[Pw_forum] Bamidele Ibrahim Adetunji wants to share new pictures with you
An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20121026/e34be789/attachment-0001.html
[Pw_forum] CIF to PWSCF
Hi Ben One problem is that the QE input files contains not only the structure, but parameters for the quantum calculation. So, we have to edit the file, using copy and paste when possible. The main problem is that the CIF files contains olny the atomic coordinates that are non-equivalent by the symmetry of tha space group of the crystal. I use gdis (comes in Ubuntu distributions) to convert to other less crystallographic format, like that of SIESTA. This automates the generation of the symmetry equivalent positions that are not in the CIF. You can also generate the coordinates using The inconvenient is that it generates the conventional cell, rather than the primitive cell. Then I use vim or gedit to manully set the input file. Linux distributions are plenty of programs for chemistry and physics. I have seen that the babel code can read the CIF format and convert to many more. There is also a serious intenet option using the bilbao crystallographic server. This tool is recognized by crystallographers in the International Tables for Crsytallgraphy, so it is a trustable tool. http://www.cryst.ehu.es/ There, you can use the programs TRANSTRU or STRCONVERT. What you need is to convert the structure to the group P1, or just 1, and this gives all the information need to the QE input file. Then, use vim, gedit, or your favorite editor. This is not confortable at the begining, but at the end it is easy, and you may consider it as one intiation ritual (one more, right). For the case of iron, the stable crystal structure is so simple (BCC) that you can write it with the only knowledge of the lattice constants, you do not need the CIF. It is explained in the initial chapters of many (probably all) solid state physics and materials science books. I suggest you read that, otherwise you better quit using QE. Best regards Eduardo 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 > 2012/10/24 Ben Palmer >> >> Hi, >> >> I'm new to pwscf and I'm trying to find the relaxed co-ordinates for an >> Iron crystal. I've been trying to set up the initial crystal from a cif >> file. Is there a way to convert from cif to the pwscf format? >> >> Thanks >> >> Be -- -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20121026/db3c5305/attachment.html
[Pw_forum] EPW package used with QE
Dear Elie, no EPW il still just interfaced with qe version 4.0.3. There is some effort going on for aligning public part of EPW to espresso trunk. cheers Layla 2012/10/26 Marci > Hi Elie, > > I think you have better chance of getting an answer if you contact the > developers of the EPW package: > > http://epw.org.uk/Main/Contact > > Cheers, > Marton Voros > > -- > PhD student > Department of Atomic Physics > Budapest University of Technology and Economics > > On Fri, Oct 26, 2012 at 3:00 PM, Elie M > wrote: > > Dear all, > > > > I have a question about the use of the EPW package (electron phonon > > calculations using the Wannier functions) with QE. As far as I know, the > > latest version is EPW-2.3.6 which can be used in conjunction with old > > versions of QE like QE-4.0.3. > > > > (1) Does anybody know if the EPW pacakge can be compiled with the recent > > versions of QE, say QE-4.3.2? > > > > (2) If not, is there a more recent version , to be downloaded, which can > be > > used with QE-4.3.2? > > > > > > > > Thank you > > > > Elie Moujaes > > University of Nottingham > > NG7 2RD > > NOTTS > > UK > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20121026/e27ce05d/attachment.html
[Pw_forum] EPW package used with QE
Hi Elie, I think you have better chance of getting an answer if you contact the developers of the EPW package: http://epw.org.uk/Main/Contact Cheers, Marton Voros -- PhD student Department of Atomic Physics Budapest University of Technology and Economics On Fri, Oct 26, 2012 at 3:00 PM, Elie M wrote: > Dear all, > > I have a question about the use of the EPW package (electron phonon > calculations using the Wannier functions) with QE. As far as I know, the > latest version is EPW-2.3.6 which can be used in conjunction with old > versions of QE like QE-4.0.3. > > (1) Does anybody know if the EPW pacakge can be compiled with the recent > versions of QE, say QE-4.3.2? > > (2) If not, is there a more recent version , to be downloaded, which can be > used with QE-4.3.2? > > > > Thank you > > Elie Moujaes > University of Nottingham > NG7 2RD > NOTTS > UK > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] EPW package used with QE
