From eyvaz_isaev at yahoo.com  Thu Jul  1 00:03:37 2010
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Wed, 30 Jun 2010 15:03:37 -0700 (PDT)
Subject: [Pw_forum] electron-phonon coupling and pseudopotential choice
In-Reply-To: <261531277910649@web57.yandex.ru>
Message-ID: <644208.71474.qm@web65701.mail.ac4.yahoo.com>

Dear Oleg,

--- On Wed, 6/30/10, Oleg Sergeev <seoman at yandex.ru> wrote:
> i think my fault was that i didn't recalculate
> the lattice parameter for each new PP. i'll check it.
> 
I suppose, this will not fix your problem. It might be due to miscompiled ph.x. I remember, there was a comment that some compilers (I do not remember exactly which one, g95 or gfortran). Recently I had a problem with one of these compilers (on my laptop with Ubuntu 9.4) when ph.x could not read an input file.  

I tested EPI for Al using at least two different pseudopotentials (RRKJ3 type, and vbc type, though both are norm conserving), so, your problem, most likely, is not connected to pseudopotentials used.

Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com



> Oleg Sergeev,
> JIHT RAS, Moscow.
> 
> > example07 is meant to show the procedure to compute
> el-ph coupling NOT 
> > to represent a converged calculation of it.
> > Have you checked convergence of your calculation w.r.t
> . cutoff, 
> > k-points and so on.
> > Have you calculate consistently the lattice parameter
> of your system ?
> > stefano
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


      


From limch at ihpc.a-star.edu.sg  Thu Jul  1 04:04:59 2010
From: limch at ihpc.a-star.edu.sg (Lim Chiang Huay, Freda)
Date: Thu, 1 Jul 2010 10:04:59 +0800
Subject: [Pw_forum] How to set nbnd value for berry phase calculations?
In-Reply-To: <4C2AFB97.2090809@democritos.it>
References: <EA1C6ED4FAC4B144B5AB82AC0041E8B91FF3EECADE@shared-svc-exch.shared-svc.local>
	<4C2AFB97.2090809@democritos.it>
Message-ID: <EA1C6ED4FAC4B144B5AB82AC0041E8B91FF3EECBDE@shared-svc-exch.shared-svc.local>

Hi Paolo,

In such cases, is there a guideline how we should set the nbnd value to calculate the berry phase?

Should I change the pseudopotential instead to ensure that there will be even number of electrons?

Rgds,
freda

-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi
Sent: Wednesday, June 30, 2010 4:09 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] How to set nbnd value for berry phase calculations?

Lim Chiang Huay, Freda wrote:

> and from the pseudopotentials, there should be 41 electrons in a cell.
> From the manual nbnd = nelect/2.

this is true for insulators without spin polarization. If you have an
odd number of electrons, your system cannot be an insulator (and it
should be treated as spin polarized)

P.
--
Paolo Giannozzi, Democritos and University of Udine, Italy
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum

This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.

From giannozz at democritos.it  Thu Jul  1 12:29:42 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 01 Jul 2010 12:29:42 +0200
Subject: [Pw_forum] How to set nbnd value for berry phase calculations?
In-Reply-To: <EA1C6ED4FAC4B144B5AB82AC0041E8B91FF3EECBDE@shared-svc-exch.shared-svc.local>
References: <EA1C6ED4FAC4B144B5AB82AC0041E8B91FF3EECADE@shared-svc-exch.shared-svc.local>	<4C2AFB97.2090809@democritos.it>
	<EA1C6ED4FAC4B144B5AB82AC0041E8B91FF3EECBDE@shared-svc-exch.shared-svc.local>
Message-ID: <4C2C6E16.2010409@democritos.it>

Lim Chiang Huay, Freda wrote:

> In such cases, is there a guideline how we should set the nbnd value
> to calculate the berry phase?

I think that the berry phase can be calculated only in insulators.
You should use spin polarization (nspin=2) and fix the total
magnetization (tot_magnetization=1, I guess). Then you can use
any number of bands, as long as they are in sufficient number
to accommodate all electrons (the less bands, the quicker the
calculation, of course). No warranty.

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From sclauzer at sissa.it  Thu Jul  1 12:44:41 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Thu, 1 Jul 2010 12:44:41 +0200
Subject: [Pw_forum] How to set nbnd value for berry phase calculations?
In-Reply-To: <EA1C6ED4FAC4B144B5AB82AC0041E8B91FF3EECADE@shared-svc-exch.shared-svc.local>
References: <EA1C6ED4FAC4B144B5AB82AC0041E8B91FF3EECADE@shared-svc-exch.shared-svc.local>
Message-ID: <84505575-F41E-4D3A-99E4-52B08330379A@sissa.it>


Il giorno 30/giu/2010, alle ore 09.43, Lim Chiang Huay, Freda ha scritto:

> Hi all,
>  
> I?m doing Berry Phase calculations for the first time for BiFeO3. I met with some problems in setting nbnd values for the scf and nscf calculations. And I can?t find an answer in previous forum post.
>  
> I used the pseudopotentials available in the website http://www.pwscf.org/pseudo.php
> They are: 
> Bi.pbe-d-mt.UPF
> Fe.pbe-nd-rrkjus.UPF
> O.pbe-mt.UPF
> and from the pseudopotentials, there should be 41 electrons in a cell. From the manual nbnd = nelect/2.

In your cell you have 2 formula units, hence 82 electrons. Let's suppose that it is an insulator.

If you do spin-unpolarized calculations (nspin=1) you need at least 41 bands, hence nbnd in case (1) is too little.

>  
> I?ve tried different combinations of nbnd values for scf and nscf jobs and non was able to give me the polarization value.
> The following are the some selected cases and their error msg:
> Case(1)
> *.scf, nbnd=21; *.nscf, nbnd=21
> Both jobs crash
> Error for scf: too few bands


> Error for nscf: starting and expected charges differ

You cannot perform the nscf calculation if the scf one has not run successfully.

