From akohlmey at cmm.chem.upenn.edu Mon Jun 1 00:23:23 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 31 May 2009 18:23:23 -0400 Subject: [Pw_forum] Is 'stm_wfc_matching' option operational? In-Reply-To: References: Message-ID: <1243808603.3912.4772.camel@zero> On Sun, 2009-05-31 at 13:52 -0700, pushpa raghani wrote: > Hi, dear pushpa, > Is the option 'stm_wfc_matching' operational in post processing? In > 3.2.3 version, it says that stm_wfc_matching is presently disabled. In > 4.0 version, it doesn't say anything, so I guess it should be working why? > there? However, I get the error 'option stm_wfc_matching does not > work'. I tried this both on symmetric and asymmetric slab. Any ideas? well, the "does not work" should give you an answer. i don't really now about the code in question, but if you see messages like that, it usually means that the code is either partially implemented or has some know bugs or something else that can only be fixed by somebody carefully looking at the implementation. cheers, axel. > Many Thanks, > Pushpa > (Stanford University) > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Mon Jun 1 00:26:47 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 31 May 2009 18:26:47 -0400 Subject: [Pw_forum] will mixing_beta affect the calculation result? In-Reply-To: <9758779.11461243804706825.JavaMail.coremail@bj163app41.163.com> References: <9758779.11461243804706825.JavaMail.coremail@bj163app41.163.com> Message-ID: <1243808807.3912.4776.camel@zero> On Mon, 2009-06-01 at 05:18 +0800, duchl06 wrote: > Dear pwscf users > i thought the mixing_beta only affect the convergence velocity, but > when i did a scf calculation recently, i got different result using > different mixing_beta (the total energy have a disparity about 0.03ry > when the mixing_beta chosen 0.7 and 0.2, this is very huge ), i do > not know what happened. your wavefunction converged to different (local) minima. > will mixing_beta affect the calculation result? it should not, but you have proof that it does. however, it is quite likely that there are some other issues with your input. > are there any error in my calculation or i have a misunderstanding on > the mixing_beta? without actually seeing the input, nobody can tell. cheers, axel. > thank you! > Du > > > > ______________________________________________________________________ > ?????????? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From kazempoor2000 at yahoo.com Mon Jun 1 15:58:44 2009 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Mon, 1 Jun 2009 06:58:44 -0700 (PDT) Subject: [Pw_forum] charge state Message-ID: <793682.378.qm@web112509.mail.gq1.yahoo.com> Dear users In simulation of charged defect in bulk? ,makov-payne correction are used. But the terms that add to correct the total energy need to count madeulun constant. I study TiO2 in tetragonal cell( the size of cell is 2*2*3). How can I obtain madeulung constant? thanks? a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090601/c69f49cf/attachment.htm From marzari at MIT.EDU Mon Jun 1 16:31:18 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 01 Jun 2009 10:31:18 -0400 Subject: [Pw_forum] charge state In-Reply-To: <793682.378.qm@web112509.mail.gq1.yahoo.com> References: <793682.378.qm@web112509.mail.gq1.yahoo.com> Message-ID: <4A23E636.9070005@mit.edu> ali kazempoor wrote: > Dear users > In simulation of charged defect in bulk ,makov-payne correction are > used. But the terms that add to correct the total energy need to count > madeulun constant. I study TiO2 in tetragonal cell( the size of cell is > 2*2*3). How can I obtain madeulung constant? > thanks a lot Charged defects in the bulk are fairly tricky - you could use (I presume) a Makov-Payne correction using the dielectric constant of TiO2, abut you still need to make sure you have some absolute reference (e.g. the average of the electrostatic potential away from the defect). I believe there is quite a lot of recent literature (e.g. PA Schultz); note also that the second term in original Makov-Payne correction is not correct - see Dabo et al PRB 77, 115139 (2008). nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From pushpajnc at gmail.com Mon Jun 1 17:42:14 2009 From: pushpajnc at gmail.com (pushpa raghani) Date: Mon, 1 Jun 2009 08:42:14 -0700 Subject: [Pw_forum] Is 'stm_wfc_matching' option operational? In-Reply-To: <1243808603.3912.4772.camel@zero> References: <1243808603.3912.4772.camel@zero> Message-ID: Dear Axel, > Is the option 'stm_wfc_matching' operational in post processing? In > 3.2.3 version, it says that stm_wfc_matching is presently disabled. In > 4.0 version, it doesn't say anything, so I guess it should be working why? In the version 3.2.3, it is clearly stated that 'stm_wfc_matching is presently disabled'. When the version changes to 4.0, why would one remove something which is informative and still holds true? 'does not work' could as well mean that it does not work for this particular system! Many thanks for your answer. Pushpa On Sun, May 31, 2009 at 3:23 PM, Axel Kohlmeyer wrote: > On Sun, 2009-05-31 at 13:52 -0700, pushpa raghani wrote: > > Hi, > > dear pushpa, > > > Is the option 'stm_wfc_matching' operational in post processing? In > > 3.2.3 version, it says that stm_wfc_matching is presently disabled. In > > 4.0 version, it doesn't say anything, so I guess it should be working > > why? > > > there? However, I get the error 'option stm_wfc_matching does not > > work'. I tried this both on symmetric and asymmetric slab. Any ideas? > > well, the "does not work" should give you an answer. i don't really > now about the code in question, but if you see messages like that, it > usually means that the code is either partially implemented or has > some know bugs or something else that can only be fixed by somebody > carefully looking at the implementation. > > cheers, > axel. > > > Many Thanks, > > Pushpa > > (Stanford University) > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > 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/20090601/102193ce/attachment.htm From giannozz at democritos.it Mon Jun 1 18:03:52 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 1 Jun 2009 18:03:52 +0200 Subject: [Pw_forum] Is 'stm_wfc_matching' option operational? In-Reply-To: References: <1243808603.3912.4772.camel@zero> Message-ID: <5C5989F7-4B91-4D4C-B14E-94514B90E151@democritos.it> Hi Pushpa > In the version 3.2.3, it is clearly stated that 'stm_wfc_matching > is presently disabled'. > When the version changes to 4.0, why would one remove something > which is informative > and still holds true? maybe because it was deemed obsolete. As far as I know, that option has not been working for years. Maybe it is straightforward to re-implement it, but it requires some work. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Mon Jun 1 18:15:27 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 1 Jun 2009 18:15:27 +0200 Subject: [Pw_forum] about atom occupied factor In-Reply-To: <2687ee6de6958ea3017f94505a0e7359.squirrel@buzon.cimav.edu.mx> References: <2687ee6de6958ea3017f94505a0e7359.squirrel@buzon.cimav.edu.mx> Message-ID: <94874C52-2E66-4C63-86FC-6EF6C501FEA6@democritos.it> On May 31, 2009, at 20:35 , Javier Camarillo Cisneros wrote: > The occupied factor between .1 to 1 is the factor of times that > a atom > appears on one position, shared with other atom. > For example, I need specified two different atom (Fe 25% and Ti > 75%) > to the same position at one octahedral site on Aurivillius crystal. > This crystal is formed to 196 atoms, so is not possible create 4 > times the lattice to incorporate at the same time the 3 Ti and the > 1 Fe. than you need virtual crystal approximation. I don't know how satisfactory VCA can be in this case, though Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sgowtham at mtu.edu Mon Jun 1 19:12:36 2009 From: sgowtham at mtu.edu (Gowtham) Date: Mon, 1 Jun 2009 13:12:36 -0400 (EDT) Subject: [Pw_forum] Request: Help needed in parallel compilation of 4.0.5 Message-ID: Dear Sir/Madam, We, in our research group, are trying to compile parallel version of Quantum Espresso v4.0.5 on our beowulf linux cluster. Several of our attempts over the past couple weeks have failed. Even when parallel compilation seems to have succeeded, we notice no difference in performance between serial & parallel runs. If the fellow users of Quantum Espresso could please guide as with configure/Makefile tips/tricks, we will greatly appreciate it. The cluster is 64-bit, built using NPACI ROCKS software along with Red Hat Enterprise Linux. It has Intel v9.1 compilers, with which we have compiled several other programs (VASP/SIESTA/SMEAGOL) and they all seem to be running fine with SGE job submission engine. Thanks in advance for your time and help! Best regards, Gowtham -- Gowtham Department of Physics Michigan Tech University Houghton, MI http://sgowtham.net/ From akohlmey at cmm.chem.upenn.edu Mon Jun 1 20:11:01 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 01 Jun 2009 14:11:01 -0400 Subject: [Pw_forum] Request: Help needed in parallel compilation of 4.0.5 In-Reply-To: References: Message-ID: <1243879861.3912.4867.camel@zero> On Mon, 2009-06-01 at 13:12 -0400, Gowtham wrote: > Dear Sir/Madam, dear gowtham, > If the fellow users of Quantum Espresso could please > guide as with configure/Makefile tips/tricks, we > will greatly appreciate it. there is _plenty_ of advice in the mailing list archives. most likely somebody else has already stumbled across the problems that you are seeing. there are many discussions on how to run efficiently and how to compile on linux platforms. if you don't see a difference between parallel or serial compiles, than this can have many reasons. you have to provide examples and proof that you are actually running a parallel executable and show how you are running it. cheers, axel. > The cluster is 64-bit, built using NPACI ROCKS > software along with Red Hat Enterprise Linux. It > has Intel v9.1 compilers, with which we have compiled > several other programs (VASP/SIESTA/SMEAGOL) and > they all seem to be running fine with SGE job > submission engine. > Thanks in advance for your time and help! > > Best regards, > Gowtham > > -- > Gowtham > Department of Physics > Michigan Tech University > Houghton, MI > > http://sgowtham.net/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From bipulrr at gmail.com Mon Jun 1 22:08:19 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 2 Jun 2009 01:38:19 +0530 Subject: [Pw_forum] about Pseudopotential generation Message-ID: <3a749910906011308q54a76558ja6b65f1c4b5154f2@mail.gmail.com> Dear Pwscf users, 1. I want to generate the PP of some rare earth elements having f-electrons. There is a code in espresso folder, named atomic_doc/pseudo-gen So can I generate nice PP (ultra-soft) from the script ld1.x, so that I can calculate the electronic and phonon properties? 2. There is another programme named uspp-xxx which i got from the pwscf site only. Is that script is same as the above one, or better one? regards -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India From sophia.nishad at gmail.com Tue Jun 2 01:17:05 2009 From: sophia.nishad at gmail.com (Sophia Nishad) Date: Mon, 1 Jun 2009 18:17:05 -0500 Subject: [Pw_forum] separating optical and acoustic phonon modes Message-ID: <8a0137e60906011617p6991e456u53a597a2d47ab39e@mail.gmail.com> Hi Eyvaz, Would it be possible to get a copy of the code as mentioned at: http://www.democritos.it/pipermail/pw_forum/2009-February/011502.html Thanks, -- Sophia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090601/28c0debc/attachment.htm From sophia.nishad at gmail.com Tue Jun 2 01:18:17 2009 From: sophia.nishad at gmail.com (Sophia Nishad) Date: Mon, 1 Jun 2009 18:18:17 -0500 Subject: [Pw_forum] separating optical and acoustic phonon modes In-Reply-To: <8a0137e60906011617p6991e456u53a597a2d47ab39e@mail.gmail.com> References: <8a0137e60906011617p6991e456u53a597a2d47ab39e@mail.gmail.com> Message-ID: <8a0137e60906011618l4e4c7e9ew53f6a9324d9ce9a6@mail.gmail.com> Sorry, the link should be: http://www.democritos.it/pipermail/pw_forum/2009-February/011511.html On Mon, Jun 1, 2009 at 6:17 PM, Sophia Nishad wrote: > Hi Eyvaz, > > Would it be possible to get a copy of the code as mentioned at: > http://www.democritos.it/pipermail/pw_forum/2009-February/011502.html > > Thanks, > -- > Sophia > -- Sophia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090601/97431f0b/attachment-0001.htm From padmaja_patnaik at yahoo.co.uk Tue Jun 2 06:54:57 2009 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Tue, 2 Jun 2009 04:54:57 +0000 (GMT) Subject: [Pw_forum] which pseudopotential are LDA+GGA Message-ID: <280763.1608.qm@web26104.mail.ukl.yahoo.com> Dear all how to know which pseudopotentials are using both LDA and GGA? Its not mentioned clearly in all files. 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/20090602/99c508fb/attachment.htm From degironc at sissa.it Tue Jun 2 10:53:52 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 02 Jun 2009 10:53:52 +0200 Subject: [Pw_forum] which pseudopotential are LDA+GGA In-Reply-To: <280763.1608.qm@web26104.mail.ukl.yahoo.com> References: <280763.1608.qm@web26104.mail.ukl.yahoo.com> Message-ID: <4A24E8A0.5070107@sissa.it> NO pseudopotential is using both LDA and GGA. pseudopotentials are genererated according to ONE given XC functional and should be used with it. the functional used in the generation is written clearly in the pseudopotential file (UPF) and often is also clearly specified in the pseudopotential name. stefano Padmaja Patnaik wrote: > Dear all > > how to know which pseudopotentials are using both LDA and GGA? Its not > mentioned clearly in all files. > > 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 > From eyvaz_isaev at yahoo.com Tue Jun 2 11:37:11 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 2 Jun 2009 02:37:11 -0700 (PDT) Subject: [Pw_forum] separating optical and acoustic phonon modes Message-ID: <596773.52482.qm@web65701.mail.ac4.yahoo.com> Hi, Sophia, OK, I will send the code to you. Bests, Eyvaz. P.S. I am glad coming back to the forum. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Tue, 6/2/09, Sophia Nishad wrote: > From: Sophia Nishad > Subject: Re: [Pw_forum] separating optical and acoustic phonon modes > To: "PWSCF Forum" > Date: Tuesday, June 2, 2009, 3:18 AM > Sorry, the link should be: > http://www.democritos.it/pipermail/pw_forum/2009-February/011511.html > > On Mon, Jun 1, 2009 at 6:17 PM, > Sophia Nishad > wrote: > > Hi Eyvaz, > > Would it be possible to get a copy of the code as mentioned > at: > http://www.democritos.it/pipermail/pw_forum/2009-February/011502.html > > > > Thanks, > -- > Sophia > > > > > -- > Sophia > > > -----Inline Attachment Follows----- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From rgonzalezh at unal.edu.co Tue Jun 2 14:58:22 2009 From: rgonzalezh at unal.edu.co (Rafael Julian Gonzalez Hernandez) Date: Tue, 02 Jun 2009 07:58:22 -0500 Subject: [Pw_forum] Different results Message-ID: Dear all, I am doing a spin-polarized slab calculation for (0001)GaN 2x2 surface. I have a problem here with the total force and magnetization values. 1- First, I have performed relax calculations and I found: a)INPUT_FILE: &CONTROL title = 'clean (0001)GaN' , calculation = 'relax' , restart_mode = 'from_scratch' , outdir = './tmp' , pseudo_dir = '/usr/local/espresso-4.0.5/pseudo' , prefix = 'relaxation' , etot_conv_thr = 1.0D-5 , forc_conv_thr = 1.0D-4 , nstep = 200 , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 4, celldm(1) = 12.162279408229, celldm(3) = 3.196395659, nat = 36, ntyp = 3, ecutwfc = 30 , ecutrho = 300 , occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , nspin = 2 , starting_magnetization(1) = +0.7, starting_magnetization(2) = +0.7, starting_magnetization(3) = +0.1, / &ELECTRONS electron_maxstep = 200, conv_thr = 1.0D-8 , startingpot = 'atomic' , startingwfc = 'atomic' , mixing_mode = 'plain' , mixing_beta = 0.20 , mixing_ndim = 8, diagonalization = 'david' , diago_david_ndim = 4 , / &IONS ion_dynamics = 'bfgs' , phase_space = 'full' , pot_extrapolation = 'second_order' , wfc_extrapolation = 'second_order' , upscale = 50.0D0 , trust_radius_max = 0.5D0 , trust_radius_min = 1.0D-5 , trust_radius_ini = 0.4D0 , ... a)OUTPUT_FILE: ! total energy = -3168.48291997 Ry total magnetization = 0.01 Bohr mag/cell absolute magnetization = 0.01 Bohr mag/cell Total force = 0.000115 Total SCF correction = 0.000007 2- After, with the same conditions I have taken the final positions of my relax calculation and I have performed scf calculations, but I have different results: b) calculation = 'scf' starting_magnetization(1) = +0.70, starting_magnetization(2) = +0.70, starting_magnetization(3) = +0.10, I found: ! total energy = -3168.48291732 Ry total magnetization = 0.30 Bohr mag/cell absolute magnetization = 0.31 Bohr mag/cell Total force = 0.054697 Total SCF correction = 0.000239 c) calculation = 'scf' starting_magnetization(1) = +0.01, starting_magnetization(2) = +0.01, starting_magnetization(3) = +0.01, I found: ! total energy = -3168.48291963 Ry total magnetization = 0.11 Bohr mag/cell absolute magnetization = 0.12 Bohr mag/cell Total force = 0.054783 Total SCF correction = 0.000141 Could anyone help me with this? Thank you, Rafael Juli?n Gonz?lez H. Departamento de Fisica Universidad Nacional de Colombia Bogot?, Colombia. rgonzalezh at unal.edu.co From chuchun.fu at cea.fr Tue Jun 2 14:58:15 2009 From: chuchun.fu at cea.fr (chu-chun fu) Date: Tue, 02 Jun 2009 14:58:15 +0200 Subject: [Pw_forum] constrained_magnetization Message-ID: <4A2521E7.5070905@cea.fr> Dear PWscf developers and users, I would like to know if there is any possibility to constrain the magnitud of magnetic moment of only one type of atoms in a 'multi-component' system, when using 'atomic constrained-magnetization' ? Thanks in advance Chu Chun -- Chu Chun FU DEN/DMN/SRMP CEA-Saclay 91191 Gif-sur-yvette Cedex France Tel: +33 1 69 08 29 32 Fax: +33 1 69 08 68 67 E-mail: chuchun.fu at cea.fr From anvari_meh at physics.iust.ac.ir Tue Jun 2 16:53:06 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Tue, 02 Jun 2009 18:23:06 +0330 Subject: [Pw_forum] choosing ecutwfc through vc-rx Message-ID: Hi In the following steps I want to become sure about understanding your answers. For checking my calculations I did as below 1. Performed scf calculations for my material with arbitary cell parameters(around experimental value), with fix but small k-points(8x8x1 for 2D sample). Then try to use different ecutwfc & its corresponding ecutrho to achieve convergency in energy 2. Then I used achievd ecutwfc & ecutrho in vc-rx to get optimized cell parameters & atomic positions. Again with small k-points. 3. Finally did scf calculation again with these calculated parameters & chech energy convergency vs k-points. you said that you have choose high ecutwfc or ecutrho (depend on your pps) in vc-rx .(?) if I do it would I have to use this high ecut wfc in other steps such as phonon calculations? By the way pbe pps are ultra soft but if you check C.pbe-van _bm.UPF you will see that suggested ecutwfc & ecut rho is 25,100 respectively(?) Best Regards Mehrnaz Iran University Of science & Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090602/2587b3e5/attachment.htm From mambom1902 at yahoo.com Wed Jun 3 03:26:42 2009 From: mambom1902 at yahoo.com (loc duong ding) Date: Tue, 2 Jun 2009 18:26:42 -0700 (PDT) Subject: [Pw_forum] Dispersion interaction in PWscf Message-ID: <669302.23887.qm@web38803.mail.mud.yahoo.com> Dear all, Are there some modifications?for dispersion interactions in Pwscf??How can I set up that?modification in the? input files? Sincerely,?----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com From aryjunior at gmail.com Wed Jun 3 03:30:40 2009 From: aryjunior at gmail.com (Ary Junior) Date: Tue, 2 Jun 2009 22:30:40 -0300 Subject: [Pw_forum] Error after compile with -i8 ifort option Message-ID: <4c9c61c20906021830q2876bcc4oac1c528508e12cda@mail.gmail.com> Hi, if I compile espresso-4.0.4 with ifort and -i8 option I get the error: Program PWSCF v.4.0.4 starts ... Today is 2Jun2009 at 14:46: 4 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW 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 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from invmat : error #********** error in DGETRF %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I've take a look in ESPRESSO_HOME/flib/invmat.f90 but the error don't say much. Thank you very much! Ary Junior -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090602/ac2ccd74/attachment.htm From akohlmey at cmm.chem.upenn.edu Wed Jun 3 03:52:46 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 02 Jun 2009 21:52:46 -0400 Subject: [Pw_forum] Error after compile with -i8 ifort option In-Reply-To: <4c9c61c20906021830q2876bcc4oac1c528508e12cda@mail.gmail.com> References: <4c9c61c20906021830q2876bcc4oac1c528508e12cda@mail.gmail.com> Message-ID: <1243993966.3912.6368.camel@zero> On Tue, 2009-06-02 at 22:30 -0300, Ary Junior wrote: > Hi, if I compile espresso-4.0.4 with ifort and -i8 option I get the > error: > > Program PWSCF v.4.0.4 starts ... > Today is 2Jun2009 at 14:46: 4 > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or > PAW > > 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 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %% > from invmat : error #********** > error in DGETRF > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %% > stopping ... > > I've take a look in ESPRESSO_HOME/flib/invmat.f90 but the error don't > say much. of course not! it is insignificant anyways, as the error comes from the LAPACK subroutine DGETRF(). if you compile with -i8 (which is violating the fortran standard, btw) you have to link with a BLAS/LAPACK that is compatible. if you link with one that is not compatible, you may get errors like this one, as lapack is basically seeing garbage (it expects a 32bit integer where you place a 64-bit integer). cheers, axel. > > Thank you very much! > > Ary Junior > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Wed Jun 3 04:07:04 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 02 Jun 2009 22:07:04 -0400 Subject: [Pw_forum] Dispersion interaction in PWscf In-Reply-To: <669302.23887.qm@web38803.mail.mud.yahoo.com> References: <669302.23887.qm@web38803.mail.mud.yahoo.com> Message-ID: <1243994824.3912.6397.camel@zero> On Tue, 2009-06-02 at 18:26 -0700, loc duong ding wrote: > Dear all, > > Are there some modifications for dispersion interactions in Pwscf? How can I set up that modification in the input files? if you are looking for empirical corrections a la DFT+D, then the answer is: not yet. there is an old hard-coded implementation in the FPMD branch, but that works only for alkanes. since the topic is coming up repeatedly, you can check the mailing list archives for more details and discussions. cheers, axel. > Sincerely, ----------------------------------------------- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From bipulrr at gmail.com Wed Jun 3 09:30:11 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Wed, 3 Jun 2009 13:00:11 +0530 Subject: [Pw_forum] Calculation at high pressure Message-ID: <3a749910906030030j1ec64fcdg784558127895d8e2@mail.gmail.com> Dear PWSCF users, I am doing electronic and phonon calculations on LaSb in its zero and high pressure. The LaSb around 10GPa shows a phase transition from B1 to tetragonal (BCT) structure. So I want to calculate the phonon properties of LaSb at BCT structure at 10GPa. So can anybody tell me what I have to put in my input file to put a pressure of 10GPa so that I can get all +ve frequencies at BCT structure? regards -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090603/f8f55fb4/attachment.htm From paulatto at sissa.it Wed Jun 3 09:34:15 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 3 Jun 2009 09:34:15 +0200 (CEST) Subject: [Pw_forum] Calculation at high pressure In-Reply-To: <3a749910906030030j1ec64fcdg784558127895d8e2@mail.gmail.com> References: <3a749910906030030j1ec64fcdg784558127895d8e2@mail.gmail.com> Message-ID: <33675.78.12.165.148.1244014455.squirrel@webmail.sissa.it> In data 03 giugno 2009 alle ore 09:30:11, Bipul Rakshit ha scritto: > So I want to calculate the phonon properties of LaSb at BCT structure at > 10GPa. So can anybody tell me what I have to put in my input file to put > a pressure of 10GPa so that I can get all +ve frequencies at BCT structure? You can specify a target pressure in variable-cell relaxation (look for the "press" keyword in the &cell namelist). You can have the stress/pressure printed in a normal scf calculation setting tstress=.true. in the control namelist, regards > > regards > -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From giannozz at democritos.it Wed Jun 3 09:38:29 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 03 Jun 2009 09:38:29 +0200 Subject: [Pw_forum] Dispersion interaction in PWscf In-Reply-To: <1243994824.3912.6397.camel@zero> References: <669302.23887.qm@web38803.mail.mud.yahoo.com> <1243994824.3912.6397.camel@zero> Message-ID: <4A262875.9010702@democritos.it> Axel Kohlmeyer wrote: > if you are looking for empirical corrections a la DFT+D, > then the answer is: not yet. but maybe coming soon. There is an implementation of DFT-D that sooner or later should percolate into the cvs tree. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From bipulrr at gmail.com Wed Jun 3 09:50:01 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Wed, 3 Jun 2009 13:20:01 +0530 Subject: [Pw_forum] Calculation at high pressure In-Reply-To: <33675.78.12.165.148.1244014455.squirrel@webmail.sissa.it> References: <3a749910906030030j1ec64fcdg784558127895d8e2@mail.gmail.com> <33675.78.12.165.148.1244014455.squirrel@webmail.sissa.it> Message-ID: <3a749910906030050o5052c5beg99a2d5f0e0ce1486@mail.gmail.com> Dear Lorenzo Paulatto, Just one more thing to ask. Since I want to do phonon of BCT at 10 GPa, and its equilibrium lattice parameter is 4.09 Ang (at zero pressure), so I have to perform first a variable-cell-relaxation calculation setting target pressure at 10GPa, and then the calculation gives a lattice constant. Using that lattice constant I have to perform the phonon calculation which give me +ve frequencies. Am i right? regards On Wed, Jun 3, 2009 at 1:04 PM, Lorenzo Paulatto wrote: > In data 03 giugno 2009 alle ore 09:30:11, Bipul Rakshit > ha scritto: > > So I want to calculate the phonon properties of LaSb at BCT structure at > > 10GPa. So can anybody tell me what I have to put in my input file to put > > a pressure of 10GPa so that I can get all +ve frequencies at BCT > structure? > > You can specify a target pressure in variable-cell relaxation (look for > the "press" keyword in the &cell namelist). You can have the > stress/pressure printed in a normal scf calculation setting tstress=.true. > in the control namelist, > > regards > > > > > regards > > > > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by SquirrelMail http://www.squirrelmail.org/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090603/f05c7fcc/attachment.htm From paulatto at sissa.it Wed Jun 3 10:48:34 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 03 Jun 2009 10:48:34 +0200 Subject: [Pw_forum] which pseudopotential are LDA+GGA In-Reply-To: <280763.1608.qm@web26104.mail.ukl.yahoo.com> References: <280763.1608.qm@web26104.mail.ukl.yahoo.com> Message-ID: In data 02 giugno 2009 alle ore 06:54:57, Padmaja Patnaik ha scritto: > how to know which pseudopotentials are using both LDA and GGA? Its not > mentioned clearly in all files. Dear Padmaja, please have a look at the text-file Doc/nomefile.upf in the QE directory, it explains everything. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From paulatto at sissa.it Wed Jun 3 10:48:33 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 03 Jun 2009 10:48:33 +0200 Subject: [Pw_forum] about Pseudopotential generation In-Reply-To: <3a749910906011308q54a76558ja6b65f1c4b5154f2@mail.gmail.com> References: <3a749910906011308q54a76558ja6b65f1c4b5154f2@mail.gmail.com> Message-ID: In data 01 giugno 2009 alle ore 22:08:19, Bipul Rakshit ha scritto: > So can I generate nice PP (ultra-soft) from the script ld1.x, so that > I can calculate the electronic and phonon properties? It is a bit more than a script, and yes it can generate norm-conserving, ultrasoft and PAW datasets. Please see the documentation in atomic_doc/ directory, and the examples in various subdirectories you'll find there. > 2. There is another programme named uspp-xxx which i got from the > pwscf site only. Is that script is same as the above one, or better > one? Probably it's some very old version. > regards regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From paulatto at sissa.it Wed Jun 3 10:48:34 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 03 Jun 2009 10:48:34 +0200 Subject: [Pw_forum] Different results In-Reply-To: References: Message-ID: In data 02 giugno 2009 alle ore 14:58:22, Rafael Julian Gonzalez Hernandez ha scritto: > ! total energy = -3168.48291732 Ry > total magnetization = 0.30 Bohr mag/cell > > ! total energy = -3168.48291963 Ry > total magnetization = 0.11 Bohr mag/cell Apparently there are two solutions, with different magnetization that are practically degenerate in energy. If you want and try to discriminate between the two solution you can try and reduce the smearing parameter (remember to increse the number of k-points accordingly to maintain convergence) and repeat the calculation of the final state. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From paulatto at sissa.it Wed Jun 3 11:03:31 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 03 Jun 2009 11:03:31 +0200 Subject: [Pw_forum] constrained_magnetization In-Reply-To: <4A2521E7.5070905@cea.fr> References: <4A2521E7.5070905@cea.fr> Message-ID: In data 02 giugno 2009 alle ore 14:58:15, chu-chun fu ha scritto: > Dear PWscf developers and users, > > I would like to know if there is any possibility to constrain the > magnitud of magnetic moment of only one type of atoms in a > 'multi-component' system, when using 'atomic constrained-magnetization' ? Dear Chu Chun, it looks to me like your question is a variant on the very popular "how can I fix atom X to have occupation Z". Unluckily there is no real solution to it, as in DFT (especially on a plane-wave basis set) there is no straitforward way to say to which atom a certain electron belongs. Possible solutions include LDA+U and constrained DFT, which require some knowledge and practice to use correctly. the former is explained in detail in M. Cococcioni's PhD thesis which you can find on sissa web pages: ; I don't know if the latter is officialy supported in QE. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From paulatto at sissa.it Wed Jun 3 11:05:45 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 03 Jun 2009 11:05:45 +0200 Subject: [Pw_forum] Calculation at high pressure In-Reply-To: <3a749910906030050o5052c5beg99a2d5f0e0ce1486@mail.gmail.com> References: <3a749910906030030j1ec64fcdg784558127895d8e2@mail.gmail.com> <33675.78.12.165.148.1244014455.squirrel@webmail.sissa.it> <3a749910906030050o5052c5beg99a2d5f0e0ce1486@mail.gmail.com> Message-ID: In data 03 giugno 2009 alle ore 09:50:01, Bipul Rakshit ha scritto: > Dear Lorenzo Paulatto, > Just one more thing to ask. Since I want to do phonon of BCT at 10 GPa, > and its equilibrium lattice parameter is 4.09 Ang (at zero pressure), so > I have to perform first a variable-cell-relaxation calculation setting > target > pressure at 10GPa, and then the calculation gives a lattice constant. exactly > Using that lattice constant I have to perform the phonon calculation > which give me +ve frequencies. I think so, I've no experience on phonon calculation, but if your system has an internal stress of 10 GPa all the calculation will be a 10 GPa... regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From chuchun.fu at cea.fr Wed Jun 3 11:35:06 2009 From: chuchun.fu at cea.fr (chu-chun fu) Date: Wed, 03 Jun 2009 11:35:06 +0200 Subject: [Pw_forum] constrained_magnetization In-Reply-To: References: <4A2521E7.5070905@cea.fr> Message-ID: <4A2643CA.6070909@cea.fr> Dear Lorenzo, Thank you for your response. Maybe I was not clear enough in my previous email. My question is not to give occupation Z to atom X, but local M (magnetization) to atom X. My question actually concerns the 'atomic' constrained magnetization option already implemented in PWscf (in particular version 4.0.3) by adding a 'penalty functional' as can be seen in the SUBROUTINE add_bfield, Just wonder if we can only constrain the local magnetization of only one species instead of all the atoms to respective values as fixed in the input. Thank you again in advance for your response Chu Chun Lorenzo Paulatto wrote: > In data 02 giugno 2009 alle ore 14:58:15, chu-chun fu > ha scritto: > >> Dear PWscf developers and users, >> >> I would like to know if there is any possibility to constrain the >> magnitud of magnetic moment of only one type of atoms in a >> 'multi-component' system, when using 'atomic >> constrained-magnetization' ? > > Dear Chu Chun, > it looks to me like your question is a variant on the very popular > "how can I fix atom X to have occupation Z". Unluckily there is no > real solution to it, as in DFT (especially on a plane-wave basis set) > there is no straitforward way to say to which atom a certain electron > belongs. > > Possible solutions include LDA+U and constrained DFT, which require > some knowledge and practice to use correctly. the former is explained > in detail in M. Cococcioni's PhD thesis which you can find on sissa > web pages: ; I don't know if the > latter is officialy supported in QE. > > best regards > > > --Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ -- Chu Chun FU DEN/DMN/SRMP CEA-Saclay 91191 Gif-sur-yvette Cedex France Tel: +33 1 69 08 29 32 Fax: +33 1 69 08 68 67 E-mail: chuchun.fu at cea.fr From paulatto at sissa.it Wed Jun 3 11:45:14 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 03 Jun 2009 11:45:14 +0200 Subject: [Pw_forum] constrained_magnetization In-Reply-To: <4A2643CA.6070909@cea.fr> References: <4A2521E7.5070905@cea.fr> <4A2643CA.6070909@cea.fr> Message-ID: In data 03 giugno 2009 alle ore 11:35:06, chu-chun fu ha scritto: > Thank you for your response. Maybe I was not clear enough in my previous > email. My question is not to give occupation Z to atom X, but local M > (magnetization) to atom X. My question actually concerns the 'atomic' > constrained magnetization option already implemented in PWscf (in > particular version 4.0.3) by adding a 'penalty functional' as can be > seen in the SUBROUTINE add_bfield, Well, yes I mistaken your question a bit, yet that's what constrained DFT is about. > Just wonder if we can only constrain the local magnetization of only one > species instead of all the atoms to respective values as fixed in the > input. You cannot, but you can assign a different (formally) specie to each atom doing something like this: ATOMIC_SPECIES Pd_1 106.40 Pd.pbe-paw_kj.UPF Pd_2 106.40 Pd.pbe-paw_kj.UPF Pd_3 106.40 Pd.pbe-paw_kj.UPF ATOMIC_POSITIONS Pd_1 0.000000 0.000000 0.000000 Pd_2 0.250000 -0.144340 0.408250 Pd_3 0.500000 -0.288680 0.816490 the species will be equivalent in practice, but distinct from the code point of view, hence you can assign different constraints to them. It has to be done this way because of how the symmetry analysis works: atoms of the same specie can in principle occupy equivalent positions, in which case it would make no sense to assign different properties to each of them. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From chuchun.fu at cea.fr Wed Jun 3 12:40:32 2009 From: chuchun.fu at cea.fr (chu-chun fu) Date: Wed, 03 Jun 2009 12:40:32 +0200 Subject: [Pw_forum] constrained_magnetization In-Reply-To: References: <4A2521E7.5070905@cea.fr> <4A2643CA.6070909@cea.fr> Message-ID: <4A265320.2000404@cea.fr> Dear Lorenzo, Thanks again. I am aware of the calculation procedure you described in your previous email, i.e. to asign as different species that are not equivalent from electronic point of view bu equivalent as chemical species. However, concrning atomic magnetization constraint, it requires to asign one fixed value to each species, and what I asked was about the possibility to constrain certain species (atoms) while leaving other species (atoms) free from magnetic constraint. I just wonder I may probably do it by modify the subroutine add_bfield ? But just want to be sure. Will appreciate if possible that you let me know which subroutines would be modified to do such a constraint ? Best Regards Chu Chun Lorenzo Paulatto wrote: > In data 03 giugno 2009 alle ore 11:35:06, chu-chun fu > ha scritto: > >> Thank you for your response. Maybe I was not clear enough in my previous >> email. My question is not to give occupation Z to atom X, but local M >> (magnetization) to atom X. My question actually concerns the 'atomic' >> constrained magnetization option already implemented in PWscf (in >> particular version 4.0.3) by adding a 'penalty functional' as can be >> seen in the SUBROUTINE add_bfield, > > Well, yes I mistaken your question a bit, yet that's what constrained > DFT is about. > >> Just wonder if we can only constrain the local magnetization of only one >> species instead of all the atoms to respective values as fixed in the >> input. > > You cannot, but you can assign a different (formally) specie to each > atom doing something like this: > > ATOMIC_SPECIES > Pd_1 106.40 Pd.pbe-paw_kj.UPF > Pd_2 106.40 Pd.pbe-paw_kj.UPF > Pd_3 106.40 Pd.pbe-paw_kj.UPF > ATOMIC_POSITIONS > Pd_1 0.000000 0.000000 0.000000 > Pd_2 0.250000 -0.144340 0.408250 > Pd_3 0.500000 -0.288680 0.816490 > > the species will be equivalent in practice, but distinct from the code > point of view, hence you can assign different constraints to them. It > has to be done this way because of how the symmetry analysis works: > atoms of the same specie can in principle occupy equivalent positions, > in which case it would make no sense to assign different properties to > each of them. > > best regards > > > --Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ -- Chu Chun FU DEN/DMN/SRMP CEA-Saclay 91191 Gif-sur-yvette Cedex France Tel: +33 1 69 08 29 32 Fax: +33 1 69 08 68 67 E-mail: chuchun.fu at cea.fr From paulatto at sissa.it Wed Jun 3 12:55:52 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 03 Jun 2009 12:55:52 +0200 Subject: [Pw_forum] constrained_magnetization In-Reply-To: <4A265320.2000404@cea.fr> References: <4A2521E7.5070905@cea.fr> <4A2643CA.6070909@cea.fr> <4A265320.2000404@cea.fr> Message-ID: In data 03 giugno 2009 alle ore 12:40:32, chu-chun fu ha scritto: > Will appreciate if possible that you let me know which subroutines would > be modified to do such a constraint ? Well, in add_bfield you can change lambda from a scalar to an array of size ntyp[es] (or even nat[oms]!) and apply zero penalty to the species you want to leave free. It can be done the "proper" way, so that you can read it from the input file, but it is a bit cumbersome; it would require changes in Modules/input_parameters.f90 and PW/input.f90 and it may have possible unexpected side-effect in other parts of add_bfield. Just hard-coding it in add_bfield.f90 should work for you, but if you want to add it as a code feature you are very welcome. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From cristian.degliesposti at unibo.it Wed Jun 3 15:36:18 2009 From: cristian.degliesposti at unibo.it (Cristian Degli Esposti Boschi) Date: Wed, 03 Jun 2009 15:36:18 +0200 Subject: [Pw_forum] Installing QE 4.0.5 on Mac Pro 64-bit and gfortran In-Reply-To: References: Message-ID: <4A267C52.9080206@unibo.it> >Have you tried with 4.3.x for instance (not Apple build)? There should >be also 4.4.x available. I have just tried to compile with gcc 4.3.3 (GCC build). The configure step is like this: sudo ./configure --disable-parallel CC=gcc-4 CFLAGS="-m64" FFLAGS="-m64" F90FLAGS="-m64" CPPFLAGS="-m64" LDFLAGS="-m64" (gcc-4 means 4.3.3 on our Mac Pro). When I try 64-bit compilation the errors with fft_scalar are still there... (for instance "Symbol ... at (1) already has basic type of INTEGER"). I searched in Google for this type of errors with gfortran and it is likely that Axel Kohlmeyer is right: >ok. now that explains something. your default compiler installation >is a 32-bit version. those have a limited address space of about >2GB. this is why you are running out of memory. when you change >to 64-bit mode, this is resolved. however, you cannot just change >make.sys. you have to re-run configure and pass the -m64 flag >with the compiler flags (for c, f77 _and_ f90) and then compilation >should work. in 64-bit mode some parts of the fortran and c code >in Q-E have to be adjusted due to the difference in pointer size >vs. the default integer size compared to 32-bit mode. So, where and how should I fix the pointer size vs. the default integer size? Thanks again. Cristian -- ___________________________________________________ Cristian Degli Esposti Boschi CNR, CNISM, Unita' di Ricerca di Bologna, c/o Dipartimento di Fisica, Universita' di Bologna viale Berti-Pichat, 6/2, 40127, Bologna, Italia tel. ++39 051 2095114 fax ++39 051 2095113 e-mail: cristian.degliesposti -AT- unibo.it web: http://www.df.unibo.it/fismat/theory ___________________________________________________ From giannozz at democritos.it Wed Jun 3 15:51:15 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 3 Jun 2009 15:51:15 +0200 Subject: [Pw_forum] Installing QE 4.0.5 on Mac Pro 64-bit and gfortran In-Reply-To: <4A267C52.9080206@unibo.it> References: <4A267C52.9080206@unibo.it> Message-ID: <6F4261F2-2F7F-469B-812C-8A3FB2688A4F@democritos.it> On Jun 3, 2009, at 15:36 , Cristian Degli Esposti Boschi wrote: > So, where and how should I fix the pointer size vs. the default > integer > size? include/fft_defs.h --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From jwgonzal2 at yahoo.es Thu Jun 4 05:03:18 2009 From: jwgonzal2 at yahoo.es (=?iso-8859-1?Q?Jhon_W=2E_Gonz=E1lez?=) Date: Thu, 4 Jun 2009 03:03:18 +0000 (GMT) Subject: [Pw_forum] SCF correction problem in relaxation In-Reply-To: <49976.78.12.170.167.1243679396.squirrel@webmail.sissa.it> References: <515069.78539.qm@web27604.mail.ukl.yahoo.com> <49976.78.12.170.167.1243679396.squirrel@webmail.sissa.it> Message-ID: <412919.47338.qm@web27605.mail.ukl.yahoo.com> Thaks, but I have tried several configurations including: * mixing_mode = 'local-TF' and 'plain' * conv_thr = 1.0D-7, 1.0D-6, 1.0D-5, 1.0D-4, 1.0D-3, 1.0D-2, 1.0D-1 and always get the same warning "SCF correction compared to forces is too large, reduce conv_thr" Jhon W. Gonz?lez Universidad T?cnica Federico Santa Mar?a Fono (56) (32) 2654623 Fax (56) (32) 2797656 Casilla 110-VALPARAISO Avenida Espa?a 1680 239-0123 VALPARAISO CHILE for QE forum: http://www.democritos.it/mailman/listinfo/pw_forum ----- Mensaje original ---- De: Lorenzo Paulatto Para: PWSCF Forum Enviado: s?bado, 30 de mayo, 2009 6:29:56 Asunto: Re: [Pw_forum] SCF correction problem in relaxation Dear John, it means that your convergence threshold is too big: > conv_thr = 1.0D-5 , it is at least 10 and at most 10 thousand times larger than an acceptable convergence threshiold. Either increase it or increase the upscale parameter. regards P.S. you could also try and search the mailing list archive: please note that the same question has been asked and answered no more than 7 days ago. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From positronium at gmail.com Thu Jun 4 05:47:01 2009 From: positronium at gmail.com (Lex Kemper) Date: Wed, 03 Jun 2009 23:47:01 -0400 Subject: [Pw_forum] SCF correction problem in relaxation In-Reply-To: <412919.47338.qm@web27605.mail.ukl.yahoo.com> References: <515069.78539.qm@web27604.mail.ukl.yahoo.com> <49976.78.12.170.167.1243679396.squirrel@webmail.sissa.it> <412919.47338.qm@web27605.mail.ukl.yahoo.com> Message-ID: <4A2743B5.6080401@phys.ufl.edu> Dear Jhon, In that case, how about trying 1.0D-8 or 1.0D-10? Cheers, Lex Kemper Department of Physics and QTP University of Florida Jhon W. Gonz?lez wrote: > Thaks, but I have tried several configurations including: > > * mixing_mode = 'local-TF' and 'plain' > * conv_thr = 1.0D-7, 1.0D-6, 1.0D-5, 1.0D-4, 1.0D-3, 1.0D-2, 1.0D-1 > and always get the same warning "SCF correction compared to forces is too large, reduce conv_thr" > > > > Jhon W. Gonz?lez > > Universidad T?cnica Federico Santa Mar?a > Fono (56) (32) 2654623 Fax (56) (32) 2797656 > Casilla 110-VALPARAISO > Avenida Espa?a 1680 > 239-0123 VALPARAISO > CHILE > > for QE forum: http://www.democritos.it/mailman/listinfo/pw_forum > > > ----- Mensaje original ---- > De: Lorenzo Paulatto > Para: PWSCF Forum > Enviado: s?bado, 30 de mayo, 2009 6:29:56 > Asunto: Re: [Pw_forum] SCF correction problem in relaxation > > > Dear John, > it means that your convergence threshold is too big: >> conv_thr = 1.0D-5 , > it is at least 10 and at most 10 thousand times larger than an acceptable > convergence threshiold. Either increase it or increase the upscale > parameter. > > regards > > P.S. you could also try and search the mailing list archive: > > please note that the same question has been asked and answered no more > than 7 days ago. > From manoj at phys.ufl.edu Thu Jun 4 05:57:11 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Wed, 3 Jun 2009 23:57:11 -0400 (EDT) Subject: [Pw_forum] transmission calculation Message-ID: Dear PWSCF users and developers, I have been trying to do the conductance calculation for the twin boundary of Cu. I compared my results with previously done calculations and for most K points the transmission coefficients match up very well. But there are some k points that I get transmission coefficients more than 1! This is not reasonable, as the maximum value of transmission coefficient could be 1.I am getting 1.000345, and similar for other k points. Do you think transmission coefficients being more than 1 is just numerical error of the code or there is something wrong with my input file? Attached is the input file for lead and scatterign region - SCF for the LEFT lead- &control calculation='scf' pseudo_dir = '/home/manoj/espresso-4.0.1/pseudo', outdir='./', prefix='lcu', / &system ibrav =0, celldm(1)=4.82, nat= 3, ntyp= 1, ecutwfc =150.0, occupations='smearing', smearing='gaussian', degauss=0.02, ecutrho=500 / &electrons conv_thr = 1.0e-8 mixing_beta=0.7 / ATOMIC_SPECIES Cu 63.55 Cu.pz-d-rrkjus.UPF ATOMIC_POSITIONS Cu 0.0 0.0 0.0 Cu -0.5 0.288675134 0.81649658 Cu -1.0 0.577350269 1.632993162 K_POINTS (automatic) 6 6 8 1 1 1 CELL_PARAMETERS {hexagonal} 1.0 0.0 0.0 -0.5 0.8660254037844386 0.0 0.0 0.0 2.449489743 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SCF for the RIGHT lead- &control calculation='scf' pseudo_dir = '/home/manoj/espresso-4.0.1/pseudo', outdir='./', prefix='rcu', / &system ibrav =0, celldm(1)=4.82, nat= 3, ntyp= 1, ecutwfc =150.0, occupations='smearing', smearing='gaussian', degauss=0.02, ecutrho=500 / &electrons conv_thr = 1.0e-8 mixing_beta=0.7 / ATOMIC_SPECIES Cu 63.55 Cu.pz-d-rrkjus.UPF ATOMIC_POSITIONS Cu 0.0 0.0 0.0 Cu 0.5 -0.288675134 0.81649658 Cu 1.0 -0.577350269 1.632993162 K_POINTS (automatic) 6 6 8 1 1 1 CELL_PARAMETERS {hexagonal} 1.0 0.0 0.0 -0.5 0.8660254037844386 0.0 0.0 0.0 2.449489743 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SCF for SCATTERING region- &control calculation='scf' pseudo_dir = '/home/manoj/espresso-4.0.1/pseudo', outdir='./', prefix='scu', / &system ibrav =0, celldm(1)=4.82, nat= 12, ntyp= 1, ecutwfc =150.0, occupations='smearing', smearing='gaussian', degauss=0.02, ecutrho=500 / &electrons conv_thr = 1.0e-8 mixing_beta=0.7 / ATOMIC_SPECIES Cu 63.55 Cu.pz-d-rrkjus.UPF ATOMIC_POSITIONS Cu 0.0 0.0 0.0 Cu -0.5 0.288675134 0.816496581 Cu -1.0 0.577350269 1.632993162 Cu -0.5 0.288675134 2.449489743 Cu 0.0 0.0 3.265986324 Cu 0.5 -0.288675134 4.082482905 Cu 1.0 -0.577350269 4.898979486 Cu 1.5 -0.866025404 5.715476066 Cu 2.0 -1.154700538 6.531972647 Cu 1.5 -0.866025404 7.348469228 Cu 1.0 -0.577350269 8.164965809 Cu 0.5 -0.288675134 8.981462390 K_POINTS (automatic) 6 6 4 1 1 1 CELL_PARAMETERS {hexagonal} 1.0 0.0 0.0 -0.5 0.866025403 0.0 0.0 0.0 9.797958971 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input file for conductance part- &inputcond outdir='./' prefixs='scu' prefixl='lcu' prefixr='rcu' tran_file ='trans.twin' ikind=2 ecut2d=200 energy0=0.0 denergy=0.0 ewind=101.d0 epsproj=1.d-6 nz1=25 bds=3.265986324 / 6 0.5000000 -0.5000000 1 4.2584095E-17 0.5000000 1 0.250000000 0.0000000 1 0.1666667 0.1666667 1 -1.2775231E-16 -0.2500000 1 0.2500000 -0.2500001 1 1 0.0 Regards, Manoj Srivastava University of Florida, Gainesville, FL From gregor.mali at ki.si Thu Jun 4 08:38:03 2009 From: gregor.mali at ki.si (Gregor Mali) Date: Thu, 4 Jun 2009 08:38:03 +0200 Subject: [Pw_forum] PAW dataset for Mn, NC PPs for GIPAW for Mn and Li In-Reply-To: <412919.47338.qm@web27605.mail.ukl.yahoo.com> References: <515069.78539.qm@web27604.mail.ukl.yahoo.com><49976.78.12.170.167.1243679396.squirrel@webmail.sissa.it> <412919.47338.qm@web27605.mail.ukl.yahoo.com> Message-ID: <8C0B47760A05FB4AB504C9BCAD32D256E5DF5E@postar.ki.si> Dear PWscf users, I am studying hyperfine interaction of lithium nuclei in some lithium manganese silicates. I hope that an insight into the interaction could be obtained by calculating spin-polarization at Li position (or in a small sphere around Li), or by using the GIPAW module. In the former case (spin-polarization) I would like to use the PAW approach, since, as far as I understand, it improves the accuracy on the core. I kindly ask, whether someone is willing to share a PAW dataset for Mn, or an input file for generation of such a dataset, as well as norm-conserving pseudopotentials for Li and Mn, convenient for use with GIPAW. Thank you very much in advance. Gregor Mali National Institute of Chemistry Ljubljana, Slovenia From bipulrr at gmail.com Thu Jun 4 09:31:46 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Thu, 4 Jun 2009 13:01:46 +0530 Subject: [Pw_forum] problem in updating cvs version Message-ID: <3a749910906040031h3d06ed8eue839adb3ebbd47c9@mail.gmail.com> Dear Pwscf users, I am using remote parallel computers for calculation. When I try to update the cvs version with the following commands.... *For sh/ksh/bash, use export CVS_RSH=ssh export CVSROOT=:pserver:cvsanon at democritos.sissa.it:/home/cvs * * Then: cvs login and enter password: /cvsanon/* it gives me the following error *cvs [login aborted]: connect to democritos.sissa.it(147.122.10.31):2401 failed: Connection timed out* -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090604/a48a3362/attachment.htm From paulatto at sissa.it Thu Jun 4 10:02:05 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 04 Jun 2009 10:02:05 +0200 Subject: [Pw_forum] SCF correction problem in relaxation In-Reply-To: <412919.47338.qm@web27605.mail.ukl.yahoo.com> References: <515069.78539.qm@web27604.mail.ukl.yahoo.com> <49976.78.12.170.167.1243679396.squirrel@webmail.sissa.it> <412919.47338.qm@web27605.mail.ukl.yahoo.com> Message-ID: In data 04 giugno 2009 alle ore 05:03:18, Jhon W. Gonz?lez ha scritto: > and always get the same warning "SCF correction compared to forces is > too large, reduce conv_thr" When the forces are ~zero the SCF correction will always be large compared to them. What counts is if the forces are small enough for you to consider the calculation converged. Zero +/- zero is still zero. In any case you can get rid of the message by setting i.e. upscale=1.e+5 which will allow the program to reduce the convergence threshold down to insane levels, preventing the message from displaying. But is this what you really want? regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From paulatto at sissa.it Thu Jun 4 10:06:59 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 04 Jun 2009 10:06:59 +0200 Subject: [Pw_forum] problem in updating cvs version In-Reply-To: <3a749910906040031h3d06ed8eue839adb3ebbd47c9@mail.gmail.com> References: <3a749910906040031h3d06ed8eue839adb3ebbd47c9@mail.gmail.com> Message-ID: In data 04 giugno 2009 alle ore 09:31:46, Bipul Rakshit ha scritto: > *cvs [login aborted]: connect to democritos.sissa.it(147.122.10.31):2401 > failed: Connection timed out* There was a fierce thunderstorm half an hour ago, and this could explain the problem connecting to the server; yet I have to advise you that the CVS repository has been moved to qe-forge.org a couple of months ago: the branch on the democrito server is no longer updated. Please see this page for details on how to get the cvs version from the forge. I think there is a way to transfer the local setting to make a previous cvs directory point to the new repository, but I don't know how to do it. You can always get a fresh check-out and then replace the files... best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From mambom1902 at yahoo.com Thu Jun 4 10:38:11 2009 From: mambom1902 at yahoo.com (loc duong ding) Date: Thu, 4 Jun 2009 01:38:11 -0700 (PDT) Subject: [Pw_forum] Problem with parallel running by mpich2 Message-ID: <49911.66582.qm@web38804.mail.mud.yahoo.com> Dear developers and all users, I use MPICH2 to run PWSCF. I get?a problem. When I?run PWSCF by command: mpiexec -machinefile /home/loc/machinefile -n 8 pw.x -npool 2 test there is nothing: No error, no announcement. When?I test the input file?( C8OOH_11.txt) by command: pw.x? test ? it runs well even though very slow. ? To test MPICH2, I use that to run another small structure and no problem. ? Have any one met this problem??What is the possible reason of this problem? ? This is my input file: ? ?&CONTROL ????? calculation = 'relax', ????? prefix='C8OOH_1H2', ????? restart_mode = 'restart', ????? pseudo_dir ='/home/loc/espresso-4.0/pseudo', ????? outdir='./' ????? tstress = .true. , ????? tprnfor = .true. , ????? nstep =? 200? , ????? etot_conv_thr = 1.0E-4 , ????? forc_conv_thr = 1.0D-3 , ????? dt = 20 , / &SYSTEM ????? ibrav= 14,? celldm(1) = 18.89399, celldm(2)= 0.99629,celldm(3)= 1.05229, celldm(4)= 0.109, celldm(5)= -0.1598,celldm(6)= -0.504, nat = 88, ntyp = 3, nspin=2, ????? ecutwfc =35, ecutrho = 210, occupations='smearing', degauss=0.0001, ????? starting_magnetization(1) = 0.0, ????? starting_magnetization(2) = 0.3, ????? starting_magnetization(3) = 0.5??? / &ELECTRONS ??? startingwfc = 'atomic' ??? mixing_mode = 'plain' ??? mixing_beta = 0.6 ??? conv_thr = 1.0e-6 ??? electron_maxstep= 250 / &IONS ??? upscale = 15 / &CELL ?? cell_dynamics = 'bfgs' , ?? press = 0.00 , ?? wmass =? 0.00150000? , ?? press_conv_thr = 0.5, / ATOMIC_SPECIES ?C? 12.011? C.pbe-rrkjus.UPF ?O? 15.9994 O.pbe-rrkjus.UPF ?H? 1.008?? H.pbe-rrkjus.UPF ATOMIC_POSITIONS {angstrom} C??? 2.97500??? 1.96900??? 7.98400 C??? 0.44200??? 1.99500??? 8.00700 C??? 1.74300?? -0.16900??? 7.98800 C??? 1.70600??? 2.71300??? 7.63300 C??? 2.93300??? 0.57400??? 8.01100 C??? 0.48500??? 0.56000??? 8.20500 O??? 1.62100??? 2.83300??? 6.18300 C?? -0.80500?? -0.17900??? 8.19100 O?? -0.18900??? 0.06300??? 9.47200 C?? -0.15900??? 1.96900?? 13.18800 C??? 1.14200?? -0.19400?? 13.16500 C??? 2.33300??? 0.54800?? 13.18600 C?? -1.40500?? -0.20600?? 13.36700 C?? -0.11700??? 0.53400?? 13.38400 O?? -0.79200??? 0.02000?? 14.65100 C??? 1.10500??? 2.68600?? 12.80800 O??? 1.01600??? 2.79700?? 11.35900 C??? 4.22300??? 2.69000??? 8.01100 C??? 2.37500??? 1.94400?? 13.15900 C??? 3.62200??? 2.66500?? 13.18700 H??? 2.43200??? 3.27000??? 5.83300 H??? 1.77600??? 3.31500?? 11.00400 C??? 7.97200??? 1.96900??? 7.98400 C??? 5.43900??? 1.99500??? 8.00700 C??? 6.74100?? -0.16900??? 7.98800 C??? 6.70300??? 2.71300??? 7.63300 C??? 7.93100??? 0.57400??? 8.01100 C??? 5.48200??? 0.56000??? 8.20500 O??? 6.61800??? 2.83300??? 6.18300 C??? 4.19300?? -0.17900??? 8.19100 O??? 4.80800??? 0.06300??? 9.47200 C??? 4.83800??? 1.96900?? 13.18800 C??? 6.14000?? -0.19400?? 13.16500 C??? 7.33100??? 0.54800?? 13.18600 C??? 3.59300?? -0.20600?? 13.36700 C??? 4.88000??? 0.53400?? 13.38400 O??? 4.20600??? 0.02000?? 14.65100 C??? 6.10200??? 2.68600?? 12.80800 O??? 6.01300??? 2.79700?? 11.35900 C??? 9.22000??? 2.69000??? 8.01100 C??? 7.37200??? 1.94400?? 13.15900 C??? 8.62000??? 2.66500?? 13.18700 H??? 7.43000??? 3.27000??? 5.83300 H??? 6.77400??? 3.31500?? 11.00400 C??? 5.46300??? 6.27000??? 7.98400 C??? 2.93000??? 6.29500??? 8.00700 C??? 4.23100??? 4.13100??? 7.98800 C??? 4.19400??? 7.01300??? 7.63300 C??? 5.42100??? 4.87400??? 8.01100 C??? 2.97300??? 4.86000??? 8.20500 O??? 4.10900??? 7.13300??? 6.18300 C??? 1.68300??? 4.12100??? 8.19100 O??? 2.29900??? 4.36300??? 9.47200 C??? 2.32900??? 6.26900?? 13.18800 C??? 3.63000??? 4.10600?? 13.16500 C??? 4.82100??? 4.84800?? 13.18600 C??? 1.08300??? 4.09400?? 13.36700 C??? 2.37100??? 4.83400?? 13.38400 O??? 1.69600??? 4.32000?? 14.65100 C??? 3.59300??? 6.98600?? 12.80800 O??? 3.50400??? 7.09700?? 11.35900 C??? 6.71100??? 6.99100??? 8.01100 C??? 4.86300??? 6.24400?? 13.15900 C??? 6.11000??? 6.96600?? 13.18700 H??? 4.92000??? 7.57000??? 5.83300 H??? 4.26400??? 7.61500?? 11.00400 C??? 0.46500??? 6.27000??? 7.98400 C?? -2.06800??? 6.29500??? 8.00700 C?? -0.76600??? 4.13100??? 7.98800 C?? -0.80400??? 7.01300??? 7.63300 C??? 0.42400??? 4.87400??? 8.01100 C?? -2.02500??? 4.86000??? 8.20500 O?? -0.88900??? 7.13300??? 6.18300 C?? -3.31400??? 4.12100??? 8.19100 O?? -2.69900??? 4.36300??? 9.47200 C?? -2.66900??? 6.26900?? 13.18800 C?? -1.36700??? 4.10600?? 13.16500 C?? -0.17600??? 4.84800?? 13.18600 C?? -3.91400??? 4.09400?? 13.36700 C?? -2.62600??? 4.83400?? 13.38400 O?? -3.30100??? 4.32000?? 14.65100 C?? -1.40500??? 6.98600?? 12.80800 O?? -1.49300??? 7.09700?? 11.35900 C??? 1.71300??? 6.99100??? 8.01100 C?? -0.13400??? 6.24400?? 13.15900 C??? 1.11300??? 6.96600?? 13.18700 H?? -0.07700??? 7.57000??? 5.83300 H?? -0.73300??? 7.61500?? 11.00400 K_POINTS {automatic} 4 4 1 0 0 0 I appreciate your help! ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com From paulatto at sissa.it Thu Jun 4 10:43:43 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 04 Jun 2009 10:43:43 +0200 Subject: [Pw_forum] Problem with parallel running by mpich2 In-Reply-To: <49911.66582.qm@web38804.mail.mud.yahoo.com> References: <49911.66582.qm@web38804.mail.mud.yahoo.com> Message-ID: In data 04 giugno 2009 alle ore 10:38:11, loc duong ding ha scritto: > there is nothing: No error, no announcement. Dear loc Duong Ding, doesn't it even print the first dozen of lines? If it does, it may just be the usual problem with input redirection: try feeding the input file by using the syntax mpich2 [...] pw.x -in input.in [...] which is more parallel safe. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From sclauzer at sissa.it Thu Jun 4 15:07:47 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 4 Jun 2009 15:07:47 +0200 Subject: [Pw_forum] transmission calculation In-Reply-To: References: Message-ID: <20090604150747.7wmvdoafxcg44sww@webmail.sissa.it> Quoting Manoj Srivastava : > Dear PWSCF users and developers, > I have been trying to do the conductance calculation for the twin > boundary of Cu. I compared my results with previously done calculations > and for most K points the transmission coefficients match up very well. > But there are some k points that I get transmission coefficients more than > 1! This is not reasonable, as the maximum value of transmission > coefficient could be 1.I am getting 1.000345, and similar for other k > points. Which k-points? How many channels are there? Please send me the output file or post the relevant part of it. > Do you think transmission coefficients being more than 1 is just > numerical error of the code or there is something wrong with my input > file? Attached is the input file for lead and scatterign region - Transmission coefficients should be between 0 and 1. In the code there are many levels of approximation. Some of them may affect the results. Usually the two relevant parameters one needs to adjust are epsproj and ewind. Why are you tweaking the others? Have you tried the default? > ecutwfc =150.0, Why such a high value? You are using US, aren't you? > ATOMIC_POSITIONS > Cu 0.0 0.0 0.0 > Cu -0.5 0.288675134 0.81649658 > Cu -1.0 0.577350269 1.632993162 > > K_POINTS (automatic) > 6 6 8 1 1 1 > CELL_PARAMETERS {hexagonal} > 1.0 0.0 0.0 > -0.5 0.8660254037844386 0.0 > 0.0 0.0 2.449489743 This shouldn't be an issue, but you could try to use ibrav=4 instead of ibrav=0 and specify atomic positions such that all atoms are inside the first primitive cell (i.e. the one with R=0) > > / > 6 > 0.5000000 -0.5000000 1 > 4.2584095E-17 0.5000000 1 Why don't you specify 0.00000 instead? Should not matter anyway. Gabriele Sclauzero SISSA & Democritos > 0.250000000 0.0000000 1 > 0.1666667 0.1666667 1 > -1.2775231E-16 -0.2500000 1 > 0.2500000 -0.2500001 1 > 1 > 0.0 > > > Regards, > Manoj Srivastava > University of Florida, > Gainesville, FL > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From zhaohscas at yahoo.com.cn Fri Jun 5 12:29:14 2009 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Fri, 5 Jun 2009 18:29:14 +0800 Subject: [Pw_forum] temperature dependent density functional theory Message-ID: <807115539.20090605182914@yahoo.com.cn> Dear all, I've learned that time dependent density functional theory, but never learned that how to something like temperature dependent density functional theory. I want to know whether it is possible to do temperature dependent density functional theory within the frame of DFT? Kind regards, -- Hongsheng Zhao Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences GnuPG DSA: 0xD108493 2009-6-5 From akohlmey at cmm.chem.upenn.edu Fri Jun 5 15:02:06 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 05 Jun 2009 09:02:06 -0400 Subject: [Pw_forum] temperature dependent density functional theory In-Reply-To: <807115539.20090605182914@yahoo.com.cn> References: <807115539.20090605182914@yahoo.com.cn> Message-ID: <1244206926.3912.9729.camel@zero> On Fri, 2009-06-05 at 18:29 +0800, Hongsheng Zhao wrote: > Dear all, > > I've learned that time dependent density functional theory, but never > learned that how to something like temperature dependent density > functional theory. I want to know whether it is possible to do > temperature dependent density functional theory within the frame of > DFT? dear hongsheng zhao, would you mind to explain to ignorant people like me, what "Temperature dependent DFT" would encompass. thanks, axel. > Kind regards, -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From zhaohscas at yahoo.com.cn Fri Jun 5 15:50:27 2009 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Fri, 5 Jun 2009 21:50:27 +0800 Subject: [Pw_forum] temperature dependent density functional theory In-Reply-To: <1244206926.3912.9729.camel@zero> References: <807115539.20090605182914@yahoo.com.cn> <1244206926.3912.9729.camel@zero> Message-ID: <646457566.20090605215027@yahoo.com.cn> On Friday, June 5, 2009 at 21:02, akohlmey at cmm.chem.upenn.edu wrote: > On Fri, 2009-06-05 at 18:29 +0800, Hongsheng Zhao wrote: >> Dear all, >> >> I've learned that time dependent density functional theory, but never >> learned that how to something like temperature dependent density >> functional theory. I want to know whether it is possible to do >> temperature dependent density functional theory within the frame of >> DFT? > dear hongsheng zhao, > would you mind to explain to ignorant people like > me, Perhaps this should be said by me :-) > what "Temperature dependent DFT" would encompass. In my mind, all the first principles/ab initio calculations only work under 0K, so I want to know whether can I do the first principles/ab initio calculations under other temperatures other than 0K, especially under some temperatures around room temperature? Kind regards, -- Hongsheng Zhao Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences GnuPG DSA: 0xD108493 2009-6-5 From akohlmey at cmm.chem.upenn.edu Fri Jun 5 17:18:49 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 05 Jun 2009 11:18:49 -0400 Subject: [Pw_forum] temperature dependent density functional theory In-Reply-To: <646457566.20090605215027@yahoo.com.cn> References: <807115539.20090605182914@yahoo.com.cn> <1244206926.3912.9729.camel@zero> <646457566.20090605215027@yahoo.com.cn> Message-ID: <1244215129.3912.9743.camel@zero> > > what "Temperature dependent DFT" would encompass. > > In my mind, all the first principles/ab initio calculations only work > under 0K, so I want to know whether can I do the first principles/ab > initio calculations under other temperatures other than 0K, especially > under some temperatures around room temperature? first of all, the way people talk about ab initio being calculations at OK usually has to be seen in the context of geometry optimizations. this approach generally uses the time independent DFT formalism and thus the Born-Oppenheimer approximation and with in that approximation you can very well do molecular dynamics, i.e. a system at temperature different from OK. you can do this with pw.x but also in cp.x using the car-parrinello hamiltonian. of course there is the effect of temperature to the electronic structure, but that is is generally very small, unless you go to very high temperatures. this can be treated as well, but require some more complicated to use methods. in most cases, you should be just fine by applying a finite temperature to your atoms and using normal DFT. cheers, axel. > > Kind regards, -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From zhaohscas at yahoo.com.cn Fri Jun 5 18:09:49 2009 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Sat, 6 Jun 2009 00:09:49 +0800 Subject: [Pw_forum] temperature dependent density functional theory In-Reply-To: <1244215129.3912.9743.camel@zero> References: <807115539.20090605182914@yahoo.com.cn> <1244206926.3912.9729.camel@zero> <646457566.20090605215027@yahoo.com.cn> <1244215129.3912.9743.camel@zero> Message-ID: <1144531918.20090606000949@yahoo.com.cn> On Friday, June 5, 2009 at 23:18, akohlmey at cmm.chem.upenn.edu wrote: >> > what "Temperature dependent DFT" would encompass. >> >> In my mind, all the first principles/ab initio calculations only work >> under 0K, so I want to know whether can I do the first principles/ab >> initio calculations under other temperatures other than 0K, especially >> under some temperatures around room temperature? > first of all, the way people talk about ab initio being calculations > at OK usually has to be seen in the context of geometry optimizations. > this approach generally uses the time independent DFT formalism and > thus the Born-Oppenheimer approximation and with in that approximation > you can very well do molecular dynamics, i.e. a system at temperature > different from OK. you can do this with pw.x but also in cp.x using > the car-parrinello hamiltonian. > of course there is the effect of temperature to the electronic > structure, but that is is generally very small, unless you go > to very high temperatures. this can be treated as well, but require > some more complicated to use methods. in most cases, you should be > just fine by applying a finite temperature to your atoms and using > normal DFT. By what means/parameters can I apply a finite temperature to my system? Kind regards, -- Hongsheng Zhao Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences GnuPG DSA: 0xD108493 2009-6-6 From akohlmey at cmm.chem.upenn.edu Fri Jun 5 18:17:44 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 05 Jun 2009 12:17:44 -0400 Subject: [Pw_forum] temperature dependent density functional theory In-Reply-To: <1144531918.20090606000949@yahoo.com.cn> References: <807115539.20090605182914@yahoo.com.cn> <1244206926.3912.9729.camel@zero> <646457566.20090605215027@yahoo.com.cn> <1244215129.3912.9743.camel@zero> <1144531918.20090606000949@yahoo.com.cn> Message-ID: <1244218664.3912.9764.camel@zero> On Sat, 2009-06-06 at 00:09 +0800, Hongsheng Zhao wrote: > By what means/parameters can I apply a finite temperature to my > system? set calculation type to 'md' and check out the documentation of the &ions namelist in pw.x you can select the thermostatting method and the target or initial temperature. similarly so for cp.x cheers, axel. > > Kind regards, -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From manoj at phys.ufl.edu Fri Jun 5 18:33:26 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Fri, 5 Jun 2009 12:33:26 -0400 (EDT) Subject: [Pw_forum] transmission calculation In-Reply-To: <20090604150747.7wmvdoafxcg44sww@webmail.sissa.it> Message-ID: Dear Gabriele, Thanks for your response. On Thu, 4 Jun 2009, Gabriele Sclauzero wrote: > Quoting Manoj Srivastava : > > > Dear PWSCF users and developers, > > I have been trying to do the conductance calculation for the twin > > boundary of Cu. I compared my results with previously done calculations > > and for most K points the transmission coefficients match up very well. > > But there are some k points that I get transmission coefficients more than > > 1! This is not reasonable, as the maximum value of transmission > > coefficient could be 1.I am getting 1.000345, and similar for other k > > points. > > Which k-points? How many channels are there? Please send me the output > file or post the relevant part of it. There are quiet a few k points for which transmission is more than 1. For example- k( 3) = ( 0.2500000 0.0000000), wk = 0.1666667 ngper, shell number = 317 133 ngper, n2d = 317 317 Nchannels of the left tip = 1 k1(2pi/a) k2(2pi/a) E-Ef (eV) 0.0634548 0.0000000 0.0000000 Nchannels of the right tip = 1 k1(2pi/a) k2(2pi/a) E-Ef (eV) 0.1266351 0.0000000 0.0000000 to transmit T_ij for propagating states: 1 --> 1 1.0000806 1.00008 Eigenchannel decomposition: @ 1 0.00000 1.00008 1.00000 E-Ef(ev), T(x2 spins) = 0.0000000 2.0001613 Also for another k point - k( 5) = ( 0.0000000 -0.2500000), wk = 0.1666667 ngper, shell number = 317 133 ngper, n2d = 317 317 Nchannels of the left tip = 1 k1(2pi/a) k2(2pi/a) E-Ef (eV) 0.0634548 0.0000000 0.0000000 Nchannels of the right tip = 1 k1(2pi/a) k2(2pi/a) E-Ef (eV) 0.1266351 0.0000000 0.0000000 to transmit T_ij for propagating states: 1 --> 1 1.0000806 1.00008 Eigenchannel decomposition: @ 1 0.00000 1.00008 1.00000 E-Ef(ev), T(x2 spins) = 0.0000000 2.0001613 > > > Do you think transmission coefficients being more than 1 is just > > numerical error of the code or there is something wrong with my input > > file? Attached is the input file for lead and scatterign region - > > Transmission coefficients should be between 0 and 1. In the code there > are many levels of approximation. Some of them may affect the results. > Usually the two relevant parameters one needs to adjust are epsproj > and ewind. Why are you tweaking the others? Have you tried the default? > > > > > > ecutwfc =150.0, > > Why such a high value? You are using US, aren't you? I started with low value of ecutwfc, but my transmission was more than 1, so I started increasing ecutwfc, but still no change. And, yes I am using USPP. > > > > ATOMIC_POSITIONS > > Cu 0.0 0.0 0.0 > > Cu -0.5 0.288675134 0.81649658 > > Cu -1.0 0.577350269 1.632993162 > > > > K_POINTS (automatic) > > 6 6 8 1 1 1 > > CELL_PARAMETERS {hexagonal} > > 1.0 0.0 0.0 > > -0.5 0.8660254037844386 0.0 > > 0.0 0.0 2.449489743 > > This shouldn't be an issue, but you could try to use ibrav=4 instead > of ibrav=0 and specify atomic positions such that all atoms are inside > the first primitive cell (i.e. the one with R=0) Setting ibrav=4 or setting ibrav=0 and manually specify unit cell should give me the same results, I believe. What is R=0 ? > > > > > > > > > / > > 6 > > 0.5000000 -0.5000000 1 > > 4.2584095E-17 0.5000000 1 > > Why don't you specify 0.00000 instead? Should not matter anyway. Yes, it does not matter. > > Gabriele Sclauzero > > > SISSA & Democritos > > > > 0.250000000 0.0000000 1 > > 0.1666667 0.1666667 1 > > -1.2775231E-16 -0.2500000 1 > > 0.2500000 -0.2500001 1 > > 1 > > 0.0 > > > > > > Regards, > > Manoj Srivastava > > University of Florida, > > Gainesville, FL > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ---------------------------------------------------------------- > 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 > Regards, Manoj From kyin.cn at gmail.com Sat Jun 6 06:16:54 2009 From: kyin.cn at gmail.com (Kun Yin) Date: Sat, 06 Jun 2009 12:16:54 +0800 Subject: [Pw_forum] temperature dependent density functional theory In-Reply-To: <1144531918.20090606000949@yahoo.com.cn> References: <807115539.20090605182914@yahoo.com.cn> <1244206926.3912.9729.camel@zero> <646457566.20090605215027@yahoo.com.cn> <1244215129.3912.9743.camel@zero> <1144531918.20090606000949@yahoo.com.cn> Message-ID: <1244261814.6871.18.camel@dejavu> On Sat, 2009-06-06 at 00:09 +0800, Hongsheng Zhao wrote: > By what means/parameters can I apply a finite temperature to my > system? > Dear Zhao, You can extend to finite temperature by two means depending your specific system: (1) ab-initio molecular dynamics (e.g. CPMD) This method usually is applied to molecular systems or liquid systems or surface, interface. It takes more time to compute such calculations and system size can not be very large. (2) phonon calculations (e.g. DFPT or frozen phonon method) This method usually is applied to solid system which is far from melting. The DFPT is implemented in Quantum-ESPRESSO, see examples related ph.x In a word, if you want to consider "temperature", you should have some method to calculate the contribution of nuclei motions. Cheers, Kun YIN, PhD candidate Nanjing University, China From zhaohscas at yahoo.com.cn Sat Jun 6 06:44:34 2009 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Sat, 6 Jun 2009 12:44:34 +0800 Subject: [Pw_forum] temperature dependent density functional theory In-Reply-To: <1244261814.6871.18.camel@dejavu> References: <807115539.20090605182914@yahoo.com.cn> <1244206926.3912.9729.camel@zero> <646457566.20090605215027@yahoo.com.cn> <1244215129.3912.9743.camel@zero> <1144531918.20090606000949@yahoo.com.cn> <1244261814.6871.18.camel@dejavu> Message-ID: <136661673.20090606124434@yahoo.com.cn> On Saturday, June 6, 2009 at 12:16, kyin.cn at gmail.com wrote: > On Sat, 2009-06-06 at 00:09 +0800, Hongsheng Zhao wrote: >> By what means/parameters can I apply a finite temperature to my >> system? >> > Dear Zhao, > You can extend to finite temperature by two means depending your > specific system: > (1) ab-initio molecular dynamics (e.g. CPMD) > This method usually is applied to molecular systems or liquid systems or > surface, interface. It takes more time to compute such calculations and > system size can not be very large. > (2) phonon calculations (e.g. DFPT or frozen phonon method) > This method usually is applied to solid system which is far from > melting. The DFPT is implemented in Quantum-ESPRESSO, see examples > related ph.x > In a word, if you want to consider "temperature", you should have some > method to calculate the contribution of nuclei motions. Thanks very much for your help. Kind regards, -- Hongsheng Zhao Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences GnuPG DSA: 0xD108493 2009-6-6 From kazempoor2000 at yahoo.com Sat Jun 6 09:20:24 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Sat, 6 Jun 2009 00:20:24 -0700 (PDT) Subject: [Pw_forum] charhe simulation Message-ID: <4975.81624.qm@web112503.mail.gq1.yahoo.com> Dear all I have a question about charge simulation. In common DFT simulation with neutral charge we have Ewald sum that describe charge-charge interaction . This sum is not problematic . But when we simulate for example ionization energy, we have to use correction like makov-payne . In both case we have charge -charge interaction . What is the differences between two case? Thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 From anvari_meh at physics.iust.ac.ir Sat Jun 6 14:15:15 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Sat, 06 Jun 2009 15:45:15 +0330 Subject: [Pw_forum] missing q-points Message-ID: Dear all I tried to calculate phonon dispersion for graphene in uniform grid (nq1=2, nq2=2, nq3=1). In graphene .dyn0 file exist two points, but after nscf calculations & phonon performance the code couldn't find same q-points so in q2r.x I have this error from init : error # 1 missing q-point(s)! I checked archive & I saw maybe the problem is due to fftw so I install fftw 3.1.2, but yet I have the problem .what can I do? Mehrnaz Iran University Of Science & Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090606/d45f4d1a/attachment.htm From phylyh at nus.edu.sg Sat Jun 6 14:13:40 2009 From: phylyh at nus.edu.sg (Lu Yunhao) Date: Sat, 6 Jun 2009 20:13:40 +0800 Subject: [Pw_forum] How to set the ensemble when doing molecule dynamics calculation with pw.x Message-ID: <000001c9e6a0$3a3557a0$ab4f8489@nusa0bcf64b485> Dear All Can the pw.x code do molecule dynamic calculation with NVE ensemble? I search the Manu and can not find any descriptions about ensemble. Best wishes, Yunhao Resear Fellow NUS -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090606/a3821fcf/attachment.htm From akohlmey at cmm.chem.upenn.edu Sat Jun 6 16:32:47 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 06 Jun 2009 10:32:47 -0400 Subject: [Pw_forum] charhe simulation In-Reply-To: <4975.81624.qm@web112503.mail.gq1.yahoo.com> References: <4975.81624.qm@web112503.mail.gq1.yahoo.com> Message-ID: <1244298767.3912.9865.camel@zero> On Sat, 2009-06-06 at 00:20 -0700, ali kazempour wrote: > Dear all > I have a question about charge simulation. > In common DFT simulation with neutral charge we have Ewald sum that > describe charge-charge interaction . This sum is not problematic . But the ewald sum is a _method_ to efficiently compute (or rather approximate) the _coulomb contribution_ to the total energy per unitcell in a crystal. > when we simulate for example ionization energy, we have to use > correction like makov-payne . In both case we have charge -charge > interaction . What is the differences between two case? if you take out an electron, you will have a charged unit cell, and due to periodic boundary conditions, this will happen in _every_ unitcell. this is effectively an unphysical situation and such a crystal is not stable. however, you can still do calculations of such systems, if you ignore the g=0 term in the ewald sum. this will lead to an error in the total energy, but it is independent of the positions of the atoms or ions and thus the forces will still be correct. cheers, axel. > Thanks a lot > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Sat Jun 6 16:37:16 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 06 Jun 2009 10:37:16 -0400 Subject: [Pw_forum] How to set the ensemble when doing molecule dynamics calculation with pw.x In-Reply-To: <000001c9e6a0$3a3557a0$ab4f8489@nusa0bcf64b485> References: <000001c9e6a0$3a3557a0$ab4f8489@nusa0bcf64b485> Message-ID: <1244299036.3912.9870.camel@zero> On Sat, 2009-06-06 at 20:13 +0800, Lu Yunhao wrote: > Dear All > Can the pw.x code do molecule dynamic calculation with NVE ensemble? yes, of course! > I search the Manu and can not find any descriptions about ensemble. well, all you have to do is to a) have a constant number of atoms, b) a constant volume, and c) _not_ control the temperature. a) is trivial (you cannot add or remove atoms anyways) b) is simple, too (this is the default) c) only requires a look at the documentation of the &ions namelist. check out "tempw" it cannot get much simpler. axel. > > > Best wishes, > > Yunhao > > Resear Fellow > > NUS > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From gbilalbegovic at gmail.com Sat Jun 6 20:00:00 2009 From: gbilalbegovic at gmail.com (Goranka Bilalbegovic) Date: Sat, 6 Jun 2009 20:00:00 +0200 Subject: [Pw_forum] gipaw quartz example Message-ID: <7332fead0906061100i14b7e860t58c46b0d992b237@mail.gmail.com> Hello, In the GIPAW example for quartz, the nuclear quadrupole moment of 17^O is written as: Q_efg(2)= +2.55 (also in the qe-forge CVS Repository). According to P. Pyykko: Mol. Phys. 106 (2008) 1965-1974, it should be: Q_efg(2)= -2.56. This new and revised "Year-2008 Nuclear Quadrupole Moments" table by Prof. Pekka Pyykko is also available at: http://www.chem.helsinki.fi/~pyykko/Q2008.pdf The same value is on the WebElements: http://www.webelements.com/oxygen/nmr.html Best regards, Goranka --- Goranka Bilalbegovic, Department of Physics, Faculty of Science, University of Zagreb, Croatia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090606/78bcb042/attachment.htm From helen at fh.huji.ac.il Sun Jun 7 11:09:54 2009 From: helen at fh.huji.ac.il (Helen) Date: Sun, 7 Jun 2009 12:09:54 +0300 Subject: [Pw_forum] EXX routine Message-ID: <006201c9e74f$b9153fe0$cd604084@fh.huji.ac.il> I've been using the EXX routine to calculate electronic structure. The routine can calculate the orbital energies at the k-points used in the scf calculation. In an effort to calculate the electronic structure for a general k-point I have been adding the general k-point with an infinitesimal weight to the list of k-points used in the scf calculation along with its symmetry points e.g for nq=4,4,1 K_POINTS 18 0.0000000 0.0000000 0.0000000 0.03125 -0.2500000 0.2500000 -0.2500000 0.25000 0.5000000 -0.5000000 0.5000000 0.12500 0.0000000 0.5000000 0.0000000 0.18750 0.7500000 -0.2500000 0.7500000 0.75000 0.5000000 0.0000000 0.5000000 0.37500 0.0000000 -1.0000000 0.0000000 0.09375 -0.5000000 -1.0000000 0.0000000 0.18750 0.0000000 0.0000000 0.001000 0.0000001 0.2500000 0.2500000 0.25100 0.0000001 0.5000000 0.5000000 0.501000 0.0000001 0.7500000 0.7500000 0.751000 0.0000001 0.0000000 0.0000000 0.501000 0.0000001 0.2500000 0.2500000 0.751000 0.0000001 0.5000000 0.5000000 1.001000 0.0000001 0.0000000 0.0000000 1.001000 0.0000001 0.25 0.25 1.251 0.0000001 0.0 0.0 1.501 0.0000001 This method works fine for LDA routines. It also works OK with the functional we made (BNL, which is a type of hybrid functional of LDA and explicit exchange) when the weight given to the explicit exchange is small. However when I use only the explicit exchange routine or the EXX routine has a more significant weight than LDA, I get spurious results for the general k-point. For example when q=4,4,1 for bulk Si I get at k=0,0,0 orbital energies 3.3785eV and 11.6304eV but at k=0,0,0.001 orbital energies 2.7821eV and 11.8583eV when the energies at k=0,0,0.001 should be almost the same as those at k=0,0,0 This problem doesn't occur when q=1,1,1 and occurs to a lesser extent when q=2,2,1. The results for the 'normal' k-points are fine the problem is only with the general k-point. Can anybody (especially Dr. de Gironcoli) explain this problem? Thank you for your help, Dr. Helen Eisenberg, Fritz-Haber Center for Molecular Dynamics, Hebrew University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090607/36501b96/attachment.htm From marzari at MIT.EDU Sun Jun 7 11:33:31 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Sun, 07 Jun 2009 05:33:31 -0400 Subject: [Pw_forum] EXX routine In-Reply-To: <006201c9e74f$b9153fe0$cd604084@fh.huji.ac.il> References: <006201c9e74f$b9153fe0$cd604084@fh.huji.ac.il> Message-ID: <4A2B896B.8070507@mit.edu> Helen wrote: > This method works fine for LDA routines. It also works OK with the > functional we made (BNL, which is a type of hybrid functional of LDA and > explicit exchange) when the weight given to the explicit exchange is > small. However when I use only the explicit exchange routine or the EXX > routine has a more significant weight than LDA, I get spurious results > for the general k-point. I'll indeed let Stefano chip in, or any other - one question that comes to mind is this: would the results change if you had a much tighter tolerance for convergence ? The code has "global" tolerance thresholds, to which the quasi-empty k-points do not contribute. I think the Davidson algorithm should diagonalize equally well the quasi-empty, but if it struggles, the code will not recognize their struggle. Another naive comment: couldn't you use the nscf or bands option, to diagonalize a posteriori the Hamiltonian at any arbitary point ? A few more points: I am not sure with which precision the code reads the weights (maybe your small weights are read as zero) - and what it does if the sum of the weights is not normalized to 1.0 or 2.0 (as in your case). Last sanity check: what happens if you also give k=0,0,0 a second time, but with the almost-zero weight ? All the best, nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From helen at fh.huji.ac.il Sun Jun 7 13:44:26 2009 From: helen at fh.huji.ac.il (Helen) Date: Sun, 7 Jun 2009 14:44:26 +0300 Subject: [Pw_forum] EXX routine References: <006201c9e74f$b9153fe0$cd604084@fh.huji.ac.il> <4A2B896B.8070507@mit.edu> Message-ID: <007701c9e765$4f2fdde0$cd604084@fh.huji.ac.il> Thank you for your reply, > I'll indeed let Stefano chip in, or any other - one question that comes > to mind is this: would the results change if you had a much tighter > tolerance for convergence ? > > The code has "global" tolerance thresholds, to which the quasi-empty > k-points do not contribute. I think the Davidson algorithm should > diagonalize equally well the quasi-empty, but if it struggles, the code > will not recognize their struggle. I had tried increasing convergence tolerances but it didn't help > A few more points: I am not sure with which precision the > code reads the weights (maybe your small weights are read as > zero) - and what it does if the sum of the weights > is not normalized to 1.0 or 2.0 (as in your case). I checked this within the EXX code, and it is OK > Last sanity check: what happens if you also give k=0,0,0 > a second time, but with the almost-zero weight ? > This is a very good idea, I have just checked it, with strange results, when I do the normal 8 k-points and add at the end k=0,0,0 weight=0.0000001 then I get the correct results. But when I add at the end both k=0,0,0 and k=0.5,0.5,0.5 and k=0,0,1 (the symmetry points needed for nq=2,2,1) all with negligible weights I get wrong results for the orbital energies of k=0,0,0. I will look more closely why this may be happening, Thanks for your help, Helen Fritz-Haber Center, HebrewUniversity From eyvaz_isaev at yahoo.com Mon Jun 8 00:06:24 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 7 Jun 2009 15:06:24 -0700 (PDT) Subject: [Pw_forum] missing q-points Message-ID: <531731.98563.qm@web65704.mail.ac4.yahoo.com> Dear Mehrnaz, The problem is not related to FFTW libraries, it is rather a symmetry problem. Check k-points with the same nq1,nq2, and nq3 (and the same symmetry) with k_points.x. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Sat, 6/6/09, Mehrnaz Anvari wrote: > From: Mehrnaz Anvari > Subject: [Pw_forum] missing q-points > To: pw_forum at pwscf.org > Date: Saturday, June 6, 2009, 4:15 PM > > > > > > > > > > > > > Dear > all > I > tried to > calculate phonon dispersion for graphene in uniform grid > (nq1=2, > nq2=2, nq3=1). In graphene .dyn0 file exist two points, but > after > nscf calculations & phonon performance the code > couldn't find > same q-points so in q2r.x I have this error > > from > init : > error # 1 > > missing > q-point(s)! > I > checked > archive & I saw maybe the problem is due to fftw so I > install > fftw 3.1.2, but yet I have the problem .what can I > do? > Mehrnaz > Iran > University > Of Science & Technology > > > > > > -----Inline Attachment Follows----- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From marc at fq.edu.uy Mon Jun 8 02:03:23 2009 From: marc at fq.edu.uy (marc at fq.edu.uy) Date: Sun, 7 Jun 2009 21:03:23 -0300 (UYT) Subject: [Pw_forum] about forces in CP chemical reactions Message-ID: <50367.190.134.25.202.1244419403.squirrel@webmail.fq.edu.uy> Hi all To do a CP on a chemical reaction, I plan follow steps, minimizing electrons, minimizing ions,randomize positions, finding maximum time step compatible with ficticious electron mass, then the recommendations said to verify forces,comparing BO vs CP forces in several simulations points, as in 2006 Tangley paper, where delta rms between both forces is calculated. There is some recommend delta rms value to chemical reactions ? If not, because depends on system, as I understood which must be done is work with a smaller ficticious mass or do BOMD, could someone clear me this point or signal some seminal job to follow ? Thanking in advance your help and support. Best Regards Marc Segovia Catedra de Quimica Cuantica DETEMA- Facultad de Quimica Universidad de la Republica Uruguay ccbg.fq.edu.uy From somesh.kb at gmail.com Mon Jun 8 07:44:39 2009 From: somesh.kb at gmail.com (Somesh Kumar Bhattacharya) Date: Mon, 8 Jun 2009 07:44:39 +0200 Subject: [Pw_forum] about forces in CP chemical reactions In-Reply-To: <50367.190.134.25.202.1244419403.squirrel@webmail.fq.edu.uy> References: <50367.190.134.25.202.1244419403.squirrel@webmail.fq.edu.uy> Message-ID: Hii Marc, Am sorry to say that I didn't understand what you want. : > Hi all > > To do a CP on a chemical reaction, I plan follow steps, > minimizing electrons, minimizing ions,randomize positions, finding > maximum time step compatible with ficticious electron mass, then the > recommendations said to verify forces,comparing BO vs CP > forces in several simulations points, as in 2006 Tangley paper, where > delta rms between both forces is calculated. > There is some recommend delta rms value to chemical reactions ? What chemical reaction do you want to study?? > If not, because depends on system, as I understood which must be done is > work with a smaller ficticious mass or do BOMD, could someone clear me > this point or signal some seminal job to follow ? http://www.democritos.it/pipermail/pw_forum/2006-April/004004.html > > Thanking in advance your help and support. > > Best Regards > > Marc Segovia > Catedra de Quimica Cuantica > DETEMA- Facultad de Quimica > Universidad de la Republica > Uruguay > ccbg.fq.edu.uy > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Somesh Kr. Bhattacharya Post Doctoral Fellow Room No. 263, Leonardo Building, The Abdus Salam International Centre for Theoretical Physics Strada Costiera, 11 I-34014 Trieste Italy Phone: +39-040-2240399 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090608/a9bbb642/attachment.htm From zdw2000 at gmail.com Mon Jun 8 11:00:23 2009 From: zdw2000 at gmail.com (Wei Zhou) Date: Mon, 8 Jun 2009 17:00:23 +0800 Subject: [Pw_forum] can the pwscf soft do optical conductivity calculations? Message-ID: <3e36a8fc0906080200l2be9f12ew2d3866e7f43f9db5@mail.gmail.com> I just want to do optical conductivity of metal ,so ................. thank you in advance -- ZhouDawei JiLin Universiyt ,ChangChun ,China zdw2000 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090608/b86465ae/attachment.htm From marc at fq.edu.uy Mon Jun 8 13:29:47 2009 From: marc at fq.edu.uy (marc at fq.edu.uy) Date: Mon, 8 Jun 2009 08:29:47 -0300 (UYT) Subject: [Pw_forum] about forces in CP chemical reactions In-Reply-To: References: <50367.190.134.25.202.1244419403.squirrel@webmail.fq.edu.uy> Message-ID: <36713.200.40.206.198.1244460587.squirrel@webmail.fq.edu.uy> Hi Somesh Many thanks for your answer, I have the post that you refer, and read the paper refered, I understand that they said that a forces difference analysis between CP and BO must be done, but also said that they supposse that for chemical reactions the situtation is more delicate, so my question is general about chemical reactions with CP, with criteria are used to check that is running fine, just conserved energy, and delta rms between forces ? I hope now is more clear Best Regards Marc Marc Segovia Catedra de Quimica Cuantica DETEMA- Facultad de Quimica Universidad de la Republica Uruguay ccbg.fq.edu.uy > Hii Marc, > > Am sorry to say that I didn't understand what you want. > : > >> Hi all >> >> To do a CP on a chemical reaction, I plan follow steps, >> minimizing electrons, minimizing ions,randomize positions, finding >> maximum time step compatible with ficticious electron mass, then the >> recommendations said to verify forces,comparing BO vs CP >> forces in several simulations points, as in 2006 Tangley paper, where >> delta rms between both forces is calculated. >> There is some recommend delta rms value to chemical reactions ? > > > What chemical reaction do you want to study?? > > >> If not, because depends on system, as I understood which must be done >> is >> work with a smaller ficticious mass or do BOMD, could someone clear me >> this point or signal some seminal job to follow ? > > > http://www.democritos.it/pipermail/pw_forum/2006-April/004004.html > > > > >> >> Thanking in advance your help and support. >> >> Best Regards >> >> Marc Segovia >> Catedra de Quimica Cuantica >> DETEMA- Facultad de Quimica >> Universidad de la Republica >> Uruguay >> ccbg.fq.edu.uy >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Somesh Kr. Bhattacharya > Post Doctoral Fellow > Room No. 263, > Leonardo Building, > The Abdus Salam International Centre for Theoretical Physics > Strada Costiera, 11 > I-34014 Trieste > Italy > Phone: +39-040-2240399 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Mon Jun 8 14:45:14 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 08 Jun 2009 14:45:14 +0200 Subject: [Pw_forum] transmission calculation In-Reply-To: References: Message-ID: <4A2D07DA.6030906@sissa.it> Dear Manoj Manoj Srivastava wrote: > Dear Gabriele, > Thanks for your response. > On Thu, 4 Jun 2009, Gabriele Sclauzero wrote: > >> Quoting Manoj Srivastava : >> >>> Dear PWSCF users and developers, >>> I have been trying to do the conductance calculation for the twin >>> boundary of Cu. I compared my results with previously done calculations >>> and for most K points the transmission coefficients match up very well. >>> But there are some k points that I get transmission coefficients more than >>> 1! This is not reasonable, as the maximum value of transmission >>> coefficient could be 1.I am getting 1.000345, and similar for other k >>> points. >> Which k-points? How many channels are there? Please send me the output >> file or post the relevant part of it. > > There are quiet a few k points for which transmission is more than 1. I tried to reproduce your calculation and indeed I find transmission coefficients greater than 1. However I think that the problem is in your setup rather than in the program itself. In order for the scf potential to match smoothly across the border between left lead and scattering region, you should include in the leftmost part of the scattering region (SR) a certain number of replicas of the left lead. Being your lead quite long, maybe one replica is sufficient (you should however check if the complex band structure obtained from the leftmost replica in the SR agrees sufficiently with those obtained from the left lead), but in your setup only a part of the left lead is reproduced at the beginning of the SR and I think this is not enough. The same applies to the right lead, which should be included at the rightmost part of the SR (there the situation of your setup seems even worst, since only the atom at the border matches this needing). HTH GS > For example- > k( 3) = ( 0.2500000 0.0000000), wk = 0.1666667 > > ngper, shell number = 317 133 > ngper, n2d = 317 317 > Nchannels of the left tip = 1 > k1(2pi/a) k2(2pi/a) E-Ef (eV) > > 0.0634548 0.0000000 0.0000000 > Nchannels of the right tip = 1 > k1(2pi/a) k2(2pi/a) E-Ef (eV) > > 0.1266351 0.0000000 0.0000000 > to transmit > T_ij for propagating states: > 1 --> 1 1.0000806 > 1.00008 > Eigenchannel decomposition: > @ 1 0.00000 1.00008 > 1.00000 > E-Ef(ev), T(x2 spins) = 0.0000000 2.0001613 > > Also for another k point - > > k( 5) = ( 0.0000000 -0.2500000), wk = 0.1666667 > > ngper, shell number = 317 133 > ngper, n2d = 317 317 > Nchannels of the left tip = 1 > k1(2pi/a) k2(2pi/a) E-Ef (eV) > > 0.0634548 0.0000000 0.0000000 > Nchannels of the right tip = 1 > k1(2pi/a) k2(2pi/a) E-Ef (eV) > > 0.1266351 0.0000000 0.0000000 > to transmit > T_ij for propagating states: > 1 --> 1 1.0000806 > 1.00008 > Eigenchannel decomposition: > @ 1 0.00000 1.00008 > 1.00000 > E-Ef(ev), T(x2 spins) = 0.0000000 2.0001613 > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From kazempoor2000 at yahoo.com Mon Jun 8 14:47:08 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Mon, 8 Jun 2009 05:47:08 -0700 (PDT) Subject: [Pw_forum] vc-relax Message-ID: <688426.31424.qm@web112512.mail.gq1.yahoo.com> Dear all I want to study defect in TiO2. For a supercell with 2*2*3(72 atoms) size , Do I relax the atomic position and lattice parameter simultaneously (vc relax)or not?what about bigger supercell? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 From sclauzer at sissa.it Mon Jun 8 14:54:30 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 08 Jun 2009 14:54:30 +0200 Subject: [Pw_forum] missing q-points In-Reply-To: References: Message-ID: <4A2D0A06.8040700@sissa.it> Mehrnaz Anvari wrote: > Dear all > I tried to calculate phonon dispersion for graphene in uniform grid > (nq1=2, nq2=2, nq3=1). In graphene .dyn0 file exist two points, but > after nscf calculations & phonon performance the code couldn't find same > q-points so in q2r.x I have this error > from init : error # 1 > missing q-point(s)! I understood what you want to do, but not quite how you tried to do it. Please post the input files for all the steps you followed and possibly part of the output file where you find the error message (as well as the version of QE used), otherwise it would be difficult to identify your problem. GS > I checked archive & I saw maybe the problem is due to fftw so I install > fftw 3.1.2, but yet I have the problem .what can I do? > Mehrnaz > Iran University Of Science & Technology > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From paulatto at sissa.it Mon Jun 8 14:55:32 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 08 Jun 2009 14:55:32 +0200 Subject: [Pw_forum] vc-relax In-Reply-To: <688426.31424.qm@web112512.mail.gq1.yahoo.com> References: <688426.31424.qm@web112512.mail.gq1.yahoo.com> Message-ID: In data 08 giugno 2009 alle ore 14:47:08, ali kazempour ha scritto: > > Dear all > I want to study defect in TiO2. For a supercell with 2*2*3(72 atoms) > size , Do I relax the atomic position and lattice parameter > simultaneously (vc relax)or not?what about bigger supercell? Dear Ali, it depends on the system you want to simulate! In other words, if you assume the density of defects to be small, you'll expect the defective supercell to be forced, by the surrounding flawless crystal, to have the same lattice parameter as the unperturbed TiO2. E.g. if you remove a single Oxygen from the middle of a big TiO2 crystal it does not provide enough energy to force the entire crystal to change its lattice parameter, there may be a local strain which you account by taking a big enough supercell. As periodic-boundary condition always imply a relatively high density of defects (one every 12 unit cells, in your case) you have to use the lattice parameter of unpertubed TiO2, and only relax the atoms positions (which will move to compensate the local strain). The system will actually feel a stress, but that's exactly what's happening in the experiment. On the other hand, if you want to study a system with a high density of defects, in your case about 1 every 12 unit cells, than you have to relax the cell parameters together with the ionic positions. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From akohlmey at cmm.chem.upenn.edu Mon Jun 8 15:57:35 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 08 Jun 2009 09:57:35 -0400 Subject: [Pw_forum] about forces in CP chemical reactions In-Reply-To: <36713.200.40.206.198.1244460587.squirrel@webmail.fq.edu.uy> References: <50367.190.134.25.202.1244419403.squirrel@webmail.fq.edu.uy> <36713.200.40.206.198.1244460587.squirrel@webmail.fq.edu.uy> Message-ID: <1244469455.3912.10148.camel@zero> On Mon, 2009-06-08 at 08:29 -0300, marc at fq.edu.uy wrote: hi marc, > Hi Somesh > > Many thanks for your answer, I have the post that you refer, and read the > paper refered, I understand that they said that a forces difference > analysis between CP and BO must be done, but also said that they supposse > that for chemical reactions the situtation is more delicate, so my > question is general about chemical reactions with CP, with criteria are > used to check that is running fine, just conserved energy, and delta rms > between forces ? this is not the problem. the problem with chemical reactions is that the electronic structure changes significantly, which in turn will need the fictitious degrees of freedom (suddenly) to run faster for a while. because of that, the choice of fictitious mass will affect the effective barrier that you are seeing. also, you will have some irreversible transfer of energy from the ionic degrees of freedom to the fictitious degrees of freedom, which will increase your distance from the born-oppenheimer surface. the problem is: decreasing the fictitious mass will keep you closer to the BO surface, but the CP method will eventually break down and also become very inefficient due to the requirement of a very small timestep, but to assess how much a specific choice of fictitious mass (and timestep) will affect a specific system, is very hard to predict. since there are references to the tangney paper. while i believe that this is a very valuable study, its choice of setups to compare are very extreme and thus not representative to the typical choices of parameters which are generally quite safe, unless you have a system that is not "behaving well". the best choices depend strongly on the masses of the lightest atoms in the system, so it is impossible to give a general recommendation other than: try it out, see if it behaves well (i.e. the fictitious dynamics is stable w/o a thermostat) and matches OK with some reference BO snapshots). due to more efficient ways of achieving convergence and effective wavefunction extrapolation schemes that help to counter one of the biggest disadvantages of BO dynamics, the choice of BO over CP seems to become more popular these days. cheers, axel. > I hope now is more clear > > Best Regards > > Marc > > Marc Segovia > Catedra de Quimica Cuantica > DETEMA- Facultad de Quimica > Universidad de la Republica > Uruguay > ccbg.fq.edu.uy > > > > > Hii Marc, > > > > Am sorry to say that I didn't understand what you want. > > : > > > >> Hi all > >> > >> To do a CP on a chemical reaction, I plan follow steps, > >> minimizing electrons, minimizing ions,randomize positions, finding > >> maximum time step compatible with ficticious electron mass, then the > >> recommendations said to verify forces,comparing BO vs CP > >> forces in several simulations points, as in 2006 Tangley paper, where > >> delta rms between both forces is calculated. > >> There is some recommend delta rms value to chemical reactions ? > > > > > > What chemical reaction do you want to study?? > > > > > >> If not, because depends on system, as I understood which must be done > >> is > >> work with a smaller ficticious mass or do BOMD, could someone clear me > >> this point or signal some seminal job to follow ? > > > > > > http://www.democritos.it/pipermail/pw_forum/2006-April/004004.html > > > > > > > > > >> > >> Thanking in advance your help and support. > >> > >> Best Regards > >> > >> Marc Segovia > >> Catedra de Quimica Cuantica > >> DETEMA- Facultad de Quimica > >> Universidad de la Republica > >> Uruguay > >> ccbg.fq.edu.uy > >> > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > > > > > > > > -- > > Somesh Kr. Bhattacharya > > Post Doctoral Fellow > > Room No. 263, > > Leonardo Building, > > The Abdus Salam International Centre for Theoretical Physics > > Strada Costiera, 11 > > I-34014 Trieste > > Italy > > Phone: +39-040-2240399 > > _______________________________________________ > > 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 -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From marc at fq.edu.uy Mon Jun 8 19:33:46 2009 From: marc at fq.edu.uy (marc at fq.edu.uy) Date: Mon, 8 Jun 2009 14:33:46 -0300 (UYT) Subject: [Pw_forum] about forces in CP chemical reactions In-Reply-To: <1244469455.3912.10148.camel@zero> References: <50367.190.134.25.202.1244419403.squirrel@webmail.fq.edu.uy> <36713.200.40.206.198.1244460587.squirrel@webmail.fq.edu.uy> <1244469455.3912.10148.camel@zero> Message-ID: <64656.200.40.206.198.1244482426.squirrel@webmail.fq.edu.uy> Thank you Axel, the point is understood.regards.marc > On Mon, 2009-06-08 at 08:29 -0300, marc at fq.edu.uy wrote: > > hi marc, > >> Hi Somesh >> >> Many thanks for your answer, I have the post that you refer, and read >> the >> paper refered, I understand that they said that a forces difference >> analysis between CP and BO must be done, but also said that they >> supposse >> that for chemical reactions the situtation is more delicate, so my >> question is general about chemical reactions with CP, with criteria are >> used to check that is running fine, just conserved energy, and delta rms >> between forces ? > > this is not the problem. the problem with chemical reactions is that > the electronic structure changes significantly, which in turn will > need the fictitious degrees of freedom (suddenly) to run faster for > a while. because of that, the choice of fictitious mass will affect > the effective barrier that you are seeing. also, you will have some > irreversible transfer of energy from the ionic degrees of freedom > to the fictitious degrees of freedom, which will increase your distance > from the born-oppenheimer surface. the problem is: decreasing the > fictitious mass will keep you closer to the BO surface, but the > CP method will eventually break down and also become very inefficient > due to the requirement of a very small timestep, but to assess how > much a specific choice of fictitious mass (and timestep) will affect > a specific system, is very hard to predict. > > since there are references to the tangney paper. while i believe that > this is a very valuable study, its choice of setups to compare are > very extreme and thus not representative to the typical choices of > parameters which are generally quite safe, unless you have a system > that is not "behaving well". the best choices depend strongly on > the masses of the lightest atoms in the system, so it is impossible > to give a general recommendation other than: try it out, see if it > behaves well (i.e. the fictitious dynamics is stable w/o a thermostat) > and matches OK with some reference BO snapshots). due to more efficient > ways of achieving convergence and effective wavefunction extrapolation > schemes that help to counter one of the biggest disadvantages of BO > dynamics, the choice of BO over CP seems to become more popular these > days. > > cheers, > axel. > >> I hope now is more clear >> >> Best Regards >> >> Marc >> >> Marc Segovia >> Catedra de Quimica Cuantica >> DETEMA- Facultad de Quimica >> Universidad de la Republica >> Uruguay >> ccbg.fq.edu.uy >> >> >> >> > Hii Marc, >> > >> > Am sorry to say that I didn't understand what you want. >> > : >> > >> >> Hi all >> >> >> >> To do a CP on a chemical reaction, I plan follow steps, >> >> minimizing electrons, minimizing ions,randomize positions, finding >> >> maximum time step compatible with ficticious electron mass, then the >> >> recommendations said to verify forces,comparing BO vs CP >> >> forces in several simulations points, as in 2006 Tangley paper, where >> >> delta rms between both forces is calculated. >> >> There is some recommend delta rms value to chemical reactions ? >> > >> > >> > What chemical reaction do you want to study?? >> > >> > >> >> If not, because depends on system, as I understood which must be >> done >> >> is >> >> work with a smaller ficticious mass or do BOMD, could someone clear >> me >> >> this point or signal some seminal job to follow ? >> > >> > >> > http://www.democritos.it/pipermail/pw_forum/2006-April/004004.html >> > >> > >> > >> > >> >> >> >> Thanking in advance your help and support. >> >> >> >> Best Regards >> >> >> >> Marc Segovia >> >> Catedra de Quimica Cuantica >> >> DETEMA- Facultad de Quimica >> >> Universidad de la Republica >> >> Uruguay >> >> ccbg.fq.edu.uy >> >> >> >> _______________________________________________ >> >> Pw_forum mailing list >> >> Pw_forum at pwscf.org >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> > >> > >> > >> > -- >> > Somesh Kr. Bhattacharya >> > Post Doctoral Fellow >> > Room No. 263, >> > Leonardo Building, >> > The Abdus Salam International Centre for Theoretical Physics >> > Strada Costiera, 11 >> > I-34014 Trieste >> > Italy >> > Phone: +39-040-2240399 >> > _______________________________________________ >> > 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 > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From phylyh at nus.edu.sg Tue Jun 9 03:53:37 2009 From: phylyh at nus.edu.sg (Lu Yunhao) Date: Tue, 9 Jun 2009 09:53:37 +0800 Subject: [Pw_forum] How to set the ensemble when doing molecule In-Reply-To: Message-ID: <000901c9e8a5$1adc8fc0$ab4f8489@nusa0bcf64b485> If I set ion_temperature= 'not_controlled', the tempw is still used and meaningful? I attach part of my input file as follows. Is it right? By the way, I add electric field along Z direction. &CONTROL title = 'MD-contT' , calculation = 'md' , prefix='MD-contT', restart_mode = 'from_scratch' , tefield=.true., outdir = '/home/phylyh/Au_gr-check/MD-contT/tmp' , pseudo_dir = '/home/phylyh/pseudo_dir' , dt=40, nstep=500, &IONS ion_dynamics='verlet', ion_temperature='rescale-v', tempw=300.D0, nraise=1, tolp=100, pot_extrapolation='second-order', wfc_extrapolation='second-order' / Message: 5 Date: Sat, 06 Jun 2009 10:37:16 -0400 From: Axel Kohlmeyer Subject: Re: [Pw_forum] How to set the ensemble when doing molecule dynamics calculation with pw.x To: PWSCF Forum Message-ID: <1244299036.3912.9870.camel at zero> Content-Type: text/plain On Sat, 2009-06-06 at 20:13 +0800, Lu Yunhao wrote: > Dear All > Can the pw.x code do molecule dynamic calculation with NVE ensemble? yes, of course! > I search the Manu and can not find any descriptions about ensemble. well, all you have to do is to a) have a constant number of atoms, b) a constant volume, and c) _not_ control the temperature. a) is trivial (you cannot add or remove atoms anyways) b) is simple, too (this is the default) c) only requires a look at the documentation of the &ions namelist. check out "tempw" it cannot get much simpler. axel. > > > Best wishes, > > Yunhao > > Resear Fellow > > NUS > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. ------------------------------ From akohlmey at cmm.chem.upenn.edu Tue Jun 9 04:34:55 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 8 Jun 2009 22:34:55 -0400 Subject: [Pw_forum] How to set the ensemble when doing molecule In-Reply-To: <000901c9e8a5$1adc8fc0$ab4f8489@nusa0bcf64b485> References: <000901c9e8a5$1adc8fc0$ab4f8489@nusa0bcf64b485> Message-ID: <7b6913e90906081934p534fa40v2660e90a90b6e492@mail.gmail.com> On Mon, Jun 8, 2009 at 9:53 PM, Lu Yunhao wrote: > If I set ion_temperature= 'not_controlled', the tempw is still used and > meaningful? yes. it will set the initial temperature. > I attach part of my input file as follows. Is it right? By the way, I add > electric field along Z direction. if you add an electric field, you _don't_ do an NVE ensemble by not controlling the temperature. the external field will create energy, i.e. you'll have a non-equilibrium system. > > &CONTROL > ? ? ? ? ? ? ? ? title = 'MD-contT' , > ? ? ? ? ? ? ? ? calculation = 'md' , > ? ? ? ? ? ? ? ?prefix='MD-contT', > ? ? ? ? ? ? ? ?restart_mode = 'from_scratch' , > ? ? ? ? ? ? ? ? tefield=.true., > ? ? ? ? ? ? ? ? ?outdir = '/home/phylyh/Au_gr-check/MD-contT/tmp' , > ? ? ? ? ? ? ? ? ?pseudo_dir = '/home/phylyh/pseudo_dir' , > ? ? ? ? ? ? ? ? dt=40, > ? ? ? ? ? ? ? ? nstep=500, > &IONS > ? ?ion_dynamics='verlet', > ? ?ion_temperature='rescale-v', > ? ?tempw=300.D0, > ? ?nraise=1, > ? ?tolp=100, if you use rescale and tolp, you are not in a defined ensemble either. since you remove or add energy to your system in an arbitrary way. cheers, axel. > ? ?pot_extrapolation='second-order', > ? ?wfc_extrapolation='second-order' > / > > > > Message: 5 > Date: Sat, 06 Jun 2009 10:37:16 -0400 > From: Axel Kohlmeyer > Subject: Re: [Pw_forum] How to set the ensemble when doing molecule > ? ? ? ?dynamics calculation with pw.x > To: PWSCF Forum > Message-ID: <1244299036.3912.9870.camel at zero> > Content-Type: text/plain > > On Sat, 2009-06-06 at 20:13 +0800, Lu Yunhao wrote: >> Dear All > >> Can the pw.x code do molecule dynamic calculation with NVE ensemble? > > yes, of course! > >> I search the Manu and can not find any descriptions about ensemble. > > well, all you have to do is to a) have a constant number of atoms, > b) a constant volume, and c) _not_ control the temperature. > > a) is trivial (you cannot add or remove atoms anyways) > b) is simple, too (this is the default) > c) only requires a look at the documentation of the &ions > ? namelist. check out "tempw" > > > it cannot get much simpler. > ? ?axel. >> >> >> Best wishes, >> >> Yunhao >> >> Resear Fellow >> >> NUS >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer ? akohlmey at cmm.chem.upenn.edu ? http://www.cmm.upenn.edu > ? Center for Molecular Modeling ? -- ? University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, ?fax: 1-215-573-6233, ?office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From mambom1902 at yahoo.com Tue Jun 9 05:03:17 2009 From: mambom1902 at yahoo.com (loc duong ding) Date: Mon, 8 Jun 2009 20:03:17 -0700 (PDT) Subject: [Pw_forum] Problem with parallel running by mpich2 In-Reply-To: References: Message-ID: <338657.51336.qm@web38804.mail.mud.yahoo.com> > doesn't it even print the first dozen of lines? If it does, it may just be? > the usual problem with input redirection: try feeding the input file by? > using the syntax >?? mpich2 [...] pw.x -in input.in [...] > which is more parallel safe. > > regards > > > -- > Lorenzo Paulatto It is solved.?Thank you very much, Prof. Lorenzo Paullatto. Sincerely,?----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com From mambom1902 at yahoo.com Tue Jun 9 08:03:40 2009 From: mambom1902 at yahoo.com (loc duong ding) Date: Mon, 8 Jun 2009 23:03:40 -0700 (PDT) Subject: [Pw_forum] Problem when compile Quantum espresso (CVS) Message-ID: <700031.57815.qm@web38803.mail.mud.yahoo.com> ?Dear developers and users, ? I complie QE (CVS version) with my PC with Ferdora linux and Cywin without any problem.? However, when I try to complie with my cluster (Centos, i686-pc-linux-gnu,? architecture ia32), I have a problem. The error message is: ? In file casino2upf.f90:98? ????? REAL*8, ALLOCATABLE :: wavefunc(:) ?????????????????????? 1 ?Error: Attribute at (1) is not allowed in a TYPE definition ??In file casino2upf.f90:304 ???????? IF ( ALLOCATED(mtail%wavefunc) ) THEN ???????????????????????????????????? 1 ?Error: 'wavefunc' at (1) is not a member of the 'wavfun_list' structure ??In file casino2upf.f90:308 ??????????? ALLOCATE( mtail%wavefunc(mesh_) ) ?????????????????????????????????? 1 ?Error: 'wavefunc' at (1) is not a member of the 'wavfun_list' structure ??In file casino2upf.f90:309 ???????? ELSE ??????????? 1 ?Error: Unexpected ELSE statement at (1) ??In file casino2upf.f90:310 ??????????? ALLOCATE( mtail%wavefunc(mesh_) ) ?????????????????????????????????? 1 ?Error: 'wavefunc' at (1) is not a member of the 'wavfun_list' structure ??In file casino2upf.f90:311 ???????? END IF ?????????? 1 ?Error: Expecting END DO statement at (1) ??In file casino2upf.f90:317 ???????? READ(j, *, err=300) (mtail%wavefunc(ir),ir=1,mesh_) ?????????????????????????? 1 ?Error: Expected variable in READ statement at (1) ??In file casino2upf.f90:352 ???????? chi_(ir:,i) = mptr%wavefunc(ir) ?????????????????????????????????? 1 ?Error: 'wavefunc' at (1) is not a member of the 'wavfun_list' structure ??In file casino2upf.f90:354 ????? deallocate( mptr%wavefunc ) ????????????????????????????? 1 ?Error: 'wavefunc' at (1) is not a member of the 'wavfun_list' structure ?make[1]: *** [casino2upf.o] Error 1 ?make[1]: Leaving directory `/home/loc/espresso/upftools' ?make: *** [upf] Error 2 ? I don't know where this error come from. Could you give me some instructions for? solving this error? I am running QE4.0 in this cluster. ? Sincerely,? Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com ? From giannozz at democritos.it Tue Jun 9 08:18:11 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 9 Jun 2009 08:18:11 +0200 Subject: [Pw_forum] Problem when compile Quantum espresso (CVS) In-Reply-To: <700031.57815.qm@web38803.mail.mud.yahoo.com> References: <700031.57815.qm@web38803.mail.mud.yahoo.com> Message-ID: On Jun 9, 2009, at 8:03 , loc duong ding wrote: > REAL*8, ALLOCATABLE :: wavefunc(:) > 1 > Error: Attribute at (1) is not allowed in a TYPE definition allocatable arrays in derived types are not allowed in fortran-90 standard but only in fortran-95 standard (e.g. old versions of gfortran do not like them). You need a fortran-95 compiler to complile recent versions of q-e. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From marzari at MIT.EDU Tue Jun 9 09:39:38 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Tue, 09 Jun 2009 03:39:38 -0400 Subject: [Pw_forum] [Fwd: Re: [Fwd: gipaw quartz example]] Message-ID: <4A2E11BA.2010708@mit.edu> -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu -------------- next part -------------- An embedded message was scrubbed... From: Francesco Mauri Subject: Re: [Fwd: [Pw_forum] gipaw quartz example] Date: Tue, 09 Jun 2009 09:36:30 +0200 Size: 6021 Url: http://www.democritos.it/pipermail/pw_forum/attachments/20090609/033fc606/attachment.eml From phylyh at nus.edu.sg Tue Jun 9 10:13:43 2009 From: phylyh at nus.edu.sg (Lu Yunhao) Date: Tue, 9 Jun 2009 16:13:43 +0800 Subject: [Pw_forum] How to set the ensemble when doing molecule In-Reply-To: Message-ID: <002f01c9e8da$34211e30$ab4f8489@nusa0bcf64b485> Yes, you are quite right. Now, I just try to compare results with different parameter. If I set ion_temperature='not_controlled', the nraise=1, and tolp=100, are still used or have some other meaning. When I do NVE MD in E-field, the following setting is right? ion_dynamics='verlet', ion_temperature= 'rescale-v' , tempw=300.D0, nraise=1, tolp=100, Thanks a lot Best wishes, Yunhao NUS Message: 2 Date: Mon, 8 Jun 2009 22:34:55 -0400 From: Axel Kohlmeyer Subject: Re: [Pw_forum] How to set the ensemble when doing molecule To: PWSCF Forum Message-ID: <7b6913e90906081934p534fa40v2660e90a90b6e492 at mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 On Mon, Jun 8, 2009 at 9:53 PM, Lu Yunhao wrote: > If I set ion_temperature= 'not_controlled', the tempw is still used and > meaningful? yes. it will set the initial temperature. > I attach part of my input file as follows. Is it right? By the way, I add > electric field along Z direction. if you add an electric field, you _don't_ do an NVE ensemble by not controlling the temperature. the external field will create energy, i.e. you'll have a non-equilibrium system. > > &CONTROL > ? ? ? ? ? ? ? ? title = 'MD-contT' , > ? ? ? ? ? ? ? ? calculation = 'md' , > ? ? ? ? ? ? ? ?prefix='MD-contT', > ? ? ? ? ? ? ? ?restart_mode = 'from_scratch' , > ? ? ? ? ? ? ? ? tefield=.true., > ? ? ? ? ? ? ? ? ?outdir = '/home/phylyh/Au_gr-check/MD-contT/tmp' , > ? ? ? ? ? ? ? ? ?pseudo_dir = '/home/phylyh/pseudo_dir' , > ? ? ? ? ? ? ? ? dt=40, > ? ? ? ? ? ? ? ? nstep=500, > &IONS > ? ?ion_dynamics='verlet', > ? ?ion_temperature='rescale-v', > ? ?tempw=300.D0, > ? ?nraise=1, > ? ?tolp=100, if you use rescale and tolp, you are not in a defined ensemble either. since you remove or add energy to your system in an arbitrary way. cheers, axel. > ? ?pot_extrapolation='second-order', > ? ?wfc_extrapolation='second-order' > / > > > > Message: 5 > Date: Sat, 06 Jun 2009 10:37:16 -0400 > From: Axel Kohlmeyer > Subject: Re: [Pw_forum] How to set the ensemble when doing molecule > ? ? ? ?dynamics calculation with pw.x > To: PWSCF Forum > Message-ID: <1244299036.3912.9870.camel at zero> > Content-Type: text/plain > > On Sat, 2009-06-06 at 20:13 +0800, Lu Yunhao wrote: >> Dear All > >> Can the pw.x code do molecule dynamic calculation with NVE ensemble? > > yes, of course! > >> I search the Manu and can not find any descriptions about ensemble. > > well, all you have to do is to a) have a constant number of atoms, > b) a constant volume, and c) _not_ control the temperature. > > a) is trivial (you cannot add or remove atoms anyways) > b) is simple, too (this is the default) > c) only requires a look at the documentation of the &ions > ? namelist. check out "tempw" > > > it cannot get much simpler. > ? ?axel. >> >> >> Best wishes, >> >> Yunhao >> >> Resear Fellow >> >> NUS >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer ? akohlmey at cmm.chem.upenn.edu ? http://www.cmm.upenn.edu > ? Center for Molecular Modeling ? -- ? University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, ?fax: 1-215-573-6233, ?office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. ------------------------------ Message: 3 Date: Mon, 8 Jun 2009 20:03:17 -0700 (PDT) From: loc duong ding Subject: Re: [Pw_forum] Problem with parallel running by mpich2 To: pw_forum at pwscf.org Message-ID: <338657.51336.qm at web38804.mail.mud.yahoo.com> Content-Type: text/plain; charset=iso-8859-1 > doesn't it even print the first dozen of lines? If it does, it may just be? > the usual problem with input redirection: try feeding the input file by? > using the syntax >?? mpich2 [...] pw.x -in input.in [...] > which is more parallel safe. > > regards > > > -- > Lorenzo Paulatto It is solved.?Thank you very much, Prof. Lorenzo Paullatto. Sincerely,?----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com ------------------------------ Message: 4 Date: Mon, 8 Jun 2009 23:03:40 -0700 (PDT) From: loc duong ding Subject: [Pw_forum] Problem when compile Quantum espresso (CVS) To: PWscf forum Message-ID: <700031.57815.qm at web38803.mail.mud.yahoo.com> Content-Type: text/plain; charset=iso-8859-1 ?Dear developers and users, ? I complie QE (CVS version) with my PC with Ferdora linux and Cywin without any problem.? However, when I try to complie with my cluster (Centos, i686-pc-linux-gnu,? architecture ia32), I have a problem. The error message is: ? In file casino2upf.f90:98? ????? REAL*8, ALLOCATABLE :: wavefunc(:) ?????????????????????? 1 ?Error: Attribute at (1) is not allowed in a TYPE definition ??In file casino2upf.f90:304 ???????? IF ( ALLOCATED(mtail%wavefunc) ) THEN ???????????????????????????????????? 1 ?Error: 'wavefunc' at (1) is not a member of the 'wavfun_list' structure ??In file casino2upf.f90:308 ??????????? ALLOCATE( mtail%wavefunc(mesh_) ) ?????????????????????????????????? 1 ?Error: 'wavefunc' at (1) is not a member of the 'wavfun_list' structure ??In file casino2upf.f90:309 ???????? ELSE ??????????? 1 ?Error: Unexpected ELSE statement at (1) ??In file casino2upf.f90:310 ??????????? ALLOCATE( mtail%wavefunc(mesh_) ) ?????????????????????????????????? 1 ?Error: 'wavefunc' at (1) is not a member of the 'wavfun_list' structure ??In file casino2upf.f90:311 ???????? END IF ?????????? 1 ?Error: Expecting END DO statement at (1) ??In file casino2upf.f90:317 ???????? READ(j, *, err=300) (mtail%wavefunc(ir),ir=1,mesh_) ?????????????????????????? 1 ?Error: Expected variable in READ statement at (1) ??In file casino2upf.f90:352 ???????? chi_(ir:,i) = mptr%wavefunc(ir) ?????????????????????????????????? 1 ?Error: 'wavefunc' at (1) is not a member of the 'wavfun_list' structure ??In file casino2upf.f90:354 ????? deallocate( mptr%wavefunc ) ????????????????????????????? 1 ?Error: 'wavefunc' at (1) is not a member of the 'wavfun_list' structure ?make[1]: *** [casino2upf.o] Error 1 ?make[1]: Leaving directory `/home/loc/espresso/upftools' ?make: *** [upf] Error 2 ? I don't know where this error come from. Could you give me some instructions for? solving this error? I am running QE4.0 in this cluster. ? Sincerely,? Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com ? ------------------------------ Message: 5 Date: Tue, 9 Jun 2009 08:18:11 +0200 From: Paolo Giannozzi Subject: Re: [Pw_forum] Problem when compile Quantum espresso (CVS) To: PWSCF Forum Message-ID: Content-Type: text/plain; charset=US-ASCII; format=flowed On Jun 9, 2009, at 8:03 , loc duong ding wrote: > REAL*8, ALLOCATABLE :: wavefunc(:) > 1 > Error: Attribute at (1) is not allowed in a TYPE definition allocatable arrays in derived types are not allowed in fortran-90 standard but only in fortran-95 standard (e.g. old versions of gfortran do not like them). You need a fortran-95 compiler to complile recent versions of q-e. Paolo --- Paolo Giannozzi, Dept of Physics, University of 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 24, Issue 12 **************************************** From phylyh at nus.edu.sg Tue Jun 9 10:17:09 2009 From: phylyh at nus.edu.sg (Lu Yunhao) Date: Tue, 9 Jun 2009 16:17:09 +0800 Subject: [Pw_forum] =?gb2312?b?tPC4tDogIEhvdyB0byBzZXQgdGhlIGVuc2VtYmxl?= =?gb2312?b?IHdoZW4gZG9pbmcgbW9sZWN1bGU=?= Message-ID: <003301c9e8da$af25e2a0$ab4f8489@nusa0bcf64b485> It is possible to do MD with initial T=0K? it seems the tempw can not be set to zero. -----????----- ???: Lu Yunhao [mailto:phylyh at nus.edu.sg] ????: 2009?6?9? 16:14 ???: 'pw_forum at pwscf.org' ??: Re: [Pw_forum] How to set the ensemble when doing molecule Yes, you are quite right. Now, I just try to compare results with different parameter. If I set ion_temperature='not_controlled', the nraise=1, and tolp=100, are still used or have some other meaning. When I do NVE MD in E-field, the following setting is right? ion_dynamics='verlet', ion_temperature= 'rescale-v' , tempw=300.D0, nraise=1, tolp=100, Thanks a lot Best wishes, Yunhao NUS Message: 2 Date: Mon, 8 Jun 2009 22:34:55 -0400 From: Axel Kohlmeyer Subject: Re: [Pw_forum] How to set the ensemble when doing molecule To: PWSCF Forum Message-ID: <7b6913e90906081934p534fa40v2660e90a90b6e492 at mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 On Mon, Jun 8, 2009 at 9:53 PM, Lu Yunhao wrote: > If I set ion_temperature= 'not_controlled', the tempw is still used and > meaningful? yes. it will set the initial temperature. > I attach part of my input file as follows. Is it right? By the way, I add > electric field along Z direction. if you add an electric field, you _don't_ do an NVE ensemble by not controlling the temperature. the external field will create energy, i.e. you'll have a non-equilibrium system. > > &CONTROL > ? ? ? ? ? ? ? ? title = 'MD-contT' , > ? ? ? ? ? ? ? ? calculation = 'md' , > ? ? ? ? ? ? ? ?prefix='MD-contT', > ? ? ? ? ? ? ? ?restart_mode = 'from_scratch' , > ? ? ? ? ? ? ? ? tefield=.true., > ? ? ? ? ? ? ? ? ?outdir = '/home/phylyh/Au_gr-check/MD-contT/tmp' , > ? ? ? ? ? ? ? ? ?pseudo_dir = '/home/phylyh/pseudo_dir' , > ? ? ? ? ? ? ? ? dt=40, > ? ? ? ? ? ? ? ? nstep=500, > &IONS > ? ?ion_dynamics='verlet', > ? ?ion_temperature='rescale-v', > ? ?tempw=300.D0, > ? ?nraise=1, > ? ?tolp=100, if you use rescale and tolp, you are not in a defined ensemble either. since you remove or add energy to your system in an arbitrary way. cheers, axel. > ? ?pot_extrapolation='second-order', > ? ?wfc_extrapolation='second-order' > / > > > > Message: 5 > Date: Sat, 06 Jun 2009 10:37:16 -0400 > From: Axel Kohlmeyer > Subject: Re: [Pw_forum] How to set the ensemble when doing molecule > ? ? ? ?dynamics calculation with pw.x > To: PWSCF Forum > Message-ID: <1244299036.3912.9870.camel at zero> > Content-Type: text/plain > > On Sat, 2009-06-06 at 20:13 +0800, Lu Yunhao wrote: >> Dear All > >> Can the pw.x code do molecule dynamic calculation with NVE ensemble? > > yes, of course! > >> I search the Manu and can not find any descriptions about ensemble. > > well, all you have to do is to a) have a constant number of atoms, > b) a constant volume, and c) _not_ control the temperature. > > a) is trivial (you cannot add or remove atoms anyways) > b) is simple, too (this is the default) > c) only requires a look at the documentation of the &ions > ? namelist. check out "tempw" > > > it cannot get much simpler. > ? ?axel. >> >> >> Best wishes, >> >> Yunhao >> >> Resear Fellow >> >> NUS >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer ? akohlmey at cmm.chem.upenn.edu ? http://www.cmm.upenn.edu > ? Center for Molecular Modeling ? -- ? University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, ?fax: 1-215-573-6233, ?office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. ------------------------------ Message: 3 Date: Mon, 8 Jun 2009 20:03:17 -0700 (PDT) From: loc duong ding Subject: Re: [Pw_forum] Problem with parallel running by mpich2 To: pw_forum at pwscf.org Message-ID: <338657.51336.qm at web38804.mail.mud.yahoo.com> Content-Type: text/plain; charset=iso-8859-1 > doesn't it even print the first dozen of lines? If it does, it may just be? > the usual problem with input redirection: try feeding the input file by? > using the syntax >?? mpich2 [...] pw.x -in input.in [...] > which is more parallel safe. > > regards > > > -- > Lorenzo Paulatto It is solved.?Thank you very much, Prof. Lorenzo Paullatto. Sincerely,?----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com ------------------------------ Message: 4 Date: Mon, 8 Jun 2009 23:03:40 -0700 (PDT) From: loc duong ding Subject: [Pw_forum] Problem when compile Quantum espresso (CVS) To: PWscf forum Message-ID: <700031.57815.qm at web38803.mail.mud.yahoo.com> Content-Type: text/plain; charset=iso-8859-1 ?Dear developers and users, ? I complie QE (CVS version) with my PC with Ferdora linux and Cywin without any problem.? However, when I try to complie with my cluster (Centos, i686-pc-linux-gnu,? architecture ia32), I have a problem. The error message is: ? In file casino2upf.f90:98? ????? REAL*8, ALLOCATABLE :: wavefunc(:) ?????????????????????? 1 ?Error: Attribute at (1) is not allowed in a TYPE definition ??In file casino2upf.f90:304 ???????? IF ( ALLOCATED(mtail%wavefunc) ) THEN ???????????????????????????????????? 1 ?Error: 'wavefunc' at (1) is not a member of the 'wavfun_list' structure ??In file casino2upf.f90:308 ??????????? ALLOCATE( mtail%wavefunc(mesh_) ) ?????????????????????????????????? 1 ?Error: 'wavefunc' at (1) is not a member of the 'wavfun_list' structure ??In file casino2upf.f90:309 ???????? ELSE ??????????? 1 ?Error: Unexpected ELSE statement at (1) ??In file casino2upf.f90:310 ??????????? ALLOCATE( mtail%wavefunc(mesh_) ) ?????????????????????????????????? 1 ?Error: 'wavefunc' at (1) is not a member of the 'wavfun_list' structure ??In file casino2upf.f90:311 ???????? END IF ?????????? 1 ?Error: Expecting END DO statement at (1) ??In file casino2upf.f90:317 ???????? READ(j, *, err=300) (mtail%wavefunc(ir),ir=1,mesh_) ?????????????????????????? 1 ?Error: Expected variable in READ statement at (1) ??In file casino2upf.f90:352 ???????? chi_(ir:,i) = mptr%wavefunc(ir) ?????????????????????????????????? 1 ?Error: 'wavefunc' at (1) is not a member of the 'wavfun_list' structure ??In file casino2upf.f90:354 ????? deallocate( mptr%wavefunc ) ????????????????????????????? 1 ?Error: 'wavefunc' at (1) is not a member of the 'wavfun_list' structure ?make[1]: *** [casino2upf.o] Error 1 ?make[1]: Leaving directory `/home/loc/espresso/upftools' ?make: *** [upf] Error 2 ? I don't know where this error come from. Could you give me some instructions for? solving this error? I am running QE4.0 in this cluster. ? Sincerely,? Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com ? ------------------------------ Message: 5 Date: Tue, 9 Jun 2009 08:18:11 +0200 From: Paolo Giannozzi Subject: Re: [Pw_forum] Problem when compile Quantum espresso (CVS) To: PWSCF Forum Message-ID: Content-Type: text/plain; charset=US-ASCII; format=flowed On Jun 9, 2009, at 8:03 , loc duong ding wrote: > REAL*8, ALLOCATABLE :: wavefunc(:) > 1 > Error: Attribute at (1) is not allowed in a TYPE definition allocatable arrays in derived types are not allowed in fortran-90 standard but only in fortran-95 standard (e.g. old versions of gfortran do not like them). You need a fortran-95 compiler to complile recent versions of q-e. Paolo --- Paolo Giannozzi, Dept of Physics, University of 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 24, Issue 12 **************************************** From mambom1902 at yahoo.com Tue Jun 9 10:48:36 2009 From: mambom1902 at yahoo.com (loc duong ding) Date: Tue, 9 Jun 2009 01:48:36 -0700 (PDT) Subject: [Pw_forum] Problem when compile Quantum espresso (CVS) Message-ID: <826416.66333.qm@web38808.mail.mud.yahoo.com> The problem have been?solved by Daniel's instructions. >Dear Loc, >The main error is at the beginning: >In file casino2upf.f90:98 >???? REAL*8, ALLOCATABLE :: wavefunc(:) ?>????????????????????? 1 >Error: Attribute at (1) is not allowed in a TYPE definition >in fact, ALLOCATABLE arrays are not allowed in a TYPE block, at least in fortran90 (maybe they are in >fortran95). >If you need this file, you can either try to use another compiler (intel 11 should work) >If you don't need to use casino2upf (it convert a pseudopotential written in CASINO >to unified pseudopotential format UPF), I suggest you to compile PWscf as "make pw" >or "make pwall", this will prevent the compilation of casino2upf. >If you need this file, you can either try to use another compiler (intel 11 should work) >or modify the casino2upf.f90 by replacing the "ALLOCATABLE" attribute at line 98 >with "POINTER" (you can always allocate a pointer). >cheers >daniel ?----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com From akohlmey at cmm.chem.upenn.edu Tue Jun 9 15:13:37 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 09 Jun 2009 09:13:37 -0400 Subject: [Pw_forum] =?utf-8?b?562U5aSNOiBIb3cgdG8gc2V0IHRoZSBlbnNlbWJsZSB3?= =?utf-8?q?hen_doing_molecule?= In-Reply-To: <003301c9e8da$af25e2a0$ab4f8489@nusa0bcf64b485> References: <003301c9e8da$af25e2a0$ab4f8489@nusa0bcf64b485> Message-ID: <1244553217.5214.19.camel@zero> On Tue, 2009-06-09 at 16:17 +0800, Lu Yunhao wrote: > It is possible to do MD with initial T=0K? it seems the tempw can not be set > to zero. just set it to 0.1 or alike. that is pretty well the same thing. if your system is of high potential energy, it doesn't matter, if you system is not, the atoms won't move anyways. it is hard for me to see how you can get meaningful dynamics out of the kind of setup you are describing, as your requirements to the MD and the properties of the system seem to contradict each other. axel. -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From rfaccio at fq.edu.uy Tue Jun 9 15:38:54 2009 From: rfaccio at fq.edu.uy (Ricardo Faccio) Date: Tue, 9 Jun 2009 10:38:54 -0300 Subject: [Pw_forum] LDA pseudo for F Message-ID: <003001c9e907$a2327b30$0402a8c0@ricardof> Dear PWscf users I wonder if any of you could send me a LDA pseudo for fluoride. Thanks in advance. Ricardo ------------------------------------------------------------------------- Dr. Ricardo Faccio Prof. Adjunto de F?sica Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA Facultad de Qu?mica, Universidad de la Rep?blica Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio at fq.edu.uy Phone: 598 2 924 98 59 598 2 929 06 48 Fax: 598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm --------------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090609/457e872a/attachment.htm From baroni at sissa.it Tue Jun 9 21:21:35 2009 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 9 Jun 2009 21:21:35 +0200 Subject: [Pw_forum] LDA pseudo for F In-Reply-To: <003001c9e907$a2327b30$0402a8c0@ricardof> References: <003001c9e907$a2327b30$0402a8c0@ricardof> Message-ID: <2B479569-E0F1-44D6-9FF2-8D3046C140B6@sissa.it> Ricardo: you mean fluorine, I guess .?... On Jun 9, 2009, at 3:38 PM, Ricardo Faccio wrote: > Dear PWscf users > I wonder if any of you could send me a LDA pseudo for fluoride. > Thanks in advance. > Ricardo > ------------------------------------------------------------------------- > Dr. Ricardo Faccio > Prof. Adjunto de F?sica > Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA > Facultad de Qu?mica, Universidad de la Rep?blica > Av. Gral. Flores 2124, C.C. 1157 > C.P. 11800, Montevideo, Uruguay. > E-mail: rfaccio at fq.edu.uy > Phone: 598 2 924 98 59 > 598 2 929 06 48 > Fax: 598 2 9241906 > Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm > --------------------------------------------------------------------------------- > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090609/49181f3c/attachment.htm From rfaccio at fq.edu.uy Tue Jun 9 22:30:46 2009 From: rfaccio at fq.edu.uy (Ricardo Faccio) Date: Tue, 9 Jun 2009 17:30:46 -0300 Subject: [Pw_forum] LDA pseudo for F References: <003001c9e907$a2327b30$0402a8c0@ricardof> <2B479569-E0F1-44D6-9FF2-8D3046C140B6@sissa.it> Message-ID: <006e01c9e941$2bb4b920$0402a8c0@ricardof> Dear Stefano Yes! I mean fluorine. Thanks Ricardo ------------------------------------------------------------------------- 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 --------------------------------------------------------------------------------- ----- Original Message ----- From: Stefano Baroni To: PWSCF Forum Sent: Tuesday, June 09, 2009 4:21 PM Subject: Re: [Pw_forum] LDA pseudo for F Ricardo: you mean fluorine, I guess .?... On Jun 9, 2009, at 3:38 PM, Ricardo Faccio wrote: Dear PWscf users I wonder if any of you could send me a LDA pseudo for fluoride. Thanks in advance. Ricardo ------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------ _______________________________________________ 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/20090609/1244bd1f/attachment.htm From juanlopez415 at gmail.com Tue Jun 9 22:32:45 2009 From: juanlopez415 at gmail.com (Juan Manuel Lopez) Date: Tue, 9 Jun 2009 16:32:45 -0400 Subject: [Pw_forum] LDA pseudo for F In-Reply-To: <2B479569-E0F1-44D6-9FF2-8D3046C140B6@sissa.it> References: <003001c9e907$a2327b30$0402a8c0@ricardof> <2B479569-E0F1-44D6-9FF2-8D3046C140B6@sissa.it> Message-ID: Dear PWSCF users, Some body can help me about to make a good input (scf.in) for a supercell with around 100 atoms, including Cobalt and Organic molecules. Because I try with the example input, but does not converge. -- Best regards, -------------------------------------- Juan M. Lopez Encarnacion -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090609/f93f6437/attachment.htm From amosleffler at gmail.com Tue Jun 9 22:34:12 2009 From: amosleffler at gmail.com (Amos Leffler) Date: Tue, 9 Jun 2009 13:34:12 -0700 Subject: [Pw_forum] Problem with running CP Message-ID: <61b264610906091334k196c377at658e51f161768684@mail.gmail.com> Dear forum, I have been trying to run the attached file which is based on that in Example18. The flle in Example18 runs properly but my modified version does not. I have noted the information in the "Users Guide" , p28ff. If I leave out the EOF entries after each of the "Atomic Positions" the entire file reads in but no output is generated. Adding the EOF after the first Atomic_Positions, the output stops with the message "running the calculation with fixed ions...\c" . Is there more detailed information on using CP either in espresso itself or elsewhere? Thanks for your help. Amos Leffler -------------- next part -------------- A non-text attachment was scrubbed... Name: run_example2 Type: application/octet-stream Size: 9419 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090609/0c1490a1/attachment-0001.obj From somesh.kb at gmail.com Tue Jun 9 23:11:28 2009 From: somesh.kb at gmail.com (Somesh Kumar Bhattacharya) Date: Tue, 9 Jun 2009 23:11:28 +0200 Subject: [Pw_forum] Problem with running CP In-Reply-To: <61b264610906091334k196c377at658e51f161768684@mail.gmail.com> References: <61b264610906091334k196c377at658e51f161768684@mail.gmail.com> Message-ID: Dear Amos, I tried running your file ( one you attached with this mail) ................ and get the error : =------------------------------------------------------------------------------= CP: variable-cell Car-Parrinello molecular dynamics using norm-conserving and ultrasoft Vanderbilt pseudopotentials Version: 4.0.3 - Fri Jun 5 13:34:25 CEST 2009 Authors: Alfredo Pasquarello, Kari Laasonen, Andrea Trave, Roberto Car, Paolo Giannozzi, Nicola Marzari, Carlo Cavazzoni, Guido Chiarotti, Sandro Scandolo, Paolo Focher, Gerardo Ballabio, and others =------------------------------------------------------------------------------= This run was started on: 23: 3:55 9Jun2009 Serial Build Warning: card EOF ignored Warning: card $ECHO " RUNNING THE CALCULATION WITH FIXED IONS...\C" ignored Warning: card $CP_COMMAND < CO.CP.START.IN > CO.CP.START.OUT ignored Warning: card CHECK_FAILURE $? ignored Warning: card $ECHO " DONE" ignored Warning: card CAT > CO.CP.RESTART.IN << EOF ignored Warning: card &CONTROL ignored Warning: card CALCULATION='CP', ignored Warning: card RESTART_MODE='FROM_SCRATCH', ignored Warning: card NSTEP=50, IPRINT=50, ISAVE=50, ignored Warning: card DT=15.0, ignored Warning: card NDR=91, NDW=92, ignored Warning: card PSEUDO_DIR='$PSEUDO_DIR/', ignored Warning: card OUTDIR='$TMP_DIR/', ignored Warning: card / ignored Warning: card &SYSTEM ignored Warning: card IBRAV = 0, ignored Warning: card NAT = 28, ignored Warning: card NTYP = 2, ignored Warning: card ECUTWFC = 24.D0, ignored Warning: card ECUTRHO = 144.D0, ignored Warning: card NR1B=16, NR2B=16, NR3B=16, ignored Warning: card QCUTZ=150., Q2SIGMA=2.0, ECFIXED=16.0, ignored Warning: card / ignored Warning: card &ELECTRONS ignored Warning: card ELECTRON_DYNAMICS='DAMP', ELECTRON_DAMPING=0.2, ignored Warning: card EMASS=700., EMASS_CUTOFF=3., ignored Warning: card &IONS ignored Warning: card ION_DYNAMICS='NONE', ignored Warning: card ION_RADIUS(1) = 1.0, ION_RADIUS(2) =1.0, ignored Warning: card / ignored %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from card_cell_parameters : error # 2 two occurrences %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... 2 I think its because with ibrav = 0, you need to add the card cell_parameters. Did you tried that ???? Somesh On Tue, Jun 9, 2009 at 10:34 PM, Amos Leffler wrote: > Dear forum, > I have been trying to run the attached file which is based on > that in Example18. The flle in Example18 runs properly but my > modified version does not. I have noted the information in the "Users > Guide" , p28ff. If I leave out the EOF entries after each of the > "Atomic Positions" the entire file reads in but no output is > generated. Adding the EOF after the first Atomic_Positions, the output > stops with the message "running the calculation with fixed ions...\c" > . Is there more detailed information on using CP either in espresso > itself or elsewhere? > Thanks for your help. > > Amos Leffler > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Somesh Kr. Bhattacharya Post Doctoral Fellow Room No. 263, Leonardo Building, The Abdus Salam International Centre for Theoretical Physics Strada Costiera, 11 I-34014 Trieste Italy Phone: +39-040-2240399 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090609/b87664a6/attachment.htm From akohlmey at cmm.chem.upenn.edu Tue Jun 9 23:26:53 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 09 Jun 2009 17:26:53 -0400 Subject: [Pw_forum] Problem with running CP In-Reply-To: <61b264610906091334k196c377at658e51f161768684@mail.gmail.com> References: <61b264610906091334k196c377at658e51f161768684@mail.gmail.com> Message-ID: <1244582813.5214.957.camel@zero> On Tue, 2009-06-09 at 13:34 -0700, Amos Leffler wrote: > Dear forum, dear amos, > I have been trying to run the attached file which is based on > that in Example18. The flle in Example18 runs properly but my what platform are you running on: OS type/version, CPU, fortran compiler? > modified version does not. I have noted the information in the "Users > Guide" , p28ff. If I leave out the EOF entries after each of the > "Atomic Positions" the entire file reads in but no output is this _cannot_ work. this is due to shell scripting and has little to do with pw.x/cp.x itself. there are some linux versions that use a /bin/sh implementation that is very minimalistic (but standard compliant), while the run_example scripts tend to depend some some common extensions. you have to leave the EOFs in, but you can try replacing /bin/sh with /bin/bash. > generated. Adding the EOF after the first Atomic_Positions, the output > stops with the message "running the calculation with fixed ions...\c" > . Is there more detailed information on using CP either in espresso > itself or elsewhere? there should be a large number of error messages. this has nothing to do with cp.x. the run_example script just automates the process of generating input files and running them. in general, it is better for manual runs to modify the individual input files, if you are not an expert in bourne shell scripting. cheers, axel. > Thanks for your help. > > Amos Leffler > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From phylyh at nus.edu.sg Wed Jun 10 05:22:30 2009 From: phylyh at nus.edu.sg (Lu Yunhao) Date: Wed, 10 Jun 2009 11:22:30 +0800 Subject: [Pw_forum] How to set the ensemble when doing MD In-Reply-To: Message-ID: <000001c9e97a$b04c4480$ab4f8489@nusa0bcf64b485> Sorry, my questions are somewhat confused. I just want to compare MD calculations at different temperatures under Electric Field. I am also interested in what will happen if the total energy is constant (NVE). Do you have some experience on this? Now, my question (maybe the last one) is: If I set ion_temperature="not_controlled", the "tolp" and "nraise" are still meaningful or have some other meanings? Many thanks. Message: 2 Date: Tue, 09 Jun 2009 09:13:37 -0400 From: Axel Kohlmeyer Subject: Re: [Pw_forum] ??: How to set the ensemble when doing molecule To: PWSCF Forum Message-ID: <1244553217.5214.19.camel at zero> Content-Type: text/plain On Tue, 2009-06-09 at 16:17 +0800, Lu Yunhao wrote: > It is possible to do MD with initial T=0K? it seems the tempw can not be set > to zero. just set it to 0.1 or alike. that is pretty well the same thing. if your system is of high potential energy, it doesn't matter, if you system is not, the atoms won't move anyways. it is hard for me to see how you can get meaningful dynamics out of the kind of setup you are describing, as your requirements to the MD and the properties of the system seem to contradict each other. axel. -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From dalcorso at sissa.it Wed Jun 10 09:44:56 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Wed, 10 Jun 2009 09:44:56 +0200 Subject: [Pw_forum] LDA pseudo for F In-Reply-To: <006e01c9e941$2bb4b920$0402a8c0@ricardof> References: <003001c9e907$a2327b30$0402a8c0@ricardof> <2B479569-E0F1-44D6-9FF2-8D3046C140B6@sissa.it> <006e01c9e941$2bb4b920$0402a8c0@ricardof> Message-ID: <1244619896.3256.0.camel@dhpc-5-03.sissa.it> On Tue, 2009-06-09 at 17:30 -0300, Ricardo Faccio wrote: > Dear Stefano > Yes! I mean fluorine. There is one in atomic/pseudo_library/LDA/SR HTH Andrea > Thanks > Ricardo > ------------------------------------------------------------------------- > 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 > --------------------------------------------------------------------------------- > ----- Original Message ----- > From: Stefano Baroni > To: PWSCF Forum > Sent: Tuesday, June 09, 2009 4:21 PM > Subject: Re: [Pw_forum] LDA pseudo for F > > > Ricardo: you mean fluorine, I guess .?... > > On Jun 9, 2009, at 3:38 PM, Ricardo Faccio wrote: > > > Dear PWscf users > > I wonder if any of you could send me a LDA pseudo for > > fluoride. > > Thanks in advance. > > Ricardo > > ------------------------------------------------------------------------- > > 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 > > > > > > > ______________________________________________________________ > > _______________________________________________ > 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 -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From anvari_meh at physics.iust.ac.ir Wed Jun 10 11:22:14 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Wed, 10 Jun 2009 12:52:14 +0330 Subject: [Pw_forum] missing q-points Message-ID: Hi First I have to say as Eyvaz had suggested I ran my ph.x code for same nq1,nq2,nq3 (2,2,2) but I get the previous error. I ran kpoints.x but I did'nt understand how could it help me, because I have done scf calculations with 12x12x1 grid and I have got same k as I got from kpoints.x. In the following as you wanted you could check some parts of my input & output. scf calculations / &system ibrav = 0 , celldm(1) =4.92 , nat= 2, ntyp= 1, ecutwfc =35, ecutrho=500 , occupations='smearing', degauss=0.02, smearing='m-p', / &electrons diagonalization='cg' mixing_beta = 0.7 conv_thr = 1.0d-9 / ATOMIC_SPECIES C 12.0107 C.pbe-van_bm.UPF CELL_PARAMETERS HEXAGONAL 0.947945153 0.000000000 0.000000000 -0.473972577 0.820944584 0.000000000 0.000000000 0.000000000 10.017908940 ATOMIC_POSITIONS {crystal} C 0.000000000 0.000000000 0.000000000 C 0.333333300 0.666666700 0.000000000 K_POINTS AUTOMATIC 12 12 1 1 1 1 phonon calculations tr2_ph=1.0d-14, prefix='Graphene', ldisp=.true., nq1=2, nq2=2, nq3=1 amass(1)=12.0107, outdir='/home/mehrnaz/scratch/tmp2/', fildyn='graphene.dyn', / q2r.out nqs= 1 q= 0.00000000 0.00000000 0.00000000 reading force constants from file graphene.dyn2 nqs= 1 q= 0.00000000 -0.60905451 0.00000000 from init : error # 1 missing q-point(s)! stopping ... Mehrnaz Iran University Of Science & Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090610/6fc5283b/attachment.htm From paulatto at sissa.it Wed Jun 10 11:01:32 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 10 Jun 2009 11:01:32 +0200 Subject: [Pw_forum] SCF calculation does not converge (was: LDA pseudo for F) In-Reply-To: References: <003001c9e907$a2327b30$0402a8c0@ricardof> <2B479569-E0F1-44D6-9FF2-8D3046C140B6@sissa.it> Message-ID: In data 09 giugno 2009 alle ore 22:32:45, Juan Manuel Lopez ha scritto: > Dear PWSCF users, > > Some body can help me about to make a good input (scf.in) for a supercell > with around 100 atoms, including Cobalt and Organic molecules. Because I > try with the example input, but does not converge. > Dear Juan, I assume you mistakenly sent this email before finishing to write it, if you want us to check your input, we should be able to read it! best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From marzari at MIT.EDU Wed Jun 10 11:02:45 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 10 Jun 2009 05:02:45 -0400 Subject: [Pw_forum] How to set the ensemble when doing MD In-Reply-To: <000001c9e97a$b04c4480$ab4f8489@nusa0bcf64b485> References: <000001c9e97a$b04c4480$ab4f8489@nusa0bcf64b485> Message-ID: <4A2F76B5.9080907@mit.edu> Lu Yunhao wrote: > Sorry, my questions are somewhat confused. I just want to compare MD > calculations at different temperatures under Electric Field. I am also > interested in what will happen if the total energy is constant (NVE). Do you > have some experience on this? Dear Lu, one comment - I suspect that the electric fields you need to apply in order to see some effects on these small cell sizes and time scales need to be huge and unphysical. Maybe not - probably the best references would be looking at some ab-initio MD done by Pasquarello (I believe on HCl) and later by Car and Sharma, with the goal in mind of calculating the static limit of the dielectric constant (i.e. to take into account, in a liquid, also of the ionic screening). nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From sclauzer at sissa.it Wed Jun 10 15:31:02 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 10 Jun 2009 15:31:02 +0200 Subject: [Pw_forum] missing q-points In-Reply-To: References: Message-ID: <4A2FB596.7000902@sissa.it> I tried to reproduce your error but I couldn't. I've used the cvs version of QE on my Linux Intel PC and I could obtain the interatomic force constants without any error message. Here is the output from q2r [sclauzer at brenta:~/tmp/Graphene]$ /scratch/sclauzer-exec/espresso-4.1CVS/bin/q2r.x < anvari.q2r.in | tee anvari.q2r.out reading grid info from file graphene.dyn0 reading force constants from file graphene.dyn1 Dielectric Tensor not found nqs= 1 q= 0.00000000 0.00000000 0.00000000 reading force constants from file graphene.dyn2 nqs= 3 q= 0.00000000 -0.60905451 0.00000000 q= 0.52745668 0.30452725 0.00000000 q= -0.52745668 0.30452725 0.00000000 q-space grid ok, #points = 4 fft-check warning: sum of imaginary terms = .8800000E-06 If you used an older version of QE, please try with the latest 4.0.5 or the CVS one. Regards, Gabriele Mehrnaz Anvari wrote: > > Hi > First I have to say as Eyvaz had suggested I ran my ph.x code for same > nq1,nq2,nq3 (2,2,2) but I get the previous error. I ran kpoints.x but I > did'nt understand how could it help me, because I have done scf > calculations with 12x12x1 grid and I have got same k as I got from > kpoints.x. > In the following as you wanted you could check some parts of my input & > output. > _*scf calculations*_ > / > &system > ibrav = 0 , celldm(1) =4.92 , nat= 2, ntyp= 1, > ecutwfc =35, ecutrho=500 , occupations='smearing', degauss=0.02, > smearing='m-p', > / > &electrons > diagonalization='cg' > mixing_beta = 0.7 > conv_thr = 1.0d-9 > / > ATOMIC_SPECIES > C 12.0107 C.pbe-van_bm.UPF > CELL_PARAMETERS HEXAGONAL > 0.947945153 0.000000000 0.000000000 > -0.473972577 0.820944584 0.000000000 > 0.000000000 0.000000000 10.017908940 > ATOMIC_POSITIONS {crystal} > C 0.000000000 0.000000000 0.000000000 > C 0.333333300 0.666666700 0.000000000 > K_POINTS AUTOMATIC > 12 12 1 1 1 1 > > _*phonon calculations*_ > > tr2_ph=1.0d-14, > prefix='Graphene', > ldisp=.true., > nq1=2, nq2=2, nq3=1 > amass(1)=12.0107, > outdir='/home/mehrnaz/scratch/tmp2/', > fildyn='graphene.dyn', > / > > _*q2r.out*_ > nqs= 1 > q= 0.00000000 0.00000000 0.00000000 > reading force constants from file graphene.dyn2 > nqs= 1 > q= 0.00000000 -0.60905451 0.00000000 > > from init : error # 1 > missing q-point(s)! > stopping ... > Mehrnaz > Iran University Of Science & Technology > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From hayden at umbc.edu Wed Jun 10 16:03:14 2009 From: hayden at umbc.edu (Michael Hayden) Date: Wed, 10 Jun 2009 10:03:14 -0400 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system Message-ID: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> PWSCF users, I am trying to get Quantum Espresso going on my Mac. I am completely new to this kind of thing, but think I have done everything correctly yet the Espresso config process says, "Parallel environment not detected (is this a parallel machine?)" every time I run it. Here are my particulars: 1. MacPro with 2 x 3 GHz Quad-core Xeon-Intel processors, running OS X (10.5.7) 2. I downloaded gfortran from MacResearch.org. It is installed in / usr/local/bin. 3. I downloaded OpenMPI version 1.3.2, unpacked and installed it with the following command in /usr/local, sudo ./configure --with-mpi-f90-size=medium FC=gfortran F77=gfortran FCFLAGS=-m64 FFLAGS=-m64 CXXFLAGS=-m64 CFLAGS=-m64 Everything seems to be fine, with the libraries in /usr/local/lib and the binaries in /usr/local/bin. 4. I downloaded Quantum Espresso v4.0.5 and unpacked it in /usr/ local. I ran the config as follows: sudo ./configure LD_LIBS=/usr/local/lib MPI_LIBS=/usr/local/lib FFT_LIBS=/usr/local/lib MPIF77=mpif77 MPIF90=mpif90 ARCH=mac686 MPICC=mpic++ The output is here: checking build system type... i686-apple-darwin9.7.0 checking architecture... mac686 checking for ifort... no checking for g95... no checking for gfortran... gfortran checking for Fortran 77 compiler default output file name... a.out checking whether the Fortran 77 compiler works... yes checking whether we are cross compiling... yes checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes checking for mpif90... mpif90 checking whether we are using the GNU Fortran 77 compiler... no checking whether mpif90 accepts -g... no checking version of mpif90... unknown, assuming gfortran setting F90... gfortran setting MPIF90... mpif90 checking for cc... cc checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ANSI C... none needed setting CC... cc checking how to run the C preprocessor... cc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for int *... yes checking size of int *... 