Marci and Layla, Thank you both for your replies. I will also contact the EPW group for further information Elie Date: Fri, 26 Oct 2012 15:20:19 +0200 From: lmartinsa...@gmail.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] EPW package used with QE Dear Elie, no EPW il still just interfaced with qe version 4.0.3. There is some effort going on for aligning public part of EPW to espresso trunk. cheers Layla 2012/10/26 Marci Hi Elie, I think you have better chance of getting an answer if you contact the developers of the EPW package: http://epw.org.uk/Main/Contact Cheers, Marton Voros -- PhD student Department of Atomic Physics Budapest University of Technology and Economics On Fri, Oct 26, 2012 at 3:00 PM, Elie M wrote: > Dear all, > > I have a question about the use of the EPW package (electron phonon > calculations using the Wannier functions) with QE. As far as I know, the > latest version is EPW-2.3.6 which can be used in conjunction with old > versions of QE like QE-4.0.3. > > (1) Does anybody know if the EPW pacakge can be compiled with the recent > versions of QE, say QE-4.3.2? > > (2) If not, is there a more recent version , to be downloaded, which can be > used with QE-4.3.2? > > > > Thank you > > Elie Moujaes > University of Nottingham > NG7 2RD > NOTTS > UK > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum at pwscf.org http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum at pwscf.org http://pwscf.org/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20121026/f766ee04/attachment.html
[Pw_forum] EPW package used with QE
Dear all, I have a question about the use of the EPW package (electron phonon calculations using the Wannier functions) with QE. As far as I know, the latest version is EPW-2.3.6 which can be used in conjunction with old versions of QE like QE-4.0.3. (1) Does anybody know if the EPW pacakge can be compiled with the recent versions of QE, say QE-4.3.2? (2) If not, is there a more recent version , to be downloaded, which can be used with QE-4.3.2? Thank you Elie MoujaesUniversity of NottinghamNG7 2RDNOTTSUK -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20121026/e237bb84/attachment.html
[Pw_forum] Phonon DOS per polarization
On 26 October 2012 07:55, Bo Qiu <200210qb at gmail.com> wrote: > Dear Dr. Paulatto, > > Thanks a lot for the explanations! I'm actually writing a small code to > order phonon bands based on eigenvector continuities on a 3d grid. Thanks > for pointing out there is already such option in matdyn.x, I'll definitely > check it out. I have finished a preliminary test for my code on Al for a > band crossing along Gamma-K direction -- it seems to be well captured, > but band orderings are wrong at some random point where there is actually > no band crossing. I'll try to figure it out and also referring to the > matdyn.f90 to see what else I can do. > On the other hand, I think for electronic band structures one will have > the same problem with band ordering -- though most of time people are only > interested about those very few bands near Fermi level. I wonder in the > case of electronic band structure whether continuity of wavefunction should > be used to deal with band ordering with band crossing? Thanks a lot! > > The bands.x code already does that, i.e. it sorts the bands using the overlap of wavefunctions at consequent k-points. Again, this is an option that works well for line plots, but I'm not sure it always make sense to use in a 3D dispersion. Or at least, it would need to be modified to sort according to neighboring points, not just according to the previous point in the input list. It is not very hard to do, but a bit boring as it requires a rethinking of the code structures. bests -- Dr. 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 -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20121026/5785dab2/attachment.html
[Pw_forum] IMPORTANT: QE Open Invitation to Contribute