>  
> Case(2)
> *.scf, nbnd=43; *.nscf, nbnd=42
> Scf converged. Nscf crashed.
> Error for nscf: Polarization only for insulators and no empty bands

The code prevents one from doing Berry's phase calculations for ferromagnetic insulators (though I don't know if these systems actually exist...). There is a check that stops the calculation if nbnd /= nelec/2, which is always the case for these systems (see below). I don't know if there is something from the theoretical point of view that prevents one from doing such calculation. 

In any case, the number of bands in the nscf run is too small to include all occupied spin-up states.

>  
> Case(3)
> *.scf, nbnd=42; *.nscf, nbnd=42
> Scf converged. Nscf crashed.
> Error for scf: too few spin up bands

Since you calculation is spin-polarized there will be an unbalance between the number of occupied spin-up and spin-down bands, hence you need the code to compute more than 42 bands. This stems from the fact that in the pwscf code the number of total spin-up bands (i.e. occuppied+empty=nbnd) is equal to the total number of spin-down bands.

> Error for nscf: starting and expected charges differ

As above.


HTH

GS

>  
> My input files are as follows:
> SCF JOB:
> &control
>     calculation  = 'scf',
>     restart_mode = 'from_scratch'
>     pseudo_dir   = '/Home6/cc/ihpclimc/BP_CAL/PPOT'
>     outdir       = '/Scratch/ihpclimc/BERRY_PHASE_CALCULATIONS/Try_BP/OUTDIR',
>  /
>  &system
>     ibrav=5
>     celldm(1)=10.6523,
>     celldm(4)=0.50988,
>     nat=10
>     ntyp=3
>     nbnd=42
>     ecutwfc=50.0
>     occupations = 'fixed'
>     degauss=0.00
>     nspin=2
>     multiplicity=5
>     lda_plus_u=.true.
>     Hubbard_U(2)=6
>  /
>  &electrons
>     conv_thr = 1e-12,
>     mixing_beta=0.3,
>     diagonalization='cg',
> /
> ATOMIC_SPECIES
>   Bi   209.0      Bi.pbe-d-mt.UPF
>   Fe    55.85     Fe.pbe-nd-rrkjus.UPF
>   O     16.00     O.pbe-mt.UPF
>  
> ATOMIC_POSITIONS crystal
>   Bi    0.000    0.000    0.000         0       0       0
>   Bi    0.500    0.500    0.500         0       0       0
>   Fe    0.219    0.219    0.219
>   Fe    0.719    0.719    0.719
>   O     0.445    0.032    0.897
>   O     0.897    0.445    0.032
>   O     0.032    0.897    0.445
>   O     1.397    0.532    0.945
>   O     0.532    0.945    1.397
>   O     0.945    1.397    0.532
>  
> K_POINTS {automatic}
>   1 1 1 1 1 1
>  
> NSCF JOB:
> &control
>     calculation  = 'nscf',
>     pseudo_dir   = '/Home6/cc/ihpclimc/BP_CAL/PPOT'
>     outdir       = '/Scratch/ihpclimc/BERRY_PHASE_CALCULATIONS/Try_BP/OUTDIR',
>     lberry       = .true.
>     gdir         = 3
>     nppstr       = 7
>  /
>  &system
>     ibrav=5
>     celldm(1)=10.6523,
>     celldm(4)=0.50988,
>     nat=10
>     ntyp=3
>     nbnd=42
>     ecutwfc=50.0
>     occupations = 'fixed'
>     degauss=0.00
>     nspin=2
>     multiplicity=5
>     lda_plus_u=.true.
>     Hubbard_U(2)=6
>  /
>  &electrons
>     conv_thr = 1e-12,
>     mixing_beta=0.3,
>     diagonalization='cg',
> /
> ATOMIC_SPECIES
>   Bi   209.0      Bi.pbe-d-mt.UPF
>   Fe    55.85     Fe.pbe-nd-rrkjus.UPF
>   O     16.00     O.pbe-mt.UPF
>  
> ATOMIC_POSITIONS crystal
>   Bi    0.000    0.000    0.000         0       0       0
>   Bi    0.500    0.500    0.500         0       0       0
>   Fe    0.219    0.219    0.219
>   Fe    0.719    0.719    0.719
>   O     0.445    0.032    0.897
>   O     0.897    0.445    0.032
>   O     0.032    0.897    0.445
>   O     1.397    0.532    0.945
>   O     0.532    0.945    1.397
>   O     0.945    1.397    0.532
>  
> K_POINTS {automatic}
>   4 4 4 1 1 1
>  
>  
> Can anyone help?
>  
> Thanks,
> Rgds
>  
> Freda Lim
> Institute of High Performance Computing
> 1 Fusionopolis Way, #16-16 Connexis
> Singapore 138632
> Email: limch at ihpc.a-star.edu.sg
>  
>  
> 
> This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.
> _______________________________________________
> 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

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From marzari at MIT.EDU  Thu Jul  1 16:25:49 2010
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 01 Jul 2010 15:25:49 +0100
Subject: [Pw_forum] ultrasoft Cs pseudopotential
In-Reply-To: <AANLkTik7_5YtO1R9TNq45MadLaAgjrWq1AZ_67SbiJDe@mail.gmail.com>
References: <AANLkTinEpsnx8fMvBAxyUZDHRUYb_npA0igU8puCGfC7@mail.gmail.com>
	<AANLkTik7_5YtO1R9TNq45MadLaAgjrWq1AZ_67SbiJDe@mail.gmail.com>
Message-ID: <4C2CA56D.3000607@mit.edu>



Dear Suza W,

There is a norm-conserving PBE pseudo on the website, with all the 
details needed to
generate again using LDA.

