From li.chengyang at wmich.edu Thu Dec 1 00:00:59 2011 From: li.chengyang at wmich.edu (Chengyang Li) Date: Wed, 30 Nov 2011 18:00:59 -0500 (EST) Subject: [Pw_forum] DC & BEC In-Reply-To: Message-ID: <724530996.1374139.1322694059759.JavaMail.root@wmu-mailstore05> Dear Suza It seems like BaTiO3 is not a simple cubic structure, so you should not choose ibrav=1. Chengyang ----- Original Message ----- > From: "Suza W" > To: "PWSCF Forum" > Sent: Wednesday, November 30, 2011 3:32:15 PM > Subject: [Pw_forum] DC & BEC > Dear All, > Being an epitome of ferroelectric, BaTiO3 has extensively been > studied using PWSCF. However,? unfortunately, with several > standard available USPP, I encounter? following unphysical? results :? > ??????? > ???? Dielectric constant in cartesian axis > ????????? (-8142842.391767483?????? 0.000000000?????? 0.000000000 ) > ????????? (?????? 0.000000000-8142842.391767481?????? 0.000000000 ) > ????????? (?????? 0.000000000?????? 0.000000000-8142842.391767476 ) > ????????? Effective charges (d Force / dE) in cartesian axis > ?????????? atom????? 1?? Ba > ????? Ex? (??? -1136.43937??????? 0.00000??????? 0.00000 ) > ????? Ey? (??????? 0.00000??? -1136.43937??????? 0.00000 ) > ????? Ez? (??????? 0.00000??????? 0.00000??? -1136.43937 ) > ?????????? atom????? 2?? Ti > ????? Ex? (??? -1874.03151??????? 0.00000??????? 0.00000 ) > ????? Ey? (??????? 0.00000??? -1874.03151??????? 0.00000 ) > ????? Ez? (??????? 0.00000??????? 0.00000??? -1874.03151 ) > ?????????? atom????? 3?? O? > ????? Ex? (????? 931.42284??????? 0.00000??????? 0.00000 ) > ????? Ey? (??????? 0.00000???? 1067.39482??????? 0.00000 ) > ????? Ez? (??????? 0.00000??????? 0.00000???? 1067.39482 ) > ?????????? atom????? 4?? O? > ????? Ex? (???? 1067.39482??????? 0.00000??????? 0.00000 ) > ????? Ey? (??????? 0.00000????? 931.42284??????? 0.00000 ) > ????? Ez? (??????? 0.00000??????? 0.00000???? 1067.39482 ) > ?????????? atom????? 5?? O? > ????? Ex? (???? 1067.39482??????? 0.00000??????? 0.00000 ) > ????? Ey? (??????? 0.00000???? 1067.39482??????? 0.00000 ) > ????? Ez? (??????? 0.00000??????? 0.00000????? 931.42284 ) > Any suggestion for correcting these errors will be highly > appreciated.? > Here goes the input file which renders such a blunder.? > ?&system > ??? ibrav =? 1, > ??? celldm(1) = 7.5589, > ??? nat = 5, > ??? ntyp=3, > ??? ecutwfc = 30.0, > ??????? ecutrho = 240.0, > ?/ > ?&electrons > ??? diagonalization = 'david' > ??? conv_thr =? 1.0d-9 > ??? mixing_beta = 0.7 > ?/ > ?&ions > ?/ > ?&cell > ?/ > ATOMIC_SPECIES > ?Ba? 137.327?????? Ba.pbe-nsp-van.UPF > ?Ti?? 47.867?????? Ti.pbe-sp-van_ak.UPF > ?O??? 15.9994????? O.pbe-van_ak.UPF > ATOMIC_POSITIONS (alat) > Ba? 0.0? 0.0? 0.0 > Ti? 0.5? 0.5? 0.5 > O? 0.0? 0.5? 0.5 > O? 0.5? 0.0? 0.5 > O? 0.5? 0.5? 0.0 > K_POINTS {automatic} > ?8 8 8? 1 1 1 > Thanking you, > Yours sincerely, > Suza W > PhD Student > Department of Materials Science > Bangalore > _______________________________________________ > 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/20111130/c6ce41b6/attachment-0001.htm From dstrubbe at berkeley.edu Thu Dec 1 02:15:37 2011 From: dstrubbe at berkeley.edu (David Strubbe) Date: Wed, 30 Nov 2011 17:15:37 -0800 Subject: [Pw_forum] dvscf for dielectric response Message-ID: For phonon calculations, one can ask for the 'dvscf' file containing the change in self-consistent potential for each mode to be written. Can the corresponding quantity be written for dielectric response? I have not been able to see a way to do this currently implemented. David Strubbe UC Berkeley -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111130/8b96ebaa/attachment.htm From chenhanghuipwscf at gmail.com Thu Dec 1 05:40:19 2011 From: chenhanghuipwscf at gmail.com (Hanghui Chen) Date: Wed, 30 Nov 2011 23:40:19 -0500 Subject: [Pw_forum] pseudopotential Message-ID: To QE developers, I am now trying to simulate some XAS spectrum. In order to take into account the electron-hole interaction, I need to generate a pseudo potential which has a hole in the 1s state of O. I am wondering whether such a special psp of O is equivalent to a psp of F with reference configuration 1s^{1}2s^{2}2p^{5} i.e. +1 configuration but with one electron missing in the 1s state? Is that the way to generate such a special O psp? Thank you very much. Hanghui Chen Department of Physics Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111130/25da01a1/attachment.htm From giannozz at democritos.it Thu Dec 1 08:35:05 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 1 Dec 2011 08:35:05 +0100 Subject: [Pw_forum] dynmat.x - segmentation fault error In-Reply-To: References: <70DAA912-9C42-4868-AD01-C9C68EAF4F50@democritos.it> Message-ID: <09EF9833-FC50-4FED-A7B4-923002A62880@democritos.it> On Nov 30, 2011, at 19:46 , Kacper Dru?bicki wrote: > I get the following error while trying to diagonalize the dynamic > matrix > for the 186 atomic system. > > Reading Dynamical Matrix from file matdyn > ...Force constants read > ...epsilon and Z* read > Segmentation fault too much memory used. Unfortunately the code "dynmat" uses a disproportionate amount of memory to enforce the Acoustic Sum Rule with sophisticated algorithms. You need to modify the code in such a way that 1) it doesn't use large automatic arrays, and 2) it allocates only those arrays that are actually needed. Then you may still need to switch to asr='simple' P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Thu Dec 1 08:39:38 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 1 Dec 2011 08:39:38 +0100 Subject: [Pw_forum] DC & BEC In-Reply-To: References: Message-ID: On Nov 30, 2011, at 22:32 , Suza W wrote: > Dielectric constant in cartesian axis > > (-8142842.391767483 0.000000000 0.000000000 ) > ( 0.000000000-8142842.391767481 0.000000000 ) > ( 0.000000000 0.000000000-8142842.391767476 ) typically this happens when the gap is very small. IIRC, cubic BaTiO3 is unstable, by the way. It also yields occasionally funny results if you start from atomic wavefunctions (converging to a fake scf charge): verify that you get the same results if you use "startingwfc='random'" P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From tone.kokalj at ijs.si Thu Dec 1 08:48:02 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 01 Dec 2011 08:48:02 +0100 Subject: [Pw_forum] PWgui Locate Error In-Reply-To: <518201ccafa9$f9414580$ebc3d080$@w2agz.com> References: <518201ccafa9$f9414580$ebc3d080$@w2agz.com> Message-ID: <1322725682.3260.5.camel@catalyst.ijs.si> On Wed, 2011-11-30 at 13:49 -0800, W2AGZ wrote: > As far as I can tell, all my tcl/tk libs are current. > > ************************************************* > > > > ERROR: failed to locate object from identifier path_inter_nimages Thanks for reporting this. The reason seems to be related to some remnants of the NEB in PWgui, which has been stripped from pw.x (to a separate neb.x). The problem will be fixed! Regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From nicola.marzari at epfl.ch Thu Dec 1 09:37:19 2011 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Thu, 01 Dec 2011 09:37:19 +0100 Subject: [Pw_forum] DC & BEC In-Reply-To: References: Message-ID: <4ED73CBF.4070903@epfl.ch> Dear Suza, slightly puzzling - one thing I recall is that these perovskites can reach an incorrect ground state where some of the higher occupied eigenstates have converged to even higher unoccupied states (this is in principle possible with some of the iterative algorithms used e.g. in PWSCF or VASP). This is typically cured by using startignwfc="atomic+random" - it looks like this has now become the default in pwscf, but depending on the version you use it might not have been the case. LEt us know, nicola On 11/30/11 10:32 PM, Suza W wrote: > > Dear All, > > Being an epitome of ferroelectric, BaTiO3 has extensively been > studied using PWSCF. However, unfortunately, with several > standard available USPP, I encounter following unphysical results : > > Dielectric constant in cartesian axis > > (-8142842.391767483 0.000000000 0.000000000 ) > ( 0.000000000-8142842.391767481 0.000000000 ) > ( 0.000000000 0.000000000-8142842.391767476 ) > > Effective charges (d Force / dE) in cartesian axis > > atom 1 Ba > Ex ( -1136.43937 0.00000 0.00000 ) > Ey ( 0.00000 -1136.43937 0.00000 ) > Ez ( 0.00000 0.00000 -1136.43937 ) > atom 2 Ti > Ex ( -1874.03151 0.00000 0.00000 ) > Ey ( 0.00000 -1874.03151 0.00000 ) > Ez ( 0.00000 0.00000 -1874.03151 ) > atom 3 O > Ex ( 931.42284 0.00000 0.00000 ) > Ey ( 0.00000 1067.39482 0.00000 ) > Ez ( 0.00000 0.00000 1067.39482 ) > atom 4 O > Ex ( 1067.39482 0.00000 0.00000 ) > Ey ( 0.00000 931.42284 0.00000 ) > Ez ( 0.00000 0.00000 1067.39482 ) > atom 5 O > Ex ( 1067.39482 0.00000 0.00000 ) > Ey ( 0.00000 1067.39482 0.00000 ) > Ez ( 0.00000 0.00000 931.42284 ) > > Any suggestion for correcting these errors will be highly appreciated. > Here goes the input file which renders such a blunder. > &system > ibrav = 1, > celldm(1) = 7.5589, > nat = 5, > ntyp=3, > ecutwfc = 30.0, > ecutrho = 240.0, > / > &electrons > diagonalization = 'david' > conv_thr = 1.0d-9 > mixing_beta = 0.7 > / > &ions > / > &cell > / > ATOMIC_SPECIES > Ba 137.327 Ba.pbe-nsp-van.UPF > Ti 47.867 Ti.pbe-sp-van_ak.UPF > O 15.9994 O.pbe-van_ak.UPF > ATOMIC_POSITIONS (alat) > Ba 0.0 0.0 0.0 > Ti 0.5 0.5 0.5 > O 0.0 0.5 0.5 > O 0.5 0.0 0.5 > O 0.5 0.5 0.0 > K_POINTS {automatic} > 8 8 8 1 1 1 > > Thanking you, > Yours sincerely, > Suza W > PhD Student > Department of Materials Science > Bangalore > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL From giannozz at democritos.it Thu Dec 1 10:06:22 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 01 Dec 2011 10:06:22 +0100 Subject: [Pw_forum] dynmat.x - segmentation fault error In-Reply-To: References: <70DAA912-9C42-4868-AD01-C9C68EAF4F50@democritos.it> Message-ID: <1322730382.30265.2.camel@fe12lx.fisica.uniud.it> Try to replace routine set_asr in dynmat.f90 with the attached version - no warranty P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy -------------- next part -------------- A non-text attachment was scrubbed... Name: set_asr.f90 Type: text/x-fortran Size: 13412 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111201/92f1b9a6/attachment.bin From matteo.calandra at impmc.jussieu.fr Thu Dec 1 10:54:51 2011 From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra) Date: Thu, 01 Dec 2011 10:54:51 +0100 Subject: [Pw_forum] pseudopotential (Hanghui Chen) In-Reply-To: References: Message-ID: <4ED74EEB.9040601@impmc.jussieu.fr> Le 01/12/11 09:38, pw_forum-request at pwscf.org a ?crit : > > Message: 2 > Date: Wed, 30 Nov 2011 23:40:19 -0500 > From: Hanghui Chen > Subject: [Pw_forum] pseudopotential > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > To QE developers, > I am now trying to simulate some XAS spectrum. In order to take into > account the electron-hole interaction, I need to generate a pseudo > potential which has a hole in the 1s state of O. I am wondering whether > such a special psp of O is equivalent to a psp of F with reference > configuration 1s^{1}2s^{2}2p^{5} i.e. +1 configuration but with one > electron missing in the 1s state? Is that the way to generate such a > special O psp? > Thank you very much. > > Hanghui Chen > Department of Physics > Yale University > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111130/25da01a1/attachment-0001.htm Dear H. Chen, you can take O.star1s-pbe-van_gipaw.UPF available in the pseudopotential repository of QE http://www.quantum-espresso.org/pseudo/1.3/html/O.html This is what you look for. You can see calculations made with this pseudo in the following papers: http://link.aps.org/doi/10.1103/PhysRevB.80.075102 http://xxx.lanl.gov/abs/1111.3225 http://link.aps.org/doi/10.1103/PhysRevB.81.115115 All the best, M. -- * * * * Matteo Calandra, Directeur de Recherche (DR2) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 23, 3eme etage, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111201/d5f2a63c/attachment.htm From mpayami at aeoi.org.ir Thu Dec 1 12:49:09 2011 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Thu, 1 Dec 2011 15:19:09 +0330 Subject: [Pw_forum] FFLAGS in make.sys References: Message-ID: Dear QE Developers,I noticed that the FFLAGS variable in the make.sys is used in F90FLAGS before it is defined:-------------------------------------# compiler flags: C, F90, F77 # C flags must include DFLAGS and IFLAGS # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax CFLAGS = -O3 $(DFLAGS) $(IFLAGS) F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS = -O2 -assume byterecl -g -traceback -par-report0 -vec-report0 -openmp ------------------------------------------This is seen in old versions either.Is it a mistake?Best regards,Mahmoud Payami,AEOI, Tehran, Iran From giannozz at democritos.it Thu Dec 1 17:13:36 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 1 Dec 2011 17:13:36 +0100 Subject: [Pw_forum] FFLAGS in make.sys In-Reply-To: References: Message-ID: On Dec 1, 2011, at 12:49 , Mahmoud Payami wrote: > Dear QE Developers,I noticed that the FFLAGS variable > in the make.sys is used in F90FLAGS before it is defined not a problem (I think): the language used by make is smarter than fortran! Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From payam.norouzzadeh at gmail.com Thu Dec 1 17:51:03 2011 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Thu, 1 Dec 2011 10:51:03 -0600 Subject: [Pw_forum] Equation of state Message-ID: Hello Quantum Espresso users As you know the code ev.f90 fits the data in E-V curve to some equation of states like Birch 1st order,Birch 2nd order,Keane and Murnaghan. Does anyone know any paper,text or resource to discuss about these equations of states and their details? Best regards,Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111201/30d1635e/attachment-0001.htm From giannozz at democritos.it Thu Dec 1 18:05:14 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 01 Dec 2011 18:05:14 +0100 Subject: [Pw_forum] Equation of state In-Reply-To: References: Message-ID: <1322759114.30633.15.camel@fe12lx.fisica.uniud.it> On Thu, 2011-12-01 at 10:51 -0600, Payam Norouzzadeh wrote: > Does anyone know any paper,text or resource to discuss about these > equations of states and their details? the wikipedia page is not bad: http://en.wikipedia.org/wiki/Birch-Murnaghan_equation_of_state P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From michelepisarra at yahoo.it Thu Dec 1 18:07:37 2011 From: michelepisarra at yahoo.it (Michele Pisarra) Date: Thu, 1 Dec 2011 17:07:37 +0000 (GMT) Subject: [Pw_forum] wavefunction and symmetries Message-ID: <1322759257.96795.YahooMailNeo@web27003.mail.ukl.yahoo.com> Hi everyone. I calculated the eigenvalues and wavefunctions for different k point inside the first Brillouin Zone. My system is a Graphene Monolayer. Because of the complexity of the?calculation I?have to do with the eigenfunctions, I need to exploit the symmetry of the Brillouin Zone.? I calculated the band structure in k points connected one to another by symmetry operations, for instance the 6 K points of the 2D graphene lattice. In fact I find out that the corresponding eigenvalues for?each K point?differ very slightly. I obtained also the eigenvectors using the pw_export utility of the package, but I wasn't able to find the connection between the eigenvectors. I noticed that the number of planewaves used for the k points linked by the symmetry connection is the same, but the palnewaves used are different, of corse. I know that the code exploit the symmetries so?my question is?can anyone tell me what is the connection between the eigenfunction corresponding to?k points connected by symmetry operations? If there is any, of corse. Thank you. ?Michele Pisarra, PhD Student, Dipartimento di Fisica, Universit? della Calabria Via P. Bucci, Cubo 31 C VI piano, 87036, Rende (CS), Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111201/4679b98a/attachment.htm From giannozz at democritos.it Thu Dec 1 18:10:48 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 01 Dec 2011 18:10:48 +0100 Subject: [Pw_forum] dvscf for dielectric response In-Reply-To: References: Message-ID: <1322759448.30633.19.camel@fe12lx.fisica.uniud.it> On Wed, 2011-11-30 at 17:15 -0800, David Strubbe wrote: > For phonon calculations, one can ask for the 'dvscf' file > containing the change in self-consistent potential for > each mode to be written. Can the corresponding quantity > be written for dielectric response? it can, but it requires modifying the code. Or maybe you can use fildrho, but you have first to understand how it works (it's almost undocumented) P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From suza.rri at gmail.com Thu Dec 1 18:33:42 2011 From: suza.rri at gmail.com (Suza W) Date: Thu, 1 Dec 2011 18:33:42 +0100 Subject: [Pw_forum] DC & BEC In-Reply-To: References: Message-ID: Dear Paolo & Nicola, Thanks a lot, startignwfc="atomic+random" rocks. Yours sincerely, Suza W. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111201/9cf31100/attachment.htm From Michael.Mehl at nrl.navy.mil Thu Dec 1 18:43:11 2011 From: Michael.Mehl at nrl.navy.mil (Mike Mehl) Date: Thu, 01 Dec 2011 12:43:11 -0500 Subject: [Pw_forum] Equation of state In-Reply-To: References: Message-ID: <4ED7BCAF.7080300@nrl.navy.mil> For more detail on many other physically plausible equations of state, see: @Book{anderson95:eos, author = {Orson L. Anderson}, title = {Equations of State of Solids for Geophysical and Ceramic Science}, publisher = {Oxford University Press}, year = 1995, number = 31, series = {Oxford Monographs on Geology and Geophysics}, address = {New York, Oxford}, keywords = {Equation of State}, isbn = {0-19-505606-X}, cardcat = {QE501.3.A53}} There is no indication of proofreading for this book, but it does have a lot of information on possible equations of state. As it is geared towards experiment there is more discussion of P(V) behavior than E(V). On 12/01/2011 11:51 AM, Payam Norouzzadeh wrote: > Hello Quantum Espresso users > > As you know the code ev.f90 fits the data in E-V curve to some equation > of states like Birch 1st order,Birch 2nd order,Keane and Murnaghan. > Does anyone know any paper,text or resource to discuss about these > equations of states and their details? > -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC From giannozz at democritos.it Thu Dec 1 21:41:03 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 1 Dec 2011 21:41:03 +0100 Subject: [Pw_forum] PlotPhon Questions...Again In-Reply-To: <2cea01ccae64$54384c00$fca8e400$@w2agz.com> References: <2cea01ccae64$54384c00$fca8e400$@w2agz.com> Message-ID: <72F5742F-2CAC-4C1A-B0A8-0B0A20E8F714@democritos.it> On Nov 29, 2011, at 7:58 , W2AGZ wrote: > Is there today a generally agreed-upon standard formulation for > space groups, especially for those symmetries less than cubic, > hexagonal, tetragonal, and orthorhombic? > I don't think there is any P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Thu Dec 1 22:32:15 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 1 Dec 2011 22:32:15 +0100 Subject: [Pw_forum] wavefunction and symmetries In-Reply-To: <1322759257.96795.YahooMailNeo@web27003.mail.ukl.yahoo.com> References: <1322759257.96795.YahooMailNeo@web27003.mail.ukl.yahoo.com> Message-ID: <0426B46C-5126-4BAC-93AC-72D64676067E@democritos.it> On Dec 1, 2011, at 18:07 , Michele Pisarra wrote: > can anyone tell me what is the connection between the > eigenfunction corresponding to k points connected by > symmetry operations? If there is any, of course. some time ago I wrote these notes. I am not sure they are correct, though. -------------- next part -------------- A non-text attachment was scrubbed... Name: simmetria.pdf Type: application/pdf Size: 60527 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111201/92c176a6/attachment-0001.pdf -------------- next part -------------- P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From michelepisarra at yahoo.it Fri Dec 2 16:10:54 2011 From: michelepisarra at yahoo.it (Michele Pisarra) Date: Fri, 2 Dec 2011 15:10:54 +0000 (GMT) Subject: [Pw_forum] wavefunction and symmetries In-Reply-To: <0426B46C-5126-4BAC-93AC-72D64676067E@democritos.it> References: <1322759257.96795.YahooMailNeo@web27003.mail.ukl.yahoo.com> <0426B46C-5126-4BAC-93AC-72D64676067E@democritos.it> Message-ID: <1322838654.56392.YahooMailNeo@web27002.mail.ukl.yahoo.com> Ok! Thank you. It?is what I was looking for. ?Michele Pisarra, PhD Student, Dipartimento di Fisica, Universit? della Calabria Via P. Bucci, Cubo 31 C VI piano, 87036, Rende (CS), Italy ________________________________ Da: Paolo Giannozzi A: Michele Pisarra ; PWSCF Forum Inviato: Gioved? 1 Dicembre 2011 22:32 Oggetto: Re: [Pw_forum] wavefunction and symmetries On Dec 1, 2011, at 18:07 , Michele Pisarra wrote: > can anyone tell me what is the connection between the > eigenfunction corresponding to k points connected by > symmetry operations? If there is any, of course. some time ago I wrote these notes. I am not sure they are correct, though. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111202/52e0b0cf/attachment.htm From hasanx at gmail.com Fri Dec 2 18:32:11 2011 From: hasanx at gmail.com (HASAN SAHIN) Date: Fri, 2 Dec 2011 19:32:11 +0200 Subject: [Pw_forum] Problem with Raman and Infrared Active Modes: SOLVED Message-ID: Dear Users, In my previous e-mails I was asking about the eigenmodes that are both Raman and IR active. Now I think it is solved. When I calculate eigenfrequencies at gamma point, I had noticed that all the modes are both Raman and IR active as follows omega( 4 - 5) = 102.9 [cm-1] --> E L_3 I+R omega( 6 - 7) = 156.9 [cm-1] --> E L_3 I+R omega( 8 - 8) = 402.0 [cm-1] --> A_1 L_1 I+R omega( 9 - 10) = 719.8 [cm-1] --> E L_3 I+R omega( 11 - 11) = 831.9 [cm-1] --> A_1 L_1 I+R omega( 12 - 12) = 1042.2 [cm-1] --> A_1 L_1 I+R Therefore I have tried to improve my calculation by -increasing number of kpoints in scf part -increasing ecutwfc and ecutrho -using different pseudopotentials -setting crystal structure as perfectly symmetric but none of these improvements could give reasonable result about Raman activity. However, problem was solved by taking the values of tr2_ph less than 1.0d-24. In this case we see that the modes becomes only Raman (or only IR) active as follows omega( 4 - 5) = 104.8 [cm-1] --> E_g L_3 R omega( 6 - 7) = 165.5 [cm-1] --> E_u L_3' I omega( 8 - 8) = 398.5 [cm-1] --> A_1g L_1 R omega( 9 - 10) = 715.3 [cm-1] --> E_g L_3 R omega( 11 - 11) = 827.6 [cm-1] --> A_2u L_2' I omega( 12 - 12) = 1042.5 [cm-1] --> A_1g L_1 R I also would like to thank Martin Andersson, Paolo Giannozzi, Stefano Baroni, Andrea Dal Corso very much for their valuable comments and suggestions. -- *SINCERELY ########################################## Hasan Sahin Bilkent University National Nanotechnology Research Center http://www.bilkent.edu.tr/~shasan/ http://www.researcherid.com/rid/G-4747-2010 ##########################################* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111202/e7301127/attachment.htm From giacsport at libero.it Sat Dec 3 03:20:02 2011 From: giacsport at libero.it (giacsport at libero.it) Date: Sat, 3 Dec 2011 03:20:02 +0100 (CET) Subject: [Pw_forum] metallic BP? Message-ID: <3375660.7676171322878802207.JavaMail.root@wmail28> Dear All, I am doing calculations on a 2 atom primitive cell of Boron Phosphide. What I obtain from the "scf" calculation is a system that "should be" metallic.... Indeed "highest occupied, lowest unoccupied level (ev): 6.1092 5.4104" -->( As far as I understand, Homo lies 0.7 eV above the LUMO) but of course this system is a wide-gap semiconductor. I am not able to figure out the reason for such behaviour. I have tested the same system (rhombohedral cell, a=b=c=6.06 Bohr, alpha=beta=gamma=60deg) in several machines finding always the same result. I attach the input file and the header of the two pseudos (USPP/GGA) I am using. Thanks in advance for any comments. My best, Giacomo &control calculation = 'scf' restart_mode='from_scratch', prefix='BP', tprnfor = .true., tstress = .true., wf_collect=.true., pseudo_dir='/home/giacomo/GGA/', outdir='/home/giacomo/GGA/' / &system ibrav= 4, celldm(1) =6.061296108, celldm(3)=1, nat= 2, ntyp= 2, ecutwfc =50., nbnd = 50, / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES B 10.811 B.UPF P 30.974 P.UPF ATOMIC_POSITIONS (crystal) B 0.0 0.0 0.0 P 0.25000 0.25000 0.250000 K_POINTS (automatic) 6 6 6 0 0 0 For BORON: Generated using Vanderbilt code, version 7 3 5 Author: unknown Generation date: 20 6 2004 Automatically converted from original format 0 The Pseudo was generated with a Non-Relativistic Calculation 1.00000000000E+00 Local Potential cutoff radius nl pn l occ Rcut Rcut US E pseu 2S 2 0 2.00 10.00000000000 1.50000000000 -0.69693392995 2P 2 1 1.00 10.00000000000 1.53000000000 -0.26855658626 0 Version Number B Element US Ultrasoft pseudopotential T Nonlinear Core Correction SLA PW GGX GGC PW91 Exchange-Correlation functional 3.00000000000 Z valence -5.70038942945 Total energy 0.0000000 0.0000000 Suggested cutoff for wfc and rho 1 Max angular momentum component 781 Number of points in mesh 2 4 Number of Wavefunctions, Number of Projectors Wavefunctions nl l occ 2S 0 2.00 2P 1 1.00 --------------------------------- For PHOSPHORUS Generated using Vanderbilt code, version 7 3 5 Author: unknown Generation date: 20 6 2004 Automatically converted from original format 1 The Pseudo was generated with a Scalar-Relativistic Calculation 1.60000000000E+00 Local Potential cutoff radius nl pn l occ Rcut Rcut US E pseu 3S 3 0 2.00 10.00000000000 1.70000000000 -1.03015496458 3P 3 1 3.00 10.00000000000 1.70000000000 -0.40774343239 0 Version Number P Element US Ultrasoft pseudopotential T Nonlinear Core Correction SLA PW GGX GGC PW91 Exchange-Correlation functional 5.00000000000 Z valence -17.57767183737 Total energy 0.0000000 0.0000000 Suggested cutoff for wfc and rho 2 Max angular momentum component 903 Number of points in mesh 2 5 Number of Wavefunctions, Number of Projectors Wavefunctions nl l occ 3S 0 2.00 3P 1 3.00 ------------------------------------------ Giacomo Giorgi Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan From germaneau at gucas.ac.cn Sat Dec 3 16:32:09 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Sat, 03 Dec 2011 10:32:09 -0500 Subject: [Pw_forum] metallic BP? In-Reply-To: <522876633.08659@test1.gucas.ac.cn> References: <522876633.08659@test1.gucas.ac.cn> Message-ID: <4EDA40F9.5000805@gucas.ac.cn> Hey Giacomo, Forgive my ignorance but why do you say that the "scf" calculation is a system that "should be" metallic ? To me it has a band gap of .7 ev. What do you mean by wide band gap semiconductor ? What band gap value do you expect to get? May be the wide band gap behavior you mention does not occur at 0K. I guess you double checked whether your system is fully relaxed. ?ric. On 12/02/2011 09:20 PM, giacsport at libero.it wrote: > Dear All, > I am doing calculations on a 2 atom primitive cell of Boron > Phosphide. What I obtain from the "scf" calculation is a system that "should > be" metallic.... Indeed > > "highest occupied, lowest unoccupied level (ev): 6.1092 > 5.4104" -->( As far as I understand, Homo lies 0.7 eV above the > LUMO) > > but of course this system is a wide-gap semiconductor. > I am not able to figure out the reason for such behaviour. I have tested the > same system (rhombohedral cell, a=b=c=6.06 Bohr, alpha=beta=gamma=60deg) in > several machines finding always the same result. I attach the input file and > the header of the two pseudos (USPP/GGA) I am using. > Thanks in advance for any comments. > My best, > Giacomo > > > > > > > &control > calculation = 'scf' > restart_mode='from_scratch', > prefix='BP', > tprnfor = .true., > tstress = .true., > wf_collect=.true., > pseudo_dir='/home/giacomo/GGA/', > outdir='/home/giacomo/GGA/' > / > &system > ibrav= 4, celldm(1) =6.061296108, celldm(3)=1, > nat= 2, ntyp= 2, > ecutwfc =50., nbnd = 50, > / > &electrons > diagonalization='david' > mixing_mode = 'plain' > mixing_beta = 0.7 > conv_thr = 1.0d-8 > / > ATOMIC_SPECIES > B 10.811 B.UPF > P 30.974 P.UPF > ATOMIC_POSITIONS (crystal) > B 0.0 0.0 0.0 > P 0.25000 0.25000 0.250000 > K_POINTS (automatic) > 6 6 6 0 0 0 > > > > > > > > > For BORON: > > > Generated using Vanderbilt code, version 7 3 5 > Author: unknown Generation date: 20 6 2004 > Automatically converted from original format > 0 The Pseudo was generated with a Non-Relativistic Calculation > 1.00000000000E+00 Local Potential cutoff radius > nl pn l occ Rcut Rcut US E pseu > 2S 2 0 2.00 10.00000000000 1.50000000000 -0.69693392995 > 2P 2 1 1.00 10.00000000000 1.53000000000 -0.26855658626 > > > > > 0 Version Number > B Element > US Ultrasoft pseudopotential > T Nonlinear Core Correction > SLA PW GGX GGC PW91 Exchange-Correlation functional > 3.00000000000 Z valence > -5.70038942945 Total energy > 0.0000000 0.0000000 Suggested cutoff for wfc and rho > 1 Max angular momentum component > 781 Number of points in mesh > 2 4 Number of Wavefunctions, Number of Projectors > Wavefunctions nl l occ > 2S 0 2.00 > 2P 1 1.00 > > --------------------------------- > > > > For PHOSPHORUS > > > Generated using Vanderbilt code, version 7 3 5 > Author: unknown Generation date: 20 6 2004 > Automatically converted from original format > 1 The Pseudo was generated with a Scalar-Relativistic Calculation > 1.60000000000E+00 Local Potential cutoff radius > nl pn l occ Rcut Rcut US E pseu > 3S 3 0 2.00 10.00000000000 1.70000000000 -1.03015496458 > 3P 3 1 3.00 10.00000000000 1.70000000000 -0.40774343239 > > > > > 0 Version Number > P Element > US Ultrasoft pseudopotential > T Nonlinear Core Correction > SLA PW GGX GGC PW91 Exchange-Correlation functional > 5.00000000000 Z valence > -17.57767183737 Total energy > 0.0000000 0.0000000 Suggested cutoff for wfc and rho > 2 Max angular momentum component > 903 Number of points in mesh > 2 5 Number of Wavefunctions, Number of Projectors > Wavefunctions nl l occ > 3S 0 2.00 > 3P 1 3.00 > > > > > ------------------------------------------ > Giacomo Giorgi > > Department of Chemical System Engineering, > School of Engineering, The University of Tokyo > 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111203/26afe8dd/attachment-0001.htm From giacsport at libero.it Sat Dec 3 09:39:37 2011 From: giacsport at libero.it (giacsport at libero.it) Date: Sat, 3 Dec 2011 09:39:37 +0100 (CET) Subject: [Pw_forum] metallic BP? Message-ID: <16063440.7536041322901577105.JavaMail.root@wmail42> Hi Eric, sorry. I expressed my point maybe in a misleading way...I mean, i found a gap metallic (Homo is highest in energy than Lumo) but the system is reported to be a wide bandgap semiconductor (Gap > 2. eV)"highest occupied, lowest unoccupied level (ev): 6.1092 5.4104"HOMO=6.109 LUMO=5.4104 (as far as I understand)....the gap is 0.7 eV only if you switch HOMO and LUMO The structure is the experimental one I found from a previous paper and it was optimized with Gaussian PBC Thanks,G ----Messaggio originale---- Da: germaneau at gucas.ac.cn Data: 03/12/2011 16.32 A: "giacsport at libero.it", "PWSCF Forum" Ogg: Re: [Pw_forum] metallic BP? Hey Giacomo, Forgive my ignorance but why do you say that the "scf" calculation is a system that "should be" metallic ? To me it has a band gap of .7 ev. What do you mean by wide band gap semiconductor ? What band gap value do you expect to get? May be the wide band gap behavior you mention does not occur at 0K. I guess you double checked whether your system is fully relaxed. ?ric. On 12/02/2011 09:20 PM, giacsport at libero.it wrote: Dear All, I am doing calculations on a 2 atom primitive cell of Boron Phosphide. What I obtain from the "scf" calculation is a system that "should be" metallic.... Indeed "highest occupied, lowest unoccupied level (ev): 6.1092 5.4104" -->( As far as I understand, Homo lies 0.7 eV above the LUMO) but of course this system is a wide-gap semiconductor. I am not able to figure out the reason for such behaviour. I have tested the same system (rhombohedral cell, a=b=c=6.06 Bohr, alpha=beta=gamma=60deg) in several machines finding always the same result. I attach the input file and the header of the two pseudos (USPP/GGA) I am using. Thanks in advance for any comments. My best, Giacomo &control calculation = 'scf' restart_mode='from_scratch', prefix='BP', tprnfor = .true., tstress = .true., wf_collect=.true., pseudo_dir='/home/giacomo/GGA/', outdir='/home/giacomo/GGA/' / &system ibrav= 4, celldm(1) =6.061296108, celldm(3)=1, nat= 2, ntyp= 2, ecutwfc =50., nbnd = 50, / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES B 10.811 B.UPF P 30.974 P.UPF ATOMIC_POSITIONS (crystal) B 0.0 0.0 0.0 P 0.25000 0.25000 0.250000 K_POINTS (automatic) 6 6 6 0 0 0 For BORON: Generated using Vanderbilt code, version 7 3 5 Author: unknown Generation date: 20 6 2004 Automatically converted from original format 0 The Pseudo was generated with a Non-Relativistic Calculation 1.00000000000E+00 Local Potential cutoff radius nl pn l occ Rcut Rcut US E pseu 2S 2 0 2.00 10.00000000000 1.50000000000 -0.69693392995 2P 2 1 1.00 10.00000000000 1.53000000000 -0.26855658626 0 Version Number B Element US Ultrasoft pseudopotential T Nonlinear Core Correction SLA PW GGX GGC PW91 Exchange-Correlation functional 3.00000000000 Z valence -5.70038942945 Total energy 0.0000000 0.0000000 Suggested cutoff for wfc and rho 1 Max angular momentum component 781 Number of points in mesh 2 4 Number of Wavefunctions, Number of Projectors Wavefunctions nl l occ 2S 0 2.00 2P 1 1.00 --------------------------------- For PHOSPHORUS Generated using Vanderbilt code, version 7 3 5 Author: unknown Generation date: 20 6 2004 Automatically converted from original format 1 The Pseudo was generated with a Scalar-Relativistic Calculation 1.60000000000E+00 Local Potential cutoff radius nl pn l occ Rcut Rcut US E pseu 3S 3 0 2.00 10.00000000000 1.70000000000 -1.03015496458 3P 3 1 3.00 10.00000000000 1.70000000000 -0.40774343239 0 Version Number P Element US Ultrasoft pseudopotential T Nonlinear Core Correction SLA PW GGX GGC PW91 Exchange-Correlation functional 5.00000000000 Z valence -17.57767183737 Total energy 0.0000000 0.0000000 Suggested cutoff for wfc and rho 2 Max angular momentum component 903 Number of points in mesh 2 5 Number of Wavefunctions, Number of Projectors Wavefunctions nl l occ 3S 0 2.00 3P 1 3.00 ------------------------------------------ Giacomo Giorgi Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Be the change you wish to see in the world ? Mahatma Gandhi ? Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111203/efd48493/attachment.htm From giannozz at democritos.it Sat Dec 3 11:04:57 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 3 Dec 2011 11:04:57 +0100 Subject: [Pw_forum] metallic BP? In-Reply-To: <16063440.7536041322901577105.JavaMail.root@wmail42> References: <16063440.7536041322901577105.JavaMail.root@wmail42> Message-ID: On Dec 3, 2011, at 9:39 , giacsport at libero.it wrote: > The structure is the experimental one I found from a previous paper > and it was optimized with Gaussian PBC are you sure? it yields very high forces and a very large stress. It also has just 2 symmetries. Reminder to everybody reporting problems: - if you use pseudopotentials from www.quantum-espresso.org, please do not change the names of pseudopotential files - please always report the version of QE you are using P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Dec 3 11:10:02 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 3 Dec 2011 11:10:02 +0100 Subject: [Pw_forum] Problem with Raman and Infrared Active Modes: SOLVED In-Reply-To: References: Message-ID: On Dec 2, 2011, at 18:32 , HASAN SAHIN wrote: > omega( 4 - 5) = 102.9 [cm-1] --> E > L_3 I+R > omega( 6 - 7) = 156.9 [cm-1] --> E > L_3 I+R > omega( 8 - 8) = 402.0 [cm-1] --> A_1 > L_1 I+R > omega( 9 - 10) = 719.8 [cm-1] --> E > L_3 I+R > omega( 11 - 11) = 831.9 [cm-1] --> A_1 L_1 I+R > omega( 12 - 12) = 1042.2 [cm-1] --> A_1 L_1 I+R no inversion symmetry > omega( 4 - 5) = 104.8 [cm-1] --> E_g > L_3 R > omega( 6 - 7) = 165.5 [cm-1] --> E_u > L_3' I > omega( 8 - 8) = 398.5 [cm-1] --> A_1g L_1 R > omega( 9 - 10) = 715.3 [cm-1] --> E_g L_3 R > omega( 11 - 11) = 827.6 [cm-1] --> A_2u L_2' I > omega( 12 - 12) = 1042.5 [cm-1] --> A_1g L_1 R inversion symmetry (note the "g" and "u", standing for "gerade", even, and "ungerade", odd). In presence of inversion symmetry, Raman-active modes are even, Infrared-active modes are odd P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From germaneau at gucas.ac.cn Sun Dec 4 02:25:35 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Sat, 03 Dec 2011 20:25:35 -0500 Subject: [Pw_forum] metallic BP? In-Reply-To: <522899362.05761@gscas.net.cn> References: <522899362.05761@gscas.net.cn> Message-ID: <4EDACC0F.9010409@gucas.ac.cn> I'm sorry, you expressed correctly. Can you tell us what pressure and forces you got? What was energy difference between the two last scf steps? ?ric. On 12/03/2011 03:39 AM, giacsport at libero.it wrote: > > Hi Eric, > > sorry. I expressed my point maybe in a > misleading way...I mean, i found a gap metallic (Homo is highest in > energy than Lumo) but the system is reported to be a wide bandgap > semiconductor (Gap > 2. eV) > > "highest occupied, lowest unoccupied level (ev): 6.1092 5.4104" > > HOMO=6.109 LUMO=5.4104 (as far as I understand)....the gap is 0.7 eV > only if you switch HOMO and LUMO > > The structure is the experimental one I found from a previous paper > and it was optimized with Gaussian PBC > > > Thanks, > > G > > > ----Messaggio originale---- > Da: germaneau at gucas.ac.cn > Data: 03/12/2011 16.32 > A: "giacsport at libero.it", "PWSCF > Forum" > Ogg: Re: [Pw_forum] metallic BP? > > Hey Giacomo, > > Forgive my ignorance but why do you say that the "scf" calculation > is a system that "should be" metallic ? > To me it has a band gap of .7 ev. > What do you mean by wide band gap semiconductor ? > What band gap value do you expect to get? > May be the wide band gap behavior you mention does not occur at 0K. > I guess you double checked whether your system is fully relaxed. > > ?ric. > > On 12/02/2011 09:20 PM, giacsport at libero.it wrote: >> Dear All, >> I am doing calculations on a 2 atom primitive cell of Boron >> Phosphide. What I obtain from the "scf" calculation is a system that "should >> be" metallic.... Indeed >> >> "highest occupied, lowest unoccupied level (ev): 6.1092 >> 5.4104" -->( As far as I understand, Homo lies 0.7 eV above the >> LUMO) >> >> but of course this system is a wide-gap semiconductor. >> I am not able to figure out the reason for such behaviour. I have tested the >> same system (rhombohedral cell, a=b=c=6.06 Bohr, alpha=beta=gamma=60deg) in >> several machines finding always the same result. I attach the input file and >> the header of the two pseudos (USPP/GGA) I am using. >> Thanks in advance for any comments. >> My best, >> Giacomo >> >> >> >> >> >> >> &control >> calculation = 'scf' >> restart_mode='from_scratch', >> prefix='BP', >> tprnfor = .true., >> tstress = .true., >> wf_collect=.true., >> pseudo_dir='/home/giacomo/GGA/', >> outdir='/home/giacomo/GGA/' >> / >> &system >> ibrav= 4, celldm(1) =6.061296108, celldm(3)=1, >> nat= 2, ntyp= 2, >> ecutwfc =50., nbnd = 50, >> / >> &electrons >> diagonalization='david' >> mixing_mode = 'plain' >> mixing_beta = 0.7 >> conv_thr = 1.0d-8 >> / >> ATOMIC_SPECIES >> B 10.811 B.UPF >> P 30.974 P.UPF >> ATOMIC_POSITIONS (crystal) >> B 0.0 0.0 0.0 >> P 0.25000 0.25000 0.250000 >> K_POINTS (automatic) >> 6 6 6 0 0 0 >> >> >> >> >> >> >> >> >> For BORON: >> >> >> Generated using Vanderbilt code, version 7 3 5 >> Author: unknown Generation date: 20 6 2004 >> Automatically converted from original format >> 0 The Pseudo was generated with a Non-Relativistic Calculation >> 1.00000000000E+00 Local Potential cutoff radius >> nl pn l occ Rcut Rcut US E pseu >> 2S 2 0 2.00 10.00000000000 1.50000000000 -0.69693392995 >> 2P 2 1 1.00 10.00000000000 1.53000000000 -0.26855658626 >> >> >> >> >> 0 Version Number >> B Element >> US Ultrasoft pseudopotential >> T Nonlinear Core Correction >> SLA PW GGX GGC PW91 Exchange-Correlation functional >> 3.00000000000 Z valence >> -5.70038942945 Total energy >> 0.0000000 0.0000000 Suggested cutoff for wfc and rho >> 1 Max angular momentum component >> 781 Number of points in mesh >> 2 4 Number of Wavefunctions, Number of Projectors >> Wavefunctions nl l occ >> 2S 0 2.00 >> 2P 1 1.00 >> >> --------------------------------- >> >> >> >> For PHOSPHORUS >> >> >> Generated using Vanderbilt code, version 7 3 5 >> Author: unknown Generation date: 20 6 2004 >> Automatically converted from original format >> 1 The Pseudo was generated with a Scalar-Relativistic Calculation >> 1.60000000000E+00 Local Potential cutoff radius >> nl pn l occ Rcut Rcut US E pseu >> 3S 3 0 2.00 10.00000000000 1.70000000000 -1.03015496458 >> 3P 3 1 3.00 10.00000000000 1.70000000000 -0.40774343239 >> >> >> >> >> 0 Version Number >> P Element >> US Ultrasoft pseudopotential >> T Nonlinear Core Correction >> SLA PW GGX GGC PW91 Exchange-Correlation functional >> 5.00000000000 Z valence >> -17.57767183737 Total energy >> 0.0000000 0.0000000 Suggested cutoff for wfc and rho >> 2 Max angular momentum component >> 903 Number of points in mesh >> 2 5 Number of Wavefunctions, Number of Projectors >> Wavefunctions nl l occ >> 3S 0 2.00 >> 3P 1 3.00 >> >> >> >> >> ------------------------------------------ >> Giacomo Giorgi >> >> Department of Chemical System Engineering, >> School of Engineering, The University of Tokyo >> 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Dr. ?ric Germaneau > > > Graduate University of Chinese Academy of Sciences > College of Physical Sciences > Yuquan Road 19A > Beijing 100049 > China > > /Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/ > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111203/a2822dc4/attachment-0001.htm From elie.moujaes at hotmail.co.uk Sat Dec 3 14:53:03 2011 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Sat, 3 Dec 2011 13:53:03 +0000 Subject: [Pw_forum] band structure for a 72 C atom supercell Message-ID: Dear all, I computed the electronic band structure of a 72 Carbon atom supercell but the result shows a lot of wiggles in the energies? Do I have to use more points or might it be due to something else? You will find the ps plot attached Regards Elie MoujaesUnIVERISTY od NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111203/560ba7cf/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: GB72.bands.ps Type: application/postscript Size: 49174 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111203/560ba7cf/attachment-0001.ps From kalamaillist at gmail.com Sat Dec 3 17:01:59 2011 From: kalamaillist at gmail.com (WF) Date: Sun, 4 Dec 2011 00:01:59 +0800 Subject: [Pw_forum] band structure for a 72 C atom supercell Message-ID: <000801ccb1d4$e8038670$b80a9350$@gmail.com> At Sat, 3 Dec 2011 13:53:03 +0000, Elie M writes: >Dear all, >I computed the electronic band structure of a 72 Carbon atom supercell but the result shows a lot of wiggles in the ? energies? Do I have to use more points or might it be due to something else? >You will find the ps plot attached >Regards >Elie MoujaesUnIVERISTY od NottinghamNG7 2RDUK In my experience the band structure plotted by plotband.x may give unphysical band crossing. You can just plot the raw data in the original order to avoid this, however band-crossing will be totally lost. -------------------------------------------------- Wu Feng Chemistry and Molecular Engineering, Peking University -------------------------------------------------- From elie.moujaes at hotmail.co.uk Sat Dec 3 17:08:00 2011 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Sat, 3 Dec 2011 16:08:00 +0000 Subject: [Pw_forum] band structure for a 72 C atom supercell In-Reply-To: <000801ccb1d4$e8038670$b80a9350$@gmail.com> References: <000801ccb1d4$e8038670$b80a9350$@gmail.com> Message-ID: Dear Wu, Thanks for your reply. Is there any other executable that does this?what about Gnuplot? does it follow the same procedure or is different? Thanks again Elie > From: kalamaillist at gmail.com > To: pw_forum at pwscf.org > Date: Sun, 4 Dec 2011 00:01:59 +0800 > Subject: Re: [Pw_forum] band structure for a 72 C atom supercell > > At Sat, 3 Dec 2011 13:53:03 +0000, Elie M writes: > > >Dear all, > >I computed the electronic band structure of a 72 Carbon atom supercell but > the result shows a lot of wiggles in the ? energies? Do I have to use more > points or might it be due to something else? > >You will find the ps plot attached > >Regards > > >Elie MoujaesUnIVERISTY od NottinghamNG7 2RDUK > > In my experience the band structure plotted by plotband.x may give > unphysical band crossing. You can just plot the raw data in the original > order to avoid this, however band-crossing will be totally lost. > > -------------------------------------------------- > Wu Feng > Chemistry and Molecular Engineering, Peking University > -------------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111203/0ad80547/attachment.htm From omipet2000 at yahoo.com Sat Dec 3 21:10:05 2011 From: omipet2000 at yahoo.com (Omileke Peter) Date: Sat, 3 Dec 2011 12:10:05 -0800 (PST) Subject: [Pw_forum] Atomic position for Li15Si4 Message-ID: <1322943005.96057.YahooMailNeo@web120016.mail.ne1.yahoo.com> Dear all, ?????????? Please, I have problem in knowing the atomic position of Li15Si4 (space group is l43d). I will be very glad if someone could help me out.Thanks in advance for your suggestion.? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111203/2cc85ed7/attachment.htm From tb283 at cornell.edu Sat Dec 3 21:59:26 2011 From: tb283 at cornell.edu (Turan Birol) Date: Sat, 3 Dec 2011 15:59:26 -0500 Subject: [Pw_forum] Problem with Raman and Infrared Active Modes: SOLVED In-Reply-To: References: Message-ID: The Isotropy Software has a module, called SMODES, that does a full analysis of phonon modes; including their Raman/Infrared activity. It uses 'simple' group theory only, and the only input it needs is the structure: Therefore, it cannot be affected by any lack of convergence or other errors in the DF(P)T calculation. I suggest always using SMODES -before- doing a phonon calculation to know what to expect. You can access SMODES at http://stokes.byu.edu/smodes.html Best, Turan. ------- PhD Candidate, Cornell University On Sat, Dec 3, 2011 at 5:10 AM, Paolo Giannozzi wrote: > > On Dec 2, 2011, at 18:32 , HASAN SAHIN wrote: > >> ? ? ?omega( ?4 - ?5) ? = ? ? ? ? 