[Pw_forum] How to start and use QE open source simulation
yoseph Getachew
yosmanche at gmail.com
Tue Jun 16 17:50:49 CEST 2009
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:
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> 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/>
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>>
>> ------------------------------------------------------------------------
>>
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>
> --
>
>
> 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
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> ------------------------------
>
> 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.
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> ****************************************
>
--
peace,yoseph
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