Alkali metals have very soft pseudopotentials to begin with, so you 
should be fine.


                nicola

Suza W wrote:
> Dear QE USERS,
>  
>      QE pseudo site does not have Cs ultrasoft pseudo-potential.
>      Can you anybody help me to get the ultasoft (LDA&GGA) 
> pseudo-potential for Cs?
>      I have got the following link in the forum : 
> http://www.fisica.uniud.it/~giannozz/public/Cs.tar.gz 
> <http://www.fisica.uniud.it/%7Egiannozz/public/Cs.tar.gz>
>      but not able to open this. It seems that the above link is dead.
>      Any help in this regard will be highly appreciated.
>
>  Yours sincerely,
>  
>  Suza W.
>  Ph. D. student
>  RRI, India
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
---------------------------------------------------------------------
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 


From suza.rri at gmail.com  Thu Jul  1 16:50:28 2010
From: suza.rri at gmail.com (Suza W)
Date: Thu, 1 Jul 2010 16:50:28 +0200
Subject: [Pw_forum] ultrasoft Cs pseudopotential
In-Reply-To: <4C2CA56D.3000607@mit.edu>
References: <AANLkTinEpsnx8fMvBAxyUZDHRUYb_npA0igU8puCGfC7@mail.gmail.com>
	<AANLkTik7_5YtO1R9TNq45MadLaAgjrWq1AZ_67SbiJDe@mail.gmail.com>
	<4C2CA56D.3000607@mit.edu>
Message-ID: <AANLkTimfz9edaSic6ZXNkgHiUbuTwr1vFYPAylUyxep5@mail.gmail.com>

 Dear Nicola,

 Thanks a lot for your reply. The pseudo mentioned by you has one electron
in valence. However,
 from PW-FORUM, I came to know that it might be better to use 9 valence
electrons in case of Cesium (Cs).
 May I get a Cs Ultra-soft  PP (LDA & GGA), preferably with 9 electrons in
valence, from your USPP collection?

 Yours sincerely,
 Suza

On Thu, Jul 1, 2010 at 4:25 PM, Nicola Marzari <marzari at mit.edu> wrote:

>
>
> Dear Suza W,
>
> There is a norm-conserving PBE pseudo on the website, with all the
> details needed to
> generate again using LDA.
>
> Alkali metals have very soft pseudopotentials to begin with, so you
> should be fine.
>
>
>                nicola
>
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From marzari at MIT.EDU  Thu Jul  1 17:28:47 2010
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 01 Jul 2010 16:28:47 +0100
Subject: [Pw_forum] ultrasoft Cs pseudopotential
In-Reply-To: <AANLkTimfz9edaSic6ZXNkgHiUbuTwr1vFYPAylUyxep5@mail.gmail.com>
References: <AANLkTinEpsnx8fMvBAxyUZDHRUYb_npA0igU8puCGfC7@mail.gmail.com>	<AANLkTik7_5YtO1R9TNq45MadLaAgjrWq1AZ_67SbiJDe@mail.gmail.com>	<4C2CA56D.3000607@mit.edu>
	<AANLkTimfz9edaSic6ZXNkgHiUbuTwr1vFYPAylUyxep5@mail.gmail.com>
Message-ID: <4C2CB42F.8080706@mit.edu>

Suza W wrote:
>
>
>  Dear Nicola,
>  
>  Thanks a lot for your reply. The pseudo mentioned by you has one 
> electron in valence. However,  
>  from PW-FORUM, I came to know that it might be better to use 9 
> valence electrons in case of Cesium (Cs).
>  May I get a Cs Ultra-soft  PP (LDA & GGA), preferably with 9 
> electrons in valence, from your USPP collection?
>  
>  Yours sincerely,
>  Suza


Dear Suza,

the few psuedos we generated are all public, and I do not have a Cs with 
9 electrons -
neither norm-conserving nor USPP.

The one on the database has non-linear core corrections, so it should be 
quite good.
Other option for you is to learn on how to generate pseudos - there is
a tutorial by Andrea Dal Corso on the quantum=espresso page (Santa Barbara
school).

             nicola


-- 
---------------------------------------------------------------------
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 


From chenhanghuipwscf at gmail.com  Thu Jul  1 23:45:15 2010
From: chenhanghuipwscf at gmail.com (hanghui chen)
Date: Thu, 1 Jul 2010 17:45:15 -0400
Subject: [Pw_forum] Hubbard U in the version 4.2
Message-ID: <AANLkTil-yllVI_JjKaX739rFySdT2X2hEN5dLoQPKWS6@mail.gmail.com>

Dear QE developers,
       My previous email which reports a possible bug in the version 4.2 is
pending because the attached input and output files are too large. Now I
want to give a brief report here: I tried Hubbard U in the latest version
4.2 and found the contribution of Hubbard U to the total energy is always
zero and more mysteriously the code crashes right before the forces are
calculated. I am just wondering if any one else has the same problem when
turning on the Hubbard U in the version 4.2.
       Thank you very much.

Hanghui Chen
Department of Physics
Yale University
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From sclauzer at sissa.it  Fri Jul  2 10:41:51 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Fri, 02 Jul 2010 10:41:51 +0200
Subject: [Pw_forum] Hubbard U in the version 4.2
In-Reply-To: <AANLkTil-yllVI_JjKaX739rFySdT2X2hEN5dLoQPKWS6@mail.gmail.com>
References: <AANLkTil-yllVI_JjKaX739rFySdT2X2hEN5dLoQPKWS6@mail.gmail.com>
Message-ID: <4C2DA64F.2090000@sissa.it>

Dear Hanghui,

    have you try to run the lda+U tests in the tests/ folder? Do they 
crash too? Have you tried to run example 25? On my desktop both work 
with espresso-4.2.


On 07/01/2010 11:45 PM, hanghui chen wrote:
> Dear QE developers,
>        My previous email which reports a possible bug in the version 
> 4.2 is pending because the attached input and output files are too large. 