102.9 ?[cm-1] ? --> E >> L_3 ? ? ? ? ?I+R >> ? ? ?omega( ?6 - ?7) ? = ? ? ? ? 156.9 ?[cm-1] ? --> E >> L_3 ? ? ? ? ?I+R >> ? ? ?omega( ?8 - ?8) ? = ? ? ? ? 402.0 ?[cm-1] ? --> A_1 >> L_1 ? ? ? ?I+R >> ? ? ?omega( ?9 - 10) ?= ? ? ? ? 719.8 ?[cm-1] ? --> E >> L_3 ? ? ? ? ?I+R >> ? ? ?omega( 11 - 11) = ? ? ? ? 831.9 ?[cm-1] ? --> A_1 ?L_1 ? ? ? ?I+R >> ? ? ?omega( 12 - 12) = ? ? ? 1042.2 ?[cm-1] ? --> A_1 ?L_1 ? ? ? ?I+R > > no inversion symmetry > >> ? ? ?omega( ?4 - ?5) ? = ? ? ? ?104.8 ?[cm-1] ? --> E_g >> L_3 ? ? ? ? ?R >> ? ? ?omega( ?6 - ?7) ? = ? ? ? ?165.5 ?[cm-1] ? --> E_u >> L_3' ? ? ? ? I >> ? ? ?omega( ?8 - ?8) ? = ? ? ? ?398.5 ?[cm-1] ? --> A_1g L_1 ? ? ? ? R >> ? ? ?omega( ?9 - 10) ?= ? ? ? ?715.3 ?[cm-1] ? --> E_g ?L_3 ? ? ? ? ?R >> ? ? ?omega( 11 - 11) = ? ? ? ?827.6 ?[cm-1] ? --> A_2u L_2' ? ? ? ?I >> ? ? ?omega( 12 - 12) = ? ? ? 1042.5 ?[cm-1] ? --> A_1g L_1 ? ? ? ?R > > inversion symmetry (note the "g" and "u", standing for "gerade", even, > and "ungerade", odd). In presence of inversion symmetry, Raman-active > modes are even, Infrared-active modes are odd > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giacsport at libero.it Sun Dec 4 02:11:42 2011 From: giacsport at libero.it (giacsport at libero.it) Date: Sun, 4 Dec 2011 02:11:42 +0100 (CET) Subject: [Pw_forum] metallic BP? Message-ID: <7372700.7691481322961102326.JavaMail.defaultUser@defaultHost> Hi Paolo, thanks for the reply and escuse me for the previous lacking description of the problem. I have a question that you for sure will be able to reply. It seems that I was able to fix the problem. I will try to explain. In my first attempt I was using the Primitive Cell of BP consisting of two atoms. It is a rhombohedral cell, a=b=c=6.06 Bohr and alpha=beta=gamma=60 deg (ibrav= 4, celldm(1) =6.06, celldm(3)=1) B 0.0000 0.0000 0.0000 P 1.1373 1.1373 1.1373 -2 0.0000 2.2745 2.2745 -2 2.2745 0.0000 2.2745 -2 2.2745 2.2745 0.0000 (first 2 lines atomic coordinates, last three the lattice vectors) reported in the Supplementary Materials of THE JOURNAL OF CHEMICAL PHYSICS 123, 174101 (2005) It gave as result that strange bandgap I reported before (formally no gap). espresso.4.1.3 (both serial and parallel) Then I used exactly the same atomic position and configuration (2 atoms, 1 B and 1 P) but with the lattice parameters of the Conventional Cell (ibrav= 2, celldm(1) =8.575576536) and in this case I found perfect agreement (of course with some obvious DFT underestimation of the gap). Thus, as far as I understand, if I have the Primitive Cell coordinates I have to use in any case the Conventional Cell lattice vectors. Is it correct? Thanks in advance and excuse me once more! My very best, Giacomo ---------------------------------- Giacomo GIORGI Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Ja >----Messaggio originale---- >Da: giannozz at democritos.it >Data: 03/12/2011 11.04 >A: , "PWSCF Forum" >Ogg: Re: [Pw_forum] metallic BP? > > >On Dec 3, 2011, at 9:39 , giacsport at libero.it wrote: > >> The structure is the experimental one I found from a previous paper >> and it was optimized with Gaussian PBC > >are you sure? it yields very high forces and a very large stress. >It also has just 2 symmetries. > >Reminder to everybody reporting problems: >- if you use pseudopotentials from www.quantum-espresso.org, > please do not change the names of pseudopotential files >- please always report the version of QE you are using > >P. >--- >Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >Phone +39-0432-558216, fax +39-0432-558222 > > > > > From lfhuang at theory.issp.ac.cn Sun Dec 4 09:51:31 2011 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Sun, 04 Dec 2011 16:51:31 +0800 Subject: [Pw_forum] =?utf-8?q?band_structure_for_a_72__C_atom_supercell?= Message-ID: <20111204085131.3620.qmail@ms.hfcas.ac.cn> Dear Elie: This problem is just caused by the fact that the bands at each k point are not sorted according to their symmetry. It probably has been mentioned many times on this Forum. You can have a look at the difference between the magnitude sorting and symmetry sorting in the web page below: http://blog.sciencenet.cn/home.php?mod=space&uid=345795&do=blog&id=422819 where phonon dispersions of graphene are given as examples, and the basic algorithm should be applicable to the symmetry sorting of electronic band dispersions. I don't known whether the symmetry sorting of electronic band dispersions have been realized in QE. If not, I may do this job when time permits. Hope this be of some use to you. Best Wishes! Yours Sincerely, L. F. Huang ------ ====================================================================== L.F.Huang ?????, Electronic Structure and Phonon Physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591440(office) Fax: 86-551-5591434 ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111204/74d42621/attachment.htm From kalamaillist at gmail.com Sun Dec 4 10:03:30 2011 From: kalamaillist at gmail.com (WF) Date: Sun, 4 Dec 2011 17:03:30 +0800 Subject: [Pw_forum] band structure for a 72 C atom supercell Message-ID: <000001ccb263$9bb88790$d32996b0$@gmail.com> > Dear Wu, > Thanks for your reply. Is there any other executable that does this?what about Gnuplot? does it follow the same procedure or is different? > Thanks again > Elie The band information can be found in the stdout of pw.x in text. Any graph tool include gnuplot and xmgrace should be OK to display them, however it may be necessary to rearrange the data to an usable format by yourself. -------------------------------------------------- Wu Feng Chemistry and Molecular Engineering, Peking University -------------------------------------------------- From giannozz at democritos.it Sun Dec 4 11:05:13 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 4 Dec 2011 11:05:13 +0100 Subject: [Pw_forum] metallic BP? In-Reply-To: <7372700.7691481322961102326.JavaMail.defaultUser@defaultHost> References: <7372700.7691481322961102326.JavaMail.defaultUser@defaultHost> Message-ID: <0C816D37-F954-4B73-95DA-034FAC92F1E5@democritos.it> On Dec 4, 2011, at 2:11 , giacsport at libero.it wrote: > In my first attempt I was using the Primitive Cell of BP consisting > of two > atoms. It is a rhombohedral cell, a=b=c=6.06 Bohr and > alpha=beta=gamma=60 deg > (ibrav= 4, celldm(1) =6.06, celldm(3)=1) > > B 0.0000 0.0000 0.0000 > P 1.1373 1.1373 1.1373 > -2 0.0000 2.2745 2.2745 > -2 2.2745 0.0000 2.2745 > -2 2.2745 2.2745 0.0000 > > (first 2 lines atomic coordinates, last three the lattice vectors) > reported in the Supplementary Materials of THE JOURNAL OF CHEMICAL > PHYSICS > 123, 174101 (2005) the authors are for sure working at OCSA: Office for Complication of Simple Affairs. The above structure is known to everybody not working at OCSA as "zincblende": fcc lattice with two atoms. > P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Dec 4 12:17:46 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 4 Dec 2011 12:17:46 +0100 Subject: [Pw_forum] Phonon benchmark Message-ID: I am looking for a realistic phonon calculation, to be used as a benchmark to identify bottlenecks and improve performances on parallel machines. The ideal benchmark should have about 100 atoms (let's say in the 50- to 200-atom range) and run on up to a few hundreds processors. If you have something like this and you are willing to provide it for testing, please contact me Paolo --- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giacsport at libero.it Sun Dec 4 12:22:17 2011 From: giacsport at libero.it (giacsport at libero.it) Date: Sun, 4 Dec 2011 12:22:17 +0100 (CET) Subject: [Pw_forum] R: Re: metallic BP? Message-ID: <8265323.8031651322997737908.JavaMail.root@wmail44> Thanks Paolo! I only wonder if in this case both people working at OCSE and at Tokyo University should specify ibrav=2 (cubic, since the structure is ZB) or ibrav=4 (rhombohedral, since angles are 60 deg)... :) Thanks once more! Best, G >----Messaggio originale---- >Da: giannozz at democritos.it >Data: 04/12/2011 11.05 >A: "giacsport at libero.it", "PWSCF Forum" >Ogg: Re: [Pw_forum] metallic BP? > > >On Dec 4, 2011, at 2:11 , giacsport at libero.it wrote: > >> In my first attempt I was using the Primitive Cell of BP consisting >> of two >> atoms. It is a rhombohedral cell, a=b=c=6.06 Bohr and >> alpha=beta=gamma=60 deg >> (ibrav= 4, celldm(1) =6.06, celldm(3)=1) >> >> B 0.0000 0.0000 0.0000 >> P 1.1373 1.1373 1.1373 >> -2 0.0000 2.2745 2.2745 >> -2 2.2745 0.0000 2.2745 >> -2 2.2745 2.2745 0.0000 >> >> (first 2 lines atomic coordinates, last three the lattice vectors) >> reported in the Supplementary Materials of THE JOURNAL OF CHEMICAL >> PHYSICS >> 123, 174101 (2005) > >the authors are for sure working at OCSA: Office for Complication of >Simple Affairs. >The above structure is known to everybody not working at OCSA as >"zincblende": >fcc lattice with two atoms. >> > > >P. >--- >Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >Phone +39-0432-558216, fax +39-0432-558222 > > > > > From giannozz at democritos.it Sun Dec 4 12:44:53 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 4 Dec 2011 12:44:53 +0100 Subject: [Pw_forum] R: Re: metallic BP? In-Reply-To: <8265323.8031651322997737908.JavaMail.root@wmail44> References: <8265323.8031651322997737908.JavaMail.root@wmail44> Message-ID: <79B59F97-D331-4855-9457-BFC6A35219D2@democritos.it> On Dec 4, 2011, at 12:22 , giacsport at libero.it wrote: > I only wonder if in this case both people working at OCSA > and at Tokyo University should specify ibrav=2 they should > or ibrav=4 (rhombohedral, since angles are 60 deg)... :) they shouldn't, because ibrav=4 means "hexagonal lattice": axis "a" along x, axis "b" at 120 degree with axis "a", axis "c" orthogonal to the plane formed by axis "a" and "b", as explained in much detail in the documentation. If you really plan to apply to a position at OCSA, you may prove your ability to complicate simple things by choosing ibrav=5 or (recent QE versions only) ibrav=-5: this is a trigonal (rhombohedral) lattice, with 3-fold axis around <001> (ibrav=5) or <111> (ibrav=-5) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From baroni at sissa.it Sun Dec 4 19:12:27 2011 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 4 Dec 2011 19:12:27 +0100 Subject: [Pw_forum] wavefunction and symmetries In-Reply-To: <0426B46C-5126-4BAC-93AC-72D64676067E@democritos.it> References: <1322759257.96795.YahooMailNeo@web27003.mail.ukl.yahoo.com> <0426B46C-5126-4BAC-93AC-72D64676067E@democritos.it> Message-ID: <9855C8B9-C17E-4370-A219-B2D9403EA2D8@sissa.it> Dear Michele, if you need something more basic, you may want to take a glance at one of the many textbooks on group theory (such as Tinkham's or Gold & Knox's, or Lax's), or an old textbook on electronic-structure theory (my favorite one is still Bassani & Patori Parravicini's). SB On Dec 1, 2011, at 10:32 PM, Paolo Giannozzi wrote: > > On Dec 1, 2011, at 18:07 , Michele Pisarra wrote: > >> can anyone tell me what is the connection between the >> eigenfunction corresponding to k points connected by >> symmetry operations? If there is any, of course. > > some time ago I wrote these notes. I am not sure they are > correct, though. > > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111204/7b3df15f/attachment.htm From giacsport at libero.it Mon Dec 5 00:56:08 2011 From: giacsport at libero.it (giacsport at libero.it) Date: Mon, 5 Dec 2011 00:56:08 +0100 (CET) Subject: [Pw_forum] R: Re: R: Re: metallic BP? Message-ID: <14417355.1189311323042968441.JavaMail.defaultUser@defaultHost> Thanks Paolo! Very clear. I got the point. Best, Giacomo P.S.: I keep you posted about the status of my application at OCSA... ;) >----Messaggio originale---- >Da: giannozz at democritos.it >Data: 04/12/2011 12.44 >A: "giacsport at libero.it", "PWSCF Forum" >Ogg: Re: [Pw_forum] R: Re: metallic BP? > > >On Dec 4, 2011, at 12:22 , giacsport at libero.it wrote: > >> I only wonder if in this case both people working at OCSA >> and at Tokyo University should specify ibrav=2 > >they should > >> or ibrav=4 (rhombohedral, since angles are 60 deg)... :) > >they shouldn't, because ibrav=4 means "hexagonal lattice": >axis "a" along x, axis "b" at 120 degree with axis "a", axis >"c" orthogonal to the plane formed by axis "a" and "b", as >explained in much detail in the documentation. > >If you really plan to apply to a position at OCSA, you may >prove your ability to complicate simple things by choosing >ibrav=5 or (recent QE versions only) ibrav=-5: this is a >trigonal (rhombohedral) lattice, with 3-fold axis around <001> >(ibrav=5) or <111> (ibrav=-5) > >P. >--- >Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >Phone +39-0432-558216, fax +39-0432-558222 > > > > > From gabriele.sclauzero at epfl.ch Mon Dec 5 08:56:34 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Mon, 5 Dec 2011 08:56:34 +0100 Subject: [Pw_forum] band structure for a 72 C atom supercell In-Reply-To: <20111204085131.3620.qmail@ms.hfcas.ac.cn> References: <20111204085131.3620.qmail@ms.hfcas.ac.cn> Message-ID: Dear Elie and Huang, Il giorno 04/dic/2011, alle ore 09.51, lfhuang ha scritto: > Dear Elie: > This problem is just caused by the fact that the bands at each k point are not sorted according to their symmetry. The bands from pw.x are sorted according to their energy eigenvalue, if you want them sorted "by symmetry" you need to use bands.x after the nscf run. Please have a look at Doc/INPUT_BANDS.txt, the input is very simple. You can choose between two different "sorting" algorithms, one built directly upon symmetry properties of the wavefunctions, and another which uses the overlaps between wavefunctions at neighboring k-points. > It probably has been mentioned many times on this Forum. Indeed, it has. > I don't known whether the symmetry sorting of electronic band dispersions have been realized in QE. It is implemented in PP/sym_band.f90 Regards, Gabriele > If not, I may do this job when time permits. > > Hope this be of some use to you. > > Best Wishes! > > Yours Sincerely, > L. F. Huang > > ------ > ====================================================================== > L.F.Huang ?????, Electronic Structure and Phonon Physics > ====================================================================== > Add: Research Laboratory for Computational Materials Sciences, > Instutue of Solid State Physics,the Chinese Academy of Sciences, > P.O.Box 1129, Hefei 230031, P.R.China > Tel: 86-551-5591440(office) > Fax: 86-551-5591434 > ====================================================================== > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111205/a1e5172c/attachment.htm From lfhuang at theory.issp.ac.cn Mon Dec 5 10:00:29 2011 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Mon, 05 Dec 2011 17:00:29 +0800 Subject: [Pw_forum] =?utf-8?q?band_structure_for_a_72__C_atom_supercell?= Message-ID: <20111205090029.14146.qmail@ms.hfcas.ac.cn> Dear Prof. Sclauzero: Thanks very much for your helpful information! Best Wishes! Yours Sincerely, L. F. Huang > Date: Mon, 5 Dec 2011 08:56:34 +0100 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] band structure for a 72 C atom supercell > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset="utf-8" > > Dear Elie and Huang, > > Il giorno 04/dic/2011, alle ore 09.51, lfhuang ha scritto: > > > Dear Elie: > > This problem is just caused by the fact that the bands at each k point are not sorted according to their symmetry. > > The bands from pw.x are sorted according to their energy eigenvalue, if you want them sorted "by symmetry" you need to use bands.x after the nscf run. > Please have a look at Doc/INPUT_BANDS.txt, the input is very simple. You can choose between two different "sorting" algorithms, one built directly upon symmetry properties of the wavefunctions, and another which uses the overlaps between wavefunctions at neighboring k-points. > > > It probably has been mentioned many times on this Forum. > > Indeed, it has. > > > I don't known whether the symmetry sorting of electronic band dispersions have been realized in QE. > > It is implemented in PP/sym_band.f90 > > > Regards, > > > Gabriele > > > If not, I may do this job when time permits. > > > > Hope this be of some use to you. > > > > Best Wishes! > > > > Yours Sincerely, > > L. F. Huang > > > > ------ > > ====================================================================== > > L.F.Huang ?????, Electronic Structure and Phonon Physics > > ====================================================================== > > Add: Research Laboratory for Computational Materials Sciences, > > Instutue of Solid State Physics,the Chinese Academy of Sciences, > > P.O.Box 1129, Hefei 230031, P.R.China > > Tel: 86-551-5591440(office) > > Fax: 86-551-5591434 > > ====================================================================== > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > ------ ====================================================================== L.F.Huang ?????, Electronic Structure and Phonon Physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591440(office) Fax: 86-551-5591434 ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111205/e5c2cb90/attachment.htm From lily_physics at yahoo.com.sg Mon Dec 5 10:13:12 2011 From: lily_physics at yahoo.com.sg (Lily Anh) Date: Mon, 5 Dec 2011 17:13:12 +0800 (SGT) Subject: [Pw_forum] vc-md temperature increases Message-ID: <1323076392.89294.YahooMailNeo@web77407.mail.sg1.yahoo.com> Hi all, I am running a 'vc-md' calculation with PW.X in QE v4.1.1. The system is bcc-Fe supercell of 16 atoms. The target temperature were set to 600 K in the input file while the temperature goes up all the way to more than 1000 K. I tried with a much larger supercell (128 atoms), this problem still happens. Does anyone know how to fix this? Many thanks! Lily I attached my input file here: &control ? ? calculation='vc-md', ? ? restart_mode=from_scratch', ? ? prefix='Fe', ? ? pseudo_dir = '/pseudo/', ? ? outdir='/tmp/' etot_conv_thr = 1d-5, ? ? forc_conv_thr = 1d-4, ? ? tprnfor=.true., ? ? tstress=.true., ? ? dt=10.0, ? ? nstep=100000 ?/ ?&system ? ?nosym=.t., ibrav = 0, celldm(1) =9.3,nat= ?16, nbnd=300,ntyp= 1, ecutwfc=40,ecutrho=400,occupations='smearing', smearing='mp', degauss=0.02 ?/ ?&electrons mixing_mode='TF' mixing_beta= 0.7 ?/ ?&ions ? ? ion_dynamics='beeman' ? ? ion_temperature='rescaling' ?! ?method of temperature control ? ? tempw=600, ? ? ? ? ! ?target temperature ? ? tolp=30 ? ? ? ? ? ?! ?tolerance for the temperature / ?&cell ? ? cell_dynamics='pr' ? ? press=2000, ?/ ATOMIC_SPECIES Fe ? ?55.847 ?Fe.pbe-sp-van.UPF CELL_PARAMETERS {cubic} 1.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 1.00 ATOMIC_POSITIONS {crystal} Fe ? ? ?0 ? ? ? 0 ? ? ? 0 Fe ? ? ?0.25 ? ?0.25 ? ?0.25 Fe ? ? ?0.5 ? ? 0 ? ? ? 0 Fe ? ? ?0.75 ? ?0.25 ? ?0.25 Fe ? ? ?0 ? ? ? 0.5 ? ? 0 Fe ? ? ?0.25 ? ?0.75 ? ?0.25 Fe ? ? ?0.5 ? ? 0.5 ? ? 0 Fe ? ? ?0.75 ? ?0.75 ? ?0.25 Fe ? ? ?0 ? ? ? 0 ? ? ? 0.5 Fe ? ? ?0.25 ? ?0.25 ? ?0.75 Fe ? ? ?0.5 ? ? 0 ? ? ? 0.5 Fe ? ? ?0.75 ? ?0.25 ? ?0.75 Fe ? ? ?0 ? ? ? 0.5 ? ? 0.5 Fe ? ? ?0.25 ? ?0.75 ? ?0.75 Fe ? ? ?0.5 ? ? 0.5 ? ? 0.5 Fe ? ? ?0.75 ? ?0.75 ? ?0.75 K_POINTS { automatic } 4 4 4 0 0 0 Here is the temperature values during the MD ? ? ?Ekin = ? ? 0.08550401 Ry ? ?T = ? ?0.0 K ?Etot = -3974.76493424 ? ? ?Ekin = ? ? 0.08545553 Ry ? ?T = ?529.1 K ?Etot = -3974.76491196 ? ? ?Ekin = ? ? 0.08523972 Ry ? ?T = ?528.4 K ?Etot = -3974.76491592 ? ? ?Ekin = ? ? 0.08488325 Ry ? ?T = ?527.5 K ?Etot = -3974.76492105 ? ? ?Ekin = ? ? 0.08438872 Ry ? ?T = ?526.2 K ?Etot = -3974.76492687 ? ? ?Ekin = ? ? 0.08375063 Ry ? ?T = ?524.7 K ?Etot = -3974.76494262 ? ? ?Ekin = ? ? 0.08298072 Ry ? ?T = ?522.9 K ?Etot = -3974.76496009 ? ? ?Ekin = ? ? 0.08208596 Ry ? ?T = ?520.8 K ?Etot = -3974.76497988 ? ? ?Ekin = ? ? 0.08108295 Ry ? ?T = ?518.4 K ?Etot = -3974.76499060 ? ? ?Ekin = ? ? 0.07996422 Ry ? ?T = ?515.9 K ?Etot = -3974.76500658 ? ? ?Ekin = ? ? 0.07874892 Ry ? ?T = ?513.0 K ?Etot = -3974.76501879 ? ? ?Ekin = ? ? 0.07744342 Ry ? ?T = ?510.0 K ?Etot = -3974.76502953 ? ? ?Ekin = ? ? 0.07604792 Ry ? ?T = ?506.7 K ?Etot = -3974.76504879 ? ? ?Ekin = ? ? 0.07458876 Ry ? ?T = ?503.3 K ?Etot = -3974.76506076 ? ? ?Ekin = ? ? 0.07307428 Ry ? ?T = ?499.6 K ?Etot = -3974.76507026 ? ? ?Ekin = ? ? 0.07151519 Ry ? ?T = ?495.8 K ?Etot = -3974.76507785 ? ? ?Ekin = ? ? 0.06992683 Ry ? ?T = ?491.9 K ?Etot = -3974.76508190 ? ? ?Ekin = ? ? 0.06831764 Ry ? ?T = ?487.9 K ?Etot = -3974.76508757 ? ? ?Ekin = ? ? 0.06669444 Ry ? ?T = ?483.7 K ?Etot = -3974.76510303 ? ? ?Ekin = ? ? 0.06507583 Ry ? ?T = ?479.5 K ?Etot = -3974.76512546 ? ? ?Ekin = ? ? 0.06348366 Ry ? ?T = ?475.1 K ?Etot = -3974.76514805 ? ? ?Ekin = ? ? 0.06193603 Ry ? ?T = ?470.8 K ?Etot = -3974.76516928 ? ? ?Ekin = ? ? 0.06044488 Ry ? ?T = ?466.4 K ?Etot = -3974.76519330 ? ? ?Ekin = ? ? 0.05903489 Ry ? ?T = ?462.0 K ?Etot = -3974.76521261 ? ? ?Ekin = ? ? 0.05771662 Ry ? ?T = ?457.6 K ?Etot = -3974.76523302 ? ? ?Ekin = ? ? 0.05651069 Ry ? ?T = ?453.3 K ?Etot = -3974.76525200 ? ? ?Ekin = ? ? 0.05543666 Ry ? ?T = ?449.1 K ?Etot = -3974.76526613 ? ? ?Ekin = ? ? 0.05451365 Ry ? ?T = ?445.0 K ?Etot = -3974.76527508 ? ? ?Ekin = ? ? 0.05374637 Ry ? ?T = ?441.0 K ?Etot = -3974.76528988 ? ? ?Ekin = ? ? 0.05315721 Ry ? ?T = ?437.1 K ?Etot = -3974.76530747 ? ? ?Ekin = ? ? 0.05277633 Ry ? ?T = ?433.4 K ?Etot = -3974.76531355 ? ? ?Ekin = ? ? 0.05261350 Ry ? ?T = ?429.9 K ?Etot = -3974.76531535 ? ? ?Ekin = ? ? 0.05268058 Ry ? ?T = ?426.7 K ?Etot = -3974.76531828 ? ? ?Ekin = ? ? 0.05299435 Ry ? ?T = ?423.7 K ?Etot = -3974.76532130 ? ? ?Ekin = ? ? 0.05356950 Ry ? ?T = ?421.0 K ?Etot = -3974.76532740 ? ? ?Ekin = ? ? 0.05441763 Ry ? ?T = ?418.6 K ?Etot = -3974.76534001 ? ? ?Ekin = ? ? 0.05556545 Ry ? ?T = ?416.5 K ?Etot = -3974.76534845 ? ? ?Ekin = ? ? 0.05702061 Ry ? ?T = ?414.8 K ?Etot = -3974.76535951 ? ? ?Ekin = ? ? 0.05880261 Ry ? ?T = ?413.5 K ?Etot = -3974.76536810 ? ? ?Ekin = ? ? 0.06092253 Ry ? ?T = ?412.6 K ?Etot = -3974.76537615 ? ? ?Ekin = ? ? 0.06339679 Ry ? ?T = ?412.1 K ?Etot = -3974.76538052 ? ? ?Ekin = ? ? 0.06622640 Ry ? ?T = ?412.0 K ?Etot = -3974.76539202 ? ? ?Ekin = ? ? 0.06943072 Ry ? ?T = ?412.4 K ?Etot = -3974.76540230 ? ? ?Ekin = ? ? 0.07301810 Ry ? ?T = ?413.4 K ?Etot = -3974.76541371 ? ? ?Ekin = ? ? 0.07700134 Ry ? ?T = ?414.8 K ?Etot = -3974.76542210 ? ? ?Ekin = ? ? 0.08139225 Ry ? ?T = ?416.8 K ?Etot = -3974.76542358 ? ? ?Ekin = ? ? 0.08618992 Ry ? ?T = ?419.3 K ?Etot = -3974.76542521 ? ? ?Ekin = ? ? 0.09139929 Ry ? ?T = ?422.4 K ?Etot = -3974.76542710 ? ? ?Ekin = ? ? 0.09702375 Ry ? ?T = ?426.2 K ?Etot = -3974.76542895 ? ? ?Ekin = ? ? 0.10306465 Ry ? ?T = ?430.5 K ?Etot = -3974.76543106 ? ? ?Ekin = ? ? 0.10952168 Ry ? ?T = ?435.4 K ?Etot = -3974.76543338 ? ? ?Ekin = ? ? 0.11639279 Ry ? ?T = ?441.0 K ?Etot = -3974.76543565 ? ? ?Ekin = ? ? 0.12367355 Ry ? ?T = ?447.3 K ?Etot = -3974.76543806 ? ? ?Ekin = ? ? 0.13135747 Ry ? ?T = ?454.2 K ?Etot = -3974.76544066 ? ? ?Ekin = ? ? 0.13943498 Ry ? ?T = ?461.8 K ?Etot = -3974.76544481 ? ? ?Ekin = ? ? 0.14789548 Ry ? ?T = ?470.0 K ?Etot = -3974.76545002 ? ? ?Ekin = ? ? 0.15672727 Ry ? ?T = ?478.9 K ?Etot = -3974.76545493 ? ? ?Ekin = ? ? 0.16591506 Ry ? ?T = ?488.6 K ?Etot = -3974.76545971 ? ? ?Ekin = ? ? 0.17544087 Ry ? ?T = ?498.9 K ?Etot = -3974.76546486 ? ? ?Ekin = ? ? 0.18528602 Ry ? ?T = ?509.9 K ?Etot = -3974.76546866 ? ? ?Ekin = ? ? 0.19542620 Ry ? ?T = ?521.5 K ?Etot = -3974.76547325 ? ? ?Ekin = ? ? 0.20583571 Ry ? ?T = ?533.9 K ?Etot = -3974.76547954 ? ? ?Ekin = ? ? 0.21647613 Ry ? ?T = ?546.9 K ?Etot = -3974.76549741 ? ? ?Ekin = ? ? 0.22730110 Ry ? ?T = ?560.5 K ?Etot = -3974.76554452 ? ? ?Ekin = ? ? 0.23831627 Ry ? ?T = ?574.8 K ?Etot = -3974.76558181 ? ? ?Ekin = ? ? 0.24947252 Ry ? ?T = ?589.8 K ?Etot = -3974.76562279 ? ? ?Ekin = ? ? 0.26074557 Ry ? ?T = ?605.3 K ?Etot = -3974.76565485 ? ? ?Ekin = ? ? 0.27207612 Ry ? ?T = ?621.4 K ?Etot = -3974.76569597 ? ? ?Ekin = ? ? 0.28344542 Ry ? ?T = ?638.1 K ?Etot = -3974.76572250 ? ? ?Ekin = ? ? 0.29479651 Ry ? ?T = ?655.3 K ?Etot = -3974.76574618 ? ? ?Ekin = ? ? 0.30606129 Ry ? ?T = ?673.0 K ?Etot = -3974.76579053 ? ? ?Ekin = ? ? 0.31721730 Ry ? ?T = ?691.2 K ?Etot = -3974.76582817 ? ? ?Ekin = ? ? 0.32824936 Ry ? ?T = ?709.8 K ?Etot = -3974.76582822 ? ? ?Ekin = ? ? 0.33906198 Ry ? ?T = ?728.8 K ?Etot = -3974.76583611 ? ? ?Ekin = ? ? 0.34961260 Ry ? ?T = ?748.2 K ?Etot = -3974.76584414 ? ? ?Ekin = ? ? 0.35984903 Ry ? ?T = ?768.0 K ?Etot = -3974.76585498 ? ? ?Ekin = ? ? 0.36972011 Ry ? ?T = ?788.0 K ?Etot = -3974.76587088 ? ? ?Ekin = ? ? 0.37917783 Ry ? ?T = ?808.2 K ?Etot = -3974.76589051 ? ? ?Ekin = ? ? 0.38818195 Ry ? ?T = ?828.7 K ?Etot = -3974.76590575 ? ? ?Ekin = ? ? 0.39668256 Ry ? ?T = ?849.3 K ?Etot = -3974.76591947 ? ? ?Ekin = ? ? 0.40463122 Ry ? ?T = ?870.0 K ?Etot = -3974.76593441 ? ? ?Ekin = ? ? 0.41198588 Ry ? ?T = ?890.7 K ?Etot = -3974.76594819 ? ? ?Ekin = ? ? 0.41870194 Ry ? ?T = ?911.5 K ?Etot = -3974.76596318 ? ? ?Ekin = ? ? 0.42474052 Ry ? ?T = ?932.2 K ?Etot = -3974.76597798 ? ? ?Ekin = ? ? 0.43006276 Ry ? ?T = ?952.8 K ?Etot = -3974.76599394 ? ? ?Ekin = ? ? 0.43463419 Ry ? ?T = ?973.2 K ?Etot = -3974.76601082 ? ? ?Ekin = ? ? 0.43842410 Ry ? ?T = ?993.5 K ?Etot = -3974.76602797 ? ? ?Ekin = ? ? 0.44140452 Ry ? ?T = 1013.5 K ?Etot = -3974.76604568 ? ? ?Ekin = ? ? 0.44355191 Ry ? ?T = 1033.2 K ?Etot = -3974.76606390 ? ? ?Ekin = ? ? 0.44484735 Ry ? ?T = 1052.5 K ?Etot = -3974.76608252 ? ? ?Ekin = ? ? 0.44527696 Ry ? ?T = 1071.5 K ?Etot = -3974.76610132 ? ? ?Ekin = ? ? 0.44483203 Ry ? ?T = 1089.9 K ?Etot = -3974.76612027 ? ? ?Ekin = ? ? 0.44350967 Ry ? ?T = 1108.0 K ?Etot = -3974.76613930 ? ? ?Ekin = ? ? 0.44131301 Ry ? ?T = 1125.4 K ?Etot = -3974.76615836 ? ? ?Ekin = ? ? 0.43825157 Ry ? ?T = 1142.3 K ?Etot = -3974.76617740 ? ? ?Ekin = ? ? 0.43434138 Ry ? ?T = 1158.6 K ?Etot = -3974.76619636 ? ? ?Ekin = ? ? 0.42960510 Ry ? ?T = 1174.2 K ?Etot = -3974.76621514 ? ? ?Ekin = ? ? 0.42407189 Ry ? ?T = 1189.2 K ?Etot = -3974.76623361 ? ? ?Ekin = ? ? 0.41777725 Ry ? ?T = 1203.5 K ?Etot = -3974.76625163 ? ? ?Ekin = ? ? 0.41076253 Ry ? ?T = 1217.0 K ?Etot = -3974.76626910 ? ? ?Ekin = ? ? 0.19721000 Ry ? ?T = 1221.1 K ?Etot = -3974.97458774 ? ? ?Ekin = ? ? 0.19183941 Ry ? ?T = 1204.4 K ?Etot = -3974.97459002 ? ? ?Ekin = ? ? 0.18636543 Ry ? ?T = 1187.6 K ?Etot = -3974.97459773 ? ? ?Ekin = ? ? 0.18083022 Ry ? ?T = 1170.6 K ?Etot = -3974.97460510 ? ? ?Ekin = ? ? 0.17526808 Ry ? ?T = 1153.5 K ?Etot = -3974.97461296 ? ? ?Ekin = ? ? 0.16971356 Ry ? ?T = 1136.4 K ?Etot = -3974.97462467 ? ? ?Ekin = ? ? 0.16420699 Ry ? ?T = 1119.3 K ?Etot = -3974.97463108 ? ? ?Ekin = ? ? 0.15877522 Ry ? ?T = 1102.3 K ?Etot = -3974.97464047 ? ? ?Ekin = ? ? 0.15345494 Ry ? ?T = 1085.4 K ?Etot = -3974.97464581 ? ? ?Ekin = ? ? 0.14826952 Ry ? ?T = 1068.6 K ?Etot = -3974.97465340 ? ? ?Ekin = ? ? 0.14324982 Ry ? ?T = 1052.1 K ?Etot = -3974.97466117 ? ? ?Ekin = ? ? 0.13842282 Ry ? ?T = 1035.9 K ?Etot = -3974.97466503 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111205/54e6de6a/attachment-0001.htm From elie.moujaes at hotmail.co.uk Mon Dec 5 14:55:38 2011 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Mon, 5 Dec 2011 13:55:38 +0000 Subject: [Pw_forum] band structure for a 72 C atom supercell In-Reply-To: References: <20111204085131.3620.qmail@ms.hfcas.ac.cn>, Message-ID: Dear Professor Sclauzero, Thanks very much for this important piece of information, Elie From: gabriele.sclauzero at epfl.ch Date: Mon, 5 Dec 2011 08:56:34 +0100 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] band structure for a 72 C atom supercell Dear Elie and Huang, Il giorno 04/dic/2011, alle ore 09.51, lfhuang ha scritto:Dear Elie: This problem is just caused by the fact that the bands at each k point are not sorted according to their symmetry. The bands from pw.x are sorted according to their energy eigenvalue, if you want them sorted "by symmetry" you need to use bands.x after the nscf run.Please have a look at Doc/INPUT_BANDS.txt, the input is very simple. You can choose between two different "sorting" algorithms, one built directly upon symmetry properties of the wavefunctions, and another which uses the overlaps between wavefunctions at neighboring k-points. It probably has been mentioned many times on this Forum. Indeed, it has. I don't known whether the symmetry sorting of electronic band dispersions have been realized in QE. It is implemented in PP/sym_band.f90 Regards, Gabriele If not, I may do this job when time permits. Hope this be of some use to you. Best Wishes! Yours Sincerely, L. F. Huang ------ ====================================================================== L.F.Huang ?????, Electronic Structure and Phonon Physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591440(office) Fax: 86-551-5591434 ====================================================================== _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111205/bc064034/attachment.htm From baroni at sissa.it Mon Dec 5 14:48:14 2011 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 5 Dec 2011 14:48:14 +0100 Subject: [Pw_forum] Atomic position for Li15Si4 In-Reply-To: <1322943005.96057.YahooMailNeo@web120016.mail.ne1.yahoo.com> References: <1322943005.96057.YahooMailNeo@web120016.mail.ne1.yahoo.com> Message-ID: A google search gave me the following papers as the first two hits: http://www.sciencedirect.com/science/article/pii/S0013468608009663 http://jap.aip.org/resource/1/japiau/v102/i5/p053704_s1 They both contain a table with the crystal structure you are looking after. I am afraid I do not have the right to post here the pdf files, but you may want to ask the authors to send you an "electronic reprint". Stefano B On Dec 3, 2011, at 9:10 PM, Omileke Peter wrote: > Dear all, > Please, I have problem in knowing the atomic position of Li15Si4 (space group is l43d). > I will be very glad if someone could help me out.Thanks in advance for your suggestion. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111205/428fc9f1/attachment.htm From Michael.Mehl at nrl.navy.mil Mon Dec 5 15:36:19 2011 From: Michael.Mehl at nrl.navy.mil (Mike Mehl) Date: Mon, 05 Dec 2011 09:36:19 -0500 Subject: [Pw_forum] vc-md temperature increases In-Reply-To: <1323076392.89294.YahooMailNeo@web77407.mail.sg1.yahoo.com> References: <1323076392.89294.YahooMailNeo@web77407.mail.sg1.yahoo.com> Message-ID: <4EDCD6E3.60904@nrl.navy.mil> Since BCC Fe is magnetic, I suspect you will get better results by adding nspin=2, to your &system block. On 12/05/2011 04:13 AM, Lily Anh wrote: > Hi all, > > I am running a 'vc-md' calculation with PW.X in QE v4.1.1. The system is > bcc-Fe supercell of 16 atoms. The target temperature were set to 600 K > in the input file while the temperature goes up all the way to more than > 1000 K. I tried with a much larger supercell (128 atoms), this problem > still happens. > > Does anyone know how to fix this? > > Many thanks! > Lily > > > > I attached my input file here: > > &system > nosym=.t., ibrav = 0, celldm(1) =9.3,nat= 16, nbnd=300,ntyp= 1, > ecutwfc=40,ecutrho=400,occupations='smearing', smearing='mp', degauss=0.02 > / > &electrons > mixing_mode='TF' > mixing_beta= 0.7 > / -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC From cyrille.barreteau at cea.fr Mon Dec 5 15:47:02 2011 From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille) Date: Mon, 5 Dec 2011 14:47:02 +0000 Subject: [Pw_forum] RE : vc-md temperature increases In-Reply-To: <4EDCD6E3.60904@nrl.navy.mil> References: <1323076392.89294.YahooMailNeo@web77407.mail.sg1.yahoo.com>, <4EDCD6E3.60904@nrl.navy.mil> Message-ID: <6E80B49CBC3D9F4694B510228B88EE3C016B7B@E-EXDAGE-A1.extra.cea.fr> Dear Lily, Indeed the non magnetic ground state of iron is fcc therefore if you start from bcc your system is very unhappy. As suggested by Mike you should set nspin=2. However do not forget that by doing vc-md you will move atoms according to a given "molecular" temperature but you will totally ignore the spin temperature which is another complicated story:-) Any hint to do a spin+molecular dynamic from ab-initio would be very welcome:-) Some attempts to do it from empirical models have been proposed but this remains rather tricky. good luck.. cyrille ============================================================ Cyrille Barreteau phone : +33 (0)1 69 08 29 51 CEA Saclay cellphone: +33 (0)6 47 53 66 52 IRAMIS, SPCSI, Bat. 462 fax : +33 (0)1 69 08 84 46 91191 Gif sur Yvette Cedex email: cyrille.barreteau at cea.fr FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ ============================================================== ________________________________________ De : pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] de la part de Mike Mehl [Michael.Mehl at nrl.navy.mil] Date d'envoi : lundi 5 d?cembre 2011 15:36 ? : Lily Anh; PWSCF Forum Objet : Re: [Pw_forum] vc-md temperature increases Since BCC Fe is magnetic, I suspect you will get better results by adding nspin=2, to your &system block. On 12/05/2011 04:13 AM, Lily Anh wrote: > Hi all, > > I am running a 'vc-md' calculation with PW.X in QE v4.1.1. The system is > bcc-Fe supercell of 16 atoms. The target temperature were set to 600 K > in the input file while the temperature goes up all the way to more than > 1000 K. I tried with a much larger supercell (128 atoms), this problem > still happens. > > Does anyone know how to fix this? > > Many thanks! > Lily > > > > I attached my input file here: > > &system > nosym=.t., ibrav = 0, celldm(1) =9.3,nat= 16, nbnd=300,ntyp= 1, > ecutwfc=40,ecutrho=400,occupations='smearing', smearing='mp', degauss=0.02 > / > &electrons > mixing_mode='TF' > mixing_beta= 0.7 > / -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Mon Dec 5 16:10:35 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 05 Dec 2011 16:10:35 +0100 Subject: [Pw_forum] vc-md temperature increases In-Reply-To: <1323076392.89294.YahooMailNeo@web77407.mail.sg1.yahoo.com> References: <1323076392.89294.YahooMailNeo@web77407.mail.sg1.yahoo.com> Message-ID: <1323097835.6749.51.camel@fe12lx.fisica.uniud.it> On Mon, 2011-12-05 at 17:13 +0800, Lily Anh wrote: > > I am running a 'vc-md' calculation with PW.X in QE v4.1.1. The system > is bcc-Fe supercell of 16 atoms. The target temperature were set to > 600 K in the input file while the temperature goes up all the way to > more than 1000 K. velocity rescaling is present in the variable-cell MD algorithm but it is not actually activated. You will need to initialize variables "ntimes" and "ntcheck", used by subroutine "vcmove" in PW/vcsubs.f90, to the number of thermalization steps to be performed and to the number of steps between thermalizations; or to use the development version (just fixed, maybe) P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From lily_physics at yahoo.com.sg Tue Dec 6 02:49:20 2011 From: lily_physics at yahoo.com.sg (Lily Anh) Date: Tue, 6 Dec 2011 09:49:20 +0800 (SGT) Subject: [Pw_forum] vc-md temperature increases In-Reply-To: <1323097835.6749.51.camel@fe12lx.fisica.uniud.it> References: <1323076392.89294.YahooMailNeo@web77407.mail.sg1.yahoo.com> <1323097835.6749.51.camel@fe12lx.fisica.uniud.it> Message-ID: <1323136160.74985.YahooMailNeo@web77407.mail.sg1.yahoo.com> Hi Paolo, Thanks for the reply. I added the following lines in the &ions section: ? ? ntcheck=100, ? ? ? ! ?temperature is checked every ntcheck timesteps ? ? ntimes=10 ? ? ? ? ?! ?maximum number of velocity rescaling and the calculation crashes "? ? from ?read_namelists ?: error # ? ? ? ?88 ? ? ? reading namelist ions" How to fix this? Lily ________________________________ From: Paolo Giannozzi To: Lily Anh ; PWSCF Forum Sent: Monday, 5 December 2011, 23:10 Subject: Re: [Pw_forum] vc-md temperature increases On Mon, 2011-12-05 at 17:13 +0800, Lily Anh wrote: > > I am running a 'vc-md' calculation with PW.X in QE v4.1.1. The system > is bcc-Fe supercell of 16 atoms. The target temperature were set to > 600 K in the input file while the temperature goes up all the way to > more than 1000 K. velocity rescaling is present in the variable-cell MD algorithm but it is not actually activated. You will need to initialize variables "ntimes" and "ntcheck", used by subroutine "vcmove" in PW/vcsubs.f90, to the number of thermalization steps to be performed and to the number of steps between thermalizations; or to use the development version (just fixed, maybe) P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111206/8903e422/attachment.htm From giannozz at democritos.it Tue Dec 6 08:26:00 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 6 Dec 2011 08:26:00 +0100 Subject: [Pw_forum] vc-md temperature increases In-Reply-To: <1323136160.74985.YahooMailNeo@web77407.mail.sg1.yahoo.com> References: <1323076392.89294.YahooMailNeo@web77407.mail.sg1.yahoo.com> <1323097835.6749.51.camel@fe12lx.fisica.uniud.it> <1323136160.74985.YahooMailNeo@web77407.mail.sg1.yahoo.com> Message-ID: On Dec 6, 2011, at 2:49 , Lily Anh wrote: > I added the following lines in the &ions section: > > ntcheck=100, ! temperature is checked every ntcheck > timesteps > ntimes=10 ! maximum number of velocity rescaling > > and the calculation crashes " from read_namelists : error > # 88 you need to modify the code, not input data P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From lily_physics at yahoo.com.sg Tue Dec 6 09:24:15 2011 From: lily_physics at yahoo.com.sg (Lily Anh) Date: Tue, 6 Dec 2011 16:24:15 +0800 (SGT) Subject: [Pw_forum] study the phase transition with vc-md or vc-cp Message-ID: <1323159855.86279.YahooMailNeo@web77404.mail.sg1.yahoo.com> Hi all, Is it possible to observe the??spontaneous?phase transitions by the vc-md (PW.X) or vc-cp (CP.X) simulations staring from the initial structure input? If possible, what should we do? Any discussion is ?helpful? Regards & Thank you Lily -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111206/3f5d3fb0/attachment.htm From landaulev at 163.com Tue Dec 6 10:17:06 2011 From: landaulev at 163.com (jinxi) Date: Tue, 6 Dec 2011 17:17:06 +0800 (CST) Subject: [Pw_forum] local DOS: how to set nrmin and nrmax Message-ID: <50b1c044.1b1c9.13412a9832f.Coremail.landaulev@163.com> Dear all: I try to get local DOS using projwfc.x, but i can't understand the description in "INPUT_projwfc": how to set parameters irmin and irmax? I've read the input files in example16, but i still don't know how to locate the local DOS by irmin and irmax. Are there general methods to calculate the number and position of grid points? If there are some general references (books, articles, presentations) for the basic knowledge, please recommend to me. Many thanks! best wishes jinxi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111206/e4eb2517/attachment.htm From sh.shapt at gmail.com Tue Dec 6 10:55:34 2011 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Tue, 6 Dec 2011 09:55:34 +0000 Subject: [Pw_forum] Query about O.pbe-rrkjus.UPF Pseudopotential Message-ID: Hi, is O.pbe-rrkjus.UPFa norm conserving pseudopotential or ultrasoft pseudopotential ? Best Shapt IIT Mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111206/7b885b06/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Tue Dec 6 10:58:07 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 06 Dec 2011 10:58:07 +0100 Subject: [Pw_forum] Query about O.pbe-rrkjus.UPF Pseudopotential In-Reply-To: References: Message-ID: In data 06 December 2011 alle ore 10:55:34, Shaptrishi Sharma ha scritto: > O.pbe-rrkjus.UPFa > norm conserving pseudopotential or ultrasoft pseudopotential ? Dear Shaptrishi, it is ultrasoft. Hint: if you open it with a tex teditor you'll find this line: US Ultrasoft pseudopotential best regards -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From giannozz at democritos.it Tue Dec 6 11:02:23 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 6 Dec 2011 11:02:23 +0100 Subject: [Pw_forum] Query about O.pbe-rrkjus.UPF Pseudopotential In-Reply-To: References: Message-ID: <10DE08F4-B675-4DA2-BA4E-95DF05A7B2DB@democritos.it> On Dec 6, 2011, at 10:58 , Lorenzo Paulatto wrote: > Hint: if you open it with a tex teditor you'll find this line: > US Ultrasoft pseudopotential further hint: in the pseudopotential page, there is a link to a page describing the naming convention used for UPF files: http://www.quantum-espresso.org/wiki/index.php/ Naming_convention_for_the_pseudopotential P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From degliesposti at bo.imm.cnr.it Tue Dec 6 18:38:23 2011 From: degliesposti at bo.imm.cnr.it (Cristian Degli Esposti Boschi) Date: Tue, 06 Dec 2011 18:38:23 +0100 Subject: [Pw_forum] Display of forces in a pure scf run Message-ID: <4EDE530F.1030704@bo.imm.cnr.it> Dear developers, I have a very basic question, that I had never realized so far and has been asked by a students of mine... If I set to .TRUE. the logical fields tstress and tprnfor in the &CONTROL stanza of the pw.x input during a pure scf calculation, how are the forces on the ions calculated? What do the displayed values represent if only a scf calculation is performed and the ionic coordinates are not allowed to change? Thanks for your time. -- Cristian Degli Esposti Boschi CNR-IMM, Sezione di Bologna, via Gobetti, 101, 40129, Bologna, Italia tel. ++39 051 6399152, fax ++39 051 6399216 degliesposti -AT- bo.imm.cnr.it From baroni at sissa.it Tue Dec 6 19:54:13 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 6 Dec 2011 19:54:13 +0100 Subject: [Pw_forum] Display of forces in a pure scf run In-Reply-To: <4EDE530F.1030704@bo.imm.cnr.it> References: <4EDE530F.1030704@bo.imm.cnr.it> Message-ID: <17E821D9-E096-4274-905E-B818F0B0D2C6@sissa.it> Cristian, I may have misunderstood your question, and I confess to know very little of the tstress and tprnfor variables, but forces in pw.x (as well as in most other ab-iition codes) are calculated via the Hellmann-Feynman (HF) theorem. The HF theorem does not require any finite displacements to calculate forces, which are instead used to "move" the ions (either to optimized the geometry or to perform ab-initio molecular dynamics). If the question was not as simple as the answer actually implies, others may want ti add a less trivial answer ... Regards, Stefano On Dec 6, 2011, at 6:38 PM, Cristian Degli Esposti Boschi wrote: > Dear developers, > > I have a very basic question, that I had never realized so far and has > been asked by a students of mine... > > If I set to .TRUE. the logical fields tstress and tprnfor in the > &CONTROL stanza of the pw.x input during a pure scf calculation, > how are the forces on the ions calculated? What do the displayed > values represent if only a scf calculation is performed and > the ionic coordinates are not allowed to change? > > Thanks for your time. > > -- > Cristian Degli Esposti Boschi > CNR-IMM, Sezione di Bologna, > via Gobetti, 101, 40129, Bologna, Italia > tel. ++39 051 6399152, fax ++39 051 6399216 > degliesposti -AT- bo.imm.cnr.it > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111206/7c5ecb28/attachment.htm From akohlmey at gmail.com Tue Dec 6 20:02:21 2011 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Tue, 6 Dec 2011 14:02:21 -0500 Subject: [Pw_forum] Display of forces in a pure scf run In-Reply-To: <4EDE530F.1030704@bo.imm.cnr.it> References: <4EDE530F.1030704@bo.imm.cnr.it> Message-ID: On Tue, Dec 6, 2011 at 12:38 PM, Cristian Degli Esposti Boschi < degliesposti at bo.imm.cnr.it> wrote: > Dear developers, > > I have a very basic question, that I had never realized so far and has > been asked by a students of mine... > > If I set to .TRUE. the logical fields tstress and tprnfor in the > &CONTROL stanza of the pw.x input during a pure scf calculation, > how are the forces on the ions calculated? What do the displayed > values represent if only a scf calculation is performed and > the ionic coordinates are not allowed to change? > since stefano already answered the first part, here an answer to the second part. the forces and stress reported represent the instantaneous forces and stress of the given conformation. no more, no less. they are uniquely defined by the atom positions and the electronic structure method (and its parameters) and that is it. no motion needs to be considered. ciao, axel. > > Thanks for your time. > > -- > Cristian Degli Esposti Boschi > CNR-IMM, Sezione di Bologna, > via Gobetti, 101, 40129, Bologna, Italia > tel. ++39 051 6399152, fax ++39 051 6399216 > degliesposti -AT- bo.imm.cnr.it > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111206/0bebe2b6/attachment.htm From prasenjit.jnc at gmail.com Wed Dec 7 05:16:53 2011 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Wed, 7 Dec 2011 09:46:53 +0530 Subject: [Pw_forum] neb calculation Message-ID: Dear all, I am using neb.x in QE-4.3.2 to do neb calculations. However, unlike the older versions, I do not see the PW.out (containing the outputs of the scf calculations for each image) file for each of the images in the directories containing the wavefunction files for the images of the path. Do I need to set some parameters in the input file ? My neb input file is: BEGIN BEGIN_PATH_INPUT &PATH ! restart_mode = 'restart' string_method = 'neb' nstep_path = 50 num_of_images=5 use_freezing=.true. opt_scheme='broyden' first_last_opt=.false. !CI_scheme='auto' !ds=0.7 k_max=0.6169 k_min=0.6169 / END_PATH_INPUT BEGIN_ENGINE_INPUT &control outdir='/gpfs/scratch/userexternal/pghosh00/Rhn-MgO/Rh3/neb-walk-1', pseudo_dir = '/gpfs/scratch/userexternal/pghosh00/pseudo', ! max_seconds = 18000, ! restart_mode='restart' nstep = 100 wf_collect=.true. prefix='Rh2_rot_neb_1' wf_collect=.true. / &system ibrav= 0, celldm(1) =5.68, nat= 131, ntyp= 3, ecutwfc =30.0, ecutrho=240, occupations='smearing', smearing='gaussian', degauss=0.002, starting_magnetization(3)=0.5, nspin=2, / &electrons mixing_mode = 'local-TF' mixing_beta = 0.2 conv_thr = 1.0d-7 electron_maxstep=150 ! startingpot='file' ! startingwfc='file' / &ions / ATOMIC_SPECIES Mg 24.305 Mg.pbe-n-rrkjus.UPF O 15.999 O.pbe-rrkjus.UPF Rh 102.90550 Rh.pbe-nd-rrkjus.UPF BEGIN_POSITIONS FIRST_IMAGE ATOMIC_POSITIONS crystal Mg 0.000000000 0.000000000 0.000000000 0 0 0 Mg 0.000000000 0.250000000 0.000000000 0 0 0 Mg 0.000000000 0.500000000 0.000000000 0 0 0 Mg 0.000000000 0.750000000 0.000000000 0 0 0 Mg 0.250000000 0.000000000 0.000000000 0 0 0 ...... LAST_IMAGE ATOMIC_POSITIONS crystal Mg 0.000000000 0.000000000 0.000000000 0 0 0 Mg 0.000000000 0.250000000 0.000000000 0 0 0 Mg 0.000000000 0.500000000 0.000000000 0 0 0 Mg 0.000000000 0.750000000 0.000000000 0 0 0 Mg 0.250000000 0.000000000 0.000000000 0 0 0 Mg 0.250000000 0.250000000 0.000000000 0 0 0 Mg 0.250000000 0.500000000 0.000000000 0 0 0 Mg 0.250000000 0.750000000 0.000000000 0 0 0 Mg 0.500000000 0.000000000 0.000000000 0 0 0 ........... END_POSITIONS CELL_PARAMETERS {cubic} 4.0 0.0 0.0 0.0 4.0 0.0 0.0 0.0 7.77682129982394366197 K_POINTS {automatic} 2 2 1 1 1 1 END_ENGINE_INPUT END With regards, Prasenjit PRASENJIT GHOSH, Assistant Professor, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 From kalamaillist at gmail.com Wed Dec 7 09:28:26 2011 From: kalamaillist at gmail.com (WF) Date: Wed, 7 Dec 2011 16:28:26 +0800 Subject: [Pw_forum] A minor mistype in INPUT_PW doc? Message-ID: <000d01ccb4ba$3421d150$9c6573f0$@gmail.com> Dear QE developers, Today I find a word seems mistyped in Doc/INPUT_PW.html and INPUT_PW.txt in the k-points description part. Syntax: K_POINTS tpiba | crystal | tbiba_b | crystal_b Is the "tbiba_b" should be tpiba_b as used elsewhere? Thanks. -------------------------------------------------- Wu Feng Chemistry and Molecular Engineering, Peking University -------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111207/fd79a558/attachment.htm From landaulev at 163.com Wed Dec 7 09:20:20 2011 From: landaulev at 163.com (jinxi) Date: Wed, 7 Dec 2011 16:20:20 +0800 (CST) Subject: [Pw_forum] projwfc.x meet error Message-ID: <1489d92a.a0f6.134179be942.Coremail.landaulev@163.com> Dear all: When I calculate PDOS using projwfc.x, I meet error like this: Calling projwave .... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 10 error while reading from file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... But example08 and example16 are OK, I guess there's something wrong with my pseudopotential file. I attached the pp file (from the psilibrary), here's the first few lines: Generated using "atomic" code by A. Dal Corso (Quantum ESPRESSO distribution) Author: TM Generation date: 17Oct2011 Pseudopotential type: NC Element: Si Functional: PBE Suggested minimum cutoff for wavefunctions: 0. Ry Suggested minimum cutoff for charge density: 0. Ry The Pseudo was generated with a Scalar-Relativistic Calculation L component and cutoff radius for Local Potential: 2 1.8000 Valence configuration: nl pn l occ Rcut Rcut US E pseu 3S 1 0 2.00 1.800 1.800 -0.794728 3P 2 1 2.00 1.800 1.800 -0.299963 Generation configuration: 3S 1 0 2.00 1.800 1.800 -0.794724 3P 2 1 2.00 1.800 1.800 -0.299964 3D 3 2 0.00 1.800 1.800 0.100000 Pseudization used: troullier-martins functional="PBE" z_valence="4.000000000000000E+000" total_psenergy="-9.286635279439430E+000" wfc_cutoff="0.000000000000000E+000" rho_cutoff="0.000000000000000E+000" l_max="2" l_max_rho="4" l_local="2" mesh_size="1141" number_of_wfc="2" number_of_proj="2"/> 6.513442611103688E-005 6.595371633350159E-005 6.678331195832729E-005 6.762334261151813E-005 ................... how can i modify the file to pass reading wavefunctions? many thanks!! jinxi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111207/cf7f4705/attachment.htm From giannozz at democritos.it Wed Dec 7 09:46:40 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 7 Dec 2011 09:46:40 +0100 Subject: [Pw_forum] A minor mistype in INPUT_PW doc? In-Reply-To: <000d01ccb4ba$3421d150$9c6573f0$@gmail.com> References: <000d01ccb4ba$3421d150$9c6573f0$@gmail.com> Message-ID: <006DA806-C946-4F5B-86DC-71CC3B650CFA@democritos.it> On Dec 7, 2011, at 9:28 , WF wrote: > Is the ?tbiba_b? should be tpiba_b as used elsewhere? > yes. It is fixed in the next version. Thank you P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Dec 7 09:51:18 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 7 Dec 2011 09:51:18 +0100 Subject: [Pw_forum] projwfc.x meet error In-Reply-To: <1489d92a.a0f6.134179be942.Coremail.landaulev@163.com> References: <1489d92a.a0f6.134179be942.Coremail.landaulev@163.com> Message-ID: On Dec 7, 2011, at 9:20 , jinxi wrote: > I guess there's something wrong with my pseudopotential file. there is nothing wrong in your pseudopotential file P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From gabriele.sclauzero at epfl.ch Wed Dec 7 09:57:24 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Wed, 7 Dec 2011 09:57:24 +0100 Subject: [Pw_forum] projwfc.x meet error In-Reply-To: <1489d92a.a0f6.134179be942.Coremail.landaulev@163.com> References: <1489d92a.a0f6.134179be942.Coremail.landaulev@163.com> Message-ID: <38651F13-64A1-4643-932C-88E32BAB934E@epfl.ch> Dear Jinxi, please include your affiliation in your next posts. Il giorno 07/dic/2011, alle ore 09.20, jinxi ha scritto: > > Dear all: > When I calculate PDOS using projwfc.x, I meet error like this: > Calling projwave .... > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from davcio : error # 10 > error while reading from file > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > stopping ... This is pretty self explanatory: there has been an error while reading from file (in this case the wavefunctions, *.wfc* files), probably because the file(s) is (are) corrupted or because you ran the postprocessing on a different number of processors than for the previous pw.x calculation. > But example08 and example16 are OK, I guess there's something wrong with my pseudopotential file. I don't think you can blame your PP file. I think you should search for possible reasons giving this error in the user guide, the FAQ, and in the forum archives. > > how can i modify the file to pass reading wavefunctions? I don't understand completely what you meant here. The wavefunctions are needed by projwfc.x, you can't run this calculation if you don't have them. The wavefunctions are automatically written by pw.x at the end of the run. In some cases, you may need to use the wf_collect option (see input description in Doc/). HTH GS > many thanks!! > jinxi > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111207/4a6bc855/attachment.htm From baroni at sissa.it Wed Dec 7 10:07:30 2011 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 7 Dec 2011 10:07:30 +0100 Subject: [Pw_forum] study the phase transition with vc-md or vc-cp In-Reply-To: <1323159855.86279.YahooMailNeo@web77404.mail.sg1.yahoo.com> References: <1323159855.86279.YahooMailNeo@web77404.mail.sg1.yahoo.com> Message-ID: Dear Lily, the answer, as it often is, is "it depends". Different crystal structures are usually separated by an enthalpy barrier, whose crossing is a "rare event" if its height is sufficiently high. In order to observe the transition in an actual MD run, you have to either overheat or overload the system, or to bias the dynamics using one of the many available techniques, the most powerful and popular one probably being metadyamics. I am no expert in this field, but I think that the problem has been extensively treated in the literature. References that naturally occur to me are the original paper by Parrinello and Raman, or the more recent one by Parrinello and Laio on metadynamics (as well as others coauthored by R. Martonak, specifically on crystal-structure sampling), as well as the literature citing these articles. HTH - SB On Dec 6, 2011, at 9:24 AM, Lily Anh wrote: > Hi all, > > Is it possible to observe the spontaneous phase transitions by the vc-md (PW.X) or vc-cp (CP.X) simulations staring from the initial structure input? If possible, what should we do? > > Any discussion is helpful? > > Regards & Thank you > Lily > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111207/545b63b5/attachment.htm From landaulev at 163.com Wed Dec 7 10:29:27 2011 From: landaulev at 163.com (jinxi) Date: Wed, 7 Dec 2011 17:29:27 +0800 (CST) Subject: [Pw_forum] projwfc.x meet error In-Reply-To: <38651F13-64A1-4643-932C-88E32BAB934E@epfl.ch> References: <38651F13-64A1-4643-932C-88E32BAB934E@epfl.ch> <1489d92a.a0f6.134179be942.Coremail.landaulev@163.com> Message-ID: <5aa0d4a4.b932.13417db2ddf.Coremail.landaulev@163.com> Dear Sclauzero: Thanks for remind me. The error message: from davcio : error # 10 But how can i know what is ''error number 10?'' i 've set ''wf_collect = .true.'' many thanks!! ____________________________________________________________ jinxi State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry & Chemical Engineering, Xiamen University, Xiamen, 361005, P.R.China _________________________________________________ At 2011-12-07 16:57:24,"Gabriele Sclauzero" wrote: Dear Jinxi, please include your affiliation in your next posts. Il giorno 07/dic/2011, alle ore 09.20, jinxi ha scritto: Dear all: When I calculate PDOS using projwfc.x, I meet error like this: Calling projwave .... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 10 error while reading from file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... This is pretty self explanatory: there has been an error while reading from file (in this case the wavefunctions, *.wfc* files), probably because the file(s) is (are) corrupted or because you ran the postprocessing on a different number of processors than for the previous pw.x calculation. But example08 and example16 are OK, I guess there's something wrong with my pseudopotential file. I don't think you can blame your PP file. I think you should search for possible reasons giving this error in the user guide, the FAQ, and in the forum archives. how can i modify the file to pass reading wavefunctions? I don't understand completely what you meant here. The wavefunctions are needed by projwfc.x, you can't run this calculation if you don't have them. The wavefunctions are automatically written by pw.x at the end of the run. In some cases, you may need to use the wf_collect option (see input description in Doc/). HTH GS many thanks!! jinxi _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111207/6b334d6d/attachment-0001.htm From giannozz at democritos.it Wed Dec 7 10:42:50 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 7 Dec 2011 10:42:50 +0100 Subject: [Pw_forum] projwfc.x meet error In-Reply-To: <5aa0d4a4.b932.13417db2ddf.Coremail.landaulev@163.com> References: <38651F13-64A1-4643-932C-88E32BAB934E@epfl.ch> <1489d92a.a0f6.134179be942.Coremail.landaulev@163.com> <5aa0d4a4.b932.13417db2ddf.Coremail.landaulev@163.com> Message-ID: On Dec 7, 2011, at 10:29 , jinxi wrote: > But how can i know what is ''error number 10?'' by searching the documentation and the archives of the mailing list? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From henod2001 at yahoo.com Wed Dec 7 13:04:23 2011 From: henod2001 at yahoo.com (henry odhiambo) Date: Wed, 7 Dec 2011 04:04:23 -0800 (PST) Subject: [Pw_forum] Hexagonal lattice equivalent of fcc(rocksalt-like) phase change Ge2Sb2Te5 (GST) Message-ID: <1323259463.45540.YahooMailClassic@web121017.mail.ne1.yahoo.com> Hello everyone, ? The face-centered-cubic (fcc) structure of the phase-change material Ge2Sb2Te5 (GST) can be approximated by an equivalent hexagonal structure. May somebody assist me with or direct me to where I can find the atomic coordinates for?this equivalent hexagonal structure for GST. ? Regards, Henry Otunga. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111207/b2a7ad4e/attachment.htm From gabriele.sclauzero at epfl.ch Wed Dec 7 14:33:26 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Wed, 7 Dec 2011 14:33:26 +0100 Subject: [Pw_forum] projwfc.x meet error In-Reply-To: <5aa0d4a4.b932.13417db2ddf.Coremail.landaulev@163.com> References: <38651F13-64A1-4643-932C-88E32BAB934E@epfl.ch> <1489d92a.a0f6.134179be942.Coremail.landaulev@163.com> <5aa0d4a4.b932.13417db2ddf.Coremail.landaulev@163.com> Message-ID: <7D1F0F15-1E01-4BA2-94E9-F8EB626649B6@epfl.ch> Dear Jinxi, davcio is the subroutine dedicated to input/output of restart files. The error code is related to the value of some internal variable when the code crashed and sometimes it might be useful to identify better at which point it stopped, but you shouldn't attach any special meaning to that number. Just check that your files are not corrupted and that you do things properly. Regards, GS Il giorno 07/dic/2011, alle ore 10.29, jinxi ha scritto: > Dear Sclauzero: > Thanks for remind me. > The error message: > from davcio : error # 10 > But how can i know what is ''error number 10?'' > i 've set ''wf_collect = .true.'' > many thanks!! > ____________________________________________________________ > jinxi > State Key Laboratory of Physical Chemistry of Solid Surfaces, > Department of Chemistry, College of Chemistry & Chemical Engineering, > Xiamen University, Xiamen, 361005, P.R.China > _________________________________________________ > > At 2011-12-07 16:57:24,"Gabriele Sclauzero" wrote: > Dear Jinxi, > > please include your affiliation in your next posts. > > Il giorno 07/dic/2011, alle ore 09.20, jinxi ha scritto: > >> >> Dear all: >> When I calculate PDOS using projwfc.x, I meet error like this: >> Calling projwave .... >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from davcio : error # 10 >> error while reading from file >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> stopping ... > > > This is pretty self explanatory: there has been an error while reading from file (in this case the wavefunctions, *.wfc* files), probably because the file(s) is (are) corrupted or because you ran the postprocessing on a different number of processors than for the previous pw.x calculation. > >> But example08 and example16 are OK, I guess there's something wrong with my pseudopotential file. > > I don't think you can blame your PP file. I think you should search for possible reasons giving this error in the user guide, the FAQ, and in the forum archives. > >> >> how can i modify the file to pass reading wavefunctions? > > I don't understand completely what you meant here. The wavefunctions are needed by projwfc.x, you can't run this calculation if you don't have them. The wavefunctions are automatically written by pw.x at the end of the run. In some cases, you may need to use the wf_collect option (see input description in Doc/). > > > HTH > > > GS > >> many thanks!! >> jinxi >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111207/73f988d3/attachment.htm From degliesposti at bo.imm.cnr.it Wed Dec 7 16:23:53 2011 From: degliesposti at bo.imm.cnr.it (Cristian Degli Esposti Boschi) Date: Wed, 07 Dec 2011 16:23:53 +0100 Subject: [Pw_forum] Display of forces in a pure scf run In-Reply-To: References: Message-ID: <4EDF8509.4080606@bo.imm.cnr.it> Dear Stefano and Axel, thanks for your replies. Actually question can be rephrased as follows. Thanks to the Hellmann-Feynman theorem in order to compute the ionic forces I need only the partial derivatives of the total energy with respect to the ionic coordinates (see for instance 7.5 and 7.8 in Payne et al., RMP 64, p. 1045). If no real displacements of the atoms are needed to compute these derivatives, then I guess that they can be simply calculated as expectation values of the Hamiltonian on the current wavefunction because they can written down once a (parametrized) expression of the ionic potential is chosen. Am I right? Thanks for still devoting time to this... -- Cristian Degli Esposti Boschi CNR-IMM, Sezione di Bologna, via Gobetti, 101, 40129, Bologna, Italia tel. ++39 051 6399152, fax ++39 051 6399216 degliesposti -AT- bo.imm.cnr.it From alam_215 at yahoo.com Wed Dec 7 16:55:11 2011 From: alam_215 at yahoo.com (alamgir kabir) Date: Wed, 7 Dec 2011 07:55:11 -0800 (PST) Subject: [Pw_forum] projwfc.x meet error In-Reply-To: <7D1F0F15-1E01-4BA2-94E9-F8EB626649B6@epfl.ch> References: <38651F13-64A1-4643-932C-88E32BAB934E@epfl.ch> <1489d92a.a0f6.134179be942.Coremail.landaulev@163.com> <5aa0d4a4.b932.13417db2ddf.Coremail.landaulev@163.com> <7D1F0F15-1E01-4BA2-94E9-F8EB626649B6@epfl.ch> Message-ID: <1323273311.651.YahooMailNeo@web38808.mail.mud.yahoo.com> Dear Jinxi, I got the same problem few days back, and fortunately it is solved now. The thing is davcio is for reading from input and writing to the output, now if you scf calculation is done in different number of processor than your Projwfc.x than it get problem while reading from input. So please check if your pw.x calculation and projwfc.x caculation have same number of processor or not. Thank you. Alamgir Kabir PhD Student University of Central Florida U.S.A ________________________________ From: Gabriele Sclauzero To: PWSCF Forum Sent: Wednesday, December 7, 2011 8:33 AM Subject: Re: [Pw_forum] projwfc.x meet error Dear Jinxi, ? ? davcio is the subroutine dedicated to input/output of restart files. The error code is related to the value of some internal variable when the code crashed and sometimes it might be useful to identify better at which point it stopped, but you shouldn't attach any special meaning to that number. Just check that your files are not corrupted and that you do things properly. Regards, GS Il giorno 07/dic/2011, alle ore 10.29, jinxi ha scritto: Dear Sclauzero: >?? Thanks for remind me. >?? The error message: >???? from davcio : error #??????? 10 >???But how can i know what is ''error number 10?'' >???i?'ve set?''wf_collect = .true.''? >many thanks!! >____________________________________________________________ >jinxi >State Key Laboratory of Physical Chemistry of Solid Surfaces, >Department of Chemistry, College of Chemistry & Chemical Engineering, >Xiamen University, Xiamen, 361005,?P.R.China >_________________________________________________ > >At 2011-12-07 16:57:24,"Gabriele?Sclauzero"? wrote: > >Dear Jinxi, >> >> >>? ? please include your affiliation in your next posts.? >> >> >>Il giorno 07/dic/2011, alle ore 09.20, jinxi ha scritto: >> >>?Dear all: >>>When I calculate PDOS using projwfc.x, I meet error like this: >>>? Calling projwave .... >>>?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%???? >>>???? from davcio : error #??????? 10 >>>???? error while reading from file >>>?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%???? >>>???? stopping ... >>> >> >> >> >> >>This is pretty self explanatory: there has been an error while reading from file (in this case the wavefunctions, *.wfc* files), probably because the file(s) is (are) corrupted or because you ran the postprocessing on a different number of processors than for the previous pw.x calculation. >> >>But example08 and example16 are OK, I?guess there's something wrong with my pseudopotential file. >> >> >>I don't think you can blame your PP file. I think you should search for possible reasons giving this error in the user guide, the FAQ, and in the forum archives.? >> >>? >>>how can i modify the file to pass reading wavefunctions? >> >> >>I don't understand completely what you meant here. The wavefunctions are needed by projwfc.x, you can't run this calculation if you don't have them. The wavefunctions are automatically written by pw.x at the end of the run. In some cases, you may need to use the wf_collect option (see input description in Doc/). >> >> >> >> >>HTH >> >> >> >> >>GS >> >>many thanks!! >>>jinxi >>>? >>>? >>> >>>_______________________________________________ >>>Pw_forum mailing list >>>Pw_forum at pwscf.org >>>http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >>? Gabriele Sclauzero,?EPFL SB ITP CSEA >>?? PH H2 462, Station 3,?CH-1015 Lausanne >> >> >> >> >> >> >> > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > ? Gabriele Sclauzero,?EPFL SB ITP CSEA ?? PH H2 462, Station 3,?CH-1015 Lausanne _______________________________________________ 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/20111207/d81aee2b/attachment-0001.htm From baroni at sissa.it Wed Dec 7 21:37:28 2011 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 7 Dec 2011 21:37:28 +0100 Subject: [Pw_forum] Display of forces in a pure scf run In-Reply-To: <4EDF8509.4080606@bo.imm.cnr.it> References: <4EDF8509.4080606@bo.imm.cnr.it> Message-ID: On Dec 7, 2011, at 4:23 PM, Cristian Degli Esposti Boschi wrote: > Dear Stefano and Axel, thanks for your replies. Actually question can be > rephrased as follows. Thanks to the Hellmann-Feynman theorem > in order to compute the ionic forces I need only the partial > derivatives of the total energy with respect to the ionic coordinates this is not what you need, this is *the* definition of ionic force: $\mathbf{F}_I=\frac{\partial E}{\partial\mathbf{R}_I}$, with obvious notation and hopefully no LaTeX errors ... > (see for instance 7.5 and 7.8 in Payne et al., RMP 64, p. 1045). > If no real displacements of the atoms are needed to compute > these derivatives, then I guess that they can be simply calculated > as expectation values of the Hamiltonian on the current wavefunction NO: they can be computed as expectation values of the derivative of the external potential wrt ionic coordinates > because they can written down once a (parametrized) expression of the > ionic potential is chosen. Am I right? I am afraid you aren't, but I am not sure because I could not quite understand your last statement. There is nothing to choose in the parametric dependence of the external potential on the ionic coordinates. It depends the way it must [something like v(r-R), if the notation is clear enough ...], not the way we choose ... > > Thanks for still devoting time to this... you are most wlcome, as long as we can help ... S. --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111207/97b4623c/attachment.htm From permeakra at gmail.com Thu Dec 8 08:57:24 2011 From: permeakra at gmail.com (=?UTF-8?B?0J/QtdGA0LzRj9C60L7QsiDQldCy0LPQtdC90LjQuQ==?=) Date: Thu, 08 Dec 2011 11:57:24 +0400 Subject: [Pw_forum] newbie question: K-points, funtional choise and PP generation/use Message-ID: <4EE06DE4.1020702@gmail.com> Hi! I'd like to use quantum espresso in research of properties of MoS2 nanoparticles, modified with Co and Ni. This basically means calculations with 20 to 60 atoms of modified MoS2 slab and 10 to 30 atoms of interacting molecule, as well as 1- and 3-dimensional periodic calculations with same number of atoms. The atomic species of interest are: Mo, S, Co, Ni, H, C, N, O, K, Na, Li. Before performing real calculations I'd like to reproduce geometry of several basic with reasonable agreement with expreimental data. The problem is choise of PP/functional pair. For some time I was stick with b3lyp and pbe functionals of gaussian-03 package with full-electron non-periodic calculations, wich resulted in good agreement with experimental data. However, I cannot find PPs for this functionals for QE and full-electron approach is a little too much for my new systems. With quick research I was able to generate simple PP for H atom, but got 0.78 A H-H bond length instead of 0.74, and runned into incompatibility of ultrasoft PP and Gamma algorithm. So, I decided to stop and search for advise. The questions are: 1. Can someone point a good review about PP approximation (both math and use)? 2. As well as planewave approach for basis sets (It is completly new for me, I used only GTO basis sets before) ? 3. And possibly a good library of PP (espetially interested in desription of generation procedure) ? 4. What the hell are K-points, given in K_points sections and how should I choose them for ultrasoft PP ? 5. Are geometry and energy errors in QE/DFT systematic, i.e. can I use some corrections coefficient or I should work with them as random values? Of course, I'm going at least to try to find and read reference articles for QE, yet my math skills are not very hight. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111208/31689c2b/attachment.htm From joerg.buchwald at iom-leipzig.de Thu Dec 8 11:48:03 2011 From: joerg.buchwald at iom-leipzig.de (=?UTF-8?B?SsO2cmc=?= Buchwald) Date: Thu, 8 Dec 2011 11:48:03 +0100 Subject: [Pw_forum] Al pseudopotential and elastic properties Message-ID: <20111208114803.4dfeaa60@PC-Mayr-Mitarb6.pc-flexi> Hi, does anyone has any experiences with the Al pseudopotentials and the elastic constants? I was testing Al.pbe-n-van.UPF with which I could reproduce the elastic constant and the cohesive energy quite well, but using the output of the stress matrix I get a way too high results for C11(>150GPa) at a strain of 0.001. Appliying strains about >3%, I get results which are quite relastic for C11(90-110 GPa). I thought that this has something to do whith the kind of approximation, so I also created a ultrasoft (PZ-)LDA potential with the vanderbilt code and tried the normconserving Al.pz-vbc.UPF, which gave me similar results. I applied the strain by stretching the cell vectors and performing a 'relax'-simulation. This is my input file for a rel. strain of 0.003: --- &control calculation='relax' prefix='Al-test11', pseudo_dir='/home/jbuchw/espresso-4.3.2/pseudo' outdir = '/home/jbuchw/scratch', tstress=.true. disk_io='none' etot_conv_thr=1.0D-10 forc_conv_thr=1.0D-10 / &system ibrav= 0, celldm(1) =7.6271186 nat= 4, ntyp= 1, ecutwfc = 85.0 occupations='smearing' smearing='mp' degauss=0.0007 / &electrons diagonalization='david' mixing_mode='plain' conv_thr=1.0D-10 / &ions bfgs_ndim=3 / &cell ! cell_dofree='yz' / ATOMIC_SPECIES Al 26.981539 Al.pbe-n-van.UPF ATOMIC_POSITIONS crystal Al 0.00 0.00 0.00 Al 0.50 0.50 0.00 Al 0.00 0.50 0.50 Al 0.50 0.00 0.50 K_POINTS automatic 14 14 14 0 0 0 CELL_PARAMETERS 0.9995541042 0.000000000 0.000000000 0.000000000 0.996564411 0.000000000 0.000000000 0.000000000 0.996564411 -- Am I doing something wrong, or does it have something to do with the pseudopotential? Regards, J?rg PS: I also tried to get C11 by the second derivative the Energy fitting quadratic function which gave me C11=75.6GPa but this would assume that the elastic constant is constant over the strain range(which could be showed that's not the case for small strains(<0.01) using the numerical second derivative). -- Leibniz-Institut fuer Oberflaechenmodifizierung e.V. Permoserstrasse 15 04318 Leipzig GERMANY Phone: +49 341 / 235-3367 Web: http://www.uni-leipzig.de/~agmayr From nicola.marzari at epfl.ch Thu Dec 8 12:03:14 2011 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Thu, 08 Dec 2011 12:03:14 +0100 Subject: [Pw_forum] Al pseudopotential and elastic properties In-Reply-To: <20111208114803.4dfeaa60@PC-Mayr-Mitarb6.pc-flexi> References: <20111208114803.4dfeaa60@PC-Mayr-Mitarb6.pc-flexi> Message-ID: <4EE09972.9070500@epfl.ch> Dear Joerg, typically you have to use much higher cutoffs to converge the stress matrix, than what is needed to converge the relative shape of the potential energy surface. I.e. increasing the cutoff beyond your values would only lower the potental energy surface, but not really change its shape, while it would still change the stress matrix. Of course, it could also be bad luck brought by using mp smearing, rather than mv smearing. These codes can be quite sensitive. :-) nicola On 12/8/11 11:48 AM, J?rg Buchwald wrote: > Hi, > does anyone has any experiences with the Al pseudopotentials and the > elastic constants? > I was testing Al.pbe-n-van.UPF with which I could reproduce the elastic > constant and the cohesive energy quite well, but using the output of > the stress matrix I get a way too high results for C11(>150GPa) at a > strain of 0.001. Appliying strains about>3%, I get results which are > quite relastic for C11(90-110 GPa). I thought that this has something > to do whith the kind of approximation, so I also created a ultrasoft > (PZ-)LDA potential with the vanderbilt code and tried the > normconserving Al.pz-vbc.UPF, which gave me similar results. > I applied the strain by stretching the cell vectors and performing a > 'relax'-simulation. > This is my input file for a rel. strain of 0.003: > --- > &control > calculation='relax' > prefix='Al-test11', > pseudo_dir='/home/jbuchw/espresso-4.3.2/pseudo' > outdir = '/home/jbuchw/scratch', > tstress=.true. > disk_io='none' > etot_conv_thr=1.0D-10 > forc_conv_thr=1.0D-10 > / > &system > ibrav= 0, > celldm(1) =7.6271186 > nat= 4, > ntyp= 1, > ecutwfc = 85.0 > occupations='smearing' > smearing='mp' > degauss=0.0007 > / > &electrons > diagonalization='david' > mixing_mode='plain' > conv_thr=1.0D-10 > / > &ions > bfgs_ndim=3 > / > &cell > ! cell_dofree='yz' > / > ATOMIC_SPECIES > Al 26.981539 Al.pbe-n-van.UPF > ATOMIC_POSITIONS crystal > Al 0.00 0.00 0.00 > Al 0.50 0.50 0.00 > Al 0.00 0.50 0.50 > Al 0.50 0.00 0.50 > K_POINTS automatic > 14 14 14 0 0 0 > CELL_PARAMETERS > 0.9995541042 0.000000000 0.000000000 > 0.000000000 0.996564411 0.000000000 > 0.000000000 0.000000000 0.996564411 > -- > Am I doing something wrong, or does it have something to do with the > pseudopotential? > Regards, > J?rg > > > PS: I also tried to get C11 by the second derivative the Energy fitting > quadratic function which gave me C11=75.6GPa but this would assume that > the elastic constant is constant over the strain range(which could be > showed that's not the case for small strains(<0.01) using the > numerical second derivative). > > > -- ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL From akohlmey at gmail.com Thu Dec 8 14:02:23 2011 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Thu, 08 Dec 2011 08:02:23 -0500 Subject: [Pw_forum] newbie question: K-points, funtional choise and PP generation/use In-Reply-To: <4EE06DE4.1020702@gmail.com> References: <4EE06DE4.1020702@gmail.com> Message-ID: <1323349343.3490.137.camel@zero> On Thu, 2011-12-08 at 11:57 +0400, ???????? ??????? wrote: > Hi! I'd like to use quantum espresso in research of properties of MoS2 > nanoparticles, modified with Co and Ni. This basically means > calculations with 20 to 60 atoms of modified MoS2 slab and 10 to 30 > atoms of interacting molecule, as well as 1- and 3-dimensional > periodic calculations with same number of atoms. The atomic species of > interest are: Mo, S, Co, Ni, H, C, N, O, K, Na, Li. > > Before performing real calculations I'd like to reproduce geometry of > several basic with reasonable agreement with expreimental data. The > problem is choise of PP/functional pair. For some time I was stick > with b3lyp and pbe functionals of gaussian-03 package with > full-electron non-periodic calculations, wich resulted in good > agreement with experimental data. However, I cannot find PPs for this > functionals for QE and full-electron approach is a little too much for > my new systems. With quick research I was able to generate simple PP > for H atom, but got 0.78 A H-H bond length instead of 0.74, and > runned into incompatibility of ultrasoft PP and Gamma algorithm. So, > I decided to stop and search for advise. > > The questions are: > 1. Can someone point a good review about PP approximation (both > math and use)? try the introductory book by jorge kohanoff http://www.amazon.com/Electronic-Structure-Calculations-Solids-Molecules/dp/0521815916 > 1. As well as planewave approach for basis sets (It is completly > new for me, I used only GTO basis sets before) ? same recommendation as before. > 1. And possibly a good library of PP (espetially interested in > desription of generation procedure) ? Q-E has an extensive on-line library of pseudopotentials > 1. What the hell are K-points, given in K_points sections and how > should I choose them for ultrasoft PP ? some recommendation as for your first question. i highly recommend to not start any serious calculations before you understand what k-points are good for. it will save you a lot of time. > 1. Are geometry and energy errors in QE/DFT systematic, i.e. can > I use some corrections coefficient or I should work with them > as random values? DFT is as good (or bad) in QE as it is in other applications. however, with a plane wave basis set, you don't have to worry about basis set superposition errors anymore and the size of the basis set is effectively controlled by a single parameter (the plane wave cutoff). with ultra-soft pseudopotentials, you also need to worry about the density cutoff (for others anything beyond 4x the wavefunction cutoff is a waste of CPU time and memory), which depends on how much "softer" the potential has been made relative to the original norm-conserving potential that it was derived from. > Of course, I'm going at least to try to find and read reference > articles for QE, yet my math skills are not very hight. that would only be the second step. from your questions it is obvious, that you first need a general introduction to solid state physics and electronic structure calculations in that environment. the kohanoff book is a very good introduction for people with the kind of background that you seem to have and thus should serve you well to provide the background knowledge before you look into the details of the implementation and special methods. cheers, axel. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From chenhanghuipwscf at gmail.com Thu Dec 8 21:46:54 2011 From: chenhanghuipwscf at gmail.com (Hanghui Chen) Date: Thu, 8 Dec 2011 15:46:54 -0500 Subject: [Pw_forum] XSpectrum Message-ID: To QE developers, In the examples of X-ray Spectrum calculations, I noticed that for diamond, there are two different calculations. In one of them (the so-called Z approximation), 8 normal carbon atoms are employed. In the other one (Z+1 approximation), in addition to 7 normal carbon atoms, a special carbon atom is employed with a fixed hole in its valence (basically, it is N atom. Correct me if I am wrong.) What I am confused is that in the Z+1 approximation, the input file specifies the number of electron to be 8*4=32. Since the special carbon atom has valence 5 (instead of 4), the system is charged. However, my understanding of x-ray absorption is that an incoming photon excites an electron from 1s state into the conduction band. If that is the case, then why not run a charge neutral calculation, i.e. nele = 7*4+5=33, and the resulting system is metallic? Thank you. Hanghui Chen Department of Physics Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111208/ec30486d/attachment.htm From eariel99 at gmail.com Fri Dec 9 13:33:03 2011 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Fri, 9 Dec 2011 13:33:03 +0100 Subject: [Pw_forum] why is the tetrahedron interpolated DOS step-like? Message-ID: Dear all, I would like to know if the step-like aspect of a DOS calculated with the tetrahedron interpolation is what is expected to be. Please, take a look at the figures attached. I would expect something soft or at least a polygonal line with slope. I have looked at flib/dost.f90 and checked that the interpolation formulae are the same of the Bloechl's article OK. I am sorry to ask such a basic question, but I am puzzled since a long time, and tired of soften the stepped line with an additional program. Thanks in advance -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez "*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices, pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n que le es otorgada. Pero la grandeza del hombre est? precisamente en querer mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay grandeza que conquistar, puesto que all? todo es jerarqu?a establecida, inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio, reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su grandeza, su m?xima medida en el Reino de este Mundo*". Alejo Carpentier, El reino de este mundo, (1949). Translate from spanish here http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111209/946491a6/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: dos-tetra.jpeg Type: image/jpeg Size: 42328 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111209/946491a6/attachment-0002.jpeg -------------- next part -------------- A non-text attachment was scrubbed... Name: dos-tetra2.jpeg Type: image/jpeg Size: 33191 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111209/946491a6/attachment-0003.jpeg From eariel99 at gmail.com Fri Dec 9 13:56:16 2011 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Fri, 9 Dec 2011 13:56:16 +0100 Subject: [Pw_forum] Al pseudopotential and elastic properties Message-ID: Hi J?rg, Not certainly with Al, but with other elements I have some experience in elastic constants. I think you are doing things fine, but anyway I have a few comments 1) Using Ultrasoft pseudos I recently needed to use a cutoff of 60 Ry to obtain results converged and consistent when calculated either the energy or the stress tensor. You are using 85 Ry, OK, but be carefull the pseudo is defined in a discrete grid and using a very high cutoff may introduce noise. You may consider also using more k-points, specially to reproduce the tiny energy differences with a strain of 0.001. 2) In my case, using a lower cutoff, the constants obtained from the stress tensor were better than those obtained form the energy. This trend is the opposite of yours, or you may have error cancellation. 3) A strain of 0.001 is really low, check that the plot of E vs strain and stress vs strain is not noisy. I guess that is way you have such low *etot_conv_thr and** forc_conv_thr=1.0D-10* 4) Investigate how are the elastic constants measured (typically by ultrasound) and what is the typical strain involved in the measurements. *5) PS: I also tried to get C11 by the second derivative the Energy fitting*>* quadratic function which gave me C11=75.6GPa but this would assume that*>* the elastic constant is constant over the strain range(which could be*>* showed that's not the case for small strains(<0.01) using the*>* numerical second derivative).* You may add cubic and quartic terms to the fit, and the second derivative should become independent on the range if DFT calculation is well converged.. On 12/8/11 11:48 AM, J?rg Buchwald wrote: >* Hi,*>* does anyone has any experiences with the Al pseudopotentials and the*>* elastic constants?*>* I was testing Al.pbe-n-van.UPF with which I could reproduce the elastic*>* constant and the cohesive energy quite well, but using the output of*>* the stress matrix I get a way too high results for C11(>150GPa) at a*>* strain of 0.001. Appliying strains about>3%, I get results which are*>* quite relastic for C11(90-110 GPa). I thought that this has something*>* to do whith the kind of approximation, so I also created a ultrasoft*>* (PZ-)LDA potential with the vanderbilt code and tried the*>* normconserving Al.pz-vbc.UPF, which gave me similar results.*>* I applied the strain by stretching the cell vectors and performing a*>* 'relax'-simulation.*>* This is my input file for a rel. strain of 0.003:*>* ---*>* &control*>* calculation='relax'*>* prefix='Al-test11',*>* pseudo_dir='/home/jbuchw/espresso-4.3.2/pseudo'*>* outdir = '/home/jbuchw/scratch',*>* tstress=.true.*>* disk_io='none'*>* etot_conv_thr=1.0D-10*>* forc_conv_thr=1.0D-10*>* /*>* &system*>* ibrav= 0,*>* celldm(1) =7.6271186*>* nat= 4,*>* ntyp= 1,*>* ecutwfc = 85.0*>* occupations='smearing'*>* smearing='mp'*>* degauss=0.0007*>* /*>* &electrons*>* diagonalization='david'*>* mixing_mode='plain'*>* conv_thr=1.0D-10*>* /*>* &ions*>* bfgs_ndim=3*>* /*>* &cell*>* ! cell_dofree='yz'*>* /*>* ATOMIC_SPECIES*>* Al 26.981539 Al.pbe-n-van.UPF*>* ATOMIC_POSITIONS crystal*>* Al 0.00 0.00 0.00*>* Al 0.50 0.50 0.00*>* Al 0.00 0.50 0.50*>* Al 0.50 0.00 0.50*>* K_POINTS automatic*>* 14 14 14 0 0 0*>* CELL_PARAMETERS*>* 0.9995541042 0.000000000 0.000000000*>* 0.000000000 0.996564411 0.000000000*>* 0.000000000 0.000000000 0.996564411*>* --*>* Am I doing something wrong, or does it have something to do with the*>* pseudopotential?*>* Regards,*>* J?rg*>**>**>* PS: I also tried to get C11 by the second derivative the Energy fitting*>* quadratic function which gave me C11=75.6GPa but this would assume that*>* the elastic constant is constant over the strain range(which could be*>* showed that's not the case for small strains(<0.01) using the*>* numerical second derivative).* -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez "*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices, pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n que le es otorgada. Pero la grandeza del hombre est? precisamente en querer mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay grandeza que conquistar, puesto que all? todo es jerarqu?a establecida, inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio, reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su grandeza, su m?xima medida en el Reino de este Mundo*". Alejo Carpentier, El reino de este mundo, (1949). Translate from spanish here http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111209/9ec46c3d/attachment.htm From giannozz at democritos.it Fri Dec 9 14:14:07 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 9 Dec 2011 14:14:07 +0100 Subject: [Pw_forum] why is the tetrahedron interpolated DOS step-like? In-Reply-To: References: Message-ID: On Dec 9, 2011, at 13:33 , Eduardo Ariel Menendez Proupin wrote: > I would like to know if the step-like aspect of a DOS calculated with > the tetrahedron interpolation is what is expected to be. Please, take > a look at the figures attached. your system is quasi-1d, or at least, the k-point grid is, am I correct? In that case, I am afraid that what you get is what you should get. I am actually surprised that it works at all! Notice that the "steps" in tetrahedron DOS exactly correspond to the "peaks" in gaussian DOS. Paolo (guilty of the tetrahedron implementation) --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From eariel99 at gmail.com Fri Dec 9 15:41:38 2011 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Fri, 9 Dec 2011 15:41:38 +0100 Subject: [Pw_forum] why is the tetrahedron interpolated DOS step-like? Message-ID: The system is 1-D, with a 18 angstrom wide supercell. I suspected that 1-D tetrahedra are not very tetrahedral, and used a 2x2x28 k-points grid. It gives the same result than with a 1x1x28 grid, and the DOS numbers differ in the third decimal digit. Eduardo On Dec 9, 2011, at 13:33 , Eduardo Ariel Menendez Proupin wrote: >* I would like to know if the step-like aspect of a DOS calculated with*>* the tetrahedron interpolation is what is expected to be. Please, take*>* a look at the figures attached.* your system is quasi-1d, or at least, the k-point grid is, am I correct? In that case, I am afraid that what you get is what you should get. I am actually surprised that it works at all! Notice that the "steps" in tetrahedron DOS exactly correspond to the "peaks" in gaussian DOS. Paolo (guilty of the tetrahedron implementation) -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez "*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices, pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n que le es otorgada. Pero la grandeza del hombre est? precisamente en querer mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay grandeza que conquistar, puesto que all? todo es jerarqu?a establecida, inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio, reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su grandeza, su m?xima medida en el Reino de este Mundo*". Alejo Carpentier, El reino de este mundo, (1949). Translate from spanish here http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111209/0d4f15e3/attachment.htm From baroni at sissa.it Fri Dec 9 18:55:29 2011 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 9 Dec 2011 18:55:29 +0100 Subject: [Pw_forum] XSpectrum In-Reply-To: References: Message-ID: <6975FF39-81A6-4E65-8999-A3881AC705D7@sissa.it> Because in that case the code would assume that the excited electron occupies the lowest available conduction state, whereas in the experiment that you are correctly describing the core electron would be excited to some high-lying conduction band. On more physical grounds, the code simulates photoionization process, rather that than a photoexcitation one. When the final energy of the excited electron is high enough, however, the two processes are indistinguishable. SB On Dec 8, 2011, at 9:46 PM, Hanghui Chen wrote: > To QE developers, > In the examples of X-ray Spectrum calculations, I noticed that for diamond, there are two different calculations. In one of them (the so-called Z approximation), 8 normal carbon atoms are employed. In the other one (Z+1 approximation), in addition to 7 normal carbon atoms, a special carbon atom is employed with a fixed hole in its valence (basically, it is N atom. Correct me if I am wrong.) What I am confused is that in the Z+1 approximation, the input file specifies the number of electron to be 8*4=32. Since the special carbon atom has valence 5 (instead of 4), the system is charged. However, my understanding of x-ray absorption is that an incoming photon excites an electron from 1s state into the conduction band. If that is the case, then why not run a charge neutral calculation, i.e. nele = 7*4+5=33, and the resulting system is metallic? > Thank you. > > Hanghui Chen > Department of Physics > Yale University > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111209/a4432af8/attachment-0001.htm From baroni at sissa.it Fri Dec 9 18:59:38 2011 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 9 Dec 2011 18:59:38 +0100 Subject: [Pw_forum] why is the tetrahedron interpolated DOS step-like? In-Reply-To: References: Message-ID: Eduardo: you may want to rehearse the theory of critical points, such as explained in many solid-state texts, my favorite one (at least in this field) still being Bassani and Pastori Parravicini's. SB On Dec 9, 2011, at 1:33 PM, Eduardo Ariel Menendez Proupin wrote: > Dear all, > > I would like to know if the step-like aspect of a DOS calculated with the tetrahedron interpolation is what is expected to be. Please, take a look at the figures attached. I would expect something soft or at least a polygonal line with slope. > > I have looked at flib/dost.f90 and checked that the interpolation formulae are the same of the Bloechl's article OK. > I am sorry to ask such a basic question, but I am puzzled since a long time, and tired of soften the stepped line with an additional program. > Thanks in advance > -- > > > Eduardo Menendez Proupin > Departamento de Qu?mica Fisica Aplicada > Facultad de Ciencias > Universidad Aut?noma de Madrid > 28049 Madrid, Spain > Phone: +34 91 497 6706 > > On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez > > "Padece, espera y trabaja para gentes que nunca conocer? y que a su vez padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices, pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n que le es otorgada. Pero la grandeza del hombre est? precisamente en querer mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay grandeza que conquistar, puesto que all? todo es jerarqu?a establecida, inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio, reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su grandeza, su m?xima medida en el Reino de este Mundo". > Alejo Carpentier, El reino de este mundo, (1949). > > Translate from spanish here http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111209/16c3817b/attachment.htm From eariel99 at gmail.com Fri Dec 9 19:37:02 2011 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Fri, 9 Dec 2011 19:37:02 +0100 Subject: [Pw_forum] why is the tetrahedron interpolated DOS step-like? Message-ID: >Eduardo: you may want to rehearse the theory of critical points, such as explained in many solid-state texts, my favorite one (at least in this field) still being Bassani and Pastori Parravicini's. SB Stefano, Thank you. You are right if the system is 2D, but in this case it is quasi-1D. The 1-D Van Hove singularitu is appreciated in the large energy scale of the plot between -6 and -4 eV. Maybe the steps in the low energy scale reveal that a quasi-1D system with a finite k-point sampling is an effective bi-dimensionality with a smaller energy scale, with as many bands as k-points. I do not think that you are meaning that, as k-points sampling is not a matter of solid state textbooks. Thanks, and nice weekend Eduardo On Dec 9, 2011, at 1:33 PM, Eduardo Ariel Menendez Proupin wrote: >* Dear all,*>* *>* I would like to know if the step-like aspect of a DOS calculated with the tetrahedron interpolation is what is expected to be. Please, take a look at the figures attached. I would expect something soft or at least a polygonal line with slope. *>* *>* I have looked at flib/dost.f90 and checked that the interpolation formulae are the same of the Bloechl's article OK.