4 checking malloc.h usability... no checking malloc.h presence... no checking for malloc.h... no checking for gfortran... gfortran checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes setting F77... gfortran using F90... gfortran setting FFLAGS... -O3 setting F90FLAGS... $(FFLAGS) -x f95-cpp-input setting FFLAGS_NOOPT... -O0 setting CFLAGS... -O3 setting CPP... cpp setting CPPFLAGS... -P -traditional setting LD... mpif90 setting LDFLAGS... setting AR... ar setting ARFLAGS... ruv setting ARFLAGS_DYNAMIC...ruv checking whether make sets $(MAKE)... yes checking whether Fortran files must be preprocessed... no checking how to get verbose linking output from gfortran... -v checking for Fortran libraries of gfortran... -lcrt1.10.5.o -L/usr/ local/lib/gcc/i386-apple-darwin9.0.0/4.3.0 -L/usr/local/lib/gcc/i386- apple-darwin9.0.0/4.3.0/../../.. -lgfortranbegin -lgfortran -lgcc_s. 10.5 -lSystem checking for dummy main to link with Fortran libraries... rm: conftest.dSYM: is a directory none checking for Fortran name-mangling scheme... rm: conftest.dSYM: is a directory lower case, underscore, no extra underscore checking for library containing dgemm... none required checking for library containing zggev... -llapack setting BLAS_LIBS... -latlas setting LAPACK_LIBS... -llapack setting FFT_LIBS... /usr/local/lib checking for library containing fftwnd... no setting MASS_LIBS... setting MPI_LIBS... /usr/local/lib checking for library containing mpi_init... no setting DFLAGS... -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW setting IFLAGS... -I../include setting FDFLAGS... $(DFLAGS) checking for ranlib... ranlib setting RANLIB... ranlib configure: creating ./config.status config.status: creating include/fft_defs.h config.status: creating make.sys config.status: creating configure.msg config.status: creating include/c_defs.h config.status: include/c_defs.h is unchanged -------------------------------------------------------------------- ESPRESSO can take advantage of several optimized numerical libraries (essl, fftw, mkl...). This configure script attempts to find them, but may fail if they have been installed in non-standard locations. If a required library is not found, the local copy will be compiled. The following libraries have been found: BLAS_LIBS= -latlas LAPACK_LIBS= -llapack FFT_LIBS=/usr/local/lib MPI_LIBS=/usr/local/lib Please check if this is what you expect. If any libraries are missing, you may specify a list of directories to search and retry, as follows: ./configure LIBDIRS="list of directories, separated by spaces" Parallel environment not detected (is this a parallel machine?). Configured for compilation of serial executables. For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex). My PATH is : /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/ lib:/usr/X11/bin and I have set LD_LIBRARY_PATH and DYLD_LIBRARY_PATH to /usr/local/lib in my startup shell script. I have not "made" Espresso yet because of the "parallel environment not detected" comment. Does anyone see the mistake I am making? I'd really appreciate any guidance whatsoever. Michael Michael Hayden Professor and Chair Department of Physics, UMBC 1000 Hilltop Circle Baltimore, MD 21250 410-455-3199 410-455-1072 fax Research Lab http://userpages.umbc.edu/~hayden/polymers.html Wiki page http://thzpolymers.pbworks.com Materials and Devices for Information Technology Research http://stc-mditr.org/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090610/b38d5043/attachment-0001.htm From giannozz at democritos.it Wed Jun 10 16:23:42 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 10 Jun 2009 16:23:42 +0200 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> Message-ID: <637375ED-A261-47F5-9660-327BE0944328@democritos.it> On Jun 10, 2009, at 16:03 , Michael Hayden wrote: > [...] the Espresso config process says, > "Parallel environment not detected (is this a parallel machine?)" > every time I run it. and rightly so, because: > setting MPI_LIBS... /usr/local/lib > checking for library containing mpi_init... no You shouldn't provide any argument to configure unless it is needed. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From hayden at umbc.edu Wed Jun 10 16:38:06 2009 From: hayden at umbc.edu (Michael Hayden) Date: Wed, 10 Jun 2009 10:38:06 -0400 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: <637375ED-A261-47F5-9660-327BE0944328@democritos.it> References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> <637375ED-A261-47F5-9660-327BE0944328@democritos.it> Message-ID: Paolo, Thanks. I initially didn't supply any arguments but got the same results. In fact, I have tried all permutations or arguments and non- arguments. Mike On Jun 10, 2009, at 10:23 AM, Paolo Giannozzi wrote: > On Jun 10, 2009, at 16:03 , Michael Hayden wrote: > >> [...] the Espresso config process says, >> "Parallel environment not detected (is this a parallel machine?)" >> every time I run it. > > and rightly so, because: > >> setting MPI_LIBS... /usr/local/lib >> checking for library containing mpi_init... no > > > You shouldn't provide any argument to configure unless it is needed. > > P. > --- > Paolo Giannozzi, Dept of Physics, University of 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 Jun 10 16:44:15 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 10 Jun 2009 16:44:15 +0200 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> <637375ED-A261-47F5-9660-327BE0944328@democritos.it> Message-ID: On Jun 10, 2009, at 16:38 , Michael Hayden wrote: > I initially didn't supply any arguments but got the same results likely you got the same result but for a different reason, printed somewhere in the output of configure. Unless configure finds a working parallel compiler (mpif90 in your case) and working mpi libraries, it will not produce a make.sys file that is suitable for parallel compilation. Note that well-configured parallel compilers should find mpi libraries without any need to specify where they are P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From eyvaz_isaev at yahoo.com Wed Jun 10 16:58:19 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 10 Jun 2009 07:58:19 -0700 (PDT) Subject: [Pw_forum] missing q-points Message-ID: <24528.33027.qm@web65710.mail.ac4.yahoo.com> Hi, If you use kpoints.x to generate 2x2x1 k-mesh for graphene you will find 2 q-points with weights 1 and 3, respectively (total 4 points, reduced to 2 by symmetry). But according to your message q2r.x reports only 2 points totally (1+1) that is incorrect (2x2x1 = 4) . Different number of q-points usually tells us something is wrong. As example, for WC-type structure with c/a \approx 1 the use of 4x4x2 grid leads to the same error, but 4x4x4 is OK. At the same time, usually 4x4x2 is OK for hexagonal structures. Hopefully, now you understand why I asked you to generate q-points. So, you could first generate q-points using kpoints.x, calculate the dynamical matrices for these q-points and then apply q2r.x. Or follow Gabriele's advice. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Wed, 6/10/09, Gabriele Sclauzero wrote: > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] missing q-points > To: "PWSCF Forum" > Date: Wednesday, June 10, 2009, 5:31 PM > I tried to reproduce your error but I > couldn't. I've used the cvs version of QE on my > Linux Intel PC and I could obtain the interatomic force > constants without any error > message. Here is the output from q2r > > [sclauzer at brenta:~/tmp/Graphene]$ > /scratch/sclauzer-exec/espresso-4.1CVS/bin/q2r.x < > anvari.q2r.in | tee anvari.q2r.out > ???reading grid info from file > graphene.dyn0 > ???reading force constants from file > graphene.dyn1 > ???Dielectric Tensor not found > ???nqs=? ? ? ? ? > ? 1 > ? q=???0.00000000? > 0.00000000? 0.00000000 > ???reading force constants from file > graphene.dyn2 > ???nqs=? ? ? ? ? > ? 3 > ? q=???0.00000000 -0.60905451? > 0.00000000 > ? q=???0.52745668? > 0.30452725? 0.00000000 > ? q=? -0.52745668? 0.30452725? > 0.00000000 > > ? ? ???q-space grid ok, #points > =? ? 4 > > ? ? ???fft-check warning: sum of > imaginary terms = .8800000E-06 > > If you used an older version of QE, please try with the > latest 4.0.5 or the CVS one. > > Regards, > > Gabriele > > Mehrnaz Anvari wrote: > > > > Hi > > First I have to say as Eyvaz had suggested I ran my > ph.x code for same > > nq1,nq2,nq3 (2,2,2) but I get the previous error. I > ran kpoints.x but I > > did'nt understand how could it help me, because I have > done scf > > calculations with 12x12x1 grid and I have got same k > as I got from > > kpoints.x. > > In the following as you wanted you could check some > parts of my input & > > output. > > _*scf calculations*_ > > / > > &system > > ibrav = 0 , celldm(1) =4.92 , nat= 2, ntyp= 1, > > ecutwfc =35, ecutrho=500 , occupations='smearing', > degauss=0.02, > > smearing='m-p', > > / > > &electrons > > diagonalization='cg' > > mixing_beta = 0.7 > > conv_thr = 1.0d-9 > > / > > ATOMIC_SPECIES > > C 12.0107 C.pbe-van_bm.UPF > > CELL_PARAMETERS HEXAGONAL > > 0.947945153 0.000000000 0.000000000 > > -0.473972577 0.820944584 0.000000000 > > 0.000000000 0.000000000 10.017908940 > > ATOMIC_POSITIONS {crystal} > > C 0.000000000 0.000000000 0.000000000 > > C 0.333333300 0.666666700 0.000000000 > > K_POINTS AUTOMATIC > > 12 12 1 1 1 1 > > > > _*phonon calculations*_ > > > > tr2_ph=1.0d-14, > > prefix='Graphene', > > ldisp=.true., > > nq1=2, nq2=2, nq3=1 > > amass(1)=12.0107, > > outdir='/home/mehrnaz/scratch/tmp2/', > > fildyn='graphene.dyn', > > / > > > > _*q2r.out*_ > > nqs= 1 > > q= 0.00000000 0.00000000 0.00000000 > > reading force constants from file graphene.dyn2 > > nqs= 1 > > q= 0.00000000 -0.60905451 0.00000000 > > > > from init : error # 1 > > missing q-point(s)! > > stopping ... > > Mehrnaz > > Iran University Of Science & Technology > > > >? > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student? ? ? > ? ? ? ? ? ? | > | c/o:???SISSA & CNR-INFM > Democritos,? ? ? ? ? ? ? > | > |? ? ? ? via Beirut 2-4, 34014 Trieste > (Italy)? ???| > | email: sclauzer at sissa.it? > ? ? ? ? ? ? ? ? > ? ? ???| > | phone: +39 040 3787 511? ? ? ? ? > ? ? ? ? ? ? ? ? | > | skype: gurlonotturno? ? ? ? ? > ? ? ? ? ? ? ? ? > ???| > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From nahidbd1 at in.com Wed Jun 10 17:53:26 2009 From: nahidbd1 at in.com (nahid bd) Date: Wed, 10 Jun 2009 21:23:26 +0530 Subject: [Pw_forum] =?utf-8?q?Doping?= Message-ID: <1244649206.ea33b4fd0fc1ea0a40344be8a8641123@mail.in.com> I am working with parent compound LaOFeAs and want to calculate scf calculation for doping F in place of O (LaO1xFxFeAs). How can I make the input file for this purpose. Input file for parent compound is given below.&CONTROL??calculation = 'scf' ,?? restartmode = 'fromscratch' ,?? outdir = '/root/temp/' ,?? pseudodir = '/root/espresso4.0.5/pseudo/' ,?? prefix = 'LaOFeAs' ,??/??&SYSTEM??ibrav = 6,??celldm(1) = 7.620676376,??celldm(3) = 2.167568466,??nat = 8,?? ntyp = 4,??ecutwfc = 50.0 ,??ecutrho = 400.0 ,??occupations = 'smearing' ,??degauss = 0.01 ,?? smearing = 'gaussian' ,??nspin = 1 ,?? ldaplusu = .false. ,??/??&ELECTRONS?? electronmaxstep = 200,?? convthr = 1.D8 ,??mixingbeta = 0.7 ,??diagonalization = 'cg' ,?? diagothrinit = 1.D2 ,??/ATOMICSPECIES?? O 15.99940O.pberrkjus.UPF????Fe 55.84700Fe.pbendrrkjus.UPF????As 74.92162As.pbenvan.UPF????La138.90550La.pbenspvan.UPF??ATOMICPOSITIONS crystal???? O0.7500000000.2500000000.000000000 ???? O0.2500000000.7500000000.000000000 ? ???Fe0.7500000000.2500000000.500000000 ????Fe0.2500000000.7500000000.500000000 ????As0.2500000000.2500000000.651660000 ????As0.7500000000.7500000000.348340000 ????La0.2500000000.2500000000.141340000 ????La0.7500000000.7500000000.858660000 ??KPOINTS automatic???? 6 6 3 0 0 0??Dear pwforum! Get Yourself a cool, short @in.com Email ID now! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090610/3cb7aae4/attachment.htm From rfaccio at fq.edu.uy Wed Jun 10 18:31:25 2009 From: rfaccio at fq.edu.uy (Ricardo Faccio) Date: Wed, 10 Jun 2009 13:31:25 -0300 Subject: [Pw_forum] LDA pseudo for F References: <003001c9e907$a2327b30$0402a8c0@ricardof><2B479569-E0F1-44D6-9FF2-8D3046C140B6@sissa.it><006e01c9e941$2bb4b920$0402a8c0@ricardof> <1244619896.3256.0.camel@dhpc-5-03.sissa.it> Message-ID: <07bf01c9e9e8$e6c7d470$0402a8c0@ricardof> Andrea Thanks! Ricardo ------------------------------------------------------------------------- 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 --------------------------------------------------------------------------------- ----- Original Message ----- From: "Dal Corso Andrea" To: "PWSCF Forum" Sent: Wednesday, June 10, 2009 4:44 AM Subject: Re: [Pw_forum] LDA pseudo for F > On Tue, 2009-06-09 at 17:30 -0300, Ricardo Faccio wrote:> Dear Stefano> > Yes! I mean fluorine. > There is one in > atomic/pseudo_library/LDA/SR > HTH > Andrea > >> Thanks> >> Ricardo> -------------------------------------------------------------------------> >> 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> ---------------------------------------------------------------------------------> >> ----- Original Message ----- > From: Stefano Baroni > >> To: PWSCF Forum > Sent: Tuesday, June 09, 2009 4:21 PM> >> Subject: Re: [Pw_forum] LDA pseudo for F> > > >> Ricardo: you mean fluorine, I guess .?... > > On Jun 9, >> 2009, at 3:38 PM, Ricardo Faccio wrote:> > > Dear PWscf >> users> > I wonder if any of you could send me a LDA pseudo for> >> > fluoride.> > Thanks in advance.> > Ricardo> >> > -------------------------------------------------------------------------> >> > 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> > > > >> > > > >> ______________________________________________________________> > >> _______________________________________________> 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-- >> Andrea Dal Corso Tel. 0039-040-3787428SISSA, Via >> Beirut 2/4 Fax. 0039-040-378752834014 Trieste (Italy) >> e-mail: dalcorso at sissa.it > > _______________________________________________Pw_forum mailing > listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > From ajs.jacques at gmail.com Wed Jun 10 19:12:49 2009 From: ajs.jacques at gmail.com (Alain Jacques) Date: Wed, 10 Jun 2009 19:12:49 +0200 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> Message-ID: <4A2FE991.1010902@gmail.com> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090610/1740da47/attachment-0001.htm From jjr19 at uakron.edu Wed Jun 10 20:13:23 2009 From: jjr19 at uakron.edu (J. J. Ramsey) Date: Wed, 10 Jun 2009 11:13:23 -0700 (PDT) Subject: [Pw_forum] File closing errors when using NEB image parallelization Message-ID: <14450.35591.qm@web50912.mail.re2.yahoo.com> I ran an NEB calcution on a small test system (input file and pseudohydrogen pseudopotential attached) and ran it two different ways: one where I ran it on 24 CPUs with nimage=3, and one where I ran it with 8 CPUs and didn't parallelize on the images (nimage=1). The latter run worked fine with no apparent errors, but the former ended with these errors, forrtl: No such file or directory forrtl: severe (28): CLOSE error, unit 4, file "Unknown" Image PC Routine Line Source pw.x 000000000086D7A6 Unknown Unknown Unknown pw.x 000000000086BAE6 Unknown Unknown Unknown pw.x 0000000000839804 Unknown Unknown Unknown pw.x 00000000007F5336 Unknown Unknown Unknown pw.x 00000000007F4F97 Unknown Unknown Unknown pw.x 00000000007F3CBB Unknown Unknown Unknown pw.x 000000000054389E Unknown Unknown Unknown pw.x 00000000004061EB Unknown Unknown Unknown pw.x 0000000000405F8A Unknown Unknown Unknown libc.so.6 00002B17DBEDE8B4 Unknown Unknown Unknown pw.x 0000000000405EAD Unknown Unknown Unknown ... repeated several times over, followed by "RETRY EXCEEDED" errors. In spite of the errors at the end, both runs, with and without image parallelization, get me the same answer, and offhand, it looks maybe as if some processes are trying to close files that had already been closed by other processes. James J. Ramsey University of Akron Civil Engineering(!) Dept. -------------- next part -------------- A non-text attachment was scrubbed... Name: test_files.tbz2 Type: application/x-bzip-compressed-tar Size: 14203 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090610/15ff461b/attachment.bin From ajs.jacques at gmail.com Thu Jun 11 01:05:05 2009 From: ajs.jacques at gmail.com (Alain Jacques) Date: Thu, 11 Jun 2009 01:05:05 +0200 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> <4A2FE991.1010902@gmail.com> Message-ID: <4A303C21.3070102@gmail.com> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090611/c9fd4f65/attachment.htm From pushpajnc at gmail.com Thu Jun 11 03:09:22 2009 From: pushpajnc at gmail.com (pushpa raghani) Date: Wed, 10 Jun 2009 18:09:22 -0700 Subject: [Pw_forum] Fully relativistic pseudo potential for Ti Message-ID: Dear all, Has anybody generated a fully relativistic pseudopotential for Ti using pbe? Thanks, Pushpa (Stanford University) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090610/e6e312b1/attachment.htm From mighfar at jncasr.ac.in Thu Jun 11 06:43:54 2009 From: mighfar at jncasr.ac.in (Mighfar Imam) Date: Thu, 11 Jun 2009 10:13:54 +0530 (IST) Subject: [Pw_forum] full-relativistic PP Message-ID: <37884.172.16.1.1.1244695434.squirrel@172.16.1.1> Dear pwscf users, Has anybody got fully relativistic pseudopoential for Fe? I will be grateful for any help. Thanks, Mighfar Imam SRF Theoretical Sciences Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore-64, India. Ph.(Lab.) +91 -(80) 22082835 cell. +919480336087 From mansourehp at gmail.com Thu Jun 11 08:23:38 2009 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Thu, 11 Jun 2009 10:53:38 +0430 Subject: [Pw_forum] gap from DOS and bandstructure Message-ID: Dear all I have calculated DOS and Bandstructure for a system. I expect to find similar gap from two runs. But they have 0.4 eV difference with each other. What is the root of this differenc? Thanks Pashangpour -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090611/e4145ae5/attachment.htm From panda.deng.pan at gmail.com Thu Jun 11 08:37:22 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Thu, 11 Jun 2009 14:37:22 +0800 Subject: [Pw_forum] gap from DOS and bandstructure In-Reply-To: References: Message-ID: Without detail no one can help you. 2009/6/11 Mansoureh Pashangpour > Dear all > I have calculated DOS and Bandstructure for a system. > I expect to find similar gap from two runs. > But they have 0.4 eV difference with each other. What is the root of this > differenc? > Thanks > Pashangpour > > _______________________________________________ > 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/20090611/ab5ea822/attachment.htm From trinh.vo at jpl.nasa.gov Thu Jun 11 09:04:47 2009 From: trinh.vo at jpl.nasa.gov (Vo, Trinh) Date: Thu, 11 Jun 2009 00:04:47 -0700 Subject: [Pw_forum] Binding energy of P-dpoed Si Message-ID: <63E24D720DCE7246ABAA722B52D23CDF0153C2478CDA@ALTPHYEMBEVSP10.RES.AD.JPL> Dear PWSCF, I plan to calculate the impurity binding energy of P-doped Si bulk. I searched literatures, and I see people used mainly Effective mass approximation (EMA) (or used first principles to obtain potential, then used EMA). According these papers, the binding energy is determined as the difference between impurity level and the minimum of the conduction band. I also found other papers by Chelikowsky et al (Nano Letters 8, 596 (2008), PRL 92, 46802 (2004)), who calculated binding energy of P-doped nanocrytals by calculating the ionization energy, I_d, of SiP system with one electron removed, and the affinity, A_p, of the pure Si system with one electron added. The binding energy is determined as: E_b = I_d - A_p I saw problems when I want to calculate E_b by Chelikowski's method, since that method only works for non-extensive system such as nanocrystals. For P-doped Si bulk (with periodic boundary condtion), I cannot calculate I_d and A_p (or there may be a way that I do not know). If using DFT, I do not know (using espresso code) how I define the binding energy properly. Is the definition of binding energy as used in EMA is still valid? I appreciate very much if you know an alternative to calculate binding energy by using DFT. Thank you, Trinh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090611/f4114e3a/attachment.htm From mansourehp at gmail.com Thu Jun 11 09:11:58 2009 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Thu, 11 Jun 2009 11:41:58 +0430 Subject: [Pw_forum] gap from DOS and bandstructure In-Reply-To: References: Message-ID: Dear ?? yes you are right. I am using LSDA+U and sigma-GGA+U for FeO. But I didn't set U_projection_type to 'file' . Do you think it might be root of error? I want to test it. ( I used starting_ns_eigenvalue in my inputs) I am look forward to hearing from you Pashangpour On Thu, Jun 11, 2009 at 11:07 AM, ?? wrote: > Without detail no one can help you. > > 2009/6/11 Mansoureh Pashangpour > >> Dear all >> I have calculated DOS and Bandstructure for a system. >> I expect to find similar gap from two runs. >> But they have 0.4 eV difference with each other. What is the root of this >> differenc? >> Thanks >> Pashangpour >> >> _______________________________________________ >> 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/20090611/b04ab046/attachment.htm From sclauzer at sissa.it Thu Jun 11 10:03:47 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 11 Jun 2009 10:03:47 +0200 Subject: [Pw_forum] gap from DOS and bandstructure In-Reply-To: References: Message-ID: <4A30BA63.5050301@sissa.it> Mansoureh Pashangpour wrote: > Dear all > I have calculated DOS and Bandstructure for a system. > I expect to find similar gap from two runs. > But they have 0.4 eV difference with each other. What is the root of > this differenc? Maybe the gap is not at the k-point where you expected it to be? Maybe something else... how to guess with such a little of information on your system (as well as about your affiliation). GS > Thanks > Pashangpour > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Thu Jun 11 10:10:56 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 11 Jun 2009 10:10:56 +0200 Subject: [Pw_forum] gap from DOS and bandstructure In-Reply-To: References: Message-ID: <4A30BC10.6070000@sissa.it> Mansoureh Pashangpour wrote: > Dear ?? > yes you are right. I am using LSDA+U and sigma-GGA+U for FeO. But I > didn't set U_projection_type to 'file' . Do you think it might be root > of error? I want to test it. Your additional piece of information doesn't help much in helping you. Anyway, why should you set U_projection to 'file' (unless you know exactly what you are doing)? Unless you want to use projectors other than the atomic wavefunctions (that you must first calculate and put in a file) you must not set it to 'file'. > ( I used starting_ns_eigenvalue in my inputs) It would be more useful if your provide your full input files. Cheers GS > I am look forward to hearing from you > Pashangpour > > On Thu, Jun 11, 2009 at 11:07 AM, ?? > wrote: > > Without detail no one can help you. > > 2009/6/11 Mansoureh Pashangpour > > > Dear all > I have calculated DOS and Bandstructure for a system. > I expect to find similar gap from two runs. > But they have 0.4 eV difference with each other. What is the > root of this differenc? > Thanks > Pashangpour > > _______________________________________________ > 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 -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From nazari at iasbs.ac.ir Thu Jun 11 14:06:17 2009 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Thu, 11 Jun 2009 13:06:17 +0100 (BST) Subject: [Pw_forum] l_mkl_p_10.1.2.024 In-Reply-To: <63E24D720DCE7246ABAA722B52D23CDF0153C2478CDA@ALTPHYEMBEVSP10.RES.AD.J PL> References: <63E24D720DCE7246ABAA722B52D23CDF0153C2478CDA@ALTPHYEMBEVSP10.RES.AD.JPL> Message-ID: <24038.213.176.122.17.1244721977.squirrel@mail.iasbs.ac.ir> Dear All, I wish to compile the espresso-4.0.5. I have installed suse 11 os, ifort and icc compiler and l_mkl_p_10.1.2.024. When I wish to run the pw.x it failes with from cdiaghg : error # 137, info =/= 0 . The reason for this error have been reported in forum. In this case it depends to blas and lapck libraries. would you please let me know what is the correct way for linking these two libraries for l_mkl_p_10.1.2.024. regards Fariba Nazari IASBS From panda.deng.pan at gmail.com Thu Jun 11 14:01:28 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Thu, 11 Jun 2009 20:01:28 +0800 Subject: [Pw_forum] Pseudoprotential for Europium Message-ID: Dear All users, I want to study the system of Eu metal. And I could not find the pseudoprotential for Eu online. Would someone tell me where to get this pseudoprotential or sent me one. I am very appriated. Have a nice day Deng Pan Nanjing University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090611/529ce29d/attachment.htm From sclauzer at sissa.it Thu Jun 11 14:20:39 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 11 Jun 2009 14:20:39 +0200 Subject: [Pw_forum] Pseudoprotential for Europium In-Reply-To: References: Message-ID: <4A30F697.4060502@sissa.it> Please follow this thread: http://www.democritos.it/pipermail/pw_forum/2009-May/012892.html ?? wrote: > Dear All users, > > I want to study the system of Eu metal. And I could not find the > pseudoprotential for Eu online. > Would someone tell me where to get this pseudoprotential or sent me > one. I am very appriated. You may also find this very useful as well: http://www.merriam-webster.com Cheers GS > > > Have a nice day > > Deng Pan > Nanjing University > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From hayden at umbc.edu Thu Jun 11 23:06:30 2009 From: hayden at umbc.edu (Michael Hayden) Date: Thu, 11 Jun 2009 17:06:30 -0400 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: <4A303C21.3070102@gmail.com> References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> <4A2FE991.1010902@gmail.com> <4A303C21.3070102@gmail.com> Message-ID: <7124F8BA-AA78-4ED5-9CBE-18FCA80B9538@umbc.edu> Alain, Again, thanks for your efforts and time. I have successfully installed and tested OpenMPI. I also configured Quant Espresso and received the "Parallel environment detected successfully, configured for compilation of parallel executables" response at the end of the config process. I then compiled it,but the end of a very long output read: ld: in /usr/local/lib, can't map file, errno=22 collect2: ld returned 1 exit status make[1]: *** [pw.x] Error 1 make: *** [pw] Error 2 This doesn't look good and I can't find any list of these errors in the user guide. I tried example01 and received (of course) this output: ERROR: /usr/local/espresso-4.0.5/bin/pw.x not existent or not executable Aborting Any ideas? cheers, Mike On Jun 10, 2009, at 7:05 PM, Alain Jacques wrote: > Hello Mike, > > Humm, sorry it didn't work as expected. My development platform runs > OSX 10.5.7. I have compiled many working openmpi versions with the > following recipe: > > export LD_LIBRARY_PATH=/opt/gcc-4.3.2/lib:$LD_LIBRARY_PATH && export > PATH=/opt/gcc-4.3.2/bin:$PATH > > ./configure --prefix=/opt/openmpi-1.2.8_gcc-4.3.2_m32 --enable- > static --enable-shared --disable-dependency-tracking --with-devel- > headers --with-wrapper-ldflags="-Wl,-search_paths_first" CC=/opt/ > gcc-4.3.2/bin/gcc LDFLAGS="-L/opt/gcc-4.3.2/lib" FC=/opt/gcc-4.3.2/ > bin/gfortran F77=/opt/gcc-4.3.2/bin/gfortran CXX=/opt/gcc-4.3.2/bin/g > ++ CPP=/opt/gcc-4.3.2/bin/cpp CFLAGS="-m32 -O3 -march=native" > CXXFLAGS="-m32 -O3 -march=native" FCFLAGS="-m32 -O3 -march=native" > FFLAGS="-m32 -O3 -march=native" > > As you understand, my homemade gcc/gfortran lives in /opt/gcc-4.3.2/ > bin and I install the corresponding openmpi in /opt/ > openmpi-1.2.8_gcc-4.3.2_m32. Same story with openmpi up to version > 1.3.2 and gcc up to 4.4.0. The -m32 flag is there to specify 32bit > binaries (-m64 will build 64bit openmpi for the corresponding > binaries, adapt the LDFLAGS too). I am quite convinced that the > error message you receive comes from a mixture with Apple provided > openmpi libs without gfortran support. > And when it is done, in order to compile or run mpi software, I add > the path to the new openmpi binaries and libs in front with a: > > export PATH=/opt/openmpi-1.2.8_gcc-4.3.2_m32/bin:$PATH && export > DYLD_LIBRARY_PATH=/opt/openmpi-1.2.8_gcc-4.3.2_m32/lib: > $DYLD_LIBRARY_PATH > > i.e. I end with a PATH=/opt/openmpi-1.2.8_gcc-4.3.2_m32/bin:/opt/ > gcc-4.3.2/bin:xxx and DYLD_LIBRARY_PATH=/opt/ > openmpi-1.2.8_gcc-4.3.2_m32/lib:/opt/gcc-4.3.2:xxx where xxx is the > original content of the variables. > > Kind regards, > > Alain > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090611/1c93570e/attachment.htm From amosleffler at gmail.com Thu Jun 11 23:53:41 2009 From: amosleffler at gmail.com (Amos Leffler) Date: Thu, 11 Jun 2009 14:53:41 -0700 Subject: [Pw_forum] Problem with running CP In-Reply-To: References: <61b264610906091334k196c377at658e51f161768684@mail.gmail.com> Message-ID: <61b264610906111453p757f462fseda88e24f528c2dd@mail.gmail.com> Dear Somesh, Thanks for your reply. I did add the card cell parameters. However, noted something interesting. The following was written in the co.cp.start.out;file " from cell_base_init error # 1 cell parameter in alat without celldm(1)" . I thought that if you used ibrav = 0, you dont need the celldm( ) values. Also my run did not give the output that you sent me which shows that everything below EOF was ignored. I ve no idea why this is the case. Amos Leffler unaffiliated On Tue, Jun 9, 2009 at 2:11 PM, Somesh Kumar Bhattacharya wrote: > Dear Amos, > > I tried running your file ( one you attached with this mail) > ................ and get the error : > =------------------------------------------------------------------------------= > > CP: variable-cell Car-Parrinello molecular dynamics > using norm-conserving and ultrasoft Vanderbilt pseudopotentials > > Version: 4.0.3 - Fri Jun 5 13:34:25 CEST 2009 > Authors: Alfredo Pasquarello, Kari Laasonen, Andrea Trave, Roberto Car, > Paolo Giannozzi, Nicola Marzari, Carlo Cavazzoni, Guido Chiarotti, > Sandro Scandolo, Paolo Focher, Gerardo Ballabio, and others > > =------------------------------------------------------------------------------= > > This run was started on: 23: 3:55 9Jun2009 > > Serial Build > Warning: card EOF ignored > Warning: card $ECHO " RUNNING THE CALCULATION WITH FIXED IONS...\C" ignored > Warning: card $CP_COMMAND < CO.CP.START.IN > CO.CP.START.OUT ignored > Warning: card CHECK_FAILURE $? ignored > Warning: card $ECHO " DONE" ignored > Warning: card CAT > CO.CP.RESTART.IN << EOF ignored > Warning: card &CONTROL ignored > Warning: card CALCULATION='CP', ignored > Warning: card RESTART_MODE='FROM_SCRATCH', ignored > Warning: card NSTEP=50, IPRINT=50, ISAVE=50, ignored > Warning: card DT=15.0, ignored > Warning: card NDR=91, NDW=92, ignored > Warning: card PSEUDO_DIR='$PSEUDO_DIR/', ignored > Warning: card OUTDIR='$TMP_DIR/', ignored > Warning: card / ignored > Warning: card &SYSTEM ignored > Warning: card IBRAV = 0, ignored > Warning: card NAT = 28, ignored > Warning: card NTYP = 2, ignored > Warning: card ECUTWFC = 24.D0, ignored > Warning: card ECUTRHO = 144.D0, ignored > Warning: card NR1B=16, NR2B=16, NR3B=16, ignored > Warning: card QCUTZ=150., Q2SIGMA=2.0, ECFIXED=16.0, ignored > Warning: card / ignored > Warning: card &ELECTRONS ignored > Warning: card ELECTRON_DYNAMICS='DAMP', ELECTRON_DAMPING=0.2, ignored > Warning: card EMASS=700., EMASS_CUTOFF=3., ignored > Warning: card &IONS ignored > Warning: card ION_DYNAMICS='NONE', ignored > Warning: card ION_RADIUS(1) = 1.0, ION_RADIUS(2) =1.0, ignored > Warning: card / ignored > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from card_cell_parameters : error # 2 > two occurrences > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > 2 > > I think its because with ibrav = 0, you need to add the card > cell_parameters. > > Did you tried that ???? > > Somesh > > > On Tue, Jun 9, 2009 at 10:34 PM, Amos Leffler wrote: >> >> Dear forum, >> I have been trying to run the attached file which is based on >> that in Example18. The flle in Example18 runs properly but my >> modified version does not. I have noted the information in the "Users >> Guide" , p28ff. If I leave out the EOF entries after each of the >> "Atomic Positions" the entire file reads in but no output is >> generated. Adding the EOF after the first Atomic_Positions, the output >> stops with the message "running the calculation with fixed ions...\c" >> . Is there more detailed information on using CP either in espresso >> itself or elsewhere? >> Thanks for your help. >> >> Amos Leffler >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Somesh Kr. Bhattacharya > Post Doctoral Fellow > Room No. 263, > Leonardo Building, > The Abdus Salam International Centre for Theoretical Physics > Strada Costiera, 11 > I-34014 Trieste > Italy > Phone: +39-040-2240399 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From amosleffler at gmail.com Fri Jun 12 00:01:15 2009 From: amosleffler at gmail.com (Amos Leffler) Date: Thu, 11 Jun 2009 15:01:15 -0700 Subject: [Pw_forum] Problem with running CP In-Reply-To: <1244582813.5214.957.camel@zero> References: <61b264610906091334k196c377at658e51f161768684@mail.gmail.com> <1244582813.5214.957.camel@zero> Message-ID: <61b264610906111501w3686599bue7903d2e457a4f6@mail.gmail.com> Dear Axel, If what you suggest that the problem with my file is in the the "bin/sh" statement which does the program run properly with the file from example18? Another person sent me the output when he ran my file and it did give a large number of errors all saying that the lines below EOF were ignored. I did get an error message saying that the program expected celldm(1) but I thought this was not used with ibrav =0. ? Amos Leffler unaffiliated On Tue, Jun 9, 2009 at 2:26 PM, Axel Kohlmeyer wrote: > On Tue, 2009-06-09 at 13:34 -0700, Amos Leffler wrote: >> Dear forum, > > dear amos, > >> I have been trying to run the attached file which is based on >> that in Example18. The flle in Example18 runs properly but my > > what platform are you running on: OS type/version, CPU, fortran > compiler? > >> modified version does not. I have noted the information in the "Users >> Guide" , p28ff. If I leave out the EOF entries after each of the >> "Atomic Positions" the entire file reads in but no output is > > this _cannot_ work. this is due to shell scripting and has little > to do with pw.x/cp.x itself. there are some linux versions that use > a /bin/sh implementation that is very minimalistic (but standard > compliant), while the run_example scripts tend to depend some > some common extensions. you have to leave the EOFs in, but you > can try replacing /bin/sh with /bin/bash. > >> generated. Adding the EOF after the first Atomic_Positions, the output >> stops with the message "running the calculation with fixed ions...\c" >> . Is there more detailed information on using CP either in espresso >> itself or elsewhere? > > there should be a large number of error messages. > > this has nothing to do with cp.x. the run_example script > just automates the process of generating input files and > running them. in general, it is better for manual runs to > modify the individual input files, if you are not an expert > in bourne shell scripting. > > cheers, > axel. > >> Thanks for your help. >> >> Amos Leffler >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From akohlmey at cmm.chem.upenn.edu Fri Jun 12 00:07:37 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 11 Jun 2009 18:07:37 -0400 Subject: [Pw_forum] Problem with running CP In-Reply-To: <61b264610906111501w3686599bue7903d2e457a4f6@mail.gmail.com> References: <61b264610906091334k196c377at658e51f161768684@mail.gmail.com> <1244582813.5214.957.camel@zero> <61b264610906111501w3686599bue7903d2e457a4f6@mail.gmail.com> Message-ID: <1244758057.2901.115.camel@zero> On Thu, 2009-06-11 at 15:01 -0700, Amos Leffler wrote: > Dear Axel, > If what you suggest that the problem with my file is in the > the "bin/sh" statement which does the program run properly with the > file from example18? amos, good point. nevertheless, you must not remove the EOF entries. they are essential and that is what probably threw me off-track. > Another person sent me the output when he ran my file and it > did give a large number of errors all saying that the lines below EOF that e-mail is a complete fluke, since that person was obviously running the script as input to cp.x and not as a shell script in the proper location. > were ignored. I did get an error message saying that the program > expected celldm(1) but I thought this was not used with ibrav =0. ? please have a closer look at INPUT_CP. you are placing the CELL_PARAMETERS section _before_ ATOMIC_SPECIES, whereas the input description requires it to come _after_ ATOMIC_POSITIONS. if you do not follow the input syntax, calculations won't start. cheers, axel. > Amos Leffler > unaffiliated > > On Tue, Jun 9, 2009 at 2:26 PM, Axel > Kohlmeyer wrote: > > On Tue, 2009-06-09 at 13:34 -0700, Amos Leffler wrote: > >> Dear forum, > > > > dear amos, > > > >> I have been trying to run the attached file which is based on > >> that in Example18. The flle in Example18 runs properly but my > > > > what platform are you running on: OS type/version, CPU, fortran > > compiler? > > > >> modified version does not. I have noted the information in the "Users > >> Guide" , p28ff. If I leave out the EOF entries after each of the > >> "Atomic Positions" the entire file reads in but no output is > > > > this _cannot_ work. this is due to shell scripting and has little > > to do with pw.x/cp.x itself. there are some linux versions that use > > a /bin/sh implementation that is very minimalistic (but standard > > compliant), while the run_example scripts tend to depend some > > some common extensions. you have to leave the EOFs in, but you > > can try replacing /bin/sh with /bin/bash. > > > >> generated. Adding the EOF after the first Atomic_Positions, the output > >> stops with the message "running the calculation with fixed ions...\c" > >> . Is there more detailed information on using CP either in espresso > >> itself or elsewhere? > > > > there should be a large number of error messages. > > > > this has nothing to do with cp.x. the run_example script > > just automates the process of generating input files and > > running them. in general, it is better for manual runs to > > modify the individual input files, if you are not an expert > > in bourne shell scripting. > > > > cheers, > > axel. > > > >> Thanks for your help. > >> > >> Amos Leffler > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > ======================================================================= > > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > > Center for Molecular Modeling -- University of Pennsylvania > > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > > ======================================================================= > > If you make something idiot-proof, the universe creates a better idiot. > > > > _______________________________________________ > > 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 -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From wshen02 at gmail.com Fri Jun 12 00:12:09 2009 From: wshen02 at gmail.com (=?ISO-2022-JP?B?GyRCSjhEQBsoQg==?=) Date: Thu, 11 Jun 2009 15:12:09 -0700 Subject: [Pw_forum] Dear all, where can I get the detailed instructions to get the right pseudopotentials? Message-ID: <2c9df8a80906111512l77e8e348o61a3d03118ba0058@mail.gmail.com> I followed the way on the ld1.x explanation page in quantum espresso,and I find the pseudopotential I get never provide the correct result. anybody who have the experience to get the pseudopotential please tell me where I can get the detailed instruction on making pseudopotential? Thanks Wen Shen Ph.D candidate Georgetown University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090611/530ef652/attachment.htm From somesh.kb at gmail.com Fri Jun 12 00:15:45 2009 From: somesh.kb at gmail.com (Somesh Kumar Bhattacharya) Date: Thu, 11 Jun 2009 23:15:45 +0100 Subject: [Pw_forum] Problem with running CP In-Reply-To: <61b264610906111453p757f462fseda88e24f528c2dd@mail.gmail.com> References: <61b264610906091334k196c377at658e51f161768684@mail.gmail.com> <61b264610906111453p757f462fseda88e24f528c2dd@mail.gmail.com> Message-ID: hi amos, you should try running each job seperately. i assume you are perhaps in the begining stage of using QE. please do one job at a time instead of running running it as a set of jobs using some script. anyway, am attaching a simple input file for you ............ try running it with suitable modifications what ever you want ........... Axel, you are right ... i didn't run it as a shell script ........................ so may be i came up with such errors ...................................... On Thu, Jun 11, 2009 at 10:53 PM, Amos Leffler wrote: > Dear Somesh, > Thanks for your reply. I did add the card cell parameters. > However, noted something interesting. The following was written in > the co.cp.start.out;file > " from cell_base_init error # 1 > cell parameter in alat without celldm(1)" . > I thought that if you used ibrav = 0, you dont need the celldm( ) values. > Also my run did not give the output that you sent me which shows that > everything below EOF was ignored. I ve no idea why this is the case. > Amos Leffler > unaffiliated > > On Tue, Jun 9, 2009 at 2:11 PM, Somesh Kumar > Bhattacharya wrote: > > Dear Amos, > > > > I tried running your file ( one you attached with this mail) > > ................ and get the error : > > > =------------------------------------------------------------------------------= > > > > CP: variable-cell Car-Parrinello molecular dynamics > > using norm-conserving and ultrasoft Vanderbilt pseudopotentials > > > > Version: 4.0.3 - Fri Jun 5 13:34:25 CEST 2009 > > Authors: Alfredo Pasquarello, Kari Laasonen, Andrea Trave, Roberto > Car, > > Paolo Giannozzi, Nicola Marzari, Carlo Cavazzoni, Guido Chiarotti, > > Sandro Scandolo, Paolo Focher, Gerardo Ballabio, and others > > > > > =------------------------------------------------------------------------------= > > > > This run was started on: 23: 3:55 9Jun2009 > > > > Serial Build > > Warning: card EOF ignored > > Warning: card $ECHO " RUNNING THE CALCULATION WITH FIXED IONS...\C" > ignored > > Warning: card $CP_COMMAND < CO.CP.START.IN > > CO.CP.START.OUT ignored > > Warning: card CHECK_FAILURE $? ignored > > Warning: card $ECHO " DONE" ignored > > Warning: card CAT > CO.CP.RESTART.IN << EOF > ignored > > Warning: card &CONTROL ignored > > Warning: card CALCULATION='CP', ignored > > Warning: card RESTART_MODE='FROM_SCRATCH', ignored > > Warning: card NSTEP=50, IPRINT=50, ISAVE=50, ignored > > Warning: card DT=15.0, ignored > > Warning: card NDR=91, NDW=92, ignored > > Warning: card PSEUDO_DIR='$PSEUDO_DIR/', ignored > > Warning: card OUTDIR='$TMP_DIR/', ignored > > Warning: card / ignored > > Warning: card &SYSTEM ignored > > Warning: card IBRAV = 0, ignored > > Warning: card NAT = 28, ignored > > Warning: card NTYP = 2, ignored > > Warning: card ECUTWFC = 24.D0, ignored > > Warning: card ECUTRHO = 144.D0, ignored > > Warning: card NR1B=16, NR2B=16, NR3B=16, ignored > > Warning: card QCUTZ=150., Q2SIGMA=2.0, ECFIXED=16.0, ignored > > Warning: card / ignored > > Warning: card &ELECTRONS ignored > > Warning: card ELECTRON_DYNAMICS='DAMP', ELECTRON_DAMPING=0.2, ignored > > Warning: card EMASS=700., EMASS_CUTOFF=3., ignored > > Warning: card &IONS ignored > > Warning: card ION_DYNAMICS='NONE', ignored > > Warning: card ION_RADIUS(1) = 1.0, ION_RADIUS(2) =1.0, ignored > > Warning: card / ignored > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from card_cell_parameters : error # 2 > > two occurrences > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > stopping ... > > 2 > > > > I think its because with ibrav = 0, you need to add the card > > cell_parameters. > > > > Did you tried that ???? > > > > Somesh > > > > > > On Tue, Jun 9, 2009 at 10:34 PM, Amos Leffler > wrote: > >> > >> Dear forum, > >> I have been trying to run the attached file which is based on > >> that in Example18. The flle in Example18 runs properly but my > >> modified version does not. I have noted the information in the "Users > >> Guide" , p28ff. If I leave out the EOF entries after each of the > >> "Atomic Positions" the entire file reads in but no output is > >> generated. Adding the EOF after the first Atomic_Positions, the output > >> stops with the message "running the calculation with fixed ions...\c" > >> . Is there more detailed information on using CP either in espresso > >> itself or elsewhere? > >> Thanks for your help. > >> > >> Amos Leffler > >> > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > > > > > > > > -- > > Somesh Kr. Bhattacharya > > Post Doctoral Fellow > > Room No. 263, > > Leonardo Building, > > The Abdus Salam International Centre for Theoretical Physics > > Strada Costiera, 11 > > I-34014 Trieste > > Italy > > Phone: +39-040-2240399 > > > > _______________________________________________ > > 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 > -- Somesh Kr. Bhattacharya Post Doctoral Fellow Room No. 263, Leonardo Building, The Abdus Salam International Centre for Theoretical Physics Strada Costiera, 11 I-34014 Trieste Italy Phone: +39-040-2240399 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090611/bbd8f7fb/attachment-0001.htm -------------- next part -------------- &control calculation = 'fpmd' restart_mode='from_scratch', prefix='Na-atom', nstep = 5000, iprint=100, isave= 100, dt=3.0, ndr=50, ndw=51, etot_conv_thr = 1.d-8, max_seconds = 21000, pseudo_dir = '/home/somesh/QE/espresso-4.0.3/pseudo/', outdir='.' / &system ibrav = 1, celldm(1) = 37.7943233, nat= 1, ntyp= 1, ecutwfc =100.0, nelec = 1, nr1b = 40, nr2b = 40, nr3b = 40 / &electrons electron_dynamics='damp', electron_damping=0.2, startingwfc='random', orthogonalization = 'ortho', emass=400., emass_cutoff=3., / &ions ion_dynamics='none', ion_radius(1)=0.8, / &cell cell_dynamics = 'none' / ATOMIC_SPECIES Na 22.987770 Na.blyp-tm.nc.UPF ATOMIC_POSITIONS {crystal} Na 0.500000000 0.500000000 0.500000000 0 0 0 1 From carlos_viol at yahoo.com.br Fri Jun 12 08:00:33 2009 From: carlos_viol at yahoo.com.br (Carlos Eduardo Viol Barbosa) Date: Thu, 11 Jun 2009 23:00:33 -0700 (PDT) Subject: [Pw_forum] Surface Stress Message-ID: <289064.20818.qm@web65602.mail.ac4.yahoo.com> Dear all Can I use in someway the information of the stress tensor (given by pw.x in the end of output) to determine the surface stress in a specific direction? Thank you Carlos E. Viol Barbosa Laboratorio Nazionale TASC Area Science Park Basovizza S.S. 14 Km 163.5 34012 Trieste, Italy From giannozz at democritos.it Fri Jun 12 09:06:45 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 12 Jun 2009 09:06:45 +0200 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: <7124F8BA-AA78-4ED5-9CBE-18FCA80B9538@umbc.edu> References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> <4A2FE991.1010902@gmail.com> <4A303C21.3070102@gmail.com> <7124F8BA-AA78-4ED5-9CBE-18FCA80B9538@umbc.edu> Message-ID: <4A31FE85.9030900@democritos.it> Michael Hayden wrote: > ld: in /usr/local/lib, can't map file, errno=22 > collect2: ld returned 1 exit status > make[1]: *** [pw.x] Error 1 > make: *** [pw] Error 2 > > This doesn't look good and I can't find any list of these errors in the > user guide. the user guide contains information only on quantum espresso related errors. This is not one: it is a problem with the linker. I guess it means that one of the libraries you are trying to link is not a library file Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Fri Jun 12 09:08:10 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 12 Jun 2009 09:08:10 +0200 Subject: [Pw_forum] Dear all, where can I get the detailed instructions to get the right pseudopotentials? In-Reply-To: <2c9df8a80906111512l77e8e348o61a3d03118ba0058@mail.gmail.com> References: <2c9df8a80906111512l77e8e348o61a3d03118ba0058@mail.gmail.com> Message-ID: <4A31FEDA.80804@democritos.it> ?? wrote: > anybody who have the experience to get the pseudopotential please tell > me where I can get the detailed instruction on making pseudopotential? there are some notes in atomic_doc/pseudo-gen.tex P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From kazempoor2000 at yahoo.com Fri Jun 12 09:31:58 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Fri, 12 Jun 2009 00:31:58 -0700 (PDT) Subject: [Pw_forum] single and triplet states Message-ID: <356039.44555.qm@web112515.mail.gq1.yahoo.com> Dear all The electronic structure of a Ga vacancy in GaAs bulk material can be qualitatively understood in terms of four dangling bonds which are centered at the four As atoms around the missing Ga. In an undistorted situation (Td symmetry) these four dangling bonds give rise to two energy levels : one singlet (a1) and one triplet(t2) . When Ga situated at surface Ga -terminated , the As neighbors becomes three instead of four and four Ga vacancy at surface by comparison with Ga vacancy at bulk, t2 splitts. My question is when I simulate the Ga vacancy in the bulk , I only see one defect -induced level . How can I understand that this level is singlet or triplet? Also, how can I find the relation between number of dangling bonds around the defects and splitting of the states? Thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 From kazempoor2000 at yahoo.com Fri Jun 12 09:33:11 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Fri, 12 Jun 2009 00:33:11 -0700 (PDT) Subject: [Pw_forum] single and triplet states Message-ID: <95475.1367.qm@web112512.mail.gq1.yahoo.com> Dear all The electronic structure of a Ga vacancy in GaAs bulk material can be qualitatively understood in terms of four dangling bonds which are centered at the four As atoms around the missing Ga. In an undistorted situation (Td symmetry) these four dangling bonds give rise to two energy levels : one singlet (a1) and one triplet(t2) . When Ga situated at surface Ga -terminated , the As neighbors becomes three instead of four and four Ga vacancy at surface by comparison with Ga vacancy at bulk, t2 splitts. My question is when I simulate the Ga vacancy in the bulk , I only see one defect -induced level . How can I understand that this level is singlet or triplet? Also, how can I find the relation between number of dangling bonds around the defects and splitting of the states? Thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 From paulatto at sissa.it Fri Jun 12 11:12:04 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 12 Jun 2009 11:12:04 +0200 Subject: [Pw_forum] Dear all, where can I get the detailed instructions to get the right pseudopotentials? In-Reply-To: <2c9df8a80906111512l77e8e348o61a3d03118ba0058@mail.gmail.com> References: <2c9df8a80906111512l77e8e348o61a3d03118ba0058@mail.gmail.com> Message-ID: In data 12 giugno 2009 alle ore 00:12:09, ?? ha scritto: > I find the pseudopotential I get never provide the correct result. > anybody who have the experience to get the pseudopotential please tell me > where I can get the detailed instruction on making pseudopotential? Dear Wen Shen, *after* reading the notes from Paolo Giannozzi you have to study the problem in a systematic way. The starting point is the periodic table of elements, it is not called "periodic" by chance. Elements tend to have similar properties to the ones above and under them, from a pseudopotential generation point of view also elements close to the right or to the left are "similar." You can pick the example file from atomic_doc/pseudo_library and adapt them to similar elements. Notice how the cutoff radiuses are related to the physical radiuses of the orbitals: , , r_max, which are all printed during the all-electron calculation. Be careful about the syntax: ld1.x is very picky, try to not use more variables than are actually necessary. If you are trying to do an ultrasoft pseudopotential start with a signle projector per channel, than look at the logarithmic derivative (good range: -10:+10Ry) and add the second projectors (one at a time) trying to move the inevitable ghost-state as high in energy as possible. Do systematic generations, e.g. write a small script that generates a dozen of different pseudopotentials with all parameters equal but one, and plot their logarithmic derivatives. Look at all the derivatives: which value will be better for the parameter. Finally, keep in mind that light elements are easier, and elements with d orbitals are harder, elements from the first 3 or 4 columns will likely require one or two semi-core states to be include in valence. Lanthanides and actinides can take one week of work, especially if you have little experience. That's about it, if you have a specific input don't be afraid to ask for help. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From sclauzer at sissa.it Fri Jun 12 14:25:49 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 12 Jun 2009 14:25:49 +0200 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: <7124F8BA-AA78-4ED5-9CBE-18FCA80B9538@umbc.edu> References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> <4A2FE991.1010902@gmail.com> <4A303C21.3070102@gmail.com> <7124F8BA-AA78-4ED5-9CBE-18FCA80B9538@umbc.edu> Message-ID: <4A32494D.6080304@sissa.it> Sorry Michael, I can't understand why you're continuing having problems in compiling. It should be not a "mission-impossible" kind of task, you simply need to have working compilers and mpi wrappers (which you seem to have now) and maybe tweak a bit with the configure options. I compiled openmpi 1.3 on top of gfortran and Apple's gcc on MacOSX 10.5.7 (although I really _strongly_ suggest you to use Intel compilers if you want to do serious calculations on your Intel desktop... you may discover that you're wasting half of the time just to save an hundred dollars or so), and I haven't met any problem. Michael Hayden wrote: > Alain, > > Again, thanks for your efforts and time. > > I > have successfully installed and tested OpenMPI. I also configured Quant Espresso and received the "Parallel environment detected successfully, configured for compilation of parallel executables" > response at the end of the config process. > > I then compiled it,but the end of a very long output read: > > ld: in /usr/local/lib, can't map file, errno=22 > collect2: ld returned 1 exit status > make[1]: *** [pw.x] Error 1 > make: *** [pw] Error 2 Most probably you have a problem in your environment variables (check if PATH, LD_LIBRARY_PATH and DYLD_LIBRARY_PATH are what you expect them to be, i.e. with the path to the MPI version you want to use listed _first_) or you miscompiled openmpi. Honestly I don't see any need to feed so many parameters as suggested by Alain to the configure of openmpi (unless you know exactly what they mean, maybe Alain does, I do not...). You simply need to specify CC, CXX, F77, FC (and --prefix option, since it is not wise to overwrite Apple's compiler files). If something goes wrong in the configure you may need to add some others. Cheers GS > > This doesn't look good and I can't find any list of these errors in the > user guide. I tried example01 and received (of course) this output: > ERROR: /usr/local/espresso-4.0.5/bin/pw.x not existent or not executable > Aborting > > Any ideas? > > cheers, > Mike > > > On Jun 10, 2009, at 7:05 PM, Alain Jacques wrote: > >> Hello Mike, >> >> Humm, sorry it didn't work as expected. My development platform runs >> OSX 10.5.7. I have compiled many working openmpi versions with the >> following recipe: >> >> export LD_LIBRARY_PATH=/opt/gcc-4.3.2/lib:$LD_LIBRARY_PATH && export >> PATH=/opt/gcc-4.3.2/bin:$PATH >> >> ./configure --prefix=/opt/openmpi-1.2.8_gcc-4.3.2_m32 --enable-static >> --enable-shared --disable-dependency-tracking --with-devel-headers >> --with-wrapper-ldflags="-Wl,-search_paths_first" >> CC=/opt/gcc-4.3.2/bin/gcc LDFLAGS="-L/opt/gcc-4.3.2/lib" >> FC=/opt/gcc-4.3.2/bin/gfortran F77=/opt/gcc-4.3.2/bin/gfortran >> CXX=/opt/gcc-4.3.2/bin/g++ CPP=/opt/gcc-4.3.2/bin/cpp CFLAGS="-m32 -O3 >> -march=native" CXXFLAGS="-m32 -O3 -march=native" FCFLAGS="-m32 -O3 >> -march=native" FFLAGS="-m32 -O3 -march=native" >> >> As you understand, my homemade gcc/gfortran lives in >> /opt/gcc-4.3.2/bin and I install the corresponding openmpi in >> /opt/openmpi-1.2.8_gcc-4.3.2_m32. Same story with openmpi up to >> version 1.3.2 and gcc up to 4.4.0. The -m32 flag is there to specify >> 32bit binaries (-m64 will build 64bit openmpi for the corresponding >> binaries, adapt the LDFLAGS too). I am quite convinced that the error >> message you receive comes from a mixture with Apple provided openmpi >> libs without gfortran support. >> And when it is done, in order to compile or run mpi software, I add >> the path to the new openmpi binaries and libs in front with a: >> >> export PATH=/opt/openmpi-1.2.8_gcc-4.3.2_m32/bin:$PATH && export >> DYLD_LIBRARY_PATH=/opt/openmpi-1.2.8_gcc-4.3.2_m32/lib:$DYLD_LIBRARY_PATH >> >> i.e. I end with a >> PATH=/opt/openmpi-1.2.8_gcc-4.3.2_m32/bin:/opt/gcc-4.3.2/bin:xxx and >> DYLD_LIBRARY_PATH=/opt/openmpi-1.2.8_gcc-4.3.2_m32/lib:/opt/gcc-4.3.2:xxx >> where xxx is the original content of the variables. >> >> Kind regards, >> >> Alain >> > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From ajs.jacques at gmail.com Fri Jun 12 15:56:44 2009 From: ajs.jacques at gmail.com (Alain Jacques) Date: Fri, 12 Jun 2009 15:56:44 +0200 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: <4A32494D.6080304@sissa.it> References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> <4A2FE991.1010902@gmail.com> <4A303C21.3070102@gmail.com> <7124F8BA-AA78-4ED5-9CBE-18FCA80B9538@umbc.edu> <4A32494D.6080304@sissa.it> Message-ID: <4A325E9C.7030400@gmail.com> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090612/4147e069/attachment.htm From cristian.degliesposti at unibo.it Fri Jun 12 16:19:33 2009 From: cristian.degliesposti at unibo.it (Cristian Degli Esposti Boschi) Date: Fri, 12 Jun 2009 16:19:33 +0200 Subject: [Pw_forum] QE 4.0.5 64-bit serial installed on Mac Pro with gcc 4.3.3 and gfortran Message-ID: <4A3263F5.3070109@unibo.it> Dear all, I only want to report briefly that eventually it seems that I managed to install QE 4.0.5 on a Mac Pro with 2 64-bit Intel Xeon processors. For the moment I have compiled a serial build (didn't try a parallel one yet) with gfortran and gcc 4.3.3 from the FINK package. Both pw.x and cp.x seem to run properly. Mac OSX (10.5) apparently defaults to 32-bits, and I experienced memory limitations also with other applications. So I wanted 64-bit compilation. Therefore I issued sudo ./configure --disable-parallel CC=gcc-4 CFLAGS="-m64" CPPFLAGS="-m64" LDFLAGS="-m64" FFLAGS="-m64" Note that I didn't set the "-m64" option in F90FLAGS, since this would result in compilation errors with iotk sources. Then, in order to have compatibility between lapack_atlas and dlamch at the 64-bit level I had to modify manually make.sys as follows FFLAGS_NOOPT = -O0 -m64 (I use lapack shipped with the QE package). Hope this helps and thanks for all the suggestions. Cristian -- ___________________________________________________ Cristian Degli Esposti Boschi CNR, CNISM, Unita' di Ricerca di Bologna, c/o Dipartimento di Fisica, Universita' di Bologna viale Berti-Pichat, 6/2, 40127, Bologna, Italia tel. ++39 051 2095114 fax ++39 051 2095113 e-mail: cristian.degliesposti -AT- unibo.it web: http://www.df.unibo.it/fismat/theory ___________________________________________________ From hayden at umbc.edu Fri Jun 12 16:46:47 2009 From: hayden at umbc.edu (Michael Hayden) Date: Fri, 12 Jun 2009 10:46:47 -0400 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: <4A325E9C.7030400@gmail.com> References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> <4A2FE991.1010902@gmail.com> <4A303C21.3070102@gmail.com> <7124F8BA-AA78-4ED5-9CBE-18FCA80B9538@umbc.edu> <4A32494D.6080304@sissa.it> <4A325E9C.7030400@gmail.com> Message-ID: <51CD7518-BCF3-4FC7-A112-51A18EA48C55@umbc.edu> Alain, I tried your tweak but got the same result at the end of the make all: mpif90 -o pw.x \ pwscf.o ../Modules/atom.o ../Modules/autopilot.o ../Modules/ basic_algebra_routines.o ../Modules/berry_phase.o ../Modules/ bfgs_module.o ../Modules/cell_base.o ../Modules/check_stop.o ../ Modules/clocks.o ../Modules/constants.o ../Modules/ constraints_module.o ../Modules/control_flags.o ../Modules/ descriptors.o ../Modules/dspev_drv.o ../Modules/electrons_base.o ../ Modules/error_handler.o ../Modules/exc_t.o ../Modules/fft_base.o ../ Modules/fft_parallel.o ../Modules/fft_scalar.o ../Modules/ fft_types.o ../Modules/functionals.o ../Modules/input_parameters.o ../ Modules/io_files.o ../Modules/io_global.o ../Modules/ions_base.o ../ Modules/ions_nose.o ../Modules/kind.o ../Modules/mp_global.o ../ Modules/mp_wave.o ../Modules/mp.o ../Modules/mp_base.o ../Modules/ metagga.o ../Modules/metadyn_base.o ../Modules/metadyn_io.o ../Modules/ metadyn_vars.o ../Modules/path_base.o ../Modules/path_formats.o ../ Modules/path_variables.o ../Modules/path_opt_routines.o ../Modules/ path_io_routines.o ../Modules/path_reparametrisation.o ../Modules/ parallel_include.o ../Modules/parameters.o ../Modules/parser.o ../ Modules/paw_variables.o ../Modules/printout_base.o ../Modules/ pseudo_types.o ../Modules/ptoolkit.o ../Modules/radial_grids.o ../ Modules/random_numbers.o ../Modules/read_cards.o ../Modules/ read_namelists.o ../Modules/read_ncpp.o ../Modules/read_upf_v1.o ../ Modules/read_upf_v2.o ../Modules/read_uspp.o ../Modules/recvec.o ../ Modules/shmem_include.o ../Modules/splinelib.o ../Modules/ stick_base.o ../Modules/task_groups.o ../Modules/timestep.o ../Modules/ upf_to_internal.o ../Modules/uspp.o ../Modules/upf.o ../Modules/ version.o ../Modules/vxc_t.o ../Modules/vxcgc.o ../Modules/ wavefunctions.o ../Modules/wave_base.o ../Modules/write_upf_v2.o ../ Modules/xml_io_base.o ../Modules/zhpev_drv.o libpw.a ../flib/ ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a ../flib/ lapack.a ../flib/blas.a /usr/local/lib /usr/local/lib ld: in /usr/local/lib, can't map file, errno=22 collect2: ld returned 1 exit status make[1]: *** [pw.x] Error 1 make: *** [pw] Error 2 Just to be clear. My paths are set in my .profile as such: export PATH=/usr/local/bin:/usr/local/lib:$PATH export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH export DYLD_LIBRARY_PATH=/usr/local/lib:$DYLD_LIBRARY_PATH I have installed and compiled FFTW, gfortran, and OpenMPI in /usr/ local. Espresso-4.0.5 is also installed in /usr/local I agree that it looks like there is some problem with the libraries, but I don't see it. still trying, Mike On Jun 12, 2009, at 9:56 AM, Alain Jacques wrote: > > A possible problem may come from a mixture with the blas and lapack > dylibs provided by Apple. If configure tells you that it finds > suitable linear algebra with -latlas and -lblas and a make pw stops > at the final link complaining about missing functions then I am > afraid it is the case. May I suggest to try the following tweak. > Configure (I use ./configure --prefix=/Users/Shared/Applications/ > espresso-4.0.5 MPIF90=mpif90 F90=gfortran F77=gfortran CC=gcc - with > correct PATH and DYLD_LIBRARY_PATH) then edit the make.sys and > modify the following 2 lines to the built-in libs BLAS_LIBS = ../ > flib/blas.a and LAPACK_LIBS = ../flib/lapack.a. Make pw and tell us > if it goes up to the end. >> I compiled openmpi 1.3 on top of gfortran and Apple's gcc on MacOSX >> 10.5.7 (although I >> really _strongly_ suggest you to use Intel compilers if you want to >> do serious >> calculations on your Intel desktop... you may discover that you're >> wasting half of the >> time just to save an hundred dollars or so), and I haven't met any >> problem. >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090612/8eeb4452/attachment.htm From giannozz at democritos.it Fri Jun 12 17:05:16 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 12 Jun 2009 17:05:16 +0200 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: <51CD7518-BCF3-4FC7-A112-51A18EA48C55@umbc.edu> References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> <4A2FE991.1010902@gmail.com> <4A303C21.3070102@gmail.com> <7124F8BA-AA78-4ED5-9CBE-18FCA80B9538@umbc.edu> <4A32494D.6080304@sissa.it> <4A325E9C.7030400@gmail.com> <51CD7518-BCF3-4FC7-A112-51A18EA48C55@umbc.edu> Message-ID: <194EA790-5DBB-4D54-975C-B6F62F4ECFE9@democritos.it> On Jun 12, 2009, at 16:46 , Michael Hayden wrote: > mpif90 -o pw.x [...] /usr/local/lib /usr/local/lib you are linking "/usr/local/lib" (a directory)... > ld: in /usr/local/lib, can't map file, errno=22 and the linker complains Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sagarambavale at yahoo.co.in Fri Jun 12 17:05:34 2009 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Fri, 12 Jun 2009 20:35:34 +0530 (IST) Subject: [Pw_forum] homo-lumo and conductance Message-ID: <882340.96939.qm@web94611.mail.in2.yahoo.com> Dear all, I am studying ballistic conductance through a molecule attached to Al electrode. The k-pt grid used for scf calculation of scattering region made of molecule and few layers of electrode, is 2 2 10 1 1 1. I want to see effect of HOMO-LUMO levels of molecule on transmission. Is it sensible to find HOMO-LUMO levels of molecule using separate calculation of isolated molecule with gamma point? How about bandstructure that I got from 20 k-pt calculation of scattering region periodic in z-direction? Thank you.. Sagar Ambavale PhD student M.S. University of Baroda India Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090612/5796f8ac/attachment.htm From hayden at umbc.edu Fri Jun 12 17:22:14 2009 From: hayden at umbc.edu (Michael Hayden) Date: Fri, 12 Jun 2009 11:22:14 -0400 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: <194EA790-5DBB-4D54-975C-B6F62F4ECFE9@democritos.it> References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> <4A2FE991.1010902@gmail.com> <4A303C21.3070102@gmail.com> <7124F8BA-AA78-4ED5-9CBE-18FCA80B9538@umbc.edu> <4A32494D.6080304@sissa.it> <4A325E9C.7030400@gmail.com> <51CD7518-BCF3-4FC7-A112-51A18EA48C55@umbc.edu> <194EA790-5DBB-4D54-975C-B6F62F4ECFE9@democritos.it> Message-ID: Paolo, Do you know the cause of this? My paths are set in my .profile as such: export PATH=/usr/local/bin:/usr/local/lib:$PATH export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH export DYLD_LIBRARY_PATH=/usr/local/lib:$DYLD_LIBRARY_PATH This was my ./configure command: ./configure --prefix=/usr/local/espresso-4.0.5 MPIF90=mpif90 CC=gcc F77=gfortran F90=gfortran MPIF77=mpif77 CXX=g++ MPICC=mpic++ FFT_LIBS=/ usr/local/lib LAPACK_LIBS=/usr/local/espresso-4.0.5/flib/lapack.a BLAS_LIBS=/usr/local/espresso-4.0.5/flib/blas.a Mike On Jun 12, 2009, at 11:05 AM, Paolo Giannozzi wrote: > > On Jun 12, 2009, at 16:46 , Michael Hayden wrote: > >> mpif90 -o pw.x [...] /usr/local/lib /usr/local/lib > > you are linking "/usr/local/lib" (a directory)... > >> ld: in /usr/local/lib, can't map file, errno=22 > > > and the linker complains > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of 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/20090612/96de5eb8/attachment.htm From paulatto at sissa.it Fri Jun 12 17:27:16 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 12 Jun 2009 17:27:16 +0200 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> <4A2FE991.1010902@gmail.com> <4A303C21.3070102@gmail.com> <7124F8BA-AA78-4ED5-9CBE-18FCA80B9538@umbc.edu> <4A32494D.6080304@sissa.it> <4A325E9C.7030400@gmail.com> <51CD7518-BCF3-4FC7-A112-51A18EA48C55@umbc.edu> <194EA790-5DBB-4D54-975C-B6F62F4ECFE9@democritos.it> Message-ID: In data 12 giugno 2009 alle ore 17:22:14, Michael Hayden ha scritto: > MPICC=mpic++ Dear Mychael, this could be a problem: c++ compilers can compile c code, but they will "mangle" the name of functions, and this can cause the linking phase to fail. Furthermore, QE does not incldue any c++ file, you can safely ignore all c++ related configure options and variables. Try setting "MPICC=mpicc" instead, best regards. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From giannozz at democritos.it Fri Jun 12 17:41:06 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 12 Jun 2009 17:41:06 +0200 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> <4A2FE991.1010902@gmail.com> <4A303C21.3070102@gmail.com> <7124F8BA-AA78-4ED5-9CBE-18FCA80B9538@umbc.edu> <4A32494D.6080304@sissa.it> <4A325E9C.7030400@gmail.com> <51CD7518-BCF3-4FC7-A112-51A18EA48C55@umbc.edu> <194EA790-5DBB-4D54-975C-B6F62F4ECFE9@democritos.it> Message-ID: <21965115-2247-4B7B-9774-AEE5AEF05781@democritos.it> On Jun 12, 2009, at 17:22 , Michael Hayden wrote: > This was my ./configure command: the less arguments you give to configure, the better > ./configure --prefix=/usr/local/espresso-4.0.5 MPIF90=mpif90 CC=gcc > F77=gfortran F90=gfortran MPIF77=mpif77 CXX=g++ MPICC=mpic++ > FFT_LIBS=/usr/local/lib FFT_LIBS=/usr/local/lib, so the linker will try (and fail in doing so) to load /usr/local/lib . MPIF77, CXX, MPICC are not used. > LAPACK_LIBS=/usr/local/espresso-4.0.5/flib/lapack.a BLAS_LIBS=/usr/ > local/espresso-4.0.5/flib/blas.a Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sclauzer at sissa.it Fri Jun 12 17:42:05 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 12 Jun 2009 17:42:05 +0200 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> <4A2FE991.1010902@gmail.com> <4A303C21.3070102@gmail.com> <7124F8BA-AA78-4ED5-9CBE-18FCA80B9538@umbc.edu> <4A32494D.6080304@sissa.it> <4A325E9C.7030400@gmail.com> <51CD7518-BCF3-4FC7-A112-51A18EA48C55@umbc.edu> <194EA790-5DBB-4D54-975C-B6F62F4ECFE9@democritos.it> Message-ID: <4A32774D.6090906@sissa.it> Michael Hayden wrote: > Paolo, > > Do you know the cause of this? Yes > > My paths are set in my .profile as such: > export PATH=/usr/local/bin:/usr/local/lib:$PATH > export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH > export DYLD_LIBRARY_PATH=/usr/local/lib:$DYLD_LIBRARY_PATH > > This was my ./configure command: > ./configure --prefix=/usr/local/espresso-4.0.5 MPIF90=mpif90 CC=gcc > F77=gfortran F90=gfortran MPIF77=mpif77 CXX=g++ MPICC=mpic++ > FFT_LIBS=/usr/local/lib this line above should be FFT_LIBS=-L/usr/local/lib -lfftw or something similar, since it was not meant to be a library path, but a linking command (please see espresso user guide and troubleshooting) > LAPACK_LIBS=/usr/local/espresso-4.0.5/flib/lapack.a > BLAS_LIBS=/usr/local/espresso-4.0.5/flib/blas.a this instead is fine since it gives a path to an object file (better, an archive of object files) > > Mike HTH GS > > > > On Jun 12, 2009, at 11:05 AM, Paolo Giannozzi wrote: > >> >> On Jun 12, 2009, at 16:46 , Michael Hayden wrote: >> >>> mpif90 -o pw.x [...] /usr/local/lib /usr/local/lib >> >> you are linking "/usr/local/lib" (a directory)... >> >>> ld: in /usr/local/lib, can't map file, errno=22 >> >> >> and the linker complains >> >> Paolo >> --- >> Paolo Giannozzi, Dept of Physics, University of 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 >> > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Fri Jun 12 18:14:46 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 12 Jun 2009 18:14:46 +0200 Subject: [Pw_forum] homo-lumo and conductance In-Reply-To: <882340.96939.qm@web94611.mail.in2.yahoo.com> References: <882340.96939.qm@web94611.mail.in2.yahoo.com> Message-ID: <4A327EF6.7020206@sissa.it> ambavale sagar wrote: > Dear all, > I am studying ballistic conductance through a molecule attached to Al > electrode. Including Al surfaces on both sides? > The k-pt grid used for scf calculation of scattering region > made of molecule and few layers of electrode, is 2 2 10 1 1 1. If so, this k-point grid looks a bit lousy to me. Unless you use a very large supercell in the transverse directions (xy, since z is the transport direction in pwcond), you should take more k-points along that directions. Along z, instead, you need less k-points (10 seems really too much to me). Along z you must include enough slabs before and after the junction with the molecule such that the scf potential at the borders of the cell is close enough to the scf potential of bulk Al. You can have a look at this paper in order to get an idea: Smogunov et al., Phys. Rev. B 78, 014423 (2008) > I want to > see effect of HOMO-LUMO levels of molecule on transmission. Is it > sensible to find HOMO-LUMO levels of molecule using separate calculation > of isolated molecule with gamma point? How about bandstructure that I > got from 20 k-pt calculation of scattering region periodic in z-direction? I'm not sure I got your questions. Of course if you study the ballistic conductance through the molecule in the tunneling regime, the result will be very sensitive to the position of the HOMO and LUMO levels of the molecule. Depending on how strong is the binding between the molecule and the electrodes the position and width of these levels will be modified more or less by the hybridization with the metal states. In order to find the position of the HOMO and LUMO in the coupled system you can look at the PDOS on the atoms of the molecule (if not too complex) and compare it with the corresponding PDOS of the isolated molecule. Another solution might be to build Wannier functions of the HOMO and LUMO and project onto them, but I never tried this solution. Anyway, you should be careful when trusting DFT results in this kind of system, since common XC functionals can mismatch the HOMO-LUMO gap of several eV and there could also be problems in getting a reliable alignment with the Fermi level of the metal. Since in weakly coupled junctions the conductance is very sensitive to the exact position of the molecular levels involved in the tunneling and to the decaying behavior of their tails, this issues can lead to errors of 1 or several orders of magnitude. Cheers GS > > Thank you. > > Sagar Ambavale > PhD student > M.S. University of Baroda > India > > ------------------------------------------------------------------------ > Explore and discover exciting holidays and getaways with Yahoo! India > Travel Click here! > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From hayden at umbc.edu Fri Jun 12 19:47:41 2009 From: hayden at umbc.edu (Michael Hayden) Date: Fri, 12 Jun 2009 13:47:41 -0400 Subject: [Pw_forum] installing OpenMPI and Quantum Espresso on a Mac OS X system In-Reply-To: <21965115-2247-4B7B-9774-AEE5AEF05781@democritos.it> References: <9E929E0E-B449-4414-A1D9-834A1264FB30@umbc.edu> <4A2FE991.1010902@gmail.com> <4A303C21.3070102@gmail.com> <7124F8BA-AA78-4ED5-9CBE-18FCA80B9538@umbc.edu> <4A32494D.6080304@sissa.it> <4A325E9C.7030400@gmail.com> <51CD7518-BCF3-4FC7-A112-51A18EA48C55@umbc.edu> <194EA790-5DBB-4D54-975C-B6F62F4ECFE9@democritos.it> <21965115-2247-4B7B-9774-AEE5AEF05781@democritos.it> Message-ID: Paolo, Alain, Gabriele, I took Paolo's advice and configured with no arguments and then it complied straight away. Example01 ran fine. Thanks to all of you for getting me started. Now it's on to learning how to launch parallel jobs and then to do some real science. cheers, Mike On Jun 12, 2009, at 11:41 AM, Paolo Giannozzi wrote: >> the less arguments you give to configure, the better > From amosleffler at gmail.com Fri Jun 12 23:12:15 2009 From: amosleffler at gmail.com (Amos Leffler) Date: Fri, 12 Jun 2009 14:12:15 -0700 Subject: [Pw_forum] Problem with running CP In-Reply-To: <1244758057.2901.115.camel@zero> References: <61b264610906091334k196c377at658e51f161768684@mail.gmail.com> <1244582813.5214.957.camel@zero> <61b264610906111501w3686599bue7903d2e457a4f6@mail.gmail.com> <1244758057.2901.115.camel@zero> Message-ID: <61b264610906121412t5e457619w3591b682a2f3e7d9@mail.gmail.com> Dear Axel, You are correct about the placement of CELL_PARAMETERS. I put it after the ATOMIC_POSITIONS and just tried to run the first part of the program but it still wont run. Do you know if anyone has tried to use cp with a cubic cell? Attached is the first input file and the output file so you can see. It looks proper to me but it is easy to miss small things.There is no out file. Amos Leffler unaffiliated On Thu, Jun 11, 2009 at 3:07 PM, Axel Kohlmeyer wrote: > On Thu, 2009-06-11 at 15:01 -0700, Amos Leffler wrote: >> Dear Axel, >> If what you suggest that the problem with my file is in the >> the "bin/sh" statement which does the program run properly with the >> file from example18? > > amos, > > good point. nevertheless, you must not remove the EOF entries. > they are essential and that is what probably threw me off-track. > >> Another person sent me the output when he ran my file and it >> did give a large number of errors all saying that the lines below EOF > > that e-mail is a complete fluke, since that person was obviously > running the script as input to cp.x and not as a shell script > in the proper location. > >> were ignored. I did get an error message saying that the program >> expected celldm(1) but I thought this was not used with ibrav =0. ? > > please have a closer look at INPUT_CP. > > you are placing the CELL_PARAMETERS section _before_ ATOMIC_SPECIES, > whereas the input description requires it to come _after_ > ATOMIC_POSITIONS. if you do not follow the input syntax, > calculations won't start. > > cheers, > axel. > > > >> Amos Leffler >> unaffiliated >> >> On Tue, Jun 9, 2009 at 2:26 PM, Axel >> Kohlmeyer wrote: >> > On Tue, 2009-06-09 at 13:34 -0700, Amos Leffler wrote: >> >> Dear forum, >> > >> > dear amos, >> > >> >> I have been trying to run the attached file which is based on >> >> that in Example18. The flle in Example18 runs properly but my >> > >> > what platform are you running on: OS type/version, CPU, fortran >> > compiler? >> > >> >> modified version does not. I have noted the information in the "Users >> >> Guide" , p28ff. If I leave out the EOF entries after each of the >> >> "Atomic Positions" the entire file reads in but no output is >> > >> > this _cannot_ work. this is due to shell scripting and has little >> > to do with pw.x/cp.x itself. there are some linux versions that use >> > a /bin/sh implementation that is very minimalistic (but standard >> > compliant), while the run_example scripts tend to depend some >> > some common extensions. you have to leave the EOFs in, but you >> > can try replacing /bin/sh with /bin/bash. >> > >> >> generated. Adding the EOF after the first Atomic_Positions, the output >> >> stops with the message "running the calculation with fixed ions...\c" >> >> . Is there more detailed information on using CP either in espresso >> >> itself or elsewhere? >> > >> > there should be a large number of error messages. >> > >> > this has nothing to do with cp.x. the run_example script >> > just automates the process of generating input files and >> > running them. in general, it is better for manual runs to >> > modify the individual input files, if you are not an expert >> > in bourne shell scripting. >> > >> > cheers, >> > axel. >> > >> >> Thanks for your help. >> >> >> >> Amos Leffler >> >> _______________________________________________ >> >> Pw_forum mailing list >> >> Pw_forum at pwscf.org >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> > >> > -- >> > ======================================================================= >> > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu >> > Center for Molecular Modeling -- University of Pennsylvania >> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 >> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 >> > ======================================================================= >> > If you make something idiot-proof, the universe creates a better idiot. >> > >> > _______________________________________________ >> > 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 > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > 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: run_example3 Type: application/octet-stream Size: 4416 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090612/6c56b15c/attachment.obj From amosleffler at gmail.com Fri Jun 12 23:19:34 2009 From: amosleffler at gmail.com (Amos Leffler) Date: Fri, 12 Jun 2009 14:19:34 -0700 Subject: [Pw_forum] Problem with running CP In-Reply-To: References: <61b264610906091334k196c377at658e51f161768684@mail.gmail.com> Message-ID: <61b264610906121419j7a15a669wb47e3f7638fcfd8@mail.gmail.com> Dear Somesh, Axel told me why you got the output that you did. I just tried the first potion of the file corrected but it still wont run. It is attached so you can see if there is any obvious error. Amos Leffler On Tue, Jun 9, 2009 at 2:11 PM, Somesh Kumar Bhattacharya wrote: > Dear Amos, > > I tried running your file ( one you attached with this mail) > ................ and get the error : > =------------------------------------------------------------------------------= > > CP: variable-cell Car-Parrinello molecular dynamics > using norm-conserving and ultrasoft Vanderbilt pseudopotentials > > Version: 4.0.3 - Fri Jun 5 13:34:25 CEST 2009 > Authors: Alfredo Pasquarello, Kari Laasonen, Andrea Trave, Roberto Car, > Paolo Giannozzi, Nicola Marzari, Carlo Cavazzoni, Guido Chiarotti, > Sandro Scandolo, Paolo Focher, Gerardo Ballabio, and others > > =------------------------------------------------------------------------------= > > This run was started on: 23: 3:55 9Jun2009 > > Serial Build > Warning: card EOF ignored > Warning: card $ECHO " RUNNING THE CALCULATION WITH FIXED IONS...