Dear All, Our research group (Theory and Simulation of Materials at EPFL) has been developing several new features within QE, some in ready-to-use status, others in progress and could benefit from porting assistance. Some of these developments are tightly knitted within main executables such as cp and pw, others are with more specific packages or even, would serve as a super-structure for QE. Therefore the effort of porting/implementation assistance would vary. Below is this list of contributions we would be happy to make, with a brief description and contact address for each. Best, emine kucukbenli, postdoc at theos, epfl, switzerland http://theossrv1.epfl.ch * * * * ENVIRON(MENT) Module that includes - implicit solvent - surface tension, - electronic-enthalpy functional (quantum volume), - periodic boundary corrections in real space. The module is already compatible with the last SVN version of QE, in perfect shape to be included, technically, but for scientific reasons we would still keep its usage monitored for some 6-12 months more. Electrochemistry routines are in development, on top of SVN version. Contact: Oliviero Andreussi oliviero.andreussi at epfl.ch NON KOOPMAN'S-SIC Built on QE v.4.1; Has modifications to CP and Modules and it introduces a new directory ACF90, which contains functions for periodic-image corrections for systems with 3d, 2d, 1d periodicity. Non Koopman's-Self Interaction Correction has several parts in different stages of development and porting: -ACF90: updated version of Auxiliary Function library by Ismaila Dabo -Orbital-density-dependent (ODD) functionals: PZ, NK0, NK, NKI, NKIPZ, NKPZ -Complex wavefunctions minimization (feature necessary for orbital dependent functionals) -Hartree-Fock and Hybrid functionals in CP. -(Still under development), support for minimization of ODD functionals on a non-orthogonal basis set. - (Just started implementation, this might include some additional subroutine in the PP), support for band structure calculations from gamma point wavefunctions (unfolding of gamma-point band structure), support for computing self-consistent U via Orbital-dependent functionals. -PP support for plotting orbital dependent potentials, and for computing photoemission spectra (Linh Nguyen) The porting of the code to SVN version is already in progress, A hybrid GIT/SVN repository which can be syncronized one way with QE is present, albeit we woud appreciate some help. Contact: Giovanni Borghi: gio.borghi at gmail.com Linh Nguyen: linh.nguyen at epfl.ch Andrea Ferretti: andrea.ferretti at nano.cnr.it Ismaila Dabo: daboi at cermics.enpc.fr HUBBARD U+V We have recently started a local porting of the U+V routines of Coccoccioni et al. to SVN version. Possibly there is replication of work here, between us, Burak Himmetoglu (w Cococcioni) and Davide Ceresoli. Related current developments include: GIPAW+U+V (on SVN version of QE) and EPR+PAW (on SVN version of QE) Contact : Emine Kucukbenli emine.kucukbenli at epfl.ch AIDA: A High-throughput Platform interfaced to QE in its latest SVN version. AIDA is a high throughput calculation platform which has been developed in collaboration with Boris Kozisky from Bosch US. Its main purpose is to automatically create QE input files, launch jobs on HPC clusters and to store the resulting data in a database. As it is a separate code, AIDA does not require any modifications to repository however would benefit greatly from standardization of elements written in save directory and easily parsable data files. We have also very recently started to work on this issue by rearranging the content of data-file.xml with Simone Ziraldo (ziraldo at sissa.it) from SISSA, who has already developed the xml input feature that can be found in the SVN version of the code. The continuing developments on reogranization of data-file.xml is in a new branch of QE repository. Contact : Andrea Cepellotti andrea.cepellotti at epfl.ch Giovanni Pizzi giovanni.pizzi at epfl.ch * * * * -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20121026/b7c1bb03/attachment-0001.html
[Pw_forum] two conventions in postprocessing pp.x
On Fri, 2012-10-26 at 11:52 +0200, Cristian Degli Esposti Boschi wrote: > Dear developers, > plot_num = 1: is this the potential or the potential energy the potential energy. See the first lines of INPUT_PW.*: All quantities whose dimensions are not explicitly specified are in RYDBERG ATOMIC UNITS. Charge is "number" charge (i.e. not multiplied by e); potentials are in energy units (i.e. they are multiplied by e) > iflag = 0: does the spherical average include a normalization factor > 1/(4 pi) or not? Apparently it doesn't. Routine PP/src/chdens.f90, line 540 or so: ! spherically averaged charge: rho0(|r|) = int rho(r) dOmega ! rho0(r) = 4pi \sum_G rho(G) j_0(|G||r|) You may want to check whether this is actually what the code does in the following lines P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] two conventions in postprocessing pp.x
