[Pw_forum] Pw_forum Digest, Vol 125, Issue 4

Yuhit Gupta yuhitgupta349 at gmail.com
Wed Dec 6 05:25:38 CET 2017


Thank you Dr. Mitsuaki Kawamura,
For your precious advice and  time.

Kind Regards
Yuhit Gupta
Research Scholar
S.L.I.E.T LONGOWAL
INDIA

On 04-Dec-2017 10:35 PM, <pw_forum-request at pwscf.org> wrote:

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> Today's Topics:
>
>    1. Re: problem in relaxing gold cluster (Ari P Seitsonen)
>    2. Re: Error in routine sym_rho_init_shell (4): lone vector
>       (Manoar Hossain)
>    3. Re: (no subject) (Mitsuaki Kawamura)
>    4. Re: problem in relaxing gold cluster (David Foster)
>    5. SOC pseudopotential (Eliya Asmani)
>    6. Re: Phonon dispersion with LO-TO splitting (Barnali Bhattacharya)
>    7. Re: SOC pseudopotential (Lorenzo Paulatto)
>    8. Re: Error in routine sym_rho_init_shell (4): lone vector
>       (Paolo Giannozzi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 3 Dec 2017 12:38:03 +0100 (CET)
> From: Ari P Seitsonen <Ari.P.Seitsonen at iki.fi>
> Subject: Re: [Pw_forum] problem in relaxing gold cluster
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <alpine.DEB.2.20.1712031229420.5423 at kubo.chimie.ens.fr>
> Content-Type: text/plain; charset="iso-8859-15"
>
>
> Dear Haja Zareyi,
>
>    [Next time with affiliation please :) ]
>
>    'hgh' in the name of the pseudo potential => it is norm-conserving, no
> need to specify 'ecutrho'. Did you check that the 'ecutwfc' was
> sufficient for a reasonable convergence?
>
>      Greetings from Lviv/Lemberg,
>
>         apsi
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=
> -=*=-=*=-=*=-=*=-
>    Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
>      Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris
>      Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935
>
>
> On Sun, 3 Dec 2017, hajar zareyi wrote:
>
> > Dear all,
> >
> > I am trying to relax gold cluster but the structure is going to break
> apart. there is my input file
> >
> > ?&CONTROL
> > calculation = 'relax' ,
> > restart_mode = 'from_scratch' ,
> > outdir="./TMP",
> > pseudo_dir ="./", ? ? ? ??
> > tprnfor ? = .true.
> > tstress = .true.
> > prefix = 'AU',
> > /
> > &SYSTEM
> > ibrav = 1,
> > celldm(1) = 34.75,
> > nat = 13,
> > ntyp = 1,
> > ecutwfc = 45 ,
> > ecutrho = 500, ? ? ? ? ? ? ? ? ? ? ??
> > occupations = 'smearing' ,
> > degauss= 0.01 ,
> > smearing= 'gaussian',
> > /
> > ?&ELECTRONS
> > mixing_mode = 'local-TF' ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ??
> > mixing_beta = 0.7
> > conv_thr = 1.D-6 ,?
> > /
> > ?&IONS
> > /
> > ?&CELL
> > /
> > ATOMIC_SPECIES
> > Au ? ?196.966657 ? Au.blyp-d-hgh.UPF
> > ATOMIC_POSITIONS (angstrom)
> > Au 7.0000000 10.0000000 10.0000000
> > Au 8.3600000 7.6440000 10.0000000
> > Au 11.0800000 7.6440000 10.0000000
> > Au 12.4400000 10.0000000 10.0000000
> > Au 11.0800000 12.3560000 10.0000000
> > Au 8.3600000 12.3560000 10.0000000
> > Au 9.7200000 10.0000000 ?10.0000000
> > Au 9.7238155 8.4315277 ?7.777622
> > Au 8.3424810 10.7842271 ?7.780175
> > Au 11.0523480 10.8179223 ?7.78000
> > Au 9.7238155 8.4315277 ?12.2223780
> > Au 8.3328179 10.7673656 ?12.2200000
> > Au 11.0523480 10.8179223 ?12.2200000
> >
> > K_POINTS gamma
> >
> > is there any one to help me to correct it
> >
> > ?
> >
> >
> > --
> > This message has been scanned for viruses and dangerous content by
> > KNTU Antispam System (E.F.A. Project), and is believed to be clean.