*>* I am sorry to ask such a basic question, but I am puzzled since a long time, and tired of soften the stepped line with an additional program. *>* Thanks in advance* -- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111209/0fbda415/attachment.htm From avallabh at purdue.edu Sun Dec 11 06:31:11 2011 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Sun, 11 Dec 2011 00:31:11 -0500 (EST) Subject: [Pw_forum] query on e-ph matrix element Message-ID: <1468233968.209665.1323581471095.JavaMail.root@mailhub016.itcs.purdue.edu> Dear users, I am trying to calculate e-ph matrix element (g) for Aluminium as a function of q (phonon wave vector) and nu(index of the phonon branch). I had gone thru the source code "elphon.f90" for this purpose. I could figure out all the variables like k,i,j,q but not nu. I see a variable 'imode0' which i cannot figure out its purpose. Can someone please help me with identifying the nu ? Also is there an efficient way to estimate g from the values of lambda and gamma ? Thanks Ajit From padmaja_patnaik at yahoo.co.uk Mon Dec 12 06:11:31 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Mon, 12 Dec 2011 05:11:31 +0000 (GMT) Subject: [Pw_forum] spin density plot in real space Message-ID: <1323666691.50147.YahooMailNeo@web28516.mail.ukl.yahoo.com> Dear All I have a doubt regarding density plot. How can we plot the spin density in real space? Thanks in advance regards, ? Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111212/db904666/attachment.htm From fratesi at mater.unimib.it Mon Dec 12 09:47:59 2011 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Mon, 12 Dec 2011 09:47:59 +0100 Subject: [Pw_forum] local DOS: how to set nrmin and nrmax In-Reply-To: <50b1c044.1b1c9.13412a9832f.Coremail.landaulev@163.com> References: <50b1c044.1b1c9.13412a9832f.Coremail.landaulev@163.com> Message-ID: <4EE5BFBF.5050700@mater.unimib.it> Dear Jinxi, the definition of irmin and irmax depends on your choice of the volume where the local DOS has to be integrated. Reasonable numbers go from 1 (first point in the FFT grid) to N (last point in the FFT grid) where N is output by pw.x (see "FFT grid:"). Points in real space going from irmin to irmax are included. This is done for the three dimensions independently. So suppose you want to take a volume which goes from the origin of the unit cell to half of it in the three dimensions (12.5% of total volume), and your FFT grid contains 64x64x50 points, then you would set: irmin(1)=1 irmax(1)=32 irmin(2)=1 irmax(2)=32 irmin(3)=1 irmax(3)=25 HTH Guido PS: Unless for specialized applications, you might perhaps be interested in the "projected" (on the atomic wavefunctions) rather than "local" DOS, both are computed by projwfc.x. Il 12/06/2011 10:17 AM, jinxi ha scritto: > Dear all: > I try to get local DOS using projwfc.x, but i can't understand the > description in "INPUT_projwfc": how to set parameters irmin and irmax? > I've read the input files in example16, but i still don't know how to > locate the local DOS by irmin and irmax. Are there general methods to > calculate the number and position of grid points? > If there are some general references (books, articles, presentations) > for the basic knowledge, please recommend to me. > Many thanks! > best wishes > jinxi > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca From jean-roch.huntzinger at univ-montp2.fr Mon Dec 12 10:02:27 2011 From: jean-roch.huntzinger at univ-montp2.fr (Jean-Roch Huntzinger) Date: Mon, 12 Dec 2011 10:02:27 +0100 Subject: [Pw_forum] example09 segfault - ramtns used but not allocated in dynmatrix.f90 Message-ID: <201112121002.27711.jean-roch.huntzinger@univ-montp2.fr> Dear all, The attached patch solves a segfault in example09 on qe 4.3.2 compiled with gfortran 4.5.3 [or equally with 4.5.0 or 4.6.2] : running normal mode calculation for CH4..../run_example: line 226: 4939 Segmentation fault (core dumped) $PH_COMMAND < ch4.nm.in > ch4.nm.out Using gdb shows that lraman was false; in this case ramtns is never allocated, hence the evaluation of the expression ramtns*omega/fpi*convfact failed during the call to write_dyn_mat_header, line 152 of dynmatrix.f90. The userguide warns about segfaults, but here it does not sound like a compiler bug. Is this correct ? Should I file a bug report ? Jean-Roch Huntzinger -- L2C/SMC UMR 5221 - Universit? Montpellier 2, CNRS - France -------------- next part -------------- A non-text attachment was scrubbed... Name: dynmatrix.f90.patch Type: text/x-patch Size: 1143 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111212/7cfcbd72/attachment.bin From yccheng.nju at gmail.com Mon Dec 12 11:10:01 2011 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Mon, 12 Dec 2011 13:10:01 +0300 Subject: [Pw_forum] QE Blue Gene/P Scalapack Message-ID: Dear PWscf users, We are having problems to run Quantum espresso 4.3.2 compiled with scalapack on Blue Gene/P system. It seems the code is not feeding a positive definite matrix to scalapack funtion. The makefile is as attached. The version compiled without scalapack is working fine though, using the same input data. Here is the error message: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from rdiaghg : error # 1 problems computing cholesky positive %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% The following is the make.sys file with scalapack. Is this problem related to our configuration or to scalapack install on our Blue Gene/P system? Would you please help me to solve this problem? Thank you in advance. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% # make.sys. Generated from make.sys.in by configure. # compilation rules .SUFFIXES : .SUFFIXES : .o .c .f .f90 # most fortran compilers can directly preprocess c-like directives: use # $(MPIF90) $(F90FLAGS) -c $< # if explicit preprocessing by the C preprocessor is needed, use: # $(CPP) $(CPPFLAGS) $< -o $*.F90 # $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o # remember the tabulator in the first column !!! .f90.o: $(MPIF90) $(F90FLAGS) -c $< # .f.o and .c.o: do not modify .f.o: $(F77) $(FFLAGS) -c $< .c.o: $(CC) $(CFLAGS) -c $< # DFLAGS = precompilation options (possible arguments to -D and -U) # used by the C compiler and preprocessor # FDFLAGS = as DFLAGS, for the f90 compiler # See include/defs.h.README for a list of options and their meaning # With the exception of IBM xlf, FDFLAGS = $(DFLAGS) # For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas DFLAGS = -D__MASS -D__AIX -D__XLF -D__LINUX_ESSL -D__MPI -D__PARA -D__SCALAPACK -D__FFTW FDFLAGS = -D__MASS,-D__AIX,-D__XLF,-D__LINUX_ESSL,-D__MPI,-D__PARA,-D__SCALAPACK,-D__FFTW # IFLAGS = how to locate directories where files to be included are # In most cases, IFLAGS = -I../include IFLAGS = -I../include # MOD_FLAGS = flag used by f90 compiler to locate modules # Each Makefile defines the list of needed modules in MODFLAGS MOD_FLAG = -I # Compilers: fortran-90, fortran-77, C # If a parallel compilation is desired, MPIF90 should be a fortran-90 # compiler that produces executables for parallel execution using MPI # (such as for instance mpif90, mpf90, mpxlf90,...); # otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...) # If you have a parallel machine but no suitable candidate for MPIF90, # try to specify the directory containing "mpif.h" in IFLAGS # and to specify the location of MPI libraries in MPI_LIBS MPIF90 = mpixlf90_r #F90 = bgxlf90_r CC = bgxlc_r F77 = bgxlf_r # C preprocessor and preprocessing flags - for explicit preprocessing, # if needed (see the compilation rules above) # preprocessing flags must include DFLAGS and IFLAGS CPP = cpp CPPFLAGS = -P -traditional $(DFLAGS) $(IFLAGS) # compiler flags: C, F90, F77 # C flags must include DFLAGS and IFLAGS # F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax CFLAGS = -qarch=450d -qtune=450 -O3 $(DFLAGS) $(IFLAGS) F90FLAGS = $(FFLAGS) -qsuffix=cpp=f90 -WF,$(FDFLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS = -qarch=450d -qtune=450 -q32 -qalias=noaryovrlp:nointptr -O3 -qstrict -qdpc=e # compiler flags without optimization for fortran-77 # the latter is NEEDED to properly compile dlamch.f, used by lapack FFLAGS_NOOPT = -q32 -O0 # Linker, linker-specific flags (if any) # Typically LD coincides with F90 or MPIF90, LD_LIBS is empty LD = mpixlf90_r LDFLAGS = -q32 -Wl,--allow-multiple-definition -qextname LD_LIBS = # External Libraries (if any) : blas, lapack, fft, MPI # If you have nothing better, use the local copy : # BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a # BLAS_LIBS_SWITCH = external BLAS_LIBS = -L/opt/share/ibmmath/essl/4.4/lib/ -lesslbg BLAS_LIBS_SWITCH = external # If you have nothing better, use the local copy : # LAPACK_LIBS = /your/path/to/espresso/LAPACK/lapack.a # LAPACK_LIBS_SWITCH = external # The following lapack libraries will be available in flib/ : # ../flib/lapack.a : contains all needed routines # ../flib/lapack_atlas.a: only routines not present in the Atlas library # For IBM machines with essl (-D__ESSL): load essl BEFORE lapack ! # remember that LAPACK_LIBS precedes BLAS_LIBS in loading order LAPACK_LIBS = -L/opt/share/ibmmath/essl/4.4/lib/ -lesslbg /opt/share/math_libraries/lapack/ppc64/IBM/lapack_BGP.a /opt/share/math_libraries/lapack/ppc64/IBM/blas_BGP.a LAPACK_LIBS_SWITCH = external SCALAPACK_LIBS = -L/opt/share/math_libraries/scalapack/ppc64/IBM/lib -lscalapack_bgp -lblacsF77init_bgp -lblacs_bgp -lblacsCinit_bgp -llapack_bgp -L/opt/share/ibmmath/essl/4.4/lib/ -lesslbg # nothing needed here if the the internal copy of FFTW is compiled # (needs -D__FFTW in DFLAGS) FFT_LIBS = -L/opt/share/ibmmath/essl/4.4/lib/ -lesslbg # For parallel execution, the correct path to MPI libraries must # be specified in MPI_LIBS (except for IBM if you use mpxlf) MPI_LIBS = # IBM-specific: MASS libraries, if available and if -D__MASS is defined in FDFLAGS MASS_LIBS = -L/opt/ibmcmp/xlmass/bg/4.4/bglib -lmassv # ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv AR = ar ARFLAGS = ruv # ranlib command. If ranlib is not needed (it isn't in most cases) use # RANLIB = echo RANLIB = ranlib # all internal and external libraries - do not modify FLIB_TARGETS = all LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a LIBS = $(SCALAPACK_LIBS) $(LAPACK_LIBS) $(FFT_LIBS) $(BLAS_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS) # topdir for linking espresso libs with plugins TOPDIR = /home/ying/espresso %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -- 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/20111212/c6b6c760/attachment.htm From giannozz at democritos.it Mon Dec 12 11:44:52 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 12 Dec 2011 11:44:52 +0100 Subject: [Pw_forum] query on e-ph matrix element In-Reply-To: <1468233968.209665.1323581471095.JavaMail.root@mailhub016.itcs.purdue.edu> References: <1468233968.209665.1323581471095.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: <1323686692.21852.34.camel@fe12lx.fisica.uniud.it> On Sun, 2011-12-11 at 00:31 -0500, Ajit Vallabhaneni wrote: > I had gone thru the source code "elphon.f90" for this purpose. wow! you are a brave man > I could figure out all the variables like k,i,j,q but not nu. > I see a variable 'imode0' which i cannot figure out its purpose. > Can someone please help me with identifying the nu ? the el-ph matrix elements are calculated for each irrep, i.e. displacement patterns transforming into each other under the symmetry operations of the small group of each wavevector. There are nirr irreps, each having dimension npert(irr). The code runs over irreps: irr=1,..,nirr, then over irrep components: ipert=1,..,npert(irr), and imode0+ipert is the index of each displacement pattern. Only when the el-phon coefficient "gamma" is calculated are phonon modes (contained in matrix "dyn") actually used. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Mon Dec 12 11:49:59 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 12 Dec 2011 11:49:59 +0100 Subject: [Pw_forum] example09 segfault - ramtns used but not allocated in dynmatrix.f90 In-Reply-To: <201112121002.27711.jean-roch.huntzinger@univ-montp2.fr> References: <201112121002.27711.jean-roch.huntzinger@univ-montp2.fr> Message-ID: <1323686999.21852.39.camel@fe12lx.fisica.uniud.it> On Mon, 2011-12-12 at 10:02 +0100, Jean-Roch Huntzinger wrote: > The attached patch solves a segfault in example09 > [...] Should I file a bug report ? too late: it was fixed a few days ago. Thank you anyway! http://qe-forge.org/scm/viewvc.php?view=rev&root=q-e&sortby=date&revision=8244 P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Mon Dec 12 12:20:31 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 12 Dec 2011 12:20:31 +0100 Subject: [Pw_forum] QE Blue Gene/P Scalapack In-Reply-To: References: Message-ID: <1323688831.21852.58.camel@fe12lx.fisica.uniud.it> On Mon, 2011-12-12 at 13:10 +0300, ??? wrote: > Is this problem related to our configuration or to scalapack install > on our Blue Gene/P system? hard to say. Is scalapack working for other input data? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From damien.connetable at ensiacet.fr Mon Dec 12 12:55:28 2011 From: damien.connetable at ensiacet.fr (damien) Date: Mon, 12 Dec 2011 12:55:28 +0100 Subject: [Pw_forum] problem with phonon code Message-ID: <4EE5EBB0.3020007@ensiacet.fr> Dear developers, I have a problem with the phonon code. It crashes with this comment: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 8 from diropn : error # 99 error opening yalo3.mixd %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 7 from diropn : error # 99 error opening yalo3.mixd %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I do not arrive to understand the origin of this crash. The problem appears after some self consistent calculations (with the versions: 4.13, 4.2 and 4.3). Maybe it is specific to the machine (cluster Altix ICE 8200 with 352 nodes)? What can I do to solve this problem? thank you for your help sincerely yours D. Conn?table -------------- next part -------------- A non-text attachment was scrubbed... Name: damien_connetable.vcf Type: text/x-vcard Size: 411 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111212/42dce599/attachment.vcf From aaghafari at yahoo.com Mon Dec 12 14:04:16 2011 From: aaghafari at yahoo.com (ali ghafari) Date: Mon, 12 Dec 2011 05:04:16 -0800 (PST) Subject: [Pw_forum] B3LYP and fhi2upf.x Message-ID: <1323695056.99285.YahooMailNeo@web161402.mail.bf1.yahoo.com> Dear QS users I want to use B3LYP which is hybrid functional. As I saw in the mailing list, I have to consider two points 1- using input_dft='B3LYP' in the &system 2 - using norm-conserving PPs. But the problem is that QE don't have any norm-conserving PPs for Cu, Ca, and O. Therefore I tried to use fhi2upf.x for converting Abinit PPs to QE. I did following steps and finally the program give me PP while several parameters are zero in the PPs such as Rcut, Rcut US, and E pseu. Furthermore, I couldn't use it in the calculation.? ? I attached several lines of PPs for Cu Is it Ok or wrong? Best wishes Ali *********************************************** 1)? /home/........../espresso-4.3.2/upftools/fhi2upf.x 2) Input file >? Cu.GGA.fhi 3) Confirm or modify l max, l loc (read:? 3? 0) > 2 04) Wavefunction # 1: label (e.g. 4s), occupancy > 4S, 2 ?? Wavefunction # 2: label (e.g. 4s), occupancy > 3D, 9 ?? Wavefunction # 3: label (e.g. 4s), occupancy > 4p, 0 Pseudopotential successfully converted Output PP file in UPF format :? Cu.GGA.fhi.UPF? ************************************ ? ??? Generated using Fritz-Haber code ??? Author: Author: unknown ??? Generation date: Generation date: as well ??? Pseudopotential type: SL ??? Element: Cu ??? Functional: PBE ??? Suggested minimum cutoff for wavefunctions:?? 0. Ry ??? Suggested minimum cutoff for charge density:?? 0. Ry ??? The Pseudo was generated with a Non-Relativistic Calculation ??? L component and cutoff radius for Local Potential:? 0?? 0.0000 ??? Valence configuration: ??? nl pn? l?? occ?????? Rcut??? Rcut US?????? E pseu ??? 4S? 4? 0? 2.00????? 0.000????? 0.000???? 0.000000 ??? 3D? 3? 2? 9.00????? 0.000????? 0.000???? 0.000000 ??? 4p? 4? 1? 0.00????? 0.000????? 0.000???? 0.000000 ??? Generation configuration: not available. ??? Comment: ??? copper, fhi98PP : Trouiller-Martins-type, GGA Perdew/Burke/Ernzerhof (1996), l= ? ? ? ? ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111212/7abb8a54/attachment-0001.htm From giannozz at democritos.it Mon Dec 12 14:15:41 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 12 Dec 2011 14:15:41 +0100 Subject: [Pw_forum] B3LYP and fhi2upf.x In-Reply-To: <1323695056.99285.YahooMailNeo@web161402.mail.bf1.yahoo.com> References: <1323695056.99285.YahooMailNeo@web161402.mail.bf1.yahoo.com> Message-ID: <1323695741.21852.70.camel@fe12lx.fisica.uniud.it> On Mon, 2011-12-12 at 05:04 -0800, ali ghafari wrote: > finally the program give me PP while several parameters are zero in > the PPs such as Rcut, Rcut US, and E pseu. this is completely irrelevant > Furthermore, I couldn't use it in the calculation. Why? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Mon Dec 12 14:21:27 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 12 Dec 2011 14:21:27 +0100 Subject: [Pw_forum] problem with phonon code In-Reply-To: <4EE5EBB0.3020007@ensiacet.fr> References: <4EE5EBB0.3020007@ensiacet.fr> Message-ID: <1323696087.21852.74.camel@fe12lx.fisica.uniud.it> On Mon, 2011-12-12 at 12:55 +0100, damien wrote: > from diropn : error # 99 > error opening yalo3.mixd > Maybe it is specific to the machine (cluster Altix ICE 8200 with 352 nodes)? more likely, to the file system. Are you writing to a parallel file system? Try to write to a file system that is local to each CPU P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From damien.connetable at ensiacet.fr Mon Dec 12 14:46:04 2011 From: damien.connetable at ensiacet.fr (damien) Date: Mon, 12 Dec 2011 14:46:04 +0100 Subject: [Pw_forum] problem with phonon code In-Reply-To: <1323696087.21852.74.camel@fe12lx.fisica.uniud.it> References: <4EE5EBB0.3020007@ensiacet.fr> <1323696087.21852.74.camel@fe12lx.fisica.uniud.it> Message-ID: <4EE6059C.8080106@ensiacet.fr> How to do this? Is there a specific option with espresso? Above, you will find the pbs script for the machine. sincerely damien conn?table #!/bin/sh #PBS -l select=4:ncpus=8:mpiprocs=8 #PBS -l place=excl #PBS -l walltime=50:00:00 #PBS -N test #PBS -m abe #PBS -j eo #PBS -M damien.connetable at ensiacet.fr cd $PBS_O_WORKDIR cp $PBS_NODEFILE nodes uniq nodes export OMP_NUM_THREADS=1 export MPI_GROUP_MAX=64 mpiexec_mpt -np 32 pw.x -npool 4 < scf.in > scf.out mpiexec_mpt -np 32 ph.x -npool 4 < ph.in > ph.out Le 12/12/2011 14:21, Paolo Giannozzi a ?crit : > On Mon, 2011-12-12 at 12:55 +0100, damien wrote: > >> from diropn : error # 99 >> error opening yalo3.mixd >> Maybe it is specific to the machine (cluster Altix ICE 8200 with 352 nodes)? > more likely, to the file system. Are you writing to a parallel file > system? Try to write to a file system that is local to each CPU > > P. -------------- next part -------------- A non-text attachment was scrubbed... Name: damien_connetable.vcf Type: text/x-vcard Size: 411 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111212/d4df587f/attachment.vcf From giannozz at democritos.it Mon Dec 12 14:48:49 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 12 Dec 2011 14:48:49 +0100 Subject: [Pw_forum] neb calculation In-Reply-To: References: Message-ID: <1323697729.21852.80.camel@fe12lx.fisica.uniud.it> On Wed, 2011-12-07 at 09:46 +0530, Prasenjit Ghosh wrote: > I am using neb.x in QE-4.3.2 to do neb calculations. However, unlike > the older versions, I do not see the PW.out (containing the outputs of > the scf calculations for each image) file for each of the images in > the directories containing the wavefunction files for the images of > the path. > > Do I need to set some parameters in the input file ? no, this is something done directly by the code. I think, however, that all images are supposed to print a PW.out file into the working directory of each image. Look into NEB/compute_scf.f90, line 267 and following: ! ! ... unit stdout is connected to the appropriate file ! IF ( ionode ) THEN ! INQUIRE( UNIT = stdout, OPENED = opnd ) IF ( opnd ) CLOSE( UNIT = stdout ) OPEN( UNIT = stdout, FILE = TRIM( tmp_dir ) // 'PW.out', & STATUS = 'UNKNOWN', POSITION = 'APPEND' ) ! END IF "ionode" should be set to "true" for each root processor of each image P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From avallabh at purdue.edu Mon Dec 12 15:23:15 2011 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Mon, 12 Dec 2011 09:23:15 -0500 (EST) Subject: [Pw_forum] query on e-ph matrix element In-Reply-To: <1323686692.21852.34.camel@fe12lx.fisica.uniud.it> Message-ID: <2022858514.212264.1323699795186.JavaMail.root@mailhub016.itcs.purdue.edu> Dear Paolo, Thanks for your response. But i am not sure i understand it completely. Are you implying that "g" cannot be calculated for a particular phonon (of specific q and nu) ? I am not entirely familiar with the concepts of irreducible representation. But in the expression for "g", there is a omega_nu,q and also the derivative of V_SCF with respect to displacement along a particular nu for a given q. Thanks Ajit From iyad.ne at gmail.com Mon Dec 12 16:44:43 2011 From: iyad.ne at gmail.com (IYAD AL-QASIR) Date: Mon, 12 Dec 2011 10:44:43 -0500 Subject: [Pw_forum] B3LYP and fhi2upf.x In-Reply-To: <1323695056.99285.YahooMailNeo@web161402.mail.bf1.yahoo.com> References: <1323695056.99285.YahooMailNeo@web161402.mail.bf1.yahoo.com> Message-ID: Hello, - You do not need to worry about the first ( information) block of your PP file. So no need to specify the values of rcut, .... - Did you try to use the converted pp in QE? if so, did it run? if not, what was the message you got? Kindest Regards, Iyad n Mon, Dec 12, 2011 at 8:04 AM, ali ghafari wrote: > Dear QS users > I want to use B3LYP which is hybrid functional. As I saw in the mailing > list, I have to consider two points > 1- using input_dft='B3LYP' in the &system > 2 - using norm-conserving PPs. > But the problem is that QE don't have any norm-conserving PPs for Cu, Ca, > and O. Therefore I tried to use fhi2upf.x for converting Abinit PPs to QE. > I did following steps and finally the program give me PP while several > parameters are zero in the PPs such as Rcut, Rcut US, and E pseu. > Furthermore, I couldn't use it in the calculation. > I attached several lines of PPs for Cu > > Is it Ok or wrong? > Best wishes > Ali > > *********************************************** > 1) /home/........../espresso-4.3.2/upftools/fhi2upf.x > 2) Input file > Cu.GGA.fhi > 3) Confirm or modify l max, l loc (read: 3 0) > 2 0 > 4) Wavefunction # 1: label (e.g. 4s), occupancy > 4S, 2 > Wavefunction # 2: label (e.g. 4s), occupancy > 3D, 9 > Wavefunction # 3: label (e.g. 4s), occupancy > 4p, 0 > > Pseudopotential successfully converted > Output PP file in UPF format : Cu.GGA.fhi.UPF > ************************************ > > > Generated using Fritz-Haber code > Author: Author: unknown > Generation date: Generation date: as well > Pseudopotential type: SL > Element: Cu > Functional: PBE > > Suggested minimum cutoff for wavefunctions: 0. Ry > Suggested minimum cutoff for charge density: 0. Ry > The Pseudo was generated with a Non-Relativistic Calculation > L component and cutoff radius for Local Potential: 0 0.0000 > > Valence configuration: > nl pn l occ Rcut Rcut US E pseu > 4S 4 0 2.00 0.000 0.000 0.000000 > 3D 3 2 9.00 0.000 0.000 0.000000 > 4p 4 1 0.00 0.000 0.000 0.000000 > > Generation configuration: not available. > Comment: > copper, fhi98PP : Trouiller-Martins-type, GGA Perdew/Burke/Ernzerhof > (1996), l= > > > > > author="Author: unknown" > date="Generation date: as well" > comment="copper, fhi98PP : Trouiller-Martins-type, GGA > Perdew/Burke/Ernzerhof (1996), l=" > element="Cu" > pseudo_type="SL" > relativistic="no" > is_ultrasoft="F" > is_paw="F" > is_coulomb="F" > has_so="F" > has_wfc="F" > has_gipaw="F" > paw_as_gipaw="F" > core_correction="F" > functional="PBE" > z_valence="1.100000000000000E+001" > total_psenergy="0.000000000000000E+000" > wfc_cutoff="0.000000000000000E+000" > rho_cutoff="0.000000000000000E+000" > l_max="2" > l_max_rho="0" > l_local="0" > mesh_size="525" > number_of_wfc="3" > number_of_proj="2"/> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- _______________________________ IYAD I. AL-QASIR, PhD Research Associate Department of Nuclear Engineering North Carolina State University Campus Box 7909 2500 Stinson Dr. Raleigh, NC 27695-7909 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111212/8f2948b5/attachment.htm From akohlmey at gmail.com Mon Dec 12 16:48:55 2011 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 12 Dec 2011 10:48:55 -0500 Subject: [Pw_forum] spin density plot in real space In-Reply-To: <1323666691.50147.YahooMailNeo@web28516.mail.ukl.yahoo.com> References: <1323666691.50147.YahooMailNeo@web28516.mail.ukl.yahoo.com> Message-ID: On Mon, Dec 12, 2011 at 12:11 AM, Padmaja Patnaik wrote: > Dear All > > I have a doubt regarding density plot. How can we plot the spin density in > real space? the difference between the spin up and spin down densities? axel > Thanks in advance > regards, > > Padmaja Patnaik > Research Scholar > Dept of Physics > IIT Bombay > Mumbai, India > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From giannozz at democritos.it Mon Dec 12 17:40:32 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 12 Dec 2011 17:40:32 +0100 Subject: [Pw_forum] query on e-ph matrix element In-Reply-To: <2022858514.212264.1323699795186.JavaMail.root@mailhub016.itcs.purdue.edu> References: <2022858514.212264.1323699795186.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: <1323708032.814.0.camel@fe12lx.fisica.uniud.it> On Mon, 2011-12-12 at 09:23 -0500, Ajit Vallabhaneni wrote: > Are you implying that "g" cannot be calculated for a particular > phonon (of specific q and nu) ? no, I am not implying. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From avallabh at purdue.edu Tue Dec 13 00:44:27 2011 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Mon, 12 Dec 2011 18:44:27 -0500 (EST) Subject: [Pw_forum] query on e-ph matrix element In-Reply-To: <1323708032.814.0.camel@fe12lx.fisica.uniud.it> Message-ID: <1570540781.214786.1323733467777.JavaMail.root@mailhub016.itcs.purdue.edu> Dear Paolo Can you please explain what the variable "zdotc" in elphon.f90 exactly does? I think it calculates the derivative of the potential. It is declared as an external variable but i couldnot figure out the location it has been calculated. Can you show me the the path as well where it is calculated ? Thanks Ajit From akohlmey at gmail.com Tue Dec 13 00:57:43 2011 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 12 Dec 2011 18:57:43 -0500 Subject: [Pw_forum] query on e-ph matrix element In-Reply-To: <1570540781.214786.1323733467777.JavaMail.root@mailhub016.itcs.purdue.edu> References: <1323708032.814.0.camel@fe12lx.fisica.uniud.it> <1570540781.214786.1323733467777.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: On Mon, Dec 12, 2011 at 6:44 PM, Ajit Vallabhaneni wrote: > Dear Paolo > > ? ? ?Can you please explain what the variable "zdotc" in elphon.f90 exactly does? I think it calculates the derivative of the potential. ?It is declared as an external variable but i couldnot figure out the location it has been calculated. Can you show me the the path as well where it is calculated ? zdotc is not a variable but a BLAS function: NAME ZDOTC - forms the dot product of a vector SYNOPSIS DOUBLE COMPLEX FUNCTION ZDOTC(N,ZX,INCX,ZY,INCY) INTEGER INCX,INCY,N DOUBLE COMPLEX ZX(*),ZY(*) PURPOSE ZDOTC forms the dot product of a vector. please note the difference in the meaning of "external" between C and Fortran. ;) cheers, axel. > > Thanks > Ajit > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From ptao10b at imr.ac.cn Tue Dec 13 08:43:04 2011 From: ptao10b at imr.ac.cn (=?GBK?B?zNXF9A==?=) Date: Tue, 13 Dec 2011 15:43:04 +0800 (CST) Subject: [Pw_forum] How to achieve the convergence of Ecutrho? Message-ID: Dear all, I've asked sevral people about the convergence criteria of Ecutrho test. They point out that the convergence will be achieved when the difference between two adjacent scf calculation is smaller than 0.1 meV. However, they are not very sure about the step length. From my view, the step length may pose huge effects on our calculation. Consider the cases of step lengths are 100 Ry and 0.00001Ry respectively, the latter will be convergent immediately while the former will not be so fast. For the resons above, I'm really confused now. And could any nice guy show me the strict judgement of the convergence for Ecutrho? Thank you very much! Yours, Plato Tao -- ------------------------------------------------------------------- PH.D. candidate Peng Tao Magnetism and Magnetic Materials Division National Laboratory for Material Science Institute of Metal Research, Chinese Academy of Sciences Phone +86-024-83978751 ------------------------------------------------------------------- From kalamaillist at gmail.com Tue Dec 13 10:03:33 2011 From: kalamaillist at gmail.com (WF) Date: Tue, 13 Dec 2011 17:03:33 +0800 Subject: [Pw_forum] How to achieve the convergence of Ecutrho? Message-ID: <001201ccb976$1a5ddbe0$4f1993a0$@gmail.com> >Dear all, > >I've asked sevral people about the convergence criteria of Ecutrho test. They point out that the convergence will be achieved when the difference between two adjacent scf calculation is smaller than 0.1 meV. However, they are not very sure about the step length. From my view, the step length may pose huge effects on our calculation. Consider the cases of step lengths are 100 Ry and 0.00001Ry respectively, the latter will be convergent immediately while the former will not be so fast. >For the resons above, I'm really confused now. And could any nice guy show me the strict judgement of the convergence for Ecutrho? Thank you very much! The convergence of Ecutrho comes from the balance of time and accuracy, so the judgment is based on your own system and there is no universal one. Typically, 1Ry~10Ry should be step length under most circumstance, as one can reach the convergence reasonably fast while the additional time cost from the more than enough Ecutrho will be in the same order of magnitude as 10%, an acceptable value. ------------------------------------------------------------ Wu Feng, Chemistry and Molecular Engineering, Peking University ------------------------------------------------------------ From fratesi at mater.unimib.it Tue Dec 13 10:10:43 2011 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Tue, 13 Dec 2011 10:10:43 +0100 Subject: [Pw_forum] How to achieve the convergence of Ecutrho? In-Reply-To: References: Message-ID: <4EE71693.2030606@mater.unimib.it> Dear Plato Tao, as for any convergence parameter, the criterion is analogue to the epsilon-delta definition in calculus. Namely, if Q is the quantity you want to have converged (say, the total energy) within an accuracy \epsilon (the value of \epsilon depending on your own needs), with respect to a convergence parameter x (say, the cutoff): if |Q(\infty) - Q(x)| < \epsilon for all x >= x', then x' is the value of the parameter ensuring you convergence. Notice that this does not imply anything about how fast you reach convergence, so a criterion only based on differences between consecutive steps (x,x+dx,x+2dx...) is ill defined as it depends on dx. You have to estimate the value of Q(\infty), e.g. by extrapolation to large values of x, and see when your error with respect to this virtually exact result is lower than the accuracy you want to achieve. Best wishes, Guido Il 12/13/2011 08:43 AM, ?? ha scritto: > Dear all, > > I've asked sevral people about the convergence criteria of Ecutrho test. They point out that the convergence will be achieved when the difference between two adjacent scf calculation is smaller than 0.1 meV. However, they are not very sure about the step length. From my view, the step length may pose huge effects on our calculation. Consider the cases of step lengths are 100 Ry and 0.00001Ry respectively, the latter will be convergent immediately while the former will not be so fast. > > For the resons above, I'm really confused now. And could any nice guy show me the strict judgement of the convergence for Ecutrho? Thank you very much! > > Yours, > Plato Tao > > -- > ------------------------------------------------------------------- > PH.D. candidate Peng Tao > Magnetism and Magnetic Materials Division > National Laboratory for Material Science > Institute of Metal Research, Chinese Academy of Sciences > Phone +86-024-83978751 > ------------------------------------------------------------------- > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From flux_ray12 at 163.com Tue Dec 13 11:19:22 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Tue, 13 Dec 2011 18:19:22 +0800 (CST) Subject: [Pw_forum] How to achieve the convergence of Ecutrho? In-Reply-To: References: Message-ID: <9d6f8d0.1018e.13436ef0911.Coremail.flux_ray12@163.com> Actually, the standard of convergency for cut-off energy is not how much dE the system gained, but whether dE/dCut is near to 0 enough. Definitely, such a threahold, for dE/dCut, is also determined by yourself. The example from you was too extreme. Thinking about 100Ry as step, your result are too rough to hold the slope information. But when 10^(-5)Ry was using, even though it should give the very fine dE/dCut information as well, the results may be not good due to the accuracy of DFT, numerical methods, and computer limitation ( please consider the length of float and double float variable ). P.S.: Therefore, I think such question is not the one of sci. & tech. rather than your thinking method. This may be the reason that no person reply such a post in emuch. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2011-12-13 15:43:04,"??" wrote: >Dear all, > >I've asked sevral people about the convergence criteria of Ecutrho test. They point out that the convergence will be achieved when the difference between two adjacent scf calculation is smaller than 0.1 meV. However, they are not very sure about the step length. From my view, the step length may pose huge effects on our calculation. Consider the cases of step lengths are 100 Ry and 0.00001Ry respectively, the latter will be convergent immediately while the former will not be so fast. > >For the resons above, I'm really confused now. And could any nice guy show me the strict judgement of the convergence for Ecutrho? Thank you very much! > >Yours, >Plato Tao > >-- >------------------------------------------------------------------- >PH.D. candidate Peng Tao >Magnetism and Magnetic Materials Division >National Laboratory for Material Science >Institute of Metal Research, Chinese Academy of Sciences >Phone +86-024-83978751 >------------------------------------------------------------------- > > > > >_______________________________________________ >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/20111213/07d5406c/attachment.htm From demyant at gmail.com Tue Dec 13 19:47:50 2011 From: demyant at gmail.com (=?ISO-8859-1?B?RGVtauluIFRhbeFz?=) Date: Tue, 13 Dec 2011 19:47:50 +0100 Subject: [Pw_forum] el_phon Message-ID: Dear Users! I want to modify the phonon code in /PH to obtain the electron-phonon matrix elements. I want to write it out in a file. If I good understand, the matrix elements are stored in the elph.f90 file (in the module el_phon). Is not it? -- Demj?n Tam?s -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111213/bf95976f/attachment.htm From liweig at mtu.edu Tue Dec 13 21:10:04 2011 From: liweig at mtu.edu (Liwei Geng) Date: Tue, 13 Dec 2011 15:10:04 -0500 (EST) Subject: [Pw_forum] software to draw phonon spectra for windows In-Reply-To: Message-ID: <905930393.558741323807004746.JavaMail.root@zcs-mbs03.it.mtu.edu> Dear all, Could anyone please suggest me some free software to draw phonon spectra under windows XP systems? Great thanks! Best regards, Liwei -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111213/c10e93eb/attachment.htm From flux_ray12 at 163.com Wed Dec 14 02:19:33 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Wed, 14 Dec 2011 09:19:33 +0800 (CST) Subject: [Pw_forum] software to draw phonon spectra for windows In-Reply-To: <905930393.558741323807004746.JavaMail.root@zcs-mbs03.it.mtu.edu> References: <905930393.558741323807004746.JavaMail.root@zcs-mbs03.it.mtu.edu> Message-ID: <7e1b66b0.10925.1343a272dd2.Coremail.flux_ray12@163.com> Cygwin + gnuplot is a good choice~ Or, you can use the OriginLab or QtiPlot demo version. At 2011-12-14 04:10:04,"Liwei Geng" wrote: Dear all, Could anyone please suggest me some free software to draw phonon spectra under windows XP systems? Great thanks! Best regards, Liwei -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111214/1822d1d7/attachment.htm From gabriele.sclauzero at epfl.ch Wed Dec 14 11:09:11 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Wed, 14 Dec 2011 11:09:11 +0100 Subject: [Pw_forum] Dear Dr. Sclauzero, In-Reply-To: <002101ccb9cf$519e00e0$f4da02a0$@sas.upenn.edu> References: <002101ccb9cf$519e00e0$f4da02a0$@sas.upenn.edu> Message-ID: Dear Dr. Chan-Woo, you should post such question on the Forum. Also other QE developers or users could give a useful reply and take part to the discussion, or just be interested in it because experiencing a similar problem. Last but not least, me, like many other users and developers, have chosen to give their contribution to the whole community of QE users through the Forum. In my opinion, it's not fair to address these people with private messages asking for help, as if they were "help-desks". Briefly, I think that your problem stems exactly from that fix which I proposed and is now included in the latest PWscf version. That fix will actually introduce a problem if the atomic wave function which you want to use for making projections have zero occupations. I thought that this would never be the case, but probably one should not exclude it a priori. A further problem arises if you generate such a pseudopotential (Ce with zero 4f occupation) and want to use it for making the LDA+U projections on the empty states, since the LD1 code usually saves in the PP file only the wavefunctions with nonzero occupations. First, you should check if you PP has the 4f wavefunctions. If it does, you can remove the check upf(nt)%oc(n) > 0.D0 as a quick fix. If not, then you need to regenerate the PP. Regards, GS Il giorno 13/dic/2011, alle ore 20.42, Chan-Woo Lee ha scritto: > Dear Dr. Sclauzero: > > May be I sent email to your old email address. > > Please find forwarded email and thank you in advance! > > Sincerely, > > Chan-Woo > > P.S. One quick question. Did you happen to get the answer about http://www.democritos.it/pipermail/pw_forum/2010-July/017622.html ? As you see from my Ce.upf, in initial configuration, 4f is empty. I did it intentionally as I generated the psp for oxide applications (CeO2, Ce2O3, etc) ? Is it safe to make modification from the link? > > > > From: Chan-Woo Lee [mailto:leechanw at sas.upenn.edu] > Sent: Tuesday, December 13, 2011 11:10 AM > To: 'sclauzer at sissa.it' > Cc: leechanw at sas.upenn.edu > Subject: Dear Dr. Sclauzero, > > Dear Dr. Gabriele Sclauzero, > > Hello, my name is Chan-Woo Lee, working at Chemistry department of UPenn as a postoc. I email you as I saw a lot of your posts on PW_Forum about DFT+U. It looks like I have similar issue with Jia Chen, http://www.democritos.it/pipermail/pw_forum/2010-July/017602.html . > > My problem is that in applying U to Ce (in CeO2), I got somewhat weird occupation matrix (both in Cerium oxide and single Ce atom in a box). > > Anyway, if you don?t mind, may I ask your help on my problem? If yes, I will email you with Ce.upf, output file, and input file. > > Thank you in advance and it will be VERY helpful for me to fix my problem if you can provide me some advice on the problem. > > > > Sincerely, > > Chan-Woo > > > > > > > > ------- > Chan-Woo Lee, Ph.D. > Postdoctoral Research Associate > > Room 265 > Department of Chemistry > University of Pennsylvania > 231 South 34th Street > Philadelphia, PA 19104-6323 > Phone: 1-215-898-3564 (Office) > Email: leechanw at sas.upenn.edu > > ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111214/eb9f822d/attachment.htm From michelepisarra at yahoo.it Wed Dec 14 14:07:13 2011 From: michelepisarra at yahoo.it (Michele Pisarra) Date: Wed, 14 Dec 2011 13:07:13 +0000 (GMT) Subject: [Pw_forum] 1D systems In-Reply-To: <1322759257.96795.YahooMailNeo@web27003.mail.ukl.yahoo.com> References: <1322759257.96795.YahooMailNeo@web27003.mail.ukl.yahoo.com> Message-ID: <1323868033.96646.YahooMailNeo@web27001.mail.ukl.yahoo.com> Dear QE users, I used QE to calculate the wave functins of several types of?carbon nanotubes. To simulate the 1D nature of this system I used?cell parameters such that two of the?lattice displacement vectors are much larger than the other one. However this choice lead to?a reciprocal space with two very small vectors?and so?to a very large number of plane waves in the basis set, ecut being fixed. I need to reduce the number of plane waves as?much as possible.?I tried to make different runs?using different lengths for the?two?"irrelevant"?vectors and I found that decreasing this lenght decreases the total energy. However I don't think that the total energy is the good parameter to look at in my case, because the decreasing of the total energy can be due to the interaction between the replica of the system that I want to be zero. So I need a criterion to find the best configuration. Can anyone help me? Thank you. Michele Pisarra, PhD Student, Dipartimento di Fisica, Universit? della Calabria Via P. Bucci, Cubo 31 C VI piano, 87036, Rende (CS), Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111214/e76a40ce/attachment-0001.htm From pmoreira at ifi.unicamp.br Wed Dec 14 14:57:56 2011 From: pmoreira at ifi.unicamp.br (pmoreira at ifi.unicamp.br) Date: Wed, 14 Dec 2011 11:57:56 -0200 Subject: [Pw_forum] from cdiaghg : error # 2012 diagonalization (ZHEGV*) failed Message-ID: <5e4db3b40cc27bfa7acdd1fb99d47b5e.squirrel@ifgw.mail.ifi.unicamp.br> I tried to run QE but the followinhg error is happening: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from : error # 2012 diagonalization (ZHEGV*) failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% My input follows below. The atomic positions were cut, because they are long and were checked with XCrysDen. I am trying to model an apatite.I did some tests suggested on user manual (cdiaghg error), but I cannot figure out where my problem is, but I think it is with the pseudo-potentials. If someone could a point some direction, I would be grateful, With best regards, Pedro Moreira Material Science pos-doc State University of Campinas, Brazil #################################################################### &control calculation='relax', restart_mode='from_scratch', pseudo_dir = '/home/des01/dekoning/pmoreira/espresso-4.3.2/pseudo/', outdir='/home/des01/dekoning/pmoreira/espresso-4.3.2/tmp/', prefix='apatite', tprnfor = .true., tstress = .true., verbosity = 'high', etot_conv_thr = 3.50e-5, forc_conv_thr = 2.50e-4 / &system ibrav = 4, celldm(1) = 18.864, celldm(3) = 0.7295, nat = 352, ntyp = 4, nosym = .true., ecutwfc = 52.0, ecutrho = 600.0, occupations = 'smearing', smearing = 'gaussian', degauss = 0.07, / &electrons diagonalization = 'cg', conv_thr = 1.0e-8, / &ions / ATOMIC_SPECIES P 30.9738 P.pbe-n-van.UPF Ca 40.0780 Ca.pbe-nsp-van.UPF O 15.9994 O.pbe-van_bm.UPF H 1.00794 H.pbe-van_ak.UPF ATOMIC_POSITIONS {angstrom} . . . K_POINTS automatic 6 4 6 0 0 0 From azadi at uni-mainz.de Wed Dec 14 18:34:55 2011 From: azadi at uni-mainz.de (Azadi, Sam) Date: Wed, 14 Dec 2011 17:34:55 +0000 Subject: [Pw_forum] Hybrid functional pressure Message-ID: <96C11A37-041E-4849-98EC-4265A2510101@uni-mainz.de> Dear QE users, As it's written in README file of EXX_examples directory, corresponding formula of stress calculation using hybrid functionals have not yet been coded in quantum espresso. But by choosing "tstress = .true." in scf input file, there is a value for stress in scf output