Dear developers, in order to perform some quantitative calculations we would need to know precisely the conventions used in the postprocessing output of pp.x regarding the following points: plot_num = 1: is this the potential or the potential energy, that is, in atomic units is there a multiplicative factor e=sqrt(2) (electric charge) or not? iflag = 0: does the sperichal average include a normalization factor 1/(4 pi) or not? Alternatively, we may check the appropriate code: which one? Thanks a lot 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 email: degliesposti -AT- bo.imm.cnr.it web: www.bo.imm.cnr.it/site/staff/personal_pages/degliesposti/
[Pw_forum] CIF to PWSCF
c On Thu, Oct 25, 2012 at 4:02 PM, Yue-Wen Fang wrote: > one way is to write a script to convert them! > i usually use castep in Materials Studio to convert the CIF files. > > Best! > >\fgff\\ftR > 2012/10/24 Ben Palmer >> >> Hi, >> >> I'm new to pwscf and I'm trying to find the relaxed co-ordinates for an >> Iron crystal. I've been trying to set up the initial crystal from a cif >> file. Is there a way to convert from cif to the pwscf format? >> >> Thanks >> >> Ben >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > > -- > > Yue-Wen Fang > East China Normal Univ, China > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] phonon branch sorting
Dear Bo and Lorenzo, I have one more suggestion on the issue of phonon branch sorting. I ran into this problem a while back, while working on a project on thermal transport in indium arsenide nanowires. I ended up using an sorting algorithm that Keith Refson developed for use with phonon calculations in the CASTEP code. This script works by calculating overlap matrices between eigenvectors at neighboring q-points. Keith recently licensed this script as GPL and I have written a tool to convert the matdyn phonon output to the CASTEP phonon format. For my project, I found that as long as you have a fairly dense mesh of q-points, it worked very well. I am planning to put these scripts up on the web soon once I have a short example run to go with it. I'll send a note to the PWSCF forum when it is ready. Bo, in the meantime, I would be happy to send you the scripts if you are interested. Best regards, Derek Derek Stewart, Ph. D. Senior Research Associate http://sites.google.com/site/dft4nano/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 On 10/26/2012 8:00 AM, Lorenzo Paulatto wrote: > On 26 October 2012 07:55, Bo Qiu <200210qb at gmail.com > <mailto:200210qb at gmail.com>> wrote: > > Dear Dr. Paulatto, > > Thanks a lot for the explanations! I'm actually writing a small > code to order phonon bands based on eigenvector continuities on a > 3d grid. Thanks for pointing out there is already such option in > matdyn.x, I'll definitely check it out. I have finished a > preliminary test for my code on Al for a band crossing along > Gamma-K direction -- it seems to be well captured, but band > orderings are wrong at some random point where there is actually > no band crossing. I'll try to figure it out and also referring to > the matdyn.f90 to see what else I can do. > On the other hand, I think for electronic band structures one will > have the same problem with band ordering -- though most of time > people are only interested about those very few bands near Fermi > level. I wonder in the case of electronic band structure whether > continuity of wavefunction should be used to deal with band > ordering with band crossing? Thanks a lot! > > > The bands.x code already does that, i.e. it sorts the bands using the > overlap of wavefunctions at consequent k-points. Again, this is an > option that works well for line plots, but I'm not sure it always make > sense to use in a 3D dispersion. Or at least, it would need to be > modified to sort according to neighboring points, not just according > to the previous point in the input list. It is not very hard to do, > but a bit boring as it requires a rethinking of the code structures. > > bests > > -- > Dr. Lorenzo Paulatto > IdR @ IMPMC -- CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www-int.impmc.upmc.fr/~paulatto/ > <http://www-int.impmc.upmc.fr/%7Epaulatto/> > mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20121026/fb458362/attachment.html