> >
>
> ------------------------------
>
> Message: 2
> Date: Sun, 3 Dec 2017 18:39:36 +0530
> From: Manoar Hossain <manoarphy at niser.ac.in>
> Subject: Re: [Pw_forum] Error in routine sym_rho_init_shell (4): lone
>         vector
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
>         <CADj-Gb9D7LudTe=0TS+d_uPEkjxLx4AzRFAS7eMyeprFnyUQkQ@
> mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Paolo,
>
> Thanks for your kind reply but
>
> "(12.330460450=7.1189946603*sqrt(3))" ------(A)
>
> Your first suggestion (A) is not working, can you please enlighten me why ?
> Also what is the permanent solution ?
> Here I attached the relevant files.
>
> Thanks in advance.
>
>
>
>
> Regards,
>
> On Fri, Dec 1, 2017 at 10:03 PM, Paolo Giannozzi <p.giannozzi at gmail.com>
> wrote:
>
> > On Thu, Nov 30, 2017 at 3:02 PM, Manoar Hossain <manoarphy at niser.ac.in>
> > wrote:
> >
> > can anybody please tell me why this is happening ?
> >>
> >
> > the code recognizes hexagonal symmetry in your data. In order to
> > symmetrize the charge density, the code needs to reorganize G-vectors in
> > such a way that only entire shells of G-vectors are present on each
> > processor. Since however your lattice vectors are not exactly hexagonal,
> > the algorithm may fail in some unfortunate cases, ending up with half a
> > shell on one processor, half a shell on another one. Unfortunately there
> is
> > no easy workaround, but ...
> >
> > And without reducing (or changing) the lattice parameter then how one can
> >> get rid of this error ?
> >>
> >
> > ... if you specify your lattice vectors as
> >
> > CELL_PARAMETERS
> >    7.1189946603   12.330460450   0.000000000
> >   -7.1189946603   12.330460450   0.000000000
> >   0.0000000       0.0000000    19.000000000
> >
> > (12.330460450=7.1189946603*sqrt(3)) instead of
> >
> > CELL_PARAMETERS
> >    7.1189946603   12.330463153   0.000000000
> >   -7.1189946603   12.330463153   0.000000000
> >    0.0000000       0.0000000    19.000000000
> >
> > it works. As a rule, it is a good idea to use "exact" lattice vectors (by
> > specifying ibrav, or the space group) instead of user-supplied lattice
> > vectors whenever symmetry is important.
> >
> > Paolo
> > --
> > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> > 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://pwscf.org/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Manoar Hossain
> Research Scholar
> School of Physical Sciences
> NISER, Bhubaneswar
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> ------------------------------
>
> Message: 3
> Date: Sun, 3 Dec 2017 22:57:23 +0900
> From: "Mitsuaki Kawamura" <mkawamura at issp.u-tokyo.ac.jp>
> Subject: Re: [Pw_forum] (no subject)
> To: "'PWSCF Forum'" <pw_forum at pwscf.org>
> Message-ID: <006e01d36c3e$a5572400$f0056c00$@issp.u-tokyo.ac.jp>
> Content-Type: text/plain;       charset="utf-8"
>
> Dear Yuhit
>
> You forgot to write the subject and your affiliation.
> The following things may help you.
>
> Examples of QE
> http://qe-forge.org/gf/download/frsrelease/244/1115/qe-6.2-examples.tar.gz
> Tutorial slides
> http://www.quantum-espresso.org/tutorials/
> List of schools, workshops, and tutorials
> http://www.quantum-espresso.org/complete-qe-schools-
> workshops-and-tutorials/
>
> If some school of QE will be held in your country (or somewhere), you
> should join that.
>
> Best regards,
> Mitsuaki Kawamura
>
> --
> ------------------------------------------------------
> Dr. Mitsuaki Kawamura
> Software Advancement Team
> Supercomputer Section
> Materials Design and Characterization Laboratory
> The Institute for Solid State Physics, Kashiwa, Japan
> e-mail : mkawamura at issp.u-tokyo.ac.jp
> ------------------------------------------------------
>
> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
> Behalf Of Yuhit Gupta
> Sent: Sunday, December 3, 2017 12:05 AM
> To: pw_forum at pwscf.org
> Subject: [Pw_forum] (no subject)
>
> I want to learn the Quantum espresso for doing pw,ph and pp.x calculation
> please suggest how to start
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 3 Dec 2017 15:36:54 +0000 (UTC)
> From: David Foster <davidfoster751 at yahoo.com>
> Subject: Re: [Pw_forum] problem in relaxing gold cluster
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <1993135738.667109.1512315414408 at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi I suggest some points for you:
> 1-You can use ibrav=0 (instead of ibrav=1) and a big box (diameter of your
> cluster+10 A in each direction). place the cluster in the center of the
> box.2- reduce mixing_beta3- leave the mixing_mode to be its default value.