file. My question is, is it reliable ? Yours S.A From akohlmey at gmail.com Wed Dec 14 18:47:06 2011 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Wed, 14 Dec 2011 12:47:06 -0500 Subject: [Pw_forum] Hybrid functional pressure In-Reply-To: <96C11A37-041E-4849-98EC-4265A2510101@uni-mainz.de> References: <96C11A37-041E-4849-98EC-4265A2510101@uni-mainz.de> Message-ID: On Wed, Dec 14, 2011 at 12:34 PM, Azadi, Sam wrote: > Dear QE users, > > As it's written in README file of EXX_examples directory, corresponding formula of stress calculation > using hybrid functionals have not yet been coded in quantum espresso. > But by choosing "tstress = .true." in scf input file, there is a value for stress in scf output file. > My question is, is it reliable ? how can it be, if the exact exchange contribution is missing? axel. > > Yours > S.A > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From bdslipun at gmail.com Wed Dec 14 18:56:52 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Wed, 14 Dec 2011 23:26:52 +0530 Subject: [Pw_forum] md simulation Message-ID: i am a new user of quantum espresso i want to the cp molecular dyanamics to study some materials having solid to liquid transition but i donot know how to represent supercell of any structure and how to calculate the T/P graph for a liquid system is there any reference available to know more about the simulation and making supercell for different systems Bd SAHOO BARC MUMBAI -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111214/085291ef/attachment.htm From baroni at sissa.it Wed Dec 14 19:19:21 2011 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 14 Dec 2011 19:19:21 +0100 Subject: [Pw_forum] 1D systems In-Reply-To: <1323868033.96646.YahooMailNeo@web27001.mail.ukl.yahoo.com> References: <1322759257.96795.YahooMailNeo@web27003.mail.ukl.yahoo.com> <1323868033.96646.YahooMailNeo@web27001.mail.ukl.yahoo.com> Message-ID: <64520B6F-6531-4988-A26F-EAE8D02CCDBF@sissa.it> Dear Michele, I think what you are doing is (generally speaking) correct. Having the two in-plane lattice vectors larger than the diameter of the tube would allow for some "vacuum" between neighboring periodic images of our tube, so as to simulate to some extent an isolated tube. This is what is called the "supercell" technique. Note that the physical parameter to monitor is the ratio between the distance between neighboring tubes (i.e. the length of the in-plane lattice vectors) and the diameter of the tube, *NOT* the length of the lattice vector parallel to the cube. As a general rule, you should check the convergence of the physical quantity you are interested in (be it the total energy, some orbital energies, some other physical properties ...) with respect to the inter-tube distance. The total energy, in particular, *HAS* to converge. If it does not, this means that you are doing something different from what you have described (and, probably, from what you think you are doing ...). If 1 day of careful inspection of the input data and of the results, plus discussions with your peers and supervisor(s) does not produce any results, you may want to consider reverting to us with some more details on what is going on ... HTH - Stefano B On Dec 14, 2011, at 2:07 PM, Michele Pisarra wrote: > Dear QE users, > I used QE to calculate the wave functins of several types of carbon nanotubes. To simulate the 1D nature of this system I used cell parameters such that two of the lattice displacement vectors are much larger than the other one. However this choice lead to a reciprocal space with two very small vectors and so to a very large number of plane waves in the basis set, ecut being fixed. I need to reduce the number of plane waves as much as possible. I tried to make different runs using different lengths for the two "irrelevant" vectors and I found that decreasing this lenght decreases the total energy. However I don't think that the total energy is the good parameter to look at in my case, because the decreasing of the total energy can be due to the interaction between the replica of the system that I want to be zero. So I need a criterion to find the best configuration. Can anyone help me? > Thank you. > > Michele Pisarra, PhD Student, > Dipartimento di Fisica, Universit? della Calabria > Via P. Bucci, Cubo 31 C VI piano, 87036, Rende (CS), Italy > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111214/4175b14b/attachment.htm From baroni at sissa.it Wed Dec 14 19:24:38 2011 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 14 Dec 2011 19:24:38 +0100 Subject: [Pw_forum] md simulation In-Reply-To: References: Message-ID: <10CF99FD-B880-4EF4-9621-E65A916CC590@sissa.it> Your question is not specific to to CP, nor to QE. If I were you, I wouldn't dare to tackle any ab-initio calculation of crystal/amorphous melting (a highly non trivial problem), before being sure you understand all the theoretical and practical subtelties, which you learn from a textbook in statistical mechanics (the former) or (classical) computer simulations (the latter). A good starting point may be Frenkel & Smit's "understanding molecular simulations". HTH - SB On Dec 14, 2011, at 6:56 PM, bhabya sahoo wrote: > i am a new user of quantum espresso > i want to the cp molecular dyanamics to study some materials > having solid to liquid transition but i donot know how to represent supercell of any structure > and how to calculate the T/P graph for a liquid system > > > is there any reference available > to know more about the simulation and making supercell for different systems > > > > > > Bd SAHOO > BARC > MUMBAI > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111214/01a46a27/attachment-0001.htm From giannozz at democritos.it Wed Dec 14 19:35:53 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 14 Dec 2011 19:35:53 +0100 Subject: [Pw_forum] Hybrid functional pressure In-Reply-To: <96C11A37-041E-4849-98EC-4265A2510101@uni-mainz.de> References: <96C11A37-041E-4849-98EC-4265A2510101@uni-mainz.de> Message-ID: On Dec 14, 2011, at 18:34 , Azadi, Sam wrote: > As it's written in README file of EXX_examples directory, > corresponding formula of stress calculation using hybrid > functionals have not yet been coded in quantum espresso. I am quite sure they have. The README should be updated P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From baroni at sissa.it Wed Dec 14 19:42:27 2011 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 14 Dec 2011 19:42:27 +0100 Subject: [Pw_forum] Hybrid functional pressure In-Reply-To: References: <96C11A37-041E-4849-98EC-4265A2510101@uni-mainz.de> Message-ID: In any event, you can make sure by comparing the result you get with some finite-difference calculations, being aware of the usual caveats about the slow convergence of stress wrt kinetic-energy cutoff. SB On Dec 14, 2011, at 7:35 PM, Paolo Giannozzi wrote: > > On Dec 14, 2011, at 18:34 , Azadi, Sam wrote: > >> As it's written in README file of EXX_examples directory, >> corresponding formula of stress calculation using hybrid >> functionals have not yet been coded in quantum espresso. > > I am quite sure they have. The README should be updated > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111214/ae424d8a/attachment.htm From flux_ray12 at 163.com Thu Dec 15 02:51:50 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 15 Dec 2011 09:51:50 +0800 (CST) Subject: [Pw_forum] Does QE support the old MPICH and gfortran? Message-ID: <60c40be6.25cc.1343f6b1a25.Coremail.flux_ray12@163.com> Dear QE developer and users: I borrowed a cluster from other department. During configure the QE package, both of v4.3.2 and v4.1.3, it showed "Parallel environment not detected". Then I checked ./install/config.log ( in QE v4.3.2 ), and found the error message like: configure:2884: mpif90 -V >&5 f95: '-V' must come at the start of the command line configure:2887: $? = 1 configure:2895: checking whether we are using the GNU Fortran compiler configure:2914: mpif90 -c -g -O2 conftest.F >&5 configure:2920: $? = 0 configure:2937: result: yes configure:2943: checking whether mpif90 accepts -g configure:2960: mpif90 -c -g conftest.f90 >&5 configure:2966: $? = 0 configure:2982: result: yes configure:3353: WARNING: parallel compiler mpif90 uses gfortran, but serial compiler mpif90 was detected configure:3355: WARNING: assuming F90=gfortran, discarding mpif90 The cluster is running on Fedora release 8. mpi version is mpif90 for 1.2.7 (release) of : 2005/11/04 11:54:51, which was compiled by gfortran ( gcc version 4.1.2 20070925 (Red Hat 4.1.2-33) ). Each node is based on Intel dual-core CPU. The parallel environment can be detected by Abinit ( unfortunately, Abinit cannot pass the mpi compiling as well, even I tried Abinit v5.3.5, which was released in 2007 ). Do I have to use an older version ( ealier than 4.1.3 ) QE? Or, are there some other methods to overcome this problem? Since this cluster does not belong to our lab, we cannot update the mpi version and install ifort. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111215/edaca07c/attachment.htm From cwandtj at gmail.com Thu Dec 15 04:22:34 2011 From: cwandtj at gmail.com (Chan-Woo Lee) Date: Wed, 14 Dec 2011 22:22:34 -0500 Subject: [Pw_forum] Application of LDA+U to Ce psp with zero 4f occupation Message-ID: <003f01ccbad8$ccf87900$66e96b00$@gmail.com> I am trying to apply Hubbard U (DFT+U) to Ce in cerium based oxides including CeO2 and Ce2O3. However, as you see from header of Ce psp (see [I] below), our Ce psp (RRKJ, generated by OPIUM) is designed to have zero 4f occupation. When I applied +U to Ce using QE V4.3.1, I got following error message: from offset_atom_wfc : error # 9 wrong offset So, I searched previous threads and I figured out that I needed to modify QE code (http://www.democritos.it/pipermail/pw_forum/2010-July/017622.html). I did modification and recompiled QE code. It looked fine but I found weird energetics for reduction of CeO2 to Ce2O3 in comparison with data from PRB 75, 035109 (2007). So, I looked into output files and found out that occupation matrix for both CeO2 and Ce2O3 are somewhat unphysical (at least for me): *U_eff=0.01 eV Tr[ns(na)] CeO2 = 1.1690424 Ce2O3 = 1.3908759 *U_eff=3.0 eV Tr[ns(na)] CeO2 = 0.9963736 Ce2O3 = 1.2650403 *U_eff=9.0 eV Tr[ns(na)] CeO2 = 0.5972449 Ce2O3 = 1.1056369 I thought that even with non-orthogonal terms, at least Tr[ns(na)] for CeO2 should be very close to 0.0 as Ce exists as Ce4+ in CeO2 (with ionic picture) and should have empty 4f state. With analyzing Ce psp itself, I wanted to know whether the modification of QE discussed above is safe or not. Answer of Dr. Sclauzero to my question was as follows: "Briefly, I think that your problem stems exactly from that fix which I proposed and is now included in the latest PWscf version. That fix will actually introduce a problem if the atomic wave function which you want to use for making projections have zero occupations. I thought that this would never be the case, but probably one should not exclude it a priori. A further problem arises if you generate such a pseudopotential (Ce with zero 4f occupation) and want to use it for making the LDA+U projections on the empty states, since the LD1 code usually saves in the PP file only the wavefunctions with nonzero occupations. First, you should check if you PP has the 4f wavefunctions. If it does, you can remove the check upf(nt)%oc(n) > 0.D0 as a quick fix. If not, then you need to regenerate the PP". Based on his comment, I did some test calculations after modifying our Ce psp--simply made zero 4f occupation as nonzero, 0.01 (In (I), 430 0.00 --> 430 0.01). However, there is no total E change between the calculation with Ce psp of zero 4f occupation and that with nonzero 4f occupation (E difference <0.001/CeO2). Also, change in Tr[ns(na)] is minute (e.g. 0.9938046 --> 0.9963736) My questions to QE users are: - Maybe I need to fill 4f more? - Do you have any explanations about why is occupation matrix sum close to 1.0 not 0.0? Again, while there are some non-orthogonal terms, I think that for CeO2 Tr[ns(na)] for Ce should be close to zero not one. Did I miss something? - How about using starting_ns_eigenvalue? By the way, while I tried to use this, I couldn't understand instruction. For instance, in example below ([II]), if I want to make initial occupations as zero, how can I do? In starting_ns_eigenvalue(m,ispin,I), I can see that I should have starting_ns_eigenvalue(m,1,1) and starting_ns_eigenvalue(m,2,1) if U is applied to spin-up and spin-down for atomic species 1. Then how about m? m=1,2,3,4,5,6, and 7? If not, what will be desirable values for m? Thank you for your advice and comments in advance. P.S. I post this while there is existing post regarding the questions above because: 1) The title of the existing post is not suitable and will never be easy for QE users to search. 2) I am not comfortable with adding threads under the post which contains my personal emails (not for the forum) which violate my privacy. ++++++++++++++++++++++++++++++ [I] [Atom] Ce 15 # norb: number of orbitals 100 2.00 -643.0 # nlm occ eigen(- means auto-generate) 200 2.00 -77.4 210 6.00 -68.4 300 2.00 -10.0 310 6.00 -6.0 320 10.0 -6.4 400 2.00 -6.4 410 6.00 -6.0 420 10.0 -6.0 500 2.00 -2.4 510 6.00 -2.0 600 0.00 -1.0 610 0.00 -1.0 520 0.00 -1.0 430 0.00 -1.9 +++++++++++++++++++++++++++++++ [II] U( 1) = 3.0000 U( 2) = 0.0000 alpha( 1) = 0.0000 alpha( 2) = 0.0000 atom 1 Tr[ns(na)]= 2.0000000 atom 1 spin 1 eigenvalues: 0.1428571 0.1428571 0.1428571 0.1428571 0.1428571 0.1428571 0.1428571 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 6 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 7 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 0.143 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.143 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.143 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.143 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.143 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.143 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.143 ------- Chan-Woo Lee, Ph.D. Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia, PA 19104-6323 Phone: 1-215-898-3564 (Office) Email: leechanw at sas.upenn.edu / cwandtj at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111214/f3815e8a/attachment-0001.htm From matteo at umn.edu Thu Dec 15 08:09:32 2011 From: matteo at umn.edu (Matteo Cococcioni) Date: Thu, 15 Dec 2011 01:09:32 -0600 Subject: [Pw_forum] Application of LDA+U to Ce psp with zero 4f occupation In-Reply-To: <003f01ccbad8$ccf87900$66e96b00$@gmail.com> References: <003f01ccbad8$ccf87900$66e96b00$@gmail.com> Message-ID: On Wed, Dec 14, 2011 at 9:22 PM, Chan-Woo Lee wrote: > I am trying to apply Hubbard U (DFT+U) to Ce in cerium based oxides > including CeO2 and Ce2O3. However, as you see from header of Ce psp (see > [I] below), our Ce psp (RRKJ, generated by OPIUM) is designed to have zero > 4f occupation. When I applied +U to Ce using QE V4.3.1, I got following > error message:**** > > ** ** > > from offset_atom_wfc : error # 9**** > > wrong offset**** > > ** ** > > So, I searched previous threads and I figured out that I needed to modify > QE code (http://www.democritos.it/pipermail/pw_forum/2010-July/017622.html). > **** > > ** ** > > I did modification and recompiled QE code. It looked fine but I found > weird energetics for reduction of CeO2 to Ce2O3 in comparison with data > from PRB 75, 035109 (2007). So, I looked into output files and found out > that occupation matrix for both CeO2 and Ce2O3 are somewhat unphysical (at > least for me):**** > > ** ** > > *U_eff=0.01 eV **** > > ** ** > > Tr[ns(na)] **** > > CeO2 = 1.1690424**** > > Ce2O3 = 1.3908759**** > > ** ** > > *U_eff=3.0 eV **** > > ** ** > > Tr[ns(na)] **** > > CeO2 = 0.9963736**** > > Ce2O3 = 1.2650403 **** > > ** ** > > *U_eff=9.0 eV **** > > ** ** > > Tr[ns(na)] **** > > CeO2 = 0.5972449 **** > > Ce2O3 = 1.1056369 > Dear Chan-Woo, I have no experience with Ce oxides. I will only offer a couple of considerations. 1) don't expect exact correspondence between the "nominal" valence state of an ion you can guess from the stoichiometry of the compound and from the periodic table, with the occupations computed as projections of KS states on atomic orbitals. The situation in crystal could be different (e.g., there could be some degree of hybridization) and the result you get depends critically on how you define the occupations of specific orbitals (and there are many different ways to do this). 2) orthogonalizing atomic wave functions makes a significant difference in many case. Have you tried this? regards, Matteo > **** > > ** ** > > I thought that even with non-orthogonal terms, at least Tr[ns(na)] for > CeO2 should be very close to 0.0 as Ce exists as Ce4+ in CeO2 (with ionic > picture) and should have empty 4f state. With analyzing Ce psp itself, I > wanted to know whether the modification of QE discussed above is safe or > not. **** > > ** ** > > Answer of Dr. Sclauzero to my question was as follows:**** > > ** ** > > "Briefly, I think that your problem stems exactly from that fix which I > proposed and is now included in the latest PWscf version. That fix will > actually introduce a problem if the atomic wave function which you want to > use for making projections have zero occupations. I thought that this would > never be the case, but probably one should not exclude it a priori. A > further problem arises if you generate such a pseudopotential (Ce with zero > 4f occupation) and want to use it for making the LDA+U projections on the > empty states, since the LD1 code usually saves in the PP file only the > wavefunctions with nonzero occupations. First, you should check if you PP > has the 4f wavefunctions. If it does, you can remove the check > upf(nt)%oc(n) > 0.D0 as a quick fix. If not, then you need to regenerate > the PP".**** > > ** ** > > ** ** > > Based on his comment, I did some test calculations after modifying our Ce > psp--simply made zero 4f occupation as nonzero, 0.01 (In (I), 430 0.00 --> > 430 0.01). However, there is no total E change between the calculation with > Ce psp of zero 4f occupation and that with nonzero 4f occupation (E > difference <0.001/CeO2). Also, change in Tr[ns(na)] is minute (e.g. > 0.9938046 --> 0.9963736)**** > > ** ** > > ** ** > > My questions to QE users are:**** > > ** ** > > - Maybe I need to fill 4f more? **** > > - Do you have any explanations about why is occupation matrix sum close to > 1.0 not 0.0? Again, while there are some non-orthogonal terms, I think that > for CeO2 Tr[ns(na)] for Ce should be close to zero not one. Did I miss > something?**** > > - How about using starting_ns_eigenvalue? By the way, while I tried to use > this, I couldn't understand instruction. For instance, in example below > ([II]), if I want to make initial occupations as zero, how can I do? In > starting_ns_eigenvalue(m,ispin,I), I can see that I should have > starting_ns_eigenvalue(m,1,1) and starting_ns_eigenvalue(m,2,1) if U is > applied to spin-up and spin-down for atomic species 1. Then how about m? > m=1,2,3,4,5,6, and 7? If not, what will be desirable values for m?**** > > ** ** > > Thank you for your advice and comments in advance.**** > > ** ** > > ** ** > > P.S. I post this while there is existing post regarding the questions > above because:**** > > ** ** > > 1) The title of the existing post is not suitable and will never be easy > for QE users to search. **** > > 2) I am not comfortable with adding threads under the post which contains > my personal emails (not for the forum) which violate my privacy. **** > > ** ** > > ** ** > > ** ** > > ** ** > > ** ** > > ++++++++++++++++++++++++++++++**** > > ** ** > > [I]**** > > ** ** > > [Atom]**** > > Ce**** > > 15 # norb: number of orbitals**** > > 100 2.00 -643.0 # nlm occ eigen(- means auto-generate)**** > > 200 2.00 -77.4**** > > 210 6.00 -68.4**** > > 300 2.00 -10.0**** > > 310 6.00 -6.0**** > > 320 10.0 -6.4**** > > 400 2.00 -6.4**** > > 410 6.00 -6.0**** > > 420 10.0 -6.0**** > > 500 2.00 -2.4**** > > 510 6.00 -2.0**** > > 600 0.00 -1.0**** > > 610 0.00 -1.0**** > > 520 0.00 -1.0**** > > 430 0.00 -1.9**** > > ** ** > > ** ** > > +++++++++++++++++++++++++++++++**** > > [II]**** > > ** ** > > U( 1) = 3.0000 U( 2) = 0.0000**** > > alpha( 1) = 0.0000 alpha( 2) = 0.0000**** > > atom 1 Tr[ns(na)]= 2.0000000**** > > atom 1 spin 1**** > > eigenvalues: 0.1428571 0.1428571 0.1428571 0.1428571 0.1428571 0.1428571 > 0.1428571**** > > eigenvectors**** > > 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 > 0.0000000**** > > 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 > 0.0000000**** > > 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 > 0.0000000**** > > 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 > 0.0000000**** > > 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 > 0.0000000**** > > 6 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 > 0.0000000**** > > 7 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 > 1.0000000**** > > occupations**** > > 0.143 0.000 0.000 0.000 0.000 0.000 0.000**** > > 0.000 0.143 0.000 0.000 0.000 0.000 0.000**** > > 0.000 0.000 0.143 0.000 0.000 0.000 0.000**** > > 0.000 0.000 0.000 0.143 0.000 0.000 0.000**** > > 0.000 0.000 0.000 0.000 0.143 0.000 0.000**** > > 0.000 0.000 0.000 0.000 0.000 0.143 0.000**** > > 0.000 0.000 0.000 0.000 0.000 0.000 0.143**** > > ** ** > > ** ** > > ** ** > > ** ** > > ** ** > > *------- > Chan-Woo Lee, Ph.D.* > > * * > > *Department of Chemistry > University of Pennsylvania > 231 South 34th Street > Philadelphia, PA 19104-6323 > Phone: 1-215-898-3564 (Office) > *Email: leechanw at sas.upenn.edu / cwandtj at gmail.com**** > > ** ** > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111215/1e5611ae/attachment.htm From bamideleibrahim at yahoo.com Thu Dec 15 09:19:55 2011 From: bamideleibrahim at yahoo.com (bamidele ibrahim) Date: Thu, 15 Dec 2011 00:19:55 -0800 (PST) Subject: [Pw_forum] how to construct supercell for an fcc crystal compound Message-ID: <1323937195.73618.YahooMailNeo@web39402.mail.mud.yahoo.com> Dear all, ?? I have been working on series of zinc blende semiconductors materials in recent time. I am now interested in doping some of the compound with differents element in other to alter the crystal structures(i.e introducing impurities). I know i need to build a supercell for my compound but, i don't understand how to do it. I went through all the examples files, but none was able to give the information. I will be delighted if you can all come to my aid. for example ZnSe with atomic position of (0,0,0) and (0.25,0.25,0.25). How do i build a supercell for this compound? ? Adetunji Bamidele Ibrahim Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111215/4a22c064/attachment.htm From giannozz at democritos.it Thu Dec 15 09:32:01 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 15 Dec 2011 09:32:01 +0100 Subject: [Pw_forum] Does QE support the old MPICH and gfortran? In-Reply-To: <60c40be6.25cc.1343f6b1a25.Coremail.flux_ray12@163.com> References: <60c40be6.25cc.1343f6b1a25.Coremail.flux_ray12@163.com> Message-ID: On Dec 15, 2011, at 2:51 , GAO Zhe wrote: > During configure the QE package, both of v4.3.2 and v4.1.3, > it showed "Parallel environment not detected" > [...] > configure:3353: WARNING: parallel compiler mpif90 uses gfortran, > but serial compiler mpif90 was detected > configure:3355: WARNING: assuming F90=gfortran, discarding mpif90 this is an unrelated error that has no consequences. There should be another error that causes "configure" not to recognize the parallel environment. Anyway: if mpif90 uses gfortran, it will not compile properly QE unless it is a recent version. It doesn't seem to be your case. If you cannot modify the software on the machine, the only thing you may try is to install on a private directory a working compiler (e.g. intel) and a mpi wrapper for it. Not sure it will work, though, in your case. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From davide.ceresoli at istm.cnr.it Thu Dec 15 09:42:13 2011 From: davide.ceresoli at istm.cnr.it (Davide Ceresoli) Date: Thu, 15 Dec 2011 09:42:13 +0100 Subject: [Pw_forum] Hybrid functional pressure In-Reply-To: <96C11A37-041E-4849-98EC-4265A2510101@uni-mainz.de> References: <96C11A37-041E-4849-98EC-4265A2510101@uni-mainz.de> Message-ID: <4EE9B2E5.2040304@istm.cnr.it> Dear Sam, I hope I have implemented correctly the formula found in: Phys. Rev. B 73, 125120 (2006). As suggested by Stefano Baroni I test it by applying finite deformations to an fcc-silicon cell. I recall that it worked well for the diagonal components of the stress, although it converges extremely slowly with respect to q-points (not k-points, but nq1, nq2, nq3). For the off-diagonal components (i.e. shear modulus), I couldn't achieve convergence. The answer to your question is: we need more testing. Maybe you can help by testing the two approaches (the formula and the finite deformations) on your system and then let us know. Best, Davide On 01/-10/-28163 08:59 PM, Azadi, Sam wrote: > Dear QE users, > > As it's written in README file of EXX_examples directory, corresponding formula of stress calculation > using hybrid functionals have not yet been coded in quantum espresso. > But by choosing "tstress =true." in scf input file, there is a value for stress in scf output file. > My question is, is it reliable ? > > Yours > S.A > > -- ------------------------------------------------------------ Davide Ceresoli - davide.ceresoli at istm.cnr.it CNR-ISTM via Golgi 19, 20133 Milan, Italy Phone: +39-02-50314276 Skype: dceresoli Mobile: +39-347-1001570 From baroni at sissa.it Thu Dec 15 10:11:04 2011 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 15 Dec 2011 10:11:04 +0100 Subject: [Pw_forum] how to construct supercell for an fcc crystal compound In-Reply-To: <1323937195.73618.YahooMailNeo@web39402.mail.mud.yahoo.com> References: <1323937195.73618.YahooMailNeo@web39402.mail.mud.yahoo.com> Message-ID: The same way you would "by hands". First draw (physically with pencil and paper, or just mentally if you have a good 3D imagination) a zincblende crystal structure with many unit cells repeated in the three dimensions. Give different atoms different colors. ZnSe can be colored with just two colors (say, green and red, plus possibly black to draw bonds). Then highlight the atoms that you want to turn into impurities using a different color (say, blue), arranging them in periodic array (i.e. one every 2/3/you-name-it elementary cells). Which crystal structure has the artificial crystal you have built? The unit cell of this artificial crystal will be your unit cell: it will contain many atoms ... Do it by yourself: you will learn a lot ... (and it may be fun!) - SB On Dec 15, 2011, at 9:19 AM, bamidele ibrahim wrote: > Dear all, > I have been working on series of zinc blende semiconductors materials in recent time. > I am now interested in doping some of the compound with differents element in other to alter > the crystal structures(i.e introducing impurities). I know i need to build a supercell for my compound but, > i don't understand how to do it. I went through all the examples files, but none was able to give the information. I will > be delighted if you can all come to my aid. for example ZnSe with atomic position of (0,0,0) and (0.25,0.25,0.25). > How do i build a supercell for this compound? > > Adetunji Bamidele Ibrahim > Department of physics,University of Agriculture, > Abeokuta, Ogun State,Nigeria. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111215/92161329/attachment.htm From habdslam at yahoo.fr Thu Dec 15 10:40:27 2011 From: habdslam at yahoo.fr (Abdeslam Houari) Date: Thu, 15 Dec 2011 09:40:27 +0000 (GMT) Subject: [Pw_forum] Re : how to construct supercell for an fcc crystal compound In-Reply-To: <1323937195.73618.YahooMailNeo@web39402.mail.mud.yahoo.com> Message-ID: <1323942027.41776.YahooMailClassic@web27406.mail.ukl.yahoo.com> Hi; Just look to your ZnSe face centered cubic unit cell with 2 atoms, as a simple cubic cell with 8 atoms (4 Zn abd 4 Se) .. If you multiply it (repeat it) 2 times along the three spatial directions (x, y and z axis) you will obtain a larger simple cubic cell which contain 8 unit cell, which mean with 8x8=64 atoms (32 Zn and 32 Se). You can by simple multiplication along the three dimension of the space create a cell as large as you want... not necessary cubic !! The next step is to do the substitution in this 64-atoms cell by taking off one Zn atom, for instance, and replace it by the desired one, let say Mn for instance. You will obtain the final desired unit cell that you will use in calculations, which now contains 31 Zn atoms, 32 Se atoms and 1 Mn atom. The best way to proceed is to keep away the computer and do thing by hands, with three different color pencils on a paper sheet... When the procedure is well understood do it in computer... Good luck Abdus-salam ======================================= Abdesalem HOUARI ------------------------------------------------------------------------------------------- Department of physics, Theoretical Physics Laboratory University of Bejaia-06000. Algeria. E-mail:?abdeslam.houari at univ-bejaia.dz & habdslam at yahoo.fr https://sites.google.com/site/houariabdeslam/homepage Phone: +213 34 21 53 04 Fax: +213 34 21 59 86 Cell phone: +213 551 36 29 01 (emergency only !!) ======================================== --- En date de?: Jeu 15.12.11, bamidele ibrahim a ?crit?: De: bamidele ibrahim Objet: [Pw_forum] how to construct supercell for an fcc crystal compound ?: "pw_forum at pwscf.org" Date: Jeudi 15 d?cembre 2011, 9h19 Dear all,?? I have been working on series of zinc blende semiconductors materials in recent time. I am now interested in doping some of the compound with differents element in other to alterthe crystal structures(i.e introducing impurities). I know i need to build a supercell for my compound but, i don't understand how to do it. I went through all the examples files, but none was able to give the information. I willbe delighted if you can all come to my aid. for example ZnSe with atomic position of (0,0,0) and (0.25,0.25,0.25). How do i build a supercell for this compound? ?Adetunji Bamidele Ibrahim Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. -----La pi?ce jointe associ?e suit----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111215/053e041d/attachment.htm From glapenna at iccom.cnr.it Thu Dec 15 11:21:38 2011 From: glapenna at iccom.cnr.it (Giovanni La Penna) Date: Thu, 15 Dec 2011 11:21:38 +0100 (CET) Subject: [Pw_forum] Re : how to construct supercell for an fcc crystal compound In-Reply-To: <1323942027.41776.YahooMailClassic@web27406.mail.ukl.yahoo.com> References: <1323942027.41776.YahooMailClassic@web27406.mail.ukl.yahoo.com> Message-ID: In the past I used an utility of DL_POLY (a package widely used for simulations of empirical models of liquids, solids and partially ordered systems, membranes, liquid crystals, etc.): http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/ The utility was genlat.f (hopefully still contained in the open-source distributed version DL_POLY_CLASSIC). Any reminiscence in the latgen subroutine of QE? I see latgen.f is still used. As for an application, see for instance: http://arxiv.org/abs/1108.3396 However, I agree that if the things are not too complicated, the best is typing coordinates into an XYZ file, after a bit of manual drawing. Finally, watching at the result with some 3d-rendering graphic package. Giovanni La Penna (Cnr-ICCOM) ============================================================ Giovanni La Penna - National research council (Cnr) Institute for chemistry of organo-metallic compounds (Iccom) via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy tel.: +39 055 522-5264, fax: +39 055 522-5203 e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna skype: giovannilapenna ============================================================ From mohnish.iitk at gmail.com Thu Dec 15 11:23:19 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Thu, 15 Dec 2011 15:53:19 +0530 Subject: [Pw_forum] Re : how to construct supercell for an fcc crystal compound In-Reply-To: References: <1323942027.41776.YahooMailClassic@web27406.mail.ukl.yahoo.com> Message-ID: The best way is to sit for sometime and write your own code implementing periodic boundary condition. Writing the code may enhance you understanding of the periodicity in the crystal. On Thu, Dec 15, 2011 at 3:51 PM, Giovanni La Penna wrote: > > In the past I used an utility of DL_POLY (a package widely used for > simulations of empirical models of liquids, solids and partially > ordered systems, membranes, liquid crystals, etc.): > > http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/ > > The utility was genlat.f (hopefully still contained in > the open-source distributed version DL_POLY_CLASSIC). > Any reminiscence in the latgen subroutine of QE? > > I see latgen.f is still used. > As for an application, see for instance: > http://arxiv.org/abs/1108.3396 > > However, I agree that if the things are not too complicated, > the best is typing coordinates into an XYZ file, after > a bit of manual drawing. Finally, watching at the result with > some 3d-rendering graphic package. > > Giovanni La Penna (Cnr-ICCOM) > > ============================================================ > Giovanni La Penna - National research council (Cnr) > Institute for chemistry of organo-metallic compounds (Iccom) > via Madonna del Piano 10, > I-50019 Sesto Fiorentino, Firenze, Italy > tel.: +39 055 522-5264, fax: +39 055 522-5203 > e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna > skype: giovannilapenna > ============================================================ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111215/02b570af/attachment-0001.htm From giuseppe.mattioli at mlib.ism.cnr.it Thu Dec 15 11:37:30 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Thu, 15 Dec 2011 11:37:30 +0100 Subject: [Pw_forum] Re : how to construct supercell for an fcc crystal compound In-Reply-To: References: <1323942027.41776.YahooMailClassic@web27406.mail.ukl.yahoo.com> Message-ID: <201112151137.30979.giuseppe.mattioli@mlib.ism.cnr.it> If you like Cartesian coordinates in Angstrom units, then xcrysden makes the job... You can read your pw.x unit-cell output file, replicate the cell, and obtain an xsf file of the supercell, which may be easily rewritten as .xyz HTH Giuseppe Mattioli On Thursday 15 December 2011 11:23:19 mohnish pandey wrote: > The best way is to sit for sometime and write your own code implementing > periodic boundary condition. Writing the code may enhance you understanding > of the periodicity in the crystal. > > On Thu, Dec 15, 2011 at 3:51 PM, Giovanni La Penna wrote: > > In the past I used an utility of DL_POLY (a package widely used for > > simulations of empirical models of liquids, solids and partially > > ordered systems, membranes, liquid crystals, etc.): > > > > http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/ > > > > The utility was genlat.f (hopefully still contained in > > the open-source distributed version DL_POLY_CLASSIC). > > Any reminiscence in the latgen subroutine of QE? > > > > I see latgen.f is still used. > > As for an application, see for instance: > > http://arxiv.org/abs/1108.3396 > > > > However, I agree that if the things are not too complicated, > > the best is typing coordinates into an XYZ file, after > > a bit of manual drawing. Finally, watching at the result with > > some 3d-rendering graphic package. > > > > Giovanni La Penna (Cnr-ICCOM) > > > > ============================================================ > > Giovanni La Penna - National research council (Cnr) > > Institute for chemistry of organo-metallic compounds (Iccom) > > via Madonna del Piano 10, > > I-50019 Sesto Fiorentino, Firenze, Italy > > tel.: +39 055 522-5264, fax: +39 055 522-5203 > > e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna > > skype: giovannilapenna > > ============================================================ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From alex124678 at nc.rr.com Thu Dec 15 11:02:17 2011 From: alex124678 at nc.rr.com (Alex Shearer) Date: Thu, 15 Dec 2011 02:02:17 -0800 Subject: [Pw_forum] how to construct supercell for an fcc crystal compound In-Reply-To: References: <1323937195.73618.YahooMailNeo@web39402.mail.mud.yahoo.com> Message-ID: <4EE9C5A9.9080706@nc.rr.com> If you know the form of the basic repeating unit (The un-doped zincblende structure would be a good place to start), it may be useful to use a molecule building program that has tools designed for periodic systems. I have had success with gaussview; the GUI is relatively intuitive and the coordinates stored in the .com file of the supercell you create can be copied directly into the corresponding section of the PW script (though be mindful of what length units are being used). The key to gview is the PBC (periodic boundary conditions) menu; there are several tutorials online with detailed instructions regarding this part of the program. If gaussview isn't available, I have heard good reviews of other programs that may have similar or even better features - the one that comes to mind is Avogadro but I'm sure there are others too. All that being said, I agree with professor Baroni that trying the construction by hand is educational; as a new user of QE I tried by hand a couple times for different crystal faces before 'cheating' and using a program. Best of luck, Alex Shearer C.B. Harris Group University of California, Berkeley On 12/15/2011 1:11 AM, Stefano Baroni wrote: > The same way you would "by hands". First draw (physically with pencil > and paper, or just mentally if you have a good 3D imagination) a > zincblende crystal structure with many unit cells repeated in the > three dimensions. Give different atoms different colors. ZnSe can be > colored with just two colors (say, green and red, plus possibly black > to draw bonds). Then highlight the atoms that you want to turn into > impurities using a different color (say, blue), arranging them in > periodic array (i.e. one every 2/3/you-name-it elementary cells). > Which crystal structure has the artificial crystal you have built? The > unit cell of this artificial crystal will be your unit cell: it will > contain many atoms ... Do it by yourself: you will learn a lot ... > (and it may be fun!) - SB > > On Dec 15, 2011, at 9:19 AM, bamidele ibrahim wrote: > >> Dear all, >> I have been working on series of zinc blende semiconductors >> materials in recent time. >> I am now interested in doping some of the compound with differents >> element in other to alter >> the crystal structures(i.e introducing impurities). I know i need to >> build a supercell for my compound but, >> i don't understand how to do it. I went through all the examples >> files, but none was able to give the information. I will >> be delighted if you can all come to my aid. for example ZnSe with >> atomic position of (0,0,0) and (0.25,0.25,0.25). >> How do i build a supercell for this compound? >> Adetunji Bamidele Ibrahim >> Department of physics,University of Agriculture, >> Abeokuta, Ogun State,Nigeria. >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Stefano Baroni - SISSA&DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 > 406 (tel) -528 (fax) / stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale > de la pens?e - Jean Piaget > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > No virus found in this message. > Checked by AVG - www.avg.com > Version: 2012.0.1890 / Virus Database: 2108/4681 - Release Date: 12/14/11 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111215/31343f43/attachment.htm From arvifis at gmail.com Thu Dec 15 13:20:15 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Thu, 15 Dec 2011 10:20:15 -0200 Subject: [Pw_forum] how to construct supercell for an fcc crystal compound In-Reply-To: <4EE9C5A9.9080706@nc.rr.com> References: <1323937195.73618.YahooMailNeo@web39402.mail.mud.yahoo.com> <4EE9C5A9.9080706@nc.rr.com> Message-ID: Dear Bamidele Ibrahim: you can use VESTA program, it's a beatiful and friendly program to see crystal structures and make supercell, this program save the atomic positions in XYZ format. Furthermore, run on linux and win..! http://www.geocities.jp/kmo_mma/crystal/en/download-vesta.html Best. Arles V. Gil Rebaza IFLP - Argentina 2011/12/15 Alex Shearer > If you know the form of the basic repeating unit (The un-doped zincblende > structure would be a good place to start), it may be useful to use a > molecule building program that has tools designed for periodic systems. I > have had success with gaussview; the GUI is relatively intuitive and the > coordinates stored in the .com file of the supercell you create can be > copied directly into the corresponding section of the PW script (though be > mindful of what length units are being used). The key to gview is the PBC > (periodic boundary conditions) menu; there are several tutorials online > with detailed instructions regarding this part of the program. If gaussview > isn't available, I have heard good reviews of other programs that may have > similar or even better features - the one that comes to mind is Avogadro > but I'm sure there are others too. > > All that being said, I agree with professor Baroni that trying the > construction by hand is educational; as a new user of QE I tried by hand a > couple times for different crystal faces before 'cheating' and using a > program. > > Best of luck, > > Alex Shearer > C.B. Harris Group > University of California, Berkeley > > > > > On 12/15/2011 1:11 AM, Stefano Baroni wrote: > > The same way you would "by hands". First draw (physically with pencil and > paper, or just mentally if you have a good 3D imagination) a zincblende > crystal structure with many unit cells repeated in the three dimensions. > Give different atoms different colors. ZnSe can be colored with just two > colors (say, green and red, plus possibly black to draw bonds). Then > highlight the atoms that you want to turn into impurities using a different > color (say, blue), arranging them in periodic array (i.e. one every > 2/3/you-name-it elementary cells). Which crystal structure has the > artificial crystal you have built? The unit cell of this artificial crystal > will be your unit cell: it will contain many atoms ... Do it by yourself: > you will learn a lot ... (and it may be fun!) - SB > > On Dec 15, 2011, at 9:19 AM, bamidele ibrahim wrote: > > Dear all, > I have been working on series of zinc blende semiconductors materials > in recent time. > I am now interested in doping some of the compound with differents > element in other to alter > the crystal structures(i.e introducing impurities). I know i need to build > a supercell for my compound but, > i don't understand how to do it. I went through all the examples files, > but none was able to give the information. I will > be delighted if you can all come to my aid. for example ZnSe with atomic > position of (0,0,0) and (0.25,0.25,0.25). > How do i build a supercell for this compound? > > Adetunji Bamidele Ibrahim > Department of physics,University of Agriculture, > Abeokuta, Ogun State,Nigeria. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de > la pens?e - Jean Piaget > > > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > No virus found in this message. > Checked by AVG - www.avg.com > Version: 2012.0.1890 / Virus Database: 2108/4681 - Release Date: 12/14/11 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111215/e5ab5499/attachment-0001.htm From aaghafari at yahoo.com Thu Dec 15 13:29:54 2011 From: aaghafari at yahoo.com (ali ghafari) Date: Thu, 15 Dec 2011 04:29:54 -0800 (PST) Subject: [Pw_forum] Hybrid functional for non-scf Message-ID: <1323952194.22852.YahooMailNeo@web161405.mail.bf1.yahoo.com> Dear QS users Why Hybrid functionals don't implement in non-scf ? While it can be done for scf, in this situation how can I plot band structure? Best Regards Ali -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111215/17ee1029/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Thu Dec 15 13:54:14 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Thu, 15 Dec 2011 13:54:14 +0100 Subject: [Pw_forum] Hybrid functional for non-scf In-Reply-To: <1323952194.22852.YahooMailNeo@web161405.mail.bf1.yahoo.com> References: <1323952194.22852.YahooMailNeo@web161405.mail.bf1.yahoo.com> Message-ID: <201112151354.15232.giuseppe.mattioli@mlib.ism.cnr.it> Dear Ali You simply can't plot an accurate band structure. Please read the following file. It contains a bit of explanation... yourQE/examples/EXX_example/README HTH Giuseppe On Thursday 15 December 2011 13:29:54 ali ghafari wrote: > Dear QS users > > > Why Hybrid functionals don't implement in non-scf ? > While it can be done for scf, in this situation how can I plot band > structure? Best Regards > > Ali -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From canepap at wfu.edu Thu Dec 15 21:06:54 2011 From: canepap at wfu.edu (canepap at wfu.edu) Date: Thu, 15 Dec 2011 20:06:54 GMT Subject: [Pw_forum] From a friend at Zipcar Message-ID: ------------------- From a Friend at Zipcar ------------------- Hey Friend, You should join Zipcar, too! Why? It's easy—you just reserve online, let yourself in with your Zipcard and drive. It's convenient—there are thousands of Zipcars in the US, UK and Canada. It's fun—Zipcars come in every color, size and shape from hybrid to pickup. It's a sweet deal—low hourly and daily rates include fuel and insurance.