This sounds strange. How big are they? Have you tried to compress them 
and send the (g)zipped archive?

Please try to submit at least the input file, otherwise it is impossible 
to understand your problem.

> Now I want to give a brief report here: I tried Hubbard U in the 
> latest version 4.2 and found the contribution of Hubbard U to the 
> total energy is always zero and more mysteriously the code crashes 
> right before the forces are calculated. I am just wondering if any one 
> else has the same problem when turning on the Hubbard U in the version 
> 4.2.

The only strange thing I've seen in v4.2 is a string which is 
erroneously printed twice (at least on my build of QE):

atom    3   Tr[ns(na)]=   6.0000000
atom    3   spin  1
atom  3  spin  1
eigenvalues:  1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
eigenvectors

but I don't think this is the source of your problem.

GS

>        Thank you very much.
>
> Hanghui Chen
> Department of Physics
> Yale University
>
>
> _______________________________________________
> 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

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From miguel.martinez at ehu.es  Fri Jul  2 11:19:53 2010
From: miguel.martinez at ehu.es (Miguel =?ISO-8859-1?B?TWFydO1uZXo=?=)
Date: Fri, 2 Jul 2010 10:19:53 +0100
Subject: [Pw_forum] ultrasoft Cs pseudopotential
In-Reply-To: <4C2CB42F.8080706@mit.edu>
References: <AANLkTinEpsnx8fMvBAxyUZDHRUYb_npA0igU8puCGfC7@mail.gmail.com>
	<AANLkTik7_5YtO1R9TNq45MadLaAgjrWq1AZ_67SbiJDe@mail.gmail.com>
	<4C2CA56D.3000607@mit.edu>
	<AANLkTimfz9edaSic6ZXNkgHiUbuTwr1vFYPAylUyxep5@mail.gmail.com>
	<4C2CB42F.8080706@mit.edu>
Message-ID: <20100702101953.752f3f41@mark>

Dear all,

Personally, I found the PBE Cs pseudo available in the library suitable
for metallic bcc Cs. However, and probably due to charge transfer, I
found it unsuitable at higher pressures (beyond 2 GPa). I know that 1
electron sodium PPs are not really trustworthy in the fcc phase beyond
60 GPa (although results are not too far off). Alkalis plus very high
pressure has always meant extra electrons for me.

Having been asked (and just noticed), here's my 9-electron PBE pseudo.
I'm sure the ld1 masters will have suggestions to it, and they are more
than welcome (especially since I hate generating pseudopotentials with
semicore electrons).

You'll have to mkdir Cs9 before running ld1.x. However, you can use the
nice plot_dlog (located in espresso-4.2/atomic_doc/paw_library) script
to see the logarithmic derivatives. In any case, all the usual warnings
apply: "test first" and "use at your own risk". 

 &input
    title='Cs',
    prefix='Cs9/ld1',
    zed=55.0,
    rel=1,
     rlderiv=3.01,
     eminld=-5.0,
     emaxld=3.0,
     deld=0.02d0,
     nld=3,
    config='[Kr] 4d10 5s2 5p6 6s1 5d0 6p0'
    iswitch=3,
    dft='PBE',
 /
 &inputp
   lloc=-1,
   rcloc=2.6
   nlcc=.true.
   rcore=1.3
   rho0=0.0
   tm=.true.
   pseudotype=3,
     which_augfun='AE',
     new_core_ps=.true.,
   file_pseudopw='Cs.pbe-nsp-van.UPF',
   author='MMC',
 /
7
5S  1  0  2.00  0.00  1.40  2.60
6S  2  0  1.00  0.00  1.40  2.60
6S  3  0 -1.00  0.50  1.40  2.60
5P  2  1  6.00  0.00  1.60  2.00
5P  3  1  0.00 -0.05  1.60  2.00
5D  3  2  0.00  0.00  1.80  2.20
5D  4  2  0.00  0.50  1.80  2.20



Regards,

Miguel

PS: You may want to put a slight charge in the p channel. That will
mean more tests, though.

On Thu, 01 Jul 2010 16:28:47 +0100 Nicola Marzari <marzari at MIT.EDU>
wrote:
> Suza W wrote:
> >
> >
> >  Dear Nicola,
> >  
> >  Thanks a lot for your reply. The pseudo mentioned by you has one 
> > electron in valence. However,  
> >  from PW-FORUM, I came to know that it might be better to use 9 
> > valence electrons in case of Cesium (Cs).
> >  May I get a Cs Ultra-soft  PP (LDA & GGA), preferably with 9 
> > electrons in valence, from your USPP collection?
> >  
> >  Yours sincerely,
> >  Suza
> 
> 
> Dear Suza,
> 
> the few psuedos we generated are all public, and I do not have a Cs
> with 9 electrons -
> neither norm-conserving nor USPP.
> 
> The one on the database has non-linear core corrections, so it should
> be quite good.
> Other option for you is to learn on how to generate pseudos - there is
> a tutorial by Andrea Dal Corso on the quantum=espresso page (Santa
> Barbara school).
> 
>              nicola
> 
> 



-- 
----------------------------------------
Dr. Miguel Martinez Canales
   Department of Physics & Astronomy
   University College London
   Gower Street, London, WC1E 6BT (UK)
Fax:  +44 207 679 0595
Tlf:  +44 207 678 3476
----------------------------------------

 "If you have an apple and I have an apple and
 we exchange these apples then you and I will
 still each have one apple. But if you have an
 idea and I have an idea and we exchange these
 ideas, then each of us will have two ideas."