\C" ignored > Warning: card $CP_COMMAND < CO.CP.START.IN > CO.CP.START.OUT ignored > Warning: card CHECK_FAILURE $? ignored > Warning: card $ECHO " DONE" ignored > Warning: card CAT > CO.CP.RESTART.IN << EOF ignored > Warning: card &CONTROL ignored > Warning: card CALCULATION='CP', ignored > Warning: card RESTART_MODE='FROM_SCRATCH', ignored > Warning: card NSTEP=50, IPRINT=50, ISAVE=50, ignored > Warning: card DT=15.0, ignored > Warning: card NDR=91, NDW=92, ignored > Warning: card PSEUDO_DIR='$PSEUDO_DIR/', ignored > Warning: card OUTDIR='$TMP_DIR/', ignored > Warning: card / ignored > Warning: card &SYSTEM ignored > Warning: card IBRAV = 0, ignored > Warning: card NAT = 28, ignored > Warning: card NTYP = 2, ignored > Warning: card ECUTWFC = 24.D0, ignored > Warning: card ECUTRHO = 144.D0, ignored > Warning: card NR1B=16, NR2B=16, NR3B=16, ignored > Warning: card QCUTZ=150., Q2SIGMA=2.0, ECFIXED=16.0, ignored > Warning: card / ignored > Warning: card &ELECTRONS ignored > Warning: card ELECTRON_DYNAMICS='DAMP', ELECTRON_DAMPING=0.2, ignored > Warning: card EMASS=700., EMASS_CUTOFF=3., ignored > Warning: card &IONS ignored > Warning: card ION_DYNAMICS='NONE', ignored > Warning: card ION_RADIUS(1) = 1.0, ION_RADIUS(2) =1.0, ignored > Warning: card / ignored > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from card_cell_parameters : error # 2 > two occurrences > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > 2 > > I think its because with ibrav = 0, you need to add the card > cell_parameters. > > Did you tried that ???? > > Somesh > > > On Tue, Jun 9, 2009 at 10:34 PM, Amos Leffler wrote: >> >> Dear forum, >> I have been trying to run the attached file which is based on >> that in Example18. The flle in Example18 runs properly but my >> modified version does not. I have noted the information in the "Users >> Guide" , p28ff. If I leave out the EOF entries after each of the >> "Atomic Positions" the entire file reads in but no output is >> generated. Adding the EOF after the first Atomic_Positions, the output >> stops with the message "running the calculation with fixed ions...\c" >> . Is there more detailed information on using CP either in espresso >> itself or elsewhere? >> Thanks for your help. >> >> Amos Leffler >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Somesh Kr. Bhattacharya > Post Doctoral Fellow > Room No. 263, > Leonardo Building, > The Abdus Salam International Centre for Theoretical Physics > Strada Costiera, 11 > I-34014 Trieste > Italy > Phone: +39-040-2240399 > > _______________________________________________ > 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: run_example3 Type: application/octet-stream Size: 4416 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090612/efe655c9/attachment-0001.obj From akohlmey at cmm.chem.upenn.edu Fri Jun 12 23:52:35 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 12 Jun 2009 17:52:35 -0400 Subject: [Pw_forum] Problem with running CP In-Reply-To: <61b264610906121412t5e457619w3591b682a2f3e7d9@mail.gmail.com> References: <61b264610906091334k196c377at658e51f161768684@mail.gmail.com> <1244582813.5214.957.camel@zero> <61b264610906111501w3686599bue7903d2e457a4f6@mail.gmail.com> <1244758057.2901.115.camel@zero> <61b264610906121412t5e457619w3591b682a2f3e7d9@mail.gmail.com> Message-ID: <1244843555.2901.364.camel@zero> On Fri, 2009-06-12 at 14:12 -0700, Amos Leffler wrote: > Dear Axel, dear amos, > You are correct about the placement of CELL_PARAMETERS. I put > it after the ATOMIC_POSITIONS and just tried to run the first part of > the program but it still wont run. Do you know if anyone has tried to > use cp with a cubic cell? many have. me too. works just fine. it seems strange to me, however, that you use an explicit cell dimension statement for a primitive cubic cell, where specifying ibrav=1 and celldm(1)=16.0 would do the trick just fine. > Attached is the first input file and the output file so you can > see. It looks proper to me but it is easy to miss small things.There the first issue is that you put the EOF statement at the wrong place, it would have come _directly_ after the input. another problem, is that your file has tab characters instead of spaces in the coordinate section and that seems to throw off the inline parser for the atom positions. the next issue is, that you cannot run cp dynamics without an &ions namelist, even if you keep the ion positions fixed. > is no out file. there is no out file, because the line executing the code and redirecting the output is included in the .in file due to wrong placement of the EOF statement. please read up on shell scripting, if you mess with shell scripts, or modify and run .in files directly without using the wrapper scripts of the QE distribution. cheers, axel. > Amos Leffler > unaffiliated > > On Thu, Jun 11, 2009 at 3:07 PM, Axel > Kohlmeyer wrote: > > On Thu, 2009-06-11 at 15:01 -0700, Amos Leffler wrote: > >> Dear Axel, > >> If what you suggest that the problem with my file is in the > >> the "bin/sh" statement which does the program run properly with the > >> file from example18? > > > > amos, > > > > good point. nevertheless, you must not remove the EOF entries. > > they are essential and that is what probably threw me off-track. > > > >> Another person sent me the output when he ran my file and it > >> did give a large number of errors all saying that the lines below EOF > > > > that e-mail is a complete fluke, since that person was obviously > > running the script as input to cp.x and not as a shell script > > in the proper location. > > > >> were ignored. I did get an error message saying that the program > >> expected celldm(1) but I thought this was not used with ibrav =0. ? > > > > please have a closer look at INPUT_CP. > > > > you are placing the CELL_PARAMETERS section _before_ ATOMIC_SPECIES, > > whereas the input description requires it to come _after_ > > ATOMIC_POSITIONS. if you do not follow the input syntax, > > calculations won't start. > > > > cheers, > > axel. > > > > > > > >> Amos Leffler > >> unaffiliated > >> > >> On Tue, Jun 9, 2009 at 2:26 PM, Axel > >> Kohlmeyer wrote: > >> > On Tue, 2009-06-09 at 13:34 -0700, Amos Leffler wrote: > >> >> Dear forum, > >> > > >> > dear amos, > >> > > >> >> I have been trying to run the attached file which is based on > >> >> that in Example18. The flle in Example18 runs properly but my > >> > > >> > what platform are you running on: OS type/version, CPU, fortran > >> > compiler? > >> > > >> >> modified version does not. I have noted the information in the "Users > >> >> Guide" , p28ff. If I leave out the EOF entries after each of the > >> >> "Atomic Positions" the entire file reads in but no output is > >> > > >> > this _cannot_ work. this is due to shell scripting and has little > >> > to do with pw.x/cp.x itself. there are some linux versions that use > >> > a /bin/sh implementation that is very minimalistic (but standard > >> > compliant), while the run_example scripts tend to depend some > >> > some common extensions. you have to leave the EOFs in, but you > >> > can try replacing /bin/sh with /bin/bash. > >> > > >> >> generated. Adding the EOF after the first Atomic_Positions, the output > >> >> stops with the message "running the calculation with fixed ions...\c" > >> >> . Is there more detailed information on using CP either in espresso > >> >> itself or elsewhere? > >> > > >> > there should be a large number of error messages. > >> > > >> > this has nothing to do with cp.x. the run_example script > >> > just automates the process of generating input files and > >> > running them. in general, it is better for manual runs to > >> > modify the individual input files, if you are not an expert > >> > in bourne shell scripting. > >> > > >> > cheers, > >> > axel. > >> > > >> >> Thanks for your help. > >> >> > >> >> Amos Leffler > >> >> _______________________________________________ > >> >> Pw_forum mailing list > >> >> Pw_forum at pwscf.org > >> >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > > >> > -- > >> > ======================================================================= > >> > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > >> > Center for Molecular Modeling -- University of Pennsylvania > >> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > >> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > >> > ======================================================================= > >> > If you make something idiot-proof, the universe creates a better idiot. > >> > > >> > _______________________________________________ > >> > 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 > > > > -- > > ======================================================================= > > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > > Center for Molecular Modeling -- University of Pennsylvania > > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > > ======================================================================= > > If you make something idiot-proof, the universe creates a better idiot. > > > > _______________________________________________ > > 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 -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From sunyang198498 at gmail.com Sat Jun 13 00:16:34 2009 From: sunyang198498 at gmail.com (=?GB2312?B?y+/R9A==?=) Date: Fri, 12 Jun 2009 17:16:34 -0500 Subject: [Pw_forum] B_field Message-ID: <98e7a0810906121516k13108a03p7be786a1f4b3cd47@mail.gmail.com> Dear everyone: I try to appy an external magnetic field about 0.01 Ry to a bulk of paramagnetic material. By either looking at the spin polarization and the density of states, I could not find any polarization induced. Any one has an idea. It will be highly appreciated! Yang -- University of Nebraska at Lincoln From sagarambavale at yahoo.co.in Sat Jun 13 07:35:30 2009 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Sat, 13 Jun 2009 11:05:30 +0530 (IST) Subject: [Pw_forum] homo-lumo and conductance In-Reply-To: References: Message-ID: <441490.13216.qm@web94615.mail.in2.yahoo.com> Dear Gabriele, Thank you for your reply. I refered to smogunov paper but I could not understand the sentence used there : "Since the system has the supercell (artificial) 2D periodicity in the xy plane, perpendicular to the transport direction, we averaged the transmission over the corresponding 2D BZ using 21 k points in the irreducible part of the BZ." Are those 21 k-pts belong to xy plane only? what type of grid that may be? 6 6 2 1 1 1 ? In my case supercell dimensions in x and y are 25 a.u. i.e. ~12 ang which includes nearly ~9 ang. of vaccum. As you mentioned the limitation of DFT due to xc-functional, can I use DFT calculation to compare qualitatively the Transmission coefficient of same molecule with different geometries? would you please mention in detail how to find positions of HOMO, LUMO in a coupled system? regards Sagar Ambavale ________________________________ Message: 1 Date: Fri, 12 Jun 2009 18:14:46 +0200 From: Gabriele Sclauzero Subject: Re: [Pw_forum] homo-lumo and conductance To: PWSCF Forum Message-ID: <4A327EF6.7020206 at sissa.it> Content-Type: text/plain; charset=ISO-8859-1; format=flowed ambavale sagar wrote: > Dear all, > I am studying ballistic conductance through a molecule attached to Al > electrode. Including Al surfaces on both sides? > The k-pt grid used for scf calculation of scattering region > made of molecule and few layers of electrode, is 2 2 10 1 1 1. If so, this k-point grid looks a bit lousy to me. Unless you use a very large supercell in the transverse directions (xy, since z is the transport direction in pwcond), you should take more k-points along that directions. Along z, instead, you need less k-points (10 seems really too much to me). Along z you must include enough slabs before and after the junction with the molecule such that the scf potential at the borders of the cell is close enough to the scf potential of bulk Al. You can have a look at this paper in order to get an idea: Smogunov et al., Phys. Rev. B 78, 014423 (2008) > I want to > see effect of HOMO-LUMO levels of molecule on transmission. Is it > sensible to find HOMO-LUMO levels of molecule using separate calculation > of isolated molecule with gamma point? How about bandstructure that I > got from 20 k-pt calculation of scattering region periodic in z-direction? I'm not sure I got your questions. Of course if you study the ballistic conductance through the molecule in the tunneling regime, the result will be very sensitive to the position of the HOMO and LUMO levels of the molecule. Depending on how strong is the binding between the molecule and the electrodes the position and width of these levels will be modified more or less by the hybridization with the metal states. In order to find the position of the HOMO and LUMO in the coupled system you can look at the PDOS on the atoms of the molecule (if not too complex) and compare it with the corresponding PDOS of the isolated molecule. Another solution might be to build Wannier functions of the HOMO and LUMO and project onto them, but I never tried this solution. Anyway, you should be careful when trusting DFT results in this kind of system, since common XC functionals can mismatch the HOMO-LUMO gap of several eV and there could also be problems in getting a reliable alignment with the Fermi level of the metal. Since in weakly coupled junctions the conductance is very sensitive to the exact position of the molecular levels involved in the tunneling and to the decaying behavior of their tails, this issues can lead to errors of 1 or several orders of magnitude. Cheers GS > > Thank you. > > Sagar Ambavale > PhD student > M.S. University of Baroda > India > > o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o *************************** Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090613/c389e2c1/attachment.htm From smogunov at sissa.it Sat Jun 13 14:08:30 2009 From: smogunov at sissa.it (Alexandre Smogunov) Date: Sat, 13 Jun 2009 14:08:30 +0200 (CEST) Subject: [Pw_forum] homo-lumo and conductance In-Reply-To: <441490.13216.qm@web94615.mail.in2.yahoo.com> References: <441490.13216.qm@web94615.mail.in2.yahoo.com> Message-ID: Dear Sagar I suppose you use the finite width Al wires as the leads as we did in our PRB paper in 2004, then you can use 1 k point in the XY plane. But I would recommend you to use more realistic infinite (in the XY plane) surfaces as the leads as we did in our more recent papers, then you should use more k points as Gabriele suggests. 21 k poins in the XY plane (perpendiculAar to the transport z axis) corresponds to the mesh 12 12 1 1 1 1. Then you have 21 k points in the irreducible 2D BZ = 1/8 of the full 2D BZ. Regards, Alexander On Sat, 13 Jun 2009, ambavale sagar wrote: > Dear Gabriele, Thank you for your reply. I refered to smogunov paper but I could not understand the sentence used there : "Since the system has the supercell (artificial) 2D periodicity in the xy plane, perpendicular to the transport direction, we averaged the transmission over the corresponding 2D BZ using 21 k points in the irreducible part of the BZ." Are those 21 k-pts belong to xy plane only? what type of grid that may be? 6 6 2 1 1 1 ? In my case supercell dimensions in x and y are 25 a.u. i.e. ~12 ang which includes nearly ~9 ang. of vaccum. As you mentioned the limitation of DFT due to xc-functional, can I use DFT calculation to compare qualitatively the Transmission coefficient of same molecule with different geometries? would you please mention in detail how to find positions of HOMO, LUMO in a coupled system? regards Sagar Ambavale ________________________________ Message: 1 Date: Fri, 12 Jun 2009 18:14:46 +0200 From: Gabriele Sclauzero Subject: Re: [Pw_forum] homo-lumo and conductance To: PWSCF Forum Message-ID: <4A327EF6.7020206 at sissa.it> Content-Type: text/plain; charset=ISO-8859-1; format=flowed ambavale sagar wrote: > Dear all, > I am studying ballistic conductance through a molecule attached to Al > electrode. Including Al surfaces on both sides? > The k-pt grid used for scf calculation of scattering region > made of molecule and few layers of electrode, is 2 2 10 1 1 1. If so, this k-point grid looks a bit lousy to me. Unless you use a very large supercell in the transverse directions (xy, since z is the transport direction in pwcond), you should take more k-points along that directions. Along z, instead, you need less k-points (10 seems really too much to me). Along z you must include enough slabs before and after the junction with the molecule such that the scf potential at the borders of the cell is close enough to the scf potential of bulk Al. You can have a look at this paper in order to get an idea: Smogunov et al., Phys. Rev. B 78, 014423 (2008) > I want to > see effect of HOMO-LUMO levels of molecule on transmission. Is it > sensible to find HOMO-LUMO levels of molecule using separate calculation > of isolated molecule with gamma point? How about bandstructure that I > got from 20 k-pt calculation of scattering region periodic in z-direction? I'm not sure I got your questions. Of course if you study the ballistic conductance through the molecule in the tunneling regime, the result will be very sensitive to the position of the HOMO and LUMO levels of the molecule. Depending on how strong is the binding between the molecule and the electrodes the position and width of these levels will be modified more or less by the hybridization with the metal states. In order to find the position of the HOMO and LUMO in the coupled system you can look at the PDOS on the atoms of the molecule (if not too complex) and compare it with the corresponding PDOS of the isolated molecule. Another solution might be to build Wannier functions of the HOMO and LUMO and project onto them, but I never tried this solution. Anyway, you should be careful when trusting DFT results in this kind of system, since common XC functionals can mismatch the HOMO-LUMO gap of several eV and there could also be problems in getting a reliable alignment with the Fermi level of the metal. Since in weakly coupled junctions the conductance is very sensitive to the exact position of the molecular levels involved in the tunneling and to the decaying behavior of their tails, this issues can lead to errors of 1 or several orders of magnitude. Cheers GS > > Thank you. > > Sagar Ambavale > PhD student > M.S. University of Baroda > India > > o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o *************************** Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/ From shypirate at gmail.com Sat Jun 13 16:44:45 2009 From: shypirate at gmail.com (Y.P.Wang) Date: Sat, 13 Jun 2009 22:44:45 +0800 Subject: [Pw_forum] difference between sawlike and homogeneous electric field? Message-ID: Dear all: I want to know where is the difference between sawlike and homogeneous electric field? If I want to calculate the electric field effect on thin films based on slab geometry, which one is the correct choice? And I have found little infomation on how to set the calculation options except that in 'INPUT_PW', could you please point out for me where the detailed infomation is? With All Best Wishes, Y.P.Wang From bipulrr at gmail.com Sat Jun 13 22:00:10 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Sun, 14 Jun 2009 01:30:10 +0530 Subject: [Pw_forum] Elastic Constant. Message-ID: <3a749910906131300y5e92e22fl283eac075b5670f0@mail.gmail.com> Dear Pwscf user, I want to calculate the elastic constants for cubic structure for LaSb, which is having NaCl structure. Although I have written a small script for doing that. But if anybody develop any code, do he/she like to share, so that I can compare my results. Thanks -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India From baroni at sissa.it Sun Jun 14 12:01:17 2009 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 14 Jun 2009 12:01:17 +0200 Subject: [Pw_forum] Elastic Constant. In-Reply-To: <3a749910906131300y5e92e22fl283eac075b5670f0@mail.gmail.com> References: <3a749910906131300y5e92e22fl283eac075b5670f0@mail.gmail.com> Message-ID: <9041FC3A-E8F9-416C-953F-14097C1553A7@sissa.it> Dear Bipul, long ago there used to be an implementation of the linear-response approach to elastic constants by SB, Giannozzi, and Testa: % Copyright (C) 2009 The American Physical Society % Please report any problems to prola at aps.org @Article{PhysRevLett.59.2662, title = {Elastic Constants of Crystals from Linear-Response Theory}, author = {Baroni, Stefano and Giannozzi, Paolo and Testa, Andrea }, journal = {Phys. Rev. Lett.}, volume = {59}, number = {23}, pages = {2662--2665}, numpages = {3}, year = {1987}, month = {Dec}, doi = {10.1103/PhysRevLett.59.2662}, publisher = {American Physical Society} } This is no longer available, partly because of the programmers' lazyness, partly because there is not much to be gained with respect to the straightforward approach you are following. Stefano B On Jun 13, 2009, at 10:00 PM, Bipul Rakshit wrote: > Dear Pwscf user, > I want to calculate the elastic constants for cubic structure for > LaSb, which is having NaCl structure. Although I have written a small > script for doing that. But if anybody develop any code, do he/she like > to share, so that I can compare my results. > Thanks > -- > Bipul Rakshit > PhD Student, > Barkatullah University, > Bhopal 462026, > MP, India > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From yaldachem at gmail.com Sun Jun 14 17:26:55 2009 From: yaldachem at gmail.com (yaldaa kh) Date: Sun, 14 Jun 2009 08:26:55 -0700 Subject: [Pw_forum] restart-mod Message-ID: <47431d9f0906140826i3eba28f6h730ec22dd23b4187@mail.gmail.com> Dear all How can I use the option ' restart_mod=restart ' in pwscf (how does the previous file be specified)? thanks a lot yalda -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090614/2703466f/attachment.htm From panda.deng.pan at gmail.com Sun Jun 14 18:23:31 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Mon, 15 Jun 2009 00:23:31 +0800 Subject: [Pw_forum] inputs for structure Message-ID: Dear All Users, Please send me a detail instruction about the structure inputs using pwscf. I used have one but I lost its link. cheers Deng Pan Nanjing University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090615/88506d9a/attachment.htm From lanhaiping at gmail.com Sun Jun 14 18:48:22 2009 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 15 Jun 2009 00:48:22 +0800 Subject: [Pw_forum] inputs for structure In-Reply-To: References: Message-ID: Dear Deng Pan Why donot you check $QE/Doc/INPUT_PW.html for a look ? Regards, Haiping On Mon, Jun 15, 2009 at 12:23 AM, ?? wrote: > Dear All Users, > > Please send me a detail instruction about the structure inputs using > pwscf. I used have one but I lost its link. > > > cheers > > Deng Pan > Nanjing University > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090615/6625abd5/attachment.htm From lanhaiping at gmail.com Sun Jun 14 18:53:06 2009 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 15 Jun 2009 00:53:06 +0800 Subject: [Pw_forum] restart-mod In-Reply-To: <47431d9f0906140826i3eba28f6h730ec22dd23b4187@mail.gmail.com> References: <47431d9f0906140826i3eba28f6h730ec22dd23b4187@mail.gmail.com> Message-ID: Hi, when you triger on "restart " mode, the code look for the interrupted data by the setting for 'outdir'. P.S , Please supply your affiliation regards, On Sun, Jun 14, 2009 at 11:26 PM, yaldaa kh wrote: > Dear all > How can I use the option ' restart_mod=restart ' in pwscf (how does the > previous file be specified)? > thanks a lot > yalda > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090615/360e2a05/attachment.htm From paulatto at sissa.it Sun Jun 14 20:02:03 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sun, 14 Jun 2009 20:02:03 +0200 (CEST) Subject: [Pw_forum] restart-mod In-Reply-To: References: <47431d9f0906140826i3eba28f6h730ec22dd23b4187@mail.gmail.com> Message-ID: <39889.78.12.167.117.1245002523.squirrel@webmail.sissa.it> On Sun, June 14, 2009 18:53, lan haiping wrote: > Hi, > when you triger on "restart " mode, the code look for the interrupted > data by the setting for 'outdir'. ...and prefix. The savefiles are all the files named like %outdir%/%prefix%.* e tutti i files nella directory %outdir%/%prefix%.save/ cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From paulatto at sissa.it Sun Jun 14 22:09:26 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sun, 14 Jun 2009 22:09:26 +0200 (CEST) Subject: [Pw_forum] restart-mod In-Reply-To: <39889.78.12.167.117.1245002523.squirrel@webmail.sissa.it> References: <47431d9f0906140826i3eba28f6h730ec22dd23b4187@mail.gmail.com> <39889.78.12.167.117.1245002523.squirrel@webmail.sissa.it> Message-ID: <45124.78.12.167.117.1245010166.squirrel@webmail.sissa.it> In data 14 giugno 2009 alle ore 20:02:03, Lorenzo Paulatto ha scritto: e tutti i whoops, I don't know how Italian slipped in my email, it means "and all the" -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From anvari_meh at physics.iust.ac.ir Mon Jun 15 06:34:45 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Mon, 15 Jun 2009 08:04:45 +0330 Subject: [Pw_forum] missing q point Message-ID: I used new version of pakage (espresso-4.0.5) as you told me & the error was disappeared. I performed Eyvaz suggestion too, I mean that I used different grids (for nq1,nq2,nq3) for instance 2 2 2 , 4 4 4, 4 4 2,...but the error existed in all of these cases. Finally I couldn't understand main reason of this error. when I open the dyn0 file I see only kpoints with high symmetry, so it means that the program could indicate the symmetry of system but in the following it could'nt keep all of them it is so strange(?) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090615/1c6568f7/attachment.htm From panda.deng.pan at gmail.com Mon Jun 15 07:32:28 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Mon, 15 Jun 2009 13:32:28 +0800 Subject: [Pw_forum] structure of graphite Message-ID: Dear All, I was going to calculate the band of graphite with the input at the last I got a error like this. Warning: card ATOMIC_POSITIONS{CRYSTAL} ignored Warning: card C 0 0 0 ignored Warning: card C 0.3333 0.6667 0 ignored %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_cards : error # 1 atomic position info missing %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% My question why the atomic_position was ignored.Or I am appreciated for any comment to my input. input &control calculation = 'scf' restart_mode='from_scratch' prefix='C', pseudo_dir = 'home/Quantum-Espresso/espresso-4.0.3/pseudo/', outdir='/disk2/xgwan/tmp/' / &system ibrav=4, celldm(1)=2.4434, celldm(3)=8.1853, nat=2, ntyp=1, ecutwfc = 40.0, ecutrho = 400.0, occupations= 'smearing', degauss= 0.02, smearing= 'cold', / &electrons mixing_beta = 0.7 conv_thr = 1.0d-10 / ATOMIC_SPECIES C 12.0 C.pbe-van_ak.UPF ATOMIC_POSITIONS {crystal} C 0 0 0 C 0.3333 0.6667 0 K_POINTS {automatic} 8 8 2 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090615/f544f526/attachment.htm From giannozz at democritos.it Mon Jun 15 08:34:14 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 15 Jun 2009 08:34:14 +0200 Subject: [Pw_forum] structure of graphite In-Reply-To: References: Message-ID: On Jun 15, 2009, at 7:32 , ?? wrote: > Warning: card ATOMIC_POSITIONS{CRYSTAL} ignored no space between ATOMIC_POSITIONS and {CRYSTAL} > ATOMIC_POSITIONS {crystal} one space between ATOMIC_POSITIONS and {CRYSTAL} Guess what? it's the space. Details matter. A trivial concept that too many on this list seem unable to grasp. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sclauzer at sissa.it Mon Jun 15 08:48:53 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 15 Jun 2009 08:48:53 +0200 Subject: [Pw_forum] restart-mod In-Reply-To: <47431d9f0906140826i3eba28f6h730ec22dd23b4187@mail.gmail.com> References: <47431d9f0906140826i3eba28f6h730ec22dd23b4187@mail.gmail.com> Message-ID: <4A35EED5.4020805@sissa.it> In the normal usage of restart mode (e.g. when a job has been stopped because the elapsed time as reached the value specified in max_seconds, which you usaually take a bit smaller than the walltime of your job on a cluster), you simply make this change in the input file: from_scratch -> restart and launch the job again. The first input file does not need anything special, you simply describe your system and cutoffs and pwscf will save all needed data by default in the directories already mentioned by Lorenzo. GS yaldaa kh wrote: > Dear all > How can I use the option ' restart_mod=restart ' in pwscf (how does the > previous file be specified)? > thanks a lot > yalda > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Jun 15 08:50:19 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 15 Jun 2009 08:50:19 +0200 Subject: [Pw_forum] inputs for structure In-Reply-To: References: Message-ID: <4A35EF2B.7010606@sissa.it> lan haiping wrote: > Dear Deng Pan > > Why donot you check $QE/Doc/INPUT_PW.html for a look ? And you also have plenty of samples of input files in the examples/example?? directories... Regards GS > > Regards, > Haiping > > On Mon, Jun 15, 2009 at 12:23 AM, ?? > wrote: > > Dear All Users, > > Please send me a detail instruction about the structure inputs > using pwscf. I used have one but I lost its link. > > > cheers > > Deng Pan > Nanjing University > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com , hplan at pku.edu.cn > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Jun 15 09:04:03 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 15 Jun 2009 09:04:03 +0200 Subject: [Pw_forum] homo-lumo and conductance In-Reply-To: <441490.13216.qm@web94615.mail.in2.yahoo.com> References: <441490.13216.qm@web94615.mail.in2.yahoo.com> Message-ID: <4A35F263.9020205@sissa.it> ambavale sagar wrote: > Dear Gabriele, > Thank you for your reply. I refered to smogunov paper but I could not > understand the sentence used there : "Since the system has the supercell > (artificial) 2D periodicity in the xy plane, perpendicular to the > transport direction, we averaged the transmission over the corresponding > 2D BZ using 21 k points in the irreducible part of the BZ.." Are those > 21 k-pts belong to xy plane only? what type of grid that may be? 6 6 2 1 > 1 1 ? > In my case supercell dimensions in x and y are 25 a.u. i.e. ~12 ang > which includes nearly ~9 ang. of vaccum. Here Alexander already replied you. So your k_perpendicular points sampling depends if you want to study an isolated wire (thick or monoatomic), or a wire/molecule between realistic electrodes (modeled as surfaces or surfaces+tips attached to them). In the former case, if your supercell is large enough in the directions perpendicular to the transport the transmission should not depend on k_perp and you need only one k_perp-point. In the latter you need to sample accurately the 2D BZ, since the transmission depends (a lot in some cases) on k_perp. > > As you mentioned the limitation of DFT due to xc-functional, can I use > DFT calculation to compare qualitatively the Transmission coefficient of > same molecule with different geometries? I cannot say, actually. It depends on the coupling and other details. You can have a look to the recent work by Thygesen and Rubio, which try to include a GW correction in this kind of calculations. > > would you please mention in detail how to find positions of HOMO, LUMO > in a coupled system? What I would do (but fur sure there are many better methods) if I want to put, say, O_2 between electrodes is to look at the PDOS (computed by projwfc.x in the QE suite) projected onto the O atoms and compare it with the PDOS of the isolated O_2. It would give an idea of the level of hybridization between molecule and electrodes and of the position of the HOMO(LUMO)-derived levels. It could also be useful to look at the PDOS on the electrode atoms to understand which metallic states/atoms are more involved in the coupling. regards, GS > > regards > Sagar Ambavale > ------------------------------------------------------------------------ > ** > Message: 1 > Date: Fri, 12 Jun 2009 18:14:46 +0200 > From: Gabriele Sclauzero > > Subject: Re: [Pw_forum] homo-lumo and conductance > To: PWSCF Forum > > Message-ID: <4A327EF6.7020206 at sissa.it > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > ambavale sagar wrote: > > Dear all, > > I am studying ballistic conductance through a molecule attached to Al > > electrode. > > Including Al surfaces on both sides? > > > The k-pt grid used for scf calculation of scattering region > > made of molecule and few layers of electrode, is 2 2 10 1 1 1. > > If so, this k-point grid looks a bit lousy to me. Unless you use a very > large supercell in > the transverse directions (xy, since z is the transport direction in > pwcond), you should > take more k-points along that directions. Along z, instead, you need > less k-points (10 > seems really too much to me). Along z you must include enough slabs > before and after the > junction with the molecule such that the scf potential at the borders of > the cell is close > enough to the scf potential of bulk Al. > > You can have a look at this paper in order to get an idea: > Smogunov et al., Phys. Rev. B 78, 014423 (2008) > > > I want to > > see effect of HOMO-LUMO levels of molecule on transmission. Is it > > sensible to find HOMO-LUMO levels of molecule using separate calculation > > of isolated molecule with gamma point? How about bandstructure that I > > got from 20 k-pt calculation of scattering region periodic in > z-direction? > > I'm not sure I got your questions. Of course if you study the ballistic > conductance > through the molecule in the tunneling regime, the result will be very > sensitive to the > position of the HOMO and LUMO levels of the molecule. Depending on how > strong is the > binding between the molecule and the electrodes the position and width > of these levels > will be modified more or less by the hybridization with the metal states. > In order to find the position of the HOMO and LUMO in the coupled system > you can look at > the PDOS on the atoms of the molecule (if not too complex) and compare > it with the > corresponding PDOS of the isolated molecule. > Another solution might be to build Wannier functions of the HOMO and > LUMO and project onto > them, but I never tried this solution. > > Anyway, you should be careful when trusting DFT results in this kind of > system, since > common XC functionals can mismatch the HOMO-LUMO gap of several eV and > there could also be > problems in getting a reliable alignment with the Fermi level of the > metal. Since in > weakly coupled junctions the conductance is very sensitive to the exact > position of the > molecular levels involved in the tunneling and to the decaying behavior > of their tails, > this issues can lead to errors of 1 or several orders of magnitude. > > > Cheers > > GS > > > > > Thank you. > > > > Sagar Ambavale > > PhD student > > M.S. University of Baroda > > India > > > > > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it > | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > > > *************************** > > ------------------------------------------------------------------------ > Own a website.Get an unlimited package.Pay next to nothing.* Click > here!. > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Jun 15 09:50:37 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 15 Jun 2009 09:50:37 +0200 Subject: [Pw_forum] B_field In-Reply-To: <98e7a0810906121516k13108a03p7be786a1f4b3cd47@mail.gmail.com> References: <98e7a0810906121516k13108a03p7be786a1f4b3cd47@mail.gmail.com> Message-ID: <4A35FD4D.3090505@sissa.it> It seems to me that B_field can be read from input, but then is not used in the calculation. Maybe it was an older option which has been replaced by another solution. In fact I think that a better way to see the effect of an external magnetic field is to do a calculation with constrained magnetization (see INPUT_PW for documentation): this should ensure to reach the ground states, while I suspect that applying a magnetic field you could end in a metastable state, depending on the starting conditions. Regards GS ?? wrote: > Dear everyone: > > I try to appy an external magnetic field about 0.01 Ry to a bulk of > paramagnetic material. By either looking at the spin polarization and > the density of states, I could not find any polarization induced. > Any one has an idea. It will be highly appreciated! > > Yang > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From shypirate at gmail.com Mon Jun 15 11:19:18 2009 From: shypirate at gmail.com (shypirate) Date: Mon, 15 Jun 2009 17:19:18 +0800 Subject: [Pw_forum] doubt about documentation of QE Message-ID: <200906151719143151087@gmail.com> Dear All: I am reading the doc and example of QE, but it makes me confused. For example, in example30/README, 'tefield' and 'efield' is used together to add electric field to the studied system. However, in the 'INPUT_PW.html', 'tefield' is used to specified a sawlike potential, and 'efield' is used if 'lelfield=.TRUE.', at the same time, 'lelfield' is "different" from 'tefield'. All the above refered is version 4.0.5. Any suggestion is appreciated! Y.P.Wang 2009-06-15 shypirate -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090615/bc905842/attachment.htm From marzari at MIT.EDU Mon Jun 15 11:48:14 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 15 Jun 2009 05:48:14 -0400 Subject: [Pw_forum] fileutil ? Message-ID: <4A3618DE.5070906@mit.edu> Dear All, 1) if I try to generate the documentation files for QE (make all in dev-doc) I get an error message about missing the fileutil package (see error lines below). I have tcl-8.4.13-1.1 ; I searched the forum (to no avail), so maybe this is useful to others. 2) is it correct that the new source for the QE snapshots is the qe-forge CVS, and the old CVS is not maintained, and wil be discarded ? For reference to anyone reading, the new cvs instructions are: cvs -d :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e checkout espresso Thanks, nicola ---- in dev-doc: make all ../dev-tools/helpdoc INPUT_PW.def can't find package fileutil while executing "package require fileutil" (file "/home/marzari/codes/espresso/dev-tools/helpdoc.d/../../GUI/Guib/lib/tclUtils.tcl" line 41) invoked from within "source /home/marzari/codes/espresso/dev-tools/helpdoc.d/../../GUI/Guib/lib/tclUtils.tcl" ("package ifneeded" script) invoked from within "package require tclu 0.9" (file "/home/marzari/codes/espresso/dev-tools/helpdoc.d/helpdoc.tcl" line 4) invoked from within "source [file join $sourcedir helpdoc.tcl]" (file "../dev-tools/helpdoc" line 8) make: *** [INPUT_PW.html] Error 1 ---- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From tone.kokalj at ijs.si Mon Jun 15 12:22:07 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 15 Jun 2009 12:22:07 +0200 Subject: [Pw_forum] fileutil ? In-Reply-To: <4A3618DE.5070906@mit.edu> References: <4A3618DE.5070906@mit.edu> Message-ID: <1245061327.29014.38.camel@walk.ijs.si> On Mon, 2009-06-15 at 05:48 -0400, Nicola Marzari wrote: > > > Dear All, > > > 1) if I try to generate the documentation files for QE (make all in > dev-doc) actually in doc-def/ > ... I get an error message about missing the fileutil package > (see error lines below). I have tcl-8.4.13-1.1 ; I searched the > forum (to no avail), so maybe this is useful to others. fileutil is a package from the tcllib. The latter is required for the helpdoc program to function (see the dev-tools/README.helpdoc). And helpdoc is a utility that creates the QE txt and html documentation files from the *.def files. Several linux distros are based on Debian or RedHat, if you use one of them, then to install tcllib: apt-get install tcl tcllib xsltproc (for Debian-based distros) or yum install tcl tcllib xsltproc (for Redhat-based distros) (for other distros the installation of tcllib is likely analogous, i.e., replace the apt-get|yum with the corresponding package installer) Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From giannozz at democritos.it Mon Jun 15 12:50:27 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 15 Jun 2009 12:50:27 +0200 Subject: [Pw_forum] doubt about documentation of QE In-Reply-To: <200906151719143151087@gmail.com> References: <200906151719143151087@gmail.com> Message-ID: On Jun 15, 2009, at 11:19 , shypirate wrote: > For example, in example30/README, 'tefield' and 'efield' is used > together > to add electric field to the studied system. However, in the > 'INPUT_PW.html', > 'tefield' is used to specified a sawlike potential, and 'efield' is > used if > 'lelfield=.TRUE.', at the same time, 'lelfield' is "different" from > 'tefield'. > [...] Any suggestion is appreciated! you will have better luck if you read the documentation for CP: Doc/INPUT_CP, since this is what is actually used in example30. Unfortunately there is a mismatch between CP and PWscf in the definition of electric fields P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Mon Jun 15 13:13:13 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 15 Jun 2009 13:13:13 +0200 Subject: [Pw_forum] fileutil ? In-Reply-To: <4A3618DE.5070906@mit.edu> References: <4A3618DE.5070906@mit.edu> Message-ID: <1C080D0E-8CD7-4A48-A073-11BC40E49267@democritos.it> On Jun 15, 2009, at 11:48 , Nicola Marzari wrote: > 2) is it correct that the new source for the QE snapshots is the > qe-forge CVS, and the old CVS is not maintained correct. The user guide and developer manual on the wiki report the obsolete CVS location, because they are in turn no longer maintained: they have been brought back to the CVS tree. An updated version will be put on line when the new version will be released. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From hichem.bouderba at gmail.com Mon Jun 15 13:20:52 2009 From: hichem.bouderba at gmail.com (hichem bouderba) Date: Mon, 15 Jun 2009 13:20:52 +0200 Subject: [Pw_forum] ld1.x testing mode Message-ID: dear all, in INPUT_LD1.html about ecutmin,ecutmax,decut we have : " Parameters (Ry) used for test with a basis set of spherical Bessel functions j_l(qr) . The hamiltonian at fixed scf potential is diagonalized for various values of ecut: ecutmin, ecutmin+decut, ecutmin+2*decut ... up to ecutmax. This yields an indication of convergence with the corresponding plane-wave cutoff in solids, and shows in an unambiguous way if there are "ghost" states " how does ld1.x say "there is a ghost state somewhere" ? when testing a PAW with ld1.x I have the following error: " Cutoff (Ry) : 50.0 N = 1 N = 2 N = 3 E(L=0) = -3.2666 Ry -0.2491 Ry -0.0148 Ry E(L=1) = -1.8963 Ry -0.0931 Ry 0.0105 Ry E(L=2) = -0.0637 Ry 0.0203 Ry 0.0602 Ry Cutoff (Ry) : 55.0 N = 1 N = 2 N = 3 E(L=0) = -3.2666 Ry -0.2491 Ry -0.0148 Ry E(L=1) = -1.8963 Ry -0.0931 Ry 0.0105 Ry E(L=2) = -0.0637 Ry 0.0203 Ry 0.0601 Ry Cutoff (Ry) : 60.0 N = 1 N = 2 N = 3 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from rdiags : error # 73 failed to converge (factorization) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... " what does it mean ? thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090615/11d6c36f/attachment-0001.htm From sclauzer at sissa.it Mon Jun 15 15:14:56 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 15 Jun 2009 15:14:56 +0200 Subject: [Pw_forum] missing q point In-Reply-To: References: Message-ID: <4A364950.7070102@sissa.it> Mehrnaz Anvari wrote: > I used new version of pakage (espresso-4.0.5) as you told me & the error > was disappeared. I performed Eyvaz suggestion too, I mean that I used > different grids (for nq1,nq2,nq3) for instance 2 2 2 , 4 4 4, 4 4 > 2,...but the error existed in all of these cases. First of all, I don't understand why your k-point grid is not 2D (i.e. nkx, nky, 1) if you want to study graphite. >Finally I couldn't > understand main reason of this error. when I open the dyn0 file I see > only kpoints with high symmetry, so it means that the program could > indicate the symmetry of system but in the following it could'nt keep > all of them it is so strange(?) Be carefull that until a recent change in the CVS version the ph.x was overwriting pw.x data in the .save directory, so that if you do successive ph.x calculations without making a copy of that directory it may not work. Now I will try some of your problematic k-points grids and let oyu know if they work with the CVS version. GS > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Jun 15 15:17:46 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 15 Jun 2009 15:17:46 +0200 Subject: [Pw_forum] missing q point In-Reply-To: <4A364950.7070102@sissa.it> References: <4A364950.7070102@sissa.it> Message-ID: <4A3649FA.4050502@sissa.it> Gabriele Sclauzero wrote: > > Mehrnaz Anvari wrote: >> I used new version of pakage (espresso-4.0.5) as you told me & the error >> was disappeared. I performed Eyvaz suggestion too, I mean that I used >> different grids (for nq1,nq2,nq3) for instance 2 2 2 , 4 4 4, 4 4 >> 2,...but the error existed in all of these cases. > > First of all, I don't understand why your k-point grid is not 2D (i.e. nkx, nky, 1) if you > want to study graphite. Sorry, I meant graphene, not graphite, obviuosly... GS > >> Finally I couldn't >> understand main reason of this error. when I open the dyn0 file I see >> only kpoints with high symmetry, so it means that the program could >> indicate the symmetry of system but in the following it could'nt keep >> all of them it is so strange(?) > > Be carefull that until a recent change in the CVS version the ph.x was overwriting pw.x > data in the .save directory, so that if you do successive ph.x calculations without making > a copy of that directory it may not work. > > Now I will try some of your problematic k-points grids and let oyu know if they work with > the CVS version. > > GS > >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sunyang198498 at gmail.com Mon Jun 15 16:21:51 2009 From: sunyang198498 at gmail.com (=?GB2312?B?y+/R9A==?=) Date: Mon, 15 Jun 2009 09:21:51 -0500 Subject: [Pw_forum] B_field In-Reply-To: <4A35FD4D.3090505@sissa.it> References: <98e7a0810906121516k13108a03p7be786a1f4b3cd47@mail.gmail.com> <4A35FD4D.3090505@sissa.it> Message-ID: <98e7a0810906150721s44c844bubdc2a3b475606652@mail.gmail.com> Hi, Gabriele, I think you are right. I've already performed the constrained magnetization calculation. Would there be anyone introduce the way using "constrained magnetizatio". Is it fully equivalent to applying an external field? Thanks, Yang 2009/6/15 Gabriele Sclauzero : > It seems to me that B_field can be read from input, but then is not used in the > calculation. Maybe it was an older option which has been replaced by another solution. In > fact I think that a better way to see the effect of an external magnetic field is to do a > calculation with constrained magnetization (see INPUT_PW for documentation): this should > ensure to reach the ground states, while I suspect that applying a magnetic field you > could end in a metastable state, depending on the starting conditions. > > Regards > > GS > > ?? wrote: >> Dear everyone: >> >> I try to appy an external magnetic field about 0.01 Ry to a bulk of >> paramagnetic material. By either looking at the spin polarization and >> the density of states, I could not find any polarization induced. >> Any one has an idea. It will be highly appreciated! >> >> Yang >> > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- University of Nebraska at Lincoln From sclauzer at sissa.it Mon Jun 15 17:32:15 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 15 Jun 2009 17:32:15 +0200 Subject: [Pw_forum] B_field In-Reply-To: <98e7a0810906150721s44c844bubdc2a3b475606652@mail.gmail.com> References: <98e7a0810906121516k13108a03p7be786a1f4b3cd47@mail.gmail.com> <4A35FD4D.3090505@sissa.it> <98e7a0810906150721s44c844bubdc2a3b475606652@mail.gmail.com> Message-ID: <4A36697F.4070207@sissa.it> Dear Yang (from???, please sign including your affiliation, since this is the "policy" of the PW forum), ?? wrote: > Hi, Gabriele, I think you are right. I've already performed the > constrained magnetization > calculation. Would there be anyone introduce the way using > "constrained magnetizatio". > Is it fully equivalent to applying an external field? I'm not sure about this, but, since H (magnetic field) and M (magnetization) are conjugated variables, you can pass from one to the other as independent variable in the Hamiltonian via a Legendre transform. When you constrain the magnetization, the magnetic field will appear as a Lagrange multiplier, so if you use Lagrange technique you get it automatically (see PRL 53,2512 about constrained DFT). In QE things are done in a different way, actually, and Lagrange multipliers are not used. If you fix the total magnetization in collinear LSDA, the "two Fermi energies" technique is used, while in the other cases a penalty functional is added (you have to tweak a bit with the "lambda" parameter: have a look at INPUT_PW and add_bfield.f90 for more detail). Anyway the code always gives you the "Hellman-Feynman" Magnetic field, H(M), as output at the end of the run. If you build the E(M) curve you should find, in principle, the same magnetic field by computing the derivative of E(M) w.r.t. M and thus get the same H(M) curve. HTH GS > > Thanks, > > Yang > > 2009/6/15 Gabriele Sclauzero : >> It seems to me that B_field can be read from input, but then is not used in the >> calculation. Maybe it was an older option which has been replaced by another solution. In >> fact I think that a better way to see the effect of an external magnetic field is to do a >> calculation with constrained magnetization (see INPUT_PW for documentation): this should >> ensure to reach the ground states, while I suspect that applying a magnetic field you >> could end in a metastable state, depending on the starting conditions. >> >> Regards >> >> GS >> >> ?? wrote: >>> Dear everyone: >>> >>> I try to appy an external magnetic field about 0.01 Ry to a bulk of >>> paramagnetic material. By either looking at the spin polarization and >>> the density of states, I could not find any polarization induced. >>> Any one has an idea. It will be highly appreciated! >>> >>> Yang >>> >> -- >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From amosleffler at gmail.com Mon Jun 15 18:44:53 2009 From: amosleffler at gmail.com (Amos Leffler) Date: Mon, 15 Jun 2009 09:44:53 -0700 Subject: [Pw_forum] Problem with running CP In-Reply-To: <1244843555.2901.364.camel@zero> References: <61b264610906091334k196c377at658e51f161768684@mail.gmail.com> <1244582813.5214.957.camel@zero> <61b264610906111501w3686599bue7903d2e457a4f6@mail.gmail.com> <1244758057.2901.115.camel@zero> <61b264610906121412t5e457619w3591b682a2f3e7d9@mail.gmail.com> <1244843555.2901.364.camel@zero> Message-ID: <61b264610906150944m12a6ed17j4fc1ec84e5889adc@mail.gmail.com> Hi Axel, I tried your suggestions and the program ran just fine! I traced the problem back to your comment about the tab characters. When I replaced this input with spaces between input values it cured the problem. Looking at the Users Group I noted a similar suggestion by Paoli G. to somebody about a graphite problem. This suggests that the input instructions eg. "INPUT_CP" should be more specific about the input specifications. I am still new to Fortran 95 which is different from the old Fortran 77 and so I didn't realize this. This could be done without a lot of work and would be helpful. In any event my real thanks in solving this problem. Amos Leffler unaffiliated On Fri, Jun 12, 2009 at 2:52 PM, Axel Kohlmeyer wrote: > On Fri, 2009-06-12 at 14:12 -0700, Amos Leffler wrote: >> Dear Axel, > > dear amos, > > >> You are correct about the placement of CELL_PARAMETERS. I put >> it after the ATOMIC_POSITIONS and just tried to run the first part of >> the program but it still wont run. Do you know if anyone has tried to >> use cp with a cubic cell? > > many have. me too. works just fine. > > it seems strange to me, however, that you use an explicit cell > dimension statement for a primitive cubic cell, where specifying > ibrav=1 and celldm(1)=16.0 would do the trick just fine. > >> Attached is the first input file and the output file so you can >> see. It looks proper to me but it is easy to miss small things.There > > the first issue is that you put the EOF statement at the wrong > place, it would have come _directly_ after the input. > > another problem, is that your file has tab characters instead > of spaces in the coordinate section and that seems to throw off > the inline parser for the atom positions. > > the next issue is, that you cannot run cp dynamics > without an &ions namelist, even if you keep the ion > positions fixed. > > >> is no out file. > > there is no out file, because the line executing the > code and redirecting the output is included in the > .in file due to wrong placement of the EOF statement. > > please read up on shell scripting, if you mess with > shell scripts, or modify and run .in files directly > without using the wrapper scripts of the QE distribution. > > cheers, > axel. > >> Amos Leffler >> unaffiliated >> >> On Thu, Jun 11, 2009 at 3:07 PM, Axel >> Kohlmeyer wrote: >> > On Thu, 2009-06-11 at 15:01 -0700, Amos Leffler wrote: >> >> Dear Axel, >> >> If what you suggest that the problem with my file is in the >> >> the "bin/sh" statement which does the program run properly with the >> >> file from example18? >> > >> > amos, >> > >> > good point. nevertheless, you must not remove the EOF entries. >> > they are essential and that is what probably threw me off-track. >> > >> >> Another person sent me the output when he ran my file and it >> >> did give a large number of errors all saying that the lines below EOF >> > >> > that e-mail is a complete fluke, since that person was obviously >> > running the script as input to cp.x and not as a shell script >> > in the proper location. >> > >> >> were ignored. I did get an error message saying that the program >> >> expected celldm(1) but I thought this was not used with ibrav =0. ? >> > >> > please have a closer look at INPUT_CP. >> > >> > you are placing the CELL_PARAMETERS section _before_ ATOMIC_SPECIES, >> > whereas the input description requires it to come _after_ >> > ATOMIC_POSITIONS. if you do not follow the input syntax, >> > calculations won't start. >> > >> > cheers, >> > axel. >> > >> > >> > >> >> Amos Leffler >> >> unaffiliated >> >> >> >> On Tue, Jun 9, 2009 at 2:26 PM, Axel >> >> Kohlmeyer wrote: >> >> > On Tue, 2009-06-09 at 13:34 -0700, Amos Leffler wrote: >> >> >> Dear forum, >> >> > >> >> > dear amos, >> >> > >> >> >> I have been trying to run the attached file which is based on >> >> >> that in Example18. The flle in Example18 runs properly but my >> >> > >> >> > what platform are you running on: OS type/version, CPU, fortran >> >> > compiler? >> >> > >> >> >> modified version does not. I have noted the information in the "Users >> >> >> Guide" , p28ff. If I leave out the EOF entries after each of the >> >> >> "Atomic Positions" the entire file reads in but no output is >> >> > >> >> > this _cannot_ work. this is due to shell scripting and has little >> >> > to do with pw.x/cp.x itself. there are some linux versions that use >> >> > a /bin/sh implementation that is very minimalistic (but standard >> >> > compliant), while the run_example scripts tend to depend some >> >> > some common extensions. you have to leave the EOFs in, but you >> >> > can try replacing /bin/sh with /bin/bash. >> >> > >> >> >> generated. Adding the EOF after the first Atomic_Positions, the output >> >> >> stops with the message "running the calculation with fixed ions...\c" >> >> >> . Is there more detailed information on using CP either in espresso >> >> >> itself or elsewhere? >> >> > >> >> > there should be a large number of error messages. >> >> > >> >> > this has nothing to do with cp.x. the run_example script >> >> > just automates the process of generating input files and >> >> > running them. in general, it is better for manual runs to >> >> > modify the individual input files, if you are not an expert >> >> > in bourne shell scripting. >> >> > >> >> > cheers, >> >> > axel. >> >> > >> >> >> Thanks for your help. >> >> >> >> >> >> Amos Leffler >> >> >> _______________________________________________ >> >> >> Pw_forum mailing list >> >> >> Pw_forum at pwscf.org >> >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > >> >> > -- >> >> > ======================================================================= >> >> > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu >> >> > Center for Molecular Modeling -- University of Pennsylvania >> >> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 >> >> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 >> >> > ======================================================================= >> >> > If you make something idiot-proof, the universe creates a better idiot. >> >> > >> >> > _______________________________________________ >> >> > 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 >> > >> > -- >> > ======================================================================= >> > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu >> > Center for Molecular Modeling -- University of Pennsylvania >> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 >> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 >> > ======================================================================= >> > If you make something idiot-proof, the universe creates a better idiot. >> > >> > _______________________________________________ >> > 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 > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From wshen02 at gmail.com Mon Jun 15 20:02:23 2009 From: wshen02 at gmail.com (=?ISO-2022-JP?B?GyRCSjhEQBsoQg==?=) Date: Mon, 15 Jun 2009 11:02:23 -0700 Subject: [Pw_forum] hi, everybody, can anybody explain me what the problem it is here? Message-ID: <2c9df8a80906151102m74a6d2e3s4b43819a0c3a4585@mail.gmail.com> I am trying to running a trimmer of CrN, but the espresso gives the following error, from tabd : error # 1 pseudopotential not yet inserted Thanks Wen Shen Ph.D candidate Georgetown University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090615/cd41c392/attachment.htm From paulatto at sissa.it Mon Jun 15 21:20:53 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 15 Jun 2009 21:20:53 +0200 (CEST) Subject: [Pw_forum] hi, everybody, can anybody explain me what the problem it is here? In-Reply-To: <2c9df8a80906151102m74a6d2e3s4b43819a0c3a4585@mail.gmail.com> References: <2c9df8a80906151102m74a6d2e3s4b43819a0c3a4585@mail.gmail.com> Message-ID: <32891.78.12.170.124.1245093653.squirrel@webmail.sissa.it> On Mon, June 15, 2009 20:02, $BJ8D@(B wrote: > pseudopotential not yet inserted An appropriate value of U (of LDA+U) has only been inserted for an handful of well-tested elements. If you need to study some other elemens you can either: 1) write to this mailing list and hope someone will give you a good value (I cannot, but someone could) 2) look in literature for previous studies of that material 3) in Matteo Cococcioni's thesis there should be a detailed explanation on how to find a proper value for U (you can find it here: http://www.sissa.it/cm/phd.php) best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From sunyang198498 at gmail.com Mon Jun 15 23:14:37 2009 From: sunyang198498 at gmail.com (=?GB2312?B?y+/R9A==?=) Date: Mon, 15 Jun 2009 16:14:37 -0500 Subject: [Pw_forum] B_field In-Reply-To: <4A36697F.4070207@sissa.it> References: <98e7a0810906121516k13108a03p7be786a1f4b3cd47@mail.gmail.com> <4A35FD4D.3090505@sissa.it> <98e7a0810906150721s44c844bubdc2a3b475606652@mail.gmail.com> <4A36697F.4070207@sissa.it> Message-ID: <98e7a0810906151414s29c17eb5u208528bcbd22b7b6@mail.gmail.com> Dear Gabriele and any other pwscf users: Thank you for all of the informations. I do read the script of "add B_field", one thing that makes me confused is that: the main structure of the Program was written using conditional pattern, of which, I never find the "i_cons == 5" case (which should be there, you can look it up in the input.f90), which is, I guess, a core problem with my input. In my "nspin=2" calculation, there turns out a reminder in the output file: "i_cons not programmed". This is a reminder also in the "add_bfield.f90" to warn that "icons" is out of range. Actually, we just want to do a simple noncollinear calculation toward the bulk Pd. We hope to use something may be more straightfowrd (just a hope). The following is my input file: **************************************************************************************** &control calculation='scf' restart_mode='from_scratch', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' prefix='Pd' / &system ibrav = 2 celldm(1) = 7.33361 constrained_magnetization = 'total' nspin = 2 fixed_magnetization(3) = 0.01 ntyp = 1 nat=1 ecutwfc = 30.0 ecutrho = 500.0 occupations='tetrahedra' lambda=1 / &electrons conv_thr = 1.0e-8 mixing_beta = 0.1 / ATOMIC_SPECIES Pd 1.0 Pd.pz-nd-rrkjus.UPF ATOMIC_POSITIONS Pd 0.0000 0.0000 0.000 K_POINTS (automatic) 8 8 8 0 0 0 EOF echo echo "#######################################################################" echo Running PW.x for the scf calculation ... $PW_COMMAND < scf.in > scf.out echo done ***************************************************************************************** The report is: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from add_bfield : error # 1 i_cons not programmed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Overall, we just would like to add an B field to a bulk system. As Gabriele pointed out that the flag of "B_field(i)" might have been out of date. Any one has an idea about this, your suggestion is highly appreciated. Thank you so much!! Yang 2009/6/15 Gabriele Sclauzero : > Dear Yang (from???, please sign including your affiliation, since this is > the "policy" of the PW forum), > > ?? wrote: >> Hi, Gabriele, I think you are right. I've already performed the >> constrained magnetization >> calculation. Would there be anyone introduce the way using >> "constrained magnetizatio". >> Is it fully equivalent to applying an external field? > > I'm not sure about this, but, since H (magnetic field) and M (magnetization) are > conjugated variables, you can pass from one to the other as independent variable > in the Hamiltonian via a Legendre transform. When you constrain the magnetization, > the magnetic field will appear as a Lagrange multiplier, so if you use Lagrange > technique you get it automatically (see PRL 53,2512 about constrained DFT). > In QE things are done in a different way, actually, and Lagrange multipliers are not > used. If you fix the total magnetization in collinear LSDA, the "two Fermi energies" > technique is used, while in the other cases a penalty functional is added (you have to > tweak a bit with the "lambda" parameter: have a look at INPUT_PW and add_bfield.f90 for > more detail). > Anyway the code always gives you the "Hellman-Feynman" Magnetic field, H(M), as output at > the end of the run. If you build the E(M) curve you should find, in principle, the same > magnetic field by computing the derivative of E(M) w.r.t. M and thus get the same H(M) curve. > > > HTH > > GS > > > >> >> Thanks, >> >> Yang >> >> 2009/6/15 Gabriele Sclauzero : >>> It seems to me that B_field can be read from input, but then is not used in the >>> calculation. Maybe it was an older option which has been replaced by another solution. In >>> fact I think that a better way to see the effect of an external magnetic field is to do a >>> calculation with constrained magnetization (see INPUT_PW for documentation): this should >>> ensure to reach the ground states, while I suspect that applying a magnetic field you >>> could end in a metastable state, depending on the starting conditions. >>> >>> Regards >>> >>> GS >>> >>> ?? wrote: >>>> Dear everyone: >>>> >>>> I try to appy an external magnetic field about 0.01 Ry to a bulk of >>>> paramagnetic material. By either looking at the spin polarization and >>>> the density of states, I could not find any polarization induced. >>>> Any one has an idea. It will be highly appreciated! >>>> >>>> Yang >>>> >>> -- >>> >>> >>> o ------------------------------------------------ o >>> | Gabriele Sclauzero, PhD Student | >>> | c/o: SISSA & CNR-INFM Democritos, | >>> | via Beirut 2-4, 34014 Trieste (Italy) | >>> | email: sclauzer at sissa.it | >>> | phone: +39 040 3787 511 | >>> | skype: gurlonotturno | >>> o ------------------------------------------------ o >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- University of Nebraska at Lincoln From wshen02 at gmail.com Mon Jun 15 23:49:38 2009 From: wshen02 at gmail.com (=?ISO-2022-JP?B?GyRCSjhEQBsoQg==?=) Date: Mon, 15 Jun 2009 14:49:38 -0700 Subject: [Pw_forum] Dear all, a question about the tabd.f90 file Message-ID: <2c9df8a80906151449j522438f1of75055dc3cc8e6cf@mail.gmail.com> When I run the CrN trimer, I get this error from tabd:error #1 pseudopotential not yet inserted followed the two discussions on pwforum, it is due to tabd.f90 file don't have the information for Cr. So I tried to add the information for Cr in the tabd.f90 file, but whenever I input the occ_loc=4.0,5.0 or 6.0 the error always exists. The electron structure for Cr is [Ar]3d54s1 Do you have some idea about this? What should I do about this and what should be the occ_loc for Cr (in the tabd.f90 file, it says "the total number of d electrons") Thanks Wen Shen Ph.D candidate Georgetown University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090615/a7ac0f31/attachment.htm From sclauzer at sissa.it Tue Jun 16 08:43:16 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 16 Jun 2009 08:43:16 +0200 Subject: [Pw_forum] hi, everybody, can anybody explain me what the problem it is here? In-Reply-To: <2c9df8a80906151102m74a6d2e3s4b43819a0c3a4585@mail.gmail.com> References: <2c9df8a80906151102m74a6d2e3s4b43819a0c3a4585@mail.gmail.com> Message-ID: <4A373F04.50609@sissa.it> You will find the solution to your problem here: http://www.google.it/search?q=pseudopotential+not+yet+inserted+site%3Ademocritos.it GS ?? wrote: > I am trying to running a trimmer of CrN, but the espresso gives the > following error, > from tabd : error # 1 > pseudopotential not yet inserted > Thanks > > > Wen Shen > Ph.D candidate > Georgetown University > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Tue Jun 16 08:47:11 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 16 Jun 2009 08:47:11 +0200 Subject: [Pw_forum] hi, everybody, can anybody explain me what the problem it is here? In-Reply-To: <32891.78.12.170.124.1245093653.squirrel@webmail.sissa.it> References: <2c9df8a80906151102m74a6d2e3s4b43819a0c3a4585@mail.gmail.com> <32891.78.12.170.124.1245093653.squirrel@webmail.sissa.it> Message-ID: <4A373FEF.60005@sissa.it> Lorenzo Paulatto wrote: > On Mon, June 15, 2009 20:02, $BJ8D@(B wrote: >> pseudopotential not yet inserted > > An appropriate value of U (of LDA+U) has only been inserted for an handful Actually, U has to be inserted anyway in all cases. What is missing are the angular momentum (l=1,2,3 or 4) of the local orbitals which are used to build the local occupations needed by the LDA+U and the total (atomic) occupation of that subshell of orbitals. > of well-tested elements. If you need to study some other elemens you can > either: > 1) write to this mailing list and hope someone will give you a good value > (I cannot, but someone could) > 2) look in literature for previous studies of that material > 3) in Matteo Cococcioni's thesis there should be a detailed explanation on > how to find a proper value for U (you can find it here: > http://www.sissa.it/cm/phd.php) Anyway, this is a very good advice for anyone starting serious LDA+U calculations. GS > > best regards > > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Tue Jun 16 08:52:26 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 16 Jun 2009 08:52:26 +0200 Subject: [Pw_forum] Dear all, a question about the tabd.f90 file In-Reply-To: <2c9df8a80906151449j522438f1of75055dc3cc8e6cf@mail.gmail.com> References: <2c9df8a80906151449j522438f1of75055dc3cc8e6cf@mail.gmail.com> Message-ID: On Jun 15, 2009, at 23:49 , ?? wrote: > So I tried to add the information for Cr in the tabd.f90 file, > but whenever I input the occ_loc=4.0,5.0 or 6.0 the error > always exists. did you recompile? --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sclauzer at sissa.it Tue Jun 16 09:00:19 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 16 Jun 2009 09:00:19 +0200 Subject: [Pw_forum] Dear all, a question about the tabd.f90 file In-Reply-To: <2c9df8a80906151449j522438f1of75055dc3cc8e6cf@mail.gmail.com> References: <2c9df8a80906151449j522438f1of75055dc3cc8e6cf@mail.gmail.com> Message-ID: <4A374303.1090004@sissa.it> ?? wrote: > When I run the CrN trimer, I get this error > from tabd:error #1 > pseudopotential not yet inserted > followed the two discussions on pwforum, it is due to tabd.f90 file > don't have the information for Cr. > So I tried to add the information for Cr in the tabd.f90 file, but > whenever I input the occ_loc=4.0,5.0 or 6.0 the error always exists. I think you should use 5.0 (can you guess why?), but setting occ_loc to 4 or 6 should not cause any crash in the code. Your problem is another, I guess (I can only guess, since you give very little of information...) Are you putting plus U only on Cr or also on N? Are you sure that after modifying tabd the error message is the same that you report? From http://www.democritos.it/pipermail/pw_forum/2004-March/000914.html --- On Mon, 1 Mar 2004, Philippe BARANEK wrote: > Anyone of you have used pwscf with hubbard correction and > could he explain me how to use it because I must do something > wrong, each time I am trying I have got this error message > > "From set_hubbard_l : error # 1 > pseudopotential not yet inserted > Stopping" $ grep set_hubbard_l PW/*f90 $ PW/set_hubbard_l.f90:integer function set_hubbard_l(psd) result (hubbard_l) $ PW/set_hubbard_l.f90: call errore ('set_hubbard_l','pseudopotential not yet inserted', 1) if you look into PW/set_hubbard_l.f90 you will see that only for a few selected elements is the variable hubbard_l defined. If your preferred element (U, I guess) is not in the list, you have to add it: elseif (psd .eq.'Ce' .or. psd .eq.'U') then hubbard_l = 3 else ... ... Paolo --- So, if you had a look to the archives maybe you already discovered that you need to modify also the subroutine set_hubbard_l. > > The electron structure for Cr is [Ar]3d54s1 > Do you have some idea about this? > > What should I do about this and what should be the occ_loc for Cr (in > the tabd.f90 file, it says "the total number of d electrons") What do you think should be "the total number of d electrons" in this case. I hope you have at least an idea about that before using LDA+U. cheers, GS > > Thanks > > Wen Shen > Ph.D candidate > Georgetown University > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Tue Jun 16 09:34:36 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 16 Jun 2009 09:34:36 +0200 Subject: [Pw_forum] B_field In-Reply-To: <98e7a0810906151414s29c17eb5u208528bcbd22b7b6@mail.gmail.com> References: <98e7a0810906121516k13108a03p7be786a1f4b3cd47@mail.gmail.com> <4A35FD4D.3090505@sissa.it> <98e7a0810906150721s44c844bubdc2a3b475606652@mail.gmail.com> <4A36697F.4070207@sissa.it> <98e7a0810906151414s29c17eb5u208528bcbd22b7b6@mail.gmail.com> Message-ID: <4A374B0C.7090009@sissa.it> ?? wrote: > Dear Gabriele and any other pwscf users: > > Thank you for all of the informations. I do read the script of "add B_field", > one thing that makes me confused is that: the main structure of the > Program was written using conditional pattern, of which, I never find the > "i_cons == 5" case (which should be there, you can look it up in the > input.f90), which is, I guess, a core problem with my input. In my "nspin=2" > calculation, there turns out a reminder in the output file: "i_cons > not programmed". > This is a reminder also in the "add_bfield.f90" to warn that "icons" > is out of range. > > Actually, we just want to do a simple noncollinear calculation toward the > bulk Pd. We hope to use something may be more straightfowrd (just a hope). > > The following is my input file: Your input for me works just fine. This problem was fixed in v. 4.0.2, so you might need to update QE to the latest version (you can retrieve v. 4.0.5 from qe-forge.org website). There should be this line: IF (nspin ==1 .or. i_cons==0 .or. i_cons==5 ) RETURN and the subroutine does nothing for i_cons==5, since in that case the calculation is done using two Fermi energies, so that you don't need to add a magnetic field to constrain the magnetization. If you really want to add a magnetic field to the XC potential (though I'm not sure is the correct thing to do), you have to look at i_cons==4 (not i_cons==5) in add_bfield. This type of "constraint" is not considered in input.f90, but you want to reenable that option, simply add i_cons==4 just after IF ( B_field(1) /= 0.D0 .OR. & B_field(2) /= 0.D0 .OR. & B_field(3) /= 0.D0 ) THEN and it should be handled properly by add_bfield. GS > > **************************************************************************************** > > &control > calculation='scf' > restart_mode='from_scratch', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > prefix='Pd' > > > / > &system > ibrav = 2 > celldm(1) = 7.33361 > constrained_magnetization = 'total' > nspin = 2 > fixed_magnetization(3) = 0.01 > ntyp = 1 > nat=1 > ecutwfc = 30.0 > ecutrho = 500.0 > occupations='tetrahedra' > lambda=1 > / > > &electrons > conv_thr = 1.0e-8 > mixing_beta = 0.1 > / > ATOMIC_SPECIES > Pd 1.0 Pd.pz-nd-rrkjus.UPF > > ATOMIC_POSITIONS > Pd 0.0000 0.0000 0.000 > K_POINTS (automatic) > 8 8 8 0 0 0 > EOF > echo > echo "#######################################################################" > echo Running PW.x for the scf calculation ... > $PW_COMMAND < scf.in > scf.out > echo done > > ***************************************************************************************** > > The report is: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from add_bfield : error # 1 > i_cons not programmed > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > Overall, we just would like to add an B field to a bulk system. As > Gabriele pointed out that > the flag of "B_field(i)" might have been out of date. Any one has an > idea about this, your suggestion > is highly appreciated. > > Thank you so much!! > > Yang > > > > > > > > > > > 2009/6/15 Gabriele Sclauzero : >> Dear Yang (from???, please sign including your affiliation, since this is >> the "policy" of the PW forum), >> >> ?? wrote: >>> Hi, Gabriele, I think you are right. I've already performed the >>> constrained magnetization >>> calculation. Would there be anyone introduce the way using >>> "constrained magnetizatio". >>> Is it fully equivalent to applying an external field? >> I'm not sure about this, but, since H (magnetic field) and M (magnetization) are >> conjugated variables, you can pass from one to the other as independent variable >> in the Hamiltonian via a Legendre transform. When you constrain the magnetization, >> the magnetic field will appear as a Lagrange multiplier, so if you use Lagrange >> technique you get it automatically (see PRL 53,2512 about constrained DFT). >> In QE things are done in a different way, actually, and Lagrange multipliers are not >> used. If you fix the total magnetization in collinear LSDA, the "two Fermi energies" >> technique is used, while in the other cases a penalty functional is added (you have to >> tweak a bit with the "lambda" parameter: have a look at INPUT_PW and add_bfield.f90 for >> more detail). >> Anyway the code always gives you the "Hellman-Feynman" Magnetic field, H(M), as output at >> the end of the run. If you build the E(M) curve you should find, in principle, the same >> magnetic field by computing the derivative of E(M) w.r.t. M and thus get the same H(M) curve. >> >> >> HTH >> >> GS >> >> >> >>> Thanks, >>> >>> Yang >>> >>> 2009/6/15 Gabriele Sclauzero : >>>> It seems to me that B_field can be read from input, but then is not used in the >>>> calculation. Maybe it was an older option which has been replaced by another solution. In >>>> fact I think that a better way to see the effect of an external magnetic field is to do a >>>> calculation with constrained magnetization (see INPUT_PW for documentation): this should >>>> ensure to reach the ground states, while I suspect that applying a magnetic field you >>>> could end in a metastable state, depending on the starting conditions. >>>> >>>> Regards >>>> >>>> GS >>>> >>>> ?? wrote: >>>>> Dear everyone: >>>>> >>>>> I try to appy an external magnetic field about 0.01 Ry to a bulk of >>>>> paramagnetic material. By either looking at the spin polarization and >>>>> the density of states, I could not find any polarization induced. >>>>> Any one has an idea. It will be highly appreciated! >>>>> >>>>> Yang >>>>> >>>> -- >>>> >>>> >>>> o ------------------------------------------------ o >>>> | Gabriele Sclauzero, PhD Student | >>>> | c/o: SISSA & CNR-INFM Democritos, | >>>> | via Beirut 2-4, 34014 Trieste (Italy) | >>>> | email: sclauzer at sissa.it | >>>> | phone: +39 040 3787 511 | >>>> | skype: gurlonotturno | >>>> o ------------------------------------------------ o >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>> >>> >> -- >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Tue Jun 16 09:36:41 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 16 Jun 2009 09:36:41 +0200 Subject: [Pw_forum] B_field In-Reply-To: <4A374B0C.7090009@sissa.it> References: <98e7a0810906121516k13108a03p7be786a1f4b3cd47@mail.gmail.com> <4A35FD4D.3090505@sissa.it> <98e7a0810906150721s44c844bubdc2a3b475606652@mail.gmail.com> <4A36697F.4070207@sissa.it> <98e7a0810906151414s29c17eb5u208528bcbd22b7b6@mail.gmail.com> <4A374B0C.7090009@sissa.it> Message-ID: <4A374B89.9000106@democritos.it> Gabriele Sclauzero wrote: > (you can retrieve v. 4.0.5 from qe-forge.org website). no, from www.quantum-espresso.org P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Tue Jun 16 09:50:00 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 16 Jun 2009 09:50:00 +0200 Subject: [Pw_forum] File closing errors when using NEB image parallelization In-Reply-To: <14450.35591.qm@web50912.mail.re2.yahoo.com> References: <14450.35591.qm@web50912.mail.re2.yahoo.com> Message-ID: In data 10 giugno 2009 alle ore 20:13:23, J. J. Ramsey ha scritto: > ... > In spite of the errors at the end, both runs, with and without image > parallelization, get me the same answer, and offhand, it looks maybe as > if some processes are trying to close files that had already been closed > by other processes. Hallo J, sorry for not replying for so long. You problem is indeed interesting, but in my NEB calculations I've never met it. Can you provide an example input file? In theory different images use different prefix, hence they should not interfere, nevertheless there could still be some problem, e.g. some debug output that have been left in the code by mistake. If you don't want to provide an example, or if the example is massive, you could try to compile the code with debug options (on intel compiler I suggest -traceback): you should be able to spot the exact line where the offending output happens. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From sclauzer at sissa.it Tue Jun 16 10:48:37 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 16 Jun 2009 10:48:37 +0200 Subject: [Pw_forum] missing q point In-Reply-To: <4A3649FA.4050502@sissa.it> References: <4A364950.7070102@sissa.it> <4A3649FA.4050502@sissa.it> Message-ID: <4A375C65.9020900@sissa.it> Gabriele Sclauzero wrote: > > Gabriele Sclauzero wrote: >> Mehrnaz Anvari wrote: >>> I used new version of pakage (espresso-4.0.5) as you told me & the error >>> was disappeared. I performed Eyvaz suggestion too, I mean that I used >>> different grids (for nq1,nq2,nq3) for instance 2 2 2 , 4 4 4, 4 4 >>> 2,...but the error existed in all of these cases. I've tried the 442 grid with espresso-4.1CVS on my intel linux workstation. Everything seems to work fine for me. No missing q-points or something similar. This is the output from q2r.x reading grid info from file graphene.dyn0 reading force constants from file graphene.dyn1 Dielectric Tensor not found nqs= 1 q= 0.00000000 0.00000000 0.00000000 reading force constants from file graphene.dyn2 nqs= 1 q= 0.00000000 0.00000000 -0.04991061 reading force constants from file graphene.dyn3 nqs= 6 q= 0.00000000 0.30452725 0.00000000 q= 0.00000000 -0.30452725 0.00000000 q= -0.26372834 -0.15226363 0.00000000 q= 0.26372834 -0.15226363 0.00000000 q= -0.26372834 0.15226363 0.00000000 q= 0.26372834 0.15226363 0.00000000 reading force constants from file graphene.dyn4 nqs= 6 q= 0.00000000 0.30452725 -0.04991061 q= 0.00000000 -0.30452725 0.04991061 q= -0.26372834 -0.15226363 0.04991061 q= 0.26372834 -0.15226363 0.04991061 q= -0.26372834 0.15226363 0.04991061 q= 0.26372834 0.15226363 0.04991061 reading force constants from file graphene.dyn5 nqs= 3 q= 0.00000000 -0.60905451 0.00000000 q= 0.52745668 0.30452725 0.00000000 q= -0.52745668 0.30452725 0.00000000 reading force constants from file graphene.dyn6 nqs= 3 q= 0.00000000 -0.60905451 -0.04991061 q= 0.52745668 0.30452725 0.04991061 q= -0.52745668 0.30452725 0.04991061 reading force constants from file graphene.dyn7 nqs= 6 q= 0.26372834 0.45679088 0.00000000 q= -0.26372834 -0.45679088 0.00000000 q= 0.26372834 -0.45679088 0.00000000 q= 0.52745668 0.00000000 0.00000000 q= -0.52745668 0.00000000 0.00000000 q= -0.26372834 0.45679088 0.00000000 reading force constants from file graphene.dyn8 nqs= 6 q= 0.26372834 0.45679088 -0.04991061 q= -0.26372834 -0.45679088 0.04991061 q= 0.26372834 -0.45679088 -0.04991061 q= 0.52745668 0.00000000 0.04991061 q= -0.52745668 0.00000000 0.04991061 q= -0.26372834 0.45679088 0.04991061 q-space grid ok, #points = 32 fft-check warning: sum of imaginary terms = .8800000E-06 All seems fine to me! cheers, GS >> First of all, I don't understand why your k-point grid is not 2D (i.e. nkx, nky, 1) if you >> want to study graphite. > > Sorry, I meant graphene, not graphite, obviuosly... > > GS > >>> Finally I couldn't >>> understand main reason of this error. when I open the dyn0 file I see >>> only kpoints with high symmetry, so it means that the program could >>> indicate the symmetry of system but in the following it could'nt keep >>> all of them it is so strange(?) >> Be carefull that until a recent change in the CVS version the ph.x was overwriting pw.x >> data in the .save directory, so that if you do successive ph.x calculations without making >> a copy of that directory it may not work. >> >> Now I will try some of your problematic k-points grids and let oyu know if they work with >> the CVS version. >> >> GS >> >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From mozaharphysics25 at yahoo.com Tue Jun 16 12:23:45 2009 From: mozaharphysics25 at yahoo.com (Mozahar Ali) Date: Tue, 16 Jun 2009 03:23:45 -0700 (PDT) Subject: [Pw_forum] about superconducting Tc Message-ID: <192862.38526.qm@web58504.mail.re3.yahoo.com> At first I would like to give thanks to prof.Eyvaz because following his suggesions I can calculate E-P coupling.But now I would like to calculate superconducting critical temperature(Tc).Can we calculate Tc with the Quantum Espresso? if so then give?me suggesions please. Get your preferred Email name! Now you can @ymail.com and @rocketmail.com. http://mail.promotions.yahoo.com/newdomains/aa/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090616/717def5f/attachment.htm From mozaharphysics25 at yahoo.com Tue Jun 16 12:31:07 2009 From: mozaharphysics25 at yahoo.com (Mozahar Ali) Date: Tue, 16 Jun 2009 03:31:07 -0700 (PDT) Subject: [Pw_forum] about superconduting Tc Message-ID: <604464.41006.qm@web58507.mail.re3.yahoo.com> Dear all user, At first I would like to give thanks to prof.Eyvaz because following his suggesions I can calculate E-P coupling.But now I would like to calculate superconducting critical temperature(Tc).Can we calculate Tc with the Quantum Espresso? if so then give me suggesions please. New Email names for you! Get the Email name you've always wanted on the new @ymail and @rocketmail. Hurry before someone else does! http://mail.promotions.yahoo.com/newdomains/aa/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090616/1c9234ed/attachment-0001.htm From marzari at MIT.EDU Tue Jun 16 12:34:02 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Tue, 16 Jun 2009 06:34:02 -0400 Subject: [Pw_forum] about superconduting Tc In-Reply-To: <604464.41006.qm@web58507.mail.re3.yahoo.com> References: <604464.41006.qm@web58507.mail.re3.yahoo.com> Message-ID: <4A37751A.7070502@mit.edu> Mozahar Ali wrote: > Dear all user, > > At first I would like to give thanks to prof.Eyvaz because following his > suggesions I can calculate E-P coupling.But now I would like to > calculate superconducting critical temperature(Tc).Can we calculate Tc > with the Quantum Espresso? if so then give me suggesions please. Sure. 1) Plenty of literature. Start with the 1996 PRL of Mauri and de Gironcoli, and all the papers that cite that. Have also a look at the work done independently by Amy Liu, or the recent work from Calandra/Lazzeri/Mauri on el-phon coupling. 2) sign your emails with your affiliation. it's common courtesy on this forum, and not doing it raises the suspicion that you've never looked at it before. Thanks, nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From jjr19 at uakron.edu Tue Jun 16 13:05:54 2009 From: jjr19 at uakron.edu (J. J. Ramsey) Date: Tue, 16 Jun 2009 04:05:54 -0700 (PDT) Subject: [Pw_forum] File closing errors when using NEB image parallelization In-Reply-To: References: <14450.35591.qm@web50912.mail.re2.yahoo.com> Message-ID: <269325.14322.qm@web50907.mail.re2.yahoo.com> > Can you provide an example input file? Should be attached in my original e-mail. > If you don't want to provide an example, or if the example is massive, you could > try to compile the code with debug options (on intel compiler I suggest > -traceback): you should be able to spot the exact line where the offending > output happens. Thanks for the mentioning the "-traceback" option. I tried using "-g -O0" but that didn't help find the error. I'll try to see if I can get a trace. From eyvaz_isaev at yahoo.com Tue Jun 16 13:45:48 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 16 Jun 2009 04:45:48 -0700 (PDT) Subject: [Pw_forum] about superconduting Tc Message-ID: <628202.69908.qm@web65704.mail.ac4.yahoo.com> Dear Mozahar, --- On Tue, 6/16/09, Mozahar Ali wrote: > At first I would like to give thanks to prof.Eyvaz because > following his suggesions I can calculate E-P coupling. You are welcome, and that is great that you can calculate EPC constant. > But now I would like to calculate superconducting critical > temperature(Tc).Can we calculate Tc with the Quantum > Espresso? if so then give me suggesions please. > If you have the last version of lambda.f90 I posted recently to the forum, then you can easily calculate T_c according to Allen-Dynes formula. If you can not find it then let me know. Please do not forget supply your affiliation. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From jjr19 at uakron.edu Tue Jun 16 15:10:54 2009 From: jjr19 at uakron.edu (J. J. Ramsey) Date: Tue, 16 Jun 2009 06:10:54 -0700 (PDT) Subject: [Pw_forum] File closing errors when using NEB image parallelization In-Reply-To: References: <14450.35591.qm@web50912.mail.re2.yahoo.com> Message-ID: <880917.27758.qm@web50903.mail.re2.yahoo.com> ----- Original Message ---- > you could > try to compile the code with debug options (on intel compiler I suggest > -traceback): you should be able to spot the exact line where the offending > output happens. I did the traceback, and the full error messages are attached. Most of them look like this: forrtl: No such file or directory forrtl: severe (28): CLOSE error, unit 4, file "Unknown" Image PC Routine Line Source pw.x 0000000000964311 Unknown Unknown Unknown pw.x 00000000009632E5 Unknown Unknown Unknown pw.x 000000000091255A Unknown Unknown Unknown pw.x 00000000008B2762 Unknown Unknown Unknown pw.x 00000000008B1F91 Unknown Unknown Unknown pw.x 00000000008AB1B6 Unknown Unknown Unknown pw.x 0000000000609818 stop_run_ 63 stop_run.f90 pw.x 00000000004331A5 MAIN__ 85 pwscf.f90 pw.x 0000000000432FBC Unknown Unknown Unknown libc.so.6 00002B15DA942164 Unknown Unknown Unknown pw.x 0000000000432EE9 Unknown Unknown Unknown While PWscf was compiled with debugging info and the "-traceback" option, I was still compiling against my cluster's already compiled OpenMPI, which should explain why "Unknown" is repeated so much above. -------------- next part -------------- A non-text attachment was scrubbed... Name: smallerProb_PWscfNEB2_c18_v10_k4.err.gz Type: application/x-gzip Size: 1984 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090616/55086ff8/attachment.bin From sunyang198498 at gmail.com Tue Jun 16 16:59:13 2009 From: sunyang198498 at gmail.com (=?GB2312?B?y+/R9A==?=) Date: Tue, 16 Jun 2009 09:59:13 -0500 Subject: [Pw_forum] B_field In-Reply-To: <4A374B89.9000106@democritos.it> References: <98e7a0810906121516k13108a03p7be786a1f4b3cd47@mail.gmail.com> <4A35FD4D.3090505@sissa.it> <98e7a0810906150721s44c844bubdc2a3b475606652@mail.gmail.com> <4A36697F.4070207@sissa.it> <98e7a0810906151414s29c17eb5u208528bcbd22b7b6@mail.gmail.com> <4A374B0C.7090009@sissa.it> <4A374B89.9000106@democritos.it> Message-ID: <98e7a0810906160759jdad69eeo25323428107888c7@mail.gmail.com> Thank you all!! Yang 2009/6/16 Paolo Giannozzi > Gabriele Sclauzero wrote: > > > (you can retrieve v. 4.0.5 from qe-forge.org website). > > no, from www.quantum-espresso.org > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- University of Nebraska at Lincoln -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090616/9a04e05d/attachment.htm From paulatto at sissa.it Tue Jun 16 17:41:08 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 16 Jun 2009 17:41:08 +0200 Subject: [Pw_forum] File closing errors when using NEB image parallelization In-Reply-To: <880917.27758.qm@web50903.mail.re2.yahoo.com> References: <14450.35591.qm@web50912.mail.re2.yahoo.com> <880917.27758.qm@web50903.mail.re2.yahoo.com> Message-ID: In data 16 giugno 2009 alle ore 15:10:54, J. J. Ramsey ha scritto: > Image PC Routine Line > pw.x 0000000000609818 stop_run_ 63 > stop_run.f90 > pw.x 00000000004331A5 MAIN__ 85 pwscf.f90 > While PWscf was compiled with debugging info and the "-traceback" > option, I was still compiling against my cluster's already compiled > OpenMPI, which should explain why "Unknown" is repeated so much above. Not all of the "unknown", actually but what's deeper I can deduct from what is there. I cannot say it for certain, bu it looks suspiciously like a race condition, possibly related to the kind of filesystem on which the wavefunctions directory (outdir, and consequently ~/tmp, per default). If I had to bet I would say you are using ~/tmp as the default directory, and it is a normal NFS share. Anyway, it is indeed annoying but should be harmless, as long as it only happens at the end of the run. I could try and "fix" it now, but it will take some time to check for side effects. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From yosmanche at gmail.com Tue Jun 16 17:50:49 2009 From: yosmanche at gmail.com (yoseph Getachew) Date: Tue, 16 Jun 2009 18:50:49 +0300 Subject: [Pw_forum] How to start and use QE open source simulation Message-ID: Dear All , sorry but this is a very low level question. would you please inform me as to how i can install,configure, and make all the necessary steps so that i can be able to run simulations. i have tried to use the QE website but i ended up in so much more inconsistencies. for example where and how can i get and install fortan and c.xcrysden which binary or static files should i use and how should i install them. i need your specific advise on this to catch up with everybody. Regards, Yoseph Getachew ArbaMinch University, Department of Physics On 6/15/09, pw_forum-request at pwscf.org wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://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: homo-lumo and conductance (Gabriele Sclauzero) > 2. Re: B_field (Gabriele Sclauzero) > 3. doubt about documentation of QE (shypirate) > 4. fileutil ? (Nicola Marzari) > 5. Re: fileutil ? (Tone Kokalj) > 6. Re: doubt about documentation of QE (Paolo Giannozzi) > 7. Re: fileutil ? (Paolo Giannozzi) > 8. ld1.x testing mode (hichem bouderba) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 15 Jun 2009 09:04:03 +0200 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] homo-lumo and conductance > To: PWSCF Forum > Message-ID: <4A35F263.9020205 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > ambavale sagar wrote: >> Dear Gabriele, >> Thank you for your reply. I refered to smogunov paper but I could not >> understand the sentence used there : "Since the system has the supercell >> (artificial) 2D periodicity in the xy plane, perpendicular to the >> transport direction, we averaged the transmission over the corresponding >> 2D BZ using 21 k points in the irreducible part of the BZ.." Are those >> 21 k-pts belong to xy plane only? what type of grid that may be? 6 6 2 1 >> 1 1 ? >> In my case supercell dimensions in x and y are 25 a.u. i.e. ~12 ang >> which includes nearly ~9 ang. of vaccum. > > Here Alexander already replied you. So your k_perpendicular points sampling > depends if you > want to study an isolated wire (thick or monoatomic), or a wire/molecule > between realistic > electrodes (modeled as surfaces or surfaces+tips attached to them). In the > former case, if > your supercell is large enough in the directions perpendicular to the > transport the > transmission should not depend on k_perp and you need only one k_perp-point. > In the latter > you need to sample accurately the 2D BZ, since the transmission depends (a > lot in some > cases) on k_perp. > >> >> As you mentioned the limitation of DFT due to xc-functional, can I use >> DFT calculation to compare qualitatively the Transmission coefficient of >> same molecule with different geometries? > > I cannot say, actually. It depends on the coupling and other details. You > can have a look > to the recent work by Thygesen and Rubio, which try to include a GW > correction in this > kind of calculations. > >> >> would you please mention in detail how to find positions of HOMO, LUMO >> in a coupled system? > > What I would do (but fur sure there are many better methods) if I want to > put, say, O_2 > between electrodes is to look at the PDOS (computed by projwfc.x in the QE > suite) > projected onto the O atoms and compare it with the PDOS of the isolated O_2. > It would give > an idea of the level of hybridization between molecule and electrodes and of > the position > of the HOMO(LUMO)-derived levels. > It could also be useful to look at the PDOS on the electrode atoms to > understand which > metallic states/atoms are more involved in the coupling. > > regards, > > GS > > >> >> regards >> Sagar Ambavale >> ------------------------------------------------------------------------ >> ** >> Message: 1 >> Date: Fri, 12 Jun 2009 18:14:46 +0200 >> From: Gabriele Sclauzero > >> Subject: Re: [Pw_forum] homo-lumo and conductance >> To: PWSCF Forum > >> Message-ID: <4A327EF6.7020206 at sissa.it > >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> >> ambavale sagar wrote: >> > Dear all, >> > I am studying ballistic conductance through a molecule attached to Al >> > electrode. >> >> Including Al surfaces on both sides? >> >> > The k-pt grid used for scf calculation of scattering region >> > made of molecule and few layers of electrode, is 2 2 10 1 1 1. >> >> If so, this k-point grid looks a bit lousy to me. Unless you use a very >> large supercell in >> the transverse directions (xy, since z is the transport direction in >> pwcond), you should >> take more k-points along that directions. Along z, instead, you need >> less k-points (10 >> seems really too much to me). Along z you must include enough slabs >> before and after the >> junction with the molecule such that the scf potential at the borders of >> the cell is close >> enough to the scf potential of bulk Al. >> >> You can have a look at this paper in order to get an idea: >> Smogunov et al., Phys. Rev. B 78, 014423 (2008) >> >> > I want to >> > see effect of HOMO-LUMO levels of molecule on transmission. Is it >> > sensible to find HOMO-LUMO levels of molecule using separate >> calculation >> > of isolated molecule with gamma point? How about bandstructure that I >> > got from 20 k-pt calculation of scattering region periodic in >> z-direction? >> >> I'm not sure I got your questions. Of course if you study the ballistic >> conductance >> through the molecule in the tunneling regime, the result will be very >> sensitive to the >> position of the HOMO and LUMO levels of the molecule. Depending on how >> strong is the >> binding between the molecule and the electrodes the position and width >> of these levels >> will be modified more or less by the hybridization with the metal states. >> In order to find the position of the HOMO and LUMO in the coupled system >> you can look at >> the PDOS on the atoms of the molecule (if not too complex) and compare >> it with the >> corresponding PDOS of the isolated molecule. >> Another solution might be to build Wannier functions of the HOMO and >> LUMO and project onto >> them, but I never tried this solution. >> >> Anyway, you should be careful when trusting DFT results in this kind of >> system, since >> common XC functionals can mismatch the HOMO-LUMO gap of several eV and >> there could also be >> problems in getting a reliable alignment with the Fermi level of the >> metal. Since in >> weakly coupled junctions the conductance is very sensitive to the exact >> position of the >> molecular levels involved in the tunneling and to the decaying behavior >> of their tails, >> this issues can lead to errors of 1 or several orders of magnitude. >> >> >> Cheers >> >> GS >> >> > >> > Thank you. >> > >> > Sagar Ambavale >> > PhD student >> > M.S. University of Baroda >> > India >> > >> > >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it >> | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> >> >> *************************** >> >> ------------------------------------------------------------------------ >> Own a website.Get an unlimited package.Pay next to nothing.* Click >> here!. >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > > > ------------------------------ > > Message: 2 > Date: Mon, 15 Jun 2009 09:50:37 +0200 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] B_field > To: PWSCF Forum > Message-ID: <4A35FD4D.3090505 at sissa.it> > Content-Type: text/plain; charset=UTF-8; format=flowed > > It seems to me that B_field can be read from input, but then is not used in > the > calculation. Maybe it was an older option which has been replaced by another > solution. In > fact I think that a better way to see the effect of an external magnetic > field is to do a > calculation with constrained magnetization (see INPUT_PW for documentation): > this should > ensure to reach the ground states, while I suspect that applying a magnetic > field you > could end in a metastable state, depending on the starting conditions. > > Regards > > GS > > ?? wrote: >> Dear everyone: >> >> I try to appy an external magnetic field about 0.01 Ry to a bulk of >> paramagnetic material. By either looking at the spin polarization and >> the density of states, I could not find any polarization induced. >> Any one has an idea. It will be highly appreciated! >> >> Yang >> > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > > > ------------------------------ > > Message: 3 > Date: Mon, 15 Jun 2009 17:19:18 +0800 > From: "shypirate" > Subject: [Pw_forum] doubt about documentation of QE > To: "pw_forum" > Message-ID: <200906151719143151087 at gmail.com> > Content-Type: text/plain; charset="us-ascii" > > Dear All: > I am reading the doc and example of QE, but it makes me confused. > > For example, in example30/README, 'tefield' and 'efield' is used together to > add electric field to the studied system. However, in the 'INPUT_PW.html', > 'tefield' is used to specified a sawlike potential, and 'efield' is used if > 'lelfield=.TRUE.', at the same time, 'lelfield' is "different" from > 'tefield'. > > All the above refered is version 4.0.5. > > Any suggestion is appreciated! > > Y.P.Wang > > > 2009-06-15 > > > > shypirate > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090615/bc905842/attachment-0001.htm > > ------------------------------ > > Message: 4 > Date: Mon, 15 Jun 2009 05:48:14 -0400 > From: Nicola Marzari > Subject: [Pw_forum] fileutil ? > To: PWSCF Forum > Message-ID: <4A3618DE.5070906 at mit.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > > Dear All, > > > 1) if I try to generate the documentation files for QE (make all in > dev-doc) I get an error message about missing the fileutil package > (see error lines below). I have tcl-8.4.13-1.1 ; I searched the > forum (to no avail), so maybe this is useful to others. > > 2) is it correct that the new source for the QE snapshots is the > qe-forge CVS, and the old CVS is not maintained, and wil be > discarded ? For reference to anyone reading, the new cvs > instructions are: > > cvs -d :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e checkout espresso > > Thanks, > > nicola > > > ---- > in dev-doc: > make all > ../dev-tools/helpdoc INPUT_PW.def > can't find package fileutil > while executing > "package require fileutil" > (file > "/home/marzari/codes/espresso/dev-tools/helpdoc.d/../../GUI/Guib/lib/tclUtils.tcl" > line 41) > invoked from within > "source > /home/marzari/codes/espresso/dev-tools/helpdoc.d/../../GUI/Guib/lib/tclUtils.tcl" > ("package ifneeded" script) > invoked from within > "package require tclu 0.9" > (file > "/home/marzari/codes/espresso/dev-tools/helpdoc.d/helpdoc.tcl" line 4) > invoked from within > "source [file join $sourcedir helpdoc.tcl]" > (file "../dev-tools/helpdoc" line 8) > make: *** [INPUT_PW.html] Error 1 > ---- > > --------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials Science and Engineering > 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA > tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu > > > ------------------------------ > > Message: 5 > Date: Mon, 15 Jun 2009 12:22:07 +0200 > From: Tone Kokalj > Subject: Re: [Pw_forum] fileutil ? > To: PWSCF Forum > Message-ID: <1245061327.29014.38.camel at walk.ijs.si> > Content-Type: text/plain > > On Mon, 2009-06-15 at 05:48 -0400, Nicola Marzari wrote: >> >> >> Dear All, >> >> >> 1) if I try to generate the documentation files for QE (make all in >> dev-doc) > > actually in doc-def/ > >> ... I get an error message about missing the fileutil package >> (see error lines below). I have tcl-8.4.13-1.1 ; I searched the >> forum (to no avail), so maybe this is useful to others. > > > fileutil is a package from the tcllib. The latter is required for the > helpdoc program to function (see the dev-tools/README.helpdoc). And > helpdoc is a utility that creates the QE txt and html documentation > files from the *.def files. > > Several linux distros are based on Debian or RedHat, if you use one of > them, then to install tcllib: > > apt-get install tcl tcllib xsltproc (for Debian-based distros) > > or > > yum install tcl tcllib xsltproc (for Redhat-based distros) > > (for other distros the installation of tcllib is likely analogous, i.e., > replace the apt-get|yum with the corresponding package installer) > > Regards, Tone > > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > ------------------------------ > > Message: 6 > Date: Mon, 15 Jun 2009 12:50:27 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] doubt about documentation of QE > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > On Jun 15, 2009, at 11:19 , shypirate wrote: > >> For example, in example30/README, 'tefield' and 'efield' is used >> together >> to add electric field to the studied system. However, in the >> 'INPUT_PW.html', >> 'tefield' is used to specified a sawlike potential, and 'efield' is >> used if >> 'lelfield=.TRUE.', at the same time, 'lelfield' is "different" from >> 'tefield'. >> [...] Any suggestion is appreciated! > > you will have better luck if you read the documentation for CP: > Doc/INPUT_CP, since this is what is actually used in example30. > Unfortunately there is a mismatch between CP and PWscf in the > definition of electric fields > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > ------------------------------ > > Message: 7 > Date: Mon, 15 Jun 2009 13:13:13 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] fileutil ? > To: PWSCF Forum > Message-ID: <1C080D0E-8CD7-4A48-A073-11BC40E49267 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > On Jun 15, 2009, at 11:48 , Nicola Marzari wrote: > >> 2) is it correct that the new source for the QE snapshots is the >> qe-forge CVS, and the old CVS is not maintained > > correct. The user guide and developer manual on the wiki report > the obsolete CVS location, because they are in turn no longer > maintained: they have been brought back to the CVS tree. > An updated version will be put on line when the new version > will be released. > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > ------------------------------ > > Message: 8 > Date: Mon, 15 Jun 2009 13:20:52 +0200 > From: hichem bouderba > Subject: [Pw_forum] ld1.x testing mode > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > dear all, > in INPUT_LD1.html about ecutmin,ecutmax,decut we have : > " > Parameters (Ry) used for test with a basis set of spherical > Bessel functions j_l(qr) . The hamiltonian at fixed scf > potential is diagonalized for various values of ecut: > ecutmin, ecutmin+decut, ecutmin+2*decut ... up to ecutmax. > This yields an indication of convergence with the > corresponding plane-wave cutoff in solids, and shows > in an unambiguous way if there are "ghost" states > " > > how does ld1.x say "there is a ghost state somewhere" ? > > when testing a PAW with ld1.x I have the following error: > > " > Cutoff (Ry) : 50.0 > N = 1 N = 2 N = 3 > E(L=0) = -3.2666 Ry -0.2491 Ry -0.0148 Ry > E(L=1) = -1.8963 Ry -0.0931 Ry 0.0105 Ry > E(L=2) = -0.0637 Ry 0.0203 Ry 0.0602 Ry > > Cutoff (Ry) : 55.0 > N = 1 N = 2 N = 3 > E(L=0) = -3.2666 Ry -0.2491 Ry -0.0148 Ry > E(L=1) = -1.8963 Ry -0.0931 Ry 0.0105 Ry > E(L=2) = -0.0637 Ry 0.0203 Ry 0.0601 Ry > > Cutoff (Ry) : 60.0 > N = 1 N = 2 N = 3 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from rdiags : error # 73 > failed to converge (factorization) > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > " > what does it mean ? > thanks. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090615/11d6c36f/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 24, Issue 30 > **************************************** > -- peace,yoseph From jjr19 at uakron.edu Tue Jun 16 18:04:27 2009 From: jjr19 at uakron.edu (J. J. Ramsey) Date: Tue, 16 Jun 2009 09:04:27 -0700 (PDT) Subject: [Pw_forum] File closing errors when using NEB image parallelization In-Reply-To: References: <14450.35591.qm@web50912.mail.re2.yahoo.com> <880917.27758.qm@web50903.mail.re2.yahoo.com> Message-ID: <419763.82623.qm@web50910.mail.re2.yahoo.com> ----- Original Message ---- > If I had to bet I would say you are using ~/tmp as the default directory, > and it is a normal NFS share. Actually, it's a subdirectory under /usr/var/tmp, and to the best of my knowledge, it is not an NFS share. There is a bit more info, here: http://www.arl.hpc.mil/Systems/mjm_docs.html#fs Also, I had even tried out my problem on an entirely different cluster which uses the Parallel File System (http://www.osc.edu/supercomputing/computing/pvfs/index.shtml) and got the same problems. From marzari at MIT.EDU Tue Jun 16 18:27:07 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Tue, 16 Jun 2009 12:27:07 -0400 Subject: [Pw_forum] How to start and use QE open source simulation In-Reply-To: References: Message-ID: <4A37C7DB.1030803@mit.edu> yoseph Getachew wrote: > Dear All , > > sorry but this is a very low level question. > > would you please inform me as to how i can install,configure, and make > all the necessary steps so that i can be able to run simulations. i > have tried to use the QE website but i ended up in so much more > inconsistencies. > > for example where and how can i get and install fortan and c.xcrysden > which binary or static files should i use and how should i install them. > > i need your specific advise on this to catch up with everybody. > > Regards, > Yoseph Getachew > ArbaMinch University, > Department of Physics Hi Yoseph, it looks like you need to start with some basics on Linux. Do you have anyone familiar with that in the Department, or can you access some online guide ? People might have better suggestions here. At a minimum, to install Quantum ESPRESSO you need a Fortran compiler, and (I think) a C compiler. The Intel fortran and c compilers are very efficient, but would need to be downloaded from the Intel site (I have left a copy of those at Addis Abeba, not sure if it is still there - contact SibKrishna Ghoshal ). gfortran and gcc would be standard alternatives, available from many Linux distributions. nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From Giovanni.Cantele at na.infn.it Tue Jun 16 18:27:25 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Tue, 16 Jun 2009 18:27:25 +0200 Subject: [Pw_forum] How to start and use QE open source simulation In-Reply-To: References: Message-ID: <4A37C7ED.5060305@na.infn.it> yoseph Getachew wrote: > Dear All , > > sorry but this is a very low level question. > > would you please inform me as to how i can install,configure, and make > all the necessary steps so that i can be able to run simulations. i > have tried to use the QE website but i ended up in so much more > inconsistencies. > actually, it is rather hard to help you, due to loss of information. Which kind of inconsistencies? In compiling QE? At run time? It seems to me that lot of information can be found here: http://www.quantum-espresso.org/wiki/index.php/Installation there are also compiler/architecture-related issues mentioned there. The user guide is also reported within the distribution (Doc/user_guide.html). > for example where and how can i get and install fortan and c. on which system? Do you have a Linux distribution? Maybe ubuntu? I've the Intel fortran/C compiler that I freely downloaded from the Intel web site, I guest it is still free. Another possibility is gfortran, I would install it on my PC using sudo apt-get install gfortran but a different command is needed for other linux distributions. > xcrysden > which binary or static files should i use and how should i install them. > are you sure that what reported on the web site is useless for you? Go to (did you already do it?) http://www.xcrysden.org/doc/install.html I find many sections: *Installation Instructions * */How to Install the Compiled Package /* /FOR IMPATIENT: minimal installation instructions / /A Bit Longer Installation Instructions / /What xcConfigure does? / */How to Install the Source Package /* /Trouble Shooting / Someone also had the patience to suggest installation instructions for both impatient and patient users!!!!! Did you follow all the suggested steps, and in case which was the one failing? > i need your specific advise on this to catch up with everybody. > > Regards, > Yoseph Getachew > ArbaMinch University, > Department of Physics > > > Best regards, Giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it Skype contact: giocan74 From hqzhou at nju.edu.cn Wed Jun 17 09:05:37 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Wed, 17 Jun 2009 15:05:37 +0800 Subject: [Pw_forum] Elastic Constant. References: <3a749910906131300y5e92e22fl283eac075b5670f0@mail.gmail.com> <9041FC3A-E8F9-416C-953F-14097C1553A7@sissa.it> Message-ID: Stefano, The straightforward approach is tedious for orthorgonal, monolinic, trilinic systems. Should the lost implementation gain in these respects? Huiqun Zhou @Earth Sciences, Nanjing University, China ----- Original Message ----- From: "Stefano Baroni" To: "PWSCF Forum" Sent: Sunday, June 14, 2009 6:01 PM Subject: Re: [Pw_forum] Elastic Constant. > Dear Bipul, > > long ago there used to be an implementation of the linear-response > approach to elastic constants by SB, Giannozzi, and Testa: > % Copyright (C) 2009 The American Physical Society > % Please report any problems to prola at aps.org > > @Article{PhysRevLett.59.2662, > title = {Elastic Constants of Crystals from Linear-Response Theory}, > author = {Baroni, Stefano and Giannozzi, Paolo and Testa, Andrea }, > journal = {Phys. Rev. Lett.}, > volume = {59}, > number = {23}, > pages = {2662--2665}, > numpages = {3}, > year = {1987}, > month = {Dec}, > doi = {10.1103/PhysRevLett.59.2662}, > publisher = {American Physical Society} > } > This is no longer available, partly because of the programmers' > lazyness, partly because there is not much to be gained with respect > to the straightforward approach you are following. > > Stefano B > > > On Jun 13, 2009, at 10:00 PM, Bipul Rakshit wrote: > >> Dear Pwscf user, >> I want to calculate the elastic constants for cubic structure for >> LaSb, which is having NaCl structure. Although I have written a small >> script for doing that. But if anybody develop any code, do he/she like >> to share, so that I can compare my results. >> Thanks >> -- >> Bipul Rakshit >> PhD Student, >> Barkatullah University, >> Bhopal 462026, >> MP, India >> _______________________________________________ >> 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 hqzhou at nju.edu.cn Wed Jun 17 08:36:39 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Wed, 17 Jun 2009 14:36:39 +0800 Subject: [Pw_forum] Elastic Constant. References: <3a749910906131300y5e92e22fl283eac075b5670f0@mail.gmail.com> <9041FC3A-E8F9-416C-953F-14097C1553A7@sissa.it> Message-ID: Stefano, The straightforward approach is tedious for orthorgonal, monolinic, trilinic systems. Should the lost implementation gain in these respects? Huiqun Zhou @Earth Sciences, Nanjing University, China ----- Original Message ----- From: "Stefano Baroni" To: "PWSCF Forum" Sent: Sunday, June 14, 2009 6:01 PM Subject: Re: [Pw_forum] Elastic Constant. > Dear Bipul, > > long ago there used to be an implementation of the linear-response > approach to elastic constants by SB, Giannozzi, and Testa: > % Copyright (C) 2009 The American Physical Society > % Please report any problems to prola at aps.org > > @Article{PhysRevLett.59.2662, > title = {Elastic Constants of Crystals from Linear-Response Theory}, > author = {Baroni, Stefano and Giannozzi, Paolo and Testa, Andrea }, > journal = {Phys. Rev. Lett.}, > volume = {59}, > number = {23}, > pages = {2662--2665}, > numpages = {3}, > year = {1987}, > month = {Dec}, > doi = {10.1103/PhysRevLett.59.2662}, > publisher = {American Physical Society} > } > This is no longer available, partly because of the programmers' > lazyness, partly because there is not much to be gained with respect > to the straightforward approach you are following. > > Stefano B > > > On Jun 13, 2009, at 10:00 PM, Bipul Rakshit wrote: > >> Dear Pwscf user, >> I want to calculate the elastic constants for cubic structure for >> LaSb, which is having NaCl structure. Although I have written a small >> script for doing that. But if anybody develop any code, do he/she like >> to share, so that I can compare my results. >> Thanks >> -- >> Bipul Rakshit >> PhD Student, >> Barkatullah University, >> Bhopal 462026, >> MP, India >> _______________________________________________ >> 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 hqzhou at nju.edu.cn Wed Jun 17 09:02:09 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Wed, 17 Jun 2009 15:02:09 +0800 Subject: [Pw_forum] Elastic Constant. References: <3a749910906131300y5e92e22fl283eac075b5670f0@mail.gmail.com> <9041FC3A-E8F9-416C-953F-14097C1553A7@sissa.it> Message-ID: Stefano, The straightforward approach is tedious for orthorgonal, monolinic, trilinic systems. Should the lost implementation gain in these respects? Huiqun Zhou @Earth Sciences, Nanjing University, China ----- Original Message ----- From: "Stefano Baroni" To: "PWSCF Forum" Sent: Sunday, June 14, 2009 6:01 PM Subject: Re: [Pw_forum] Elastic Constant. > Dear Bipul, > > long ago there used to be an implementation of the linear-response > approach to elastic constants by SB, Giannozzi, and Testa: > % Copyright (C) 2009 The American Physical Society > % Please report any problems to prola at aps.org > > @Article{PhysRevLett.59.2662, > title = {Elastic Constants of Crystals from Linear-Response Theory}, > author = {Baroni, Stefano and Giannozzi, Paolo and Testa, Andrea }, > journal = {Phys. Rev. Lett.}, > volume = {59}, > number = {23}, > pages = {2662--2665}, > numpages = {3}, > year = {1987}, > month = {Dec}, > doi = {10.1103/PhysRevLett.59.2662}, > publisher = {American Physical Society} > } > This is no longer available, partly because of the programmers' > lazyness, partly because there is not much to be gained with respect > to the straightforward approach you are following. > > Stefano B > > > On Jun 13, 2009, at 10:00 PM, Bipul Rakshit wrote: > >> Dear Pwscf user, >> I want to calculate the elastic constants for cubic structure for >> LaSb, which is having NaCl structure. Although I have written a small >> script for doing that. But if anybody develop any code, do he/she like >> to share, so that I can compare my results. >> Thanks >> -- >> Bipul Rakshit >> PhD Student, >> Barkatullah University, >> Bhopal 462026, >> MP, India >> _______________________________________________ >> 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 hqzhou at nju.edu.cn Wed Jun 17 09:20:30 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Wed, 17 Jun 2009 15:20:30 +0800 Subject: [Pw_forum] Apology Message-ID: <7EEB4B700D6348C6861653383E296E29@RAPIDMIND> Dear list users, I apologize for sending out a post three times because of a configuration problem in my mail client. I tried twice so that there were already two unsent mails in my outbox. After I fixed the setting problem, I forgot to delete the two and tried again, so you may have received my three equivalent posts. I'm sorry for the inconvenience and apologize again. Huiqun Zhou @Earth Sciences, Nanjing University, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090617/9028e2d3/attachment.htm From ustc0200 at gmail.com Wed Jun 17 09:35:43 2009 From: ustc0200 at gmail.com (Zhu Xi) Date: Wed, 17 Jun 2009 15:35:43 +0800 Subject: [Pw_forum] Apology In-Reply-To: <7EEB4B700D6348C6861653383E296E29@RAPIDMIND> References: <7EEB4B700D6348C6861653383E296E29@RAPIDMIND> Message-ID: you are welcome . 2009/6/17, Huiqun Zhou : > > Dear list users, > > I apologize for sending out a post three times because of > a configuration problem in my mail client. I tried twice > so that there were already two unsent mails in my outbox. > After I fixed the setting problem, I forgot to delete the > two and tried again, so you may have received my three > equivalent posts. > > I'm sorry for the inconvenience and apologize again. > > Huiqun Zhou > @Earth Sciences, Nanjing University, China > > > > _______________________________________________ > 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/20090617/bb86d9c6/attachment.htm From sagarambavale at yahoo.co.in Wed Jun 17 10:10:50 2009 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Wed, 17 Jun 2009 13:40:50 +0530 (IST) Subject: [Pw_forum] Pw_forum Digest, Vol 24, Issue 30 In-Reply-To: References: Message-ID: <688347.44460.qm@web94614.mail.in2.yahoo.com> Dear Gabriele and smogunov, Yes, I do use Al- wire of finite width as reported in smogunov's 2004 paper. In this case what should be the k-pt grid for scf calculation? {for conductance calculation k_perp is set to 1} When doing calcuIation with electrode infinite in xy plane, is it necessary to use same k-pt grid for conductance and scf calculation? When doing PDOS calculation of molecule, is the gamma point calculation sufficient? Thanking you. Sagar Ambavale ---------------------------------------------------------------------- Message: 1 Date: Mon, 15 Jun 2009 09:04:03 +0200 From: Gabriele Sclauzero Subject: Re: [Pw_forum] homo-lumo and conductance To: PWSCF Forum Message-ID: <4A35F263.9020205 at sissa.it> Content-Type: text/plain; charset=ISO-8859-1; format=flowed ambavale sagar wrote: > Dear Gabriele, > Thank you for your reply. I refered to smogunov paper but I could not > understand the sentence used there : "Since the system has the supercell > (artificial) 2D periodicity in the xy plane, perpendicular to the > transport direction, we averaged the transmission over the corresponding > 2D BZ using 21 k points in the irreducible part of the BZ..." Are those > 21 k-pts belong to xy plane only? what type of grid that may be? 6 6 2 1 > 1 1 ? > In my case supercell dimensions in x and y are 25 a.u. i.e. ~12 ang > which includes nearly ~9 ang. of vaccum. Here Alexander already replied you. So your k_perpendicular points sampling depends if you want to study an isolated wire (thick or monoatomic), or a wire/molecule between realistic electrodes (modeled as surfaces or surfaces+tips attached to them). In the former case, if your supercell is large enough in the directions perpendicular to the transport the transmission should not depend on k_perp and you need only one k_perp-point. In the latter you need to sample accurately the 2D BZ, since the transmission depends (a lot in some cases) on k_perp. > > As you mentioned the limitation of DFT due to xc-functional, can I use > DFT calculation to compare qualitatively the Transmission coefficient of > same molecule with different geometries? I cannot say, actually. It depends on the coupling and other details. You can have a look to the recent work by Thygesen and Rubio, which try to include a GW correction in this kind of calculations. > > would you please mention in detail how to find positions of HOMO, LUMO > in a coupled system? What I would do (but fur sure there are many better methods) if I want to put, say, O_2 between electrodes is to look at the PDOS (computed by projwfc.x in the QE suite) projected onto the O atoms and compare it with the PDOS of the isolated O_2. It would give an idea of the level of hybridization between molecule and electrodes and of the position of the HOMO(LUMO)-derived levels. It could also be useful to look at the PDOS on the electrode atoms to understand which metallic states/atoms are more involved in the coupling.. regards, GS ICC World Twenty20 England '09 exclusively on YAHOO! CRICKET http://cricket.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090617/7d96b981/attachment.htm From sagarambavale at yahoo.co.in Wed Jun 17 10:13:57 2009 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Wed, 17 Jun 2009 13:43:57 +0530 (IST) Subject: [Pw_forum] homo-lumo and conductance Message-ID: <616570.72980.qm@web94613.mail.in2.yahoo.com> Sorry for previous mail with wrong subject line. Dear Gabriele and Smogunov, Yes, I do use Al- wire of finite width as reported in smogunov's 2004 paper. In this case what should be the k-pt grid for scf calculation? {for conductance calculation k_perp is set to 1} When doing calcuIation with electrode infinite in xy plane, is it necessary to use same k-pt grid for conductance and scf calculation? When doing PDOS calculation of molecule, is the gamma point calculation sufficient? Thanking you. Sagar Ambavale ---------------------------------------------------------------------- Message: 1 Date: Mon, 15 Jun 2009 09:04:03 +0200 From: Gabriele Sclauzero Subject: Re: [Pw_forum] homo-lumo and conductance To: PWSCF Forum Message-ID: <4A35F263.9020205 at sissa.it> Content-Type: text/plain; charset=ISO-8859-1; format=flowed ambavale sagar wrote: > Dear Gabriele, > Thank you for your reply. I refered to smogunov paper but I could not > understand the sentence used there : "Since the system has the supercell > (artificial) 2D periodicity in the xy plane, perpendicular to the > transport direction, we averaged the transmission over the corresponding > 2D BZ using 21 k points in the irreducible part of the BZ.." Are those > 21 k-pts belong to xy plane only? what type of grid that may be? 6 6 2 1 > 1 1 ? > In my case supercell dimensions in x and y are 25 a.u. i.e. ~12 ang > which includes nearly ~9 ang. of vaccum. Here Alexander already replied you. So your k_perpendicular points sampling depends if you want to study an isolated wire (thick or monoatomic), or a wire/molecule between realistic electrodes (modeled as surfaces or surfaces+tips attached to them). In the former case, if your supercell is large enough in the directions perpendicular to the transport the transmission should not depend on k_perp and you need only one k_perp-point. In the latter you need to sample accurately the 2D BZ, since the transmission depends (a lot in some cases) on k_perp. > > As you mentioned the limitation of DFT due to xc-functional, can I use > DFT calculation to compare qualitatively the Transmission coefficient of > same molecule with different geometries? I cannot say, actually. It depends on the coupling and other details. You can have a look to the recent work by Thygesen and Rubio, which try to include a GW correction in this kind of calculations. > > would you please mention in detail how to find positions of HOMO, LUMO > in a coupled system? What I would do (but fur sure there are many better methods) if I want to put, say, O_2 between electrodes is to look at the PDOS (computed by projwfc.x in the QE suite) projected onto the O atoms and compare it with the PDOS of the isolated O_2. It would give an idea of the level of hybridization between molecule and electrodes and of the position of the HOMO(LUMO)-derived levels. It could also be useful to look at the PDOS on the electrode atoms to understand which metallic states/atoms are more involved in the coupling. regards, GS ________________________________ ICC World Twenty20 England '09 exclusively on YAHOO! CRICKET Explore your hobbies and interests. Go to http://in.promos.yahoo.com/groups/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090617/1836c324/attachment.htm From sclauzer at sissa.it Wed Jun 17 10:32:39 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 17 Jun 2009 10:32:39 +0200 Subject: [Pw_forum] homo-lumo and conductance In-Reply-To: <616570.72980.qm@web94613.mail.in2.yahoo.com> References: <616570.72980.qm@web94613.mail.in2.yahoo.com> Message-ID: <4A38AA27.2090906@sissa.it> ambavale sagar wrote: > Sorry for previous mail with wrong subject line. > > Dear Gabriele and Smogunov, > Yes, I do use Al- wire of finite width as reported in smogunov's 2004 > paper. In this case what should be the k-pt grid for scf calculation? > {for conductance calculation k_perp is set to 1} For an isolated monoatomic wire or finite cross section electrode (or thick wire) you choose kx=ky=1, kz="a number large enough, such that the total energy and other interesting physical quantities are converged within your target accuracy". > When doing calcuIation with electrode infinite in xy plane, is it > necessary to use same k-pt grid for conductance and scf calculation? kx=ky=some number, which needs not to be the same in scf and transmission calculations. In the former case you have to converge the total energy, in the latter the transmission (you need to check both convergences by increasing kx=ky and looking at the result). Be aware that the convergence of the transmission may depend a lot on the scattering energy in some cases. > When doing PDOS calculation of molecule, is the gamma point calculation > sufficient? Yes, if the molecule is isolated. GS > > Thanking you. > > Sagar Ambavale > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 15 Jun 2009 09:04:03 +0200 > From: Gabriele Sclauzero > > Subject: Re: [Pw_forum] homo-lumo and conductance > To: PWSCF Forum > > Message-ID: <4A35F263.9020205 at sissa.it > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > ambavale sagar wrote: > > Dear Gabriele, > > Thank you for your reply. I refered to smogunov paper but I could not > > understand the sentence used there : "Since the system has the supercell > > (artificial) 2D periodicity in the xy plane, perpendicular to the > > transport direction, we averaged the transmission over the corresponding > > 2D BZ using 21 k points in the irreducible part of the BZ.." Are those > > 21 k-pts belong to xy plane only? what type of grid that may be? 6 6 2 1 > > 1 1 ? > > In my case supercell dimensions in x and y are 25 a..u. i.e. ~12 ang > > which includes nearly ~9 ang. of vaccum. > > Here Alexander already replied you. So your k_perpendicular points > sampling depends if you > want to study an isolated wire (thick or monoatomic), or a wire/molecule > between realistic > electrodes (modeled as surfaces or surfaces+tips attached to them). In > the former case, if > your supercell is large enough in the directions perpendicular to the > transport the > transmission should not depend on k_perp and you need only one > k_perp-point. In the latter > you need to sample accurately the 2D BZ, since the transmission depends > (a lot in some > cases) on k_perp. > > > > > As you mentioned the limitation of DFT due to xc-functional, can I use > > DFT calculation to compare qualitatively the Transmission coefficient of > > same molecule with different geometries? > > I cannot say, actually. It depends on the coupling and other details. > You can have a look > to the recent work by Thygesen and Rubio, which try to include a GW > correction in this > kind of calculations. > > > > > would you please mention in detail how to find positions of HOMO, LUMO > > in a coupled system? > > What I would do (but fur sure there are many better methods) if I want > to put, say, O_2 > between electrodes is to look at the PDOS (computed by projwfc.x in the > QE suite) > projected onto the O atoms and compare it with the PDOS of the isolated > O_2. It would give > an idea of the level of hybridization between molecule and electrodes > and of the position > of the HOMO(LUMO)-derived levels. > It could also be useful to look at the PDOS on the electrode atoms to > understand which > metallic states/atoms are more involved in the coupling. > > regards, > > GS > > > > > ------------------------------------------------------------------------ > ICC World Twenty20 England '09 exclusively on YAHOO! CRICKET > > > ------------------------------------------------------------------------ > Cricket on your mind? Visit the ultimate cricket website. Enter now! > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Wed Jun 17 10:43:15 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 17 Jun 2009 10:43:15 +0200 Subject: [Pw_forum] Elastic Constant. In-Reply-To: References: <3a749910906131300y5e92e22fl283eac075b5670f0@mail.gmail.com> <9041FC3A-E8F9-416C-953F-14097C1553A7@sissa.it> Message-ID: <4A38ACA3.7020600@democritos.it> Huiqun Zhou wrote: > The straightforward approach is tedious for orthogonal, monoclinic, triclinic > systems. Should the lost implementation gain in these respects? the lost implementation was written only for the cubic case and only for the bulk modulus, if I remember correctly. Extending it to low-symmetry cases would also be tedious! Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Wed Jun 17 11:32:41 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 17 Jun 2009 11:32:41 +0200 Subject: [Pw_forum] File closing errors when using NEB image parallelization In-Reply-To: <419763.82623.qm@web50910.mail.re2.yahoo.com> References: <14450.35591.qm@web50912.mail.re2.yahoo.com> <880917.27758.qm@web50903.mail.re2.yahoo.com> <419763.82623.qm@web50910.mail.re2.yahoo.com> Message-ID: In data 16 giugno 2009 alle ore 18:04:27, J. J. Ramsey ha scritto: > Also, I had even tried out my problem on an entirely different cluster > which uses the Parallel File System > (http://www.osc.edu/supercomputing/computing/pvfs/index.shtml) and got > the same problems. I've looked at your problem from all possible directions but I cannot find any way it could fail! Apparently it is quite simple code. I wasn't able to replicate you problem even by forcing two threads to close the same file several times each! Could you please provide more information on the compilers you have used on the two different cluster, the exact command line you have used to start the job (are you using pools?) and the output of the "env" command from pw.x point of view (i.e. you put env in you job's script). Finally, please take no offense if this sound like a stupid suggestion; the only way I could reproduce you problem was to run multiple copies of a serial-compiled executables via mpirun. Could you please double-check it is not your case? cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From jjr19 at uakron.edu Wed Jun 17 16:25:27 2009 From: jjr19 at uakron.edu (J. J. Ramsey) Date: Wed, 17 Jun 2009 07:25:27 -0700 (PDT) Subject: [Pw_forum] File closing errors when using NEB image parallelization In-Reply-To: References: <14450.35591.qm@web50912.mail.re2.yahoo.com> <880917.27758.qm@web50903.mail.re2.yahoo.com> <419763.82623.qm@web50910.mail.re2.yahoo.com> Message-ID: <967475.669.qm@web50909.mail.re2.yahoo.com> ----- Original Message ---- > Could you please provide more information on the compilers you have used > on the two different cluster On the MJM cluster (http://www.arl.hpc.mil/Systems/mjm.html), the compiler is ifort 11.0, and the LAPACK used is the *sequential* version of MKL 10.1. The MPI implementation used was OpenMPI 1.2.9. On the OSC BALE cluster (http://www.osc.edu/supercomputing/computing/bale/), the compiler was ifort 9.1, and the LAPACK used was the one bundled with the QE tarball. The MPI implementation was MVAPICH 0.9.9. > the exact command line you have used to > start the job (are you using pools?) The exact commands are as follows. On MJM: mpirun.lsf ./pw.x -nimage 3 -in "smallerProb_PWscfNEB2_c18_v10_k4.in" > "smallerProb_PWscfNEB2_c18_v10_k4.out" 2> "smallerProb_PWscfNEB2_c18_v10_k4.err" On BALE: mpiexec "$TMPDIR/pw.x" -nimage 3 -in smallerProb_PWscfNEB2_c18_v10_k4.in > smallerProb_PWscfNEB2_c18_v10_k4.out 2> smallerProb_PWscfNEB2_c18_v10_k4.err > and the output of the "env" command > from pw.x point of view (i.e. you put env in you job's script). These are attached > Finally, please take no offense if this sound like a stupid suggestion; > the only way I could reproduce you problem was to run multiple copies of a > serial-compiled executables via mpirun. Could you please double-check it > is not your case? They definitely were not compiled serially. Here is the first few lines of the output file, which is the same for both MJM and BALE (except for the date at the top): Program PWSCF v.4.0.5 starts ... Today is 17Jun2009 at 8:44:24 Parallel version (MPI) Number of processors in use: 24 path-images division: nimage = 3 R & G space division: proc/pool = 8 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW 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 initial path length = 7.5354 bohr initial inter-image distance = 1.8838 bohr calculation = neb restart_mode = from_scratch opt_scheme = broyden num_of_images = 5 nstep = 50 CI_scheme = no-CI first_last_opt = F coarse-grained phase-space = F use_freezing = F ds = 1.0000 a.u. k_max = 0.6169 a.u. k_min = 0.6169 a.u. suggested k_max = 0.6169 a.u. suggested k_min = 0.6169 a.u. path_thr = 0.0500 eV / A -------------- next part -------------- A non-text attachment was scrubbed... Name: BALE-my_env_vars.out.gz Type: application/x-gzip Size: 1352 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090617/3ab5625e/attachment.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: MJM-my_env_vars.out.gz Type: application/x-gzip Size: 2476 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090617/3ab5625e/attachment-0001.bin From chenweiguang82 at gmail.com Wed Jun 17 18:12:45 2009 From: chenweiguang82 at gmail.com (Weiguang Chen) Date: Thu, 18 Jun 2009 00:12:45 +0800 Subject: [Pw_forum] Which part is the main potential for obtaining the work function? Message-ID: <9e6d976a0906170912u19037a81l2c2b8d652341eeb1@mail.gmail.com> Hi, We know the potential of a solid state consists of V_bare(atomic core), V_hartree(Hartree contribution) and V_xc(exchange correalation) and so on. I want to know which component is the main source when we try to get the work function. Thanks -- Best Wishes ChenWeiguang ************************************************ # Chen, Weiguang # # Postgraduate, Ph. D # 75 University Road, Physics Buliding # 218 # School of Physics & Engineering # Zhengzhou University # Zhengzhou, Henan 450052 CHINA # # Tel: 86-13203730117; # E-mail:chenweiguang82 at gmail.com ; # chenweiguang82 at qq.com #********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090618/243f0e71/attachment.htm From paulatto at sissa.it Wed Jun 17 18:45:34 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 17 Jun 2009 18:45:34 +0200 Subject: [Pw_forum] Which part is the main potential for obtaining the work function? In-Reply-To: <9e6d976a0906170912u19037a81l2c2b8d652341eeb1@mail.gmail.com> References: <9e6d976a0906170912u19037a81l2c2b8d652341eeb1@mail.gmail.com> Message-ID: In data 17 giugno 2009 alle ore 18:12:45, Weiguang Chen ha scritto: > We know the potential of a solid state consists of V_bare(atomic core), > V_hartree(Hartree contribution) and V_xc(exchange correalation) and so > on. I want to know which component is the main source when we try to get > the work function. The first and the second together (plot_num=11, in pp.x); please see the example WorkFct_example in the examples/ directory of quantum-espresso regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From mastermik at gmail.com Wed Jun 17 20:40:05 2009 From: mastermik at gmail.com (Mikiyas Tsegaye) Date: Wed, 17 Jun 2009 14:40:05 -0400 Subject: [Pw_forum] phonon dispersion calculation abruptly stops Message-ID: <641C7CFB-A7E5-4B32-9B5A-27055E562471@gmail.com> Hello, I'm trying to calculate phonon dispersion for Germanium. I have the pw.x and ph.x inputs prepared as follows: ********************************************************************************************************* &control calculation='scf', restart_mode='from_scratch', prefix='FF', tprnfor = .true., pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav = 2, celldm(1) =10.56, nat= 2, ntyp= 1, ecutwfc = 22.0 / &electrons mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Ge 72.64 Ge.pz-bhs.UPF ATOMIC_POSITIONS Ge 0.00 0.00 0.00 Ge 0.25 0.25 0.25 K_POINTS 10 0.1250000 0.1250000 0.1250000 1.00 0.1250000 0.1250000 0.3750000 3.00 0.1250000 0.1250000 0.6250000 3.00 0.1250000 0.1250000 0.8750000 3.00 0.1250000 0.3750000 0.3750000 3.00 0.1250000 0.3750000 0.6250000 6.00 0.1250000 0.3750000 0.8750000 6.00 0.1250000 0.6250000 0.6250000 3.00 0.3750000 0.3750000 0.3750000 1.00 0.3750000 0.3750000 0.6250000 3.00 EOF $ECHO " running pw.x to calculate scf...\c" $PW_COMMAND < Ge.scfK.in > Ge.scfK.out check_failure $? $ECHO "done" # try the whole dispersion cat > Ge.phG.in << EOF phonons of germanium &INPUTPH amass(1) = 72.640, outdir = '$TMP_DIR/', prefix = 'FF', tr2_ph = 1.0d-14, fildyn = 'FF.dynG', ldisp = .true., nq1 = 6, nq2 = 6, nq3 = 6, / EOF $ECHO " running ph.x to calculate gamma phonons...\c" $PH_COMMAND < Ge.phG.in > Ge.phG.out check_failure $? $ECHO "done" ******************************************************************************************* Now, the scf step finishes succesfully, but the ph.x step only finishes up to a certain point: It crashes with "segementation fault". The output file Ge.phG.out shows the following: ************************************************************ Program PHONON v.4.0.5 starts ... Today is 17Jun2009 at 10:43:58 Ultrasoft (Vanderbilt) Pseudopotentials Dynamical matrices for ( 6, 6, 6,) uniform grid of q-points ( 16q-points): N xq(1) xq(2) xq(3) 1 0.00000 0.00000 0.00000 2 -0.16667 0.16667 -0.16667 3 -0.33333 0.33333 -0.33333 4 0.50000 -0.50000 0.50000 5 0.00000 0.33333 0.00000 6 -0.16667 0.50000 -0.16667 7 0.66667 -0.33333 0.66667 8 0.50000 -0.16667 0.50000 9 0.33333 0.00000 0.33333 10 0.00000 0.66667 0.00000 11 0.83333 -0.16667 0.83333 12 0.66667 -0.00000 0.66667 13 0.00000 -1.00000 0.00000 14 0.66667 -0.33333 1.00000 15 0.50000 -0.16667 0.83333 16 -0.33333 -1.00000 0.00000 bravais-lattice index = 2 lattice parameter (a_0) = 10.5600 a.u. unit-cell volume = 294.3959 (a.u.)^3 number of atoms/cell = 2 number of atomic types = 1 kinetic-energy cut-off = 22.0000 Ry charge density cut-off = 88.0000 Ry convergence threshold = 1.0E-14 beta = 0.7000 number of iterations used = 4 Exchange-correlation = SLA PZ NOGX NOGC (1100) celldm(1)= 10.56000 celldm(2)= 0.00000 celldm(3)= 0.00000 celldm(4)= 0.00000 celldm(5)= 0.00000 celldm(6)= 0.00000 crystal axes: (cart. coord. in units of a_0) a(1) = ( -0.5000 0.0000 0.5000 ) a(2) = ( 0.0000 0.5000 0.5000 ) a(3) = ( -0.5000 0.5000 0.0000 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( -1.0000 -1.0000 1.0000 ) b(2) = ( 1.0000 1.0000 1.0000 ) b(3) = ( -1.0000 1.0000 -1.0000 ) Atoms inside the unit cell: Cartesian axes site n. atom mass positions (a_0 units) 1 Ge 72.6400 tau( 1) = ( 0.00000 0.00000 0.00000 ) 2 Ge 72.6400 tau( 2) = ( 0.25000 0.25000 0.25000 ) Computing dynamical matrix for q = ( 0.00000 0.00000 0.00000 ) 49 Sym.Ops. (with q -> -q+G ) G cutoff = 248.5712 ( 4111 G-vectors) FFT grid: ( 24, 24, 24) number of k points= 10 cart. coord. in units 2pi/a_0 k( 1) = ( 0.1250000 0.1250000 0.1250000), wk = 0.0625000 k( 2) = ( 0.1250000 0.1250000 0.3750000), wk = 0.1875000 k( 3) = ( 0.1250000 0.1250000 0.6250000), wk = 0.1875000 k( 4) = ( 0.1250000 0.1250000 0.8750000), wk = 0.1875000 k( 5) = ( 0.1250000 0.3750000 0.3750000), wk = 0.1875000 k( 6) = ( 0.1250000 0.3750000 0.6250000), wk = 0.3750000 k( 7) = ( 0.1250000 0.3750000 0.8750000), wk = 0.3750000 k( 8) = ( 0.1250000 0.6250000 0.6250000), wk = 0.1875000 k( 9) = ( 0.3750000 0.3750000 0.3750000), wk = 0.0625000 k( 10) = ( 0.3750000 0.3750000 0.6250000), wk = 0.1875000 PseudoPot. # 1 for Ge read from file Ge.pz-bhs.UPF Pseudo is Norm-conserving, Zval = 4.0 Generated by new atomic code, or converted to UPF format Using radial grid of 291 points, 2 beta functions with: l(1) = 0 l(2) = 1 Atomic displacements: There are 2 irreducible representations Representation 1 3 modes - To be done Representation 2 3 modes - To be done PHONON : 0.51s CPU time, 0.58s wall time Alpha used in Ewald sum = 0.9000 Electric Fields Calculation ********************************************************************* Can anyone tell me why this is happening? --------- Mikiyas Tsegaye University of Virginia Department of Electrical and Computer Engineering Charlottesville, VA, USA From giannozz at democritos.it Wed Jun 17 22:16:26 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 17 Jun 2009 22:16:26 +0200 Subject: [Pw_forum] phonon dispersion calculation abruptly stops In-Reply-To: <641C7CFB-A7E5-4B32-9B5A-27055E562471@gmail.com> References: <641C7CFB-A7E5-4B32-9B5A-27055E562471@gmail.com> Message-ID: <815DDA55-5A2B-4A62-9068-27C7CBCAB493@democritos.it> On Jun 17, 2009, at 20:40 , Mikiyas Tsegaye wrote: > Can anyone tell me why this is happening? if it works on a different machine: lousy compiler P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From eyvaz_isaev at yahoo.com Wed Jun 17 22:35:26 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 17 Jun 2009 13:35:26 -0700 (PDT) Subject: [Pw_forum] phonon dispersion calculation abruptly stops Message-ID: <327508.99269.qm@web65712.mail.ac4.yahoo.com> Dear Mikiyas, --- On Wed, 6/17/09, Mikiyas Tsegaye wrote: Let us analyse your input files. Here is a sketch of your scf-input: > &system > ibrav = 2, celldm(1) =10.56, nat=? 2, > ntyp= 1, ecutwfc = 22.0 That means you have a semiconductor (insulator). Now from ph-input: > ldisp = .true., > nq1 = 6, nq2 = 6, nq3 = 6, I suggest ph.x starts for "Electric Field Calculations", as it does not see the keywords specific for the metallic case, but can not do it as you did not specify epsil=.true., i.e. calculate electric field corrections. By default epsil=.false., i.e. do not calculate "Electric Field Calculations" (sorry for some tautology) and then ph.x stops (most likely). A short note on the mail subject: it is not connected with "phonon dispersion" calculations, this script produces only dynamical matricies for the q-mesh specified by nq1,nq2,nq3. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Wed, 6/17/09, Mikiyas Tsegaye wrote: > From: Mikiyas Tsegaye > Subject: [Pw_forum] phonon dispersion calculation abruptly stops > To: pw_forum at pwscf.org > Date: Wednesday, June 17, 2009, 10:40 PM > Hello, > > I'm trying to calculate phonon dispersion for Germanium. > I have the pw.x and ph.x inputs prepared as follows: > ********************************************************************************************************* > &control > ? ? calculation='scf', > ? ? restart_mode='from_scratch', > ? ? prefix='FF', > ? ? tprnfor = .true., > ? ? pseudo_dir = '$PSEUDO_DIR/', > ? ? outdir='$TMP_DIR/' > / > &system > ? ? ibrav = 2, celldm(1) =10.56, nat=? 2, > ntyp= 1, > ? ? ecutwfc = 22.0 > / > &electrons > ? ? mixing_beta = 0.7 > ? ? conv_thr =? 1.0d-8 > / > ATOMIC_SPECIES > Ge? 72.64? Ge.pz-bhs.UPF > ATOMIC_POSITIONS > Ge 0.00 0.00 0.00 > Ge 0.25 0.25 0.25 > K_POINTS > 10 > ???0.1250000? 0.1250000? > 0.1250000???1.00 > ???0.1250000? 0.1250000? > 0.3750000???3.00 > ???0.1250000? 0.1250000? > 0.6250000???3.00 > ???0.1250000? 0.1250000? > 0.8750000???3.00 > ???0.1250000? 0.3750000? > 0.3750000???3.00 > ???0.1250000? 0.3750000? > 0.6250000???6.00 > ???0.1250000? 0.3750000? > 0.8750000???6.00 > ???0.1250000? 0.6250000? > 0.6250000???3.00 > ???0.3750000? 0.3750000? > 0.3750000???1.00 > ???0.3750000? 0.3750000? > 0.6250000???3.00 > > EOF > $ECHO "? running pw.x to calculate scf...\c" > $PW_COMMAND < Ge.scfK.in > Ge.scfK.out > check_failure $? > $ECHO "done" > > # try the whole dispersion > cat > Ge.phG.in << EOF > phonons of germanium > &INPUTPH > amass(1) = 72.640, > outdir = '$TMP_DIR/', > prefix = 'FF', > tr2_ph = 1.0d-14, > fildyn = 'FF.dynG', > ldisp = .true., > nq1 = 6, nq2 = 6, nq3 = 6, > / > EOF > > $ECHO "? running ph.x to calculate gamma > phonons...\c" > $PH_COMMAND < Ge.phG.in > Ge.phG.out > check_failure $? > $ECHO "done" > > ******************************************************************************************* > Now, the scf step finishes succesfully, but the ph.x step > only? > finishes up to a certain point: It crashes with > "segementation fault".? > The output file Ge.phG.out shows the following: > > ************************************************************ > > > ? ???Program PHONON? ? > v.4.0.5? starts ... > ? ???Today is 17Jun2009 at 10:43:58 > > ? ???Ultrasoft (Vanderbilt) > Pseudopotentials > > > ? ???Dynamical matrices for ( 6, 6, 6,) > uniform grid of q-points > ? ???(? 16q-points): > ? ? ???N? ? > ???xq(1)? ? > ???xq(2)? ? > ???xq(3) > ? ? ???1? > ???0.00000? > ???0.00000? ???0.00000 > ? ? ???2? ? > -0.16667? ???0.16667? ? > -0.16667 > ? ? ???3? ? > -0.33333? ???0.33333? ? > -0.33333 > ? ? ???4? > ???0.50000? ? -0.50000? > ???0.50000 > ? ? ???5? > ???0.00000? > ???0.33333? ???0.00000 > ? ? ???6? ? > -0.16667? ???0.50000? ? > -0.16667 > ? ? ???7? > ???0.66667? ? -0.33333? > ???0.66667 > ? ? ???8? > ???0.50000? ? -0.16667? > ???0.50000 > ? ? ???9? > ???0.33333? > ???0.00000? ???0.33333 > ? ? ? 10? > ???0.00000? > ???0.66667? ???0.00000 > ? ? ? 11? > ???0.83333? ? -0.16667? > ???0.83333 > ? ? ? 12? > ???0.66667? ? -0.00000? > ???0.66667 > ? ? ? 13? > ???0.00000? ? -1.00000? > ???0.00000 > ? ? ? 14? > ???0.66667? ? -0.33333? > ???1.00000 > ? ? ? 15? > ???0.50000? ? -0.16667? > ???0.83333 > ? ? ? 16? ? -0.33333? ? > -1.00000? ???0.00000 > > > > ? ???bravais-lattice index? > ???=? ? ? ? ? ? > 2 > ? ???lattice parameter > (a_0)???=? ? ? 10.5600? > a.u. > ? ???unit-cell volume? ? > ? ? ? =? ???294.3959 > (a.u.)^3 > ? ???number of atoms/cell? ? > ? =? ? ? ? ? ? 2 > ? ???number of atomic types? > ? =? ? ? ? ? ? 1 > ? ???kinetic-energy cut-off? > ? =? ? ? 22.0000? Ry > ? ???charge density cut-off? > ? =? ? ? 88.0000? Ry > ? ???convergence threshold? > ???=? ? ? 1.0E-14 > ? ???beta? ? ? ? > ? ? ? ? ? ? ? =? > ? ???0.7000 > ? ???number of iterations used =? > ? ? ? ? ? 4 > ? ???Exchange-correlation? ? > ? =? SLA? PZ???NOGX NOGC > (1100) > > > ? > ???celldm(1)=???10.56000? > celldm(2)=? ? 0.00000? celldm(3)=? > ? 0.00000 > ? ???celldm(4)=? ? > 0.00000? celldm(5)=? ? 0.00000? > celldm(6)=? ? 0.00000 > > ? ???crystal axes: (cart. coord. in > units of a_0) > ? ? ? ? ? ? > ???a(1) = ( -0.5000? 0.0000? 0.5000 > ) > ? ? ? ? ? ? > ???a(2) = (? 0.0000? 0.5000? > 0.5000 ) > ? ? ? ? ? ? > ???a(3) = ( -0.5000? 0.5000? 0.0000 > ) > > ? ???reciprocal axes: (cart. coord. in > units 2 pi/a_0) > ? ? ? ? ? ? > ???b(1) = ( -1.0000 -1.0000? 1.0000 ) > ? ? ? ? ? ? > ???b(2) = (? 1.0000? 1.0000? > 1.0000 ) > ? ? ? ? ? ? > ???b(3) = ( -1.0000? 1.0000 -1.0000 ) > > > ? ???Atoms inside the unit cell: > > ???Cartesian axes > > ? ???site n.? atom? ? > ? mass? ? ? ? > ???positions (a_0 units) > ? ? ? ? 1? ? ? ? > Ge? 72.6400???tau( 1) = (? ? > 0.00000? ? 0.00000? ??? > 0.00000? ) > ? ? ? ? 2? ? ? ? > Ge? 72.6400???tau( 2) = (? ? > 0.25000? ? 0.25000? ??? > 0.25000? ) > > ? ???Computing dynamical matrix for > ? ? ? ? ? ? ? ? > ? ? q = (? ? 0.00000? ? > 0.00000? ? 0.00000 ) > > ? ???49 Sym.Ops. (with q -> -q+G ) > > > ? ???G cutoff =? 248.5712? > (???4111 G-vectors)? > ???FFT grid: ( 24, 24,? > 24) > ? ???number of k > points=???10 > ? ? ? ? ? ? ? ? > ? ? ???cart. coord. in units > 2pi/a_0 > ? ? ? ? k(? ? 1) = > (???0.1250000???0.1250000???0.1250000), > wk =? ? > 0.0625000 > ? ? ? ? k(? ? 2) = > (???0.1250000???0.1250000???0.3750000), > wk =? ? > 0.1875000 > ? ? ? ? k(? ? 3) = > (???0.1250000???0.1250000???0.6250000), > wk =? ? > 0.1875000 > ? ? ? ? k(? ? 4) = > (???0.1250000???0.1250000???0.8750000), > wk =? ? > 0.1875000 > ? ? ? ? k(? ? 5) = > (???0.1250000???0.3750000???0.3750000), > wk =? ? > 0.1875000 > ? ? ? ? k(? ? 6) = > (???0.1250000???0.3750000???0.6250000), > wk =? ? > 0.3750000 > ? ? ? ? k(? ? 7) = > (???0.1250000???0.3750000???0.8750000), > wk =? ? > 0.3750000 > ? ? ? ? k(? ? 8) = > (???0.1250000???0.6250000???0.6250000), > wk =? ? > 0.1875000 > ? ? ? ? k(? ? 9) = > (???0.3750000???0.3750000???0.3750000), > wk =? ? > 0.0625000 > ? ? ? ? k(???10) = > (???0.3750000???0.3750000???0.6250000), > wk =? ? > 0.1875000 > > ? ???PseudoPot. # 1 for Ge read from > file Ge.pz-bhs.UPF > ? ???Pseudo is Norm-conserving, Zval > =? 4.0 > ? ???Generated by new atomic code, or > converted to UPF format > ? ???Using radial grid of? 291 > points,? 2 beta functions with: > ? ? ? ? ? ? ? ? > l(1) =???0 > ? ? ? ? ? ? ? ? > l(2) =???1 > > > ? ???Atomic displacements: > ? ???There are???2 > irreducible representations > > ? ???Representation? > ???1? ? ? 3 modes - To be > done > > ? ???Representation? > ???2? ? ? 3 modes - To be > done > ? ???PHONON? ? > ???:? ???0.51s CPU > time,? ? 0.58s wall time > > > ? ???Alpha used in Ewald sum > =???0.9000 > > ? ???Electric Fields Calculation > > ********************************************************************* > > Can anyone tell me why this is happening? > > --------- > > Mikiyas Tsegaye > University of Virginia > Department of Electrical and Computer Engineering > Charlottesville, VA, USA > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From eyvaz_isaev at yahoo.com Wed Jun 17 23:02:38 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 17 Jun 2009 14:02:38 -0700 (PDT) Subject: [Pw_forum] phonon dispersion calculation abruptly stops Message-ID: <586812.4696.qm@web65713.mail.ac4.yahoo.com> Sorry, I was incorrect regarding ph.x and epsil=.false. combination! I used your input files and everything has gone well on my notebook, including electric field corrections, even epsil=.false. Bests, Eyvaz. --- On Thu, 6/18/09, Eyvaz Isaev wrote: > From: Eyvaz Isaev > Subject: Re: [Pw_forum] phonon dispersion calculation abruptly stops > To: "PWSCF Forum" > Date: Thursday, June 18, 2009, 12:35 AM > > Dear Mikiyas, > > > --- On Wed, 6/17/09, Mikiyas Tsegaye > wrote: > > Let us analyse your input files. > > Here is a sketch of your scf-input: > > > &system > > ibrav = 2, celldm(1) =10.56, nat=? 2, > > ntyp= 1, ecutwfc = 22.0 > > That means you have a semiconductor (insulator). > > Now from ph-input: > > > ldisp = .true., > > nq1 = 6, nq2 = 6, nq3 = 6, > > I suggest ph.x starts for "Electric Field Calculations", as > it does not see the keywords specific for the metallic case, > but can not do it as you did not specify epsil=.true., i.e. > calculate electric field corrections. > By default epsil=.false., i.e. do not calculate "Electric > Field Calculations" (sorry for some tautology) and then ph.x > stops (most likely). > > A short note on the mail subject: it is not connected with > "phonon dispersion" calculations, this script produces only > dynamical matricies for the q-mesh specified by nq1,nq2,nq3. > > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of > Steel & Alloys, Russia, > Department of Physics, Chemistry, and Biology (IFM), > Linkoping University, Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, > isaev at ifm.liu.se, > eyvaz_isaev at yahoo.com > > > --- On Wed, 6/17/09, Mikiyas Tsegaye > wrote: > > > From: Mikiyas Tsegaye > > Subject: [Pw_forum] phonon dispersion calculation > abruptly stops > > To: pw_forum at pwscf.org > > Date: Wednesday, June 17, 2009, 10:40 PM > > Hello, > > > > I'm trying to calculate phonon dispersion for > Germanium. > > I have the pw.x and ph.x inputs prepared as follows: > > > ********************************************************************************************************* > > &control > > ? ? calculation='scf', > > ? ? restart_mode='from_scratch', > > ? ? prefix='FF', > > ? ? tprnfor = .true., > > ? ? pseudo_dir = '$PSEUDO_DIR/', > > ? ? outdir='$TMP_DIR/' > > / > > &system > > ? ? ibrav = 2, celldm(1) =10.56, nat=? 2, > > ntyp= 1, > > ? ? ecutwfc = 22.0 > > / > > &electrons > > ? ? mixing_beta = 0.7 > > ? ? conv_thr =? 1.0d-8 > > / > > ATOMIC_SPECIES > > Ge? 72.64? Ge.pz-bhs.UPF > > ATOMIC_POSITIONS > > Ge 0.00 0.00 0.00 > > Ge 0.25 0.25 0.25 > > K_POINTS > > 10 > > ???0.1250000? 0.1250000? > > 0.1250000???1.00 > > ???0.1250000? 0.1250000? > > 0.3750000???3.00 > > ???0.1250000? 0.1250000? > > 0.6250000???3.00 > > ???0.1250000? 0.1250000? > > 0.8750000???3.00 > > ???0.1250000? 0.3750000? > > 0.3750000???3.00 > > ???0.1250000? 0.3750000? > > 0.6250000???6.00 > > ???0.1250000? 0.3750000? > > 0.8750000???6.00 > > ???0.1250000? 0.6250000? > > 0.6250000???3.00 > > ???0.3750000? 0.3750000? > > 0.3750000???1.00 > > ???0.3750000? 0.3750000? > > 0.6250000???3.00 > > > > EOF > > $ECHO "? running pw.x to calculate scf...\c" > > $PW_COMMAND < Ge.scfK.in > Ge.scfK.out > > check_failure $? > > $ECHO "done" > > > > # try the whole dispersion > > cat > Ge.phG.in << EOF > > phonons of germanium > > &INPUTPH > > amass(1) = 72.640, > > outdir = '$TMP_DIR/', > > prefix = 'FF', > > tr2_ph = 1.0d-14, > > fildyn = 'FF.dynG', > > ldisp = .true., > > nq1 = 6, nq2 = 6, nq3 = 6, > > / > > EOF > > > > $ECHO "? running ph.x to calculate gamma > > phonons...\c" > > $PH_COMMAND < Ge.phG.in > Ge.phG.out > > check_failure $? > > $ECHO "done" > > > > > ******************************************************************************************* > > Now, the scf step finishes succesfully, but the ph.x > step > > only? > > finishes up to a certain point: It crashes with > > "segementation fault".? > > The output file Ge.phG.out shows the following: > > > > > ************************************************************ > > > > > > ? ???Program PHONON? ? > > v.4.0.5? starts ... > > ? ???Today is 17Jun2009 at 10:43:58 > > > > ? ???Ultrasoft (Vanderbilt) > > Pseudopotentials > > > > > > ? ???Dynamical matrices for ( 6, 6, 6,) > > uniform grid of q-points > > ? ???(? 16q-points): > > ? ? ???N? ? > > ???xq(1)? ? > > ???xq(2)? ? > > ???xq(3) > > ? ? ???1? > > ???0.00000? > > ???0.00000? ???0.00000 > > ? ? ???2? ? > > -0.16667? ???0.16667? ? > > -0.16667 > > ? ? ???3? ? > > -0.33333? ???0.33333? ? > > -0.33333 > > ? ? ???4? > > ???0.50000? ? -0.50000? > > ???0.50000 > > ? ? ???5? > > ???0.00000? > > ???0.33333? ???0.00000 > > ? ? ???6? ? > > -0.16667? ???0.50000? ? > > -0.16667 > > ? ? ???7? > > ???0.66667? ? -0.33333? > > ???0.66667 > > ? ? ???8? > > ???0.50000? ? -0.16667? > > ???0.50000 > > ? ? ???9? > > ???0.33333? > > ???0.00000? ???0.33333 > > ? ? ? 10? > > ???0.00000? > > ???0.66667? ???0.00000 > > ? ? ? 11? > > ???0.83333? ? -0.16667? > > ???0.83333 > > ? ? ? 12? > > ???0.66667? ? -0.00000? > > ???0.66667 > > ? ? ? 13? > > ???0.00000? ? -1.00000? > > ???0.00000 > > ? ? ? 14? > > ???0.66667? ? -0.33333? > > ???1.00000 > > ? ? ? 15? > > ???0.50000? ? -0.16667? > > ???0.83333 > > ? ? ? 16? ? -0.33333? ? > > -1.00000? ???0.00000 > > > > > > > > ? ???bravais-lattice index? > > ???=? ? ? ? ? ? > > 2 > > ? ???lattice parameter > > (a_0)???=? ? ? 10.5600? > > a.u. > > ? ???unit-cell volume? ? > > ? ? ? =? ???294.3959 > > (a.u.)^3 > > ? ???number of atoms/cell? ? > > ? =? ? ? ? ? ? 2 > > ? ???number of atomic types? > > ? =? ? ? ? ? ? 1 > > ? ???kinetic-energy cut-off? > > ? =? ? ? 22.0000? Ry > > ? ???charge density cut-off? > > ? =? ? ? 88.0000? Ry > > ? ???convergence threshold? > > ???=? ? ? 1.0E-14 > > ? ???beta? ? ? ? > > ? ? ? ? ? ? ? =? > > ? ???0.7000 > > ? ???number of iterations used =? > > ? ? ? ? ? 4 > > ? ???Exchange-correlation? ? > > ? =? SLA? PZ???NOGX NOGC > > (1100) > > > > > > ? > > ???celldm(1)=???10.56000? > > celldm(2)=? ? 0.00000? celldm(3)=? > > ? 