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Pieremanuele Learn more at http://www.zipcar.com and get $25 in free driving! Just enter mmpchffb as the promo code on your application. zipcar | wheels when you want them (TM) --------------- Need help? Contact: 1.866.494.7227 | info at zipcar.com Zipcar is the world's largest car sharing and car club service. It is an alternative to traditional car rental and car ownership. If you're 21+, share Zipcars in Atlanta, Baltimore, Boston, Chicago, London, New York, Philadelphia, Pittsburgh, Portland, San Francisco, Seattle, Toronto, Vancouver and Washington DC. Zipcars also live on campus at universities across North America. Copyright 2011 Zipcar, Inc. All rights reserved. Sent by: Zipcar, 25 First Street, 4th Floor, Cambridge, MA 02141 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111215/d3ca0d07/attachment.htm From dorabman at gmail.com Thu Dec 15 22:50:23 2011 From: dorabman at gmail.com (Hua Bao) Date: Thu, 15 Dec 2011 16:50:23 -0500 Subject: [Pw_forum] query on e-ph matrix element In-Reply-To: <1323686692.21852.34.camel@fe12lx.fisica.uniud.it> References: <1468233968.209665.1323581471095.JavaMail.root@mailhub016.itcs.purdue.edu> <1323686692.21852.34.camel@fe12lx.fisica.uniud.it> Message-ID: Dear QE-users and Paolo, Thanks for your explanation. Actually we can completely understand npert(irr). However, there is still difficulty for us to relate npert(irr) to a specific \nu. When we track the quantity "npert", we could not find out where it is modified (although we know it is defined in phcom.f90). Would you please point out the relationship between npert and \nu? Just point out which files we need to look into will be helpful. Thanks, Hua On Mon, Dec 12, 2011 at 5:44 AM, Paolo Giannozzi wrote: > On Sun, 2011-12-11 at 00:31 -0500, Ajit Vallabhaneni wrote: > > > I had gone thru the source code "elphon.f90" for this purpose. > > wow! you are a brave man > > > I could figure out all the variables like k,i,j,q but not nu. > > I see a variable 'imode0' which i cannot figure out its purpose. > > Can someone please help me with identifying the nu ? > > the el-ph matrix elements are calculated for each irrep, i.e. > displacement patterns transforming into each other under the > symmetry operations of the small group of each wavevector. > There are nirr irreps, each having dimension npert(irr). > The code runs over irreps: irr=1,..,nirr, then over irrep > components: ipert=1,..,npert(irr), and imode0+ipert is the > index of each displacement pattern. Only when the el-phon > coefficient "gamma" is calculated are phonon modes (contained > in matrix "dyn") actually used. > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111215/aaf713c1/attachment-0001.htm From ma at nano.ku.dk Fri Dec 16 14:00:09 2011 From: ma at nano.ku.dk (Martin Andersson) Date: Fri, 16 Dec 2011 14:00:09 +0100 Subject: [Pw_forum] heavier elements with empirical dispersion don't work [SOLVED] In-Reply-To: <4EEB3B73.80900@nano.ku.dk> References: <4EEB3B73.80900@nano.ku.dk> Message-ID: <4EEB40D9.6020907@nano.ku.dk> Hi all, I managed to find the small thing I missed and now it works. I attach the modified version of mm_dispersion.f90 if anyone wants to use it. Of course I say nothing about the accuracy of the DFT-D method for the heavy elements... Cheers, Martin Andersson University of Copenhagen -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: mm_dispersion.f90 Url: http://www.democritos.it/pipermail/pw_forum/attachments/20111216/911cff18/attachment.txt From ma at nano.ku.dk Fri Dec 16 13:37:07 2011 From: ma at nano.ku.dk (Martin Andersson) Date: Fri, 16 Dec 2011 13:37:07 +0100 Subject: [Pw_forum] heavier elements with empirical dispersion don't work Message-ID: <4EEB3B73.80900@nano.ku.dk> Hi, I have added parameters for elements 55-84 from Grimme's empirical dispersion to the mm_dispersion.f90 in Modules/ and recompiled the program. The program still doesn't work with Ba. The error reads: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from init_london : error # 1 atom Ba not found %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Could someone tell me what other modifications need to be done to the code in order to get it to work, please? Cheers, Martin Andersson, University of Copenhagen From giannozz at democritos.it Fri Dec 16 16:28:58 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 16 Dec 2011 16:28:58 +0100 Subject: [Pw_forum] heavier elements with empirical dispersion don't work In-Reply-To: <4EEB3B73.80900@nano.ku.dk> References: <4EEB3B73.80900@nano.ku.dk> Message-ID: On Dec 16, 2011, at 13:37 , Martin Andersson wrote: > from init_london : error # 1 > atom Ba not found try to replace in line 199 of Modules/mm_dispersion.f90 : i = atomic_number ( atom_label ( ilab ) ) with i = atomic_number ( TRIM(atom_label ( ilab )) ) If it doesn't, work, you have to print atom_label(ilab) and to go inside routine 'atomic_number' (it is in flib/ and figure out what happens (it is very simple to understand what it does) Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From dorabman at gmail.com Fri Dec 16 17:50:56 2011 From: dorabman at gmail.com (Hua Bao) Date: Fri, 16 Dec 2011 11:50:56 -0500 Subject: [Pw_forum] electron-phonon matrix element - relationship between npert and nu Message-ID: Dear Paolo and QE-users, The electron-phonon matrix element is written in terms of ibnd, jbnd, ik, ipert+imode0. (in elphon file) Based on your discussion with Ajit, I realize that ipert is the number of perturbations. However, I am still having difficulty to project nirr/npert to a specific \nu. It can be easily understand they are related, though. For a phonon wave vector q, there are \nu phonon modes. These modes are categorized into nirr irreducible representations, and each nirr has npert perturbations? Can I assume one perturbation is a component of one phonon pattern? Would you please point out the relationship between npert and \nu? Thanks, Hua -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111216/5ff26606/attachment-0001.htm From yunpengwang at live.com Sat Dec 17 11:14:49 2011 From: yunpengwang at live.com (Yunpeng Wang) Date: Sat, 17 Dec 2011 05:14:49 -0500 Subject: [Pw_forum] hybrid functional error Message-ID: Hi, I am using HSE06 hybrid functional to calculate binding energy of an atom to a molecule, because GGA gives non-consistent result compared to experimental results. The HSE06 run ends with following error after several EXX steps: ---------------------------------------------------- task # 53 from expint : error # 1 bad arguments ----------------------------------------------------- Where is the problem? best, Yun-Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111217/4d323609/attachment.htm From giannozz at democritos.it Sat Dec 17 12:40:29 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 17 Dec 2011 12:40:29 +0100 Subject: [Pw_forum] hybrid functional error In-Reply-To: References: Message-ID: <356B5E0C-E02E-4475-899A-973A5B91F0C2@democritos.it> On Dec 17, 2011, at 11:14 , Yunpeng Wang wrote: > from expint : error # 1 > bad arguments > > Where is the problem? it is where the error message says it is: in "expint" (flib/expint.f90). If you go inside the file, you will see that this error arises when * n < 0 , or * n=0,1 and x<=0, or * n>1 and x<0 The second case is the relevant one, I guess, Please specify which version of QE you are using: there have been several minor changes to the HSE routines since the first release. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Dec 17 12:42:40 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 17 Dec 2011 12:42:40 +0100 Subject: [Pw_forum] hybrid functional error In-Reply-To: <356B5E0C-E02E-4475-899A-973A5B91F0C2@democritos.it> References: <356B5E0C-E02E-4475-899A-973A5B91F0C2@democritos.it> Message-ID: <57A783A0-FAD4-4958-8123-235E3A30C3A3@democritos.it> On Dec 17, 2011, at 12:40 , Paolo Giannozzi wrote: > Please specify which version of QE you are using: there have been > several minor changes to the HSE routines since the first release. and also please specify if your calculation is spin-polarized or not. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From yunpengwang at live.com Sat Dec 17 15:12:25 2011 From: yunpengwang at live.com (Peter Wang) Date: Sat, 17 Dec 2011 22:12:25 +0800 Subject: [Pw_forum] hybrid functional error In-Reply-To: <57A783A0-FAD4-4958-8123-235E3A30C3A3@democritos.it> References: <356B5E0C-E02E-4475-899A-973A5B91F0C2@democritos.it> <57A783A0-FAD4-4958-8123-235E3A30C3A3@democritos.it> Message-ID: Hi PG: I am using QE version 4.3.2 and my system is spin-polarized. Yun-Peng -----????----- From: Paolo Giannozzi Sent: Saturday, December 17, 2011 7:42 PM To: PWSCF Forum Subject: Re: [Pw_forum] hybrid functional error On Dec 17, 2011, at 12:40 , Paolo Giannozzi wrote: > Please specify which version of QE you are using: there have been > several minor changes to the HSE routines since the first release. and also please specify if your calculation is spin-polarized or not. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From hannu.komsa at epfl.ch Sun Dec 18 15:51:03 2011 From: hannu.komsa at epfl.ch (hannu.komsa at epfl.ch) Date: Sun, 18 Dec 2011 15:51:03 +0100 Subject: [Pw_forum] hybrid functional error In-Reply-To: References: Message-ID: <20111218155103.898113bjdjo3k91z@webmail.epfl.ch> Since n is always 1, and by quickly looking at the code it should be that x>=0. Furthermore, x should be zero only if the density gradient is zero and the screening parameter is set to zero (=screening length infinity = PBE0). If you have done so, then you can fix the problem by either using PBE0 or using a very small parameter value (btw., these two approaches give slightly different results, although they should give the same). If you haven't done so, then... ? Hannu-Pekka Komsa University of Helsinki > >> from expint : error # 1 >> bad arguments >> >> Where is the problem? > > it is where the error message says it is: in "expint" (flib/expint.f90). > If you go inside the file, you will see that this error arises when > * n < 0 , or > * n=0,1 and x<=0, or > * n>1 and x<0 > The second case is the relevant one, I guess, > Please specify which version of QE you are using: there have been > several minor changes to the HSE routines since the first release. > From victor.bermudez at nrl.navy.mil Sun Dec 18 15:58:49 2011 From: victor.bermudez at nrl.navy.mil (Vic Bermudez) Date: Sun, 18 Dec 2011 09:58:49 -0500 Subject: [Pw_forum] Restarting a Geometry Optimization Message-ID: Hello, I've looked all over (manuals, tutorials, user forum posts, etc.) for an answer to this and can't find one. Can someone please provide a simple description of how, exactly, one goes about restarting a pwscf geometry optimization run that has timed out ? I know about the "restart" keyword, of course, but what files are needed from the previous run ? Is there a particular naming convention for these files that must be followed ? Is there a special subdirectory where these files have to be placed ? Thanks in Advance, Vic Bermudez Victor M. Bermudez Code 6876 U.S. Naval Research Laboratory 4555 Overlook Ave., S.W. Washington, DC 20375-5347 Phone: 202-767-6728 FAX: 202-767-1165 E-mail: victor.bermudez at nrl.navy.mil From yunpengwang at live.com Sun Dec 18 16:02:25 2011 From: yunpengwang at live.com (Peter Wang) Date: Sun, 18 Dec 2011 23:02:25 +0800 Subject: [Pw_forum] hybrid functional error In-Reply-To: <20111218155103.898113bjdjo3k91z@webmail.epfl.ch> References: <20111218155103.898113bjdjo3k91z@webmail.epfl.ch> Message-ID: I am sorry I can not get you. Do you recommand me to use PBE0 instead of HSE06? best, Yun-Peng -----????----- From: hannu.komsa at epfl.ch Sent: Sunday, December 18, 2011 10:51 PM To: pw_forum at pwscf.org Subject: Re: [Pw_forum] hybrid functional error Since n is always 1, and by quickly looking at the code it should be that x>=0. Furthermore, x should be zero only if the density gradient is zero and the screening parameter is set to zero (=screening length infinity = PBE0). If you have done so, then you can fix the problem by either using PBE0 or using a very small parameter value (btw., these two approaches give slightly different results, although they should give the same). If you haven't done so, then... ? Hannu-Pekka Komsa University of Helsinki > >> from expint : error # 1 >> bad arguments >> >> Where is the problem? > > it is where the error message says it is: in "expint" (flib/expint.f90). > If you go inside the file, you will see that this error arises when > * n < 0 , or > * n=0,1 and x<=0, or > * n>1 and x<0 > The second case is the relevant one, I guess, > Please specify which version of QE you are using: there have been > several minor changes to the HSE routines since the first release. > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Sun Dec 18 19:53:41 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 18 Dec 2011 19:53:41 +0100 Subject: [Pw_forum] Restarting a Geometry Optimization In-Reply-To: References: Message-ID: <5B5D9B5A-3D84-4EEC-87E2-1E65C052E6F1@democritos.it> On Dec 18, 2011, at 15:58 , Vic Bermudez wrote: > Can someone please provide a simple description of how, > exactly, one goes about restarting a pwscf geometry optimization > run that has timed out ? there s nothing "simple" about restarting, and in any case, "exactly" and "simple" don't match. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From degironc at sissa.it Sun Dec 18 20:03:31 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 18 Dec 2011 20:03:31 +0100 Subject: [Pw_forum] Restarting a Geometry Optimization In-Reply-To: <5B5D9B5A-3D84-4EEC-87E2-1E65C052E6F1@democritos.it> References: <5B5D9B5A-3D84-4EEC-87E2-1E65C052E6F1@democritos.it> Message-ID: <4EEE3903.60902@sissa.it> if the uncompleted job terminated smoothly (as is usually the case if the max_seconds variable was properly set) then it is sufficient to resubmit the job with the same input except that restart_mode="restart" is defined. If the job did not complete smoothly and files on the scratch area are corrupted, the simplest option is to copy the last set of coordinates from the output in the input and resubmit with restart_mode="from_scratch". this will begin a new relaxation from the last (best ?) available positions. stefano On 12/18/2011 07:53 PM, Paolo Giannozzi wrote: > On Dec 18, 2011, at 15:58 , Vic Bermudez wrote: > >> Can someone please provide a simple description of how, >> exactly, one goes about restarting a pwscf geometry optimization >> run that has timed out ? > there s nothing "simple" about restarting, and in any case, > "exactly" and "simple" don't match. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Sun Dec 18 21:36:39 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 18 Dec 2011 21:36:39 +0100 Subject: [Pw_forum] from cdiaghg : error # 2012 diagonalization (ZHEGV*) failed In-Reply-To: <5e4db3b40cc27bfa7acdd1fb99d47b5e.squirrel@ifgw.mail.ifi.unicamp.br> References: <5e4db3b40cc27bfa7acdd1fb99d47b5e.squirrel@ifgw.mail.ifi.unicamp.br> Message-ID: <85B8E9F3-C7BD-4F7D-BDA4-709AB0E77F88@democritos.it> On Dec 14, 2011, at 14:57 , pmoreira at ifi.unicamp.br wrote: > from : error # 2012 > diagonalization (ZHEGV*) failed > I did some tests suggested on user manual (cdiaghg error), > but I cannot figure out where my problem is first of all: is the error reproducible on different machines and under different conditions? the first thing to understand is whether this error actually reflects a problem in the hamiltonian or in the overlap matrix P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Dec 18 21:49:24 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 18 Dec 2011 21:49:24 +0100 Subject: [Pw_forum] electron-phonon matrix element - relationship between npert and nu In-Reply-To: References: Message-ID: On Dec 16, 2011, at 17:50 , Hua Bao wrote: > The electron-phonon matrix element is written in terms of ibnd, > jbnd, ik, ipert+imode0. (in elphon file) [...] However, I am still > having difficulty to project nirr/npert to a specific \nu. you shouldn't need to project anything. Electron-phonon matrix elements have to be symmetrized. The irrep basis is used for symmetrization. After symmetrization, the electron-phonon matrix elements are expressed in the basis of atomic displacements. Phonons are available in the basis of displacements as well. So you can forget about irreps. Or at least, this is what I remember, in at least one of the many possible ways to calculate electron-phonon coefficients. In the current development version, there are three, plus one with an external code P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Dec 18 22:03:05 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 18 Dec 2011 22:03:05 +0100 Subject: [Pw_forum] hybrid functional error In-Reply-To: References: <356B5E0C-E02E-4475-899A-973A5B91F0C2@democritos.it> <57A783A0-FAD4-4958-8123-235E3A30C3A3@democritos.it> Message-ID: On Dec 17, 2011, at 15:12 , Peter Wang wrote: > I am using QE version 4.3.2 and my system is spin-polarized. it might have been fixed by this recent change: http://qe-forge.org/scm/viewvc.php?view=rev&root=q-e&revision=8264 Not sure, though P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From permeakra at gmail.com Sun Dec 18 23:42:30 2011 From: permeakra at gmail.com (=?UTF-8?B?0J/QtdGA0LzRj9C60L7QsiDQldCy0LPQtdC90LjQuQ==?=) Date: Mon, 19 Dec 2011 02:42:30 +0400 Subject: [Pw_forum] PP generation and plotting ld1 output Message-ID: <4EEE6C56.8020304@gmail.com> Disclaimer At moment I need pseudopotentials for Mo, Co, S, H, C, O for PBE or better functional. Distribution, however, do not present PBE pseudo for Mo. So, i tried to build one, using Ru input is starting point (in distribution). When I tested pseudo built I found, that it works bad for ionic states (errors about 0.1 Ry). This means, I need either a PP with semicore or very fine tuning. The latter is a problem, since I need good performance for most states (1....6). Thus, I look forward for semicore. As I understand PP, I have to specify radii, whithin wich orbitals should be smoothed. The problem is, that to do it I need to find, where core electron density mostly end. So, here are the question. 1) Tutorials I found give some plotting comands, but do not give any advise how to plot density from specific subshell. How should I do this ? 2) Can someone tell me, are there any traps with PPs with semicore and possibly point some specific tutorials ? From avallabh at purdue.edu Mon Dec 19 02:01:44 2011 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Sun, 18 Dec 2011 20:01:44 -0500 (EST) Subject: [Pw_forum] electron-phonon matrix element - relationship between npert and nu In-Reply-To: Message-ID: <2076594508.228408.1324256504510.JavaMail.root@mailhub016.itcs.purdue.edu> Dear Paolo, Can you please refer to the variables which store the basis for atomic displacements ? Thanks AK From m.abbasnejad at gmail.com Mon Dec 19 05:41:55 2011 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Mon, 19 Dec 2011 13:41:55 +0900 Subject: [Pw_forum] X-ray diffraction Message-ID: Dear QE users, Hi, As far as I know, the Quantum ESPRESSO can calculate the K-edge X-ray absorption spectra calculation. I was wondering if it can do X-ray diffraction calculations in order to have that plot as well? Thanks in advance. Yours, Mohaddeseh Tehran university, Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111219/42001282/attachment.htm From divyasrivastava at jncasr.ac.in Mon Dec 19 06:00:55 2011 From: divyasrivastava at jncasr.ac.in (Divya Srivastava) Date: Mon, 19 Dec 2011 10:30:55 +0530 Subject: [Pw_forum] Fwd: No subject Message-ID: <1324270855.4eeec5078db8d@mercury.jncasr.ac.in> Divya Srivastava Research Associate TSU, JNCASR Jakkur, Bangalore-64 Tel: 080-2208-2834 --- Original message follows --- Subject: No subject From: Divya Srivastava To: "pw_forum-request at pwscf.org" Date: 19-12-2011 10:03 Hi I wish to do hybrid DFT on CusScS2 compound. I am not getting proper potential that I can use. If I am using "(Cu,Sc,S).pz-n-van_ak.UPF " type of potentials I am getting following error : from setup : error # 1 HYBRID XC not implemented for USPP or PAW I am using espresso-4.3 for this calculation, pbe0. Divya Srivastava Research Associate TSU, JNCASR Jakkur, Bangalore-64 Tel: 080-2208-2834 From yunpengwang at live.com Mon Dec 19 06:31:05 2011 From: yunpengwang at live.com (Yunpeng Wang) Date: Mon, 19 Dec 2011 00:31:05 -0500 Subject: [Pw_forum] Fwd: No subject In-Reply-To: <1324270855.4eeec5078db8d@mercury.jncasr.ac.in> References: <1324270855.4eeec5078db8d@mercury.jncasr.ac.in> Message-ID: because hybrid functionals work together only with norm-conserving pseudopotentials. The PP's you used are Ultrasoft PP's. Yun-Peng > Date: Mon, 19 Dec 2011 10:30:55 +0530 > From: divyasrivastava at jncasr.ac.in > To: pw_forum at pwscf.org > Subject: [Pw_forum] Fwd: No subject > > > Divya Srivastava > Research Associate > TSU, JNCASR > Jakkur, Bangalore-64 > Tel: 080-2208-2834 > > > --- Original message follows --- > Subject: No subject > From: Divya Srivastava > To: "pw_forum-request at pwscf.org" > Date: 19-12-2011 10:03 > > > Hi > I wish to do hybrid DFT on CusScS2 compound. I am not getting proper potential that I can use. > If I am using "(Cu,Sc,S).pz-n-van_ak.UPF " type of potentials I am getting following error : > from setup : error # 1 > HYBRID XC not implemented for USPP or PAW > I am using espresso-4.3 for this calculation, pbe0. > > > Divya Srivastava > Research Associate > TSU, JNCASR > Jakkur, Bangalore-64 > Tel: 080-2208-2834 > _______________________________________________ > 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/20111219/fc7149eb/attachment.htm From giannozz at democritos.it Mon Dec 19 12:48:42 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 19 Dec 2011 12:48:42 +0100 Subject: [Pw_forum] electron-phonon matrix element - relationship between npert and nu In-Reply-To: <2076594508.228408.1324256504510.JavaMail.root@mailhub016.itcs.purdue.edu> References: <2076594508.228408.1324256504510.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: <10E09777-6650-4E84-B87C-D5E9B26346FA@democritos.it> On Dec 19, 2011, at 2:01 , Ajit Vallabhaneni wrote: > Can you please refer to the variables which store the basis for > atomic displacements ? ? --- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy "Nothing is impossible for the man who doesn't have to do it himself" From giannozz at democritos.it Mon Dec 19 13:47:26 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 19 Dec 2011 13:47:26 +0100 Subject: [Pw_forum] PP generation and plotting ld1 output In-Reply-To: <4EEE6C56.8020304@gmail.com> References: <4EEE6C56.8020304@gmail.com> Message-ID: On Dec 18, 2011, at 23:42 , ???????? ??????? wrote: > 1) Tutorials I found give some plotting comands, but do not give any > advise how to plot density from specific subshell. How should I do > this ? just plot the square of the wave function. Apart from a r^2 factor and numerical factors, it is the density of that shell > 2) Can someone tell me, are there any traps with PPs with semicore "traps" i.e. pitfalls? plenty of them > and possibly point some specific tutorials ? there is a short section on the generation of semi-core PPs in atomic_doc/pseudo_gen.tex P. --- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy "Nothing is impossible for the man who doesn't have to do it himself" From kucukben at sissa.it Mon Dec 19 13:56:54 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Mon, 19 Dec 2011 13:56:54 +0100 Subject: [Pw_forum] =?utf-8?q?PP_generation_and_plotting_ld1_output?= In-Reply-To: <4EEE6C56.8020304@gmail.com> References: <4EEE6C56.8020304@gmail.com> Message-ID: <350326001555224f0fda9e0d2315e6be@sissa.it> hello, have you looked into pslibrary project in qe-forge? there is a Mo pseudo with semicore there with pbe. generated by as far as i know Andrea Dal Corso and tested. cheers emine On 18.12.2011 23:42, ???????? ??????? wrote: > Disclaimer > > At moment I need pseudopotentials for Mo, Co, S, H, C, O for PBE or > better functional. Distribution, however, do not present PBE pseudo > for > Mo. So, i tried to build one, using Ru input is starting point (in > distribution). When I tested pseudo built I found, that it works bad > for > ionic states (errors about 0.1 Ry). This means, I need either a PP > with > semicore or very fine tuning. The latter is a problem, since I need > good performance for most states (1....6). Thus, I look forward for > semicore. > > As I understand PP, I have to specify radii, whithin wich orbitals > should be smoothed. The problem is, that to do it I need to find, > where > core electron density mostly end. > > So, here are the question. > > 1) Tutorials I found give some plotting comands, but do not give any > advise how to plot density from specific subshell. How should I do > this ? > > 2) Can someone tell me, are there any traps with PPs with semicore > and > possibly point some specific tutorials ? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From permeakra at gmail.com Mon Dec 19 15:41:55 2011 From: permeakra at gmail.com (=?KOI8-R?B?5dfHxc7JyiDwxdLN0cvP1w==?=) Date: Mon, 19 Dec 2011 17:41:55 +0300 Subject: [Pw_forum] PP generation and plotting ld1 output In-Reply-To: <350326001555224f0fda9e0d2315e6be@sissa.it> References: <4EEE6C56.8020304@gmail.com> <350326001555224f0fda9e0d2315e6be@sissa.it> Message-ID: Ups, I missed it. Check sheduled, thanks 2011/12/19 Emine Kucukbenli > > hello, > have you looked into pslibrary project in qe-forge? > there is a Mo pseudo with semicore there with pbe. > generated by as far as i know Andrea Dal Corso and tested. > > cheers > emine > > On 18.12.2011 23:42, ???????? ??????? wrote: > > Disclaimer > > > > At moment I need pseudopotentials for Mo, Co, S, H, C, O for PBE or > > better functional. Distribution, however, do not present PBE pseudo > > for > > Mo. So, i tried to build one, using Ru input is starting point (in > > distribution). When I tested pseudo built I found, that it works bad > > for > > ionic states (errors about 0.1 Ry). This means, I need either a PP > > with > > semicore or very fine tuning. The latter is a problem, since I need > > good performance for most states (1....6). Thus, I look forward for > > semicore. > > > > As I understand PP, I have to specify radii, whithin wich orbitals > > should be smoothed. The problem is, that to do it I need to find, > > where > > core electron density mostly end. > > > > So, here are the question. > > > > 1) Tutorials I found give some plotting comands, but do not give any > > advise how to plot density from specific subshell. How should I do > > this ? > > > > 2) Can someone tell me, are there any traps with PPs with semicore > > and > > possibly point some specific tutorials ? > > _______________________________________________ > > 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/20111219/a5af3d11/attachment.htm From permeakra at gmail.com Mon Dec 19 15:53:28 2011 From: permeakra at gmail.com (=?KOI8-R?B?5dfHxc7JyiDwxdLN0cvP1w==?=) Date: Mon, 19 Dec 2011 17:53:28 +0300 Subject: [Pw_forum] PP generation and plotting ld1 output In-Reply-To: References: <4EEE6C56.8020304@gmail.com> Message-ID: The problem is, I cannot find, what column in ld1.x output represents subshell needed. For example, I runned computation for config '[Ar] 4s2 4p6 4d5 5s1' and got *.wfc file. I wish to plot core density and each subshell, and ideally I want plot some of them in pairs. And I'm not an experience gnuplot user and *.wfc format is not documented, or at least I wasn't able to find docs needed. The section in doc/pseudo_gen.tex is too short in my opinion. 2011/12/19 Paolo Giannozzi > > On Dec 18, 2011, at 23:42 , ???????? ??????? wrote: > > > 1) Tutorials I found give some plotting comands, but do not give any > > advise how to plot density from specific subshell. How should I do > > this ? > > just plot the square of the wave function. Apart from a r^2 factor and > numerical factors, it is the density of that shell > > > 2) Can someone tell me, are there any traps with PPs with semicore > > "traps" i.e. pitfalls? plenty of them > > > and possibly point some specific tutorials ? > > there is a short section on the generation of semi-core PPs in > atomic_doc/pseudo_gen.tex > > P. > --- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > "Nothing is impossible for the man who doesn't have to do it himself" > > > > _______________________________________________ > 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/20111219/b0b74c96/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Mon Dec 19 16:59:28 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 19 Dec 2011 16:59:28 +0100 Subject: [Pw_forum] electron-phonon matrix element - relationship between npert and nu In-Reply-To: <10E09777-6650-4E84-B87C-D5E9B26346FA@democritos.it> References: <2076594508.228408.1324256504510.JavaMail.root@mailhub016.itcs.purdue.edu> <10E09777-6650-4E84-B87C-D5E9B26346FA@democritos.it> Message-ID: On Mon, 19 Dec 2011 12:48:42 +0100, Paolo Giannozzi wrote: >> Can you please refer to the variables which store the basis for >> atomic displacements ? At the end of the phonon calculation, the phononic eigenvectors are printed at the end of the fildyn file. During the phonon calculation the symmetry-dependent patterns are stored in the variable "u" from module "modes". best regards -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From yaldachem at gmail.com Mon Dec 19 20:24:42 2011 From: yaldachem at gmail.com (yaldaa kh) Date: Mon, 19 Dec 2011 22:54:42 +0330 Subject: [Pw_forum] homo lumo Message-ID: dear all how are determined the energy of homo and lumo for a molecule in gas and adsorbed states? thanks in advance yaldaa k chemistry teacher dehkhoda highschool From tribhuwan.physics at gmail.com Tue Dec 20 10:13:33 2011 From: tribhuwan.physics at gmail.com (Tribhuwan Pandey) Date: Tue, 20 Dec 2011 14:43:33 +0530 Subject: [Pw_forum] Explanation required for file.anh_G in quantum espresso Message-ID: Hi all I am doing some calculation to calculate third-order anharmonic phonon lifetimes for Si and I came across the file si.anh_G. I would like some to help as to how to read this file. Your reply would be appreciated. Regards Tribhuwan -- * With Regards Tribhuwan Pandey Research Scholar Materials Theory and Simulation Group Materials Research Center Indian Institute of Science, Bangalore, India * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111220/e2e48911/attachment.htm From eugeniofs at iq.ufrj.br Tue Dec 20 15:44:06 2011 From: eugeniofs at iq.ufrj.br (Eugenio Furtado) Date: Tue, 20 Dec 2011 12:44:06 -0200 (BRST) Subject: [Pw_forum] core_hole In-Reply-To: <1480388252.70741.1324391588110.JavaMail.root@mail.iq.ufrj.br> Message-ID: <1421962688.70762.1324392246599.JavaMail.root@mail.iq.ufrj.br> Dear QE users, I've been tried to use the pseudo N.star1s-pbe-rrkjus.UPF , from QE pseudo database (http://www.quantum-espresso.org/pseudo/upfdetails.php?upf=N.star1s-pbe-rrkjus.UPF) in a SCF calculation (version 4.3). I follow the suggestions ( cutoff for wfc=60 and for chrg_den=600), however and unfortunately I got this: from read_upf_v2 : error # 1 Ultrasoft pseudopotentials in UPF format v.2.0.0 are affected by a bug compromising their quality. Please regenerate pseudopotential file for N Of course I understood the message... It should be updated? I know about the sensibility of the pseudopotentials when generated and used in different systems, and they should be tested to exhaustion ... But, one question: are the pseudo from the database of "general" purpose, I mean like "lanl2dz" or "sdd" are in gaussian or other MO packages? Thank you in advance! Best regards, Egn -- Eugenio Furtado de Souza Laboratorio de Modelagem Molecular-LABMMOL Universidade Federal do Rio de Janeiro Av. Athos da Silveira Ramos No 149, CT, Bloco A, sala 609 tel: (21) 2562-7132 Cidade Universit?ria, Ilha do Fund?o, Rio de Janeiro-RJ, CEP 21941-90 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111220/7706d98c/attachment.htm From baroni at sissa.it Tue Dec 20 16:20:06 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 20 Dec 2011 16:20:06 +0100 Subject: [Pw_forum] homo lumo In-Reply-To: References: Message-ID: <2D5CDCE1-C67B-40D5-ADE6-398949244B3B@sissa.it> On Dec 19, 2011, at 8:24 PM, yaldaa kh wrote: > dear all > how are determined the energy of homo and lumo for a molecule in gas > and adsorbed states? Dear Yaldaa, it's a great pleasure to welcome a highschool teacher joining this community: WELCOME ON BOARD! The two cases (gas phase and adsorbed states) are conceptually similar. What one has to do (either explicitly, if the complexity of the systems allows, or implicitly if it doesn't) is to calculate the lowest-lying "molecular orbitals" *of the entire system*. (I enclosed "molecular orbitals" in quotation marks because one has to treat the entire system - isolated molecule, if in the gas phase, or molecule+substrate if in the adsorbed state, as a unique big "molecule"). The number of calculated states must be no smaller than the number of electrons (the latter number is determined by the charge state of the overall system). Then, very simply, if you have N electrons, the N-th state will be the HOMO and the (N+1)-th the LUMO. The only difference between the two cases is that, in the adsorbed state, the "molecular orbitals" of the whole system (the only ones that have a mathematically and physically well defined meaning) will result from the hybridization of orbitals pertaining to the isolated molecule and the isolated substrate, much in the same way as molecular orbitals of an isolated molecule may be (approximately) expressed as linear combinations of atomic orbitals (LCAO). These hybridized orbitals will be strictly localized around the adsorbed molecule or delocalized all over the molecule+substrate system according to whether or not the corresponding energy is degenerate with some energy levels of the isolated substrate (two states are said "degenerate" if they have the same energy). Hope to have been clear enough and of some help. If not, do not hesitate to revert to us, and I (we) will try to be clearer ... Best wishes, Stefano Baroni > thanks in advance > yaldaa k > chemistry teacher > dehkhoda highschool > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111220/1c247bd4/attachment.htm From giannozz at democritos.it Tue Dec 20 16:37:15 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 Dec 2011 16:37:15 +0100 Subject: [Pw_forum] Explanation required for file.anh_G in quantum espresso In-Reply-To: References: Message-ID: On Dec 20, 2011, at 10:13 , Tribhuwan Pandey wrote: > I would like some to help as to how to read this file. the README in example 14 is more or less all the available documentation on anharmonic force constants P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Dec 20 22:35:00 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 Dec 2011 22:35:00 +0100 Subject: [Pw_forum] PP generation and plotting ld1 output In-Reply-To: References: <4EEE6C56.8020304@gmail.com> Message-ID: On Dec 19, 2011, at 15:53 , ??????? ???????? wrote: > I'm not an experience gnuplot user and *.wfc format is not documented there is nothing to be documented, IIRC: the first line describes the contents of the various columns P. --- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy "Nothing is impossible for the man who doesn't have to do it himself" From kacper.druzbicki at uj.edu.pl Wed Dec 21 10:54:35 2011 From: kacper.druzbicki at uj.edu.pl (=?iso-8859-2?Q?=22Kacper_Dru=BFbicki=22?=) Date: Wed, 21 Dec 2011 10:54:35 +0100 Subject: [Pw_forum] dynmat.x - segmentation fault error In-Reply-To: <1322730382.30265.2.camel@fe12lx.fisica.uniud.it> References: <70DAA912-9C42-4868-AD01-C9C68EAF4F50@democritos.it> <1322730382.30265.2.camel@fe12lx.fisica.uniud.it> Message-ID: I would like to kindly thank Prof Gianozzi for giving me the solution for the problem. Indeed, providing suggested changes was the point. Now dynmat.x works fine even for few-hundred atomic unit cells, with the only limitation of using ASR=simple. Thank you! Kacper Druzbicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Cracow, Poland phone: +48 12 6632265 ----- Original Message ----- From: Paolo Giannozzi Date: Thursday, December 1, 2011 10:06 am Subject: Re: [Pw_forum] dynmat.x - segmentation fault error To: PWSCF Forum > Try to replace routine set_asr in dynmat.f90 with the attached > version - no warranty > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Wed Dec 21 14:52:36 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 21 Dec 2011 14:52:36 +0100 Subject: [Pw_forum] core_hole In-Reply-To: <1421962688.70762.1324392246599.JavaMail.root@mail.iq.ufrj.br> References: <1421962688.70762.1324392246599.JavaMail.root@mail.iq.ufrj.br> Message-ID: On Dec 20, 2011, at 15:44 , Eugenio Furtado wrote: > Ultrasoft pseudopotentials in UPF format v.2.0.0 are affected by a > bug compromising their quality. Please regenerate pseudopotential > file for N done (courtesy of Giuseppe Mattioli who, unlike myself, keeps track of generation input): http://www.fisica.uniud.it/~giannozz/public/N.star1s-pbe- rrkjus.UPF Please report any problem with it. The file on the web server will be updated soon (1-2 months), since we are moving anyway to a new web interface. > are the pseudo from the database of "general" purpose, I mean like > "lanl2dz" > or "sdd" are in gaussian or other MO packages? never heard about "lanl2dz" or "sdd" . The pseudopotentials "should be" suitable for general usage, i.e., unless you plan to do something special, they should be ok (note that the one you found to be buggy is for special purposes: calculation of X-ray spectra). Most of them have actually been used in serious (or pretended to be such) calculations. P. --- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy "Nothing is impossible for the man who doesn't have to do it himself" From giuseppe.mattioli at mlib.ism.cnr.it Wed Dec 21 15:21:19 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Wed, 21 Dec 2011 15:21:19 +0100 Subject: [Pw_forum] core_hole In-Reply-To: References: <1421962688.70762.1324392246599.JavaMail.root@mail.iq.ufrj.br> Message-ID: <201112211521.19317.giuseppe.mattioli@mlib.ism.cnr.it> Non mi ero accorto che il "colpevole" era Eugenio Furtado... Gli ho insegnato il mese scorso a fare i conti XPS, aveva visto il mio lavoro sulle pirimidine alogenate e mi aveva contattato. Ciao G. On Wednesday 21 December 2011 14:52:36 Paolo Giannozzi wrote: > On Dec 20, 2011, at 15:44 , Eugenio Furtado wrote: > > Ultrasoft pseudopotentials in UPF format v.2.0.0 are affected by a > > bug compromising their quality. Please regenerate pseudopotential > > file for N > > done (courtesy of Giuseppe Mattioli who, unlike myself, keeps track > of generation > input): http://www.fisica.uniud.it/~giannozz/public/N.star1s-pbe- > rrkjus.UPF > Please report any problem with it. The file on the web server will be > updated > soon (1-2 months), since we are moving anyway to a new web interface. > > > are the pseudo from the database of "general" purpose, I mean like > > "lanl2dz" > > or "sdd" are in gaussian or other MO packages? > > never heard about "lanl2dz" or "sdd" . The pseudopotentials "should > be" suitable > for general usage, i.e., unless you plan to do something special, > they should be > ok (note that the one you found to be buggy is for special purposes: > calculation > of X-ray spectra). Most of them have actually been used in serious > (or pretended > to be such) calculations. > > P. > --- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > "Nothing is impossible for the man who doesn't have to do it himself" > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From giuseppe.mattioli at mlib.ism.cnr.it Wed Dec 21 15:24:56 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Wed, 21 Dec 2011 15:24:56 +0100 Subject: [Pw_forum] core_hole In-Reply-To: <201112211521.19317.giuseppe.mattioli@mlib.ism.cnr.it> References: <1421962688.70762.1324392246599.JavaMail.root@mail.iq.ufrj.br> <201112211521.19317.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <201112211524.56446.giuseppe.mattioli@mlib.ism.cnr.it> Sorry, the previous message was for Paolo only... On Wednesday 21 December 2011 15:21:19 Giuseppe Mattioli wrote: > Non mi ero accorto che il "colpevole" era Eugenio Furtado... Gli ho > insegnato il mese scorso a fare i conti XPS, aveva visto il mio lavoro > sulle pirimidine alogenate e mi aveva contattato. Ciao > G. > > On Wednesday 21 December 2011 14:52:36 Paolo Giannozzi wrote: > > On Dec 20, 2011, at 15:44 , Eugenio Furtado wrote: > > > Ultrasoft pseudopotentials in UPF format v.2.0.0 are affected by a > > > bug compromising their quality. Please regenerate pseudopotential > > > file for N > > > > done (courtesy of Giuseppe Mattioli who, unlike myself, keeps track > > of generation > > input): http://www.fisica.uniud.it/~giannozz/public/N.star1s-pbe- > > rrkjus.UPF > > Please report any problem with it. The file on the web server will be > > updated > > soon (1-2 months), since we are moving anyway to a new web interface. > > > > > are the pseudo from the database of "general" purpose, I mean like > > > "lanl2dz" > > > or "sdd" are in gaussian or other MO packages? > > > > never heard about "lanl2dz" or "sdd" . The pseudopotentials "should > > be" suitable > > for general usage, i.e., unless you plan to do something special, > > they should be > > ok (note that the one you found to be buggy is for special purposes: > > calculation > > of X-ray spectra). Most of them have actually been used in serious > > (or pretended > > to be such) calculations. > > > > P. > > --- > > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > > "Nothing is impossible for the man who doesn't have to do it himself" > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From eugeniofs at iq.ufrj.br Wed Dec 21 15:39:27 2011 From: eugeniofs at iq.ufrj.br (Eugenio Furtado) Date: Wed, 21 Dec 2011 12:39:27 -0200 (BRST) Subject: [Pw_forum] core_hole In-Reply-To: Message-ID: <1756543773.73737.1324478367222.JavaMail.root@mail.iq.ufrj.br> Dear all, >>...never heard about "lanl2dz" or "sdd" . See for example: J. Am. Chem. Soc. , 2011 , 133 (45), pp 18328?18342 and J. Am. Chem. Soc. , 2011 , 133 (43), pp 17180?17191 . They should be used in MO calculations, as far as I can see... From this moment, I'm afraid that something will change in my mind... >>http://www.fisica.uniud.it/~giannozz/public/N.star1s-pbe- rrkjus.UPF Not Found The requested URL /~giannozz/public/N.star1s-pbe- was not found on this server. Apache/1.3.4 Server at www.fisica.uniud.it Port 80 Best regards, Egn ----- Mensagem original ----- De: "Paolo Giannozzi" Para: "PWSCF Forum" Enviadas: Quarta-feira, 21 de Dezembro de 2011 11:52:36 Assunto: Re: [Pw_forum] core_hole On Dec 20, 2011, at 15:44 , Eugenio Furtado wrote: > Ultrasoft pseudopotentials in UPF format v.2.0.0 are affected by a > bug compromising their quality. Please regenerate pseudopotential > file for N done (courtesy of Giuseppe Mattioli who, unlike myself, keeps track of generation input): http://www.fisica.uniud.it/~giannozz/public/N.star1s-pbe- rrkjus.UPF Please report any problem with it. The file on the web server will be updated soon (1-2 months), since we are moving anyway to a new web interface. > are the pseudo from the database of "general" purpose, I mean like > "lanl2dz" > or "sdd" are in gaussian or other MO packages? never heard about "lanl2dz" or "sdd" . The pseudopotentials "should be" suitable for general usage, i.e., unless you plan to do something special, they should be ok (note that the one you found to be buggy is for special purposes: calculation of X-ray spectra). Most of them have actually been used in serious (or pretended to be such) calculations. P. --- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy "Nothing is impossible for the man who doesn't have to do it himself" _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Eugenio Furtado de Souza Laboratorio de Modelagem Molecular-LABMMOL Universidade Federal do Rio de Janeiro Av. Athos da Silveira Ramos No 149, CT, Bloco A, sala 609 tel: (21) 2562-7132 Cidade Universit?ria, Ilha do Fund?o, Rio de Janeiro-RJ, CEP 21941-90 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111221/a4c42697/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Wed Dec 21 15:46:31 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Wed, 21 Dec 2011 15:46:31 +0100 Subject: [Pw_forum] core_hole In-Reply-To: <1756543773.73737.1324478367222.JavaMail.root@mail.iq.ufrj.br> References: <1756543773.73737.1324478367222.JavaMail.root@mail.iq.ufrj.br> Message-ID: <201112211546.31432.giuseppe.mattioli@mlib.ism.cnr.it> Dear Eugenio > >>http://www.fisica.uniud.it/~giannozz/public/N.star1s-pbe- rrkjus.UPF > > Not Found The requested URL /~giannozz/public/N.star1s-pbe- was not found > on this server. there is an extra blank space in the address... Try with http://www.fisica.uniud.it/~giannozz/public/N.star1s-pbe-rrkjus.UPF the PP is there. Cheers Giuseppe On Wednesday 21 December 2011 15:39:27 Eugenio Furtado wrote: > Dear all, > > >>...never heard about "lanl2dz" or "sdd" . > > See for example: J. Am. Chem. Soc. , 2011 , 133 (45), pp 18328?18342 and J. > Am. Chem. Soc. , 2011 , 133 (43), pp 17180?17191 . They should be used in > MO calculations, as far as I can see... From this moment, I'm afraid that > something will change in my mind... > > >>http://www.fisica.uniud.it/~giannozz/public/N.star1s-pbe- rrkjus.UPF > > Not Found The requested URL /~giannozz/public/N.star1s-pbe- was not found > on this server. > > > Apache/1.3.4 Server at www.fisica.uniud.it Port 80 > > Best regards, > Egn > ----- Mensagem original ----- > De: "Paolo Giannozzi" > Para: "PWSCF Forum" > Enviadas: Quarta-feira, 21 de Dezembro de 2011 11:52:36 > Assunto: Re: [Pw_forum] core_hole > > On Dec 20, 2011, at 15:44 , Eugenio Furtado wrote: > > Ultrasoft pseudopotentials in UPF format v.2.0.0 are affected by a > > bug compromising their quality. Please regenerate pseudopotential > > file for N > > done (courtesy of Giuseppe Mattioli who, unlike myself, keeps track > of generation > input): http://www.fisica.uniud.it/~giannozz/public/N.star1s-pbe- > rrkjus.UPF > Please report any problem with it. The file on the web server will be > updated > soon (1-2 months), since we are moving anyway to a new web interface. > > > are the pseudo from the database of "general" purpose, I mean like > > "lanl2dz" > > or "sdd" are in gaussian or other MO packages? > > never heard about "lanl2dz" or "sdd" . The pseudopotentials "should > be" suitable > for general usage, i.e., unless you plan to do something special, > they should be > ok (note that the one you found to be buggy is for special purposes: > calculation > of X-ray spectra). Most of them have actually been used in serious > (or pretended > to be such) calculations. > > P. > --- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > "Nothing is impossible for the man who doesn't have to do it himself" > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From giannozz at democritos.it Wed Dec 21 15:50:21 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 21 Dec 2011 15:50:21 +0100 Subject: [Pw_forum] core_hole In-Reply-To: <1756543773.73737.1324478367222.JavaMail.root@mail.iq.ufrj.br> References: <1756543773.73737.1324478367222.JavaMail.root@mail.iq.ufrj.br> Message-ID: <407EFC93-B864-46DE-9C90-8006E34FEB0C@democritos.it> On Dec 21, 2011, at 15:39 , Eugenio Furtado wrote: > >>http://www.fisica.uniud.it/~giannozz/public/N.star1s-pbe- rrkjus.UPF > Not Found The requested URL /~giannozz/public/N.star1s-pbe- was not > found on this server. there is a spurious space between "pbe-" and "rrkjus" > P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From eugeniofs at iq.ufrj.br Wed Dec 21 15:52:32 2011 From: eugeniofs at iq.ufrj.br (Eugenio Furtado) Date: Wed, 21 Dec 2011 12:52:32 -0200 (BRST) Subject: [Pw_forum] core_hole In-Reply-To: <201112211546.31432.