 George Bernard Shaw 


From masoudnahali at live.com  Fri Jul  2 13:17:02 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Fri, 2 Jul 2010 11:17:02 +0000
Subject: [Pw_forum] optimizing cell parameters and choosing k-points of
	graphite
Message-ID: <COL114-W142815E0A552D85AEFB795A1CE0@phx.gbl>




One of the origins of this bad convergence is the selection of ecurho. For ultra-soft pseudo-potentials,the ecurho should be 10X of ecutwfc
and I had not considered it well. 

 
very best wishes
Masoud Nahali
SUT
 


Dear Quantum Espresso users
 
I have done a 'vc-relax' calculation to find the cell parameters of graphite.  The selected k-points are (4*4*4) and automatic.
 
obtained cell parameters:
  a         = 2.469,
  b         = 2.469,
  c         = 7.069,
 
then I used these values to 'relax' the atoms in cell (k-points were 4*4*4 too) . Finally I used the obtained cell parameters to find the proper k-points for graphite.
I performed some 'scf' calculations with different k-points and in whole of them the cell parameters and positions were what is obtained from the relax part with   4*4*4 k-points.
 
'scf' energy with different k-points:
 
k-points     energy	
 
(4*4*4): -45.5732791969 Ry 
 
(5*5*5): -45.57637408 Ry
 
(6*6*6): -45.57592043 Ry
 
(7*7*7): -45.57420434 Ry
 
(8*8*8): -45.57474553 Ry
 
(9*9*9): -45.57500776 Ry
 
(10*10*10): -45.57454272 Ry
 
(11*11*11): -45.57464463 Ry
 
(12*12*12): -45.57480118 Ry
 
(13*13*13): -45.57462800 Ry
 
(14*14*14): -45.57463705 Ry
 
(15*15*15): -45.57473135 Ry
 
(16*16*16): -45.57465384 Ry
I appreciate if one help me to find the answers to these questions:
1. Is the whole procedure plausible ?2. why a energy convergence is not occurred after selecting these high values of k-points?3. How can I find the proper k-points safely?
the input file for 'scf' calculation:
&CONTROL
  calculation  = "scf",
  pseudo_dir   = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
  outdir       = "/home/koa/tmp",
  etot_conv_thr= 1.0D-4,
  forc_conv_thr= 1.0D-3,
  nstep=150,
  /
&SYSTEM
  ibrav     = 4,
  a         = 2.469,
  b         = 2.469,
  c         = 7.069,
  cosab     = -0.5,
  cosac     = 1.0,
  cosbc     = 1.0,
  nat       = 4,
  ntyp      = 1,
  ecutwfc   = 30.D0,
  ecutrho   = 200.D0
  occupations = 'smearing'
  smearing ='mp', 
  degauss = 0.01,
  nspin = 2,
  starting_magnetization(1)= 1.0,
  /
&ELECTRONS
  conv_thr    = 1.D-6,
  mixing_beta = 0.7D0,
  diagonalization = "david",
/
&IONS
 ion_dynamics="bfgs"
/
ATOMIC_SPECIES
C  12.0107  C.pbe-van_ak.UPF
ATOMIC_POSITIONS {angstrom}
C        0.000000000   0.000000000   0.000000000
C        0.000000000   1.425534302   0.000000000
C        0.000000000   0.000000000   3.534553118
C        1.234548920   0.712767151   3.534553118
 
K_POINTS {automatic}
16 16 16 1 1 1
 
the vc-relax input: 
&CONTROL
  calculation  = "vc-relax",
  pseudo_dir   = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
  outdir       = "/home/koa/tmp",
  etot_conv_thr= 1.0D-4,
  forc_conv_thr= 1.0D-3,
  dt=70,
  nstep=150,
  /
&SYSTEM
  ibrav     = 4,
  a         = 2.456,
  b         = 2.456,
  c         = 6.696,
  cosab     = -0.5,
  cosac     = 1.0,
  cosbc     = 1.0,
  nat       = 4,
  ntyp      = 1,
  ecutwfc   = 30.D0,
  ecutrho   = 200.D0
  occupations = 'smearing'
  smearing ='mp', 
  degauss = 0.01,
  nspin = 2,
  starting_magnetization(1)= 1.0,
  /
&ELECTRONS
  conv_thr    = 1.D-6,
  mixing_beta = 0.7D0,
  diagonalization = "david",
/
&IONS
 ion_dynamics="bfgs"
/
&CELL
cell_dynamics = 'damp-w',
press = 0.0 ,
/
ATOMIC_SPECIES
C  12.0107  C.pbe-van_ak.UPF
ATOMIC_POSITIONS {angstrom}
 C                  0.00000000    0.00000000    0.00000000
 
 C                  0.00000000    1.41797226    0.00000000
 
 C                  0.00000000    0.00000000    3.34800000
 
 C                  1.22800000    0.70898613    3.34800000
 
K_POINTS {automatic}
4 4 4 1 1 1
 
very best wishes
 

  		 	   		  
_________________________________________________________________
Hotmail: Free, trusted and rich email service.
https://signup.live.com/signup.aspx?id=60969
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From arphysis at gmail.com  Fri Jul  2 14:17:42 2010
From: arphysis at gmail.com (Artem R. Khabibullin)
Date: Fri, 2 Jul 2010 16:17:42 +0400
Subject: [Pw_forum] about the variable-cell MD
Message-ID: <AANLkTillY4a0jiiiGf2Cc1zWDARroOCge-jh-c4U66aM@mail.gmail.com>

Dear colleagues,
I am beginner user of the Quantum-Espresso. My task is the simulation 32
water molecules (H2O). I have still some problems. The main of them is a
variable-cell MD with cp.x code under constantly high pressure in the (NpT -
ensemble). Another words, I am exploring 32 molecules of water under high
pressure and specific temperature. My script to this case is

# Electronical + Ionic Dynamics + NOSE thermostat on ions +

&CONTROL
title = ' Water 32 Molecules ',
calculation = 'vc-cp',
restart_mode = 'restart',
ndr = 51,
ndw = 52,
nstep = 2000,
iprint = 10,
isave = 10,
tstress = .TRUE.,
tprnfor = .TRUE.,
dt = 4.0d0,
etot_conv_thr = 1.d-9,
ekin_conv_thr = 1.d-4,
prefix = 'h2o_mol'
pseudo_dir = './pseudo/'
outdir = './tmp/'
/