0.00000 > > ? ???celldm(4)=? ? > > 0.00000? celldm(5)=? ? 0.00000? > > celldm(6)=? ? 0.00000 > > > > ? ???crystal axes: (cart. coord. in > > units of a_0) > > ? ? ? ? ? ? > > ???a(1) = ( -0.5000? 0.0000? 0.5000 > > ) > > ? ? ? ? ? ? > > ???a(2) = (? 0.0000? 0.5000? > > 0.5000 ) > > ? ? ? ? ? ? > > ???a(3) = ( -0.5000? 0.5000? 0.0000 > > ) > > > > ? ???reciprocal axes: (cart. coord. in > > units 2 pi/a_0) > > ? ? ? ? ? ? > > ???b(1) = ( -1.0000 -1.0000? 1.0000 ) > > ? ? ? ? ? ? > > ???b(2) = (? 1.0000? 1.0000? > > 1.0000 ) > > ? ? ? ? ? ? > > ???b(3) = ( -1.0000? 1.0000 -1.0000 ) > > > > > > ? ???Atoms inside the unit cell: > > > > ???Cartesian axes > > > > ? ???site n.? atom? ? > > ? mass? ? ? ? > > ???positions (a_0 units) > > ? ? ? ? 1? ? ? ? > > Ge? 72.6400???tau( 1) = (? ? > > 0.00000? ? 0.00000? ??? > > 0.00000? ) > > ? ? ? ? 2? ? ? ? > > Ge? 72.6400???tau( 2) = (? ? > > 0.25000? ? 0.25000? ??? > > 0.25000? ) > > > > ? ???Computing dynamical matrix for > > ? ? ? ? ? ? ? ? > > ? ? q = (? ? 0.00000? ? > > 0.00000? ? 0.00000 ) > > > > ? ???49 Sym.Ops. (with q -> -q+G ) > > > > > > ? ???G cutoff =? 248.5712? > > (???4111 G-vectors)? > > ???FFT grid: ( 24, 24,? > > 24) > > ? ???number of k > > points=???10 > > ? ? ? ? ? ? ? ? > > ? ? ???cart. coord. in units > > 2pi/a_0 > > ? ? ? ? k(? ? 1) = > > (???0.1250000???0.1250000???0.1250000), > > wk =? ? > > 0.0625000 > > ? ? ? ? k(? ? 2) = > > (???0.1250000???0.1250000???0.3750000), > > wk =? ? > > 0.1875000 > > ? ? ? ? k(? ? 3) = > > (???0.1250000???0.1250000???0.6250000), > > wk =? ? > > 0.1875000 > > ? ? ? ? k(? ? 4) = > > (???0.1250000???0.1250000???0.8750000), > > wk =? ? > > 0.1875000 > > ? ? ? ? k(? ? 5) = > > (???0.1250000???0.3750000???0.3750000), > > wk =? ? > > 0.1875000 > > ? ? ? ? k(? ? 6) = > > (???0.1250000???0.3750000???0.6250000), > > wk =? ? > > 0.3750000 > > ? ? ? ? k(? ? 7) = > > (???0.1250000???0.3750000???0.8750000), > > wk =? ? > > 0.3750000 > > ? ? ? ? k(? ? 8) = > > (???0.1250000???0.6250000???0.6250000), > > wk =? ? > > 0.1875000 > > ? ? ? ? k(? ? 9) = > > (???0.3750000???0.3750000???0.3750000), > > wk =? ? > > 0.0625000 > > ? ? ? ? k(???10) = > > (???0.3750000???0.3750000???0.6250000), > > wk =? ? > > 0.1875000 > > > > ? ???PseudoPot. # 1 for Ge read from > > file Ge.pz-bhs.UPF > > ? ???Pseudo is Norm-conserving, Zval > > =? 4.0 > > ? ???Generated by new atomic code, or > > converted to UPF format > > ? ???Using radial grid of? 291 > > points,? 2 beta functions with: > > ? ? ? ? ? ? ? ? > > l(1) =???0 > > ? ? ? ? ? ? ? ? > > l(2) =???1 > > > > > > ? ???Atomic displacements: > > ? ???There are???2 > > irreducible representations > > > > ? ???Representation? > > ???1? ? ? 3 modes - To be > > done > > > > ? ???Representation? > > ???2? ? ? 3 modes - To be > > done > > ? ???PHONON? ? > > ???:? ???0.51s CPU > > time,? ? 0.58s wall time > > > > > > ? ???Alpha used in Ewald sum > > =???0.9000 > > > > ? ???Electric Fields Calculation > > > > > ********************************************************************* > > > > Can anyone tell me why this is happening? > > > > --------- > > > > Mikiyas Tsegaye > > University of Virginia > > Department of Electrical and Computer Engineering > > Charlottesville, VA, USA > > _______________________________________________ > > 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 sanjeev0302 at rediffmail.com Thu Jun 18 04:35:47 2009 From: sanjeev0302 at rediffmail.com (Sanjeev K. Gupta) Date: 18 Jun 2009 02:35:47 -0000 Subject: [Pw_forum] pseudopotential converter Message-ID: <20090618023547.40037.qmail@f4mail-235-231.rediffmail.com> Dear PWSCF Users, Greetings... I want to use UPF type pseudopotential for my calculation and it is not available on espresso/pseuopotential website (www.pwscf.org). For my purpose, two things are possible 1. Generate pseudopotential using ld1.x script. and 2. to convert FHI (available on internet)to UPF using fhi2upf.x script. I tried first way, and got error (due to i have not given correct input as i did not understand pseudo-gen/test.job and input file, i have seen earlier post on PWSCF-Forum also). and for second way, i do not get any information, how i proceeds? Plz. can anybody suggest me how FHI convert to UPF using fhi2upf.x script or suggest me how i understand the input file of pseudo-gen/test.job to run for UPF pseuopotential. Thanks in advanced. Kind Regards S K Gupta S. K. Gupta PhD Candidate, Dept. of Physics, Bhavnagar University. Bhavnagar, 364 002., Gujarat. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090618/e137ac88/attachment-0001.htm From sanjeev0302 at rediffmail.com Thu Jun 18 06:55:40 2009 From: sanjeev0302 at rediffmail.com (Sanjeev K. Gupta) Date: 18 Jun 2009 04:55:40 -0000 Subject: [Pw_forum] Error in phonon dispersion calculation Message-ID: <20090618045540.28854.qmail@f4mail-235-143.rediffmail.com> Dear PWSCF Users, Greetings... When I am running my script, then I got this error, plz. suggest me what is the reason? running the scf calculation... running the phonon calculation on a 4x4x4 mesh... transforming C(q) => C(R)... recalculating omega(q) from C(R)... plotting the phonon dispersions... calculating phonon density of states .... forrtl: No such file or directory forrtl: severe (29): file not found, unit 1, file /root/$NAME/STEP_4/$NAME.444.fc Image PC Routine Line Source matdyn.x 08332420 Unknown Unknown Unknown matdyn.x 08330E80 Unknown Unknown Unknown matdyn.x 0830F3F9 Unknown Unknown Unknown matdyn.x 082D66C0 Unknown Unknown Unknown matdyn.x 082D6B97 Unknown Unknown Unknown matdyn.x 082E0B6E Unknown Unknown Unknown matdyn.x 0805182F Unknown Unknown Unknown matdyn.x 0804DFCF Unknown Unknown Unknown matdyn.x 0804D98D Unknown Unknown Unknown libc.so.6 0082DE33 Unknown Unknown Unknown matdyn.x 0804D8C1 Unknown Unknown Unknown kind regards SKG S. K. Gupta PhD Candidate, Dept. of Physics, Bhavnagar University. Bhavnagar, 364 002., Gujarat. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090618/1f7d8ab8/attachment.htm From baroni at sissa.it Thu Jun 18 07:17:19 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 18 Jun 2009 07:17:19 +0200 Subject: [Pw_forum] Elastic Constant. In-Reply-To: <4A38ACA3.7020600@democritos.it> References: <3a749910906131300y5e92e22fl283eac075b5670f0@mail.gmail.com> <9041FC3A-E8F9-416C-953F-14097C1553A7@sissa.it> <4A38ACA3.7020600@democritos.it> Message-ID: <3631C067-B3C6-49B6-BF22-84EDB3192124@sissa.it> On Jun 17, 2009, at 10:43 AM, Paolo Giannozzi wrote: > Huiqun Zhou wrote: > >> The straightforward approach is tedious for orthogonal, monoclinic, >> triclinic >> systems. Should the lost implementation gain in these respects? > > the lost implementation was written only for the cubic case and only > for > the bulk modulus, if I remember correctly. of course you do do, Paolo (the implementation was yours!) > Extending it to low-symmetry > cases would also be tedious! ... and possibly worthwhile: would you volunteer, Huiqun Zhou? Have you read the PRL paper where all this is explained? Stefano --- 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/20090618/118d66f9/attachment.htm From giannozz at democritos.it Thu Jun 18 09:25:21 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 18 Jun 2009 09:25:21 +0200 Subject: [Pw_forum] Error in phonon dispersion calculation In-Reply-To: <20090618045540.28854.qmail@f4mail-235-143.rediffmail.com> References: <20090618045540.28854.qmail@f4mail-235-143.rediffmail.com> Message-ID: On Jun 18, 2009, at 6:55 , Sanjeev K. Gupta wrote: > When I am running my script, then I got this error, plz. suggest me > what is the reason? > forrtl: No such file or directory > forrtl: severe (29): file not found, unit 1, file /root/$NAME/ > STEP_4/$NAME.444.fc no such file or directory. Check output files for errors. Check your script --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Thu Jun 18 09:28:53 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 18 Jun 2009 09:28:53 +0200 Subject: [Pw_forum] pseudopotential converter In-Reply-To: <20090618023547.40037.qmail@f4mail-235-231.rediffmail.com> References: <20090618023547.40037.qmail@f4mail-235-231.rediffmail.com> Message-ID: <61B27451-6CD5-4FDE-BF0E-658C8618838A@democritos.it> On Jun 18, 2009, at 4:35 , Sanjeev K. Gupta wrote: > Plz. can anybody suggest me how FHI convert to UPF using fhi2upf.x > script run fhi2upf.x (which is not a "script" but an executable). It will ask what it needs. It will not bite you. > or suggest me how i understand the input file of pseudo-gen/ > test.job to run > for UPF pseudopotential. the input data format is explained in Doc/INPUT_LD1.* > Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From anvari_meh at physics.iust.ac.ir Thu Jun 18 11:11:23 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Thu, 18 Jun 2009 12:41:23 +0330 Subject: [Pw_forum] missing q point Message-ID: Dear Gabriele I compeletly agree with you. I work on graphene and it seems that it is not necessary to use 2 2 2/4 4 4 grid. I just used them to see that as Eyvaz suggested my error would be diappeared or not. Now I don't have any problem with espresso-4.0.5 & thanks a lot because of your help. I have another question when I use c.blyp-mt.UPF pseudopotential and then calculate frequency in gamma point, my optical frequency is about 3400cm-1 but when I use 2 2 1 grid I gain 1528cm-1. I couldn't understand the reason of it Best Regards Mehrnaz Iran University Of science & Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090618/97183acd/attachment.htm From sclauzer at sissa.it Thu Jun 18 11:20:36 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 18 Jun 2009 11:20:36 +0200 Subject: [Pw_forum] missing q point In-Reply-To: References: Message-ID: <4A3A06E4.6000809@sissa.it> Mehrnaz Anvari wrote: > Dear Gabriele > I compeletly agree with you. I work on graphene and it seems that it is > not necessary to use 2 2 2/4 4 4 grid. I just used them to see that as > Eyvaz suggested my error would be diappeared or not. Now I don't have > any problem with espresso-4.0.5 & thanks a lot because of your help. I > have another question when I use c.blyp-mt.UPF pseudopotential and then > calculate frequency in gamma point, my optical frequency is about > 3400cm-1 but when I use 2 2 1 grid I gain 1528cm-1. I couldn't > understand the reason of it Your question is not much clear too me. Do you mean that the frequency obtained for the same q vector (0,0,0 in this case) is different if you perform a single q-point calculation w.r.t the frequency obtained when that q-point is included in a q-point grid (like the 221 you mention). This seems quite improbable to me. Or maybe you mean that when computing dispersions from the 221 grid using Fourier interpolation the result is not good at Gamma? This may be since you are using a very small grid (try to check convergence by increasing the size of the grid). Then there are many other convergence issues about cut-offs, k-point grids, PPs, ... GS > Best Regards > Mehrnaz > Iran University Of science & Technology > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From paulatto at sissa.it Thu Jun 18 11:38:58 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 18 Jun 2009 11:38:58 +0200 (CEST) Subject: [Pw_forum] File closing errors when using NEB image parallelization In-Reply-To: <967475.669.qm@web50909.mail.re2.yahoo.com> References: <14450.35591.qm@web50912.mail.re2.yahoo.com> <880917.27758.qm@web50903.mail.re2.yahoo.com> <419763.82623.qm@web50910.mail.re2.yahoo.com> <967475.669.qm@web50909.mail.re2.yahoo.com> Message-ID: <53182.78.12.166.56.1245317938.squirrel@webmail.sissa.it> I could finally reproduce the bug, a fix will come with the next version of QE, I'll send you a preliminary version, as soon as it is ready, if you wish. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From greatnaol at gmail.com Thu Jun 18 13:56:37 2009 From: greatnaol at gmail.com (Naol Regassa) Date: Thu, 18 Jun 2009 14:56:37 +0300 Subject: [Pw_forum] How to start and use QE open source simulation Message-ID: <97e4b88e0906180456t1ebabbdg2f0102be9b6247d@mail.gmail.com> Hello Yosef You can get the file for QE and XcrysDen from AAU, Materials science programe (Room 111). Try contact us when you come to Addis. We may help you on how to install, configure and start up. Tamene Regassa Student at AAU, Materials science programe On 6/17/09, pw_forum-request at pwscf.org wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://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: File closing errors when using NEB image parallelization > (J. J. Ramsey) > 2. Re: How to start and use QE open source simulation > (Nicola Marzari) > 3. Re: How to start and use QE open source simulation > (Giovanni Cantele) > 4. Re: Elastic Constant. (Huiqun Zhou) > 5. Re: Elastic Constant. (Huiqun Zhou) > 6. Re: Elastic Constant. (Huiqun Zhou) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 16 Jun 2009 09:04:27 -0700 (PDT) > From: "J. J. Ramsey" > Subject: Re: [Pw_forum] File closing errors when using NEB image > parallelization > To: PWSCF Forum > Message-ID: <419763.82623.qm at web50910.mail.re2.yahoo.com> > Content-Type: text/plain; charset=us-ascii > > > ----- Original Message ---- > >> If I had to bet I would say you are using ~/tmp as the default directory, >> >> and it is a normal NFS share. > > Actually, it's a subdirectory under /usr/var/tmp, and to the best of my > knowledge, it is not an NFS share. There is a bit more info, here: > http://www.arl.hpc.mil/Systems/mjm_docs.html#fs > > Also, I had even tried out my problem on an entirely different cluster which > uses the Parallel File System > (http://www.osc.edu/supercomputing/computing/pvfs/index.shtml) and got the > same problems. > > > > > > > ------------------------------ > > Message: 2 > Date: Tue, 16 Jun 2009 12:27:07 -0400 > From: Nicola Marzari > Subject: Re: [Pw_forum] How to start and use QE open source simulation > To: PWSCF Forum > Message-ID: <4A37C7DB.1030803 at mit.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > yoseph Getachew wrote: >> Dear All , >> >> sorry but this is a very low level question. >> >> would you please inform me as to how i can install,configure, and make >> all the necessary steps so that i can be able to run simulations. i >> have tried to use the QE website but i ended up in so much more >> inconsistencies. >> >> for example where and how can i get and install fortan and c.xcrysden >> which binary or static files should i use and how should i install them. >> >> i need your specific advise on this to catch up with everybody. >> >> Regards, >> Yoseph Getachew >> ArbaMinch University, >> Department of Physics > > > Hi Yoseph, > > it looks like you need to start with some basics on Linux. Do you > have anyone familiar with that in the Department, or can you access > some online guide ? People might have better suggestions here. > > At a minimum, to install Quantum ESPRESSO you need a Fortran compiler, > and (I think) a C compiler. The Intel fortran and c compilers are very > efficient, but would need to be downloaded from the Intel site (I have > left a copy of those at Addis Abeba, not sure if it is still there - > contact SibKrishna Ghoshal ). > > gfortran and gcc would be standard alternatives, available from many > Linux distributions. > > nicola > > > > -- > --------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials Science and Engineering > 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA > tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu > > > ------------------------------ > > Message: 3 > Date: Tue, 16 Jun 2009 18:27:25 +0200 > From: Giovanni Cantele > Subject: Re: [Pw_forum] How to start and use QE open source simulation > To: PWSCF Forum > Message-ID: <4A37C7ED.5060305 at na.infn.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > yoseph Getachew wrote: >> Dear All , >> >> sorry but this is a very low level question. >> >> would you please inform me as to how i can install,configure, and make >> all the necessary steps so that i can be able to run simulations. i >> have tried to use the QE website but i ended up in so much more >> inconsistencies. >> > actually, it is rather hard to help you, due to loss of information. > Which kind of inconsistencies? In compiling QE? At run time? > It seems to me that lot of information can be found here: > http://www.quantum-espresso.org/wiki/index.php/Installation > there are also compiler/architecture-related issues mentioned there. > The user guide is also reported within the distribution > (Doc/user_guide.html). >> for example where and how can i get and install fortan and c. > on which system? Do you have a Linux distribution? Maybe ubuntu? > I've the Intel fortran/C compiler that I freely downloaded from the > Intel web site, > I guest it is still free. > Another possibility is gfortran, I would install it on my PC using > sudo apt-get install gfortran > but a different command is needed for other linux distributions. >> xcrysden >> which binary or static files should i use and how should i install them. >> > are you sure that what reported on the web site is useless for you? > Go to (did you already do it?) > http://www.xcrysden.org/doc/install.html > I find many sections: > *Installation Instructions > * > */How to Install the Compiled Package > /* > /FOR IMPATIENT: minimal installation instructions > / > /A Bit Longer Installation Instructions > / > /What xcConfigure does? > / > */How to Install the Source Package > /* > /Trouble Shooting > / > > Someone also had the patience to suggest installation instructions for both > impatient and patient users!!!!! > Did you follow all the suggested steps, and in case which was the one > failing? > >> i need your specific advise on this to catch up with everybody. >> >> Regards, >> Yoseph Getachew >> ArbaMinch University, >> Department of Physics >> >> >> > > Best regards, > > Giovanni > > -- > > > > Dr. Giovanni Cantele > Coherentia CNR-INFM and Dipartimento di Scienze Fisiche > Universita' di Napoli "Federico II" > Complesso Universitario di Monte S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > Phone: +39 081 676910 > Fax: +39 081 676346 > E-mail: giovanni.cantele at cnr.it > giovanni.cantele at na.infn.it > Web: http://people.na.infn.it/~cantele > Research Group: http://www.nanomat.unina.it > Skype contact: giocan74 > > > > ------------------------------ > > Message: 4 > Date: Wed, 17 Jun 2009 15:05:37 +0800 > From: "Huiqun Zhou" > Subject: Re: [Pw_forum] Elastic Constant. > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Stefano, > > The straightforward approach is tedious for orthorgonal, monolinic, trilinic > systems. Should the lost implementation gain in these respects? > > Huiqun Zhou > @Earth Sciences, Nanjing University, China > > ----- Original Message ----- > From: "Stefano Baroni" > To: "PWSCF Forum" > Sent: Sunday, June 14, 2009 6:01 PM > Subject: Re: [Pw_forum] Elastic Constant. > > >> Dear Bipul, >> >> long ago there used to be an implementation of the linear-response >> approach to elastic constants by SB, Giannozzi, and Testa: >> % Copyright (C) 2009 The American Physical Society >> % Please report any problems to prola at aps.org >> >> @Article{PhysRevLett.59.2662, >> title = {Elastic Constants of Crystals from Linear-Response Theory}, >> author = {Baroni, Stefano and Giannozzi, Paolo and Testa, Andrea }, >> journal = {Phys. Rev. Lett.}, >> volume = {59}, >> number = {23}, >> pages = {2662--2665}, >> numpages = {3}, >> year = {1987}, >> month = {Dec}, >> doi = {10.1103/PhysRevLett.59.2662}, >> publisher = {American Physical Society} >> } >> This is no longer available, partly because of the programmers' >> lazyness, partly because there is not much to be gained with respect >> to the straightforward approach you are following. >> >> Stefano B >> >> >> On Jun 13, 2009, at 10:00 PM, Bipul Rakshit wrote: >> >>> Dear Pwscf user, >>> I want to calculate the elastic constants for cubic structure for >>> LaSb, which is having NaCl structure. Although I have written a small >>> script for doing that. But if anybody develop any code, do he/she like >>> to share, so that I can compare my results. >>> Thanks >>> -- >>> Bipul Rakshit >>> PhD Student, >>> Barkatullah University, >>> Bhopal 462026, >>> MP, India >>> _______________________________________________ >>> 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 >> > > ------------------------------ > > Message: 5 > Date: Wed, 17 Jun 2009 14:36:39 +0800 > From: "Huiqun Zhou" > Subject: Re: [Pw_forum] Elastic Constant. > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Stefano, > > The straightforward approach is tedious for orthorgonal, monolinic, trilinic > systems. Should the lost implementation gain in these respects? > > Huiqun Zhou > @Earth Sciences, Nanjing University, China > > ----- Original Message ----- > From: "Stefano Baroni" > To: "PWSCF Forum" > Sent: Sunday, June 14, 2009 6:01 PM > Subject: Re: [Pw_forum] Elastic Constant. > > >> Dear Bipul, >> >> long ago there used to be an implementation of the linear-response >> approach to elastic constants by SB, Giannozzi, and Testa: >> % Copyright (C) 2009 The American Physical Society >> % Please report any problems to prola at aps.org >> >> @Article{PhysRevLett.59.2662, >> title = {Elastic Constants of Crystals from Linear-Response Theory}, >> author = {Baroni, Stefano and Giannozzi, Paolo and Testa, Andrea }, >> journal = {Phys. Rev. Lett.}, >> volume = {59}, >> number = {23}, >> pages = {2662--2665}, >> numpages = {3}, >> year = {1987}, >> month = {Dec}, >> doi = {10.1103/PhysRevLett.59.2662}, >> publisher = {American Physical Society} >> } >> This is no longer available, partly because of the programmers' >> lazyness, partly because there is not much to be gained with respect >> to the straightforward approach you are following. >> >> Stefano B >> >> >> On Jun 13, 2009, at 10:00 PM, Bipul Rakshit wrote: >> >>> Dear Pwscf user, >>> I want to calculate the elastic constants for cubic structure for >>> LaSb, which is having NaCl structure. Although I have written a small >>> script for doing that. But if anybody develop any code, do he/she like >>> to share, so that I can compare my results. >>> Thanks >>> -- >>> Bipul Rakshit >>> PhD Student, >>> Barkatullah University, >>> Bhopal 462026, >>> MP, India >>> _______________________________________________ >>> 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 >> > > ------------------------------ > > Message: 6 > Date: Wed, 17 Jun 2009 15:02:09 +0800 > From: "Huiqun Zhou" > Subject: Re: [Pw_forum] Elastic Constant. > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Stefano, > > The straightforward approach is tedious for orthorgonal, monolinic, trilinic > systems. Should the lost implementation gain in these respects? > > Huiqun Zhou > @Earth Sciences, Nanjing University, China > > ----- Original Message ----- > From: "Stefano Baroni" > To: "PWSCF Forum" > Sent: Sunday, June 14, 2009 6:01 PM > Subject: Re: [Pw_forum] Elastic Constant. > > >> Dear Bipul, >> >> long ago there used to be an implementation of the linear-response >> approach to elastic constants by SB, Giannozzi, and Testa: >> % Copyright (C) 2009 The American Physical Society >> % Please report any problems to prola at aps.org >> >> @Article{PhysRevLett.59.2662, >> title = {Elastic Constants of Crystals from Linear-Response Theory}, >> author = {Baroni, Stefano and Giannozzi, Paolo and Testa, Andrea }, >> journal = {Phys. Rev. Lett.}, >> volume = {59}, >> number = {23}, >> pages = {2662--2665}, >> numpages = {3}, >> year = {1987}, >> month = {Dec}, >> doi = {10.1103/PhysRevLett.59.2662}, >> publisher = {American Physical Society} >> } >> This is no longer available, partly because of the programmers' >> lazyness, partly because there is not much to be gained with respect >> to the straightforward approach you are following. >> >> Stefano B >> >> >> On Jun 13, 2009, at 10:00 PM, Bipul Rakshit wrote: >> >>> Dear Pwscf user, >>> I want to calculate the elastic constants for cubic structure for >>> LaSb, which is having NaCl structure. Although I have written a small >>> script for doing that. But if anybody develop any code, do he/she like >>> to share, so that I can compare my results. >>> Thanks >>> -- >>> Bipul Rakshit >>> PhD Student, >>> Barkatullah University, >>> Bhopal 462026, >>> MP, India >>> _______________________________________________ >>> 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 > > > End of Pw_forum Digest, Vol 24, Issue 35 > **************************************** > From panda.deng.pan at gmail.com Thu Jun 18 14:28:24 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Thu, 18 Jun 2009 20:28:24 +0800 Subject: [Pw_forum] wrong graphite band structure Message-ID: Dear All users, I was about to calculate the graphite and I get a band structure which is inconsist with other calculation by VASP. I already have checked the K-points in BZ, the crystal structure by XCRYSDEN. And I still did not get a correct band. To confirm I use it correctly I had calculate the band structure of diamond, and this time I was right. Any comment would be helpful. Here is the input for scf run &control calculation = 'scf' restart_mode='from_scratch' prefix='C', pseudo_dir = '/Quantum-Espresso/espresso-4.0.3/pseudo/', outdir='/tmp/' / &system ibrav=4, celldm(1)=2.4434, celldm(3)=8.0, nat=2, ntyp=1, ecutwfc = 40.0, ecutrho = 400.0, occupations = 'smearing', degauss = 0.03, / &electrons mixing_beta = 0.5 conv_thr = 1.0d-9 / ATOMIC_SPECIES C 12.0 C.pbe-rrkjus.UPF ATOMIC_POSITIONS {crystal} C 0.0000000 0.0000000 0.0000000 C 0.3333333 0.6666666 0.0000000 K_POINTS {automatic} 8 8 1 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090618/bb712532/attachment-0001.htm From giannozz at democritos.it Thu Jun 18 14:38:38 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 18 Jun 2009 14:38:38 +0200 Subject: [Pw_forum] wrong graphite band structure In-Reply-To: References: Message-ID: <75897B61-041E-46BB-854E-77515B03310B@democritos.it> On Jun 18, 2009, at 14:28 , ?? wrote: > celldm(1)=2.4434, these are a.u., not A --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From chenweiguang82 at gmail.com Thu Jun 18 15:20:11 2009 From: chenweiguang82 at gmail.com (Weiguang Chen) Date: Thu, 18 Jun 2009 21:20:11 +0800 Subject: [Pw_forum] Which part is the main potential for obtaining the work function? In-Reply-To: References: <9e6d976a0906170912u19037a81l2c2b8d652341eeb1@mail.gmail.com> Message-ID: <9e6d976a0906180620j49bcb752kec876e12e24de649@mail.gmail.com> Thanks , I will try it. On Thu, Jun 18, 2009 at 12:45 AM, Lorenzo Paulatto wrote: > In data 17 giugno 2009 alle ore 18:12:45, Weiguang Chen > ha scritto: > > We know the potential of a solid state consists of V_bare(atomic core), > > V_hartree(Hartree contribution) and V_xc(exchange correalation) and so > > on. I want to know which component is the main source when we try to get > > the work function. > > The first and the second together (plot_num=11, in pp.x); please see the > example WorkFct_example in the examples/ directory of quantum-espresso > > regards > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Best Wishes ChenWeiguang ************************************************ # Chen, Weiguang # # Postgraduate, Ph. D # 75 University Road, Physics Buliding # 218 # School of Physics & Engineering # Zhengzhou University # Zhengzhou, Henan 450052 CHINA # # Tel: 86-13203730117; # E-mail:chenweiguang82 at gmail.com ; # chenweiguang82 at qq.com #********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090618/312a7e33/attachment.htm From andrea.vittadini at unipd.it Thu Jun 18 14:54:17 2009 From: andrea.vittadini at unipd.it (Andrea Vittadini) Date: Thu, 18 Jun 2009 14:54:17 +0200 Subject: [Pw_forum] wrong graphite band structure (??) In-Reply-To: References: Message-ID: <4A3A38F9.6000802@unipd.it> Dear unknown user, it seems to me that you are using wrong units for the cell dimensions. Regards, Andrea ------- Andrea Vittadini CNR-ISTM University of Padova (Italy) > Dear All users, > > I was about to calculate the graphite and I get a band structure which > is inconsist with other calculation by VASP. I already have checked the > K-points in BZ, the crystal structure by XCRYSDEN. And I still did not get a > correct band. > To confirm I use it correctly I had calculate the band structure of > diamond, and this time I was right. > Any comment would be helpful. > > Here is the input for scf run > &control > calculation = 'scf' > restart_mode='from_scratch' > prefix='C', > pseudo_dir = '/Quantum-Espresso/espresso-4.0.3/pseudo/', > outdir='/tmp/' > / > &system > ibrav=4, > celldm(1)=2.4434, > celldm(3)=8.0, > nat=2, > ntyp=1, > ecutwfc = 40.0, > ecutrho = 400.0, > occupations = 'smearing', > degauss = 0.03, > / > &electrons > mixing_beta = 0.5 > conv_thr = 1.0d-9 > / > ATOMIC_SPECIES > C 12.0 C.pbe-rrkjus.UPF > ATOMIC_POSITIONS {crystal} > C 0.0000000 0.0000000 0.0000000 > C 0.3333333 0.6666666 0.0000000 > K_POINTS {automatic} > 8 8 1 0 0 0 From panda.deng.pan at gmail.com Thu Jun 18 19:35:20 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Fri, 19 Jun 2009 01:35:20 +0800 Subject: [Pw_forum] wrong graphite band structure In-Reply-To: <75897B61-041E-46BB-854E-77515B03310B@democritos.it> References: <75897B61-041E-46BB-854E-77515B03310B@democritos.it> Message-ID: 2009/6/18 Paolo Giannozzi > > On Jun 18, 2009, at 14:28 , ?? wrote: > > > celldm(1)=2.4434, > > these are a.u., not A > Dear Paolo, Thanks for your respond, I have checked the units and I change the input to "celldm(1)=4.6189", but the band structure still seems wrong. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090619/fdfe7daf/attachment.htm From samadzare at gmail.com Thu Jun 18 21:14:22 2009 From: samadzare at gmail.com (samad zare) Date: Thu, 18 Jun 2009 23:44:22 +0430 Subject: [Pw_forum] please help quick Message-ID: hello please help me quick i want all of curve for tio2 rutile curve energy- volume curve band energy curve density curve energy up spin calculation phonon -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090618/3e815943/attachment.htm From eyvaz_isaev at yahoo.com Thu Jun 18 22:08:49 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 18 Jun 2009 13:08:49 -0700 (PDT) Subject: [Pw_forum] please help quick Message-ID: <894412.28842.qm@web65704.mail.ac4.yahoo.com> Dear Samad, You did not specify the last more wanted: send me a nice written paper!!! If you will receive all these scripts what is your contribution? So, please, open /examples directory and learn step-by-step for yourself how to calculate these values/properties. Besides, specify your affiliation when you post a message to this forum. This is the Netiquette in this forum by default. Bests and good luck with examples, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Thu, 6/18/09, samad zare wrote: > From: samad zare > Subject: [Pw_forum] please help quick > To: pw_forum at pwscf.org > Date: Thursday, June 18, 2009, 11:14 PM > hello > please help me quick > i want all of curve for tio2 rutile > curve energy- volume > curve band energy > curve ?density > curve energy up spin > calculation phonon > > > > > -----Inline Attachment Follows----- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From jtmullen at ncsu.edu Thu Jun 18 23:26:28 2009 From: jtmullen at ncsu.edu (Jeffrey Mullen) Date: Thu, 18 Jun 2009 17:26:28 -0400 Subject: [Pw_forum] Proper use of mp_barrier Message-ID: <4A3AB104.2090100@ncsu.edu> forgot my affiliation --Jeff Mullen North Carolina State University Physics From jtmullen at ncsu.edu Thu Jun 18 23:46:14 2009 From: jtmullen at ncsu.edu (Jeffrey Mullen) Date: Thu, 18 Jun 2009 17:46:14 -0400 Subject: [Pw_forum] Proper use of mp_barrier Message-ID: <4A3AB5A6.8000308@ncsu.edu> This was bounced back to me, so I am trying again... --Jeff Mullen NCSU Physics Greetings, I have added a subroutine to phonon.f90 which I only want to execute on ionode after elpsum(). I call the routine only on ionode and then call mp_barrier() to sync the processors. Until the call to mp_barrier, it works. The code only runs on the ionode and other processors do not attempt to perform any tasks. The problem is mp_barrier() doesn't "release" after the completion of the subroutine. I thought that mp_barrier() blocked until every operating processor entered mp_barrier, then it stopped blocking and allowed proper program flow. What am I doing wrong? From jtmullen at ncsu.edu Thu Jun 18 23:19:20 2009 From: jtmullen at ncsu.edu (Jeffrey Mullen) Date: Thu, 18 Jun 2009 17:19:20 -0400 Subject: [Pw_forum] Proper use of mp_barrier() Message-ID: <4A3AAF58.20804@ncsu.edu> Greetings, I have added a subroutine to phonon.f90 which I only want to execute on ionode after elpsum(). I call the routine only on ionode and then call mp_barrier() to sync the processors. Until the call to mp_barrier, it works. The code only runs on the ionode and other processors do not attempt to perform any tasks. The problem is mp_barrier() doesn't "release" after the completion of the subroutine. I thought that mp_barrier() blocked until every operating processor entered mp_barrier, then it stopped blocking and allowed proper program flow. What am I doing wrong? From baroni at sissa.it Fri Jun 19 08:09:29 2009 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 19 Jun 2009 08:09:29 +0200 Subject: [Pw_forum] please help quick In-Reply-To: References: Message-ID: <51870285-2C66-4C60-AF5C-3C12772D60A6@sissa.it> On Jun 18, 2009, at 9:14 PM, samad zare wrote: > hello > please help me quick ??? > i want all of curve for tio2 rutile > curve energy- volume > curve band energy > curve density > curve energy up spin > calculation phonon Above is a description of your reserach project (or at least part of it), which, I presume, you do not expect any of us to do. You forgot to say what "quick help" would you need. Oh, yes. You also forget to say who you are (your name) and where you work (affiliation). I understand that you are in a hurry, but this way you won't obtain much help ... Take it easy, SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090619/bd90c82d/attachment-0001.htm From trinh.vo at jpl.nasa.gov Fri Jun 19 08:10:37 2009 From: trinh.vo at jpl.nasa.gov (Vo, Trinh) Date: Thu, 18 Jun 2009 23:10:37 -0700 Subject: [Pw_forum] Calculation of affinity energy and ionization Message-ID: <63E24D720DCE7246ABAA722B52D23CDF0153C2564D86@ALTPHYEMBEVSP10.RES.AD.JPL> Hello, As a test, I performed the calculations of the ionization and affinity energy of P-doped Si nanocrystal. The steps I did as follows: 1. Relax the nanostructure 2. Remove one electron form the above relaxed structure and run scf calculation for this system to obtain ionization energy (I). 3. Add one electron the relaxed structure (in #1) , and run scf calculation to obtain the affinity energy (A). The ionization energy and the affinity energy are calculated by: A = E(n)-E(n+1) I = E(n-1)-E(n) where E is the total state total energy of the n-, (n+1)-, and (n-1)-electron systems. When I compared the values of A and I that I obtained with those by a previous work, PRL 92, 0468021 (2004), I saw a large deviation. The difference is ~0.8eV for I and ~0.4eV for A. (I used the same structure of one the structures studied in the PRL. By the courtesy, Prof. Cheliskowki sent it to me for the test purpose). The calculation in the PRL is performed with real-space ab initio pseudopotential method. Their calculations of hyperfine splitting agreed very well with experimental data. Since my results have large differences from theirs, I am not sure if the procedures that I did above are incorrect. Could you give some comments if there is anything wrong from what I did. Thank you in advance your help, Trinh Vo JPL/CalTech -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090618/5c13fd21/attachment.htm From giannozz at democritos.it Fri Jun 19 08:34:35 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 19 Jun 2009 08:34:35 +0200 Subject: [Pw_forum] Proper use of mp_barrier() In-Reply-To: <4A3AAF58.20804@ncsu.edu> References: <4A3AAF58.20804@ncsu.edu> Message-ID: <447A04E7-E3FB-4704-B6DF-1B7928C6895F@democritos.it> On Jun 18, 2009, at 23:19 , Jeffrey Mullen wrote: > call elphsum() > if(ionode) then > call check_routine() > endif > call mp_barrier() it should work, but parallelism is tricky. Are you sure the code is coming out of check_routine? does it work if you comment it? P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From nedward at MIT.EDU Fri Jun 19 08:56:13 2009 From: nedward at MIT.EDU (Nicholas E. Singh-Miller) Date: Fri, 19 Jun 2009 02:56:13 -0400 (EDT) Subject: [Pw_forum] Calculation of affinity energy and ionization In-Reply-To: <63E24D720DCE7246ABAA722B52D23CDF0153C2564D86@ALTPHYEMBEVSP10.RES.AD.JPL> References: <63E24D720DCE7246ABAA722B52D23CDF0153C2564D86@ALTPHYEMBEVSP10.RES.AD.JPL> Message-ID: Hi Trinh Vo, Because you are working within periodic boundary condtions (whereas Melnikov and Chelikowsky were not). You have some errors in the energy to consider when charging the system. Assuming that your input file is as you want it (without other sources of error). A charged system (with a compensating background) will have an error in the energy that is dependent on the size of the unit cell. It is likely that you need to correct for this, either as post processing through a scheme like Makov and Payne suggest (PRB 51, 4014) or self consistently as in PRB 77, 115139 (or references therein). I believe both are to some extent implemented in QE. Hope that helps, Nick On Thu, 18 Jun 2009, Vo, Trinh wrote: > Hello, > > As a test, I performed the calculations of the ionization and affinity energy of P-doped Si nanocrystal. The steps I did as follows: > > > 1. Relax the nanostructure > 2. Remove one electron form the above relaxed structure and run scf calculation for this system to obtain ionization energy (I). > 3. Add one electron the relaxed structure (in #1) , and run scf calculation to obtain the affinity energy (A). > > The ionization energy and the affinity energy are calculated by: > > A = E(n)-E(n+1) > I = E(n-1)-E(n) > where E is the total state total energy of the n-, (n+1)-, and (n-1)-electron systems. > > When I compared the values of A and I that I obtained with those by a previous work, PRL 92, 0468021 (2004), I saw a large deviation. The difference is ~0.8eV for I and ~0.4eV for A. (I used the same structure of one the structures studied in the PRL. By the courtesy, Prof. Cheliskowki sent it to me for the test purpose). > > The calculation in the PRL is performed with real-space ab initio pseudopotential method. Their calculations of hyperfine splitting agreed very well with experimental data. > > Since my results have large differences from theirs, I am not sure if the procedures that I did above are incorrect. Could you give some comments if there is anything wrong from what I did. > > Thank you in advance your help, > > Trinh Vo > > JPL/CalTech > > > > > > > > ***************************************** Nicholas E. Singh-Miller Prof. Marzari Group (quasiamore.mit.edu) Materials Science and Engineering Massachusetts Institute of Technology 13-4066 (617)324-0372 ***************************************** From giannozz at democritos.it Fri Jun 19 11:36:40 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 19 Jun 2009 11:36:40 +0200 Subject: [Pw_forum] wrong graphite band structure In-Reply-To: References: <75897B61-041E-46BB-854E-77515B03310B@democritos.it> Message-ID: <4A3B5C28.9050106@democritos.it> ?? wrote: > Thanks for your respond, I have checked the units and I change the > input to "celldm(1)=4.6189", but the band structure still seems wrong. why? -- Paolo Giannozzi, Democritos and University of Udine, Italy From wangqj1 at 126.com Fri Jun 19 11:06:10 2009 From: wangqj1 at 126.com (wangqj1) Date: Fri, 19 Jun 2009 17:06:10 +0800 (CST) Subject: [Pw_forum] Cannot match namelist object name ZnO Message-ID: <13665010.394251245402370017.JavaMail.coremail@bj126app81.126.com> Dear pwscf users When I relaxed the suppercell used pw.x ,it displayed "Cannot match namelist object name ZnO",but scf calculation ends well with all the scf outputs .I used version 4.0.3 . So I want to know whether the hint affect the result or not ? Whether there is no need to worry about this ? Thanks for your help ! Sincerely Q J Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090619/076ee705/attachment.htm From giannozz at democritos.it Fri Jun 19 11:49:04 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 19 Jun 2009 11:49:04 +0200 Subject: [Pw_forum] Cannot match namelist object name ZnO In-Reply-To: <13665010.394251245402370017.JavaMail.coremail@bj126app81.126.com> References: <13665010.394251245402370017.JavaMail.coremail@bj126app81.126.com> Message-ID: <4A3B5F10.6040306@democritos.it> wangqj1 wrote: > When I relaxed the suppercell used pw.x ,it displayed > "Cannot match namelist object name ZnO" look for "ZnO" inside one of the namelist and remove it P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From sclauzer at sissa.it Fri Jun 19 11:51:45 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 19 Jun 2009 11:51:45 +0200 Subject: [Pw_forum] Cannot match namelist object name ZnO In-Reply-To: <13665010.394251245402370017.JavaMail.coremail@bj126app81.126.com> References: <13665010.394251245402370017.JavaMail.coremail@bj126app81.126.com> Message-ID: <4A3B5FB1.8080302@sissa.it> wangqj1 wrote: > > Dear pwscf users > When I relaxed the suppercell used pw.x ,it displayed "Cannot match > namelist object name ZnO",but scf calculation ends well with all the scf > outputs .I used version 4.0.3 . So I want to know whether the hint > affect the result or not ? Whether there is no need to worry about this ? If you feed a wrong input to pwscf your calculation may end successfully but actually compute something different from what you have in mind. So it is always important to understand all the warnings/error from the input parser, since they signal some error in the input file. Please either provide your input file or figure out by yourself why you get that warning (most probably you placed a string in the wrong place). There is a detailed description of input keywords in Doc/INPUT_PW.txt and plenty of examples in examples/ and tests/ directories GS > Thanks for your help ! > Sincerely > Q J Wang > XiangTan University > > > > ------------------------------------------------------------------------ > 200????,????,????? > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From trinh.vo at jpl.nasa.gov Fri Jun 19 21:51:23 2009 From: trinh.vo at jpl.nasa.gov (Vo, Trinh) Date: Fri, 19 Jun 2009 12:51:23 -0700 Subject: [Pw_forum] Calculation of affinity energy and ionization In-Reply-To: References: <63E24D720DCE7246ABAA722B52D23CDF0153C2564D86@ALTPHYEMBEVSP10.RES.AD.JPL> Message-ID: <63E24D720DCE7246ABAA722B52D23CDF0153C2564DAD@ALTPHYEMBEVSP10.RES.AD.JPL> Hi Nick, Thanks for your helpful comments. I will look at the papers and post processing code. Best, Trinh -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Nicholas E. Singh-Miller Sent: Thursday, June 18, 2009 11:56 PM To: PWSCF Forum Subject: Re: [Pw_forum] Calculation of affinity energy and ionization Hi Trinh Vo, Because you are working within periodic boundary condtions (whereas Melnikov and Chelikowsky were not). You have some errors in the energy to consider when charging the system. Assuming that your input file is as you want it (without other sources of error). A charged system (with a compensating background) will have an error in the energy that is dependent on the size of the unit cell. It is likely that you need to correct for this, either as post processing through a scheme like Makov and Payne suggest (PRB 51, 4014) or self consistently as in PRB 77, 115139 (or references therein). I believe both are to some extent implemented in QE. Hope that helps, Nick On Thu, 18 Jun 2009, Vo, Trinh wrote: > Hello, > > As a test, I performed the calculations of the ionization and affinity energy of P-doped Si nanocrystal. The steps I did as follows: > > > 1. Relax the nanostructure > 2. Remove one electron form the above relaxed structure and run scf calculation for this system to obtain ionization energy (I). > 3. Add one electron the relaxed structure (in #1) , and run scf calculation to obtain the affinity energy (A). > > The ionization energy and the affinity energy are calculated by: > > A = E(n)-E(n+1) > I = E(n-1)-E(n) > where E is the total state total energy of the n-, (n+1)-, and (n-1)-electron systems. > > When I compared the values of A and I that I obtained with those by a previous work, PRL 92, 0468021 (2004), I saw a large deviation. The difference is ~0.8eV for I and ~0.4eV for A. (I used the same structure of one the structures studied in the PRL. By the courtesy, Prof. Cheliskowki sent it to me for the test purpose). > > The calculation in the PRL is performed with real-space ab initio pseudopotential method. Their calculations of hyperfine splitting agreed very well with experimental data. > > Since my results have large differences from theirs, I am not sure if the procedures that I did above are incorrect. Could you give some comments if there is anything wrong from what I did. > > Thank you in advance your help, > > Trinh Vo > > JPL/CalTech > > > > > > > > ***************************************** Nicholas E. Singh-Miller Prof. Marzari Group (quasiamore.mit.edu) Materials Science and Engineering Massachusetts Institute of Technology 13-4066 (617)324-0372 ***************************************** _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From padmaja_patnaik at yahoo.co.uk Fri Jun 19 22:23:06 2009 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Fri, 19 Jun 2009 20:23:06 +0000 (GMT) Subject: [Pw_forum] Doubt in eigenvalues Message-ID: <564271.86986.qm@web26105.mail.ukl.yahoo.com> Dear all I am doing calculations on wide band gap semiconductor with a transition metal as impurity. Doing the scf calculations, DOS calculations, finding the magnetic moment etc. My problem comes while plotting the energy levels. What I expected that, the eigen values obtained should? indicate the splitting of levels into t2 and e sublevels. As t2 is 3 fold degenerate and e is two fold, so I expected that the eigen value which is repeated three times those corresponds to t2 and that repeated twice is for e. But the results obtained is quite confusing. I observe many sets of eigen values repeated twice and? thrice near the band gap region. I am performing calculations for both the spins. And this is happening for both spins. More than one set eigenvalues are found to be repeated twice and also thrice for the same K-point value. So how to know which one is the correct eigenvalue for t2 and e levels? Am i doing something wrong? I am looking at the dos output file for this plot. Can anybody please advise on this. Thanks in advance Regards Padmaja 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/20090619/44287e0f/attachment.htm From marzari at MIT.EDU Fri Jun 19 22:33:38 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Fri, 19 Jun 2009 16:33:38 -0400 Subject: [Pw_forum] Doubt in eigenvalues In-Reply-To: <564271.86986.qm@web26105.mail.ukl.yahoo.com> References: <564271.86986.qm@web26105.mail.ukl.yahoo.com> Message-ID: <4A3BF622.2040507@mit.edu> Dear Padmaja, 1) does the impurity give rise to isolated impurity levels ? If so, I presume you should plot band dispersions, and see flat bands. Then, you could plot the shape of the eigenstates at the Gamma point (or, if they are flat, indeed anywhere else), and see which ones look like the your eg or t2g 2) you could calculate the overlap between your states at gamma and the atomic d orbitals of you transition metal - this is done by the code when doing LDA+U calculations, so there should be an easy way (that I do not know) to print them out. 3) a more complex approach would be doing wannier postprocessing, to find out which are those impurity bands. note though that the localization procedure would probably give you random mixes of these orbitals, and you need an additional diagonalization step to recover the eg/t2g. This is explained in a M. Posternak et al Phys Rev B 2002. Any other suggestions ? nicola Padmaja Patnaik wrote: > Dear all > > I am doing calculations on wide band gap semiconductor with a transition > metal as impurity. Doing the scf calculations, DOS calculations, finding > the magnetic moment etc. My problem comes while plotting the energy > levels. What I expected that, the eigen values obtained should indicate > the splitting of levels into t2 and e sublevels. As t2 is 3 fold > degenerate and e is two fold, so I expected that the eigen value which > is repeated three times those corresponds to t2 and that repeated twice > is for e. But the results obtained is quite confusing. I observe many > sets of eigen values repeated twice and thrice near the band gap > region. I am performing calculations for both the spins. And this is > happening for both spins. More than one set eigenvalues are found to be > repeated twice and also thrice for the same K-point value. So how to > know which one is the correct eigenvalue for t2 and e levels? Am i doing > something wrong? I am looking at the dos output file for this plot. > Can anybody please advise on this. > Thanks in advance > > Regards > Padmaja -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From sohrab.ismail-beigi at yale.edu Sat Jun 20 05:43:52 2009 From: sohrab.ismail-beigi at yale.edu (Sohrab Ismail-Beigi) Date: Fri, 19 Jun 2009 23:43:52 -0400 Subject: [Pw_forum] Doubt in eigenvalues In-Reply-To: References: Message-ID: <844B6385-9D7E-446E-A1F0-4553D47C8F60@yale.edu> > Message: 7 > Date: Fri, 19 Jun 2009 20:23:06 +0000 (GMT) > From: Padmaja Patnaik > Subject: [Pw_forum] Doubt in eigenvalues > To: pw_forum at pwscf.org > Message-ID: <564271.86986.qm at web26105.mail.ukl.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all > > I am doing calculations on wide band gap semiconductor with a > transition metal as impurity. Doing the scf calculations, DOS > calculations, finding the magnetic moment etc. My problem comes > while plotting the energy levels. What I expected that, the eigen > values obtained should? indicate the splitting of levels into t2 and > e sublevels. As t2 is 3 fold degenerate and e is two fold, so I > expected that the eigen value which is repeated three times those > corresponds to t2 and that repeated twice is for e. But the results > obtained is quite confusing. I observe many sets of eigen values > repeated twice and? thrice near the band gap region. I am performing > calculations for both the spins. And this is happening for both > spins. More than one set eigenvalues are found to be repeated twice > and also thrice for the same K-point value. So how to know which one > is the correct eigenvalue for t2 and e levels? Am i doing something > wrong? I am looking at the dos output file > for this plot. > Can anybody please advise on this. > Thanks in advance > > Regards > Padmaja > > Padmaja Patnaik > > Research Scholar > > Dept of Physics > > IIT Bombay > > Mumbai, India > > ------------------------------ > > Message: 8 > Date: Fri, 19 Jun 2009 16:33:38 -0400 > From: Nicola Marzari > Subject: Re: [Pw_forum] Doubt in eigenvalues > To: PWSCF Forum > Message-ID: <4A3BF622.2040507 at mit.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Dear Padmaja, > > 1) does the impurity give rise to isolated impurity levels ? If > so, I presume you should plot band dispersions, and see flat bands. > Then, you could plot the shape of the eigenstates at the Gamma point > (or, if they are flat, indeed anywhere else), and see which ones look > like the your eg or t2g > > 2) you could calculate the overlap between your states at gamma > and the atomic d orbitals of you transition metal - this is done > by the code when doing LDA+U calculations, so there should be > an easy way (that I do not know) to print them out. > > 3) a more complex approach would be doing wannier postprocessing, > to find out which are those impurity bands. note though that the > localization procedure would probably give you random mixes of these > orbitals, and you need an additional diagonalization step to recover > the > eg/t2g. This is explained in a M. Posternak et al Phys Rev B 2002. > > Any other suggestions ? > > nicola > > > Padmaja Patnaik wrote: >> Dear all >> >> I am doing calculations on wide band gap semiconductor with a >> transition >> metal as impurity. Doing the scf calculations, DOS calculations, >> finding >> the magnetic moment etc. My problem comes while plotting the energy >> levels. What I expected that, the eigen values obtained should >> indicate >> the splitting of levels into t2 and e sublevels. As t2 is 3 fold >> degenerate and e is two fold, so I expected that the eigen value >> which >> is repeated three times those corresponds to t2 and that repeated >> twice >> is for e. But the results obtained is quite confusing. I observe many >> sets of eigen values repeated twice and thrice near the band gap >> region. I am performing calculations for both the spins. And this is >> happening for both spins. More than one set eigenvalues are found >> to be >> repeated twice and also thrice for the same K-point value. So how to >> know which one is the correct eigenvalue for t2 and e levels? Am i >> doing >> something wrong? I am looking at the dos output file for this plot. >> Can anybody please advise on this. >> Thanks in advance >> >> Regards >> Padmaja > > > -- > --------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials Science and Engineering > 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA > tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 24, Issue 43 > **************************************** Dear Padmaja, I think the first thing to do is to check point (1) of Nicola's reply --- if you don't have relatively localized (i.e. weakly dispersive in k-space) bands, then you don't have localized atomic-like states to it makes little sense to talk of e2 versus t2g type orbitals to describe the eigenstates. Here is something relatively easy to try: compute atomic projected densities of states. This is accomplished by the projwfc.x program with appropriate input file (see help under INPUT_PROJWFC.txt or something very similar depending on your version). What this means is that for each atomic orbital defining your pseudopotential on each atom of your system, the program computes the local density of states versus energy projected onto that orbital (there are details on orthogonalization which don't matter here). You'd be mainly interested in looking at the local projected density of states onto the d orbitals of the transition metal impurity. See if there are large projections onto those orbitals in the vicinity of the band gap or where you believe the states should be. Note that the density of states is computed by projecting each eigenstate onto the orbitals and then summing up all the contribtuions from all the eigenstates, so if you use a narrow broadening, you can pick out individual eigenstate peaks since you know their eigenenergies from the output. The program computes not only projections onto all the d-states of an atom summed up but also onto the individual d orbitals (xy,xz,yz,3z^2- r^2,x^2-y^2): assuming your system has some symmetry and you set up your axes to be along those symmetry axes, this often means some of these very orbitals are t2g and some are e2g --- you can then check to see which particular ones have large projections at what energies. The ordering has been documented and discussed in other parts of the forum. This would be a simple first step to get things going... Best of luck, --------------------------------------------- Sohrab Ismail-Beigi Associate Professor of Applied Physics and Physics Dept. of Applied Physics Yale University P.O. Box 208284 New Haven, CT 06520 Phone: 203.432.2107 Fax: 203.432.4283 Email: sohrab.ismail-beigi at yale.edu http://volga.eng.yale.edu/ - group home page http://www.eng.yale.edu/aphy/ - dept. page w/ links http://www.eng.yale.edu/graduate -- info about graduate studies in AP and brochures From jameslipd at gmail.com Sun Jun 21 05:59:47 2009 From: jameslipd at gmail.com (JAY) Date: Sun, 21 Jun 2009 11:59:47 +0800 Subject: [Pw_forum] radius distribution function Message-ID: Dear users Could anybody send me the fortran code for calculating radius distribution function? I would like to analyze the MD results. Many thanks. -- Sincerely Jay ============================================== cn: Li, Jiaye en: Jay Y. Lee M.S. in designing and developing novel materials Research experience: *ALD precursor. ie. Metal complexes *Surface modification. ie. Indium tin oxide, SiO2 *Gas storage and adsorption. ie. Ionic Liquids Skills: *ab-initial method, DFT simulation and Force Field simulation Please contact me at: 1. jameslipd at gmail.com or 2. jameslibd at gmail.com ============================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090621/7c3e951c/attachment.htm From mozaharphysics25 at yahoo.com Sun Jun 21 07:20:33 2009 From: mozaharphysics25 at yahoo.com (Mozahar Ali) Date: Sat, 20 Jun 2009 22:20:33 -0700 (PDT) Subject: [Pw_forum] eigenvalues not converged Message-ID: <356339.29569.qm@web58507.mail.re3.yahoo.com> Dear pwscf user, After successfully completing the elph.ph run i have got an warning messege which is given below Band Structure Calculation Davidson diagonalization with overlap WARNING: 3 eigenvalues not converged WARNING: 1 eigenvalues not converged WARNING: 2 eigenvalues not converged WARNING: 3 eigenvalues not converged WARNING: 3 eigenvalues not converged WARNING: 3 eigenvalues not converged WARNING: 2 eigenvalues not converged WARNING: 2 eigenvalues not converged WARNING: 1 eigenvalues not converged WARNING: 3 eigenvalues not converged WARNING: 3 eigenvalues not converged WARNING: 2 eigenvalues not converged WARNING: 2 eigenvalues not converged WARNING: 3 eigenvalues not converged WARNING: 2 eigenvalues not converged WARNING: 1 eigenvalues not converged WARNING: 1 eigenvalues not converged WARNING: 1 eigenvalues not converged WARNING: 2 eigenvalues not converged WARNING: 3 eigenvalues not converged WARNING: 2 eigenvalues not converged WARNING: 2 eigenvalues not converged WARNING: 2 eigenvalues not converged WARNING: 1 eigenvalues not converged WARNING: 1 eigenvalues not converged WARNING: 1 eigenvalues not converged WARNING: 1 eigenvalues not converged WARNING: 1 eigenvalues not converged WARNING: 3 eigenvalues not converged WARNING: 3 eigenvalues not converged WARNING: 2 eigenvalues not converged WARNING: 2 eigenvalues not converged WARNING: 2 eigenvalues not converged WARNING: 1 eigenvalues not converged WARNING: 1 eigenvalues not converged WARNING: 1 eigenvalues not converged WARNING: 2 eigenvalues not converged WARNING: 1 eigenvalues not converged WARNING: 1 eigenvalues not converged WARNING: 1 eigenvalues not converged ethr = 4.35E-11, avg # of iterations = 41.4 But run is complete successfully. Is it serious error?Can it affect on Tc calculation? How can we remove this warning? Can anybody suggest me please? mozahar research student R.U Bangladesh New Email addresses available on Yahoo! Get the Email name you've always wanted on the new @ymail and @rocketmail. Hurry before someone else does! http://mail.promotions.yahoo.com/newdomains/aa/ From anvari_meh at physics.iust.ac.ir Sun Jun 21 14:06:50 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Sun, 21 Jun 2009 15:36:50 +0330 Subject: [Pw_forum] frequency in gamma point Message-ID: Hi(Do you mean that the frequency obtained for the same q vector (0,0,0 in this case) is different if you perform a single q-point calculation w.r.t the frequency obtained when that q-point is included in a q-point grid (like the 221 you mention). This seems quite improbable to me.)Well, I have to say that unfortunately your first assumption is correct Mehrnaz Iran University of science & technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090621/dd6a1501/attachment.htm From giannozz at democritos.it Sun Jun 21 13:44:16 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 21 Jun 2009 13:44:16 +0200 Subject: [Pw_forum] frequency in gamma point In-Reply-To: References: Message-ID: <111501CC-29FE-4510-BA43-864A17CB4B62@democritos.it> On Jun 21, 2009, at 14:06 , Mehrnaz Anvari wrote: > (Do you mean that the frequency obtained for the same q vector > (0,0,0 in this case) is different if you perform a single q-point > calculation > w.r.t the frequency obtained when that q-point is included in a q- > point grid > (like the 221 you mention). This seems quite improbable to me.) > Well, I have to say that unfortunately your first assumption is > correct you did something wrong. Remember to re-run the scf calculation, or to save and restore the data file from the scf calculation. The phonon calculation unfortunately overwrites the data file (fixed in the cvs version) Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Jun 21 13:47:05 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 21 Jun 2009 13:47:05 +0200 Subject: [Pw_forum] eigenvalues not converged In-Reply-To: <356339.29569.qm@web58507.mail.re3.yahoo.com> References: <356339.29569.qm@web58507.mail.re3.yahoo.com> Message-ID: <7B663AB4-433B-4340-85A0-B45A5AC029DC@democritos.it> On Jun 21, 2009, at 7:20 , Mozahar Ali wrote: > WARNING: 3 eigenvalues not converged > ... > ethr = 4.35E-11, avg # of iterations = 41.4 > But run is complete successfully. > Is it serious error? please see the user guide, troubleshooting section, item 1.26 P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From quantumdft at gmail.com Mon Jun 22 10:39:14 2009 From: quantumdft at gmail.com (vega lew) Date: Mon, 22 Jun 2009 16:39:14 +0800 Subject: [Pw_forum] what's the difference between 'md' in pw.x and cp.x Message-ID: <412f6c680906220139r1a687e96u1046d6e006d260cd@mail.gmail.com> Dear all, I want to perform ab initio molecular dynamics calculation via Q-E. I found both cp.x and pw.x could undertake this calculation. I wonder what's the difference between 'md' in pw.x and cp.x, and if I could achieve the same final geometry for same systems (the coordinates of atoms, temparature, box dimensions and K-ponits etc. are exactly the same) by this two methods. Do you think both 'md' calculation in pw.x and 'cp' in cp.x could be regard as the 'Car-Parrinello Molecular Dynamics' calculation and do the almost the same thing as the 'CPMD' codes copyrighted jointly by IBM Corp. thank you for reading best, vega -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090622/489dd607/attachment.htm From hqzhou at nju.edu.cn Mon Jun 22 12:38:31 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 22 Jun 2009 18:38:31 +0800 Subject: [Pw_forum] what's the difference between 'md' in pw.x and cp.x References: <412f6c680906220139r1a687e96u1046d6e006d260cd@mail.gmail.com> Message-ID: <39E0D19FF3294E7586A97FC98B878270@solarflare> 'md' in PWscf may most likely be BOMD. Zhou Huiqun ----- Original Message ----- From: vega lew To: PWSCF Forum Sent: Monday, June 22, 2009 4:39 PM Subject: [Pw_forum] what's the difference between 'md' in pw.x and cp.x Dear all, I want to perform ab initio molecular dynamics calculation via Q-E. I found both cp.x and pw.x could undertake this calculation. I wonder what's the difference between 'md' in pw.x and cp.x, and if I could achieve the same final geometry for same systems (the coordinates of atoms, temparature, box dimensions and K-ponits etc. are exactly the same) by this two methods. Do you think both 'md' calculation in pw.x and 'cp' in cp.x could be regard as the 'Car-Parrinello Molecular Dynamics' calculation and do the almost the same thing as the 'CPMD' codes copyrighted jointly by IBM Corp. thank you for reading best, vega -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** ------------------------------------------------------------------------------ _______________________________________________ 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/20090622/69a563c7/attachment.htm From giannozz at democritos.it Mon Jun 22 12:41:27 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 22 Jun 2009 12:41:27 +0200 Subject: [Pw_forum] what's the difference between 'md' in pw.x and cp.x In-Reply-To: <412f6c680906220139r1a687e96u1046d6e006d260cd@mail.gmail.com> References: <412f6c680906220139r1a687e96u1046d6e006d260cd@mail.gmail.com> Message-ID: <4A3F5FD7.9030704@democritos.it> vega lew wrote: > Do you think both 'md' calculation in pw.x and 'cp' in cp.x could be > regard as the 'Car-Parrinello Molecular Dynamics' calculation no: pw.x performs molecular dynamics (MD) with electrons on the ground state (also known as Born-Oppenheimer MD). cp.x performs Car-Parrinello MD. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From akohlmey at cmm.chem.upenn.edu Mon Jun 22 15:00:12 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 22 Jun 2009 09:00:12 -0400 Subject: [Pw_forum] what's the difference between 'md' in pw.x and cp.x In-Reply-To: <412f6c680906220139r1a687e96u1046d6e006d260cd@mail.gmail.com> References: <412f6c680906220139r1a687e96u1046d6e006d260cd@mail.gmail.com> Message-ID: <7b6913e90906220600r779396ddh2ea7748d40eec9a7@mail.gmail.com> On Mon, Jun 22, 2009 at 4:39 AM, vega lew wrote: > Dear all, > > I want to perform ab initio molecular dynamics calculation via Q-E. I found > both cp.x and pw.x could undertake this calculation. > I wonder what's the difference between 'md' in pw.x and cp.x, and if I could > achieve the same final geometry for same systems (the coordinates of atoms, > temparature, box dimensions and K-ponits etc. are exactly the same) by this > two methods. with MD you will never get the exact same end configuration out of two trajectories if there are the tiniest differences, let alone they are done with two different codes or slightly different methods. this doesn't matter, because the individual geometry doesn't matter, only the ensemble. n.b.: cp.x only supports gamma point. > Do you think both 'md' calculation in pw.x and 'cp' in cp.x could be regard > as the 'Car-Parrinello Molecular Dynamics' calculation and do the almost the > same thing as the 'CPMD' codes copyrighted jointly by IBM Corp. cp.x and CPMD have the same origin. both codes can perform CP dynamics, but also born-oppenheimer MD. however, both codes cater somewhat different communities and thus are better suited for specific but different scenarios. pw.x only does born-oppenheimer dynamics. for some systems, CP dynamics can be much more efficient, but the CP method imposes limitations, that have to be understood to do correct calculations. cheers, axel. > thank you for reading > > best, > > vega > -- > ================================================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > ****************************************************************************************************************** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, > Jiangsu, China > ****************************************************************************************************************** > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From zubaexy at gmail.com Mon Jun 22 15:27:33 2009 From: zubaexy at gmail.com (Zubaer Hossain) Date: Mon, 22 Jun 2009 08:27:33 -0500 Subject: [Pw_forum] Transport calculation tutorials Message-ID: <51ec861d0906220627p6ae6a19an10bc16c905867cd3@mail.gmail.com> Hi, I am interested to perform transport calculations. I was wondering if there were any tutorials explaining 'how to's', 'effects of finite cross-section of the leads, type of connection between leads and scattering region' etc. I read the input file description for using pwcond.x; it might be useful to learn some critical stuffs about transport calculation using QE e.g. convergence of transmission coe w.r.t k-points. A brief review/hint or pointing to any paper explaining details of QE calculations would have been great. Thanks in advance, Zubaer Department of Mechanical Science and Engineering Univ. of Illinois at Urbana-Champaign, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090622/4861873f/attachment.htm From sclauzer at sissa.it Mon Jun 22 17:39:25 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 22 Jun 2009 17:39:25 +0200 Subject: [Pw_forum] Transport calculation tutorials In-Reply-To: <51ec861d0906220627p6ae6a19an10bc16c905867cd3@mail.gmail.com> References: <51ec861d0906220627p6ae6a19an10bc16c905867cd3@mail.gmail.com> Message-ID: <4A3FA5AD.9030808@sissa.it> Hi Zubaer, Zubaer Hossain wrote: > Hi, > > I am interested to perform transport calculations. > > I was wondering if there were any tutorials explaining 'how to's', To my knowledge there are no tutorials (intended as that) about conductance calculations with QE, so far. > 'effects of finite cross-section of the leads, type of connection > between leads and scattering region' etc. I think this is system specific, not QE specific. It depends of the physical system you want to investigate and how you want to model it. > I read the input file > description for using pwcond.x; it might be useful to learn some > critical stuffs about transport calculation using QE e.g. Since Alexander will be away and busy for few days, I dare to point you to his personal web page (hoping he will not blame me...) that, though still under construction, has slides about PWCOND as well as some examples and links to all the reference papers. http://people.sissa.it/~smogunov > convergence of > transmission coe w.r.t k-points. Again, I think this is not specific of QE calculations, but of any other transport code which uses PBCs. I think you should have a look at this work by Thygesen: in journal: Phys. rev B (ISSN: ) , vol: 72, pages: 033401-1 - 033401-4, 2005 In my limited experience with k-dependent transmission calculations, I can say that the number of k_perpendicular points needed to converge the transmission can vary quite a lot depending on the cross section of your supercell and of the number of band edges in the complex band structure around the scattering energy you are considering (and this makes the convergence somehow energy-dependent). Regards GS > A brief review/hint or pointing to any > paper explaining details of QE calculations would have been great. > > Thanks in advance, > Zubaer > Department of Mechanical Science and Engineering > Univ. of Illinois at Urbana-Champaign, USA > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Jun 22 18:06:10 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 22 Jun 2009 18:06:10 +0200 Subject: [Pw_forum] Transport calculation tutorials In-Reply-To: <4A3FA5AD.9030808@sissa.it> References: <51ec861d0906220627p6ae6a19an10bc16c905867cd3@mail.gmail.com> <4A3FA5AD.9030808@sissa.it> Message-ID: <4A3FABF2.6070900@sissa.it> Gabriele Sclauzero wrote: > Hi Zubaer, > > > Since Alexander will be away and busy for few days, I dare to point you to his personal > web page (hoping he will not blame me...) that, though still under construction, has Sorry, I should not have said "under construction"... it seems actually finished and working. So you can check the material there to get an idea on how to start conductance calculations with QE. Please also have a look at the example12 (and also example22) in the examples directory of QE. GS > slides about PWCOND as well as some examples and links to all the reference papers. > > http://people.sissa.it/~smogunov > > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From zubaexy at gmail.com Mon Jun 22 18:28:29 2009 From: zubaexy at gmail.com (Zubaer Hossain) Date: Mon, 22 Jun 2009 11:28:29 -0500 Subject: [Pw_forum] Transport calculation tutorials In-Reply-To: <4A3FABF2.6070900@sissa.it> References: <51ec861d0906220627p6ae6a19an10bc16c905867cd3@mail.gmail.com> <4A3FA5AD.9030808@sissa.it> <4A3FABF2.6070900@sissa.it> Message-ID: <51ec861d0906220928y2e44325k86997c41d5d97624@mail.gmail.com> Hi Gabriele Sclauzero, Thank you for your quick reply. I was looking for modeling steps in QE and general concerns in transport calculations before I launch expensive calculations. Alexander's notes provide excellent explanations to my querries. Thank you again for referring me to the page, and thanks Alexander for his helpful notes. Thanks, Zubaer On Mon, Jun 22, 2009 at 11:06 AM, Gabriele Sclauzero wrote: > > > Gabriele Sclauzero wrote: > > Hi Zubaer, > > > > > > Since Alexander will be away and busy for few days, I dare to point you > to his personal > > web page (hoping he will not blame me...) that, though still under > construction, has > > Sorry, I should not have said "under construction"... it seems actually > finished and > working. So you can check the material there to get an idea on how to start > conductance > calculations with QE. Please also have a look at the example12 (and also > example22) in the > examples directory of QE. > > GS > > > > slides about PWCOND as well as some examples and links to all the > reference papers. > > > > http://people.sissa.it/~smogunov > > > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > 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/20090622/45fdd1b3/attachment-0001.htm From sophia.nishad at gmail.com Tue Jun 23 01:03:39 2009 From: sophia.nishad at gmail.com (Jonathan) Date: Mon, 22 Jun 2009 18:03:39 -0500 Subject: [Pw_forum] Separating Raman modes Message-ID: <8a0137e60906221603t718784b7x228e5f6684d3825c@mail.gmail.com> Dear users, I computed phonons only at the gamma point for a 64-atom binary alloy. How do I separate the three main Raman modes. Would it be possible to get some help? thanks, -- Sophia UCB, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090622/80dbcb1b/attachment.htm From quantumdft at gmail.com Tue Jun 23 07:34:48 2009 From: quantumdft at gmail.com (vega lew) Date: Tue, 23 Jun 2009 13:34:48 +0800 Subject: [Pw_forum] what's the difference between 'md' in pw.x and cp.x In-Reply-To: <7b6913e90906220600r779396ddh2ea7748d40eec9a7@mail.gmail.com> References: <412f6c680906220139r1a687e96u1046d6e006d260cd@mail.gmail.com> <7b6913e90906220600r779396ddh2ea7748d40eec9a7@mail.gmail.com> Message-ID: <412f6c680906222234h45c3ed2p886ce13e789bbe3@mail.gmail.com> Dear friends, Thank you for you time for reading and answering my questions. I realized that the ensemble is much more important than one snap of the whole run, resembling the classical MD to some extent. I used to ask "if I could achieve the same final geometry for same systems (the coordinates of atoms, temparature, box dimensions and K-ponits etc. are exactly the same) by this two methods." I didn't mean the same coordinates of the final systems. I wonder if the different methods with same input coordinates will give us the same conclusion. For example, By relax calculation by pw.x water disociative adsorption is extremely favorable at certain metal surface with a minute barrier of ~0.20 eV given by NEB method. But before the calculation we didn't know this. Suppose we know nothing about it before the ab initio MD calcualtions. We only take ab initio MD, and we put a integrated water molecule at certain site on the surface. and then we perform MD calculations of different method, such as CPMD, cp.x, pw.x(calcualtion='md'). I wonder whether the dissociative state could be acheived on the surface at very low temparature (such as 100K or below) via all the MD calculations mentioned above? From sclauzer at sissa.it Tue Jun 23 09:03:49 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 23 Jun 2009 09:03:49 +0200 Subject: [Pw_forum] radius distribution function In-Reply-To: References: Message-ID: <4A407E55.5070704@sissa.it> Dear Jay, JAY wrote: > Dear users > > Could anybody send me the fortran code for calculating radius > distribution function? I would like to analyze the MD results. Many thanks. If you meant "radial distribution function", I think you can find good recipes on how to write it on any molecular dynamics textbook, from the old classics by Frenkel-Smit or Allen-Tildesley to the modern ones. If you are really in trouble I can send you a fortran code from a course on atomistic simulations I followed at University (at the moment I'm not doing molecular dynamics calculations), but I think there are many people doing much more sophisticated things on this forum. They could help you better than me. GS > > -- > Sincerely > > Jay > > > ============================================== > cn: Li, Jiaye > en: Jay Y. Lee > > M.S. in designing and developing novel materials > > Research experience: > *ALD precursor. ie. Metal complexes > *Surface modification. ie. Indium tin oxide, SiO2 > *Gas storage and adsorption. ie. Ionic Liquids > > Skills: > *ab-initial method, DFT simulation and Force Field simulation > > Please contact me at: > 1. jameslipd at gmail.com or > 2. jameslibd at gmail.com > > ============================================== > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From alexandra.carvalho at epfl.ch Tue Jun 23 10:31:06 2009 From: alexandra.carvalho at epfl.ch (alexandra.carvalho at epfl.ch) Date: Tue, 23 Jun 2009 10:31:06 +0200 Subject: [Pw_forum] Separating Raman modes In-Reply-To: <8a0137e60906221603t718784b7x228e5f6684d3825c@mail.gmail.com> References: <8a0137e60906221603t718784b7x228e5f6684d3825c@mail.gmail.com> Message-ID: <20090623103106.17671jzible9ehu2@webmail.epfl.ch> Dear Sophia, To select which modes are Raman active you must use the selection rules. The following paper may be of help (see also the tables in it): Rosseau et al. Journal of Raman Spectroscopy 10, 253 (1981) If you are starting, I recommend having a look at the selection rules for molecules, for example in Tinkham, Group theory and Quantum mechanics (Dover, 1992,NY) pp248. Most likelly, you will be interested in the allowed transitions with highest frequency. Hope this helps, Alexandra Quoting Jonathan : > Dear users, > > I computed phonons only at the gamma point for a 64-atom binary > alloy. How do I separate the three main Raman modes. > > Would it be possible to get some help? > thanks, > -- > Sophia > UCB, USA > -- Alexandra Carvalho, Ceramics Laboratory Swiss Federal Institute of Technology of Lausanne (EPFL) From vladan.stevanovic at epfl.ch Tue Jun 23 11:29:28 2009 From: vladan.stevanovic at epfl.ch (Vladan Stevanovic) Date: Tue, 23 Jun 2009 11:29:28 +0200 Subject: [Pw_forum] Zero of the electrostatic potential ? Message-ID: <4A40A078.4060305@epfl.ch> Dear Quantum-ESPRESSO users, I am using QE for simulations of transition metal clusters. My question is where the code places the vacuum level in such calculations (nonperiodic systems in a big cell) ? To formulate differently, is it possible to compare directly KS eigenvalues from different calculations ? Thanks, Vladan Stevanovic --------------------------------------------- Assistant-doctorant EPFL SB IRRMA-GE PH H2 435 (B?timent PH) Station 3 CH-1015 Lausanne tel. : +41 (0)21 693 51 08 e-mail : vladan.stevanovic at epfl.ch --------------------------------------------- From sclauzer at sissa.it Tue Jun 23 11:46:13 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 23 Jun 2009 11:46:13 +0200 Subject: [Pw_forum] Zero of the electrostatic potential ? In-Reply-To: <4A40A078.4060305@epfl.ch> References: <4A40A078.4060305@epfl.ch> Message-ID: <4A40A465.40805@sissa.it> Vladan Stevanovic wrote: > Dear Quantum-ESPRESSO users, > > I am using QE for simulations of transition metal clusters. My question > is where the code places the vacuum level in such calculations > (nonperiodic systems in a big cell) ? To formulate differently, is it I think this question has been often posed and replied in the context of work-function calculation. Please first try a search on the archives using 'work function' or something similar as keys. You can also have a look to the example in examples/WorkFct_example in the QE folder. > possible to compare directly KS eigenvalues from different calculations ? If you want compare the distance between the eigenvalues and the Fermi energies in the respective systems, I think you can. In order to understand if you can compare the absolute (i.e. not relative to E_F) value of the eigenvalues I think you must first find the answer to your previous question. GS > > > Thanks, > Vladan Stevanovic > > --------------------------------------------- > Assistant-doctorant > EPFL SB IRRMA-GE > PH H2 435 (B?timent PH) > Station 3 > CH-1015 Lausanne > tel. : +41 (0)21 693 51 08 > e-mail : vladan.stevanovic at epfl.ch > --------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From paulatto at sissa.it Tue Jun 23 12:00:01 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 23 Jun 2009 12:00:01 +0200 Subject: [Pw_forum] Zero of the electrostatic potential ? In-Reply-To: <4A40A078.4060305@epfl.ch> References: <4A40A078.4060305@epfl.ch> Message-ID: In data 23 giugno 2009 alle ore 11:29:28, Vladan Stevanovic ha scritto: > I am using QE for simulations of transition metal clusters. My question > is where the code places the vacuum level in such calculations > (nonperiodic systems in a big cell) ? Dear Vladan, a non-periodic system in a big periodic cell is still a periodic system! Hence, the integral of the potential over any possible choice of primitive cell has to be zero. This is a sufficient condition to find the zero. > To formulate differently, is it > possible to compare directly KS eigenvalues from different calculations ? In general it is NOT possible to directly compare eigenvalues of different calculations, nevertheless they can be compared taking the Fermi energy as reference. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From degironc at sissa.it Tue Jun 23 12:08:03 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 23 Jun 2009 12:08:03 +0200 Subject: [Pw_forum] Zero of the electrostatic potential ? In-Reply-To: <4A40A078.4060305@epfl.ch> References: <4A40A078.4060305@epfl.ch> Message-ID: <4A40A983.7080108@sissa.it> The zero of the potential energy is the average electrostatic potential; as such the eigenvalues in different systems cannot be directly compared. what you need yo do is to calculate the (electrostatic) potential energy in the vacuum region where it should, at least for neutral systems, be constant and take that as the zero of the energy. In order to calculate the potential in the vacuum region one could adapt the example for the calculation of the Work Function in directory examples/WorkFct_example. stefano Vladan Stevanovic wrote: > Dear Quantum-ESPRESSO users, > > I am using QE for simulations of transition metal clusters. My question > is where the code places the vacuum level in such calculations > (nonperiodic systems in a big cell) ? To formulate differently, is it > possible to compare directly KS eigenvalues from different calculations ? > > Thanks, > Vladan Stevanovic > > --------------------------------------------- > Assistant-doctorant > EPFL SB IRRMA-GE > PH H2 435 (B?timent PH) > Station 3 > CH-1015 Lausanne > tel. : +41 (0)21 693 51 08 > e-mail : vladan.stevanovic at epfl.ch > --------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Tue Jun 23 12:07:10 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 23 Jun 2009 12:07:10 +0200 Subject: [Pw_forum] Zero of the electrostatic potential ? In-Reply-To: <4A40A078.4060305@epfl.ch> References: <4A40A078.4060305@epfl.ch> Message-ID: <8CD924AB-2D4E-402A-BF90-A3A392886FBB@democritos.it> On Jun 23, 2009, at 11:29 , Vladan Stevanovic wrote: > where the code places the vacuum level in such calculations > (nonperiodic systems in a big cell) ? To formulate differently, > is it possible to compare directly KS eigenvalues from different > calculations ? short answer: no. V(G=0) is calculated (finite or infinite systems doesn't matter) as described in the attached notes. CP and PWscf have a different definition of V(0) so you get the same eigenvalues, but displaced P. -------------- next part -------------- A non-text attachment was scrubbed... Name: plane_waves.tex Type: application/octet-stream Size: 32445 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090623/9e391ac7/attachment-0001.obj -------------- next part -------------- --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From greatnaol at gmail.com Tue Jun 23 13:58:38 2009 From: greatnaol at gmail.com (Naol Regassa) Date: Tue, 23 Jun 2009 14:58:38 +0300 Subject: [Pw_forum] smaller band gaps Message-ID: <97e4b88e0906230458l7ed16454m5cc504ef06deec73@mail.gmail.com> Dear all I was using QE.4.1 to calculate the electronic structure of SrMnO_3 employing GGA+U but I got small band gap of 0.7 eV which is semi-metal (experimentally insulator). My main concern is that DFT calculations reduce band gaps by 50%. Does this mean that I can add this error to get the correct band gap so that any body can understand it? How can one argue about this condition? Tamene Student at AAU Ethiopia On 6/23/09, pw_forum-request at pwscf.org wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://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: radius distribution function (Gabriele Sclauzero) > 2. Re: Separating Raman modes (alexandra.carvalho at epfl.ch) > 3. Zero of the electrostatic potential ? (Vladan Stevanovic) > 4. Re: Zero of the electrostatic potential ? (Gabriele Sclauzero) > 5. Re: Zero of the electrostatic potential ? (Lorenzo Paulatto) > 6. Re: Zero of the electrostatic potential ? (Stefano de Gironcoli) > 7. Re: Zero of the electrostatic potential ? (Paolo Giannozzi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 23 Jun 2009 09:03:49 +0200 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] radius distribution function > To: PWSCF Forum > Message-ID: <4A407E55.5070704 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Jay, > > JAY wrote: >> Dear users >> >> Could anybody send me the fortran code for calculating radius >> distribution function? I would like to analyze the MD results. Many >> thanks. > > If you meant "radial distribution function", I think you can find good > recipes on how to > write it on any molecular dynamics textbook, from the old classics by > Frenkel-Smit or > Allen-Tildesley to the modern ones. If you are really in trouble I can send > you a fortran > code from a course on atomistic simulations I followed at University (at the > moment I'm > not doing molecular dynamics calculations), but I think there are many > people doing much > more sophisticated things on this forum. They could help you better than me. > > GS > > > >> >> -- >> Sincerely >> >> Jay >> >> >> ============================================== >> cn: Li, Jiaye >> en: Jay Y. Lee >> >> M.S. in designing and developing novel materials >> >> Research experience: >> *ALD precursor. ie. Metal complexes >> *Surface modification. ie. Indium tin oxide, SiO2 >> *Gas storage and adsorption. ie. Ionic Liquids >> >> Skills: >> *ab-initial method, DFT simulation and Force Field simulation >> >> Please contact me at: >> 1. jameslipd at gmail.com or >> 2. jameslibd at gmail.com >> >> ============================================== >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > > > ------------------------------ > > Message: 2 > Date: Tue, 23 Jun 2009 10:31:06 +0200 > From: alexandra.carvalho at epfl.ch > Subject: Re: [Pw_forum] Separating Raman modes > To: PWSCF Forum > Message-ID: <20090623103106.17671jzible9ehu2 at webmail.epfl.ch> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Dear Sophia, > > To select which modes are Raman active you must use the selection rules. > The following paper may be of help (see also the tables in it): > > Rosseau et al. Journal of Raman Spectroscopy 10, 253 (1981) > > If you are starting, I recommend having a look at the selection rules > for molecules, for example in Tinkham, Group theory and Quantum > mechanics (Dover, 1992,NY) pp248. > > Most likelly, you will be interested in the allowed transitions with highest > frequency. > > Hope this helps, > > Alexandra > > > Quoting Jonathan : > >> Dear users, >> >> I computed phonons only at the gamma point for a 64-atom binary >> alloy. How do I separate the three main Raman modes. >> >> Would it be possible to get some help? >> thanks, >> -- >> Sophia >> UCB, USA >> > > > > -- > > Alexandra Carvalho, > Ceramics Laboratory > Swiss Federal Institute of Technology of Lausanne (EPFL) > > > > ------------------------------ > > Message: 3 > Date: Tue, 23 Jun 2009 11:29:28 +0200 > From: Vladan Stevanovic > Subject: [Pw_forum] Zero of the electrostatic potential ? > To: pw_forum at pwscf.org > Message-ID: <4A40A078.4060305 at epfl.ch> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Quantum-ESPRESSO users, > > I am using QE for simulations of transition metal clusters. My question > is where the code places the vacuum level in such calculations > (nonperiodic systems in a big cell) ? To formulate differently, is it > possible to compare directly KS eigenvalues from different calculations ? > > > Thanks, > Vladan Stevanovic > > --------------------------------------------- > Assistant-doctorant > EPFL SB IRRMA-GE > PH H2 435 (B?timent PH) > Station 3 > CH-1015 Lausanne > tel. : +41 (0)21 693 51 08 > e-mail : vladan.stevanovic at epfl.ch > --------------------------------------------- > > > > ------------------------------ > > Message: 4 > Date: Tue, 23 Jun 2009 11:46:13 +0200 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] Zero of the electrostatic potential ? > To: PWSCF Forum > Message-ID: <4A40A465.40805 at sissa.it> > Content-Type: text/plain; charset=iso-8859-1; format=flowed > > > > Vladan Stevanovic wrote: >> Dear Quantum-ESPRESSO users, >> >> I am using QE for simulations of transition metal clusters. My question >> is where the code places the vacuum level in such calculations >> (nonperiodic systems in a big cell) ? To formulate differently, is it > > I think this question has been often posed and replied in the context of > work-function > calculation. Please first try a search on the archives using 'work function' > or something > similar as keys. You can also have a look to the example in > > examples/WorkFct_example > > in the QE folder. > >> possible to compare directly KS eigenvalues from different calculations ? > > If you want compare the distance between the eigenvalues and the Fermi > energies in the > respective systems, I think you can. In order to understand if you can > compare the > absolute (i.e. not relative to E_F) value of the eigenvalues I think you > must first find > the answer to your previous question. > > > GS > > >> >> >> Thanks, >> Vladan Stevanovic >> >> --------------------------------------------- >> Assistant-doctorant >> EPFL SB IRRMA-GE >> PH H2 435 (B?timent PH) >> Station 3 >> CH-1015 Lausanne >> tel. : +41 (0)21 693 51 08 >> e-mail : vladan.stevanovic at epfl.ch >> --------------------------------------------- >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > > > ------------------------------ > > Message: 5 > Date: Tue, 23 Jun 2009 12:00:01 +0200 > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] Zero of the electrostatic potential ? > To: vladan.stevanovic at epfl.ch, "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 23 giugno 2009 alle ore 11:29:28, Vladan Stevanovic > ha scritto: >> I am using QE for simulations of transition metal clusters. My question >> is where the code places the vacuum level in such calculations >> (nonperiodic systems in a big cell) ? > > Dear Vladan, > a non-periodic system in a big periodic cell is still a periodic system! > Hence, the integral of the potential over any possible choice of primitive > cell has to be zero. This is a sufficient condition to find the zero. > >> To formulate differently, is it >> possible to compare directly KS eigenvalues from different calculations ? > > In general it is NOT possible to directly compare eigenvalues of different > calculations, nevertheless they can be compared taking the Fermi energy as > reference. > > best regards > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > > > ------------------------------ > > Message: 6 > Date: Tue, 23 Jun 2009 12:08:03 +0200 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] Zero of the electrostatic potential ? > To: vladan.stevanovic at epfl.ch, PWSCF Forum > Message-ID: <4A40A983.7080108 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > The zero of the potential energy is the average electrostatic potential; > as such the eigenvalues in different systems cannot be directly compared. > what you need yo do is to calculate the (electrostatic) potential energy > in the vacuum region where it should, at least for neutral systems, be > constant and take that as the zero of the energy. > In order to calculate the potential in the vacuum region one could adapt > the example for the calculation of the Work Function in directory > examples/WorkFct_example. > > stefano > > Vladan Stevanovic wrote: >> Dear Quantum-ESPRESSO users, >> >> I am using QE for simulations of transition metal clusters. My question >> is where the code places the vacuum level in such calculations >> (nonperiodic systems in a big cell) ? To formulate differently, is it >> possible to compare directly KS eigenvalues from different calculations ? >> > >> Thanks, >> Vladan Stevanovic >> >> --------------------------------------------- >> Assistant-doctorant >> EPFL SB IRRMA-GE >> PH H2 435 (B?timent PH) >> Station 3 >> CH-1015 Lausanne >> tel. : +41 (0)21 693 51 08 >> e-mail : vladan.stevanovic at epfl.ch >> --------------------------------------------- >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > ------------------------------ > > Message: 7 > Date: Tue, 23 Jun 2009 12:07:10 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Zero of the electrostatic potential ? > To: vladan.stevanovic at epfl.ch, PWSCF Forum > Message-ID: <8CD924AB-2D4E-402A-BF90-A3A392886FBB at democritos.it> > Content-Type: text/plain; charset="us-ascii" > > > On Jun 23, 2009, at 11:29 , Vladan Stevanovic wrote: > >> where the code places the vacuum level in such calculations >> (nonperiodic systems in a big cell) ? To formulate differently, >> is it possible to compare directly KS eigenvalues from different >> calculations ? > > short answer: no. > > V(G=0) is calculated (finite or infinite systems doesn't matter) > as described in the attached notes. CP and PWscf have a > different definition of V(0) so you get the same eigenvalues, > but displaced > > P. > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: plane_waves.tex > Type: application/octet-stream > Size: 32445 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/pw_forum/attachments/20090623/9e391ac7/attachment.obj > -------------- next part -------------- > > > --- > Paolo Giannozzi, Dept of Physics, University of 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 24, Issue 49 > **************************************** > From akohlmey at cmm.chem.upenn.edu Tue Jun 23 14:28:07 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 23 Jun 2009 08:28:07 -0400 Subject: [Pw_forum] what's the difference between 'md' in pw.x and cp.x In-Reply-To: <412f6c680906222234h45c3ed2p886ce13e789bbe3@mail.gmail.com> References: <412f6c680906220139r1a687e96u1046d6e006d260cd@mail.gmail.com> <7b6913e90906220600r779396ddh2ea7748d40eec9a7@mail.gmail.com> <412f6c680906222234h45c3ed2p886ce13e789bbe3@mail.gmail.com> Message-ID: <1245760087.5775.18.camel@zero> On Tue, 2009-06-23 at 13:34 +0800, vega lew wrote: > Dear friends, > > Thank you for you time for reading and answering my questions. > > I realized that the ensemble is much more important than one snap of > the whole run, resembling the classical MD to some extent. there is _no_ difference between classical MD and ab initio MD in this respect. the only difference between the two is how you get the forces. statistical mechanics doesn't care about the forces only about configurations and ensembles. [...] > we put a integrated water molecule at certain site on the surface. and > then we perform MD calculations of different method, such as CPMD, > cp.x, pw.x(calcualtion='md'). I wonder whether the dissociative state > could be acheived on the surface at very low temparature (such as 100K > or below) via all the MD calculations mentioned above? you have to look at this from a different perspective. what you will see, depends on the potential surfaces of the system, that you are studying. running MD allows your system to sample different local minima, provided the barriers between them are small enough. if you run at low temperature, your MD will not be very different from a geometry optimization. > From your answers, I see cp.x and CPMD of IBM CORP. is using > 'Car-Parrinello Molecular Dynamics', while the 'md' calculation in > pw.x performs born-oppenheimer MD. Paolo just told us that the > born-oppenheimer MD only perform MD at ground state. Does CPMD or cp.x > perform the MD calculation at ground state or exited state? both are methods that look at the ground state wavefunction. the CP method uses a "trick" that would allow to propagate the wavefunction without having to do a full optimization. CP can be faster, but has some approximations and limitations, e.g. CP requires a band gap and has not been implemented for k-points (at least not in the codes you mentioned, and i don't know of a code that has it, even though it should be technically possible). doing excited state calculations with DFT is a different problem, as (regular) DFT is a ground state method. cheers, axel. > > thank you very much for you time > > best, > > vega > > > -- > ================================================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > ****************************************************************************************************************** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > Nanjing, Jiangsu, China > ****************************************************************************************************************** > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From jameslipd at gmail.com Tue Jun 23 14:39:22 2009 From: jameslipd at gmail.com (JAY) Date: Tue, 23 Jun 2009 20:39:22 +0800 Subject: [Pw_forum] =?utf-8?q?radius_distribution_function_=EF=BC=88Pw=5Ff?= =?utf-8?q?orum_Digest=2C_Vol_24=2C_Issue_49=EF=BC=89?= Message-ID: Dear Gabriele Thank you for your reply. I am a new learner of fortran 90, so it is much more helpful, if you send me your source code. I will make some modification where necessary. Could you please send me a copy of that fortran code? On Tue, Jun 23, 2009 at 6:08 PM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: radius distribution function (Gabriele Sclauzero) > 2. Re: Separating Raman modes (alexandra.carvalho at epfl.ch) > 3. Zero of the electrostatic potential ? (Vladan Stevanovic) > 4. Re: Zero of the electrostatic potential ? (Gabriele Sclauzero) > 5. Re: Zero of the electrostatic potential ? (Lorenzo Paulatto) > 6. Re: Zero of the electrostatic potential ? (Stefano de Gironcoli) > 7. Re: Zero of the electrostatic potential ? (Paolo Giannozzi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 23 Jun 2009 09:03:49 +0200 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] radius distribution function > To: PWSCF Forum > Message-ID: <4A407E55.5070704 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Jay, > > JAY wrote: > > Dear users > > > > Could anybody send me the fortran code for calculating radius > > distribution function? I would like to analyze the MD results. Many > thanks. > > If you meant "radial distribution function", I think you can find good > recipes on how to > write it on any molecular dynamics textbook, from the old classics by > Frenkel-Smit or > Allen-Tildesley to the modern ones. If you are really in trouble I can send > you a fortran > code from a course on atomistic simulations I followed at University (at > the moment I'm > not doing molecular dynamics calculations), but I think there are many > people doing much > more sophisticated things on this forum. They could help you better than > me. > > GS > > > > > > > -- > > Sincerely > > > > Jay > > > > > > ============================================== > > cn: Li, Jiaye > > en: Jay Y. Lee > > > > M.S. in designing and developing novel materials > > > > Research experience: > > *ALD precursor. ie. Metal complexes > > *Surface modification. ie. Indium tin oxide, SiO2 > > *Gas storage and adsorption. ie. Ionic Liquids > > > > Skills: > > *ab-initial method, DFT simulation and Force Field simulation > > > > Please contact me at: > > 1. jameslipd at gmail.com or > > 2. jameslibd at gmail.com > > > > ============================================== > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > > > ------------------------------ > > Message: 2 > Date: Tue, 23 Jun 2009 10:31:06 +0200 > From: alexandra.carvalho at epfl.ch > Subject: Re: [Pw_forum] Separating Raman modes > To: PWSCF Forum > Message-ID: <20090623103106.17671jzible9ehu2 at webmail.epfl.ch> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Dear Sophia, > > To select which modes are Raman active you must use the selection rules. > The following paper may be of help (see also the tables in it): > > Rosseau et al. Journal of Raman Spectroscopy 10, 253 (1981) > > If you are starting, I recommend having a look at the selection rules > for molecules, for example in Tinkham, Group theory and Quantum > mechanics (Dover, 1992,NY) pp248. > > Most likelly, you will be interested in the allowed transitions with > highest > frequency. > > Hope this helps, > > Alexandra > > > Quoting Jonathan : > > > Dear users, > > > > I computed phonons only at the gamma point for a 64-atom binary > > alloy. How do I separate the three main Raman modes. > > > > Would it be possible to get some help? > > thanks, > > -- > > Sophia > > UCB, USA > > > > > > -- > > Alexandra Carvalho, > Ceramics Laboratory > Swiss Federal Institute of Technology of Lausanne (EPFL) > > > > ------------------------------ > > Message: 3 > Date: Tue, 23 Jun 2009 11:29:28 +0200 > From: Vladan Stevanovic > Subject: [Pw_forum] Zero of the electrostatic potential ? > To: pw_forum at pwscf.org > Message-ID: <4A40A078.4060305 at epfl.ch> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Quantum-ESPRESSO users, > > I am using QE for simulations of transition metal clusters. My question > is where the code places the vacuum level in such calculations > (nonperiodic systems in a big cell) ? To formulate differently, is it > possible to compare directly KS eigenvalues from different calculations ? > > > Thanks, > Vladan Stevanovic > > --------------------------------------------- > Assistant-doctorant > EPFL SB IRRMA-GE > PH H2 435 (B?timent PH) > Station 3 > CH-1015 Lausanne > tel. : +41 (0)21 693 51 08 > e-mail : vladan.stevanovic at epfl.ch > --------------------------------------------- > > > > ------------------------------ > > Message: 4 > Date: Tue, 23 Jun 2009 11:46:13 +0200 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] Zero of the electrostatic potential ? > To: PWSCF Forum > Message-ID: <4A40A465.40805 at sissa.it> > Content-Type: text/plain; charset=iso-8859-1; format=flowed > > > > Vladan Stevanovic wrote: > > Dear Quantum-ESPRESSO users, > > > > I am using QE for simulations of transition metal clusters. My question > > is where the code places the vacuum level in such calculations > > (nonperiodic systems in a big cell) ? To formulate differently, is it > > I think this question has been often posed and replied in the context of > work-function > calculation. Please first try a search on the archives using 'work > function' or something > similar as keys. You can also have a look to the example in > > examples/WorkFct_example > > in the QE folder. > > > possible to compare directly KS eigenvalues from different calculations ? > > If you want compare the distance between the eigenvalues and the Fermi > energies in the > respective systems, I think you can. In order to understand if you can > compare the > absolute (i.e. not relative to E_F) value of the eigenvalues I think you > must first find > the answer to your previous question. > > > GS > > > > > > > > Thanks, > > Vladan Stevanovic > > > > --------------------------------------------- > > Assistant-doctorant > > EPFL SB IRRMA-GE > > PH H2 435 (B?timent PH) > > Station 3 > > CH-1015 Lausanne > > tel. : +41 (0)21 693 51 08 > > e-mail : vladan.stevanovic at epfl.ch > > --------------------------------------------- > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > > > ------------------------------ > > Message: 5 > Date: Tue, 23 Jun 2009 12:00:01 +0200 > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] Zero of the electrostatic potential ? > To: vladan.stevanovic at epfl.ch, "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 23 giugno 2009 alle ore 11:29:28, Vladan Stevanovic > ha scritto: > > I am using QE for simulations of transition metal clusters. My question > > is where the code places the vacuum level in such calculations > > (nonperiodic systems in a big cell) ? > > Dear Vladan, > a non-periodic system in a big periodic cell is still a periodic system! > Hence, the integral of the potential over any possible choice of primitive > cell has to be zero. This is a sufficient condition to find the zero. > > > To formulate differently, is it > > possible to compare directly KS eigenvalues from different calculations ? > > In general it is NOT possible to directly compare eigenvalues of different > calculations, nevertheless they can be compared taking the Fermi energy as > reference. > > best regards > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > > > ------------------------------ > > Message: 6 > Date: Tue, 23 Jun 2009 12:08:03 +0200 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] Zero of the electrostatic potential ? > To: vladan.stevanovic at epfl.ch, PWSCF Forum > Message-ID: <4A40A983.7080108 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > The zero of the potential energy is the average electrostatic potential; > as such the eigenvalues in different systems cannot be directly compared. > what you need yo do is to calculate the (electrostatic) potential energy > in the vacuum region where it should, at least for neutral systems, be > constant and take that as the zero of the energy. > In order to calculate the potential in the vacuum region one could adapt > the example for the calculation of the Work Function in directory > examples/WorkFct_example. > > stefano > > Vladan Stevanovic wrote: > > Dear Quantum-ESPRESSO users, > > > > I am using QE for simulations of transition metal clusters. My question > > is where the code places the vacuum level in such calculations > > (nonperiodic systems in a big cell) ? To formulate differently, is it > > possible to compare directly KS eigenvalues from different calculations ? > > > > > Thanks, > > Vladan Stevanovic > > > > --------------------------------------------- > > Assistant-doctorant > > EPFL SB IRRMA-GE > > PH H2 435 (B?timent PH) > > Station 3 > > CH-1015 Lausanne > > tel. : +41 (0)21 693 51 08 > > e-mail : vladan.stevanovic at epfl.ch > > --------------------------------------------- > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 7 > Date: Tue, 23 Jun 2009 12:07:10 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Zero of the electrostatic potential ? > To: vladan.stevanovic at epfl.ch, PWSCF Forum > Message-ID: <8CD924AB-2D4E-402A-BF90-A3A392886FBB at democritos.it> > Content-Type: text/plain; charset="us-ascii" > > > On Jun 23, 2009, at 11:29 , Vladan Stevanovic wrote: > > > where the code places the vacuum level in such calculations > > (nonperiodic systems in a big cell) ? To formulate differently, > > is it possible to compare directly KS eigenvalues from different > > calculations ? > > short answer: no. > > V(G=0) is calculated (finite or infinite systems doesn't matter) > as described in the attached notes. CP and PWscf have a > different definition of V(0) so you get the same eigenvalues, > but displaced > > P. > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: plane_waves.tex > Type: application/octet-stream > Size: 32445 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/pw_forum/attachments/20090623/9e391ac7/attachment.obj > -------------- next part -------------- > > > --- > Paolo Giannozzi, Dept of Physics, University of 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 24, Issue 49 > **************************************** > -- Sincerely Jay ============================================== cn: Li, Jiaye en: Jay Y. Lee M.S. in designing and developing novel materials Research experience: *ALD precursor. ie. Metal complexes *Surface modification. ie. Indium tin oxide, SiO2 *Gas storage and adsorption. ie. Ionic Liquids Skills: *ab-initial method, DFT simulation and Force Field simulation Please contact me at: 1. jameslipd at gmail.com or 2. jameslibd at gmail.com ============================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090623/986ea614/attachment-0001.htm From vladan.stevanovic at epfl.ch Tue Jun 23 15:17:10 2009 From: vladan.stevanovic at epfl.ch (Vladan Stevanovic) Date: Tue, 23 Jun 2009 15:17:10 +0200 Subject: [Pw_forum] Zero of the electrostatic potential ? In-Reply-To: References: <4A40A078.4060305@epfl.ch> Message-ID: <4A40D5D6.2000105@epfl.ch> Thank you very much. Vladan Stevanovic --------------------------------------------- Assistant-doctorant EPFL SB IRRMA-GE PH H2 435 (B?timent PH) Station 3 CH-1015 Lausanne tel. : +41 (0)21 693 51 08 e-mail : vladan.stevanovic at epfl.ch --------------------------------------------- From baroni at sissa.it Tue Jun 23 16:04:54 2009 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 23 Jun 2009 16:04:54 +0200 Subject: [Pw_forum] Separating Raman modes In-Reply-To: <20090623103106.17671jzible9ehu2@webmail.epfl.ch> References: <8a0137e60906221603t718784b7x228e5f6684d3825c@mail.gmail.com> <20090623103106.17671jzible9ehu2@webmail.epfl.ch> Message-ID: Dear Sophia & Alexandra: I am not sure that group theory (which I am fond of) would help much here. For a disordered system modeled by a supercell, I see few other choices than estimating the Raman activity of each mode, and then sum the contributions from all the modes. The method by Mauri and coworkers (whose implementation status in QE is unknown to me) seems particularly suitable in this case. For those who do not know, the (non-resonant) Raman activity is given by the variation of the polarizability linearly induced by each vibrational mode (here is where selection rules ultimately come from). This "traditional" way of calculating the Raman activity is not very practical for large supercells, because it requires several polarizability calculations for each phonon mode. An alternative would be 3rd order perturbation theory, which used to be implemented in QE. A bit awkward because of complications arising from the infamous q->0 limits that plague any polarizability calculations in infinite systems. The third (and most elegant) way is Mauri and collaborators'. The first derivative of the polarizability with respect to an atomic displacements is a third derivative of the energy, once with respect to a nuclear position, twice with respect to the strength of the electroc field. By changing the order of differentiation, this can be seen as the second dericative of the force acting on atoms with respect to an applied alectric field. This can be computed by 2nd order perturbation theory in the strength of the field. An alternative is to rely on some polarizable-bond model for the polarizability and to estimate its derivative with respect to nuclear distortions using such a semi-empirical model. Hope this helps. Stefano On Jun 23, 2009, at 10:31 AM, alexandra.carvalho at epfl.ch wrote: > Dear Sophia, > > To select which modes are Raman active you must use the selection > rules. > The following paper may be of help (see also the tables in it): > > Rosseau et al. Journal of Raman Spectroscopy 10, 253 (1981) > > If you are starting, I recommend having a look at the selection rules > for molecules, for example in Tinkham, Group theory and Quantum > mechanics (Dover, 1992,NY) pp248. > > Most likelly, you will be interested in the allowed transitions with > highest > frequency. > > Hope this helps, > > Alexandra > > > Quoting Jonathan : > >> Dear users, >> >> I computed phonons only at the gamma point for a 64-atom binary >> alloy. How do I separate the three main Raman modes. >> >> Would it be possible to get some help? >> thanks, >> -- >> Sophia >> UCB, USA >> > > > > -- > > Alexandra Carvalho, > Ceramics Laboratory > Swiss Federal Institute of Technology of Lausanne (EPFL) > > _______________________________________________ > 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 [+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/20090623/d4c53fd2/attachment.htm From sclauzer at sissa.it Tue Jun 23 16:44:02 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 23 Jun 2009 16:44:02 +0200 Subject: [Pw_forum] =?utf-8?q?radius_distribution_function_=EF=BC=88Pw=5Ff?= =?utf-8?q?orum_Digest=2C_Vol_24=2C_Issue_49=EF=BC=89?= In-Reply-To: References: Message-ID: <4A40EA32.4080707@sissa.it> I don't have the code at hand in this moment. It was not 'my' code anyway. If I remember well I used that from Frenkel and Smit's book. You can download it from this website http://molsim.chem.uva.nl/frenkel_smit/README.html for instance in this case study http://molsim.chem.uva.nl/frenkel_smit/Exercise_10/index.html The subroutine which accumulate statistics for the radial distribution function should be sample_gyra.f. GS JAY wrote: > Dear Gabriele > > Thank you for your reply. I am a new learner of fortran 90, so it is > much more helpful, if you send me your source code. I will make some > modification where necessary. Could you please send me a copy of that > fortran code? > > On Tue, Jun 23, 2009 at 6:08 PM, > wrote: > > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: radius distribution function (Gabriele Sclauzero) > 2. Re: Separating Raman modes (alexandra.carvalho at epfl.ch > ) > 3. Zero of the electrostatic potential ? (Vladan Stevanovic) > 4. Re: Zero of the electrostatic potential ? (Gabriele Sclauzero) > 5. Re: Zero of the electrostatic potential ? (Lorenzo Paulatto) > 6. Re: Zero of the electrostatic potential ? (Stefano de Gironcoli) > 7. Re: Zero of the electrostatic potential ? (Paolo Giannozzi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 23 Jun 2009 09:03:49 +0200 > From: Gabriele Sclauzero > > Subject: Re: [Pw_forum] radius distribution function > To: PWSCF Forum > > Message-ID: <4A407E55.5070704 at sissa.it > > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Jay, > > JAY wrote: > > Dear users > > > > Could anybody send me the fortran code for calculating radius > > distribution function? I would like to analyze the MD results. > Many thanks. > > If you meant "radial distribution function", I think you can find > good recipes on how to > write it on any molecular dynamics textbook, from the old classics > by Frenkel-Smit or > Allen-Tildesley to the modern ones. If you are really in trouble I > can send you a fortran > code from a course on atomistic simulations I followed at University > (at the moment I'm > not doing molecular dynamics calculations), but I think there are > many people doing much > more sophisticated things on this forum. They could help you better > than me. > > GS > > > > > > > -- > > Sincerely > > > > Jay > > > > > > ============================================== > > cn: Li, Jiaye > > en: Jay Y. Lee > > > > M.S. in designing and developing novel materials > > > > Research experience: > > *ALD precursor. ie. Metal complexes > > *Surface modification. ie. Indium tin oxide, SiO2 > > *Gas storage and adsorption. ie. Ionic Liquids > > > > Skills: > > *ab-initial method, DFT simulation and Force Field simulation > > > > Please contact me at: > > 1. jameslipd at gmail.com > > or > > 2. jameslibd at gmail.com > > > > > > ============================================== > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it > | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > > > ------------------------------ > > Message: 2 > Date: Tue, 23 Jun 2009 10:31:06 +0200 > From: alexandra.carvalho at epfl.ch > Subject: Re: [Pw_forum] Separating Raman modes > To: PWSCF Forum > > Message-ID: <20090623103106.17671jzible9ehu2 at webmail.epfl.ch > > > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Dear Sophia, > > To select which modes are Raman active you must use the selection rules. > The following paper may be of help (see also the tables in it): > > Rosseau et al. Journal of Raman Spectroscopy 10, 253 (1981) > > If you are starting, I recommend having a look at the selection rules > for molecules, for example in Tinkham, Group theory and Quantum > mechanics (Dover, 1992,NY) pp248. > > Most likelly, you will be interested in the allowed transitions with > highest > frequency. > > Hope this helps, > > Alexandra > > > Quoting Jonathan >: > > > Dear users, > > > > I computed phonons only at the gamma point for a 64-atom binary > > alloy. How do I separate the three main Raman modes. > > > > Would it be possible to get some help? > > thanks, > > -- > > Sophia > > UCB, USA > > > > > > -- > > Alexandra Carvalho, > Ceramics Laboratory > Swiss Federal Institute of Technology of Lausanne (EPFL) > > > > ------------------------------ > > Message: 3 > Date: Tue, 23 Jun 2009 11:29:28 +0200 > From: Vladan Stevanovic > > Subject: [Pw_forum] Zero of the electrostatic potential ? > To: pw_forum at pwscf.org > Message-ID: <4A40A078.4060305 at epfl.ch > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Quantum-ESPRESSO users, > > I am using QE for simulations of transition metal clusters. My question > is where the code places the vacuum level in such calculations > (nonperiodic systems in a big cell) ? To formulate differently, is it > possible to compare directly KS eigenvalues from different > calculations ? > > > Thanks, > Vladan Stevanovic > > --------------------------------------------- > Assistant-doctorant > EPFL SB IRRMA-GE > PH H2 435 (B?timent PH) > Station 3 > CH-1015 Lausanne > tel. : +41 (0)21 693 51 08 > e-mail : vladan.stevanovic at epfl.ch > --------------------------------------------- > > > > ------------------------------ > > Message: 4 > Date: Tue, 23 Jun 2009 11:46:13 +0200 > From: Gabriele Sclauzero > > Subject: Re: [Pw_forum] Zero of the electrostatic potential ? > To: PWSCF Forum > > Message-ID: <4A40A465.40805 at sissa.it > > Content-Type: text/plain; charset=iso-8859-1; format=flowed > > > > Vladan Stevanovic wrote: > > Dear Quantum-ESPRESSO users, > > > > I am using QE for simulations of transition metal clusters. My > question > > is where the code places the vacuum level in such calculations > > (nonperiodic systems in a big cell) ? To formulate differently, is it > > I think this question has been often posed and replied in the > context of work-function > calculation. Please first try a search on the archives using 'work > function' or something > similar as keys. You can also have a look to the example in > > examples/WorkFct_example > > in the QE folder. > > > possible to compare directly KS eigenvalues from different > calculations ? > > If you want compare the distance between the eigenvalues and the > Fermi energies in the > respective systems, I think you can. In order to understand if you > can compare the > absolute (i.e. not relative to E_F) value of the eigenvalues I think > you must first find > the answer to your previous question. > > > GS > > > > > > > > Thanks, > > Vladan Stevanovic > > > > --------------------------------------------- > > Assistant-doctorant > > EPFL SB IRRMA-GE > > PH H2 435 (B?timent PH) > > Station 3 > > CH-1015 Lausanne > > tel. : +41 (0)21 693 51 08 > > e-mail : vladan.stevanovic at epfl.ch > > --------------------------------------------- > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it > | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > > > ------------------------------ > > Message: 5 > Date: Tue, 23 Jun 2009 12:00:01 +0200 > From: "Lorenzo Paulatto" > > Subject: Re: [Pw_forum] Zero of the electrostatic potential ? > To: vladan.stevanovic at epfl.ch , > "PWSCF Forum" > > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 23 giugno 2009 alle ore 11:29:28, Vladan Stevanovic > > ha > scritto: > > I am using QE for simulations of transition metal clusters. My > question > > is where the code places the vacuum level in such calculations > > (nonperiodic systems in a big cell) ? > > Dear Vladan, > a non-periodic system in a big periodic cell is still a periodic system! > Hence, the integral of the potential over any possible choice of > primitive > cell has to be zero. This is a sufficient condition to find the zero. > > > To formulate differently, is it > > possible to compare directly KS eigenvalues from different > calculations ? > > In general it is NOT possible to directly compare eigenvalues of > different > calculations, nevertheless they can be compared taking the Fermi > energy as > reference. > > best regards > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > > > ------------------------------ > > Message: 6 > Date: Tue, 23 Jun 2009 12:08:03 +0200 > From: Stefano de Gironcoli > > Subject: Re: [Pw_forum] Zero of the electrostatic potential ? > To: vladan.stevanovic at epfl.ch , > PWSCF Forum > > Message-ID: <4A40A983.7080108 at sissa.it > > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > The zero of the potential energy is the average electrostatic potential; > as such the eigenvalues in different systems cannot be directly > compared. > what you need yo do is to calculate the (electrostatic) potential energy > in the vacuum region where it should, at least for neutral systems, be > constant and take that as the zero of the energy. > In order to calculate the potential in the vacuum region one could adapt > the example for the calculation of the Work Function in directory > examples/WorkFct_example. > > stefano > > Vladan Stevanovic wrote: > > Dear Quantum-ESPRESSO users, > > > > I am using QE for simulations of transition metal clusters. My > question > > is where the code places the vacuum level in such calculations > > (nonperiodic systems in a big cell) ? To formulate differently, is it > > possible to compare directly KS eigenvalues from different > calculations ? > > > > > Thanks, > > Vladan Stevanovic > > > > --------------------------------------------- > > Assistant-doctorant > > EPFL SB IRRMA-GE > > PH H2 435 (B?timent PH) > > Station 3 > > CH-1015 Lausanne > > tel. : +41 (0)21 693 51 08 > > e-mail : vladan.stevanovic at epfl.ch > > --------------------------------------------- > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 7 > Date: Tue, 23 Jun 2009 12:07:10 +0200 > From: Paolo Giannozzi > > Subject: Re: [Pw_forum] Zero of the electrostatic potential ? > To: vladan.stevanovic at epfl.ch , > PWSCF Forum > > Message-ID: <8CD924AB-2D4E-402A-BF90-A3A392886FBB at democritos.it > > > Content-Type: text/plain; charset="us-ascii" > > > On Jun 23, 2009, at 11:29 , Vladan Stevanovic wrote: > > > where the code places the vacuum level in such calculations > > (nonperiodic systems in a big cell) ? To formulate differently, > > is it possible to compare directly KS eigenvalues from different > > calculations ? > > short answer: no. > > V(G=0) is calculated (finite or infinite systems doesn't matter) > as described in the attached notes. CP and PWscf have a > different definition of V(0) so you get the same eigenvalues, > but displaced > > P. > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: plane_waves.tex > Type: application/octet-stream > Size: 32445 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/pw_forum/attachments/20090623/9e391ac7/attachment.obj > -------------- next part -------------- > > > --- > Paolo Giannozzi, Dept of Physics, University of 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 24, Issue 49 > **************************************** > > > > > -- > Sincerely > > Jay > > > ============================================== > cn: Li, Jiaye > en: Jay Y. Lee > > M.S. in designing and developing novel materials > > Research experience: > *ALD precursor. ie. Metal complexes > *Surface modification. ie. Indium tin oxide, SiO2 > *Gas storage and adsorption. ie. Ionic Liquids > > Skills: > *ab-initial method, DFT simulation and Force Field simulation > > Please contact me at: > 1. jameslipd at gmail.com or > 2. jameslibd at gmail.com > > ============================================== > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From paulatto at sissa.it Tue Jun 23 17:16:22 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 23 Jun 2009 17:16:22 +0200 Subject: [Pw_forum] smaller band gaps In-Reply-To: <97e4b88e0906230458l7ed16454m5cc504ef06deec73@mail.gmail.com> References: <97e4b88e0906230458l7ed16454m5cc504ef06deec73@mail.gmail.com> Message-ID: In data 23 giugno 2009 alle ore 13:58:38, Naol Regassa ha scritto: > My main concern is that DFT calculations reduce band gaps > by 50%. DFT does not predict band gap at all, for many materials it is related to the experimental one, but on assumption can be made a priori on its precision. Anyway, you are probably doing the calculation using the experimental lattice parameter, if you relax the system to the numerical equilibrium lattice parameter, you will probably get a better gap. > Does this mean that I can add this error to get the correct > band gap so that any body can understand it? How can one argue about > this condition? No, the fact that DFT does not predict the band gap is a well known problem of the theory, if you fix it with an empirical parameter it would be not only unethical, but also quite suspicious. If you want to have accurate band gap you have to use TDDFT or DFT+GW, which are both implemented in quantum espresso (I don't know the details of them, nor which is better for your specific purpose, you'll have to read a bit of literature). best regards P.S. if you are starting a new discussion in the mailing list, please write a new email, do not reply to a previous one -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From giannozz at democritos.it Tue Jun 23 18:14:02 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 23 Jun 2009 18:14:02 +0200 Subject: [Pw_forum] Separating Raman modes In-Reply-To: References: <8a0137e60906221603t718784b7x228e5f6684d3825c@mail.gmail.com> <20090623103106.17671jzible9ehu2@webmail.epfl.ch> Message-ID: <4A40FF4A.4070108@democritos.it> Stefano Baroni wrote: > The method by Mauri and coworkers > (whose implementation status in QE is unknown to me) it is implemented, but only for the "ordinary" phonon code (i.e. not for the Gamma-specific one) and only for norm-conserving pseudopotentials Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue Jun 23 18:18:24 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 23 Jun 2009 18:18:24 +0200 Subject: [Pw_forum] smaller band gaps In-Reply-To: References: <97e4b88e0906230458l7ed16454m5cc504ef06deec73@mail.gmail.com> Message-ID: <4A410050.9090100@democritos.it> Lorenzo Paulatto wrote: > if you fix it with an empirical parameter it would be not only unethical Lorenzo, take it easy: there is nothing "ethically" wrong in trying to adjust the gap, as long as it is clearly stated P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From zubaexy at gmail.com Tue Jun 23 18:28:30 2009 From: zubaexy at gmail.com (Zubaer Hossain) Date: Tue, 23 Jun 2009 11:28:30 -0500 Subject: [Pw_forum] Separating Raman modes In-Reply-To: <4A40FF4A.4070108@democritos.it> References: <8a0137e60906221603t718784b7x228e5f6684d3825c@mail.gmail.com> <20090623103106.17671jzible9ehu2@webmail.epfl.ch> <4A40FF4A.4070108@democritos.it> Message-ID: <51ec861d0906230928p791f99a7yb86b747d6ad5facd@mail.gmail.com> How about decomposing eigenstates into that for the individual atoms and summing them for each species, since the phonon frequencies are computed already, and the eigenmodes for each frequency are known. By analyzing these quantities graphically for each species, optical frequencies of the main three modes could be detected, I think. Zubaer Department of Mechanical Science and Engineering Univ. of Illinois at Urbana-Champaign, USA On Tue, Jun 23, 2009 at 11:14 AM, Paolo Giannozzi wrote: > Stefano Baroni wrote: > > > The method by Mauri and coworkers > > (whose implementation status in QE is unknown to me) > > it is implemented, but only for the "ordinary" phonon > code (i.e. not for the Gamma-specific one) and only for > norm-conserving pseudopotentials > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > 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/20090623/b2f54fbb/attachment.htm From giannozz at democritos.it Tue Jun 23 18:35:42 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 23 Jun 2009 18:35:42 +0200 Subject: [Pw_forum] Separating Raman modes In-Reply-To: <51ec861d0906230928p791f99a7yb86b747d6ad5facd@mail.gmail.com> References: <8a0137e60906221603t718784b7x228e5f6684d3825c@mail.gmail.com> <20090623103106.17671jzible9ehu2@webmail.epfl.ch> <4A40FF4A.4070108@democritos.it> <51ec861d0906230928p791f99a7yb86b747d6ad5facd@mail.gmail.com> Message-ID: <4A41045E.5060708@democritos.it> Zubaer Hossain wrote: > How about decomposing eigenstates into that for the individual atoms and > summing them for each species, since the phonon frequencies are computed > already, and the eigenmodes for each frequency are known. By analyzing > these quantities graphically for each species, optical frequencies of > the main three modes could be detected, I think. years ago we did something similar: "Phonon Dispersions in Ga(x)Al(1-x)As Alloys", PRL 65, 84 (1990). Alloy modes were projected over crystal modes. In that particular case the "mass approximation" was giving an accurate and convenient way to calculate the dynamical matrix in relatively large supercells Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From lanhaiping at gmail.com Tue Jun 23 20:05:09 2009 From: lanhaiping at gmail.com (lan haiping) Date: Wed, 24 Jun 2009 02:05:09 +0800 Subject: [Pw_forum] hybrid functional and Wannier functions Message-ID: Dear All: I want to study electronic structures with hybrid functional. Is it possible for us to using wannier90 package to analyse related bands at present version ? Such as WFs and bands structure. Regards, Hai-Ping -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090624/ce0fac3b/attachment.htm From giannozz at democritos.it Wed Jun 24 08:58:44 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 24 Jun 2009 08:58:44 +0200 Subject: [Pw_forum] hybrid functional and Wannier functions In-Reply-To: References: Message-ID: On Jun 23, 2009, at 20:05 , lan haiping wrote: > I want to study electronic structures with hybrid functional. > Is it possible for us to using wannier90 package to analyse > related bands at present version ? I think it is Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Wed Jun 24 12:16:43 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 24 Jun 2009 12:16:43 +0200 Subject: [Pw_forum] smaller band gaps In-Reply-To: <4A410050.9090100@democritos.it> References: <97e4b88e0906230458l7ed16454m5cc504ef06deec73@mail.gmail.com> <4A410050.9090100@democritos.it> Message-ID: In data 23 giugno 2009 alle ore 18:18:24, Paolo Giannozzi ha scritto: > Lorenzo, take it easy: there is nothing "ethically" wrong in trying > to adjust the gap, as long as it is clearly stated you're right, I apologize for the rudeness. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From marzari at MIT.EDU Wed Jun 24 15:52:32 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 24 Jun 2009 09:52:32 -0400 Subject: [Pw_forum] hybrid functional and Wannier functions In-Reply-To: References: Message-ID: <4A422FA0.7030907@mit.edu> lan haiping wrote: > Dear All: > > I want to study electronic structures with hybrid functional. Is it > possible for us to using wannier90 package to analyse related bands at > present version ? Such as WFs and bands structure. wannier needs scalar products between wavefunctions, and I do not see any immediate reason why those should be different in case of a hybrid functional. so, I'd give an uninformed yes. nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From lanhaiping at gmail.com Wed Jun 24 17:46:21 2009 From: lanhaiping at gmail.com (lan haiping) Date: Wed, 24 Jun 2009 23:46:21 +0800 Subject: [Pw_forum] hybrid functional and Wannier functions In-Reply-To: <4A422FA0.7030907@mit.edu> References: <4A422FA0.7030907@mit.edu> Message-ID: Dear Paolo and Nicola : Thank you. I cannot reply email properly due to gmail is blocked by Chinese Government. It is quite a pity for us due to a so-called censorship carried out now ! regards On 6/24/09, Nicola Marzari wrote: > lan haiping wrote: >> Dear All: >> >> I want to study electronic structures with hybrid functional. Is it >> possible for us to using wannier90 package to analyse related bands at >> present version ? Such as WFs and bands structure. > > > wannier needs scalar products between wavefunctions, and I do not see > any immediate reason why those should be different in case of a hybrid > functional. so, I'd give an uninformed yes. > > nicola > > > -- > --------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials Science and Engineering > 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA > tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn From marzari at MIT.EDU Wed Jun 24 18:03:14 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 24 Jun 2009 12:03:14 -0400 Subject: [Pw_forum] smaller band gaps In-Reply-To: <97e4b88e0906230458l7ed16454m5cc504ef06deec73@mail.gmail.com> References: <97e4b88e0906230458l7ed16454m5cc504ef06deec73@mail.gmail.com> Message-ID: <4A424E42.6040401@mit.edu> Naol Regassa wrote: > Dear all > > I was using QE.4.1 to calculate the electronic structure of SrMnO_3 > employing GGA+U > but I got small band gap of 0.7 eV which is semi-metal (experimentally > insulator). My main concern is that DFT calculations reduce band gaps > by 50%. Does this mean that I can add this error to get the correct > band gap so that any body can understand it? How can one argue about > this condition? > > Tamene > Student at AAU > Ethiopia Dear Naol, it's ok to list what the GGA+U band gap is (0.7) and maybe even the plain GGA. Everyone understands that band gaps are not meant to be described correctly by DFT - the "band gap" that DFT codes calculate is that of the fictitious Kohn-Sham states, that have nothing to do, in principle, with the energy levels of real electrons or of quasiparticles. In practive it is found that the Kohn-Sham states do resemble a little bit the true band structure - albeit with a lot of variability in the band gap. LDA/GGA tend to make it smaller, hybrids larger, HSE probably quite the right ballpark. nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From miguel.martinez at ehu.es Wed Jun 24 20:49:17 2009 From: miguel.martinez at ehu.es (Miguel =?UTF-8?B?TWFydMOtbmV6?=) Date: Wed, 24 Jun 2009 20:49:17 +0200 Subject: [Pw_forum] Phonon weirdness with matdyn Message-ID: <20090624204917.3f08d4da@lcpybm> Dear espresso users, I computed a while ago the phonon DOS of Fdd2 silane (that is, face centered orthorrombic) at around 50 GPa and kept the IFC matrix. I wanted to have a look at the phonon branches and have noticed some weird behaviour. I'm trying to follow the Gamma - T - Z - Y -Gamma - Z2 path(see the Brillouin Zone in http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-kv-list?gnum=43&fig=fmm2fcgr ) Amazingly, when I come back to Gamma, the frequencies have changed. And they jump back to the "normal" levels after a step in the Gamma - Z2 line. I've tried no, simple and crystal ASR in both the q2r conversion and the matdyn run, always keeping the same ASR for the sake of consistency. In any case, the "jump" is always present. Gamma will display wrong frequencies (when compared to the frequencies directly obtanied) every time the Gamma - Y line is followed in any direction. I've used both quantum-espresso 4.0.2 compiled with ifort in an itanium and a nightly "build" from q-e forge downloaded yesterday and compiled with gfortran and run in my laptop, but that warrants no change. ?Anybody has a clue on what may be happening here? For additional weird points, this happens at both 34 and 50 GPa (I ran the phonon calculation at both pressures). I fear I've done something silly, but I just don't see it. Thanks in advance, Miguel The SCF input is: &control calculation='scf' restart_mode='from_scratch', prefix='sih4', tstress = .true. tprnfor = .true. pseudo_dir = '/home/wmbmacam/pseudo/', outdir='/scratch/wmbmacam/fdd2-phon-50/' / &system ibrav= 10, celldm(1) = 12.2211446, celldm(2) = 1.07916784, celldm(3) = 0.616658866, nat=10, ntyp= 2, ecutwfc = 45.0, ecutrho = 500.0 nr1= 72, nr2= 72, nr3= 72 / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES Si 28.0855 Si.pbe-n-van.UPF H 1.0079 H.pbe-van_ak.UPF ATOMIC_POSITIONS {crystal} Si 0.610686000000 0.389314000000 0.610686000000 Si 0.860686000000 0.639314000000 0.860686000000 H 0.444907000000 0.850471000000 0.348857000000 H 0.348857000000 0.355765000000 0.444907000000 H 0.894235000000 0.901143000000 0.399529000000 H 0.399529000000 0.805093000000 0.894235000000 H 0.385750000000 0.340750000000 0.013222000000 H 0.013222000000 0.260278000000 0.385750000000 H 0.989722000000 0.236778000000 0.909250000000 H 0.909250000000 0.864250000000 0.989722000000 K_POINTS {automatic} 12 12 12 1 1 1 The Phonon input is: &inputph tr2_ph=1.0d-14, prefix='sih4', ldisp=.true., nq1=4, nq2=4, nq3=4 amass(1)=28.0855, amass(2)=1.00794, outdir='/scratch/wmbmacam/fdd2-phon-50/', fildyn='sih4.dyn', / And finally the q2r input is: &input fildyn='sih4.dyn', zasr='crystal', flfrc='sih4.fc' / PS: I'll happily provide an eps with the full phonon branches if someone desires it. Or the sih4.dyn files. -- ---------------------------------------- Miguel Mart?nez Canales Condensed Matter Physics Dpt. UPV/EHU Faculty of Science and Technology Apdo. 644 48080 Bilbao (Spain) Fax: +34 94 601 3500 Tlf: +34 94 601 5326 ---------------------------------------- "If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." George Bernard Shaw From miguel.martinez at ehu.es Wed Jun 24 20:55:40 2009 From: miguel.martinez at ehu.es (Miguel =?UTF-8?B?TWFydMOtbmV6?=) Date: Wed, 24 Jun 2009 20:55:40 +0200 Subject: [Pw_forum] Phonon weirdness with matdyn In-Reply-To: <20090624204917.3f08d4da@lcpybm> References: <20090624204917.3f08d4da@lcpybm> Message-ID: <20090624205540.04050476@lcpybm> By the way, I forgot to mention that the discontinuity, in one case, is of 150 cm^-1, while there are three other instances of a 10% difference. -- ---------------------------------------- Miguel Mart?nez Canales Condensed Matter Physics Dpt. UPV/EHU Faculty of Science and Technology Apdo. 644 48080 Bilbao (Spain) Fax: +34 94 601 3500 Tlf: +34 94 601 5326 ---------------------------------------- "If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." George Bernard Shaw From anvari_meh at physics.iust.ac.ir Wed Jun 24 22:13:45 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Wed, 24 Jun 2009 23:43:45 +0330 Subject: [Pw_forum] frequency in gamma point Message-ID: I repeated my calculation again with clean tmp & achieved correct frequency. Thanks Mehrnaz Iran University Of science & technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090624/a4e5a657/attachment.htm From giannozz at democritos.it Wed Jun 24 21:46:05 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 24 Jun 2009 21:46:05 +0200 Subject: [Pw_forum] Phonon weirdness with matdyn In-Reply-To: <20090624204917.3f08d4da@lcpybm> References: <20090624204917.3f08d4da@lcpybm> Message-ID: On Jun 24, 2009, at 20:49 , Miguel Mart?nez wrote: > I've used both quantum-espresso 4.0.2 oops, I guess you are another victim of an ill-conceived change I introduced without a careful testing. From file Doc/BUGS (recently renamed Doc/release-notes): --- Fixed in version 4.0.4: [...] * rigid.f90: the fix introduced in v. 4.0.1 to improve convergence wasn't really correct --- Note that this affected the q2r.x + matdyn.x procedure! P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From anvari_meh at physics.iust.ac.ir Wed Jun 24 22:46:27 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Thu, 25 Jun 2009 00:16:27 +0330 Subject: [Pw_forum] CVS Message-ID: Hi I follow developer manual for updating Q_E CVS but I wasn't successfull. I did below steps setenv CVS_RSH ssh setenv CVSROOT :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e cvs login (cvsanon) but each time this error was appeared "connection timed out". what is the reason Mehrnaz -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090625/a4a50479/attachment.htm From bipulrr at gmail.com Wed Jun 24 21:55:50 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Thu, 25 Jun 2009 01:25:50 +0530 Subject: [Pw_forum] CVS In-Reply-To: References: Message-ID: <3a749910906241255k4a3578b8n7e19b4a7526e2754@mail.gmail.com> The same problem happens in my IBM sp5 machines. Then I ask my system administrative, to check the proper installation of CVS in sp5 machines. On 6/25/09, Mehrnaz Anvari wrote: > Hi > I follow developer manual for updating Q_E CVS but I wasn't successfull. I > did below steps > setenv CVS_RSH ssh > setenv CVSROOT :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e > cvs login (cvsanon) > but each time this error was appeared "connection timed out". what is the > reason > Mehrnaz > -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India From giannozz at democritos.it Wed Jun 24 22:20:57 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 24 Jun 2009 22:20:57 +0200 Subject: [Pw_forum] CVS In-Reply-To: References: Message-ID: On Jun 24, 2009, at 22:46 , Mehrnaz Anvari wrote: > I follow developer manual for updating Q_E CVS but I wasn't > successfull. you may have better luck if you follow the instructions on https://qe-forge.org/scm/?group_id=10 : === Anonymous CVS Access This project's CVS repository can be checked out through anonymous (pserver) CVS with the following instruction set. The module you wish to check out must be specified as the modulename. When prompted for a password for anonymous, simply press the Enter key. cvs -d :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e login cvs -d :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e checkout "modulename" === ("modulename"= espresso) P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From tapas.kar at usu.edu Wed Jun 24 22:40:44 2009 From: tapas.kar at usu.edu (Tapas Kar) Date: Wed, 24 Jun 2009 14:40:44 -0600 Subject: [Pw_forum] Electronic thermal conductivity Message-ID: <929483FB2C66F741972CF3CE351D3C441A5ED9AF50@exchg-be03.aggies.usu.edu> Hello, I want to estimate "Electronic thermal conductivity" or electronic contribution to thermal conductivity of some metallic nanotubes. Any suggestion how to do such calculation using QM-(such as DFT) methods. Thanks Tapas -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090624/c247e579/attachment.htm From jjr19 at uakron.edu Wed Jun 24 22:53:08 2009 From: jjr19 at uakron.edu (J. J. Ramsey) Date: Wed, 24 Jun 2009 13:53:08 -0700 (PDT) Subject: [Pw_forum] CVS In-Reply-To: References: Message-ID: <883827.1072.qm@web50901.mail.re2.yahoo.com> >I follow developer manual for updating Q_E CVS but I wasn't >successfull. I did below steps > >setenv CVS_RSH ssh > >setenv CVSROOT :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e > >cvs login (cvsanon) > >but each time this error was appeared "connection timed out". what >is the reason Just as a test, I've tried both the instructions in the Developer's Manual and at QE-Forge, and while I haven't yet gotten a "connection timed out" error, CVS just seems to hang. James J. Ramsey University of Akron Civil Engineering(!) Dept. From jjr19 at uakron.edu Wed Jun 24 22:57:15 2009 From: jjr19 at uakron.edu (J. J. Ramsey) Date: Wed, 24 Jun 2009 13:57:15 -0700 (PDT) Subject: [Pw_forum] CVS In-Reply-To: References: Message-ID: <255390.20652.qm@web50907.mail.re2.yahoo.com> >I follow developer manual for updating Q_E CVS but I wasn't >successfull. I did below steps > >setenv CVS_RSH ssh > >setenv CVSROOT :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e > >cvs login (cvsanon) > >but each time this error was appeared "connection timed out". what >is the reason Actually, while I sent my last e-mail CVS finally gave me the "Connection timed out," so I can at least confirm that it's not just you who has a problem. From eyvaz_isaev at yahoo.com Wed Jun 24 23:46:08 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 24 Jun 2009 14:46:08 -0700 (PDT) Subject: [Pw_forum] Phonon weirdness with matdyn Message-ID: <273075.1972.qm@web65709.mail.ac4.yahoo.com> Hi Miguel, Does your sih4.dyn0 contain the macroscopic dielectric constants and Born effective charges? According to your input file it should, as your system contains 4*2+1*8=16 electrons and you did not specify occupations (so, your system is considered as semiconducting). If this suggestion is true, then you have LO-TO splitting at the Gamma point, and there is no phonon weirdness. Contrary, it reflects the real behaviour of the material you studied. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Wed, 6/24/09, Miguel Mart?nez wrote: > From: Miguel Mart?nez > Subject: [Pw_forum] Phonon weirdness with matdyn > To: "PWscf Forum" > Date: Wednesday, June 24, 2009, 10:49 PM > Dear espresso users, > > I computed a while ago the phonon DOS of Fdd2 silane (that > is, face > centered orthorrombic) at around 50 GPa and kept the IFC > matrix. I > wanted to have a look at the phonon branches and have > noticed some > weird behaviour. > > I'm trying to follow the Gamma - T - Z - Y -Gamma - Z2 > path(see the > Brillouin Zone in > http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-kv-list?gnum=43&fig=fmm2fcgr > ) > > Amazingly, when I come back to Gamma, the frequencies have > changed. And > they jump back to the "normal" levels after a step in the > Gamma - Z2 > line. > > I've tried no, simple and crystal ASR in both the q2r > conversion and > the matdyn run, always keeping the same ASR for the sake > of > consistency. In any case, the "jump" is always present. > Gamma will > display wrong frequencies (when compared to the frequencies > directly > obtanied) every time the Gamma - Y line is followed in any > direction. > > I've used both quantum-espresso 4.0.2 compiled with ifort > in an itanium > and a nightly "build" from q-e forge downloaded yesterday > and compiled > with gfortran and run in my laptop, but that warrants no > change. > > ?Anybody has a clue on what may be happening here? For > additional weird > points, this happens at both 34 and 50 GPa (I ran the > phonon > calculation at both pressures). I fear I've done something > silly, but I > just don't see it. > > Thanks in advance, > > Miguel > > The SCF input is: > &control > ? ? calculation='scf' > ? ? restart_mode='from_scratch', > ? ? prefix='sih4', > ? ? tstress = .true. > ? ? tprnfor = .true. > ? ? pseudo_dir = '/home/wmbmacam/pseudo/', > ? ? outdir='/scratch/wmbmacam/fdd2-phon-50/' > / > &system > ? ? ibrav= 10, celldm(1) = 12.2211446, celldm(2) > = 1.07916784, > celldm(3) = 0.616658866, nat=10, ntyp= 2, > ? ? ecutwfc = 45.0, ecutrho = 500.0 > ? ? nr1= 72, nr2= 72, nr3= 72 > / > &electrons > ? ? conv_thr = 1.0d-8 > ? ? mixing_beta = 0.7 > / > ATOMIC_SPECIES > Si? 28.0855 Si.pbe-n-van.UPF > ? H???1.0079? H.pbe-van_ak.UPF > ATOMIC_POSITIONS {crystal} > Si 0.610686000000 0.389314000000 0.610686000000 > Si 0.860686000000 0.639314000000 0.860686000000 > H? 0.444907000000 0.850471000000 0.348857000000 > H? 0.348857000000 0.355765000000 0.444907000000 > H? 0.894235000000 0.901143000000 0.399529000000 > H? 0.399529000000 0.805093000000 0.894235000000 > H? 0.385750000000 0.340750000000 0.013222000000 > H? 0.013222000000 0.260278000000 0.385750000000 > H? 0.989722000000 0.236778000000 0.909250000000 > H? 0.909250000000 0.864250000000 0.989722000000 > K_POINTS {automatic} > 12 12 12? 1 1 1 > > > The Phonon input is: > &inputph > ? tr2_ph=1.0d-14, > ? prefix='sih4', > ? ldisp=.true., > ? nq1=4, nq2=4, nq3=4 > ? amass(1)=28.0855, > ? amass(2)=1.00794, > ? outdir='/scratch/wmbmacam/fdd2-phon-50/', > ? fildyn='sih4.dyn', > / > > And finally the q2r input is: > &input > ???fildyn='sih4.dyn', zasr='crystal', > flfrc='sih4.fc' > / > > > > PS: I'll happily provide an eps with the full phonon > branches if > someone desires it. Or the sih4.dyn files. > > -- > ---------------------------------------- > Miguel Mart?nez Canales > ???Condensed Matter Physics Dpt. > ???UPV/EHU > ???Faculty of Science and Technology > ???Apdo. 644 > ???48080 Bilbao (Spain) > Fax:? +34 94 601 3500 > Tlf:? +34 94 601 5326 > ---------------------------------------- > > "If you have an apple and I have an apple and > we exchange these apples then you and I will > still each have one apple. But if you have an > idea and I have an idea and we exchange these > ideas, then each of us will have two ideas." > > George Bernard Shaw > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sagarambavale at yahoo.co.in Thu Jun 25 07:59:15 2009 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Thu, 25 Jun 2009 11:29:15 +0530 (IST) Subject: [Pw_forum] energy origin in espresso Message-ID: <747872.95447.qm@web94609.mail.in2.yahoo.com> Dear all, Can I simply compare the energy levels of two molecules / molecule and slab calculated using espresso? I have heard that if energy origin is arbitrary (e.g. in siesta code) then one have to use a common reference to compare the levels of different calculations. For this purpose one can use e.g. take a hydrogen molecule 10 ? away from the slab or molecule, whose bonding orbital can be taken as reference. Regards Sagar Ambavale PhD student The M.S. University of Baroda India Cricket on your mind? Visit the ultimate cricket website. Enter http://cricket..yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090625/86e00228/attachment.htm From giannozz at democritos.it Thu Jun 25 08:28:20 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 25 Jun 2009 08:28:20 +0200 Subject: [Pw_forum] CVS In-Reply-To: <255390.20652.qm@web50907.mail.re2.yahoo.com> References: <255390.20652.qm@web50907.mail.re2.yahoo.com> Message-ID: <5BCAE20C-5D93-4AC6-A608-B58D9D7C9862@democritos.it> On Jun 24, 2009, at 22:57 , J. J. Ramsey wrote: >> but each time this error was appeared "connection timed out". what >> is the reason > > Actually, while I sent my last e-mail CVS finally gave me the > "Connection timed out," so I can at least confirm that it's not > just you who has a problem. the server works. There might be a network problem, but there is little that can be done other than waiting for the problem to disappear P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Thu Jun 25 08:31:15 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 25 Jun 2009 08:31:15 +0200 Subject: [Pw_forum] energy origin in espresso In-Reply-To: <747872.95447.qm@web94609.mail.in2.yahoo.com> References: <747872.95447.qm@web94609.mail.in2.yahoo.com> Message-ID: On Jun 25, 2009, at 7:59 , ambavale sagar wrote: > I have heard that if energy origin is arbitrary (e.g. in siesta code) in all codes asuming periodic boundary conditions > then one have to use a common reference to compare > the levels of different calculations. For this purpose one > can use e.g. take a hydrogen molecule 10 ? away from > the slab or molecule, whose bonding orbital can be taken > as reference. yes, this is a simple way to find a common alignment Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From padmaja_patnaik at yahoo.co.uk Thu Jun 25 10:55:48 2009 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Thu, 25 Jun 2009 08:55:48 +0000 (GMT) Subject: [Pw_forum] Problem in compilation Message-ID: <615015.48108.qm@web26108.mail.ukl.yahoo.com> Dear all I am trying to compile PWSCF latest version, espresso-4.0.5 on ubuntu. Configure is successful but gives the following error in the makw all command. test -d bin || mkdir bin if test -d iotk ; then \ ??? ( cd iotk ; if test "make" = "" ; then make? TLDEPS= lib+util ; \ ??? else make? TLDEPS= lib+util ; fi ) ; fi make[1]: Entering directory `/home/gautam/Desktop/espresso-4.0.5/iotk' cd src ; make lib+util make[2]: Entering directory `/home/gautam/Desktop/espresso-4.0.5/iotk/src' mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW -I../include?? -I./? -I../Modules? -I../iotk/src -I../PW? -I../PH -c iotk_base.f90 gfortran: byterecl: No such file or directory gfortran: unrecognized option '-nomodule' f951: error: unrecognized command line option "-assume" f951: error: unrecognized command line option "-fpp" make[2]: *** [iotk_base.o] Error 1 make[2]: Leaving directory `/home/gautam/Desktop/espresso-4.0.5/iotk/src' make[1]: *** [lib+util] Error 2 make[1]: Leaving directory `/home/gautam/Desktop/espresso-4.0.5/iotk' make: *** [libiotk] Error 2 Can anybody please advise? Thanx 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/20090625/b516d1b7/attachment.htm From giannozz at democritos.it Thu Jun 25 11:10:33 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 25 Jun 2009 11:10:33 +0200 Subject: [Pw_forum] Problem in compilation In-Reply-To: <615015.48108.qm@web26108.mail.ukl.yahoo.com> References: <615015.48108.qm@web26108.mail.ukl.yahoo.com> Message-ID: <4A433F09.7050207@democritos.it> Padmaja Patnaik wrote: > Can anybody please advise? you have a mismatch between parallel (mpif90) and serial (gfortran) compiler. This is something "configure" warns you about. Use "./configure F90=gfortran", or, better, install a mpif90 compiler that uses ifort P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Thu Jun 25 11:17:58 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 25 Jun 2009 11:17:58 +0200 Subject: [Pw_forum] Problem in compilation In-Reply-To: <4A433F09.7050207@democritos.it> References: <615015.48108.qm@web26108.mail.ukl.yahoo.com> <4A433F09.7050207@democritos.it> Message-ID: In data 25 giugno 2009 alle ore 11:10:33, Paolo Giannozzi ha scritto: > "./configure F90=gfortran", or, better, install > a mpif90 compiler that uses ifort When you compile openmpi it will use gfortran and gcc as default, even if it finds other compilers. In order to have it use the intel compiler you have to specify it explicitly: ./configure CC=icc CXX=icpc F77=ifort FC=ifort ... cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From lfhuang at theory.issp.ac.cn Thu Jun 25 11:09:26 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Thu, 25 Jun 2009 17:09:26 +0800 Subject: [Pw_forum] =?utf-8?q?Electronic_thermal_conductivity?= Message-ID: <20090625090926.10753.qmail@ms.hfcas.ac.cn> Dear Tapas Kar: In my opinion, you may need some analytical derivation after DFT calculations. I have calculated the semiclassical transport properties of the electrons in graphene. First, I calculated the band structure and electron-phonon interactions by PWSCF, and then I derived the transport properties using Boltzmann equation. Because the band structure of graphene is not complicated, it is not hard for me to understand the physics and calculate the transport properties. May these can be helpful to you. In addition, please put your own affiliation at the bottom of you email, because that is a netiquette. Best Wishes! L. F. Huang > Date: Wed, 24 Jun 2009 14:40:44 -0600 > From: Tapas Kar > Subject: [Pw_forum] Electronic thermal conductivity > To: "pw_forum at pwscf.org" > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > Hello, > I want to estimate "Electronic thermal conductivity" or electronic contribution to thermal conductivity of some metallic nanotubes. Any suggestion how to do such calculation using QM-(such as DFT) methods. > Thanks > Tapas ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090625/56a5e11b/attachment.htm From greatnaol at gmail.com Thu Jun 25 13:28:59 2009 From: greatnaol at gmail.com (Naol Regassa) Date: Thu, 25 Jun 2009 14:28:59 +0300 Subject: [Pw_forum] smaller band gaps Message-ID: <97e4b88e0906250428g7c35ed27xc8f4c294a066fa49@mail.gmail.com> Thank you Prof. nicola, Lorenzo and Paolo. I got the point. Naol (Tamene) On 6/24/09, pw_forum-request at pwscf.org wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://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: smaller band gaps (Lorenzo Paulatto) > 2. Re: Separating Raman modes (Paolo Giannozzi) > 3. Re: smaller band gaps (Paolo Giannozzi) > 4. Re: Separating Raman modes (Zubaer Hossain) > 5. Re: Separating Raman modes (Paolo Giannozzi) > 6. hybrid functional and Wannier functions (lan haiping) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 23 Jun 2009 17:16:22 +0200 > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] smaller band gaps > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 23 giugno 2009 alle ore 13:58:38, Naol Regassa > ha scritto: >> My main concern is that DFT calculations reduce band gaps >> by 50%. > > DFT does not predict band gap at all, for many materials it is related to > the experimental one, but on assumption can be made a priori on its > precision. Anyway, you are probably doing the calculation using the > experimental lattice parameter, if you relax the system to the numerical > equilibrium lattice parameter, you will probably get a better gap. > >> Does this mean that I can add this error to get the correct >> band gap so that any body can understand it? How can one argue about >> this condition? > > No, the fact that DFT does not predict the band gap is a well known > problem of the theory, if you fix it with an empirical parameter it would > be not only unethical, but also quite suspicious. If you want to have > accurate band gap you have to use TDDFT or DFT+GW, which are both > implemented in quantum espresso (I don't know the details of them, nor > which is better for your specific purpose, you'll have to read a bit of > literature). > > best regards > > P.S. if you are starting a new discussion in the mailing list, please > write a new email, do not reply to a previous one > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > > > ------------------------------ > > Message: 2 > Date: Tue, 23 Jun 2009 18:14:02 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Separating Raman modes > To: PWSCF Forum > Message-ID: <4A40FF4A.4070108 at democritos.