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <1024091775.73757.1324479152798.JavaMail.root@mail.iq.ufrj.br> Dear G. >there is an extra blank space in the address... Try with >http://www.fisica.uniud.it/~giannozz/public/N.star1s-pbe-rrkjus.UPF I 'm sorry! My bad... Works Egn ----- Mensagem original ----- De: "Giuseppe Mattioli" Para: "pw forum" Enviadas: Quarta-feira, 21 de Dezembro de 2011 12:46:31 Assunto: Re: [Pw_forum] core_hole Dear Eugenio > >>http://www.fisica.uniud.it/~giannozz/public/N.star1s-pbe- rrkjus.UPF > > Not Found The requested URL /~giannozz/public/N.star1s-pbe- was not found > on this server. there is an extra blank space in the address... Try with http://www.fisica.uniud.it/~giannozz/public/N.star1s-pbe-rrkjus.UPF the PP is there. Cheers Giuseppe On Wednesday 21 December 2011 15:39:27 Eugenio Furtado wrote: > Dear all, > > >>...never heard about "lanl2dz" or "sdd" . > > See for example: J. Am. Chem. Soc. , 2011 , 133 (45), pp 18328?18342 and J. > Am. Chem. Soc. , 2011 , 133 (43), pp 17180?17191 . They should be used in > MO calculations, as far as I can see... From this moment, I'm afraid that > something will change in my mind... > > >>http://www.fisica.uniud.it/~giannozz/public/N.star1s-pbe- rrkjus.UPF > > Not Found The requested URL /~giannozz/public/N.star1s-pbe- was not found > on this server. > > > Apache/1.3.4 Server at www.fisica.uniud.it Port 80 > > Best regards, > Egn > ----- Mensagem original ----- > De: "Paolo Giannozzi" > Para: "PWSCF Forum" > Enviadas: Quarta-feira, 21 de Dezembro de 2011 11:52:36 > Assunto: Re: [Pw_forum] core_hole > > On Dec 20, 2011, at 15:44 , Eugenio Furtado wrote: > > Ultrasoft pseudopotentials in UPF format v.2.0.0 are affected by a > > bug compromising their quality. Please regenerate pseudopotential > > file for N > > done (courtesy of Giuseppe Mattioli who, unlike myself, keeps track > of generation > input): http://www.fisica.uniud.it/~giannozz/public/N.star1s-pbe- > rrkjus.UPF > Please report any problem with it. The file on the web server will be > updated > soon (1-2 months), since we are moving anyway to a new web interface. > > > are the pseudo from the database of "general" purpose, I mean like > > "lanl2dz" > > or "sdd" are in gaussian or other MO packages? > > never heard about "lanl2dz" or "sdd" . The pseudopotentials "should > be" suitable > for general usage, i.e., unless you plan to do something special, > they should be > ok (note that the one you found to be buggy is for special purposes: > calculation > of X-ray spectra). Most of them have actually been used in serious > (or pretended > to be such) calculations. > > P. > --- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > "Nothing is impossible for the man who doesn't have to do it himself" > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Eugenio Furtado de Souza Laboratorio de Modelagem Molecular-LABMMOL Universidade Federal do Rio de Janeiro Av. Athos da Silveira Ramos No 149, CT, Bloco A, sala 609 tel: (21) 2562-7132 Cidade Universit?ria, Ilha do Fund?o, Rio de Janeiro-RJ, CEP 21941-90 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111221/3e155fba/attachment.htm From 1009ukumar at gmail.com Fri Dec 23 05:47:33 2011 From: 1009ukumar at gmail.com (Sonu Kumar) Date: Fri, 23 Dec 2011 10:17:33 +0530 Subject: [Pw_forum] SCF correction compared to forces is too large. Message-ID: Dear all QE users, During optimization, i got following message: Total force = 0.000004 Total SCF correction = 0.000001 SCF correction compared to forces is too large, reduce conv_thr Total force is less than total scf correction. Then why the message is contradicting? I used conv threshold for scf=1.0d-10. Thank you. regards, ========================================== Sonu Kumar Phd Student,Physics Department Indian Institute of Technology ,Delhi-110016, India web:-http://www.iitd.ac.in/ ========================================== From fratesi at mater.unimib.it Fri Dec 23 10:03:45 2011 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Fri, 23 Dec 2011 10:03:45 +0100 Subject: [Pw_forum] SCF correction compared to forces is too large. In-Reply-To: References: Message-ID: <4EF443F1.4040508@mater.unimib.it> Dear Sonu Kumar, in general this warning means that the forces you are computing are not very accurate, BUT relatively to their absolute value. Here, the absolute value of the force is very small so even a tiny SCF correction appears large, so the warning. You can safely ignore it because there's no harm in missing forces by 25% when they are negligible. Notice that how large a 'negligible' force depends on you and the system under investigation. In my experience this situation is not unfrequent at the end of the optimization process. I expect you could get accurate results in terms of coordinates and total energy also with a bit larger scf threshold (1d-8?). Guido Il 12/23/2011 05:47 AM, Sonu Kumar ha scritto: > Dear all QE users, > > During optimization, i got following message: > > Total force = 0.000004 Total SCF correction = 0.000001 > SCF correction compared to forces is too large, reduce conv_thr > > Total force is less than total scf correction. Then why the message > is contradicting? I used conv threshold for scf=1.0d-10. > > Thank you. > > regards, > > ========================================== > Sonu Kumar > Phd Student,Physics Department > Indian Institute of Technology ,Delhi-110016, India > web:-http://www.iitd.ac.in/ > ========================================== > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From 1009ukumar at gmail.com Fri Dec 23 10:46:01 2011 From: 1009ukumar at gmail.com (Sonu Kumar) Date: Fri, 23 Dec 2011 15:16:01 +0530 Subject: [Pw_forum] SCF correction compared to forces is too large. In-Reply-To: <4EF443F1.4040508@mater.unimib.it> References: <4EF443F1.4040508@mater.unimib.it> Message-ID: Dear Prof. Guido Fratesi Thank you very much for your reply. I also take this opportunity to wish you all a merry Christmas. !! Regards, sonu ========================================== Sonu Kumar Phd Student,Physics Department Indian Institute of Technology ,Delhi-110016, India https://profiles.google.com/1009ukumar web:-http://www.iitd.ac.in/ ========================================== On Fri, Dec 23, 2011 at 2:33 PM, Guido Fratesi wrote: > Dear Sonu Kumar, > > in general this warning means that the forces you are computing are not > very accurate, BUT relatively to their absolute value. > ?Here, the absolute value of the force is very small so even a tiny SCF > correction appears large, so the warning. You can safely ignore it > because there's no harm in missing forces by 25% when they are > negligible. Notice that how large a 'negligible' force depends on you > and the system under investigation. > ?In my experience this situation is not unfrequent at the end of the > optimization process. I expect you could get accurate results in terms > of coordinates and total energy also with a bit larger scf threshold > (1d-8?). > > Guido > > Il 12/23/2011 05:47 AM, Sonu Kumar ha scritto: >> Dear all QE users, >> >> During optimization, i got following message: >> >> ? Total force = ? ? 0.000004 ? ? Total SCF correction = ? ? 0.000001 >> ? SCF correction compared to forces is too large, reduce conv_thr >> >> Total force is ?less than total scf correction. Then why the message >> is contradicting? I used ?conv threshold for scf=1.0d-10. >> >> Thank you. >> >> regards, >> >> ========================================== >> Sonu Kumar >> Phd Student,Physics Department >> Indian Institute of Technology ,Delhi-110016, India >> web:-http://www.iitd.ac.in/ >> ========================================== >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > -- > Guido Fratesi > > Dipartimento di Scienza dei Materiali > Universita` degli Studi di Milano-Bicocca > via Cozzi 53, 20125 Milano, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From physik.shyam at gmail.com Fri Dec 23 13:59:37 2011 From: physik.shyam at gmail.com (Shyam Khambholja) Date: Fri, 23 Dec 2011 18:29:37 +0530 Subject: [Pw_forum] Phonons in CsCl type structured materials.... Message-ID: Dear all, I want to calculate phonon dispersion in CsCl type structured materials. How to generate k-points, which are to be used in matdyn.in file ?? Thanks in advance. -- Mr. Shyam G Khambholja, Research student, Depratment of Physics, Sardar Patel University, Gujarat -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111223/2d3a4b93/attachment.htm From deepak.p.thakur at gmail.com Fri Dec 23 14:53:08 2011 From: deepak.p.thakur at gmail.com (Dipak Thakur) Date: Fri, 23 Dec 2011 19:23:08 +0530 Subject: [Pw_forum] Fwd: Atoms moving into Vacuum In-Reply-To: References: Message-ID: Dear All, I am trying to optimize hydroxyapatite 1x1x2 and 1x1x1. However, the atoms in the unit cell move into vacuum above the slab. See the figure below. That is while optimization [scf] all the atoms move such that they occupy the vacuum above. I have worked with graphene but never faced such problems. Can any one help me understanding why this might be happening. Below is my input file. ---------------------------------------------------------------------------------------------------------------------------------------------- &CONTROL Calculation = "relax" , restart_mode = 'from_scratch' , outdir ='/usr/espresso-4.3.2/', pseudo_dir = '/usr/espresso-4.3.2/pseudo/', disk_io = 'default' , verbosity = 'default' , etot_conv_thr = 1.D-4 , forc_conv_thr = 1.D-3 , nstep = 500 , dt = 40 , / &SYSTEM ibrav = 0, nat = 96, ntyp = 4, ecutwfc = 10 , ecutrho = 80 , occupations = 'smearing' , degauss = 0.02 , / &ELECTRONS electron_maxstep = 300, Conv_thr = 1.0d-8 , mixing_mode = 'plain' , mixing_beta = 0.5 , diagonalization = 'cg' , diago_cg_maxiter = 50, / &IONS / CELL_PARAMETERS 17.80868385387 0.00000000000 0.00000000000 -8.90434192693 15.42277262532 0.00000000000 0.00000000000 0.00000000000 25.99871311373 ATOMIC_SPECIES Ca 40.07800 Ca.pz-n-vbc.UPF P 39.09830 P.pz-van_ak.UPF O 15.99940 O.pz-van_ak.UPF H 1.007940 H.pz-van_ak.UPF ATOMIC_POSITIONS angstrom Ca -0.4710847875E-11 5.440920259 0.1031844561E-01 Ca -0.4710847875E-11 5.440920259 6.889282188 Ca 4.711975164 2.720460129 13.74760904 Ca 4.711975164 2.720460129 6.868645296 Ca 4.711975164 2.720460129 3.449800317 Ca 4.711975164 2.720460129 10.32876406 Ca 0.4713197894E-11 5.440920259 3.429163425 Ca 0.4713197894E-11 5.440920259 10.30812717 Ca -2.355045187 8.107515277 1.719740935 Ca -2.355045187 8.107515277 8.598704677 Ca 7.067020351 0.5386511056E-01 12.03818655 Ca 7.067020351 0.5386511056E-01 5.159222806 Ca 1.225113543 2.014228680 5.159222806 Ca 1.225113543 2.014228680 12.03818655 Ca 3.486861621 6.147151708 1.719740935 Ca 3.486861621 6.147151708 8.598704677 Ca -1.131816434 2.068093790 1.719740935 Ca -1.131816434 2.068093790 8.598704677 Ca 5.843791598 6.093286598 12.03818655 Ca 5.843791598 6.093286598 5.159222806 P 2.020966148 3.007468673 1.719740935 P 2.020966148 3.007468673 8.598704677 P 2.691009016 5.153911715 12.03818655 P 2.691009016 5.153911715 5.159222806 P -1.594061198 3.253942361 5.159222806 P -1.594061198 3.253942361 12.03818655 P 6.306036362 4.907438027 1.719740935 P 6.306036362 4.907438027 8.598704677 P 5.808922982 0.2464736877 1.719740935 P 5.808922982 0.2464736877 8.598704677 P -1.096947818 7.914906700 12.03818655 P -1.096947818 7.914906700 5.159222806 O 0.8104597282 3.956637212 1.719740935 O 0.8104597282 3.956637212 8.598704677 O 3.901515436 4.204743176 12.03818655 O 3.901515436 4.204743176 5.159222806 O 6.402631853 2.680197319 5.159222806 O 6.402631853 2.680197319 12.03818655 O -1.690656689 5.481183068 1.719740935 O -1.690656689 5.481183068 8.598704677 O 0.8801969606 6.884940495 1.719740935 O 0.8801969606 6.884940495 8.598704677 O 3.831778203 1.276439893 12.03818655 O 3.831778203 1.276439893 5.159222806 O 3.343146379 3.795858018 1.719740935 O 3.343146379 3.795858018 8.598704677 O 1.368828785 4.365522369 12.03818655 O 1.368828785 4.365522369 5.159222806 O -1.615736284 4.793178702 5.159222806 O -1.615736284 4.793178702 12.03818655 O 6.327711448 3.368201686 1.719740935 O 6.327711448 3.368201686 8.598704677 O 4.465067665 0.9973206834 1.719740935 O 4.465067665 0.9973206834 8.598704677 O 0.2469074986 7.164059704 12.03818655 O 0.2469074986 7.164059704 5.159222806 O 2.023793333 2.104820002 0.4829032547 O 2.023793333 2.104820002 7.361866997 O 2.688181831 6.056560386 13.27502423 O 2.688181831 6.056560386 6.396060487 O -0.8109309257 2.805066439 3.922385126 O -0.8109309257 2.805066439 10.80134887 O 5.522906090 5.356313949 2.956578616 O 5.522906090 5.356313949 9.835542358 O 6.589226069 0.7002464373 0.4829032547 O 6.589226069 0.7002464373 7.361866997 O -1.877250905 7.461133951 13.27502423 O -1.877250905 7.461133951 6.396060487 O 2.688181831 6.056560386 3.922385126 O 2.688181831 6.056560386 10.80134887 O 2.023793333 2.104820002 2.956578616 O 2.023793333 2.104820002 9.835542358 O 5.522906090 5.356313949 0.4829032547 O 5.522906090 5.356313949 7.361866997 O -0.8109309257 2.805066439 13.27502423 O -0.8109309257 2.805066439 6.396060487 O -1.877250905 7.461133951 3.922385126 O -1.877250905 7.461133951 10.80134887 O 6.589226069 0.7002464373 2.956578616 O 6.589226069 0.7002464373 9.835542358 O 0.000000000 0.000000000 1.341397930 O 0.000000000 0.000000000 8.220361672 O 0.000000000 0.000000000 12.41652955 O 0.000000000 0.000000000 5.537565812 O 0.000000000 0.000000000 4.780879801 O 0.000000000 0.000000000 11.65984354 O 0.000000000 0.000000000 2.098083941 O 0.000000000 0.000000000 8.977047683 H 0.000000000 0.000000000 0.4182409955 H 0.000000000 0.000000000 7.297204737 H 0.000000000 0.000000000 13.33968649 H 0.000000000 0.000000000 6.460722746 H 0.000000000 0.000000000 3.857722866 H 0.000000000 0.000000000 10.73668661 H 0.000000000 0.000000000 3.021240875 H 0.000000000 0.000000000 9.900204617 K_POINTS automatic 1 1 1 0 0 0 ---------------------------------------------------------------------------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111223/f3a2bd1f/attachment.htm From giannozz at democritos.it Fri Dec 23 15:06:30 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 23 Dec 2011 15:06:30 +0100 Subject: [Pw_forum] Fwd: Atoms moving into Vacuum In-Reply-To: References: Message-ID: On Dec 23, 2011, at 14:53 , Dipak Thakur wrote: > See the figure below. I don't see any figure below P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From fratesi at mater.unimib.it Fri Dec 23 15:10:55 2011 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Fri, 23 Dec 2011 15:10:55 +0100 Subject: [Pw_forum] Fwd: Atoms moving into Vacuum In-Reply-To: References: Message-ID: <4EF48BEF.80707@mater.unimib.it> Dear Dipak Thakur, I don't know about the system and have not fully understood your problem, nor seen any figure, but I would recommend you to double check the input coordinates: you are plenty of O atoms very close to each other, see for example atom number 84 and 85 (76pm!). And, the input file you sent us does not correspond to a slab. You might want to use "K_POINTS Gamma". HTH Guido Il 12/23/2011 02:53 PM, Dipak Thakur ha scritto: > Dear All, > > I am trying to optimize hydroxyapatite 1x1x2 and 1x1x1. > However, the atoms in the unit cell move into vacuum above the slab. See > the figure below. > > That is while optimization [scf] all the atoms move such that they > occupy the vacuum above. > I have worked with graphene but never faced such problems. > > Can any one help me understanding why this might be happening. > Below is my input file. > > ---------------------------------------------------------------------------------------------------------------------------------------------- > &CONTROL > Calculation = "relax" , > restart_mode = 'from_scratch' , > outdir ='/usr/espresso-4.3.2/', > pseudo_dir = '/usr/espresso-4.3.2/pseudo/', > disk_io = 'default' , > verbosity = 'default' , > etot_conv_thr = 1.D-4 , > forc_conv_thr = 1.D-3 , > nstep = 500 , > dt = 40 , > / > &SYSTEM > ibrav = 0, > nat = 96, > ntyp = 4, > ecutwfc = 10 , > ecutrho = 80 , > occupations = 'smearing' , > degauss = 0.02 , > / > &ELECTRONS > electron_maxstep = 300, > Conv_thr = 1.0d-8 , > mixing_mode = 'plain' , > mixing_beta = 0.5 , > diagonalization = 'cg' , > diago_cg_maxiter = 50, > / > &IONS > / > CELL_PARAMETERS > 17.80868385387 0.00000000000 0.00000000000 > -8.90434192693 15.42277262532 0.00000000000 > 0.00000000000 0.00000000000 25.99871311373 > ATOMIC_SPECIES > Ca 40.07800 Ca.pz-n-vbc.UPF > P 39.09830 P.pz-van_ak.UPF > O 15.99940 O.pz-van_ak.UPF > H 1.007940 H.pz-van_ak.UPF > ATOMIC_POSITIONS angstrom > Ca -0.4710847875E-11 5.440920259 0.1031844561E-01 > Ca -0.4710847875E-11 5.440920259 6.889282188 > Ca 4.711975164 2.720460129 13.74760904 > Ca 4.711975164 2.720460129 6.868645296 > Ca 4.711975164 2.720460129 3.449800317 > Ca 4.711975164 2.720460129 10.32876406 > Ca 0.4713197894E-11 5.440920259 3.429163425 > Ca 0.4713197894E-11 5.440920259 10.30812717 > Ca -2.355045187 8.107515277 1.719740935 > Ca -2.355045187 8.107515277 8.598704677 > Ca 7.067020351 0.5386511056E-01 12.03818655 > Ca 7.067020351 0.5386511056E-01 5.159222806 > Ca 1.225113543 2.014228680 5.159222806 > Ca 1.225113543 2.014228680 12.03818655 > Ca 3.486861621 6.147151708 1.719740935 > Ca 3.486861621 6.147151708 8.598704677 > Ca -1.131816434 2.068093790 1.719740935 > Ca -1.131816434 2.068093790 8.598704677 > Ca 5.843791598 6.093286598 12.03818655 > Ca 5.843791598 6.093286598 5.159222806 > P 2.020966148 3.007468673 1.719740935 > P 2.020966148 3.007468673 8.598704677 > P 2.691009016 5.153911715 12.03818655 > P 2.691009016 5.153911715 5.159222806 > P -1.594061198 3.253942361 5.159222806 > P -1.594061198 3.253942361 12.03818655 > P 6.306036362 4.907438027 1.719740935 > P 6.306036362 4.907438027 8.598704677 > P 5.808922982 0.2464736877 1.719740935 > P 5.808922982 0.2464736877 8.598704677 > P -1.096947818 7.914906700 12.03818655 > P -1.096947818 7.914906700 5.159222806 > O 0.8104597282 3.956637212 1.719740935 > O 0.8104597282 3.956637212 8.598704677 > O 3.901515436 4.204743176 12.03818655 > O 3.901515436 4.204743176 5.159222806 > O 6.402631853 2.680197319 5.159222806 > O 6.402631853 2.680197319 12.03818655 > O -1.690656689 5.481183068 1.719740935 > O -1.690656689 5.481183068 8.598704677 > O 0.8801969606 6.884940495 1.719740935 > O 0.8801969606 6.884940495 8.598704677 > O 3.831778203 1.276439893 12.03818655 > O 3.831778203 1.276439893 5.159222806 > O 3.343146379 3.795858018 1.719740935 > O 3.343146379 3.795858018 8.598704677 > O 1.368828785 4.365522369 12.03818655 > O 1.368828785 4.365522369 5.159222806 > O -1.615736284 4.793178702 5.159222806 > O -1.615736284 4.793178702 12.03818655 > O 6.327711448 3.368201686 1.719740935 > O 6.327711448 3.368201686 8.598704677 > O 4.465067665 0.9973206834 1.719740935 > O 4.465067665 0.9973206834 8.598704677 > O 0.2469074986 7.164059704 12.03818655 > O 0.2469074986 7.164059704 5.159222806 > O 2.023793333 2.104820002 0.4829032547 > O 2.023793333 2.104820002 7.361866997 > O 2.688181831 6.056560386 13.27502423 > O 2.688181831 6.056560386 6.396060487 > O -0.8109309257 2.805066439 3.922385126 > O -0.8109309257 2.805066439 10.80134887 > O 5.522906090 5.356313949 2.956578616 > O 5.522906090 5.356313949 9.835542358 > O 6.589226069 0.7002464373 0.4829032547 > O 6.589226069 0.7002464373 7.361866997 > O -1.877250905 7.461133951 13.27502423 > O -1.877250905 7.461133951 6.396060487 > O 2.688181831 6.056560386 3.922385126 > O 2.688181831 6.056560386 10.80134887 > O 2.023793333 2.104820002 2.956578616 > O 2.023793333 2.104820002 9.835542358 > O 5.522906090 5.356313949 0.4829032547 > O 5.522906090 5.356313949 7.361866997 > O -0.8109309257 2.805066439 13.27502423 > O -0.8109309257 2.805066439 6.396060487 > O -1.877250905 7.461133951 3.922385126 > O -1.877250905 7.461133951 10.80134887 > O 6.589226069 0.7002464373 2.956578616 > O 6.589226069 0.7002464373 9.835542358 > O 0.000000000 0.000000000 1.341397930 > O 0.000000000 0.000000000 8.220361672 > O 0.000000000 0.000000000 12.41652955 > O 0.000000000 0.000000000 5.537565812 > O 0.000000000 0.000000000 4.780879801 > O 0.000000000 0.000000000 11.65984354 > O 0.000000000 0.000000000 2.098083941 > O 0.000000000 0.000000000 8.977047683 > H 0.000000000 0.000000000 0.4182409955 > H 0.000000000 0.000000000 7.297204737 > H 0.000000000 0.000000000 13.33968649 > H 0.000000000 0.000000000 6.460722746 > H 0.000000000 0.000000000 3.857722866 > H 0.000000000 0.000000000 10.73668661 > H 0.000000000 0.000000000 3.021240875 > H 0.000000000 0.000000000 9.900204617 > K_POINTS automatic > 1 1 1 0 0 0 > ---------------------------------------------------------------------------------------------------------------------------------------------- > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From michelepisarra at yahoo.it Fri Dec 23 16:34:39 2011 From: michelepisarra at yahoo.it (Michele Pisarra) Date: Fri, 23 Dec 2011 15:34:39 +0000 (GMT) Subject: [Pw_forum] Normalization of the Wave Functions Message-ID: <1324654479.51042.YahooMailNeo@web27008.mail.ukl.yahoo.com> Dear QE users, I used QE to calculate the one electron wave functions. In my calculation I found out that the one electron wave function are not normalized to unity. I searched through the forum and made some checks and I found out that these is due to the fact that I used Ultrasoft PseudoPotentials. Unfortunately what I have to do with the wave functions is memory and time consuming and is very sensitive to the number of plane waves of the basis set, so I can't use Norm Conserving PseudoPotential. However I need to enter?the one electron wave functions?in some matrix element calculations?and I don't know if I have to normalize them or I have to use them as they are given by the software. ? I take this opportunity to wish everyone a Merry Christmas. ? Thank you.Michele Pisarra, PhD Student, Dipartimento di Fisica, Universit? della Calabria Via P. Bucci, Cubo 31 C VI piano, 87036, Rende (CS), Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111223/8e3683d5/attachment.htm From akohlmey at gmail.com Fri Dec 23 16:48:13 2011 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Fri, 23 Dec 2011 10:48:13 -0500 Subject: [Pw_forum] Normalization of the Wave Functions In-Reply-To: <1324654479.51042.YahooMailNeo@web27008.mail.ukl.yahoo.com> References: <1324654479.51042.YahooMailNeo@web27008.mail.ukl.yahoo.com> Message-ID: On Fri, Dec 23, 2011 at 10:34 AM, Michele Pisarra wrote: > Dear QE users, dear michele, > I used QE to calculate the one electron wave functions. In my calculation I > found out that the one electron wave function are not normalized to unity. I > searched through the forum and made some checks and I found out that these > is due to the fact that I used Ultrasoft PseudoPotentials. Unfortunately > what I have to do with the wave functions is memory and time consuming and > is very sensitive to the number of plane waves of the basis set, so I can't > use Norm Conserving PseudoPotential. However I need to enter?the one > electron wave functions?in some matrix element calculations?and I don't know > if I have to normalize them or I have to use them as they are given by the > software. it is not as simple as that. most likely you will have to re-do your calculation with norm conserving pseudopotentials. when using ultra-soft pseudopotentials, you replace part of the wavefunction with augmentation charges or something equivalent. so in order to calculate any derivative properties, you have to recast the calculation in those terms, which can be far from trivial at times. i suggest you have a closer look at the papers describing ultra-soft pseudopotentials or an equivalent review or text book. ciao e buon natale, axel. > I take this opportunity to wish everyone a Merry Christmas. > > Thank you. > Michele Pisarra, PhD Student, > Dipartimento di Fisica, Universit? della Calabria > Via P. Bucci, Cubo 31 C VI piano, 87036, Rende (CS), Italy > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From glapenna at iccom.cnr.it Fri Dec 23 17:18:58 2011 From: glapenna at iccom.cnr.it (Giovanni La Penna) Date: Fri, 23 Dec 2011 17:18:58 +0100 (CET) Subject: [Pw_forum] Normalization of the Wave Functions In-Reply-To: References: <1324654479.51042.YahooMailNeo@web27008.mail.ukl.yahoo.com> Message-ID: I used the Kohn-Sham states output of PP analysis program and they are normalized to one with ultrasoft pseudopotentials. See below for gamma-point only (psi are real, see also comments in the PP code). Unfortunately, this implies to store all the states, as cube-files in the example below. PP input: &inputpp prefix='relax', outdir='./', filplot='state.out', plot_num=7, lsign = .true., kpoint = 1, kband = 1, / &plot nfile=1, filepp(1)='state.out', iflag=3, fileout='state_1.cube', output_format=6, / Piece of analysis C code (single precision): /* ... */ #define _REAL float #define l_sqrt sqrtf #define l_copysign copysignf #define Nabs(dumx) ((dumx) >= 0 ? (dumx) : -(dumx)) /* ... */ /* dx,dy,dz are the grid sides in a.u. (bohr) nr1x,nr2x,nr3x are the number of grid points in x,y,z input[js] is the unit of state js output from PP (state_1.cube above) */ dvol=dx*dy*dz; sum=0.; for(i1=1;i1<=nr1x;i1++) { for(j1=1;j1<=nr2x;j1++) { for(k1=1;k1<=nr3x;k1++) { fscanf(input[js],"%e ",&val); /* for ADF and CPMD this is enough. For QE... */ um=val; ut=l_sqrt(Nabs(um)); val=l_copysign(ut,um); sum+=val*val; fwrite(&val,sizeof(_REAL),1,output[is]); } } } printf ("Integral of modulus of state %d = %e\n",js,sum*dvol); /* ... */ Hoping this be useful (even though slow), my best wishes, Giovanni ============================================================ Giovanni La Penna - National research council (Cnr) Institute for chemistry of organo-metallic compounds (Iccom) via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy tel.: +39 055 522-5264, fax: +39 055 522-5203 e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna skype: giovannilapenna ============================================================ From mary_sanaii at yahoo.com Sat Dec 24 11:47:48 2011 From: mary_sanaii at yahoo.com (mary bababarghi) Date: Sat, 24 Dec 2011 02:47:48 -0800 (PST) Subject: [Pw_forum] pwcond diff leads with some shift in space Message-ID: <1324723668.26823.YahooMailClassic@web112404.mail.gq1.yahoo.com> I want to simulate the transport of a scattering region which is between two identical contacts , but these contacts have a little shift in space. In other words, the right lead at y-direction is 7Angestrum upper than left lead. I have read the pwcond_input help but couldn't understand some items. Would you please help us? ?How should I define the 'bds', 'bdr' and 'bdl' in cond.in input file? Thank you in advance Looking forward to your help. M. Sanaee -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111224/3bde1574/attachment.htm From germaneau at gucas.ac.cn Tue Dec 27 16:56:29 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Tue, 27 Dec 2011 10:56:29 -0500 Subject: [Pw_forum] Issue regarding reciprocal path in band calculation Message-ID: <4EF9EAAD.5050806@gucas.ac.cn> Dear all, After a SCF calculation of a crystal with the following cell parameters * ibrav = 14, celldm(1)=5.913520,celldm(2)=1.386316,celldm(3)=1.593551, celldm(4)=0.084426,celldm(5)=0.313644,celldm(6)=0.268903 I performed a band calculation (restart_mode='from_scratch') using the path bellow which has been generated by xcrysden. K_POINTS crystal 40 0.5000000000 0.0000000000 0.0000000000 1.0 0.4500000000 0.0000000000 0.0000000000 1.0 0.4000000000 0.0000000000 0.0000000000 1.0 0.3500000000 0.0000000000 0.0000000000 1.0 0.3000000000 0.0000000000 0.0000000000 1.0 0.2500000000 0.0000000000 0.0000000000 1.0 0.2000000000 0.0000000000 0.0000000000 1.0 0.1500000000 0.0000000000 0.0000000000 1.0 0.1000000000 0.0000000000 0.0000000000 1.0 0.0500000000 0.0000000000 0.0000000000 1.0 0.0000000000 0.0000000000 0.0000000000 1.0 0.0000000000 0.0714285714 0.0000000000 1.0 0.0000000000 0.1428571429 0.0000000000 1.0 ..... But in the output the path looks like this : number of k points= 40 cart. coord. in units 2pi/alat k( 1) = ( 0.5000000 -0.1395931 -0.1651425), wk = 0.0500000 k( 2) = ( 0.4500000 -0.1256338 -0.1486282), wk = 0.0500000 k( 3) = ( 0.4000000 -0.1116745 -0.1321140), wk = 0.0500000 k( 4) = ( 0.3500000 -0.0977152 -0.1155997), wk = 0.0500000 k( 5) = ( 0.3000000 -0.0837559 -0.0990855), wk = 0.0500000 k( 6) = ( 0.2500000 -0.0697965 -0.0825712), wk = 0.0500000 k( 7) = ( 0.2000000 -0.0558372 -0.0660570), wk = 0.0500000 k( 8) = ( 0.1500000 -0.0418779 -0.0495427), wk = 0.0500000 k( 9) = ( 0.1000000 -0.0279186 -0.0330285), wk = 0.0500000 k( 10) = ( 0.0500000 -0.0139593 -0.0165142), wk = 0.0500000 k( 11) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0500000 k( 12) = ( 0.0000000 0.0534944 -0.0000050), wk = 0.0500000 k( 13) = ( 0.0000000 0.1069887 -0.0000101), wk = 0.0500000 ..... and like this k = 0.5000-0.1396-0.1651 band energies (ev): k = 0.4500-0.1256-0.1486 band energies (ev): k = 0.4000-0.1117-0.1321 band energies (ev): k = 0.3500-0.0977-0.1156 band energies (ev): I compared the lattice and reciprocal lattice parameter in both the scf and band outputs, and they are (obviously) exactly same. So I'm just wondering what's going on here. What did I do wrong? Thank you, ?ric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111227/1765870c/attachment.htm From germaneau at gucas.ac.cn Tue Dec 27 17:00:20 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Tue, 27 Dec 2011 11:00:20 -0500 Subject: [Pw_forum] Issue regarding reciprocal path in band calculation In-Reply-To: <524952129.21934@test1.gucas.ac.cn> References: <524952129.21934@test1.gucas.ac.cn> Message-ID: <4EF9EB94.1060606@gucas.ac.cn> Dear all, I'm so sorry, please do not pay intention to my previous email. The unit is different. All my apologize for having bothered you guys just too tired. ?ric. On 12/27/2011 10:56 AM, ?ric Germaneau wrote: > Dear all, > > After a SCF calculation of a crystal with the following cell parameters > > * ibrav = 14, > celldm(1)=5.913520,celldm(2)=1.386316,celldm(3)=1.593551, > celldm(4)=0.084426,celldm(5)=0.313644,celldm(6)=0.268903 > > I performed a band calculation (restart_mode='from_scratch') using the > path bellow which has been generated by xcrysden. > > K_POINTS crystal > 40 > 0.5000000000 0.0000000000 0.0000000000 1.0 > 0.4500000000 0.0000000000 0.0000000000 1.0 > 0.4000000000 0.0000000000 0.0000000000 1.0 > 0.3500000000 0.0000000000 0.0000000000 1.0 > 0.3000000000 0.0000000000 0.0000000000 1.0 > 0.2500000000 0.0000000000 0.0000000000 1.0 > 0.2000000000 0.0000000000 0.0000000000 1.0 > 0.1500000000 0.0000000000 0.0000000000 1.0 > 0.1000000000 0.0000000000 0.0000000000 1.0 > 0.0500000000 0.0000000000 0.0000000000 1.0 > 0.0000000000 0.0000000000 0.0000000000 1.0 > 0.0000000000 0.0714285714 0.0000000000 1.0 > 0.0000000000 0.1428571429 0.0000000000 1.0 > ..... > > But in the output the path looks like this : > > number of k points= 40 > cart. coord. in units 2pi/alat > k( 1) = ( 0.5000000 -0.1395931 -0.1651425), wk = > 0.0500000 > k( 2) = ( 0.4500000 -0.1256338 -0.1486282), wk = > 0.0500000 > k( 3) = ( 0.4000000 -0.1116745 -0.1321140), wk = > 0.0500000 > k( 4) = ( 0.3500000 -0.0977152 -0.1155997), wk = > 0.0500000 > k( 5) = ( 0.3000000 -0.0837559 -0.0990855), wk = > 0.0500000 > k( 6) = ( 0.2500000 -0.0697965 -0.0825712), wk = > 0.0500000 > k( 7) = ( 0.2000000 -0.0558372 -0.0660570), wk = > 0.0500000 > k( 8) = ( 0.1500000 -0.0418779 -0.0495427), wk = > 0.0500000 > k( 9) = ( 0.1000000 -0.0279186 -0.0330285), wk = > 0.0500000 > k( 10) = ( 0.0500000 -0.0139593 -0.0165142), wk = > 0.0500000 > k( 11) = ( 0.0000000 0.0000000 0.0000000), wk = > 0.0500000 > k( 12) = ( 0.0000000 0.0534944 -0.0000050), wk = > 0.0500000 > k( 13) = ( 0.0000000 0.1069887 -0.0000101), wk = > 0.0500000 > ..... > > and like this > > k = 0.5000-0.1396-0.1651 band energies (ev): > k = 0.4500-0.1256-0.1486 band energies (ev): > k = 0.4000-0.1117-0.1321 band energies (ev): > k = 0.3500-0.0977-0.1156 band energies (ev): > > > I compared the lattice and reciprocal lattice parameter in both the > scf and band outputs, and they are (obviously) exactly same. > So I'm just wondering what's going on here. > What did I do wrong? > > Thank you, > > ?ric. > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Dr. ?ric Germaneau > > > Graduate University of Chinese Academy of Sciences > College of Physical Sciences > Yuquan Road 19A > Beijing 100049 > China > > /Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/ > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111227/1978f8cd/attachment.htm From nykondalu at gmail.com Tue Dec 27 07:05:28 2011 From: nykondalu at gmail.com (yedu kondalu) Date: Tue, 27 Dec 2011 11:35:28 +0530 Subject: [Pw_forum] Calculation of orthorhombic lattice parameters from the basis vecotrs Message-ID: Dear users, I did the structural optimization of a compound belongs to the space group *Ibam-72* (body centred orthorhombic) using variable cell (vc-relax) method. lattice parameter (alat) = 10.5862 a.u. unit-cell volume = 675.9126 (a.u.)^3 The initial basis vectors a(1) = ( 0.500000 0.529989 0.537487 ) a(2) = ( -0.500000 0.529989 0.537487 ) a(3) = ( -0.500000 -0.529989 0.537487 ) After the structural optimization the vectors are new unit-cell volume = 614.83507 a.u.^3 ( 91.10916 Ang^3 ) CELL_PARAMETERS (alat= 10.58624499) 0.529016060 0.479936985 0.510293152 -0.529016060 0.479936985 0.510293152 -0.529016060 -0.479936985 0.510293152 1. How to calculate the lattice parameters for this case ? 2. How to do the same for all the non cubic systems ? Can some body please explain me any method or reference books to do the same ? Thanking you Regards KONDAL -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111227/cd3f2b77/attachment-0001.htm From germaneau at gucas.ac.cn Tue Dec 27 20:25:07 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Tue, 27 Dec 2011 14:25:07 -0500 Subject: [Pw_forum] Calculation of orthorhombic lattice parameters from the basis vecotrs In-Reply-To: <524963411.19745@gscas.net.cn> References: <524963411.19745@gscas.net.cn> Message-ID: <4EFA1B93.5080103@gucas.ac.cn> Dear Kondal, The first line of the matrix correspond to *a*, the second to *b*, and the third to *c*. In order to get a, b, and c, just calculate the norm of the corresponding vectors. Don't forget to multiply by alat to have them in Bohr. Then, /alpha/ is the angle between vectors *b* and *c*, so you just need to calculate the dot product *b.c*. You'll get /alpha/ by doing /alpha/ = acos( *b.c* / b*c ) Finally, just do the same thing for /beta/, the angle between *a* and *c*, and /gamma/, the angle between *a* and *b*. Hope it helps, ?ric. On 12/27/2011 01:05 AM, yedu kondalu wrote: > Dear users, > > I did the structural optimization of a compound belongs to the > space group /*Ibam**-72*/ (body centred orthorhombic) using variable > cell (vc-relax) method. > > lattice parameter (alat) = 10.5862 a.u. > unit-cell volume = 675.9126 (a.u.)^3 > > The initial basis vectors > a(1) = ( 0.500000 0.529989 0.537487 ) > a(2) = ( -0.500000 0.529989 0.537487 ) > a(3) = ( -0.500000 -0.529989 0.537487 ) > > After the structural optimization the vectors are > > new unit-cell volume = 614.83507 a.u.^3 ( 91.10916 Ang^3 ) > > CELL_PARAMETERS (alat= 10.58624499) > 0.529016060 0.479936985 0.510293152 > -0.529016060 0.479936985 0.510293152 > -0.529016060 -0.479936985 0.510293152 > > 1. How to calculate the lattice parameters for this case ? > > 2. How to do the same for all the non cubic systems ? > > Can some body please explain me any method or reference books to do > the same ? > > > Thanking you > > Regards > KONDAL > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111227/7de7d96c/attachment.htm From joshiniharika20 at yahoo.in Tue Dec 27 11:16:07 2011 From: joshiniharika20 at yahoo.in (Niharika Joshi) Date: Tue, 27 Dec 2011 15:46:07 +0530 (IST) Subject: [Pw_forum] Electric field calculation Message-ID: <1324980967.54224.YahooMailNeo@web95718.mail.in.yahoo.com> Hello, Is it fine to include van der Waal forces in a electric field (sawtooth potential) calculation? -Niharika Joshi (project student, Indian Institute of Science Education and Research, Pune) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111227/0323946c/attachment.htm From trambui at u.boisestate.edu Tue Dec 27 22:44:04 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Tue, 27 Dec 2011 14:44:04 -0700 Subject: [Pw_forum] question regarding an error on pseudo potential generation output file Message-ID: Dear Everyone, I'm currently trying to generate an ultra soft pp for Cs. I did it once before with different electron configuration but the result didn't quite work as good as I expected. So now, I'm regenerated another one (also I want to include the 5s 5p and 6s for my valence) and when I ran the input file (I pasted the text below), I got an error message saying that : from ld1_readin : error # 1 only one local channel here is the input file &input title='Cs', zed=55.0, iswitch=3, rel=1, dft='PBE', config='[Kr] 4d10 5s2 5p6 6s1 ', rlderiv=4.3, eminld=-10.0, emaxld=5.0, deld=0.01d0, nld=3, / &inputp lloc=2, pseudotype=3, rho0=0.01, file_pseudopw='Cs.uspp-tb.UPF' / 6 6S 1 0 1.00 0.00 4.30 4.60 6S 1 0 0.00 1.00 4.30 4.60 5P 2 1 6.00 0.00 1.60 1.90 5P 2 1 0.00 0.50 1.60 1.90 5S 1 0 2.00 0.00 1.50 1.80 5S 1 0 0.00 0.50 1.50 1.80 Would anyone please help me understand why it caused such error above? Best Regards, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111227/c2e00f7e/attachment.htm From wangweiphysics at yahoo.com.cn Wed Dec 28 02:42:26 2011 From: wangweiphysics at yahoo.com.cn (wangwei) Date: Wed, 28 Dec 2011 09:42:26 +0800 (CST) Subject: [Pw_forum] difference between "vc-md" and "vc-relax" Message-ID: <1325036546.43104.YahooMailNeo@web15008.mail.cnb.yahoo.com> Dear, In pwscf program, what's the difference between "vc-md" and "vc-relax"? And what's the difference between "md" and "relax"? Thanks for any reply! Best wishes! wangwei Huaibei Normal University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111228/a8a9f8b6/attachment.htm From mohnish.iitk at gmail.com Wed Dec 28 06:27:21 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 28 Dec 2011 10:57:21 +0530 Subject: [Pw_forum] Electric field calculation In-Reply-To: <1324980967.54224.YahooMailNeo@web95718.mail.in.yahoo.com> References: <1324980967.54224.YahooMailNeo@web95718.mail.in.yahoo.com> Message-ID: Inclusion of van der Waals forces in electric field should not make a difference. But it should mimic the physical system which you are trying to simulate. On Tue, Dec 27, 2011 at 3:46 PM, Niharika Joshi wrote: > Hello, > Is it fine to include van der Waal forces in a electric field (sawtooth > potential) calculation? > > -Niharika Joshi > (project student, Indian Institute of Science Education and Research, Pune) > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111228/504d3380/attachment.htm From tribhuwan.physics at gmail.com Wed Dec 28 07:24:11 2011 From: tribhuwan.physics at gmail.com (Tribhuwan Pandey) Date: Wed, 28 Dec 2011 11:54:11 +0530 Subject: [Pw_forum] help regarding phonon life time calculation Message-ID: Hi all , Quatum espresso users.I am using Quantum espresso for phonon life time calculation.I have some problem in understanding the output file *file.anh_G*. If anyone of you have done those calculation before please help me. any suggestion in this matter will be appreciated Thanking you tribhuwan -- * With Regards Tribhuwan Pandey Indian Institute of Science, Bangalore, India * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111228/1a58d9e0/attachment.htm From pandey.bramha at gmail.com Wed Dec 28 11:21:21 2011 From: pandey.bramha at gmail.com (bramha pandey) Date: Wed, 28 Dec 2011 02:21:21 -0800 Subject: [Pw_forum] help regarding phonon life time calculation In-Reply-To: References: Message-ID: Dear All QE users:-- I wanted to use the QHA pakage given in espresso-4.3.2,..but there is a need of IFORT compiler which was not found and recognized by me.currently i am using gfortaran compiler in ubantu 11.2 unix version.... Thanks in advance for your kind cooperation...to get (ifort). On 12/27/11, Tribhuwan Pandey wrote: > Hi all , > Quatum espresso users.I am using Quantum espresso for phonon > life time calculation.I have some problem in understanding the output file > *file.anh_G*. If anyone of you have done those calculation before please > help me. > > > any suggestion in this matter will be appreciated > > Thanking you > tribhuwan > > -- > * > With Regards > Tribhuwan Pandey > Indian Institute of Science, Bangalore, India > > > > * > -- Thanks and Regards Bramha Prasad Pandey Assistant Professor (Electronics and Communication Engg) GLA Group of Institutions, Mathura. Ph. No. 08954143009 email id pandey.bramha at gmail.com bpglaitm at yahoo.co.in From mohnish.iitk at gmail.com Wed Dec 28 12:17:32 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 28 Dec 2011 16:47:32 +0530 Subject: [Pw_forum] help regarding phonon life time calculation In-Reply-To: References: Message-ID: You can download that from net. They will give you are license number. Its free for academic purposes. On Wed, Dec 28, 2011 at 3:51 PM, bramha pandey wrote: > Dear All QE users:-- > I wanted to use the QHA pakage given in espresso-4.3.2,..but there is > a need of IFORT compiler which was not found and recognized by > me.currently i am using gfortaran compiler in ubantu 11.2 unix > version.... > > Thanks in advance for your kind cooperation...to get (ifort). > > On 12/27/11, Tribhuwan Pandey wrote: > > Hi all , > > Quatum espresso users.I am using Quantum espresso for phonon > > life time calculation.I have some problem in understanding the output > file > > *file.anh_G*. If anyone of you have done those calculation before > please > > help me. > > > > > > any suggestion in this matter will be appreciated > > > > Thanking you > > tribhuwan > > > > -- > > * > > With Regards > > Tribhuwan Pandey > > Indian Institute of Science, Bangalore, India > > > > > > > > * > > > > > -- > Thanks and Regards > Bramha Prasad Pandey > Assistant Professor (Electronics and Communication Engg) > GLA Group of Institutions, Mathura. > Ph. No. 08954143009 > email id pandey.bramha at gmail.com > bpglaitm at yahoo.co.in > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111228/c01420f6/attachment.htm From akohlmey at gmail.com Wed Dec 28 17:14:50 2011 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Wed, 28 Dec 2011 11:14:50 -0500 Subject: [Pw_forum] help regarding phonon life time calculation In-Reply-To: References: Message-ID: On Wed, Dec 28, 2011 at 6:17 AM, mohnish pandey wrote: > You can download that from net. They will give you are license number. Its > free for academic purposes. please don't spread wrong information. the "non-commercial" versions of the intel compilers are *not* free for academic purposes. please read the licensing conditions carefully. as soon as you get *any* kind of compensation for what you use the compilers for, you are in violation of the non-commercial license. the fact that this is technically possible to download, install and use those compilers without paying for it, doesn't mean that it is legal. cheers, axel. > > On Wed, Dec 28, 2011 at 3:51 PM, bramha pandey > wrote: >> >> Dear All QE users:-- >> I wanted to use the QHA pakage given in espresso-4.3.2,..but there is >> a need of IFORT compiler which was not ?found and recognized by >> me.currently i am using gfortaran compiler in ubantu 11.2 unix >> version.... >> >> Thanks in advance for your kind cooperation...to get (ifort). >> >> On 12/27/11, Tribhuwan Pandey wrote: >> > Hi ?all , >> > ? ? ? ? ? ? ?Quatum espresso users.I am using Quantum espresso for >> > phonon >> > life time calculation.I have some problem in understanding the output >> > file >> > ? *file.anh_G*. ?If anyone of you have done those calculation before >> > please >> > help me. >> > >> > >> > any suggestion in this matter will be appreciated >> > >> > Thanking you >> > tribhuwan >> > >> > -- >> > * >> > With Regards >> > Tribhuwan Pandey >> > Indian Institute of Science, Bangalore, India >> > >> > >> > >> > * >> > >> >> >> -- >> Thanks and Regards >> Bramha Prasad Pandey >> Assistant Professor (Electronics and Communication Engg) >> GLA Group of Institutions, Mathura. >> Ph. No. 08954143009 >> email id pandey.bramha at gmail.com >> ? ? ? ? ? ?bpglaitm at yahoo.co.in >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > BTech-Mtech, IIT Kanpur > Senior Project Associate, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From bdslipun at gmail.com Thu Dec 29 06:34:20 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Thu, 29 Dec 2011 11:04:20 +0530 Subject: [Pw_forum] beta tin structure Message-ID: i want the phonon dispersion curve for beta tin structure so i gave the positions of atoms as primitive tetragonal structure having coordinates 0 0 0, .5 0 .25 , .5 .5 .5, 0 .5 .75 like 4a whychoff positions (c/a=.546) so no of atoms is 4 in the unit cell so in phonon there will be 12 branches but i have seen 6 branches so how can i put my primitive tetragonal structure having two atoms in unitcell or in other way how can i give the input for beta tin structure b d sahoo reserch scholar mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111229/025a5d51/attachment.htm From 1009ukumar at gmail.com Thu Dec 29 10:41:02 2011 From: 1009ukumar at gmail.com (Sonu Kumar) Date: Thu, 29 Dec 2011 15:11:02 +0530 Subject: [Pw_forum] orthogonality of phonon