Dear All , sorry but this is a very low level question.
would you please inform me as to how i can install,configure, and make all the necessary steps so that i can be able to run simulations. i have tried to use the QE website but i ended up in so much more inconsistencies. for example where and how can i get and install fortan and c.xcrysden which binary or static files should i use and how should i install them. i need your specific advise on this to catch up with everybody. Regards, Yoseph Getachew ArbaMinch University, Department of Physics On 6/15/09, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org> wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: homo-lumo and conductance (Gabriele Sclauzero) > 2. Re: B_field (Gabriele Sclauzero) > 3. doubt about documentation of QE (shypirate) > 4. fileutil ? (Nicola Marzari) > 5. Re: fileutil ? (Tone Kokalj) > 6. Re: doubt about documentation of QE (Paolo Giannozzi) > 7. Re: fileutil ? (Paolo Giannozzi) > 8. ld1.x testing mode (hichem bouderba) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 15 Jun 2009 09:04:03 +0200 > From: Gabriele Sclauzero <sclauzer at sissa.it> > Subject: Re: [Pw_forum] homo-lumo and conductance > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <4A35F263.9020205 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > ambavale sagar wrote: >> Dear Gabriele, >> Thank you for your reply. I refered to smogunov paper but I could not >> understand the sentence used there : "Since the system has the supercell >> (artificial) 2D periodicity in the xy plane, perpendicular to the >> transport direction, we averaged the transmission over the corresponding >> 2D BZ using 21 k points in the irreducible part of the BZ.." Are those >> 21 k-pts belong to xy plane only? what type of grid that may be? 6 6 2 1 >> 1 1 ? >> In my case supercell dimensions in x and y are 25 a.u. i.e. ~12 ang >> which includes nearly ~9 ang. of vaccum. > > Here Alexander already replied you. So your k_perpendicular points sampling > depends if you > want to study an isolated wire (thick or monoatomic), or a wire/molecule > between realistic > electrodes (modeled as surfaces or surfaces+tips attached to them). In the > former case, if > your supercell is large enough in the directions perpendicular to the > transport the > transmission should not depend on k_perp and you need only one k_perp-point. > In the latter > you need to sample accurately the 2D BZ, since the transmission depends (a > lot in some > cases) on k_perp. > >> >> As you mentioned the limitation of DFT due to xc-functional, can I use >> DFT calculation to compare qualitatively the Transmission coefficient of >> same molecule with different geometries? > > I cannot say, actually. It depends on the coupling and other details. You > can have a look > to the recent work by Thygesen and Rubio, which try to include a GW > correction in this > kind of calculations. > >> >> would you please mention in detail how to find positions of HOMO, LUMO >> in a coupled system? > > What I would do (but fur sure there are many better methods) if I want to > put, say, O_2 > between electrodes is to look at the PDOS (computed by projwfc.x in the QE > suite) > projected onto the O atoms and compare it with the PDOS of the isolated O_2. > It would give > an idea of the level of hybridization between molecule and electrodes and of > the position > of the HOMO(LUMO)-derived levels. > It could also be useful to look at the PDOS on the electrode atoms to > understand which > metallic states/atoms are more involved in the coupling. > > regards, > > GS > > >> >> regards >> Sagar Ambavale >> ------------------------------------------------------------------------ >> ** >> Message: 1 >> Date: Fri, 12 Jun 2009 18:14:46 +0200 >> From: Gabriele Sclauzero <sclauzer at sissa.it <mailto:sclauzer at sissa.it>> >> Subject: Re: [Pw_forum] homo-lumo and conductance >> To: PWSCF Forum <pw_forum at pwscf.org <mailto:pw_forum at pwscf.org>> >> Message-ID: <4A327EF6.7020206 at sissa.it <mailto:4A327EF6.7020206 at >> sissa.it>> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> >> ambavale sagar wrote: >> > Dear all, >> > I am studying ballistic conductance through a molecule attached to Al >> > electrode. >> >> Including Al surfaces on both sides? >> >> > The k-pt grid used for scf calculation of scattering region >> > made of molecule and few layers of electrode, is 2 2 10 1 1 1. >> >> If so, this k-point grid looks a bit lousy to me. Unless you use a very >> large supercell in >> the transverse directions (xy, since z is the transport direction in >> pwcond), you should >> take more k-points along that directions. Along z, instead, you need >> less k-points (10 >> seems really too much to me). Along z you must include enough slabs >> before and after the >> junction with the molecule such that the scf potential at the borders of >> the cell is close >> enough to the scf potential of bulk Al. >> >> You can have a look at this paper in order to get an idea: >> Smogunov et al., Phys. Rev. B 78, 014423 (2008) >> >> > I want to >> > see effect of HOMO-LUMO levels of molecule on transmission. Is it >> > sensible to find HOMO-LUMO levels of molecule using separate >> calculation >> > of isolated molecule with gamma point? How about bandstructure that I >> > got from 20 k-pt calculation of scattering region periodic in >> z-direction? >> >> I'm not sure I got your questions. Of