&SYSTEM
ibrav = 14,
celldm(1) = 18.65,
celldm(2) = 1.0,
celldm(3) = 1.0,
celldm(4) = 0.0,
celldm(5) = 0.0,
celldm(6) = 0.0,
nat = 96,
ntyp = 2,
nbnd = 128,
nelec = 256,
ecutwfc = 70.0,
ecfixed = 68.0,
qcutz = 68.0,
q2sigma = 8.0,
xc_type = 'BLYP',
/

&ELECTRONS
emass = 300.d0,
emass_cutoff = 2.5d0,
orthogonalization = 'ortho',
electron_dynamics = 'verlet',
electron_velocities = 'zero',
ortho_eps = 5.d-8,
ortho_max = 15,
/

&IONS
ion_dynamics = 'verlet',
ion_temperature = 'nose',
!ion_velocities = 'zero',
tempw = 277.0,
fnosep = 48,

ion_radius(1) = 0.8d0,
ion_radius(2) = 0.5d0,
/

&CELL
cell_dynamics = 'pr',
!cell_velocities = 'zero',
press = 0.2d0,
wmass = 79859.24
/

ATOMIC_SPECIES
O 16.0d0 O.BLYP.UPF 4
H 1.0079d0 H.fpmd.UPF 4

ATOMIC_POSITIONS (crystal) !(bohr)
O 0.3342 0.3858 0.1702
O 0.6681 0.0772 0.0996
O 0.4894 0.2752 0.9664
O 0.8374 0.0165 0.8885
O 0.4164 0.1406 0.5374
O 0.9200 0.2746 0.7479
O 0.9298 0.6759 0.0546
O 0.5197 0.5773 0.2470
O 0.8453 0.2308 0.2531
O 0.7080 0.4512 0.1102
O 0.6297 0.6739 0.4697
O 0.6889 0.4428 0.8100
O 0.9273 0.8859 0.2748
O 0.7260 0.9572 0.4514
O 0.9539 0.6297 0.6304
O 0.0634 0.4197 0.2665
O 0.0088 0.1409 0.5073
O 0.8042 0.4375 0.4942
O 0.6981 0.1893 0.5833
O 0.2908 0.5198 0.5234
O 0.1835 0.3971 0.7808
O 0.2450 0.2024 0.3474
O 0.3062 0.1574 0.7995
O 0.4465 0.8389 0.2161
O 0.1931 0.5738 0.0049
O 0.1879 0.9665 0.1899
O 0.0876 0.6667 0.4085
O 0.2637 0.7476 0.7879
O 0.5203 0.6329 0.7214
O 0.3714 0.8763 0.4899
O 0.7915 0.8290 0.7054
O 0.1436 0.9899 0.9297
H 0.3742 0.3360 0.0929
H 0.3150 0.3226 0.2472
H 0.9405 0.1804 0.4516
H 0.6062 0.0086 0.1372
H 0.7231 0.0354 0.0264
H 0.5460 0.2002 0.9884
H 0.5502 0.3269 0.9029
H 0.8537 0.1049 0.8480
H 0.4251 0.0432 0.5210
H 0.3722 0.1543 0.6275
H 0.7041 0.0486 0.4909
H 0.9378 0.2191 0.6620
H 0.9083 0.7339 0.1314
H 0.5940 0.5403 0.1919
H 0.4413 0.5140 0.2303
H 0.7975 0.1623 0.1939
H 0.9351 0.2490 0.2169
H 0.7495 0.3794 0.1764
H 0.7769 0.5261 0.0949
H 0.7242 0.6488 0.4514
H 0.5812 0.6156 0.4033
H 0.7610 0.3991 0.7586
H 0.7253 0.4549 0.9012
H 0.9805 0.8118 0.3158
H 0.8774 0.9234 0.3508
H 0.8266 0.9432 0.8185
H 0.6439 0.9054 0.4658
H 0.9099 0.7082 0.6739
H 0.1146 0.3475 0.3129
H 0.1177 0.4592 0.1936
H 0.0984 0.1864 0.4941
H 0.8732 0.4903 0.5432
H 0.8466 0.4047 0.4105
H 0.5983 0.1849 0.5758
H 0.7255 0.2866 0.5619
H 0.2468 0.6010 0.4948
H 0.3655 0.5512 0.5766
H 0.2218 0.4478 0.6984
H 0.2272 0.3027 0.7736
H 0.0089 0.3172 0.7749
H 0.3206 0.1756 0.4126
H 0.2308 0.1250 0.2800
H 0.2420 0.1027 0.8550
H 0.3752 0.1963 0.8703
H 0.3477 0.8559 0.1901
H 0.4738 0.7418 0.2103
H 0.0297 0.6626 0.0605
H 0.2668 0.5360 0.0599
H 0.1691 0.9883 0.0958
H 0.0952 0.9378 0.2237
H 0.0161 0.6488 0.4768
H 0.0940 0.5739 0.3729
H 0.2728 0.6995 0.8762
H 0.3551 0.7479 0.7517
H 0.5812 0.5576 0.7579
H 0.5605 0.6617 0.6349
H 0.1741 0.5139 0.9284
H 0.3026 0.8058 0.5084
H 0.4067 0.8573 0.3940
H 0.7040 0.7965 0.7365
H 0.7716 0.8608 0.6097
H 0.0148 0.6043 0.7064
H 0.1834 0.9112 0.8662
H 0.0492 0.9894 0.9207

KSOUT
2
1 4

this is 7 step, when the system is relaxing and there is the electron and
ion dynamics and then at the 7 step I have adding the pressure on system.
The value for "wmass" in CELL section I got from the previous step. During
the calculation I have one problem: in the step7.out file the value of
(XNHH0 - position of Nose' for cell) became equals to infinity from
approximately 1000-1500 time steps. Why is it?
I will be very glad for answer on this problem.