[Pw_forum] Questions about the DFPT review paper
On 25 October 2012 02:38, Caloma Trumica wrote: > Dear all, > > I do not understand why the two highlighted places in the attached DFPT > review paper are correct. > > I repeat my questions here: > > 1. Why the contributions from valence bands cancel each other? > If I remeber correctly, replace \Delta\psi from eq 28 in eq 23 > > 2. Why the left side of Eq.25 has a null eigenvalue? > > It may be better explained in Messiah "Quantum mechanics" book (1962), have you tried to have a look there? bests -- Dr. 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 -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20121026/26b99897/attachment.html
[Pw_forum] Phonon DOS per polarization
Dear Dr. Paulatto, Thanks a lot for the explanations! I'm actually writing a small code to order phonon bands based on eigenvector continuities on a 3d grid. Thanks for pointing out there is already such option in matdyn.x, I'll definitely check it out. I have finished a preliminary test for my code on Al for a band crossing along Gamma-K direction -- it seems to be well captured, but band orderings are wrong at some random point where there is actually no band crossing. I'll try to figure it out and also referring to the matdyn.f90 to see what else I can do. On the other hand, I think for electronic band structures one will have the same problem with band ordering -- though most of time people are only interested about those very few bands near Fermi level. I wonder in the case of electronic band structure whether continuity of wavefunction should be used to deal with band ordering with band crossing? Thanks a lot! Bo On Thu, Oct 25, 2012 at 5:05 PM, Lorenzo Paulatto < lorenzo.paulatto at impmc.upmc.fr> wrote: > Dear Bo, > as long as you can properly characterize the band, it is not hard to do: > you can use matdyn.x to compute the phonon in a dense grid of q-points, you > can generate it with pw.x or with the kpoint.x utility. Then load the grid > in matlab or octave or similar and integrate it properly. Since some time > ago, the matdyn code produce a *.gp code which is very practical for this > kind of analysis. > > The problem is deciding which is band X, as soon as they start to cross > deciding which is which is not trivial. There is an option in matdyn to > assign the phonon bands order using eigenvectors continuity. However, this > method works well for high-symmetry lines, but may be not so robust when > doing a 3D grid of points. Yet, it is worth trying. > > Provided all these difficulties, in many case and as long as you are > interested in a phonon band that is well separated from the others there > may be no problem at all. Finally, you can think of a specific criteria to > discriminate the bands in a specific material, but implementing it is up to > you. > > bests > > -- > Dr. Lorenzo Paulatto > IdR @ IMPMC -- CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www-int.impmc.upmc.fr/~paulatto/ > mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20121026/f6affb26/attachment.html
[Pw_forum] Phonon DOS per polarization
Dear Bo, as long as you can properly characterize the band, it is not hard to do: you can use matdyn.x to compute the phonon in a dense grid of q-points, you can generate it with pw.x or with the kpoint.x utility. Then load the grid in matlab or octave or similar and integrate it properly. Since some time ago, the matdyn code produce a *.gp code which is very practical for this kind of analysis. The problem is deciding which is band X, as soon as they start to cross deciding which is which is not trivial. There is an option in matdyn to assign the phonon bands order using eigenvectors continuity. However, this method works well for high-symmetry lines, but may be not so robust when doing a 3D grid of points. Yet, it is worth trying. Provided all these difficulties, in many case and as long as you are interested in a phonon band that is well separated from the others there may be no problem at all. Finally, you can think of a specific criteria to discriminate the bands in a specific material, but implementing it is up to you. bests -- Dr. 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 -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20121025/c7540ff0/attachment.html