course if you study the ballistic >> conductance >> through the molecule in the tunneling regime, the result will be very >> sensitive to the >> position of the HOMO and LUMO levels of the molecule. Depending on how >> strong is the >> binding between the molecule and the electrodes the position and width >> of these levels >> will be modified more or less by the hybridization with the metal states. >> In order to find the position of the HOMO and LUMO in the coupled system >> you can look at >> the PDOS on the atoms of the molecule (if not too complex) and compare >> it with the >> corresponding PDOS of the isolated molecule. >> Another solution might be to build Wannier functions of the HOMO and >> LUMO and project onto >> them, but I never tried this solution. >> >> Anyway, you should be careful when trusting DFT results in this kind of >> system, since >> common XC functionals can mismatch the HOMO-LUMO gap of several eV and >> there could also be >> problems in getting a reliable alignment with the Fermi level of the >> metal. Since in >> weakly coupled junctions the conductance is very sensitive to the exact >> position of the >> molecular levels involved in the tunneling and to the decaying behavior >> of their tails, >> this issues can lead to errors of 1 or several orders of magnitude. >> >> >> Cheers >> >> GS >> >> > >> > Thank you. >> > >> > Sagar Ambavale >> > PhD student >> > M.S. University of Baroda >> > India >> > >> > >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it <mailto:sclauzer at sissa.it> >> | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> >> >> *************************** >> >> ------------------------------------------------------------------------ >> Own a website.Get an unlimited package.Pay next to nothing.* Click >> here!. >> <http://in.rd.yahoo.com/tagline_ysb_website/*http://in.business.yahoo.com/> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > > > ------------------------------ > > Message: 2 > Date: Mon, 15 Jun 2009 09:50:37 +0200 > From: Gabriele Sclauzero <sclauzer at sissa.it> > Subject: Re: [Pw_forum] B_field > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <4A35FD4D.3090505 at sissa.it> > Content-Type: text/plain; charset=UTF-8; format=flowed > > It seems to me that B_field can be read from input, but then is not used in > the > calculation. Maybe it was an older option which has been replaced by another > solution. In > fact I think that a better way to see the effect of an external magnetic > field is to do a > calculation with constrained magnetization (see INPUT_PW for documentation): > this should > ensure to reach the ground states, while I suspect that applying a magnetic > field you > could end in a metastable state, depending on the starting conditions. > > Regards > > GS > > ?? wrote: >> Dear everyone: >> >> I try to appy an external magnetic field about 0.01 Ry to a bulk of >> paramagnetic material. By either looking at the spin polarization and >> the density of states, I could not find any polarization induced. >> Any one has an idea. It will be highly appreciated! >> >> Yang >> > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > > > ------------------------------ > > Message: 3 > Date: Mon, 15 Jun 2009 17:19:18 +0800 > From: "shypirate" <shypirate at gmail.com> > Subject: [Pw_forum] doubt about documentation of QE > To: "pw_forum" <pw_forum at pwscf.org> > Message-ID: <200906151719143151087 at gmail.com> > Content-Type: text/plain; charset="us-ascii" > > Dear All: > I am reading the doc and example of QE, but it makes me confused. > > For example, in example30/README, 'tefield' and 'efield' is used together to > add electric field to the studied system. However, in the 'INPUT_PW.html', > 'tefield' is used to specified a sawlike potential, and 'efield' is used if > 'lelfield=.TRUE.', at the same time, 'lelfield' is "different" from > 'tefield'. > > All the above refered is version 4.0.5. > > Any suggestion is appreciated! > > Y.P.Wang > > > 2009-06-15 > > > > shypirate > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090615/bc905842/attachment-0001.htm > > ------------------------------ > > Message: 4 > Date: Mon, 15 Jun 2009 05:48:14 -0400 > From: Nicola Marzari <marzari at MIT.EDU> > Subject: [Pw_forum] fileutil ? > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <4A3618DE.5070906 at mit.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > > Dear All, > > > 1) if I try to generate the documentation files for QE (make all in > dev-doc) I get an error message about missing the fileutil package > (see error lines below). I have tcl-8.4.13-1.1 ; I searched the > forum (to no avail), so maybe this is useful to others. > > 2) is it correct that the new source for the QE snapshots is the > qe-forge CVS, and the old CVS is not maintained, and wil be > discarded ? For reference to anyone reading, the new cvs > instructions are: > > cvs -d :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e checkout espresso > > Thanks, > > nicola > > > ---- > in dev-doc: > make all > ../dev-tools/helpdoc INPUT_PW.def > can't find package fileutil > while executing > "package require fileutil" > (file > "/home/marzari/codes/espresso/dev-tools/helpdoc.d/../../GUI/Guib/lib/tclUtils.tcl" > line 41) > invoked from within > "source > /home/marzari/codes/espresso/dev-tools/helpdoc.d/../../GUI/Guib/lib/tclUtils.tcl" > ("package ifneeded" script) > invoked from within > "package require tclu 0.9" > (file > "/home/marzari/codes/espresso/dev-tools/helpdoc.d/helpdoc.tcl" line 4) > invoked from within > "source [file join $sourcedir helpdoc.tcl]" > (file "../dev-tools/helpdoc" line 8) > make: *** [INPUT_PW.html] Error 1 > ---- > > --------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials Science and Engineering > 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA > tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu > > > ------------------------------ > > Message: 5 > Date: Mon, 15 Jun 2009 12:22:07 +0200 > From: Tone Kokalj <tone.kokalj at ijs.si> > Subject: Re: [Pw_forum] fileutil ? > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <1245061327.29014.38.camel at walk.ijs.si> > Content-Type: text/plain > > On Mon, 2009-06-15 at 05:48 -0400, Nicola Marzari wrote: >> >> >> Dear All, >> >> >> 1) if I try to generate the documentation files for QE (make all in >> dev-doc) > > actually in doc-def/ > >> ... I get an error message about missing the fileutil package >> (see error lines below). I have tcl-8.4.13-1.1 ; I searched the >> forum (to no avail), so maybe this is useful to others. > > > fileutil is a package from the tcllib. The latter is required for the > helpdoc program to function (see the dev-tools/README.helpdoc). And > helpdoc is a utility that creates the QE txt and html documentation > files from the *.def files. > > Several linux distros are based on Debian or RedHat, if you use one of > them, then to install tcllib: > > apt-get install tcl tcllib xsltproc (for Debian-based distros) > > or > > yum install tcl tcllib xsltproc (for Redhat-based distros) > > (for other distros the installation of tcllib is likely analogous, i.e., > replace the apt-get|yum with the corresponding package installer) > > Regards, Tone > > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > ------------------------------ > > Message: 6 > Date: Mon, 15 Jun 2009 12:50:27 +0200 > From: Paolo Giannozzi <giannozz at democritos.it> > Subject: Re: [Pw_forum] doubt about documentation of QE > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <A6A59174-0F38-41E2-B770-EC74393FFCD7 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > On Jun 15, 2009, at 11:19 , shypirate wrote: > >> For example, in example30/README, 'tefield' and 'efield' is used >> together >> to add electric field to the studied system. However, in the >> 'INPUT_PW.html', >> 'tefield' is used to specified a sawlike potential, and 'efield' is >> used if >> 'lelfield=.TRUE.', at the same time, 'lelfield' is "different" from >> 'tefield'. >> [...] Any suggestion is appreciated! > > you will have better luck if you read the documentation for CP: > Doc/INPUT_CP, since this is what is actually used in example30. > Unfortunately there is a mismatch between CP and PWscf in the > definition of electric fields > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > ------------------------------ > > Message: 7 > Date: Mon, 15 Jun 2009 13:13:13 +0200 > From: Paolo Giannozzi <giannozz at democritos.it> > Subject: Re: [Pw_forum] fileutil ? > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <1C080D0E-8CD7-4A48-A073-11BC40E49267 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > On Jun 15, 2009, at 11:48 , Nicola Marzari wrote: > >> 2) is it correct that the new source for the QE snapshots is the >> qe-forge CVS, and the old CVS is not maintained > > correct. The user guide and developer manual on the wiki report > the obsolete CVS location, because they are in turn no longer > maintained: they have been brought back to the CVS tree. > An updated version will be put on line when the new version > will be released. > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > ------------------------------ > > Message: 8 > Date: Mon, 15 Jun 2009 13:20:52 +0200 > From: hichem bouderba <hichem.bouderba at gmail.com> > Subject: [Pw_forum] ld1.x testing mode > To: pw_forum at pwscf.org > Message-ID: > <c83c8cd90906150420y4b51aaado2eff955a3429b474 at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > dear all, > in INPUT_LD1.html about ecutmin,ecutmax,decut we have : > " > Parameters (Ry) used for test with a basis set of spherical > Bessel functions j_l(qr) . The hamiltonian at fixed scf > potential is diagonalized for various values of ecut: > ecutmin, ecutmin+decut, ecutmin+2*decut ... up to ecutmax. > This yields an indication of convergence with the > corresponding plane-wave cutoff in solids, and shows > in an unambiguous way if there are "ghost" states > " > > how does ld1.x say "there is a ghost state somewhere" ? > > when testing a PAW with ld1.x I have the following error: > > " > Cutoff (Ry) : 50.0 > N = 1 N = 2 N = 3 > E(L=0) = -3.2666 Ry -0.2491 Ry -0.0148 Ry > E(L=1) = -1.8963 Ry -0.0931 Ry 0.0105 Ry > E(L=2) = -0.0637 Ry 0.0203 Ry 0.0602 Ry > > Cutoff (Ry) : 55.0 > N = 1 N = 2 N = 3 > E(L=0) = -3.2666 Ry -0.2491 Ry -0.0148 Ry > E(L=1) = -1.8963 Ry -0.0931 Ry 0.0105 Ry > E(L=2) = -0.0637 Ry 0.0203 Ry 0.0601 Ry > > Cutoff (Ry) : 60.0 > N = 1 N = 2 N = 3 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from rdiags : error # 73 > failed to converge (factorization) > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > " > what does it mean ? > thanks. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090615/11d6c36f/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 24, Issue 30 > **************************************** > -- peace,yoseph