-----------------------------------------------------------------
With best wishes, Artem R.

Dr. Artem R. Khabibullin
Department of Theoretical Physics,
Kazan Federal University.
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From marsamos at democritos.it  Fri Jul  2 14:50:07 2010
From: marsamos at democritos.it (marsamos at democritos.it)
Date: Fri, 02 Jul 2010 14:50:07 +0200
Subject: [Pw_forum] plumed for ESPRESSO-4.2 available
Message-ID: <20100702145007.szbjy0beqscgg40c@mail.democritos.it>

Dear All, the PLUMED plug-in for metadynamic calculations has been 
adapted to Quantum ESPRESSO-4.2 and is available at

http://qe-forge.org/frs/?group_id=10

There is also an additional README (README.plumed.xlc_compiler) for 
those that uses ibm machines with xlc compiler.

bests


Layla

-- 
Dr. L. Martin-Samos
tel. +39 040 3787 429
CNR-DEMOCRITOS and
International School for Advanced Studies (ISAS-SISSA)
via Beirut 2-4
34151 Trieste Italy

----------------------------------------------------------------
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From cristian.degliesposti at unibo.it  Fri Jul  2 14:47:22 2010
From: cristian.degliesposti at unibo.it (Cristian Degli Esposti Boschi)
Date: Fri, 2 Jul 2010 14:47:22 +0200
Subject: [Pw_forum] Question on last line of XSpectra input file
Message-ID: <4C2DDFDA.1060202@unibo.it>

Dear all,

if I have not missed something, in the XSpectra input documentation as 
well as in the examples I do not understand the precise meaning of the
last line after closing the &cut_occ stanza.
It seems like a repetition of the K_POINTS specification in
the input for pw. For instance if the latter is set to be "automatic"
with "1 1 1 0 0 0" I guess it means a 1x1x1 grid in k-space with zero
offset, and then I repeat the same in the XSpectra input file.

But what should I specify in the latter file if in the scf calculation
with pw I use other options for K_POINTS, for instance Gamma or
a list of points with weights? I hope the question is clear. Thanks
for your time.

Cristian

-- 
___________________________________________________
Cristian Degli Esposti Boschi
CNR, CNISM, Unita' di Ricerca di Bologna, c/o
Dipartimento di Fisica, Universita' di Bologna
viale Berti-Pichat, 6/2, 40127, Bologna, Italia
tel. ++39 051 2095114   fax ++39 051 2095113
e-mail: cristian.degliesposti -AT- unibo.it
web:    http://www.df.unibo.it/fismat/theory
___________________________________________________


From zl.liu.caep at gmail.com  Sat Jul  3 03:17:44 2010
From: zl.liu.caep at gmail.com (Zhong-Li Liu)
Date: Sat, 3 Jul 2010 09:17:44 +0800
Subject: [Pw_forum] plumed for ESPRESSO-4.2 available
In-Reply-To: <20100702145007.szbjy0beqscgg40c@mail.democritos.it>
References: <20100702145007.szbjy0beqscgg40c@mail.democritos.it>
Message-ID: <AANLkTikYB4aLg99Mg0Jn0jd11WGelXvVaWC9cZX5QWrG@mail.gmail.com>

Dear Layla,

   Can PLUMED be used for metals systems now or will this be added in the
future?

Bests

Liu



On Fri, Jul 2, 2010 at 8:50 PM, <marsamos at democritos.it> wrote:

> Dear All, the PLUMED plug-in for metadynamic calculations has been
> adapted to Quantum ESPRESSO-4.2 and is available at
>
> http://qe-forge.org/frs/?group_id=10
>
> There is also an additional README (README.plumed.xlc_compiler) for
> those that uses ibm machines with xlc compiler.
>
> bests
>
>
> Layla
>
> --
> Dr. L. Martin-Samos
> tel. +39 040 3787 429
> CNR-DEMOCRITOS and
> International School for Advanced Studies (ISAS-SISSA)
> via Beirut 2-4
> 34151 Trieste Italy
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Liu, Luoyang Normal University, Luoyang, China
E-mail: zl.liu.caep at gmail.com
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From baroni at sissa.it  Sat Jul  3 07:00:37 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Sat, 3 Jul 2010 07:00:37 +0200
Subject: [Pw_forum] plumed for ESPRESSO-4.2 available
In-Reply-To: <AANLkTikYB4aLg99Mg0Jn0jd11WGelXvVaWC9cZX5QWrG@mail.gmail.com>
References: <20100702145007.szbjy0beqscgg40c@mail.democritos.it>
	<AANLkTikYB4aLg99Mg0Jn0jd11WGelXvVaWC9cZX5QWrG@mail.gmail.com>
Message-ID: <C28624FD-0937-4959-AFE7-D816E5FE5D2B@sissa.it>

I know nothing about plumed, but that it has nothing to do with electronic structure. so, the answer is YES, as long as QE can do molecular dynamics with the system of your choice. SB

On Jul 3, 2010, at 3:17 AM, Zhong-Li Liu wrote:

> Dear Layla,
> 
>    Can PLUMED be used for metals systems now or will this be added in the future?
> 
> Bests
> 
> Liu
> 
> 
> 
> On Fri, Jul 2, 2010 at 8:50 PM, <marsamos at democritos.it> wrote:
> Dear All, the PLUMED plug-in for metadynamic calculations has been
> adapted to Quantum ESPRESSO-4.2 and is available at
> 
> http://qe-forge.org/frs/?group_id=10
> 
> There is also an additional README (README.plumed.xlc_compiler) for
> those that uses ibm machines with xlc compiler.
> 
> bests
> 
> 
> Layla
> 
> --
> Dr. L. Martin-Samos
> tel. +39 040 3787 429
> CNR-DEMOCRITOS and
> International School for Advanced Studies (ISAS-SISSA)
> via Beirut 2-4
> 34151 Trieste Italy
> 
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> 
> -- 
> Dr. Liu, Luoyang Normal University, Luoyang, China
> E-mail: zl.liu.caep at gmail.com
> _______________________________________________
> 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