eigenvectors? Message-ID: Dear all QE users, I am not getting the orthogonality of phonon eigenvectors obtained in xx.dyn file. However normalization condition is satisfied. For example: 1. for four atom unit cell, eigen vectors are: omega( 1) = -0.330081 [THz] = -11.010398 [cm-1] ( -0.000126 0.000000 -0.494472 0.000000 0.000000 0.000000 ) ( -0.000128 0.000000 -0.501752 0.000000 0.000000 0.000000 ) ( -0.000128 0.000000 -0.501868 0.000000 0.000000 0.000000 ) ( -0.000128 0.000000 -0.501868 0.000000 0.000000 0.000000 ) omega( 2) = -0.330081 [THz] = -11.010398 [cm-1] ( 0.494472 0.000000 -0.000126 0.000000 0.000000 0.000000 ) ( 0.501752 0.000000 -0.000128 0.000000 0.000000 0.000000 ) ( 0.501868 0.000000 -0.000128 0.000000 0.000000 0.000000 ) ( 0.501868 0.000000 -0.000128 0.000000 0.000000 0.000000 ) omega( 3) = -0.293090 [THz] = -9.776500 [cm-1] ( 0.000000 0.000000 0.000000 0.000000 0.499253 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.500310 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.500218 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.500218 0.000000 ) omega( 4) = 2.476743 [THz] = 82.615796 [cm-1] ( -0.506652 0.000000 -0.000002 0.000000 0.000000 0.000000 ) ( 0.559568 0.000000 0.000002 0.000000 0.000000 0.000000 ) ( 0.463782 0.000000 0.000002 0.000000 0.000000 0.000000 ) ( 0.463782 0.000000 0.000002 0.000000 0.000000 0.000000 ) omega( 5) = 2.476743 [THz] = 82.615796 [cm-1] ( -0.000002 0.000000 0.506652 0.000000 0.000000 0.000000 ) ( 0.000002 0.000000 -0.559568 0.000000 0.000000 0.000000 ) ( 0.000002 0.000000 -0.463782 0.000000 0.000000 0.000000 ) ( 0.000002 0.000000 -0.463782 0.000000 0.000000 0.000000 ) omega( 6) = 9.011016 [THz] = 300.577143 [cm-1] ( 0.000000 0.000000 0.000000 0.000000 -0.562468 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.797241 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.154980 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.154980 0.000000 ) omega( 7) = 10.988751 [THz] = 366.547723 [cm-1] ( 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ) ( 0.707107 0.000000 0.000001 0.000000 0.000000 0.000000 ) ( -0.707107 0.000000 -0.000001 0.000000 0.000000 0.000000 ) omega( 8) = 10.988751 [THz] = 366.547724 [cm-1] ( 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ) ( -0.000001 0.000000 0.707107 0.000000 0.000000 0.000000 ) ( 0.000001 0.000000 -0.707107 0.000000 0.000000 0.000000 ) omega( 9) = 11.334621 [THz] = 378.084770 [cm-1] ( 0.018232 0.000000 0.000000 0.000000 0.000000 0.000000 ) ( 0.283432 0.000000 0.000000 0.000000 0.000000 0.000000 ) ( -0.677987 0.000000 -0.000001 0.000000 0.000000 0.000000 ) ( -0.677987 0.000000 -0.000001 0.000000 0.000000 0.000000 ) omega(10) = 11.334621 [THz] = 378.084771 [cm-1] ( 0.000000 0.000000 -0.018232 0.000000 0.000000 0.000000 ) ( 0.000000 0.000000 -0.283432 0.000000 0.000000 0.000000 ) ( -0.000001 0.000000 0.677987 0.000000 0.000000 0.000000 ) ( -0.000001 0.000000 0.677987 0.000000 0.000000 0.000000 ) omega(11) = 17.157192 [THz] = 572.306135 [cm-1] ( 0.000000 0.000000 0.000000 0.000000 -0.097293 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 -0.168080 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.693644 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.693644 0.000000 ) omega(12) = 20.428646 [THz] = 681.430811 [cm-1] ( 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 -0.707107 0.000000 ) ( 0.000000 0.000000 0.000000 0.000000 0.707107 0.000000 ) My Output: mode# mode# sum of prod of modes 4 6 0.00000 5 7 0.00000 6 8 0.00000 7 9 0.00000 8 10 0.00000 9 11 0.00000 10 12 0.00000 12 5 0.00000 1 3 0.00000 2 4 0.49575 <-----why not zero. Similarly : mode# mode# sum of prod of modes 1 4 -0.00013 2 5 0.00013 3 6 0.27310 <--- 4 7 0.00000 5 8 0.00000 6 9 0.00000 7 10 0.00000 8 11 0.00000 9 12 0.00000 10 1 -0.52929<-- 11 2 0.00000 12 3 0.00000 However all modes follow the normalization conditon: mode# sum of sqr of modes 1 1.00000 2 1.00000 3 1.00000 4 1.00000 5 1.00000 6 1.00000 7 1.00000 8 1.00000 9 1.00000 10 1.00000 11 1.00000 12 1.00000 Thank you !! regards, ========================================== Sonu Kumar Phd Student,Physics Department Indian Institute of Technology ,Delhi-110016, India web:-http://www.iitd.ac.in/ ========================================== From giannozz at democritos.it Thu Dec 29 16:28:17 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 29 Dec 2011 16:28:17 +0100 Subject: [Pw_forum] Electric field calculation In-Reply-To: <1324980967.54224.YahooMailNeo@web95718.mail.in.yahoo.com> References: <1324980967.54224.YahooMailNeo@web95718.mail.in.yahoo.com> Message-ID: <201112291628.17088.giannozz@democritos.it> On Tuesday 27 December 2011 11:16, Niharika Joshi wrote: > Is it fine to include van der Waal forces in a electric field (sawtooth > potential) calculation? as far as I known there is no incompatibility between the two Paolo -- Paolo Giannozzi, Democritos and Udine University From bdslipun at gmail.com Thu Dec 29 16:54:54 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Thu, 29 Dec 2011 21:24:54 +0530 Subject: [Pw_forum] Fwd: beta tin structure In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: bhabya sahoo Date: Thu, Dec 29, 2011 at 11:04 AM Subject: beta tin structure To: PWSCF Forum i want the phonon dispersion curve for beta tin structure so i gave the positions of atoms as primitive tetragonal structure having coordinates 0 0 0, .5 0 .25 , .5 .5 .5, 0 .5 .75 like 4a whychoff positions (c/a=.546) so no of atoms is 4 in the unit cell so in phonon there will be 12 branches but i have seen 6 branches so how can i put my primitive tetragonal structure having two atoms in unitcell or in other way how can i give the input for beta tin structure b d sahoo reserch scholar mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111229/768abbfd/attachment.htm From junkermeier at yahoo.com Thu Dec 29 17:37:53 2011 From: junkermeier at yahoo.com (Chad Junkermeier) Date: Thu, 29 Dec 2011 08:37:53 -0800 (PST) Subject: [Pw_forum] NEB: wild changes in image energies Message-ID: <1325176673.85121.YahooMailNeo@web111011.mail.gq1.yahoo.com> Hello, ?I have a problem that I keep encountering when performing NEB calculations. ?I will briefly describe what is happening here, and then give a more detailed explanation below. ?In short, the NEB calculations appear to run well for some number of iterations (usually on the order of 40 or 50 iterations) and then all of the sudden weird image energies start showing up, and the activation energy starts jumping around with each iteration. More detailed explanation: Physically what I am trying to do is model the diffusion of a small molecule across a graphene surface. ?This molecule is only weakly absorbed (physisorbed) onto the surface, thus, the activation energy is going to be rather small. ?Our relaxation calculations show that van der Waals type interactions are important in this system, as should be expected for something that is weakly absorbed. ?In the NEB calculation the molecule is going from one lowest energy site to a neighboring lowest energy site that is only a few angstroms away, all of which is well within the bounds of the supercell. I am using Quantum Espresso 4.3.2 on a Cray XE6.? My input file looks like this: BEGIN BEGIN_PATH_INPUT &PATH ??restart_mode? ? ??= 'from_scratch' ??string_method?? ??= 'neb', ??ds? ? ? ? ? ? ? ??= 2.D0, ??opt_scheme? ? ? ??= "broyden", ??num_of_images?? ??= 45, ??k_max?? ? ? ? ? ??= 0.3D0, ??k_min?? ? ? ? ? ??= 0.2D0, ??CI_scheme?? ? ? ??= "auto", ??nstep_path=3000, ??use_freezing = .TRUE. ??first_last_opt = .FALSE. / END_PATH_INPUT BEGIN_ENGINE_INPUT &CONTROL prefix="TW2_u_B3_B4", pseudo_dir??= "/espresso/pseudo", outdir? ? ??= "/workspace/TW2_u_B3_B4/tmp", / &SYSTEM ??ibrav = 4, ??celldm(1)???= 37.2672889, ??celldm(3)???=??0.760623, ??nat?? ? ? ??= 144, ??ntyp? ? ? ??= 4, ecutwfc?? ??= 50.0, ecutrho?? ??= 400, occupations = "smearing", smearing? ??= "methfessel-paxton",?? degauss?? ??= 0.01,? ? ? ? london? ? ??= .TRUE. / &ELECTRONS?? ? conv_thr? ??= 0.0000001,? mixing_beta = 0.3,? electron_maxstep = 150, / ATOMIC_SPECIES C??12.0??C.pbe-van_ak.UPF H???1.0??H.pbe-van_ak.UPF? O??18.0??O.pbe-van_ak.UPF P??31.0??P.pbe-van_ak.UPF? BEGIN_POSITIONS FIRST_IMAGE ATOMIC_POSITIONS angstrom? ? ? C? ? ? ??0.000000000???0.000000000???0.000000000? ??0???0???0 C? ? ? ??1.234000000???0.710000000???0.000000000? ??0???0???0 C? ? ? ??2.465000000???0.000000000???0.000000000? ??0???0???0 C? ? ? ??3.699000000???0.710000000???0.000000000? ??0???0???0 C? ? ? ??4.930000000???0.000000000???0.000000000? ??0???0???0 . . . LAST_IMAGE? ATOMIC_POSITIONS angstrom? . . . H?? ? ??12.789295543??12.155855132???2.858948537 H?? ? ??13.430079977??11.427859045???4.385644094 H?? ? ??14.299090315??11.190357788???2.820979411 END_POSITIONS K_POINTS {gamma}?? ? ? ? END_ENGINE_INPUT END While I didn't include all of the atoms in here (since there are a lot, and I don't think this is necessarily to the resolution problem), I will note that the majority of the atoms will not move appreciably during the course of the calculation, and thus to speed up the calculation I tell the code to fix the positions of the atoms that aren't moving. I started off with values that I thought would help the code run quicker:? conv_thr? ??= 0.00001 ecutwfc?? ??= 30.0, ecutrho?? ??= 280, num_of_images?? ??= 15, electron_maxstep = 100, After finding the problem that I am writing here about, and reading everything I could find on the QE website, and within pw_forum, I slowly made changes trying to work through the problem. ?Having the number of images set to 45 in the above input file has many more images than I think I need, but one of the things that I kept reading is that having more images will decrease the likelihood of problems arising. After the first few NEB iterations a nice potential barrier curve appears and is slowly refined. ?An example of the standard output for one of the well behaved images is given below: ? ? ?------------------------------ iteration??44 ------------------------------ ? ? ?tcpu =??61713.9? ??self-consistency for image??10 ? ? ?tcpu =??61932.1? ??self-consistency for image??21 ? ? ?tcpu =??62113.6? ??self-consistency for image??28 ? ? ?tcpu =??62294.4? ??self-consistency for image??31 ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (<-) =???0.044011 eV ? ? ?image? ? ? ??energy (eV)? ? ? ??error (eV/A)? ? ? ??frozen ? ? ? ? ?1?? ??-21959.2382129? ? ? ? ? ??0.081337? ? ? ? ? ??T ? ? ? ? ?2?? ??-21959.2388966? ? ? ? ? ??0.020923? ? ? ? ? ??T ? ? ? ? ?3?? ??-21959.2381194? ? ? ? ? ??0.123092? ? ? ? ? ??T ? ? ? ? ?4?? ??-21959.2363069? ? ? ? ? ??0.164123? ? ? ? ? ??F ? ? ? ? ?5?? ??-21959.2352170? ? ? ? ? ??0.044025? ? ? ? ? ??T ? ? ? ? ?6?? ??-21959.2331629? ? ? ? ? ??0.220840? ? ? ? ? ??F ? ? ? ? ?7?? ??-21959.2301578? ? ? ? ? ??0.115291? ? ? ? ? ??T ? ? ? ? ?8?? ??-21959.2277497? ? ? ? ? ??0.199382? ? ? ? ? ??F ? ? ? ? ?9?? ??-21959.2256241? ? ? ? ? ??0.037564? ? ? ? ? ??T ? ? ? ??10?? ??-21959.2216078? ? ? ? ? ??0.257680? ? ? ? ? ??F ? ? ? ??11?? ??-21959.2173790? ? ? ? ? ??0.220445? ? ? ? ? ??F ? ? ? ??12?? ??-21959.2159181? ? ? ? ? ??0.195525? ? ? ? ? ??F ? ? ? ??13?? ??-21959.2122799? ? ? ? ? ??0.189871? ? ? ? ? ??F ? ? ? ??14?? ??-21959.2093498? ? ? ? ? ??0.070035? ? ? ? ? ??T ? ? ? ??15?? ??-21959.2075466? ? ? ? ? ??0.156424? ? ? ? ? ??F ? ? ? ??16?? ??-21959.2037818? ? ? ? ? ??0.237338? ? ? ? ? ??F ? ? ? ??17?? ??-21959.2013877? ? ? ? ? ??0.059399? ? ? ? ? ??T ? ? ? ??18?? ??-21959.2006768? ? ? ? ? ??0.168875? ? ? ? ? ??F ? ? ? ??19?? ??-21959.1986806? ? ? ? ? ??0.049577? ? ? ? ? ??T ? ? ? ??20?? ??-21959.1962718? ? ? ? ? ??0.054413? ? ? ? ? ??T ? ? ? ??21?? ??-21959.1966851? ? ? ? ? ??0.022074? ? ? ? ? ??T ? ? ? ??22?? ??-21959.1954724? ? ? ? ? ??0.053047? ? ? ? ? ??T ? ? ? ??23?? ??-21959.1942736? ? ? ? ? ??0.054956? ? ? ? ? ??T ? ? ? ??24?? ??-21959.1944583? ? ? ? ? ??0.140762? ? ? ? ? ??F ? ? ? ??25?? ??-21959.1964535? ? ? ? ? ??0.032502? ? ? ? ? ??T ? ? ? ??26?? ??-21959.1950797? ? ? ? ? ??0.210304? ? ? ? ? ??F ? ? ? ??27?? ??-21959.1987196? ? ? ? ? ??0.051561? ? ? ? ? ??T ? ? ? ??28?? ??-21959.2008371? ? ? ? ? ??0.031058? ? ? ? ? ??T ? ? ? ??29?? ??-21959.2005944? ? ? ? ? ??0.183532? ? ? ? ? ??F ? ? ? ??30?? ??-21959.2045923? ? ? ? ? ??0.059183? ? ? ? ? ??T ? ? ? ??31?? ??-21959.2074746? ? ? ? ? ??0.148483? ? ? ? ? ??F ? ? ? ??32?? ??-21959.2094894? ? ? ? ? ??0.139970? ? ? ? ? ??F ? ? ? ??33?? ??-21959.2129334? ? ? ? ? ??0.033060? ? ? ? ? ??T ? ? ? ??34?? ??-21959.2156972? ? ? ? ? ??0.237590? ? ? ? ? ??F ? ? ? ??35?? ??-21959.2188749? ? ? ? ? ??0.065209? ? ? ? ? ??T ? ? ? ??36?? ??-21959.2223341? ? ? ? ? ??0.020410? ? ? ? ? ??T ? ? ? ??37?? ??-21959.2256989? ? ? ? ? ??0.041502? ? ? ? ? ??T ? ? ? ??38?? ??-21959.2278845? ? ? ? ? ??0.206609? ? ? ? ? ??F ? ? ? ??39?? ??-21959.2309458? ? ? ? ? ??0.064352? ? ? ? ? ??T ? ? ? ??40?? ??-21959.2333476? ? ? ? ? ??0.228702? ? ? ? ? ??F ? ? ? ??41?? ??-21959.2354058? ? ? ? ? ??0.034633? ? ? ? ? ??T ? ? ? ??42?? ??-21959.2369634? ? ? ? ? ??0.053540? ? ? ? ? ??T ? ? ? ??43?? ??-21959.2383146? ? ? ? ? ??0.179708? ? ? ? ? ??F ? ? ? ??44?? ??-21959.2390413? ? ? ? ? ??0.052827? ? ? ? ? ??T ? ? ? ??45?? ??-21959.2382847? ? ? ? ? ??0.084999? ? ? ? ? ??T ? ? ?climbing image = 23 ? ? ?path length? ? ? ? ??= 18.663 bohr ? ? ?inter-image distance =??0.424 bohr If you were to plot the image number versus the energy that is given above you would find what appears to be a very well behaved curve. But after a while, all of the sudden, there is a problem with the output. ? ? ?------------------------------ iteration??45 ------------------------------ ? ? ?tcpu =??62502.4? ??self-consistency for image???4 ? ? ?tcpu =??62758.1? ??self-consistency for image???6 ? ? ?tcpu =??63006.7? ??self-consistency for image???8 ? ? ?tcpu =??63287.9? ??self-consistency for image??10 ? ? ?tcpu =??63556.1? ??self-consistency for image??11 ? ? ?tcpu =??63876.3? ??self-consistency for image??12 ? ? ?tcpu =??64126.9? ??self-consistency for image??13 ? ? ?tcpu =??64409.9? ??self-consistency for image??15 ? ? ?tcpu =??64661.2? ??self-consistency for image??16 ? ? ?tcpu =??64941.7? ??self-consistency for image??18 ? ? ?tcpu =??65190.6? ??self-consistency for image??24 ? ? ?tcpu =??65480.1? ??self-consistency for image??26 ? ? ?tcpu =??65780.1? ??self-consistency for image??29 ? ? ?tcpu =??66077.9? ??self-consistency for image??31 ? ? ?tcpu =??66317.9? ??self-consistency for image??32 ? ? ?tcpu =??66580.4? ??self-consistency for image??34 ? ? ?tcpu =??66857.5? ??self-consistency for image??38 ? ? ?tcpu =??67137.2? ??self-consistency for image??40 ? ? ?tcpu =??67386.9? ??self-consistency for image??43 ? ? ?activation energy (->) =???0.287582 eV ? ? ?activation energy (<-) =???0.287654 eV ? ? ?image? ? ? ??energy (eV)? ? ? ??error (eV/A)? ? ? ??frozen ? ? ? ? ?1?? ??-21959.2382129? ? ? ? ? ??0.081337? ? ? ? ? ??T ? ? ? ? ?2?? ??-21959.2388966? ? ? ? ? ??0.020929? ? ? ? ? ??T ? ? ? ? ?3?? ??-21959.2381194? ? ? ? ? ??0.128767? ? ? ? ? ??T ? ? ? ? ?4?? ??-21959.1561960? ? ? ? ? ??2.016407? ? ? ? ? ??T ? ? ? ? ?5?? ??-21959.2352170? ? ? ? ? ??0.054181? ? ? ? ? ??T ? ? ? ? ?6?? ??-21959.1233419? ? ? ? ? ??3.440925? ? ? ? ? ??F ? ? ? ? ?7?? ??-21959.2301578? ? ? ? ? ??0.119857? ? ? ? ? ??T ? ? ? ? ?8?? ??-21959.1295895? ? ? ? ? ??3.858443? ? ? ? ? ??F ? ? ? ? ?9?? ??-21959.2256241? ? ? ? ? ??0.031368? ? ? ? ? ??T ? ? ? ??10?? ??-21959.2007906? ? ? ? ? ??0.830489? ? ? ? ? ??T ? ? ? ??11?? ??-21958.9506305? ? ? ? ? ??4.210877? ? ? ? ? ??F ? ? ? ??12?? ??-21959.1226848? ? ? ? ? ??2.774980? ? ? ? ? ??F ? ? ? ??13?? ??-21959.1255613? ? ? ? ? ??3.306542? ? ? ? ? ??F ? ? ? ??14?? ??-21959.2093498? ? ? ? ? ??0.063904? ? ? ? ? ??T ? ? ? ??15?? ??-21959.1425146? ? ? ? ? ??2.576069? ? ? ? ? ??F ? ? ? ??16?? ??-21959.0686534? ? ? ? ? ??4.452463? ? ? ? ? ??F ? ? ? ??17?? ??-21959.2013877? ? ? ? ? ??0.051986? ? ? ? ? ??T ? ? ? ??18?? ??-21959.1237018? ? ? ? ? ??2.915400? ? ? ? ? ??F ? ? ? ??19?? ??-21959.1986806? ? ? ? ? ??0.070271? ? ? ? ? ??T ? ? ? ??20?? ??-21959.1962718? ? ? ? ? ??0.055066? ? ? ? ? ??T ? ? ? ??21?? ??-21959.1966851? ? ? ? ? ??0.022251? ? ? ? ? ??T ? ? ? ??22?? ??-21959.1954724? ? ? ? ? ??0.053511? ? ? ? ? ??T ? ? ? ??23?? ??-21959.1942736? ? ? ? ? ??0.155528? ? ? ? ? ??T ? ? ? ??24?? ??-21959.0321128? ? ? ? ? ??1.669573? ? ? ? ? ??T ? ? ? ??25?? ??-21959.1964535? ? ? ? ? ??0.033436? ? ? ? ? ??T ? ? ? ??26?? ??-21958.9641160? ? ? ? ? ??2.813188? ? ? ? ? ??F ? ? ? ??27?? ??-21959.1987196? ? ? ? ? ??0.170191? ? ? ? ? ??T ? ? ? ??28?? ??-21959.2008371? ? ? ? ? ??0.119487? ? ? ? ? ??T ? ? ? ??29?? ??-21959.0410354? ? ? ? ? ??2.100854? ? ? ? ? ??T ? ? ? ??30?? ??-21959.2045923? ? ? ? ? ??0.217405? ? ? ? ? ??T ? ? ? ??31?? ??-21959.2006761? ? ? ? ? ??0.946770? ? ? ? ? ??T ? ? ? ??32?? ??-21959.1091999? ? ? ? ? ??2.022318? ? ? ? ? ??T ? ? ? ??33?? ??-21959.2129334? ? ? ? ? ??0.033922? ? ? ? ? ??T ? ? ? ??34?? ??-21959.0832736? ? ? ? ? ??3.736941? ? ? ? ? ??F ? ? ? ??35?? ??-21959.2188749? ? ? ? ? ??0.136602? ? ? ? ? ??T ? ? ? ??36?? ??-21959.2223341? ? ? ? ? ??0.033429? ? ? ? ? ??T ? ? ? ??37?? ??-21959.2256989? ? ? ? ? ??0.038111? ? ? ? ? ??T ? ? ? ??38?? ??-21959.1226548? ? ? ? ? ??4.018138? ? ? ? ? ??F ? ? ? ??39?? ??-21959.2309458? ? ? ? ? ??0.068887? ? ? ? ? ??T ? ? ? ??40?? ??-21959.1163356? ? ? ? ? ??3.540681? ? ? ? ? ??F ? ? ? ??41?? ??-21959.2354058? ? ? ? ? ??0.069677? ? ? ? ? ??T ? ? ? ??42?? ??-21959.2369634? ? ? ? ? ??0.053677? ? ? ? ? ??T ? ? ? ??43?? ??-21959.1651795? ? ? ? ? ??2.854320? ? ? ? ? ??F ? ? ? ??44?? ??-21959.2390413? ? ? ? ? ??0.041340? ? ? ? ? ??T ? ? ? ??45?? ??-21959.2382847? ? ? ? ? ??0.084999? ? ? ? ? ??T ? ? ?climbing image = 11 ? ? ?path length? ? ? ? ??= 19.063 bohr ? ? ?inter-image distance =??0.433 bohr Where if you?plot the image number versus the energy given above you will find that many of the points lay on the same curve as in the proceeding plot, but now almost half of them are jumping to higher energies. ?When I look at the xyz output in VMD, there doesn't seem to be any change in what the images look like pre/post the start of iteration 45. I will now list some of ?the activation energies produced towards the end of the run (I stopped the code once I saw this happening again). ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (->) =???0.046128 eV ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (->) =???0.044786 eV ? ? ?activation energy (->) =???0.043951 eV ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (->) =???0.044436 eV ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (->) =???0.043939 eV ? ? ?activation energy (->) =???0.287582 eV ? ? ?activation energy (->) =???0.206100 eV ? ? ?activation energy (->) =???0.601468 eV ? ? ?activation energy (->) =???0.231222 eV ? ? ?activation energy (->) =???0.216514 eV ? ? ?activation energy (->) =???0.252992 eV ? ? ?activation energy (->) =???0.289003 eV ? ? ?activation energy (->) =???0.107865 eV ? ? ?activation energy (->) =???0.154660 eV ? ? ?activation energy (->) =???0.302177 eV ? ? ?activation energy (->) =???0.154660 eV ? ? ?activation energy (->) =???0.290079 eV You can see that the activation energy is fairly constant at about 0.04 eV for a while and then after a certain point bedlam. Any ideas would be welcome. Chad Junkermeier, Ph.D. NRC Post-Doctoral Associate U. S. Naval Research Laboratory -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111229/6c0b1d54/attachment-0001.htm From dorabman at gmail.com Thu Dec 29 23:13:15 2011 From: dorabman at gmail.com (Hua Bao) Date: Thu, 29 Dec 2011 17:13:15 -0500 Subject: [Pw_forum] Anharmonic force constants (example 14) Message-ID: Dear QE-users, I am interested in phonon lifetime calculations. Before posting this question, I have read the related posts and Debernardi' thesis. There two questions. I would really appreciate if anyone can help with any of these questions. 1. Is it possible to instruct d3.x program to output the third-order force constants (in the real space)? 2. In the output file si.anh_G, it outputs "Derivative of the force constants". How is this defined? If it is the third-order force constant, it should not be assigned to any q points. If not, how can I understand this term? Thanks, Hua -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111229/5a632056/attachment.htm From buldashev.ivan at mail.ru Fri Dec 30 05:09:43 2011 From: buldashev.ivan at mail.ru (=?UTF-8?B?0JjQstCw0L0g0JHRg9C70LTQsNGI0LXQsg==?=) Date: Fri, 30 Dec 2011 08:09:43 +0400 Subject: [Pw_forum] =?utf-8?q?Problems_with_magnetic_moment_of_fcc_iron_Bu?= =?utf-8?q?ldashev_Ivan?= Message-ID: Dear QE users, I studied the antiferromagnetic solution for fcc iron. This is my input: ? ? &control ? ? calculation='scf' ? ? restart_mode='from_scratch', ? ? pseudo_dir = '/home/buldashev/QE/pseudo/', ? ? outdir='/home/buldashev/tmp/', ? ? disk_io='high' ? ? / ? ?&system ? ?ibrav= 7, ? ?celldm(1) = 5.20, ? ?celldm(3) = 1.41421356,? ? ?nat= 2, ? ?ntyp= 2, ? ?ecutwfc = 30, ? ?ecutrho = 120, ? ?nbnd = 18, ? ?nspin = 2, ? ?starting_magnetization(1)=0.5, ? ?starting_magnetization(2)=-0.5, ? ?occupations='smearing', ? ?smearing='mp', ? ?degauss=0.04, ? ?/ ? &electrons ? ?mixing_beta = 0.05, ? ?/ ? ATOMIC_SPECIES ? Fe1 55.845 Fe.pbe-sp-van.UPF ? Fe2 55.845 Fe.pbe-sp-van.UPF ? ATOMIC_POSITIONS ? Fe1 0 0 0 ? Fe2 -0.5 -0.5 -0.5 ? K_POINTS {automatic} ? 14 14 14 0 0 0 As a result, with different parameters (nbnd=16,20; mixing_beta=0.01-0.9; smearing='mp','mv'; celldm(1) = 4-8; and different ecutwfc), were found only a non-magnetic solution, that is total magnetization = 0, absolute magnetization = 0. Nevertheless, we know that there is an antiferromagnetic solution for fcc iron. Could you please indicate the reason for the differences, or at least papers in which was solved a similar problem? Thank you. Buldashev Ivan, student. South Ural State University. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111230/7cbe50c9/attachment.htm From arvifis at gmail.com Fri Dec 30 05:46:42 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Fri, 30 Dec 2011 02:46:42 -0200 Subject: [Pw_forum] Problems with magnetic moment of fcc iron Buldashev Ivan In-Reply-To: References: Message-ID: Why ibrav=7 ..?? try with ibrav=6 , besides, use: starting_magnetization(1)= 1.0, starting_magnetization(2)=-1.0, The values of ecutwfc = 30, ecutrho = 120, has been obtained after convergence ..??? and finally, are you sure that Fe(FCC) is not a cubic structure...??? please look at the bibliography. Best..!! PhD std. Arles V. Gil Rebaza IFLP - La Plata - Argentina 2011/12/30 ???? ???????? > Dear QE users, > I studied the antiferromagnetic solution for fcc iron. > This is my input: > > &control > calculation='scf' > restart_mode='from_scratch', > pseudo_dir = '/home/buldashev/QE/pseudo/', > outdir='/home/buldashev/tmp/', > disk_io='high' > / > &system > ibrav= 7, > celldm(1) = 5.20, > celldm(3) = 1.41421356, > nat= 2, > ntyp= 2, > ecutwfc = 30, > ecutrho = 120, > nbnd = 18, > nspin = 2, > starting_magnetization(1)=0.5, > starting_magnetization(2)=-0.5, > occupations='smearing', > smearing='mp', > degauss=0.04, > / > &electrons > mixing_beta = 0.05, > / > ATOMIC_SPECIES > Fe1 55.845 Fe.pbe-sp-van.UPF > Fe2 55.845 Fe.pbe-sp-van.UPF > ATOMIC_POSITIONS > Fe1 0 0 0 > Fe2 -0.5 -0.5 -0.5 > K_POINTS {automatic} > 14 14 14 0 0 0 > > As a result, with different parameters (nbnd=16,20; mixing_beta=0.01-0.9; > smearing='mp','mv'; celldm(1) = 4-8; and different ecutwfc), were found > only a non-magnetic solution, that is total magnetization = 0, absolute > magnetization = 0. Nevertheless, we know that there is an antiferromagnetic > solution for fcc iron. Could you please indicate the reason for the > differences, or at least papers in which was solved a similar problem? > Thank you. > Buldashev Ivan, student. > South Ural State University. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111230/ddc1a5fa/attachment.htm From baroni at sissa.it Fri Dec 30 09:35:17 2011 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 30 Dec 2011 09:35:17 +0100 Subject: [Pw_forum] orthogonality of phonon eigenvectors? In-Reply-To: References: Message-ID: Phonon eigenvectors are solution of a *generalized* eigenvalue equation (see the definition in any textbook of classical mechanics, dealing with "small oscillations"). As such, they are only orthogonal if all the nuclear masses are the same (simple self-evaluation exercise: explain why). HTH - SB -- Stefano Baroni, Trieste -- swift message written and sent on the go On 29/dic/2011, at 10:41, Sonu Kumar <1009ukumar at gmail.com> wrote: > Dear all QE users, > > I am not getting the orthogonality of phonon eigenvectors > obtained in xx.dyn file. However normalization condition is satisfied. > > For example: > 1. for four atom unit cell, eigen vectors are: > > omega( 1) = -0.330081 [THz] = -11.010398 [cm-1] > ( -0.000126 0.000000 -0.494472 0.000000 0.000000 0.000000 ) > ( -0.000128 0.000000 -0.501752 0.000000 0.000000 0.000000 ) > ( -0.000128 0.000000 -0.501868 0.000000 0.000000 0.000000 ) > ( -0.000128 0.000000 -0.501868 0.000000 0.000000 0.000000 ) > omega( 2) = -0.330081 [THz] = -11.010398 [cm-1] > ( 0.494472 0.000000 -0.000126 0.000000 0.000000 0.000000 ) > ( 0.501752 0.000000 -0.000128 0.000000 0.000000 0.000000 ) > ( 0.501868 0.000000 -0.000128 0.000000 0.000000 0.000000 ) > ( 0.501868 0.000000 -0.000128 0.000000 0.000000 0.000000 ) > omega( 3) = -0.293090 [THz] = -9.776500 [cm-1] > ( 0.000000 0.000000 0.000000 0.000000 0.499253 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 0.500310 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 0.500218 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 0.500218 0.000000 ) > omega( 4) = 2.476743 [THz] = 82.615796 [cm-1] > ( -0.506652 0.000000 -0.000002 0.000000 0.000000 0.000000 ) > ( 0.559568 0.000000 0.000002 0.000000 0.000000 0.000000 ) > ( 0.463782 0.000000 0.000002 0.000000 0.000000 0.000000 ) > ( 0.463782 0.000000 0.000002 0.000000 0.000000 0.000000 ) > omega( 5) = 2.476743 [THz] = 82.615796 [cm-1] > ( -0.000002 0.000000 0.506652 0.000000 0.000000 0.000000 ) > ( 0.000002 0.000000 -0.559568 0.000000 0.000000 0.000000 ) > ( 0.000002 0.000000 -0.463782 0.000000 0.000000 0.000000 ) > ( 0.000002 0.000000 -0.463782 0.000000 0.000000 0.000000 ) > omega( 6) = 9.011016 [THz] = 300.577143 [cm-1] > ( 0.000000 0.000000 0.000000 0.000000 -0.562468 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 0.797241 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 0.154980 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 0.154980 0.000000 ) > omega( 7) = 10.988751 [THz] = 366.547723 [cm-1] > ( 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ) > ( 0.707107 0.000000 0.000001 0.000000 0.000000 0.000000 ) > ( -0.707107 0.000000 -0.000001 0.000000 0.000000 0.000000 ) > omega( 8) = 10.988751 [THz] = 366.547724 [cm-1] > ( 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ) > ( -0.000001 0.000000 0.707107 0.000000 0.000000 0.000000 ) > ( 0.000001 0.000000 -0.707107 0.000000 0.000000 0.000000 ) > omega( 9) = 11.334621 [THz] = 378.084770 [cm-1] > ( 0.018232 0.000000 0.000000 0.000000 0.000000 0.000000 ) > ( 0.283432 0.000000 0.000000 0.000000 0.000000 0.000000 ) > ( -0.677987 0.000000 -0.000001 0.000000 0.000000 0.000000 ) > ( -0.677987 0.000000 -0.000001 0.000000 0.000000 0.000000 ) > omega(10) = 11.334621 [THz] = 378.084771 [cm-1] > ( 0.000000 0.000000 -0.018232 0.000000 0.000000 0.000000 ) > ( 0.000000 0.000000 -0.283432 0.000000 0.000000 0.000000 ) > ( -0.000001 0.000000 0.677987 0.000000 0.000000 0.000000 ) > ( -0.000001 0.000000 0.677987 0.000000 0.000000 0.000000 ) > omega(11) = 17.157192 [THz] = 572.306135 [cm-1] > ( 0.000000 0.000000 0.000000 0.000000 -0.097293 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 -0.168080 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 0.693644 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 0.693644 0.000000 ) > omega(12) = 20.428646 [THz] = 681.430811 [cm-1] > ( 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 -0.707107 0.000000 ) > ( 0.000000 0.000000 0.000000 0.000000 0.707107 0.000000 ) > > My Output: > > mode# mode# sum of prod of modes > 4 6 0.00000 > 5 7 0.00000 > 6 8 0.00000 > 7 9 0.00000 > 8 10 0.00000 > 9 11 0.00000 > 10 12 0.00000 > 12 5 0.00000 > 1 3 0.00000 > 2 4 0.49575 <-----why not zero. > > Similarly : > mode# mode# sum of prod of modes > 1 4 -0.00013 > 2 5 0.00013 > 3 6 0.27310 <--- > 4 7 0.00000 > 5 8 0.00000 > 6 9 0.00000 > 7 10 0.00000 > 8 11 0.00000 > 9 12 0.00000 > 10 1 -0.52929<-- > 11 2 0.00000 > 12 3 0.00000 > > However all modes follow the normalization conditon: > mode# sum of sqr of modes > 1 1.00000 > 2 1.00000 > 3 1.00000 > 4 1.00000 > 5 1.00000 > 6 1.00000 > 7 1.00000 > 8 1.00000 > 9 1.00000 > 10 1.00000 > 11 1.00000 > 12 1.00000 > > Thank you !! > > regards, > ========================================== > Sonu Kumar > Phd Student,Physics Department > Indian Institute of Technology ,Delhi-110016, India > web:-http://www.iitd.ac.in/ > ========================================== > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From suza.rri at gmail.com Fri Dec 30 14:41:53 2011 From: suza.rri at gmail.com (Suza W) Date: Fri, 30 Dec 2011 14:41:53 +0100 Subject: [Pw_forum] orthogonality of phonon eigenvectors? In-Reply-To: References: Message-ID: Hello All, Since eigen displacements are more useful than phonon eigenvectors, it would be better if QE rather prints eigen-displacements as ABINIT does. Yours sincerely, Suza W Research Associate, RRI, India On Fri, Dec 30, 2011 at 9:35 AM, Stefano Baroni wrote: > Phonon eigenvectors are solution of a *generalized* eigenvalue equation > (see the definition in any textbook of classical mechanics, dealing with > "small oscillations"). As such, they are only orthogonal if all the nuclear > masses are the same (simple self-evaluation exercise: explain why). HTH - SB > > -- > Stefano Baroni, Trieste -- swift message written and sent on the go > > On 29/dic/2011, at 10:41, Sonu Kumar <1009ukumar at gmail.com> wrote: > > > Dear all QE users, > > > > I am not getting the orthogonality of phonon eigenvectors > > obtained in xx.dyn file. However normalization condition is satisfied. > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111230/e13bd6b4/attachment.htm From kalamaillist at gmail.com Fri Dec 30 17:18:10 2011 From: kalamaillist at gmail.com (WF) Date: Sat, 31 Dec 2011 00:18:10 +0800 Subject: [Pw_forum] How to test pseudo potential for non-metallic element? Message-ID: <002601ccc70e$a1e2b2c0$e5a81840$@gmail.com> Dear everyone, I tried to create pseudo potential for O and S ( for some uncommon functional ) for later oxides calculation. Before used in the final model, it should be checked. However, for a metallic element, it is easy to create a model with its stable elementary substance and optimized to see its lattice constant as first step verification. However for an element exists as molecule, is it a good method to test the molecule case? Is it enough to use ld1.x test only as first step verification? Thanks. ------------------------------------------------------------ Wu Feng, Chemistry and Molecular Engineering, Peking University ------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111231/3f531769/attachment.htm From lmartinsamos at gmail.com Fri Dec 30 17:32:33 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Fri, 30 Dec 2011 17:32:33 +0100 Subject: [Pw_forum] NEB: wild changes in image energies In-Reply-To: <1325176673.85121.YahooMailNeo@web111011.mail.gq1.yahoo.com> References: <1325176673.85121.YahooMailNeo@web111011.mail.gq1.yahoo.com> Message-ID: Dear Chad, as the energy barrier is very very very small maybe the use of freezing causes the algorithm to have more instabilities. bests Layla 2011/12/29 Chad Junkermeier > Hello, > I have a problem that I keep encountering when performing NEB > calculations. I will briefly describe what is happening here, and then > give a more detailed explanation below. In short, the NEB calculations > appear to run well for some number of iterations (usually on the order of > 40 or 50 iterations) and then all of the sudden weird image energies start > showing up, and the activation energy starts jumping around with each > iteration. > > > > More detailed explanation: > > Physically what I am trying to do is model the diffusion of a small > molecule across a graphene surface. This molecule is only weakly absorbed > (physisorbed) onto the surface, thus, the activation energy is going to be > rather small. Our relaxation calculations show that van der Waals type > interactions are important in this system, as should be expected for > something that is weakly absorbed. In the NEB calculation the molecule is > going from one lowest energy site to a neighboring lowest energy site that > is only a few angstroms away, all of which is well within the bounds of the > supercell. > > I am using Quantum Espresso 4.3.2 on a Cray XE6. > > > My input file looks like this: > > BEGIN > BEGIN_PATH_INPUT > &PATH > restart_mode = 'from_scratch' > string_method = 'neb', > ds = 2.D0, > opt_scheme = "broyden", > num_of_images = 45, > k_max = 0.3D0, > k_min = 0.2D0, > CI_scheme = "auto", > nstep_path=3000, > use_freezing = .TRUE. > first_last_opt = .FALSE. > / > END_PATH_INPUT > BEGIN_ENGINE_INPUT > &CONTROL > prefix="TW2_u_B3_B4", > pseudo_dir = "/espresso/pseudo", > outdir = "/workspace/TW2_u_B3_B4/tmp", > / > &SYSTEM > ibrav = 4, > celldm(1) = 37.2672889, > celldm(3) = 0.760623, > nat = 144, > ntyp = 4, > ecutwfc = 50.0, > ecutrho = 400, > occupations = "smearing", > smearing = "methfessel-paxton", > degauss = 0.01, > london = .TRUE. > / > &ELECTRONS > conv_thr = 0.0000001, > mixing_beta = 0.3, > electron_maxstep = 150, > / > ATOMIC_SPECIES > C 12.0 C.pbe-van_ak.UPF > H 1.0 H.pbe-van_ak.UPF > O 18.0 O.pbe-van_ak.UPF > P 31.0 P.pbe-van_ak.UPF > BEGIN_POSITIONS > FIRST_IMAGE > ATOMIC_POSITIONS angstrom > C 0.000000000 0.000000000 0.000000000 0 0 0 > C 1.234000000 0.710000000 0.000000000 0 0 0 > C 2.465000000 0.000000000 0.000000000 0 0 0 > C 3.699000000 0.710000000 0.000000000 0 0 0 > C 4.930000000 0.000000000 0.000000000 0 0 0 > . > . > . > LAST_IMAGE > ATOMIC_POSITIONS angstrom > . > . > . > H 12.789295543 12.155855132 2.858948537 > H 13.430079977 11.427859045 4.385644094 > H 14.299090315 11.190357788 2.820979411 > END_POSITIONS > K_POINTS {gamma} > END_ENGINE_INPUT > END > > While I didn't include all of the atoms in here (since there are a lot, > and I don't think this is necessarily to the resolution problem), I will > note that the majority of the atoms will not move appreciably during the > course of the calculation, and thus to speed up the calculation I tell the > code to fix the positions of the atoms that aren't moving. > > I started off with values that I thought would help the code run quicker: > conv_thr = 0.00001 > ecutwfc = 30.0, > ecutrho = 280, > num_of_images = 15, > electron_maxstep = 100, > > After finding the problem that I am writing here about, and reading > everything I could find on the QE website, and within pw_forum, I slowly > made changes trying to work through the problem. Having the number of > images set to 45 in the above input file has many more images than I think > I need, but one of the things that I kept reading is that having more > images will decrease the likelihood of problems arising. > > > After the first few NEB iterations a nice potential barrier curve appears > and is slowly refined. An example of the standard output for one of the > well behaved images is given below: > > ------------------------------ iteration 44 > ------------------------------ > > tcpu = 61713.9 self-consistency for image 10 > tcpu = 61932.1 self-consistency for image 21 > tcpu = 62113.6 self-consistency for image 28 > tcpu = 62294.4 self-consistency for image 31 > > activation energy (->) = 0.043939 eV > activation energy (<-) = 0.044011 eV > > image energy (eV) error (eV/A) frozen > > 1 -21959.2382129 0.081337 T > 2 -21959.2388966 0.020923 T > 3 -21959.2381194 0.123092 T > 4 -21959.2363069 0.164123 F > 5 -21959.2352170 0.044025 T > 6 -21959.2331629 0.220840 F > 7 -21959.2301578 0.115291 T > 8 -21959.2277497 0.199382 F > 9 -21959.2256241 0.037564 T > 10 -21959.2216078 0.257680 F > 11 -21959.2173790 0.220445 F > 12 -21959.2159181 0.195525 F > 13 -21959.2122799 0.189871 F > 14 -21959.2093498 0.070035 T > 15 -21959.2075466 0.156424 F > 16 -21959.2037818 0.237338 F > 17 -21959.2013877 0.059399 T > 18 -21959.2006768 0.168875 F > 19 -21959.1986806 0.049577 T > 20 -21959.1962718 0.054413 T > 21 -21959.1966851 0.022074 T > 22 -21959.1954724 0.053047 T > 23 -21959.1942736 0.054956 T > 24 -21959.1944583 0.140762 F > 25 -21959.1964535 0.032502 T > 26 -21959.1950797 0.210304 F > 27 -21959.1987196 0.051561 T > 28 -21959.2008371 0.031058 T > 29 -21959.2005944 0.183532 F > 30 -21959.2045923 0.059183 T > 31 -21959.2074746 0.148483 F > 32 -21959.2094894 0.139970 F > 33 -21959.2129334 0.033060 T > 34 -21959.2156972 0.237590 F > 35 -21959.2188749 0.065209 T > 36 -21959.2223341 0.020410 T > 37 -21959.2256989 0.041502 T > 38 -21959.2278845 0.206609 F > 39 -21959.2309458 0.064352 T > 40 -21959.2333476 0.228702 F > 41 -21959.2354058 0.034633 T > 42 -21959.2369634 0.053540 T > 43 -21959.2383146 0.179708 F > 44 -21959.2390413 0.052827 T > 45 -21959.2382847 0.084999 T > > climbing image = 23 > > path length = 18.663 bohr > inter-image distance = 0.424 bohr > > > If you were to plot the image number versus the energy that is given above > you would find what appears to be a very well behaved curve. > > > But after a while, all of the sudden, there is a problem with the output. > > > > ------------------------------ iteration 45 > ------------------------------ > > tcpu = 62502.4 self-consistency for image 4 > tcpu = 62758.1 self-consistency for image 6 > tcpu = 63006.7 self-consistency for image 8 > tcpu = 63287.9 self-consistency for image 10 > tcpu = 63556.1 self-consistency for image 11 > tcpu = 63876.3 self-consistency for image 12 > tcpu = 64126.9 self-consistency for image 13 > tcpu = 64409.9 self-consistency for image 15 > tcpu = 64661.2 self-consistency for image 16 > tcpu = 64941.7 self-consistency for image 18 > tcpu = 65190.6 self-consistency for image 24 > tcpu = 65480.1 self-consistency for image 26 > tcpu = 65780.1 self-consistency for image 29 > tcpu = 66077.9 self-consistency for image 31 > tcpu = 66317.9 self-consistency for image 32 > tcpu = 66580.4 self-consistency for image 34 > tcpu = 66857.5 self-consistency for image 38 > tcpu = 67137.2 self-consistency for image 40 > tcpu = 67386.9 self-consistency for image 43 > > activation energy (->) = 0.287582 eV > activation energy (<-) = 0.287654 eV > > image energy (eV) error (eV/A) frozen > > 1 -21959.2382129 0.081337 T > 2 -21959.2388966 0.020929 T > 3 -21959.2381194 0.128767 T > 4 -21959.1561960 2.016407 T > 5 -21959.2352170 0.054181 T > 6 -21959.1233419 3.440925 F > 7 -21959.2301578 0.119857 T > 8 -21959.1295895 3.858443 F > 9 -21959.2256241 0.031368 T > 10 -21959.2007906 0.830489 T > 11 -21958.9506305 4.210877 F > 12 -21959.1226848 2.774980 F > 13 -21959.1255613 3.306542 F > 14 -21959.2093498 0.063904 T > 15 -21959.1425146 2.576069 F > 16 -21959.0686534 4.452463 F > 17 -21959.2013877 0.051986 T > 18 -21959.1237018 2.915400 F > 19 -21959.1986806 0.070271 T > 20 -21959.1962718 0.055066 T > 21 -21959.1966851 0.022251 T > 22 -21959.1954724 0.053511 T > 23 -21959.1942736 0.155528 T > 24 -21959.0321128 1.669573 T > 25 -21959.1964535 0.033436 T > 26 -21958.9641160 2.813188 F > 27 -21959.1987196 0.170191 T > 28 -21959.2008371 0.119487 T > 29 -21959.0410354 2.100854 T > 30 -21959.2045923 0.217405 T > 31 -21959.2006761 0.946770 T > 32 -21959.1091999 2.022318 T > 33 -21959.2129334 0.033922 T > 34 -21959.0832736 3.736941 F > 35 -21959.2188749 0.136602 T > 36 -21959.2223341 0.033429 T > 37 -21959.2256989 0.038111 T > 38 -21959.1226548 4.018138 F > 39 -21959.2309458 0.068887 T > 40 -21959.1163356 3.540681 F > 41 -21959.2354058 0.069677 T > 42 -21959.2369634 0.053677 T > 43 -21959.1651795 2.854320 F > 44 -21959.2390413 0.041340 T > 45 -21959.2382847 0.084999 T > > climbing image = 11 > > path length = 19.063 bohr > inter-image distance = 0.433 bohr > > > Where if you plot the image number versus the energy given above you will > find that many of the points lay on the same curve as in the proceeding > plot, but now almost half of them are jumping to higher energies. When I > look at the xyz output in VMD, there doesn't seem to be any change in what > the images look like pre/post the start of iteration 45. > > I will now list some of the activation energies produced towards the end > of the run (I stopped the code once I saw this happening again). > > activation energy (->) = 0.043939 eV > activation energy (->) = 0.043939 eV > activation energy (->) = 0.043939 eV > activation energy (->) = 0.046128 eV > activation energy (->) = 0.043939 eV > activation energy (->) = 0.044786 eV > activation energy (->) = 0.043951 eV > activation energy (->) = 0.043939 eV > activation energy (->) = 0.043939 eV > activation energy (->) = 0.043939 eV > activation energy (->) = 0.043939 eV > activation energy (->) = 0.044436 eV > activation energy (->) = 0.043939 eV > activation energy (->) = 0.043939 eV > activation energy (->) = 0.043939 eV > activation energy (->) = 0.043939 eV > activation energy (->) = 0.043939 eV > activation energy (->) = 0.043939 eV > activation energy (->) = 0.043939 eV > activation energy (->) = 0.287582 eV > activation energy (->) = 0.206100 eV > activation energy (->) = 0.601468 eV > activation energy (->) = 0.231222 eV > activation energy (->) = 0.216514 eV > activation energy (->) = 0.252992 eV > activation energy (->) = 0.289003 eV > activation energy (->) = 0.107865 eV > activation energy (->) = 0.154660 eV > activation energy (->) = 0.302177 eV > activation energy (->) = 0.154660 eV > activation energy (->) = 0.290079 eV > > > > You can see that the activation energy is fairly constant at about 0.04 eV > for a while and then after a certain point bedlam. > > > Any ideas would be welcome. > > > > Chad Junkermeier, Ph.D. > NRC Post-Doctoral Associate > U. S. Naval Research Laboratory > > _______________________________________________ > 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/20111230/0cd1128f/attachment-0001.htm From akohlmey at gmail.com Fri Dec 30 17:39:53 2011 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Fri, 30 Dec 2011 11:39:53 -0500 Subject: [Pw_forum] How to test pseudo potential for non-metallic element? In-Reply-To: <002601ccc70e$a1e2b2c0$e5a81840$@gmail.com> References: <002601ccc70e$a1e2b2c0$e5a81840$@gmail.com> Message-ID: On Fri, Dec 30, 2011 at 11:18 AM, WF wrote: > Dear everyone, > > ???????? I tried to create pseudo potential for O and S ( for some uncommon > functional ) for later oxides calculation. Before used in the final model, > it should be checked. However, for a metallic element, it is easy to create > a model with its stable elementary substance and optimized to see its > lattice constant as first step verification. However for an element exists > as molecule, is it a good method to test the molecule case? Is it enough to > use ld1.x test only as first step verification? Thanks. you can just combine them with other known to work pseudopotentials and check a variety of compounds, e.g. H2O/H2S molecules/cluster, metal/semiconductor oxides. cheers, axel. > > > > ------------------------------------------------------------ > > Wu Feng, > > Chemistry and Molecular Engineering, Peking University > > ------------------------------------------------------------ > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From faccin.giovani at gmail.com Fri Dec 30 18:30:50 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Fri, 30 Dec 2011 13:30:50 -0400 Subject: [Pw_forum] How to test pseudo potential for non-metallic element? In-Reply-To: <002601ccc70e$a1e2b2c0$e5a81840$@gmail.com> References: <002601ccc70e$a1e2b2c0$e5a81840$@gmail.com> Message-ID: Dear Wu, To check the transferability it's good to try different electronic environments. The ld1 tests are the first thing to do. If they look ok, then try very different structures, including at least a bulk and the dimer, and compare with the literature. This will give you an idea about how transferable the pseudo is. Of course you can try molecules as well if you know what result to expect. Happy new year! Giovani Faccin UFMS / Brazil Em 30/12/2011 13:18, "WF" escreveu: > Dear everyone,**** > > I tried to create pseudo potential for O and S ( for some > uncommon functional ) for later oxides calculation. Before used in the > final model, it should be checked. However, for a metallic element, it is > easy to create a model with its stable elementary substance and optimized > to see its lattice constant as first step verification. However for an > element exists as molecule, is it a good method to test the molecule case? > Is it enough to use ld1.x test only as first step verification? Thanks.*** > * > > ** ** > > ------------------------------------------------------------**** > > Wu Feng,**** > > Chemistry and Molecular Engineering, Peking University**** > > ------------------------------------------------------------**** > > ** ** > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111230/422a0927/attachment.htm From kalamaillist at gmail.com Sat Dec 31 17:52:53 2011 From: kalamaillist at gmail.com (WF) Date: Sun, 1 Jan 2012 00:52:53 +0800 Subject: [Pw_forum] How to test pseudo potential for non-metallic element? Message-ID: <000c01ccc7dc$a6013010$f2039030$@gmail.com> Thanks for your advices and I will try it later. Happy New Year! >You can just combine them with other known to work pseudopotentials and check a variety of compounds, e.g. H2O/H2S molecules/cluster, metal/semiconductor oxides. >Cheers, > axel. >Dear Wu, >To check the transferability it's good to try different electronic environments. The ld1 tests are the first thing to do. If they look ok, then try very different structures, including at least a bulk and the dimer, and compare with the literature. This will give you an idea about how transferable the pseudo is. Of course you can try molecules as well if you know what result to expect. >Happy new year! >Giovani Faccin ------------------------------------------------------------ Wu Feng, Chemistry and Molecular Engineering, Peking University ------------------------------------------------------------