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Stefano Baroni wrote: > >> The method by Mauri and coworkers >> (whose implementation status in QE is unknown to me) > > it is implemented, but only for the "ordinary" phonon > code (i.e. not for the Gamma-specific one) and only for > norm-conserving pseudopotentials > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 3 > Date: Tue, 23 Jun 2009 18:18:24 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] smaller band gaps > To: PWSCF Forum > Message-ID: <4A410050.9090100 at democritos.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Lorenzo Paulatto wrote: > >> if you fix it with an empirical parameter it would be not only unethical > > Lorenzo, take it easy: there is nothing "ethically" wrong in trying > to adjust the gap, as long as it is clearly stated > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 4 > Date: Tue, 23 Jun 2009 11:28:30 -0500 > From: Zubaer Hossain > Subject: Re: [Pw_forum] Separating Raman modes > To: PWSCF Forum > Message-ID: > <51ec861d0906230928p791f99a7yb86b747d6ad5facd at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > How about decomposing eigenstates into that for the individual atoms and > summing them for each species, since the phonon frequencies are computed > already, and the eigenmodes for each frequency are known. By analyzing these > quantities graphically for each species, optical frequencies of the main > three modes could be detected, I think. > > Zubaer > Department of Mechanical Science and Engineering > Univ. of Illinois at Urbana-Champaign, USA > > On Tue, Jun 23, 2009 at 11:14 AM, Paolo Giannozzi > wrote: > >> Stefano Baroni wrote: >> >> > The method by Mauri and coworkers >> > (whose implementation status in QE is unknown to me) >> >> it is implemented, but only for the "ordinary" phonon >> code (i.e. not for the Gamma-specific one) and only for >> norm-conserving pseudopotentials >> >> Paolo >> -- >> Paolo Giannozzi, Democritos and University of Udine, Italy >> _______________________________________________ >> 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/20090623/b2f54fbb/attachment.html > > ------------------------------ > > Message: 5 > Date: Tue, 23 Jun 2009 18:35:42 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Separating Raman modes > To: PWSCF Forum > Message-ID: <4A41045E.5060708 at democritos.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Zubaer Hossain wrote: > >> How about decomposing eigenstates into that for the individual atoms and >> summing them for each species, since the phonon frequencies are computed >> already, and the eigenmodes for each frequency are known. By analyzing >> these quantities graphically for each species, optical frequencies of >> the main three modes could be detected, I think. > > years ago we did something similar: > "Phonon Dispersions in Ga(x)Al(1-x)As Alloys", PRL 65, 84 (1990). > Alloy modes were projected over crystal modes. In that particular > case the "mass approximation" was giving an accurate and convenient > way to calculate the dynamical matrix in relatively large supercells > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 6 > Date: Wed, 24 Jun 2009 02:05:09 +0800 > From: lan haiping > Subject: [Pw_forum] hybrid functional and Wannier functions > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear All: > > I want to study electronic structures with hybrid functional. Is it > possible for us to using wannier90 package to analyse related bands at > present version ? Such as WFs and bands structure. > > > Regards, > > Hai-Ping > > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com, hplan at pku.edu.cn > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090624/ce0fac3b/attachment-0001.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 24, Issue 52 > **************************************** > From marzari at MIT.EDU Thu Jun 25 13:40:12 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Thu, 25 Jun 2009 07:40:12 -0400 Subject: [Pw_forum] energy origin in espresso In-Reply-To: References: <747872.95447.qm@web94609.mail.in2.yahoo.com> Message-ID: <4A43621C.8030509@mit.edu> Paolo Giannozzi wrote: >> then one have to use a common reference to compare >> the levels of different calculations. For this purpose one >> can use e.g. take a hydrogen molecule 10 ? away from >> the slab or molecule, whose bonding orbital can be taken >> as reference. > > yes, this is a simple way to find a common alignment Dear Ambavale, to elaborate on Paolo's comment: this is one of the two common ways to do it. The other would be to do a plot of the electrostatic potential - far away form the slab it will become flat (unless your slab, e.g., has a surface dipole - then you'll learn you have a small problem, and need to be careful about electrostatic interactions between different charges). But suppose it will become flat - that will point to the reference zero energy of that calculation. You redo this for all calculations, and you have reference points of each of them. Use this approach, and the one where you add the hydrogen molecule. Do they give you the same results ? In principle they should - if they do not, you need to figure out what is the problem, and in the process you learn a lot about accuracy. Warmly recommended, nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From marzari at MIT.EDU Thu Jun 25 13:55:45 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Thu, 25 Jun 2009 07:55:45 -0400 Subject: [Pw_forum] Electronic thermal conductivity In-Reply-To: <20090625090926.10753.qmail@ms.hfcas.ac.cn> References: <20090625090926.10753.qmail@ms.hfcas.ac.cn> Message-ID: <4A4365C1.4070109@mit.edu> Dear Tapas, indeed - one generally calculates the electronic electrical conductivity, and then just used the Wiedemann-Franz law to estimate the electronic thermal conductivity. For the electrical conductivity, I'd be fairly impressed by Huang if he had managed to do that from el-ph calculations - the dependence on k,k+q seems to require very careful integrations to estimate lifetimes ? nicola lfhuang wrote: > Dear Tapas Kar: > In my opinion, you may need some analytical derivation after DFT > calculations. I have calculated the semiclassical transport properties > of the electrons in graphene. First, I calculated the band structure and > electron-phonon interactions by PWSCF, and then I derived the transport > properties using Boltzmann equation. Because the band structure of > graphene is not complicated, it is not hard for me to understand the > physics and calculate the transport properties. May these can be helpful > to you. In addition, please put your own affiliation at the bottom of > you email, because that is a netiquette. > Best Wishes! > L. F. Huang -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From xwzhang at uestc.edu.cn Thu Jun 25 14:13:02 2009 From: xwzhang at uestc.edu.cn (xwzhang) Date: Thu, 25 Jun 2009 20:13:02 +0800 Subject: [Pw_forum] error message: from set_irr: error # 1, one mode is zero Message-ID: <200906252013023753415@uestc.edu.cn> Dear my Pwscf friends: When I am trying to do a series phonon calculations of fcc-Fe, at some of the lattice parameters, there is an error message: %%%%%%%%%%%%%%%%%%% from set_irr: error # 1 one mode is zero %%%%%%%%%%%%%%%%%%% in the output file of ph.x. How can it been remedied? I wonder, why just some of these calculations have this error? Regards Dr. Wenxu Zhang State Key Laboratory of Electronic Thin Films and Integrated Devices, University of Electronic Science and Technology of China, Chengdu 610054 China Tel: +86-28-83201475 Fax: +86-28-83204938 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090625/046eb1f3/attachment.htm From anavat_ila at yahoo.com Thu Jun 25 14:48:36 2009 From: anavat_ila at yahoo.com (Ali Tavana) Date: Thu, 25 Jun 2009 05:48:36 -0700 (PDT) Subject: [Pw_forum] Constrained U calculations Message-ID: <967637.47073.qm@web51804.mail.re2.yahoo.com> Dear all, I want to calculate ab initio, the Hubbard U, used in the LSDA+U calculations. The linear response method mentioned in the Cococcioni et al.'s paper seems to be a non-standard method for QE. I mean specially the application of localized perturbation (Delta V) needs some thing to be done by other tools. So my question is that is there any other method of U calculation (non-LR) already examined with QE or is using the traditional LR method much simpler than what I supposed it to be? Thanks, Ali From giannozz at democritos.it Thu Jun 25 14:51:10 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 25 Jun 2009 14:51:10 +0200 Subject: [Pw_forum] error message: from set_irr: error # 1, one mode is zero In-Reply-To: <200906252013023753415@uestc.edu.cn> References: <200906252013023753415@uestc.edu.cn> Message-ID: <4A4372BE.7080000@democritos.it> xwzhang wrote: > When I am trying to do a series phonon calculations of fcc-Fe, > at some of the lattice parameters, there is an error message > from set_irr: error # 1 > one mode is zero please provide a test job P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu Jun 25 14:52:04 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 25 Jun 2009 14:52:04 +0200 Subject: [Pw_forum] error message: from set_irr: error # 1, one mode is zero In-Reply-To: <200906252013023753415@uestc.edu.cn> References: <200906252013023753415@uestc.edu.cn> Message-ID: <4A4372F4.9060605@democritos.it> even better: please go to www.qe-forge.org and file a bug report P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From miguel.martinez at ehu.es Thu Jun 25 15:25:13 2009 From: miguel.martinez at ehu.es (Miguel =?UTF-8?B?TWFydMOtbmV6?=) Date: Thu, 25 Jun 2009 15:25:13 +0200 Subject: [Pw_forum] Phonon weirdness with matdyn In-Reply-To: <273075.1972.qm@web65709.mail.ac4.yahoo.com> References: <273075.1972.qm@web65709.mail.ac4.yahoo.com> Message-ID: <20090625152513.5fd9d815@lcpybm> First of all, thanks to Paolo and Eyvaz for their answers. On Wed, 24 Jun 2009 21:46:05 +0200 Paolo Giannozzi wrote: > oops, I guess you are another victim of an ill-conceived change > I introduced without a careful testing. From file Doc/BUGS > (recently renamed Doc/release-notes): The results don't change with quantum-espresso 4.0.5 or the nightly code tarball from June 23, but I guess Eyvaz is right. On Wed, 24 Jun 2009 14:46:08 -0700 (PDT) Eyvaz Isaev wrote: > Does your sih4.dyn0 contain the macroscopic dielectric constants and > Born effective charges? As long as the number is not 0, sih4.dyn* contains both the dielectric tensor and the Born effective charges, yes. > If this suggestion is true, then you have LO-TO splitting at the > Gamma point, and there is no phonon weirdness. Contrary, it reflects > the real behaviour of the material you studied. The system is insulating, yes. It doesn't have an enormous gap, but it's still about 1 eV. I'll take a deeper look at the TO-LO splitting, because I should have known better... because epsilon_yy is noticeably larger than epsilon_xx or epsilon_zz. Thanks everybody again for suggestions and tips, Miguel -- ---------------------------------------- Miguel Mart?nez Canales Condensed Matter Physics Dpt. UPV/EHU Faculty of Science and Technology Apdo. 644 48080 Bilbao (Spain) Fax: +34 94 601 3500 Tlf: +34 94 601 5326 ---------------------------------------- "If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." George Bernard Shaw From larikamonu at gmail.com Thu Jun 25 15:51:48 2009 From: larikamonu at gmail.com (mousumi uk) Date: Thu, 25 Jun 2009 15:51:48 +0200 Subject: [Pw_forum] Ni and Pt: LDA relativistic potential Message-ID: <42e352dc0906250651t15a18be6nca976b16d97d658a@mail.gmail.com> Dear All, Am searching for two LDA relativistic pseudopotentials (like Au.rel-pz-rrkjus.UPF, as in PWSCF pseudo page) for Ni and Pt. Can any of you please help? Thanks and best regards, Mousumi Upadhyay Kahaly -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090625/fa511857/attachment.htm From tapas.kar at usu.edu Thu Jun 25 19:11:45 2009 From: tapas.kar at usu.edu (Tapas Kar) Date: Thu, 25 Jun 2009 11:11:45 -0600 Subject: [Pw_forum] Electronic thermal conductivity (ElecTC) Message-ID: <929483FB2C66F741972CF3CE351D3C441A5ED9AFE6@exchg-be03.aggies.usu.edu> Dear Prof. Huang, Thanks a lot for your reply. I would appreciate reference and reprint of your grapheme work. Is it possible to estimate ElecTC for finite size nanotubes, considering molecular model. Are molar heat capacity (Cv) and thermal energy of nanotube (terminated with hydrogen) useful to estimate Elec Thermal conductivity? Well, I am a chemist and trying to understand physics of nanocomposites. I appreciate your help and suggestion Best regards, Tapas Date: Thu, 25 Jun 2009 17:09:26 +0800 From: " lfhuang " Subject: Re: [Pw_forum] Electronic thermal conductivity To: " pw_forum " Message-ID: <20090625090926.10753.qmail at ms.hfcas.ac.cn> Content-Type: text/plain; charset="utf-8" Dear Tapas Kar: In my opinion, you may need some analytical derivation after DFT calculations. I have calculated the semiclassical transport properties of the electrons in graphene. First, I calculated the band structure and electron-phonon interactions by PWSCF, and then I derived the transport properties using Boltzmann equation. Because the band structure of graphene is not complicated, it is not hard for me to understand the physics and calculate the transport properties. May these can be helpful to you. In addition, please put your own affiliation at the bottom of you email, because that is a netiquette. Best Wishes! L. F. Huang ----------------------------------------------------------------------------------------------- Tapas Kar, Ph. D Research Assistant Professor Department of Chemistry & Biochemistry Utah State University Logan, UT 84322-0300 Tel: 435-797-7230 Fax: 435-797-3390 Email: tapas.kar at usu.edu Web: http://www.chem.usu.edu/~tapaskar/ http://www.chem.usu.edu/pages/research%20pages/webpages/tapaskar.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090625/2ce32961/attachment-0001.htm From lfhuang at theory.issp.ac.cn Fri Jun 26 03:33:02 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Fri, 26 Jun 2009 9:33:02 +0800 Subject: [Pw_forum] =?utf-8?q?Electronic_thermal_conductivity_=28ElecTC=29?= Message-ID: <20090626013302.24858.qmail@ms.hfcas.ac.cn> Dear Tapas Kar: In 2004, S. Piscanec et al. calculated the e-p interaction constants of graphite by DFPT [ref. 1], and then in 2005, they applied these constants approximately to the calculation of transport properties of carbon nanotubes [ref. 2]. You also could look at another paper on the e-p scattering in metallic SWCNT[ref. 3]. There are a lot of papers on this kind of things, and I just did the calculations for fun and practice nearly two years ago, so I had not published any paper on it. And if you want to calculate the e-ph coupling derectly in nanotubes, there will be two difficulties: (1) tremendous cpu times; (2) complicated band structures. So, in my opinion, analytical derivation should be prefered here, just like the way in [ref. 2]. In addition, I'm not a professor, and I'm a ph.D candidate. I'm sorry for having not mentioned it in my affiliation before :). [1] S. Piscanec et al., "Kohn anomalies electron-phonon interactions in graphite", PRL 93, 185503 (2004) [2] M. Lazzeri et al. "Electron transport and hot phonons in carbon nanotubes", PRL 95, 236802 (2005) [3] J. Park et al, "Electron-phonon scattering in metallic single-walled carbon nanotubes", Nano Letters 4, 517 (2004) Best Wishes! Yours Sincerely L. F. Huang > Date: Thu, 25 Jun 2009 07:55:45 -0400 > From: Nicola Marzari > Subject: Re: [Pw_forum] Electronic thermal conductivity > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > Dear Tapas, > > indeed - one generally calculates the electronic electrical > conductivity, and then just used the Wiedemann-Franz law to estimate the > electronic thermal conductivity. > > For the electrical conductivity, I'd be fairly impressed by Huang > if he had managed to do that from el-ph calculations - the dependence on > k,k+q seems to require very careful integrations to estimate lifetimes ? > > nicola > > Date: Thu, 25 Jun 2009 11:11:45 -0600 > From: Tapas Kar > Subject: Re: [Pw_forum] Electronic thermal conductivity (ElecTC) > To: "lfhuang at theory.issp.ac.cn" > Cc: "pw_forum at pwscf.org" > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > Dear Prof. Huang, > Thanks a lot for your reply. I would appreciate reference and reprint of your grapheme work. > Is it possible to estimate ElecTC for finite size nanotubes, considering molecular model. > Are molar heat capacity (Cv) and thermal energy of nanotube (terminated with hydrogen) useful to estimate Elec Thermal conductivity? > > Well, I am a chemist and trying to understand physics of nanocomposites. > I appreciate your help and suggestion > Best regards, > Tapas > > Date: Thu, 25 Jun 2009 17:09:26 +0800 > From: " lfhuang " > Subject: Re: [Pw_forum] Electronic thermal conductivity > To: " pw_forum " > Message-ID: > Content-Type: text/plain; charset="utf-8" > > Dear Tapas Kar: > In my opinion, you may need some analytical derivation after DFT calculations. I have calculated the semiclassical transport properties of the electrons in graphene. First, I calculated the band structure and electron-phonon interactions by PWSCF, and then I derived the transport properties using Boltzmann equation. Because the band structure of graphene is not complicated, it is not hard for me to understand the physics and calculate the transport properties. May these can be helpful to you. In addition, please put your own affiliation at the bottom of you email, because that is a netiquette. > Best Wishes! > L. F. Huang > > ----------------------------------------------------------------------------------------------- > Tapas Kar, Ph. D > Research Assistant Professor > Department of Chemistry & Biochemistry > Utah State University > Logan, UT 84322-0300 > > Tel: 435-797-7230 > Fax: 435-797-3390 > Email: tapas.kar at usu.edu > Web: http://www.chem.usu.edu/~tapaskar/ > http://www.chem.usu.edu/pages/research%20pages/webpages/tapaskar.html > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090625/2ce32961/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 24, Issue 56 > **************************************** > ------ ====================================================================== L.F.Huang(???) ph.D candidate ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090626/e8c63bbe/attachment.htm From quantumdft at gmail.com Fri Jun 26 08:23:00 2009 From: quantumdft at gmail.com (vega lew) Date: Fri, 26 Jun 2009 14:23:00 +0800 Subject: [Pw_forum] what's the difference between 'md' in pw.x and cp.x In-Reply-To: <1245760087.5775.18.camel@zero> References: <412f6c680906220139r1a687e96u1046d6e006d260cd@mail.gmail.com> <7b6913e90906220600r779396ddh2ea7748d40eec9a7@mail.gmail.com> <412f6c680906222234h45c3ed2p886ce13e789bbe3@mail.gmail.com> <1245760087.5775.18.camel@zero> Message-ID: <412f6c680906252323r6feb0ae5s8195f22efce054f9@mail.gmail.com> Dear sir, thank you for your so detail answer about the ab initio MD method. Now, I am much clear about this method. I have not logged on this maillist because of the blockage of google webpage (my gmail was blocked too). So sorry for the late appreciation to your kind reply to my questions. thank you again vega On Tue, Jun 23, 2009 at 8:28 PM, Axel Kohlmeyer wrote: > On Tue, 2009-06-23 at 13:34 +0800, vega lew wrote: > > Dear friends, > > > > Thank you for you time for reading and answering my questions. > > > > I realized that the ensemble is much more important than one snap of > > the whole run, resembling the classical MD to some extent. > > there is _no_ difference between classical MD and ab initio MD > in this respect. the only difference between the two is how you > get the forces. statistical mechanics doesn't care about the > forces only about configurations and ensembles. > > [...] > > > we put a integrated water molecule at certain site on the surface. and > > then we perform MD calculations of different method, such as CPMD, > > cp.x, pw.x(calcualtion='md'). I wonder whether the dissociative state > > could be acheived on the surface at very low temparature (such as 100K > > or below) via all the MD calculations mentioned above? > > you have to look at this from a different perspective. what you will > see, depends on the potential surfaces of the system, that you are > studying. running MD allows your system to sample different local > minima, provided the barriers between them are small enough. if you > run at low temperature, your MD will not be very different from > a geometry optimization. > > > From your answers, I see cp.x and CPMD of IBM CORP. is using > > 'Car-Parrinello Molecular Dynamics', while the 'md' calculation in > > pw.x performs born-oppenheimer MD. Paolo just told us that the > > born-oppenheimer MD only perform MD at ground state. Does CPMD or cp.x > > perform the MD calculation at ground state or exited state? > > both are methods that look at the ground state wavefunction. > the CP method uses a "trick" that would allow to propagate > the wavefunction without having to do a full optimization. > CP can be faster, but has some approximations and limitations, > e.g. CP requires a band gap and has not been implemented for > k-points (at least not in the codes you mentioned, and i don't > know of a code that has it, even though it should be technically > possible). > > doing excited state calculations with DFT is a different > problem, as (regular) DFT is a ground state method. > > > cheers, > axel. > > > > thank you very much for you time > > > > best, > > > > vega > > > > > > -- > > > ================================================================================== > > Vega Lew ( weijia liu) > > PH.D Candidate in Chemical Engineering > > State Key Laboratory of Materials-oriented Chemical Engineering > > College of Chemistry and Chemical Engineering > > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > > > ****************************************************************************************************************** > > Email: vegalew at gmail.com > > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > > Nanjing, Jiangsu, China > > > ****************************************************************************************************************** > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090626/f63ea5f1/attachment-0001.htm From sagarambavale at yahoo.co.in Fri Jun 26 09:39:15 2009 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Fri, 26 Jun 2009 13:09:15 +0530 (IST) Subject: [Pw_forum] Pw_forum Digest, Vol 24, Issue 55 In-Reply-To: References: Message-ID: <660990.34611.qm@web94610.mail.in2.yahoo.com> Dear Sir, Thank you very much for your kind guidance. I will do the exercise. best regards Sagar ________________________________ Message: 6 Date: Thu, 25 Jun 2009 07:40:12 -0400 From: Nicola Marzari Subject: Re: [Pw_forum] energy origin in espresso To: PWSCF Forum Message-ID: <4A43621C.8030509 at mit..edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Paolo Giannozzi wrote: >> then one have to use a common reference to compare >> the levels of different calculations. For this purpose one >> can use e.g. take a hydrogen molecule 10 ? away from >> the slab or molecule, whose bonding orbital can be taken >> as reference. > > yes, this is a simple way to find a common alignment Dear Ambavale, to elaborate on Paolo's comment: this is one of the two common ways to do it. The other would be to do a plot of the electrostatic potential - far away form the slab it will become flat (unless your slab, e.g., has a surface dipole - then you'll learn you have a small problem, and need to be careful about electrostatic interactions between different charges). But suppose it will become flat - that will point to the reference zero energy of that calculation. You redo this for all calculations, and you have reference points of each of them. Use this approach, and the one where you add the hydrogen molecule. Do they give you the same results ? In principle they should - if they do not, you need to figure out what is the problem, and in the process you learn a lot about accuracy. Warmly recommended, nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu ------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum End of Pw_forum Digest, Vol 24, Issue 55 **************************************** ICC World Twenty20 England '09 exclusively on YAHOO! CRICKET http://cricket.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090626/72b41acc/attachment.htm From l.salimi at ph.iut.ac.ir Fri Jun 26 13:56:55 2009 From: l.salimi at ph.iut.ac.ir (leila salimi) Date: Fri, 26 Jun 2009 15:26:55 +0330 (IRST) Subject: [Pw_forum] Installation pwscf Message-ID: <1041016.119301246017415311.JavaMail.root@mta.iut.ac.ir> Hi everybody, I have been trying to install the code "espresso-4.0.5" on IBM pSeries 575, a clustered SMP (Symmetric Multiprocessing) system. When I issue ./configure , every things are OK. (configure: success). However, when I run (make pwall) I always get the error. mpfort -o ph.x phonon.o \ ../Modules/atom.o ../Modules/autopilot.o ../Modules/basic_algebra_routines.o ../Modules/bfgs_module.o ../Modules/berry_phase.o ../Modules/cell_base.o ../Modules/check_stop.o ../Modules/clocks.o ../Modules/constants.o ../Modules/constraints_module.o ../Modules/control_flags.o ../Modules/descriptors.o ../Modules/dspev_drv.o ../Modules/electrons_base.o../Modules/error_handler.o ../Modules/exc_t.o ../Modules/fft_base.o ../Modules/fft_parallel.o ../Modules/fft_scalar.o ../Modules/fft_types.o ../Modules/functionals.o ../Modules/input_parameters.o ../Modules/io_files.o ../Modules/io_global.o ../Modules/ions_base.o ../Modules/ions_nose.o ../Modules/kind.o ../Modules/metadyn_base.o ../Modules/metadyn_io.o ../Modules/metadyn_vars.o ../Modules/metagga.o ../Modules/mp_global.o ../Modules/mp_wave.o ../Modules/mp.o ../Modules/mp_base.o ../Modules/parallel_include.o ../Modules/parameters.o ../Modules/parser.o ../Modules/path_base.o ../Modules/path_formats.o ../Modules/path_variables.o ../Modules/path_opt_routines.o ../Modules/path_io_routines.o ../Modules/path_reparametrisation.o ../Modules/paw_variables.o ../Modules/printout_base.o ../Modules/pseudo_types.o ../Modules/ptoolkit.o ../Modules/radial_grids.o ../Modules/random_numbers.o ../Modules/read_cards.o ../Modules/read_namelists.o ../Modules/read_ncpp.o ../Modules/read_uspp.o ../Modules/read_upf_v1.o ../Modules/read_upf_v2.o ../Modules/recvec.o ../Modules/splinelib.o ../Modules/stick_base.o ../Modules/shmem_include.o ../Modules/task_groups.o ../Modules/timestep.o ../Modules/upf_to_internal.o ../Modules/upf.o ../Modules/uspp.o ../Modules/version.o ../Modules/vxc_t.o ../Modules/vxcgc.o ../Modules/wavefunctions.o ../Modules/wave_base.o ../Modules/write_upf_v2.o ../Modules/xml_io_base.o ../Modules/zhpev_drv.o libph.a ../PW/libpw.a ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a /sara/sw/lapack/3.1.1/lib/liblapack.a /sara/sw/blas/1.0/lib/libblas.a /sara/sw/fftw3/3.1.2/lib/libfftw3f.a -lmassvp4_64 -lmass_64 /opt/ibmcmp/xlmass/5.0/lib64/libmass_64.a(erfc.s64.o): In function `_erfc': erfc.c:(.opd+0x0): multiple definition of `erfc' ../flib/flib.a(erf.o):(.opd+0x18): first defined here ld: Warning: size of symbol `erfc' changed from 616 in ../flib/flib.a(erf.o) to 1256 in /opt/ibmcmp/xlmass/5.0/lib64/libmass_64.a(erfc.s64.o) make[1]: *** [ph.x] Error 1 make[1]: Leaving directory `/gpfs/h04/mokhles/espresso-4.0.5/PH' make: *** [ph] Error 2 when I check example03 with pw.x I get this error: from cfft3d : error # 1 no scalar fft driver specified Can someone give some solution to me? Leila Salimi Isfahan University of Technology, Iran From l.salimi at ph.iut.ac.ir Fri Jun 26 14:40:42 2009 From: l.salimi at ph.iut.ac.ir (leila salimi) Date: Fri, 26 Jun 2009 16:10:42 +0330 (IRST) Subject: [Pw_forum] install pwscf In-Reply-To: <19541958.119741246019970905.JavaMail.root@mta.iut.ac.ir> Message-ID: <13218721.119791246020042354.JavaMail.root@mta.iut.ac.ir> Hi everybody, I have been trying to install the code "espresso-4.0.5" on IBM pSeries 575, a clustered SMP (Symmetric Multiprocessing) system. When I issue ./configure , every things are OK. (configure: success). However, when I run (make pwall) I always get the error. mpfort -o ph.x phonon.o \ ../Modules/atom.o ../Modules/autopilot.o ../Modules/basic_algebra_routines.o ../Modules/bfgs_module.o ../Modules/berry_phase.o ../Modules/cell_base.o ../Modules/check_stop.o ../Modules/clocks.o ../Modules/constants.o ../Modules/constraints_module.o ../Modules/control_flags.o ../Modules/descriptors.o ../Modules/dspev_drv.o ../Modules/electrons_base.o../Modules/error_handler.o ../Modules/exc_t.o ../Modules/fft_base.o ../Modules/fft_parallel.o ../Modules/fft_scalar.o ../Modules/fft_types.o ../Modules/functionals.o ../Modules/input_parameters.o ../Modules/io_files.o ../Modules/io_global.o ../Modules/ions_base.o ../Modules/ions_nose.o ../Modules/kind.o ../Modules/metadyn_base.o ../Modules/metadyn_io.o ../Modules/metadyn_vars.o ../Modules/metagga.o ../Modules/mp_global.o ../Modules/mp_wave.o ../Modules/mp.o ../Modules/mp_base.o ../Modules/parallel_include.o ../Modules/parameters.o ../Modules/parser.o ../Modules/path_base.o ../Modules/path_formats.o ../Modules/path_variables.o ../Modules/path_opt_routines.o ../Modules/path_io_routines.o ../Modules/path_reparametrisation.o ../Modules/paw_variables.o ../Modules/printout_base.o ../Modules/pseudo_types.o ../Modules/ptoolkit.o ../Modules/radial_grids.o ../Modules/random_numbers.o ../Modules/read_cards.o ../Modules/read_namelists.o ../Modules/read_ncpp.o ../Modules/read_uspp.o ../Modules/read_upf_v1.o ../Modules/read_upf_v2.o ../Modules/recvec.o ../Modules/splinelib.o ../Modules/stick_base.o ../Modules/shmem_include.o ../Modules/task_groups.o ../Modules/timestep.o ../Modules/upf_to_internal.o ../Modules/upf.o ../Modules/uspp.o ../Modules/version.o ../Modules/vxc_t.o ../Modules/vxcgc.o ../Modules/wavefunctions.o ../Modules/wave_base.o ../Modules/write_upf_v2.o ../Modules/xml_io_base.o ../Modules/zhpev_drv.o libph.a ../PW/libpw.a ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a /sara/sw/lapack/3.1.1/lib/liblapack.a /sara/sw/blas/1.0/lib/libblas.a /sara/sw/fftw3/3.1.2/lib/libfftw3f.a -lmassvp4_64 -lmass_64 /opt/ibmcmp/xlmass/5.0/lib64/libmass_64.a(erfc.s64.o): In function `_erfc': erfc.c:(.opd+0x0): multiple definition of `erfc' ../flib/flib.a(erf.o):(.opd+0x18): first defined here ld: Warning: size of symbol `erfc' changed from 616 in ../flib/flib.a(erf.o) to 1256 in /opt/ibmcmp/xlmass/5.0/lib64/libmass_64.a(erfc.s64.o) make[1]: *** [ph.x] Error 1 make[1]: Leaving directory `/gpfs/h04/mokhles/espresso-4.0.5/PH' make: *** [ph] Error 2 when I check example03 with pw.x I get this error: from cfft3d : error # 1 no scalar fft driver specified Can someone give some solution to me? Leila Salimi Isfahan University of Technology, Iran From paulatto at sissa.it Fri Jun 26 15:14:05 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 26 Jun 2009 15:14:05 +0200 (CEST) Subject: [Pw_forum] install pwscf In-Reply-To: <13218721.119791246020042354.JavaMail.root@mta.iut.ac.ir> References: <13218721.119791246020042354.JavaMail.root@mta.iut.ac.ir> Message-ID: <59873.151.65.44.46.1246022045.squirrel@webmail.sissa.it> On Fri, June 26, 2009 14:40, leila salimi wrote: > /opt/ibmcmp/xlmass/5.0/lib64/libmass_64.a(erfc.s64.o): In function > `_erfc': > erfc.c:(.opd+0x0): multiple definition of `erfc' > ../flib/flib.a(erf.o):(.opd+0x18): first defined here Dear Leila, it looks like new version of the IBM libraries has started to include the erf function, in order to work-around the problem you should: 1. edit flib/Makefile and remove the line erf.o \ 2. remove the file flib/flib.a 3. recompile > when I check example03 with pw.x I get this error: > from cfft3d : error # 1 > no scalar fft driver specified Open make.sys with a text editor, and check that -D__ESSL appears in the definition of the variable FDFLAGS. If it does not, than add it (please note that it is a comma-separated list). Than make clean and recompile. > Can someone give some solution to me? Try what I suggested and please report if it works, also please provide the full output of configure, and the make.sys, so we can try and fix it in time for the next version of quantum-espresso. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From matteo at umn.edu Fri Jun 26 17:30:51 2009 From: matteo at umn.edu (Matteo Cococcioni) Date: Fri, 26 Jun 2009 10:30:51 -0500 Subject: [Pw_forum] Constrained U calculations In-Reply-To: <967637.47073.qm@web51804.mail.re2.yahoo.com> References: <967637.47073.qm@web51804.mail.re2.yahoo.com> Message-ID: <4A44E9AB.5040707@umn.edu> Dear Ali, to apply the localized perturbation you don't need extra features. you just need to set Hubbard_alpha to some finite (small) value in the input of pwscf. You need, however, some post-processing codes to extract U from your calculations. these are contained in a Vlab tutorial linked from the webpage of quantum-espresso. Hope this helps. Matteo Ali Tavana wrote: > Dear all, > > I want to calculate ab initio, the Hubbard U, used in the LSDA+U calculations. The linear response method mentioned in the Cococcioni et al.'s paper seems to be a non-standard method for QE. I mean specially the application of localized perturbation (Delta V) needs some thing to be done by other tools. So my question is that is there any other method of U calculation (non-LR) already examined with QE or is using the traditional LR method much simpler than what I supposed it to be? > > Thanks, > Ali > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From bipulrr at gmail.com Fri Jun 26 20:47:15 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Sat, 27 Jun 2009 00:17:15 +0530 Subject: [Pw_forum] reversible transition Message-ID: <3a749910906261147x72398ae6t909a42f1e32ccc8a@mail.gmail.com> Dear PWSCF users, I am reading one paper Solid State Communications 149 (2009) 689 In which the author study the high pressure phase of Mg2Si, there he write a sentence "Both the structural phase transitions are of first-order nature and are reversible." But can anybody give me idea, how theoretically we determine whether the transitions are reversible or not? thanks -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India From streltsov.s at gmail.com Sun Jun 28 12:53:01 2009 From: streltsov.s at gmail.com (Sergey Streltsov) Date: Sun, 28 Jun 2009 12:53:01 +0200 Subject: [Pw_forum] Lu pseudopotential required Message-ID: <3a3a33f40906280353o5dfbda21ga0a55c2c997e3d4b@mail.gmail.com> Dear Pw-scf users, I'm not so qualified user in pw-scf to generate pseudopotentials, but stronly need pseudopotential for Lu. I would be very grateful if someone would be so kind to send me it. Sincerely yours, Streltsov Sergey -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090628/d2eb3505/attachment.htm From panda.deng.pan at gmail.com Sun Jun 28 13:04:04 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Sun, 28 Jun 2009 19:04:04 +0800 Subject: [Pw_forum] Lu pseudopotential required In-Reply-To: <3a3a33f40906280353o5dfbda21ga0a55c2c997e3d4b@mail.gmail.com> References: <3a3a33f40906280353o5dfbda21ga0a55c2c997e3d4b@mail.gmail.com> Message-ID: Please follow this thread: http://www.democritos.it/pipermail/pw_forum/2009-May/012892.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090628/cdd06bd9/attachment.htm From anvari_meh at physics.iust.ac.ir Sun Jun 28 14:45:17 2009 From: anvari_meh at physics.iust.ac.ir (Mehrnaz Anvari) Date: Sun, 28 Jun 2009 16:15:17 +0330 Subject: [Pw_forum] cvs Message-ID: First I have to say that finally I could connect to CVS without any problem, after password was changed from cvsanan to just press Enter key.So I downloaded & updated espresso. Now I want to know how could I get & add new program such as mm_dispersion.f90 to the PW folder? Mehrnaz Iran University of science & Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090628/60d3feb9/attachment.htm From sclauzer at sissa.it Mon Jun 29 08:53:29 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 29 Jun 2009 08:53:29 +0200 Subject: [Pw_forum] cvs In-Reply-To: References: Message-ID: <4A4864E9.3070308@sissa.it> Mehrnaz Anvari wrote: > First I have to say that finally I could connect to CVS without any > problem, after password was changed from cvsanan to just press Enter > key.So I downloaded & updated espresso. > Now I want to know how could I get & add new program such as > mm_dispersion.f90 to the PW folder? Sorry, I don't understand exactly your question. Do you want to get a file from the cvs repository (when doing 'cvs co espresso' you should get already whatever is inside the repository) or do you want to make your own addition (as a new subroutine or module, for instance) to the local copy of the program? (if your not registered as a developer on the qe-forge site your not allowed to add or modify files in the repository) GS > Mehrnaz > Iran University of science & Technology > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From daniel.forrer at unipd.it Mon Jun 29 10:51:58 2009 From: daniel.forrer at unipd.it (Daniel Forrer) Date: Mon, 29 Jun 2009 10:51:58 +0200 Subject: [Pw_forum] cvs In-Reply-To: References: Message-ID: 2009/6/28 Mehrnaz Anvari > First I have to say that finally I could connect to CVS without any > problem, after password was changed from cvsanan to just press Enter key.So > I downloaded & updated espresso. > Now I want to know how could I get & add new program such as > mm_dispersion.f90 to the PW folder? > the module for semi-empirical dispersion correction (Modules/mm_dispersion.f90) has been added recently to the CVS version. The only difference wrt the older version of the code I sent you some weeks ago is that DFT-D parameters are hardcoded and then the london_file keyword has been disabled. > Mehrnaz > Iran University of science & Technology > Regards daniel > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ---------------------------------- Daniel Forrer, Ph.D Student Dipartimento di Scienze Chimiche Universit? degli Studi di Padova V. Marzolo 1, Padova mail daniel.forrer at unipd.it tel. +39 049 8275188 skype daniel.forrer ---------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090629/a6e9797c/attachment.htm From dimpy.sharma at tyndall.ie Mon Jun 29 17:15:26 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Mon, 29 Jun 2009 16:15:26 +0100 Subject: [Pw_forum] Stress calculation in quantum espresso Message-ID: Hi Quantum espresso users I want to calculate stress for a system using quantum espresso, I know that setting tstress=true in the first namelist $ control, but that one is for vc-md. I want to calculate stress using a relax and scf calculation, Can anyone help me. Thanks Dimpy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090629/e628cb04/attachment.htm From paulatto at sissa.it Mon Jun 29 17:19:12 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 29 Jun 2009 17:19:12 +0200 Subject: [Pw_forum] Stress calculation in quantum espresso In-Reply-To: References: Message-ID: In data 29 giugno 2009 alle ore 17:15:26, Dimpy Sharma ha scritto: > I want to calculate stress for a system using quantum espresso, I know > that setting tstress=true in the first namelist $ control, Dear Dimpy, that's all you need to do. If you set tstress=.true. the stress tensor will be computed and printed, no matter the kind of calculation. If you are doin a variable-cell optimization (vc-md or vc-relax) it will than be used to optimize the cell, otherwise it will just be printed and ignored. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From Giovanni.Cantele at na.infn.it Mon Jun 29 17:20:34 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Mon, 29 Jun 2009 17:20:34 +0200 Subject: [Pw_forum] Stress calculation in quantum espresso In-Reply-To: References: Message-ID: <4A48DBC2.1060306@na.infn.it> Dimpy Sharma wrote: > > Hi Quantum espresso users > > I want to calculate stress for a system using quantum espresso, I know > that setting tstress=true in the first namelist $ control, but that > one is for vc-md. I want to calculate stress using a relax and scf > calculation, Can anyone help me. > > Thanks > > Dimpy > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > I'm quite sure that the option holds even if calculation is scf/relax. Maybe you read the documentation of pw.x +-------------------------------------------------------------------- Variable: tstress Type: LOGICAL Description: calculate stress. Set to .TRUE. if calculation='vc-md' +-------------------------------------------------------------------- The last sentence does not mean that the variable applies just to a vc-md calculation but that it is by default set to .true. in that case. Giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it Skype contact: giocan74 From yccheng.nju at gmail.com Mon Jun 29 17:10:58 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Mon, 29 Jun 2009 23:10:58 +0800 Subject: [Pw_forum] the sum of the born effective charge in phonon calculation Message-ID: Dear pwscf users, I calculated the phonon of ZnS at Gamma point. I checked the output file, and found that the sum of the born effective charge is not zero. ================================ Effective charges E-U in cartesian axis atom 1 ( -2.01782 0.00000 0.00000 ) ( 0.00000 -2.01782 0.00000 ) ( 0.00000 0.00000 -2.01782 ) atom 2 ( 2.04775 0.00000 0.00000 ) ( 0.00000 2.04775 0.00000 ) ( 0.00000 0.00000 2.04775 ) ================================ My question : 1. why the sum of the effectvie charge is not zero? 2.how to improve the calculation of born effective charge? The following is my input files: scf.in &CONTROL title = fine, prefix = 'zns' calculation = 'scf' , restart_mode = 'from_scratch' , wf_collect = .false. , outdir = './' , pseudo_dir = './' , tstress = .true. , tprnfor = .true. , nstep = 100 , / &SYSTEM ibrav = 2, celldm(1) = 10.204964632, nat = 2, ntyp = 2, ecutwfc = 80, nosym = .false. , / &ELECTRONS electron_maxstep = 100, conv_thr = 1.D-12, / ATOMIC_SPECIES S 32.066 16-S.GGA.fhi.UPF Zn 65.409 30-Zn.GGA.fhi.UPF ATOMIC_POSITIONS crystal S 0.250000000 0.250000000 0.250000000 Zn 0.000000000 0.000000000 0.000000000 K_POINTS automatic 16 16 16 0 0 0 ph.in phonon calculation for ZnS &inputph tr2_ph=1.0d-12, prefix='zns', epsil=.true., trans=.true., lraman=.true., elop=.true., amass(1)=32.066, amass(2)=65.409, outdir='./', fildyn='ZnS_IR.dynG', fildrho='ZnS_IR.drho', / 0.0 0.0 0.0 -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090629/abada723/attachment.htm From l.salimi at ph.iut.ac.ir Mon Jun 29 18:47:11 2009 From: l.salimi at ph.iut.ac.ir (leila salimi) Date: Mon, 29 Jun 2009 20:17:11 +0330 (IRST) Subject: [Pw_forum] Pw_forum Digest, Vol 24, Issue 58 In-Reply-To: Message-ID: <5289605.170441246294031737.JavaMail.root@mta.iut.ac.ir> Dear Lorenzo, Thanks for your suggestion, I've implemented what you have suggested, everything was compiled and I've run a test on example03. I'm getting this error: from ewald : error # ? ? ? ? 1 ?? ? optimal alpha not found what should I do now? Kind Regards, Leila Salimi ----- Original Message ----- From: "pw forum-request" To: "pw forum" Sent: Saturday, June 27, 2009 8:44:24 AM (GMT+0100) Europe/Berlin Subject: Pw_forum Digest, Vol 24, Issue 58 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: Pw_forum Digest, Vol 24, Issue 55 (ambavale sagar) ?? 2. Installation pwscf (leila salimi) ?? 3. install pwscf (leila salimi) ?? 4. Re: install pwscf (Lorenzo Paulatto) ?? 5. Re: Constrained U calculations (Matteo Cococcioni) ?? 6. reversible transition (Bipul Rakshit) ---------------------------------------------------------------------- Message: 1 Date: Fri, 26 Jun 2009 13:09:15 +0530 (IST) From: ambavale sagar Subject: Re: [Pw_forum] Pw_forum Digest, Vol 24, Issue 55 To: pw_forum at pwscf.org Message-ID: <660990.34611.qm at web94610.mail.in2.yahoo.com> Content-Type: text/plain; charset="utf-8" Dear Sir, Thank you very much for your kind guidance. I will do the exercise. best regards Sagar ________________________________ Message: 6 Date: Thu, 25 Jun 2009 07:40:12 -0400 From: Nicola Marzari Subject: Re: [Pw_forum] energy origin in espresso To: PWSCF Forum Message-ID: <4A43621C.8030509 at mit..edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Paolo Giannozzi wrote: >> then one have to use a common reference to compare >> the levels of different calculations. For this purpose one >> can use e.g. take a hydrogen molecule 10 ? away from >> the slab or molecule, whose bonding orbital can be taken >> as reference. > > yes, this is a simple way to find a common alignment Dear Ambavale, to elaborate on Paolo's comment: this is one of the two common ways to do it. The other would be to do a plot of the electrostatic potential - far away form the slab it will become flat (unless your slab, e.g., has a surface dipole - then you'll learn you have a small problem, and need to be careful about electrostatic interactions between different charges). But suppose it will become flat - that will point to the reference zero energy of that calculation. You redo this for all calculations, and you have reference points of each of them. Use this approach, and the one where you add the hydrogen molecule. Do they give you the same results ? In principle they should - if they do not, you need to figure out what is the problem, and in the process you learn a lot about accuracy. Warmly recommended, ?? ? ? ? ? ?nicola -- --------------------------------------------------------------------- Prof Nicola Marzari ? Department of Materials Science and Engineering 13-5066 ? MIT ? 77 Massachusetts Avenue ? Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu ------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum End of Pw_forum Digest, Vol 24, Issue 55 **************************************** ?? ? ?ICC World Twenty20 England '09 exclusively on YAHOO! CRICKET http://cricket.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090626/72b41acc/attachment.html ------------------------------ Message: 2 Date: Fri, 26 Jun 2009 15:26:55 +0330 (IRST) From: leila salimi Subject: [Pw_forum] Installation pwscf To: pw , pw forum Message-ID: <1041016.119301246017415311.JavaMail.root at mta.iut.ac.ir> Content-Type: text/plain; charset=utf-8 Hi everybody, I have been trying to install the code "espresso-4.0.5" on IBM pSeries 575, a clustered SMP (Symmetric Multiprocessing) system. When I issue ./configure , every things are OK. (configure: success). However, when I run (make pwall) I always get the error. mpfort ?-o ph.x phonon.o \ ?? ? ? ?../Modules/atom.o ../Modules/autopilot.o ../Modules/basic_algebra_routines.o ../Modules/bfgs_module.o ../Modules/berry_phase.o ../Modules/cell_base.o ../Modules/check_stop.o ../Modules/clocks.o ../Modules/constants.o ../Modules/constraints_module.o ../Modules/control_flags.o ../Modules/descriptors.o ../Modules/dspev_drv.o ../Modules/electrons_base.o../Modules/error_handler.o ../Modules/exc_t.o ../Modules/fft_base.o ../Modules/fft_parallel.o ../Modules/fft_scalar.o ../Modules/fft_types.o ../Modules/functionals.o ../Modules/input_parameters.o ../Modules/io_files.o ../Modules/io_global.o ../Modules/ions_base.o ../Modules/ions_nose.o ../Modules/kind.o ../Modules/metadyn_base.o ../Modules/metadyn_io.o ../Modules/metadyn_vars.o ../Modules/metagga.o ../Modules/mp_global.o ../Modules/mp_wave.o ../Modules/mp.o ../Modules/mp_base.o ../Modules/parallel_include.o ../Modules/parameters.o ../Modules/parser.o ../Modules/path_base.o ../Modules/path_formats.o ../Modules/path_variables ?.o ../Modules/path_opt_routines.o ../Modules/path_io_routines.o ../Modules/path_reparametrisation.o ../Modules/paw_variables.o ../Modules/printout_base.o ../Modules/pseudo_types.o ../Modules/ptoolkit.o ../Modules/radial_grids.o ../Modules/random_numbers.o ../Modules/read_cards.o ../Modules/read_namelists.o ../Modules/read_ncpp.o ../Modules/read_uspp.o ../Modules/read_upf_v1.o ../Modules/read_upf_v2.o ../Modules/recvec.o ../Modules/splinelib.o ../Modules/stick_base.o ../Modules/shmem_include.o ../Modules/task_groups.o ../Modules/timestep.o ../Modules/upf_to_internal.o ../Modules/upf.o ../Modules/uspp.o ../Modules/version.o ../Modules/vxc_t.o ../Modules/vxcgc.o ../Modules/wavefunctions.o ../Modules/wave_base.o ../Modules/write_upf_v2.o ../Modules/xml_io_base.o ../Modules/zhpev_drv.o libph.a ../PW/libpw.a ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a /sara/sw/lapack/3.1.1/lib/liblapack.a /sara/sw/blas/1.0/lib/libblas.a /sara/sw/fftw3/3.1.2/lib/libfftw3f.a ?? -lmassvp4_64 -lmass_64 /opt/ibmcmp/xlmass/5.0/lib64/libmass_64.a(erfc.s64.o): In function `_erfc': erfc.c:(.opd+0x0): multiple definition of `erfc' ../flib/flib.a(erf.o):(.opd+0x18): first defined here ld: Warning: size of symbol `erfc' changed from 616 in ../flib/flib.a(erf.o) to 1256 in /opt/ibmcmp/xlmass/5.0/lib64/libmass_64.a(erfc.s64.o) make[1]: *** [ph.x] Error 1 make[1]: Leaving directory `/gpfs/h04/mokhles/espresso-4.0.5/PH' make: *** [ph] Error 2 when I check example03 with pw.x I get this error: from ?cfft3d ?: error # ? ? ? ? 1 ?? ? ?no scalar fft driver specified Can someone give some solution to me? Leila Salimi Isfahan University of Technology, Iran ------------------------------ Message: 3 Date: Fri, 26 Jun 2009 16:10:42 +0330 (IRST) From: leila salimi Subject: [Pw_forum] install pwscf To: pw forum Message-ID: <13218721.119791246020042354.JavaMail.root at mta.iut.ac.ir> Content-Type: text/plain; charset=utf-8 Hi everybody, I have been trying to install the code "espresso-4.0.5" on IBM pSeries 575, a clustered SMP (Symmetric Multiprocessing) system. When I issue ./configure , every things are OK. (configure: success). However, when I run (make pwall) I always get the error. mpfort ?-o ph.x phonon.o \ ?? ? ? ?../Modules/atom.o ../Modules/autopilot.o ../Modules/basic_algebra_routines.o ../Modules/bfgs_module.o ../Modules/berry_phase.o ../Modules/cell_base.o ../Modules/check_stop.o ../Modules/clocks.o ../Modules/constants.o ../Modules/constraints_module.o ../Modules/control_flags.o ../Modules/descriptors.o ../Modules/dspev_drv.o ../Modules/electrons_base.o../Modules/error_handler.o ../Modules/exc_t.o ../Modules/fft_base.o ../Modules/fft_parallel.o ../Modules/fft_scalar.o ../Modules/fft_types.o ../Modules/functionals.o ../Modules/input_parameters.o ../Modules/io_files.o ../Modules/io_global.o ../Modules/ions_base.o ../Modules/ions_nose.o ../Modules/kind.o ../Modules/metadyn_base.o ../Modules/metadyn_io.o ../Modules/metadyn_vars.o ../Modules/metagga.o ../Modules/mp_global.o ../Modules/mp_wave.o ../Modules/mp.o ../Modules/mp_base.o ../Modules/parallel_include.o ../Modules/parameters.o ../Modules/parser.o ../Modules/path_base.o ../Modules/path_formats.o ../Modules/path_variables ?.o ../Modules/path_opt_routines.o ../Modules/path_io_routines.o ../Modules/path_reparametrisation.o ../Modules/paw_variables.o ../Modules/printout_base.o ../Modules/pseudo_types.o ../Modules/ptoolkit.o ../Modules/radial_grids.o ../Modules/random_numbers.o ../Modules/read_cards.o ../Modules/read_namelists.o ../Modules/read_ncpp.o ../Modules/read_uspp.o ../Modules/read_upf_v1.o ../Modules/read_upf_v2.o ../Modules/recvec.o ../Modules/splinelib.o ../Modules/stick_base.o ../Modules/shmem_include.o ../Modules/task_groups.o ../Modules/timestep.o ../Modules/upf_to_internal.o ../Modules/upf.o ../Modules/uspp.o ../Modules/version.o ../Modules/vxc_t.o ../Modules/vxcgc.o ../Modules/wavefunctions.o ../Modules/wave_base.o ../Modules/write_upf_v2.o ../Modules/xml_io_base.o ../Modules/zhpev_drv.o libph.a ../PW/libpw.a ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a /sara/sw/lapack/3.1.1/lib/liblapack.a /sara/sw/blas/1.0/lib/libblas.a /sara/sw/fftw3/3.1.2/lib/libfftw3f.a ?? -lmassvp4_64 -lmass_64 /opt/ibmcmp/xlmass/5.0/lib64/libmass_64.a(erfc.s64.o): In function `_erfc': erfc.c:(.opd+0x0): multiple definition of `erfc' ../flib/flib.a(erf.o):(.opd+0x18): first defined here ld: Warning: size of symbol `erfc' changed from 616 in ../flib/flib.a(erf.o) to 1256 in /opt/ibmcmp/xlmass/5.0/lib64/libmass_64.a(erfc.s64.o) make[1]: *** [ph.x] Error 1 make[1]: Leaving directory `/gpfs/h04/mokhles/espresso-4.0.5/PH' make: *** [ph] Error 2 when I check example03 with pw.x I get this error: from ?cfft3d ?: error # ? ? ? ? 1 ?? ? ?no scalar fft driver specified Can someone give some solution to me? Leila Salimi Isfahan University of Technology, Iran ------------------------------ Message: 4 Date: Fri, 26 Jun 2009 15:14:05 +0200 (CEST) From: "Lorenzo Paulatto" Subject: Re: [Pw_forum] install pwscf To: "PWSCF Forum" Message-ID: <59873.151.65.44.46.1246022045.squirrel at webmail.sissa.it> Content-Type: text/plain;charset=iso-8859-1 On Fri, June 26, 2009 14:40, leila salimi wrote: > ?/opt/ibmcmp/xlmass/5.0/lib64/libmass_64.a(erfc.s64.o): In function > ?`_erfc': > ?erfc.c:(.opd+0x0): multiple definition of `erfc' > ?../flib/flib.a(erf.o):(.opd+0x18): first defined here Dear Leila, it looks like new version of the IBM libraries has started to include the erf function, in order to work-around the problem you should: 1. edit flib/Makefile and remove the line erf.o \ 2. remove the file flib/flib.a 3. recompile > ?when I check example03 with pw.x I get this error: > ?from ?cfft3d ?: error # ? ? ? ? 1 > ? ? ? ?no scalar fft driver specified Open make.sys with a text editor, and check that -D__ESSL appears in the definition of the variable FDFLAGS. If it does not, than add it (please note that it is a comma-separated list). Than make clean and recompile. > ?Can someone give some solution to me? Try what I suggested and please report if it works, also please provide the full output of configure, and the make.sys, so we can try and fix it in time for the next version of quantum-espresso. best regards -- Lorenzo Paulatto SISSA ?& ?DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: ? http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- ??SISSA Webmail https://webmail.sissa.it/ ??Powered by SquirrelMail http://www.squirrelmail.org/ ------------------------------ Message: 5 Date: Fri, 26 Jun 2009 10:30:51 -0500 From: Matteo Cococcioni Subject: Re: [Pw_forum] Constrained U calculations To: PWSCF Forum Message-ID: <4A44E9AB.5040707 at umn.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear Ali, to apply the localized perturbation you don't need extra features. you just need to set Hubbard_alpha to some finite (small) value in the input of ?pwscf. You need, however, some post-processing codes to extract U from your calculations. these are contained in a Vlab tutorial linked from the webpage of quantum-espresso. Hope this helps. Matteo Ali Tavana wrote: > Dear all, > > I want to calculate ab initio, the Hubbard U, used in the LSDA+U calculations. The linear response method mentioned in the Cococcioni et al.'s paper seems to be a non-standard method for QE. I mean specially the application of localized perturbation (Delta V) needs some thing to be done by other tools. So my question is that is there any other method of U calculation (non-LR) already examined with QE or is using the traditional LR method much simpler than what I supposed it to be? > > Thanks, > Ali > > > ? ? ? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ? -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 ? ?Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ------------------------------ Message: 6 Date: Sat, 27 Jun 2009 00:17:15 +0530 From: Bipul Rakshit Subject: [Pw_forum] reversible transition To: PWSCF Forum Message-ID: ????????<3a749910906261147x72398ae6t909a42f1e32ccc8a at mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Dear PWSCF users, I am reading one paper Solid State Communications 149 (2009) 689 In which the author study the high pressure phase of Mg2Si, there he write a sentence "Both the structural phase transitions are of first-order nature and are reversible." But can anybody give me idea, how theoretically we determine whether the transitions are reversible or not? thanks -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India ------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum End of Pw_forum Digest, Vol 24, Issue 58 **************************************** From paulatto at sissa.it Mon Jun 29 19:04:51 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 29 Jun 2009 19:04:51 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 24, Issue 58 In-Reply-To: <5289605.170441246294031737.JavaMail.root@mta.iut.ac.ir> References: <5289605.170441246294031737.JavaMail.root@mta.iut.ac.ir> Message-ID: In data 29 giugno 2009 alle ore 18:47:11, leila salimi ha scritto: > from ewald : error # 1 > optimal alpha not found > > what should I do now? From what I can see, it looks like the xlf version of function erfc is not working as it should, or at least as we expect it to. It may take a while before it is possible to fix or workaround the problem in an "official" way. For now, I can propose this other temporary workaround: 1. put the line you've removed from Makefile back in there, so that the QE-internal version of erfc is compiled, 2. open include/f_defs.h and add the following line (it does not matter where): #define erfc erfc_qe 3. open PW/ewald.f90 and add the following line at the very beginning: #include "f_defs.h" 4. add the same line also at the beginning of flib/erf.f90 4. recompile This shall be enough for now (not for car-parrinello, though). I'm not sure why you're having this weird problem, I've personally compiled QE on SP5 and SP6 machines, using the xlf compiler without any such problem (although editing make.sys by hand). Can you please attach you copy of make.sys (from the QE source directory)? best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From akohlmey at cmm.chem.upenn.edu Mon Jun 29 19:36:23 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 29 Jun 2009 13:36:23 -0400 Subject: [Pw_forum] Pw_forum Digest, Vol 24, Issue 58 In-Reply-To: References: <5289605.170441246294031737.JavaMail.root@mta.iut.ac.ir> Message-ID: <1246296983.2829.540.camel@zero> On Mon, 2009-06-29 at 19:04 +0200, Lorenzo Paulatto wrote: > In data 29 giugno 2009 alle ore 18:47:11, leila salimi > ha scritto: > > from ewald : error # 1 > > optimal alpha not found > > > > what should I do now? > > From what I can see, it looks like the xlf version of function erfc is not > working as it should, or at least as we expect it to. It may take a while > before it is possible to fix or workaround the problem in an "official" > way. you may want to test if the --allow-multiple-definition flag works. this is usually required if you compile with xlf on a Linux OS with power cpu and you want to use the optimized math functions from -lmass. the linux linker by default does not allow multiple definitions of the same "symbol" that are different (checked by comparing the sizes). other linkers are more forgiving and use the first occurance of a symbol after it has been flagged as undefined. the flag from above is needed on BG/L for example when using the IBM optimized library versions. cheers, axel. > > For now, I can propose this other temporary workaround: > 1. put the line you've removed from Makefile back in there, so that the > QE-internal version of erfc is compiled, > 2. open include/f_defs.h and add the following line (it does not matter > where): > #define erfc erfc_qe > 3. open PW/ewald.f90 and add the following line at the very beginning: > #include "f_defs.h" > 4. add the same line also at the beginning of flib/erf.f90 > 4. recompile > > This shall be enough for now (not for car-parrinello, though). > > I'm not sure why you're having this weird problem, I've personally > compiled QE on SP5 and SP6 machines, using the xlf compiler without any > such problem (although editing make.sys by hand). Can you please attach > you copy of make.sys (from the QE source directory)? > > best regards > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Mon Jun 29 21:44:33 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 29 Jun 2009 15:44:33 -0400 Subject: [Pw_forum] GPGPU Programming summer school at University of Tennessee, Aug 10-14. Message-ID: <1246304673.2829.565.camel@zero> Please also see: http://illinois.edu/pc/article/2101/26850/page=1/list=list The University of Tennessee will offer a summer school course in accelerating computational chemistry with general-purpose graphics processing units (GPGPUs) from Aug. 10-14. The course is offered in coordination with the Virtual School of Computational Science and Engineering. This course will provide students with the knowledge and practical skills necessary to start exploiting the power of GPGPUs in real chemistry applications. The course is especially designed for graduate students and advanced undergraduate students in chemistry and related disciplines. Streaming video and two-way audio will link participants at the University of Tennessee (UT) to the summer school, hosted by the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign, that will provide the core instruction on device architecture, programming tools, and design of high-performance algorithms; see http://www.greatlakesconsortium.org/events/manycore/ for course information. At UT, this content will be supplemented with additional lectures, worked examples, and other materials specifically targeting the effective use of GPGPUs in computational chemistry, including quantum Monte Carlo, molecular electronic structure, and molecular dynamics. Expert assistance will be provided to enable attendees to make rapid progress on both first time use and advanced design of chemistry algorithms for GPGPUs. Students will have access to the resources of the UT Multidisciplinary Center for Future Computing that includes the latest NVIDIA GPGPUs and Intel Nehalem processors. Prerequisites are C, C++, Java, or equivalent programming knowledge and familiarity with command-line use of Linux, and each student should bring a wifi-enabled laptop. Fortran applications can employ GPGPU kernels, but kernels must be written in C/C++. Applications are due by July 15, 2009, and should be addressed to gpgpuschool at ion.chem.utk.edu. In the application please clearly indicate: * Full name * Home institution and department * Email address * Status: (graduate student, postdoc, other) * Research topic * Algorithms of interest * Programming experience Limited funds are available for partial or full support of the travel and local expenses of a few students, in particular to enable participation of underrepresented or disadvantaged groups. To apply for support, please include a brief paragraph in the application email to request and explain the need for support, and to describe the benefits that attending the workshop would have for both you and your institution. Organizers: * University of Tennessee: Robert J. Harrison, R.J. Hinde, Gregory D. Peterson * University of Illinois at Urbana-Champaign: Volodymyr Kindratenko, Thom Dunning * Stanford University: Todd Martinez * University of Pennsylvania: Michael L. Klein, Axel Kohlmeyer This workshop is supported by the National Science Foundation through the cyberenabled chemistry project "Future Computing in Chemistry." -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From shypirate at gmail.com Tue Jun 30 04:05:34 2009 From: shypirate at gmail.com (shypirate) Date: Tue, 30 Jun 2009 10:05:34 +0800 Subject: [Pw_forum] atomic position relaxition under electric field Message-ID: <200906301005320313912@gmail.com> Dear all: I have used PWscf to do atomic position relaxition under finite electric field. The electric field is applied by adding a saw-like potential to bare ionic potential. The total force calculated seems not to be convergent. And there are two questions unclear for me: 1. In atomic position relaxition, does the force from external electric field contribute to total force? 2. Will all the atoms move along the direction of external electric field as a whole? If that happens, the total energy and total force can not get convergence. Thanks for your warmly help! Y.P.Wang 2009-06-30 shypirate -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090630/ca1d1483/attachment.htm From hqzhou at nju.edu.cn Tue Jun 30 05:22:06 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Tue, 30 Jun 2009 11:22:06 +0800 Subject: [Pw_forum] Stress calculation in quantum espresso References: <4A48DBC2.1060306@na.infn.it> Message-ID: <411F972BFE0A4FD1BAC4F3BF4A099242@solarflare> But at least, this kind of description is a bit of misleading. Huiqun Zhou @Earth Sciences, Nanjing University, China > +-------------------------------------------------------------------- > Variable: tstress > > Type: LOGICAL > Description: calculate stress. Set to .TRUE. if calculation='vc-md' > +-------------------------------------------------------------------- > The last sentence does not mean that the variable applies just to a > vc-md calculation but that > it is by default set to .true. in that case. From lanhaiping at gmail.com Tue Jun 30 06:41:09 2009 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 30 Jun 2009 12:41:09 +0800 Subject: [Pw_forum] atomic position relaxition under electric field In-Reply-To: <200906301005320313912@gmail.com> References: <200906301005320313912@gmail.com> Message-ID: Hi, I have a question about your setup for simulation . Is it a slab or bulk ? If it is a bulk, you should make sure what your purpose is for applying a saw-tooth electric field. Regards, On Tue, Jun 30, 2009 at 10:05 AM, shypirate wrote: > Dear all: > I have used PWscf to do atomic position relaxition under finite electric > field. The electric field is applied by adding a saw-like potential to bare > ionic potential. The total force calculated seems not to be convergent. And > there are two questions unclear for me: > 1. In atomic position relaxition, does the force from external electric > field contribute to total force? > 2. Will all the atoms move along the direction of external electric field > as a whole? If that happens, the total energy and total force can not get > convergence. > > Thanks for your warmly help! > > Y.P.Wang > > 2009-06-30 > ------------------------------ > shypirate > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090630/507699af/attachment.htm From paulatto at sissa.it Tue Jun 30 08:17:51 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 30 Jun 2009 08:17:51 +0200 (CEST) Subject: [Pw_forum] Stress calculation in quantum espresso In-Reply-To: <411F972BFE0A4FD1BAC4F3BF4A099242@solarflare> References: <4A48DBC2.1060306@na.infn.it> <411F972BFE0A4FD1BAC4F3BF4A099242@solarflare> Message-ID: <54950.78.12.162.45.1246342671.squirrel@webmail.sissa.it> On Tue, June 30, 2009 05:22, Huiqun Zhou wrote: > But at least, this kind of description is a bit of misleading. You are right, it is a bad translation from Italian. For an Italian speaker it apears to have has a certain meaning, while the real meaning is completely different! I'll fix it. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From shypirate at gmail.com Tue Jun 30 10:02:14 2009 From: shypirate at gmail.com (shypirate) Date: Tue, 30 Jun 2009 16:02:14 +0800 Subject: [Pw_forum] Pw_forum Digest, Vol 24, Issue 61 References: Message-ID: <200906301602120364735@gmail.com> Hi: A slab is used in my simulation. Thanks! 2009-06-30 shypirate Hi, I have a question about your setup for simulation . Is it a slab or bulk ? If it is a bulk, you should make sure what your purpose is for applying a saw-tooth electric field. Regards, On Tue, Jun 30, 2009 at 10:05 AM, shypirate wrote: > Dear all: > I have used PWscf to do atomic position relaxition under finite electric > field. The electric field is applied by adding a saw-like potential to bare > ionic potential. The total force calculated seems not to be convergent. And > there are two questions unclear for me: > 1. In atomic position relaxition, does the force from external electric > field contribute to total force? > 2. Will all the atoms move along the direction of external electric field > as a whole? If that happens, the total energy and total force can not get > convergence. > > Thanks for your warmly help! > > Y.P.Wang > > 2009-06-30 > ------------------------------ > shypirate > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090630/5022aa21/attachment.htm From bipulrr at gmail.com Tue Jun 30 10:12:38 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Tue, 30 Jun 2009 13:42:38 +0530 Subject: [Pw_forum] Question about P= pressure Message-ID: <3a749910906300112u37e49f4egfb659562cbbc7d26@mail.gmail.com> Dear PWSCF users, I am doing calculation on Mg2Si. There I just want to plot Pressure vs Volume graph. So what i did, first I found the equilibrium lattice constant (P=0.0), then I reduce the lattice parameter, so the pressure increases. With that Volume vs Pressure data, I plot the graph. But when i compared with experimental VvsP, it is not at all matching. Infact my volume is far less than the experimental value. So my question is, the pressure term which we get at the end of scf run, is the pressure on the system? If the pressure is equivalent to the pressure on the system, so why I am getting such large deviation (cal. volume is very less than expt,)? Please help me in this matter. -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India From shypirate at gmail.com Tue Jun 30 10:02:14 2009 From: shypirate at gmail.com (shypirate) Date: Tue, 30 Jun 2009 16:02:14 +0800 Subject: [Pw_forum] Pw_forum Digest, Vol 24, Issue 61 References: Message-ID: <200906301602120364735@gmail.com> Hi: A slab is used in my simulation. Thanks! 2009-06-30 shypirate Hi, I have a question about your setup for simulation . Is it a slab or bulk ? If it is a bulk, you should make sure what your purpose is for applying a saw-tooth electric field. Regards, On Tue, Jun 30, 2009 at 10:05 AM, shypirate wrote: > Dear all: > I have used PWscf to do atomic position relaxition under finite electric > field. The electric field is applied by adding a saw-like potential to bare > ionic potential. The total force calculated seems not to be convergent. And > there are two questions unclear for me: > 1. In atomic position relaxition, does the force from external electric > field contribute to total force? > 2. Will all the atoms move along the direction of external electric field > as a whole? If that happens, the total energy and total force can not get > convergence. > > Thanks for your warmly help! > > Y.P.Wang > > 2009-06-30 > ------------------------------ > shypirate > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090630/5022aa21/attachment-0001.htm From paulatto at sissa.it Tue Jun 30 12:31:13 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 30 Jun 2009 12:31:13 +0200 Subject: [Pw_forum] Question about P= pressure In-Reply-To: <3a749910906300112u37e49f4egfb659562cbbc7d26@mail.gmail.com> References: <3a749910906300112u37e49f4egfb659562cbbc7d26@mail.gmail.com> Message-ID: In data 30 giugno 2009 alle ore 10:12:38, Bipul Rakshit ha scritto: > I am doing calculation on Mg2Si. There I just want to plot Pressure vs > Volume graph. > So what i did, first I found the equilibrium lattice constant (P=0.0), > then I reduce the lattice parameter, so the pressure increases. Dear Bipul, as a preliminary check, please take care that all your calculations are well converged, with respect of wavefunctions cutoff (ecutwfc), charge density cutoff (ecutrho) and number of k-points. Also note that DFT theory, although very powerful, can only predict experimental data up to its accuracy. You could try and check the literature for other DFT calculation of the same material, in order to have an idea of how accurate you can expect your calculation to be. > With that Volume vs Pressure data, I plot the graph. But when i > compared with experimental VvsP, it is not at all matching. > Infact my volume is far less than the experimental value. How much is "far less"? > So my question is, the pressure term which we get at the end of scf > run, is the pressure on the system? Yes, it is. > If the pressure is equivalent to the pressure on the system, so why I > am getting such large deviation (cal. volume is very less than expt,)? I depends on the details of your calculation, if you'll provide you input and output files we could have a look and try to spot possible source of problems. Best regards. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From paulatto at sissa.it Tue Jun 30 12:34:23 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 30 Jun 2009 12:34:23 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 24, Issue 61 In-Reply-To: <200906301602120364735@gmail.com> References: <200906301602120364735@gmail.com> Message-ID: In data 30 giugno 2009 alle ore 10:02:14, shypirate ha scritto: > Hi: > A slab is used in my simulation. > Thanks! Dear Y.P.Wang, a problem with sawtooth potential has been fixed in one of the 4.0.x releases, so please be sure to use the last available one (4.0.5). Furthermore, in the CVS version that part of code has been completely restructured in order to be more reliable, although it is not yet fully tested. If you cannot fix your problems by updating the code version, you'll have to provide further details in order to get some help. Best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From mjfmartins at ice.ufjf.br Tue Jun 30 12:52:58 2009 From: mjfmartins at ice.ufjf.br (=?ISO-8859-1?Q?MATEUS_JOS=C9_FERNANDES_MARTINS?=) Date: Tue, 30 Jun 2009 07:52:58 -0300 Subject: [Pw_forum] Error in dynmat.x calculation. Message-ID: <85d7d5fd0906300352p5ac9e537w26933f779bfb78aa@mail.gmail.com> Hello all what is the error: Reading Dynamical Matrix from file / home/mateus/FULL-2x1x1.mat %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%% from readmat: error # 1 mismatch in file reading %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Whenever the road dynmat.x this error appears. I can not find solution anywhere ... Thank you, Mateus -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090630/f2edaa0e/attachment-0001.htm From hqzhou at nju.edu.cn Tue Jun 30 13:27:20 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Tue, 30 Jun 2009 19:27:20 +0800 Subject: [Pw_forum] Stress calculation in quantum espresso References: <4A48DBC2.1060306@na.infn.it><411F972BFE0A4FD1BAC4F3BF4A099242@solarflare> <54950.78.12.162.45.1246342671.squirrel@webmail.sissa.it> Message-ID: <470CF86F503347CD8E0764219C135304@solarflare> Thanks, Lorenzo, for your quick action. Anyway, English is not our mother tongue(^o^) BTW, there are other items need to check: (1) ion_dynamics add 'bfgs' for the case of calculation = 'vc-relax' (2) pot | wfc_extrapolation please clarify if 'first_order', 'second_order' can be used in calculations other than 'md' or 'vc-md'. I used these options in 'relax' and 'vc-relax' without any errors, too. Of course, I don't know if these were really in effect. (3) ecfixed, qcutz and q2sigma in the original paper, the framework is an extension of PR dynamics to CP. Please clarify if these are effective in other dynamics (damp-w, bfgs). If possible, suggest a guide line how to set these options (there is only one example of carbon in the paper), say, qcutz should be at least N (2?) times of ecfixed, ecfixed should be ecutwfc plus alpha (5 Ry or so?), q2sigma should be one N-th of qcutz ... Sorry for adtional requests. Huiqun Zhou @Earth Sciences, Nanjing University, China ----- Original Message ----- From: "Lorenzo Paulatto" To: "PWSCF Forum" Sent: Tuesday, June 30, 2009 2:17 PM Subject: Re: [Pw_forum] Stress calculation in quantum espresso > > On Tue, June 30, 2009 05:22, Huiqun Zhou wrote: >> But at least, this kind of description is a bit of misleading. > > You are right, it is a bad translation from Italian. For an Italian > speaker it apears to have has a certain meaning, while the real meaning is > completely different! I'll fix it. > > cheers > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by SquirrelMail http://www.squirrelmail.org/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From akohlmey at cmm.chem.upenn.edu Tue Jun 30 14:43:43 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 30 Jun 2009 08:43:43 -0400 Subject: [Pw_forum] Question about P= pressure In-Reply-To: <3a749910906300112u37e49f4egfb659562cbbc7d26@mail.gmail.com> References: <3a749910906300112u37e49f4egfb659562cbbc7d26@mail.gmail.com> Message-ID: <1246365823.2829.1095.camel@zero> On Tue, 2009-06-30 at 13:42 +0530, Bipul Rakshit wrote: > Dear PWSCF users, > I am doing calculation on Mg2Si. There I just want to plot Pressure vs > Volume graph. > So what i did, first I found the equilibrium lattice constant (P=0.0), > then I reduce the lattice parameter, so the pressure increases. > > With that Volume vs Pressure data, I plot the graph. But when i > compared with experimental VvsP, it is not at all matching. > Infact my volume is far less than the experimental value. please try to act like a proper scientist and provide exact details instead of vague descriptions. _how far_ less is your volume. is it a factor? a few percent? an order of magnitude? > So my question is, the pressure term which we get at the end of scf > run, is the pressure on the system? yes. if it wasn't a lot of calculations and published paper would be far off. are you sure you computed the volume of your cell correctly? > If the pressure is equivalent to the pressure on the system, so why I > am getting such large deviation (cal. volume is very less than expt,)? how should anybody know without any details and hard facts? > Please help me in this matter. it is very difficult to help somebody making such vague statements. all one can do is guess and give vague directions. your SCF calculation may be wrong, you pseudopotentials crap, you calculation of the volume wrong, you make have mixed up units, and other things. cheers, axel. -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From lex at phys.ufl.edu Tue Jun 30 19:52:15 2009 From: lex at phys.ufl.edu (Lex Kemper) Date: Tue, 30 Jun 2009 13:52:15 -0400 Subject: [Pw_forum] WIEN2k interface Message-ID: <4A4A50CF.9070404@phys.ufl.edu> Hey everyone, I want to use a piece of code that is written to take energies, kpoints, and structures from wien2k. While it is of course possible for me to write something that parses pwscf output into wien2k output, it is a rather laborious process, so I was wondering if someone had done this already. Thanks, Lex Kemper Department of Physics University of Florida From samadzare at gmail.com Tue Jun 30 20:54:58 2009 From: samadzare at gmail.com (samad zare) Date: Tue, 30 Jun 2009 23:24:58 +0430 Subject: [Pw_forum] WIEN2k interface In-Reply-To: <4A4A50CF.9070404@phys.ufl.edu> References: <4A4A50CF.9070404@phys.ufl.edu> Message-ID: hello i have a question is differed figures in pwscf and win2k? i want use output (figure band energy and.....)win2k LIEu pwscf thankyou On 6/30/09, Lex Kemper wrote: > > Hey everyone, > > I want to use a piece of code that is written to take energies, kpoints, > and structures from wien2k. While it is of course possible for me to > write something that parses pwscf output into wien2k output, it is a > rather laborious process, so I was wondering if someone had done this > already. > > Thanks, > > > Lex Kemper > Department of Physics > University of Florida > _______________________________________________ > 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/20090630/5f9566dc/attachment.htm