>
>
> Regards
>
>  David
>
>     On Sunday, December 3, 2017, 2:49:08 PM GMT+3:30, hajar zareyi <
> zareyi.h at mail.kntu.ac.ir> wrote:
>
>  Dear all,
> I am trying to relax gold cluster but the structure is going to break
> apart. there is my input file
> ?&CONTROLcalculation = 'relax' ,restart_mode = 'from_scratch'
> ,outdir="./TMP",pseudo_dir ="./", ? ? ? ??tprnfor ? = .true.tstress =
> .true.prefix = 'AU',/&SYSTEMibrav = 1,celldm(1) = 34.75,nat = 13,ntyp =
> 1,ecutwfc = 45 ,ecutrho = 500, ? ? ? ? ? ? ? ? ? ? ??occupations =
> 'smearing' ,degauss= 0.01 ,smearing= 'gaussian',/?&ELECTRONSmixing_mode =
> 'local-TF' ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ??mixing_beta = 0.7conv_thr =
> 1.D-6 ,?/?&IONS/?&CELL/ATOMIC_SPECIESAu ? ?196.966657 ?
> Au.blyp-d-hgh.UPFATOMIC_POSITIONS (angstrom)Au 7.0000000 10.0000000
> 10.0000000Au 8.3600000 7.6440000 10.0000000Au 11.0800000 7.6440000
> 10.0000000Au 12.4400000 10.0000000 10.0000000Au 11.0800000 12.3560000
> 10.0000000Au 8.3600000 12.3560000 10.0000000Au 9.7200000 10.0000000
> ?10.0000000Au 9.7238155 8.4315277 ?7.777622Au 8.3424810 10.7842271
> ?7.780175Au 11.0523480 10.8179223 ?7.78000Au 9.7238155 8.4315277
> ?12.2223780Au 8.3328179 10.7673656 ?12.2200000Au 11.0523480 10.8179223
> ?12.2200000
> K_POINTS gamma
> is there any one to help me to correct it
> ?
>
> --
> This message has been scanned for viruses and dangerous content by
> KNTU Antispam System (E.F.A. Project), and is believed to be
> clean._______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
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> ------------------------------
>
> Message: 5
> Date: Sun, 3 Dec 2017 23:45:53 +0330
> From: Eliya Asmani <eliya6191 at gmail.com>
> Subject: [Pw_forum] SOC pseudopotential
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
>         <CANcCFp1JgRUEuodpDpontWBLA=8qk+fie+EgRFehw3_d35Ewow at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
>
> I would like to perform calculations for w and Te with SOC effect. I could
> not find full relativistic *normconserving* pseudopotential for them. As I
> know in PSlibrary, we can make  just for  Ultrasoft and PAW
> pseudopotentials.
>
> Can someone quid me to find it?
>
> Eliya Asmani,
> Postdoctoral Researcher
> School of Physics, Institute for Research in Fundamental Sciences (IPM)
> Tehran, Iran
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> ------------------------------
>
> Message: 6
> Date: Mon, 4 Dec 2017 12:04:38 +0530
> From: Barnali Bhattacharya <barnalidgbhatt at gmail.com>
> Subject: Re: [Pw_forum] Phonon dispersion with LO-TO splitting
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
>         <CANJL4CPTDQHrzcU11eyENF45kb2mwrno0V7vkWionS6ojWeYGQ at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear  Lorenzo Paulatto,
>
> Thank you for your reply. But recently I have gone  your Physical review
> paper (PHYSICAL REVIEW B *87*, 214303 (2013)
> ) where you have shown phonon dispersion with LO-TO splitting for graphene
> (Figure 2) in page 214303-4.
>
> "Figure 2 shows the calculated graphene phonon dispersion,
> the respective anharmonic broadening and the vibrational
> density of states (VDOS). The branches are labeled in the usual
> way.25 There are three acoustic branches (ZA, TA, LA) and
> three optical branches (ZO, TO, LO). ZA and ZO correspond
> to an atomic motion perpendicular to the graphene plane (*z*
> direction), all the other branches are polarized parallel to the
> plane."
>
> Being motivated by work I want to reproduce this curve. Please guide me.
>
> Thanking you
>
> Barnali Bhattacharya
>
> CSIR SRF, Assam University,
>
> Silchar-788011
>
> Assam, INDIA
>
>
> On Fri, Dec 1, 2017 at 12:03 AM, Lorenzo Paulatto <paulatz at gmail.com>
> wrote:
>
> > Dear Barnali,
> > There is no LO-TO splitting in graphene, or more precisely, it is zero.
> >
> > Kind regards
> >
> > --
> > Lorenzo Paulatto
> > Written on a virtual keyboard with real fingers
> >
> > On 30 Nov 2017 3:59 pm, "Barnali Bhattacharya" <barnalidgbhatt at gmail.com
> >
> > wrote:
> >
> > Dear QE USERS,
> >
> >
> >
> > I am trying to reproduce the phonon dispersion with LO-TO splitting of
> graphene by using quantum espresso code.
> >
> > To get LO-TO splitting, I have added epsil=.true. as well as zeu=.true.
> in the input file of ph.x.  and calculated the phonon modes at q=0 (gamma
> point).
> >
> > Then I have used dynmat.x. for getting LO-TO splitting.
> >
> > At first, I did not added the propagation direction for q in the input
> file of dynmat.x .
> >
> >  After running dynmat.x, it gives the following line in the output
> >
> > ????????????????????..
> >
> > A direction for q was not specified:TO-LO splitting will be absent
> >
> > ?????????????????.
> >
> > Then I specify the q-point like
> >
> > q(1)=0.01, q(2)=0.0, q(3)=0.00 in the input file of dynmat.x .
> >
> > As a result the above line disappear from the output and the output is
> something like that
> >
> > ????????????????????????????????????????????.
> >
> > Reading Dynamical Matrix from file dmat.gra
> >
> >      ...Force constants read
> >
> >      ...epsilon and Z* read
> >
> >      Acoustic Sum Rule: || Z*(ASR) - Z*(orig)|| =    2.089033E-02
> >
> >      Acoustic Sum Rule: ||dyn(ASR) - dyn(orig)||=    1.397683E-04
> >
> >
> >
> >      Polarizability (A^3 units)
> >
> >      multiply by 0.417318 for Clausius-Mossotti correction
> >
> >         25.389880    0.000000    0.000000
> >
> >          0.000000   25.389880    0.000000
> >
> >          0.000000    0.000000    1.110081
> >
> >
> >
> >      IR activities are in (D/A)^2/amu units
> >
> >
> >
> > # mode   [cm-1]    [THz]      IR
> >
> >     1     -0.00   -0.0000    0.0000
> >
> >     2     -0.00   -0.0000    0.0000
> >
> >     3     -0.00   -0.0000    0.0000
> >
> >     4    886.97   26.5907    0.0000
> >
> >     5   1701.94   51.0228    0.0000
> >
> >    6   1701.94   51.0228    0.0000
> >
> > ?????????????????????????????????????.
> >
> > So please tell me
> >
> > 1)  from which file LO-TO splitting can be found?
> >
> >
> >
> > 2) How can I get the phonon dispersion with LO-TO splitting of graphene?
> >
> >
> >
> >  I am waiting for any kind suggestions. For details, I am attaching here
> > the input files and the dispersion curve which I want to reproduce?
> >
> >
> >
> > Thanks in advance.
> >
> >
> >
> > Sincerely
> >
> > Barnali Bhattacharya
> >
> > CSIR SRF, Assam University,
> >
> > Silchar-788011
> >
> > Assam, INDIA
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > 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
> >
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> ------------------------------
>
> Message: 7
> Date: Mon, 4 Dec 2017 08:51:44 +0100
> From: Lorenzo Paulatto <paulatz at gmail.com>
> Subject: Re: [Pw_forum] SOC pseudopotential
> To: pw_forum at pwscf.org
> Message-ID: <a5d41d27-c9bb-2620-6dc1-8111bd36b203 at gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> > I would like to perform calculations for w and Te with SOC effect. I
> > could not find full relativistic _normconserving_ pseudopotential for
> > them.
>
> Hello,
> why do you need this specific combination? I cannot think of any code
> that can do SOC but not US. Mostly thanks to Andrea Dal Corso being the
> main author of both.
>
> That said, I was able to re-generate some of the SG15-ONCV
> pseudopotentials (which are norm-conserving) with the full-relativistic
> version of the ONCV code, without too much hassle, just spending a day
> reading the documentation and testing.
>
> Disclaimer!
> Please note that:
> 1. I am in no way related to the SG15 library or the ONCV code
> 2. I do not have time to support every code in the world.
>
> Please do NOT ask ME for help on this subject, I won't provide any.
>
> kind regards
>
>
> > As I know in PSlibrary, we can make? just for? Ultrasoft and PAW
> > pseudopotentials.
> >
> > Can someone quid me to find it?
> >
> > Eliya Asmani,
> > Postdoctoral Researcher
> > School of Physics, Institute for Research in Fundamental Sciences (IPM)
> > Tehran, Iran
> >
> >
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
> >
>
> --
> Lorenzo Paulatto - Paris
>
>
> ------------------------------
>
> Message: 8
> Date: Mon, 4 Dec 2017 10:28:16 +0100
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> Subject: Re: [Pw_forum] Error in routine sym_rho_init_shell (4): lone
>         vector
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
>         <CAPMgbCvxiWkq7TOnnvgB69cYU5EOq9stkgdisGBybprJdd0fiw at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On Sun, Dec 3, 2017 at 2:09 PM, Manoar Hossain <manoarphy at niser.ac.in>
> wrote:
>
> Thanks for your kind reply but [...] Your first suggestion (A) is not
> > working, can you please enlighten me why ?
> >
>
> I am not a Zen master. I can just explain the origin of a problem, but if
> you do not read, or do not understand, my explanations, there is nothing I
> can do. Anyway:
> 1. I am 10% sure my fix works for the input data you sent a few days ago
> 2. The input data you just sent has the same problem: input lattice vectors
> that are close to hexagonal, but not exactly hexagonal
>
>
> > Also what is the permanent solution ?
> >
>
> The permanent solution is to disable symmetry with user-supplied lattice
> vectors.
>
> Here I attached the relevant files.
> >
> > Thanks in advance.
> >
> >
> >
> >
> > Regards,
> >
> > On Fri, Dec 1, 2017 at 10:03 PM, Paolo Giannozzi <p.giannozzi at gmail.com>
> > wrote:
> >
> >> On Thu, Nov 30, 2017 at 3:02 PM, Manoar Hossain <manoarphy at niser.ac.in>
> >> wrote:
> >>
> >> can anybody please tell me why this is happening ?
> >>>
> >>
> >> the code recognizes hexagonal symmetry in your data. In order to
> >> symmetrize the charge density, the code needs to reorganize G-vectors in
> >> such a way that only entire shells of G-vectors are present on each
> >> processor. Since however your lattice vectors are not exactly hexagonal,
> >> the algorithm may fail in some unfortunate cases, ending up with half a
> >> shell on one processor, half a shell on another one. Unfortunately
> there is
> >> no easy workaround, but ...
> >>
> >> And without reducing (or changing) the lattice parameter then how one
> can
> >>> get rid of this error ?
> >>>
> >>
> >> ... if you specify your lattice vectors as
> >>
> >> CELL_PARAMETERS
> >>    7.1189946603   12.330460450   0.000000000
> >>   -7.1189946603   12.330460450   0.000000000
> >>   0.0000000       0.0000000    19.000000000
> >>
> >> (12.330460450=7.1189946603*sqrt(3)) instead of
> >>
> >> CELL_PARAMETERS
> >>    7.1189946603   12.330463153   0.000000000
> >>   -7.1189946603   12.330463153   0.000000000
> >>    0.0000000       0.0000000    19.000000000
> >>
> >> it works. As a rule, it is a good idea to use "exact" lattice vectors
> (by
> >> specifying ibrav, or the space group) instead of user-supplied lattice
> >> vectors whenever symmetry is important.
> >>
> >> Paolo
> >> --
> >> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> >> Phone +39-0432-558216 <+39%200432%20558216>, fax +39-0432-558222
> >> <+39%200432%20558222>
> >>
> >>
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://pwscf.org/mailman/listinfo/pw_forum
> >>
> >
> >
> >
> > --
> > Manoar Hossain
> > Research Scholar
> > School of Physical Sciences
> > NISER, Bhubaneswar
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
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