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From kazempoor2000 at yahoo.com  Sat Jul  3 07:48:25 2010
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Fri, 2 Jul 2010 22:48:25 -0700 (PDT)
Subject: [Pw_forum] LDA+U character
Message-ID: <623208.7771.qm@web114405.mail.gq1.yahoo.com>

Dear All
I have some questions about LDA+U nature. Does U treate like a? perturbation( I know that GW( many body peturbation method) is modified version of LDA+U? if yes why we are allowed to take U=0,1,2,........ up to large values? and why we solve system self-consistent?
Does U comute with KS-hamiltonian in every U values? I mean? does the order of states remains intact with respect to LDA or they can change?
and final question:
What is the effect of U on 
1-empty states in conduction band? (with d-character)
2-half filled states in conduction band(with d-character)
3-filled- states in conduction band (with d-character)

Thanks a lot


Ali Kazempour







Fritz-Haber-Institut              fax   : ++49-30-8413 4701

der Max-Planck-Gesellschaft

Faradayweg 4-6                    e-mail: kazempou at fhi-berlin.mpg.de

D-14 195 Berlin-Dahlem / German


      
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From hqzhou at nju.edu.cn  Sat Jul  3 08:10:55 2010
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Sat, 3 Jul 2010 14:10:55 +0800
Subject: [Pw_forum] plumed for ESPRESSO-4.2 available
References: <20100702145007.szbjy0beqscgg40c@mail.democritos.it>
Message-ID: <0D6B925C73CB4E1BA5DF2934B90CAB49@solarflare>

Layla,

Sorry for my ignorance about PLUMED. Could you please explain a little
about the differences between metadynamics in PLUMED and that in pwscf?

Any reference papers are welcome.


Huiqun Zhou
@Earth Sciences, Nanjing University, China

----- Original Message ----- 
From: <marsamos at democritos.it>
To: <pw_forum at pwscf.org>; <pw_users at pwscf.org>
Sent: Friday, July 02, 2010 8:50 PM
Subject: [Pw_forum] plumed for ESPRESSO-4.2 available


> Dear All, the PLUMED plug-in for metadynamic calculations has been 
> adapted to Quantum ESPRESSO-4.2 and is available at
> 
> http://qe-forge.org/frs/?group_id=10
> 
> There is also an additional README (README.plumed.xlc_compiler) for 
> those that uses ibm machines with xlc compiler.
> 
> bests
> 
> 
> Layla
> 
> -- 
> Dr. L. Martin-Samos
> tel. +39 040 3787 429
> CNR-DEMOCRITOS and
> International School for Advanced Studies (ISAS-SISSA)
> via Beirut 2-4
> 34151 Trieste Italy
> 
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


From baroni at sissa.it  Sat Jul  3 13:10:14 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Sat, 3 Jul 2010 13:10:14 +0200
Subject: [Pw_forum] plumed for ESPRESSO-4.2 available
In-Reply-To: <0D6B925C73CB4E1BA5DF2934B90CAB49@solarflare>
References: <20100702145007.szbjy0beqscgg40c@mail.democritos.it>
	<0D6B925C73CB4E1BA5DF2934B90CAB49@solarflare>
Message-ID: <DC83087E-21EF-4A27-ACF6-99FEF834B482@sissa.it>

as far as I understand, plumed is supposed to replave the built-in metadynamics capabilities of QE. the former will hopefully continued to be maintained in the future by a dedicated group of developers, while the latter is probably at a dead end.
am I correct, Layla?
see: http://merlino.mi.infn.it/~plumed/PLUMED/Home.html
SB

On Jul 3, 2010, at 8:10 AM, Huiqun Zhou wrote:

> Layla,
> 
> Sorry for my ignorance about PLUMED. Could you please explain a little
> about the differences between metadynamics in PLUMED and that in pwscf?
> 
> Any reference papers are welcome.
> 
> 
> Huiqun Zhou
> @Earth Sciences, Nanjing University, China
> 
> ----- Original Message ----- 
> From: <marsamos at democritos.it>
> To: <pw_forum at pwscf.org>; <pw_users at pwscf.org>
> Sent: Friday, July 02, 2010 8:50 PM
> Subject: [Pw_forum] plumed for ESPRESSO-4.2 available
> 
> 
>> Dear All, the PLUMED plug-in for metadynamic calculations has been 
>> adapted to Quantum ESPRESSO-4.2 and is available at
>> 
>> http://qe-forge.org/frs/?group_id=10
>> 
>> There is also an additional README (README.plumed.xlc_compiler) for 
>> those that uses ibm machines with xlc compiler.
>> 
>> bests
>> 
>> 
>> Layla
>> 
>> -- 
>> Dr. L. Martin-Samos
>> tel. +39 040 3787 429
>> CNR-DEMOCRITOS and
>> International School for Advanced Studies (ISAS-SISSA)
>> via Beirut 2-4
>> 34151 Trieste Italy
>> 
>> ----------------------------------------------------------------
>> This message was sent using IMP, the Internet Messaging Program.
>> 
>> _______________________________________________
>> 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

---
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







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From padmaja_patnaik at yahoo.co.uk  Sun Jul  4 21:56:23 2010
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Sun, 4 Jul 2010 19:56:23 +0000 (GMT)
Subject: [Pw_forum] Problem in DOS results
Message-ID: <364271.18487.qm@web26102.mail.ukl.yahoo.com>

Dear all

I am studying the properties of a compound semiconductor using super cell calculations. I have generated super cells by expanding the lattice constant 2times, 3 times and 4 times in all the directions. My calculations gives correct results for 2 times and 4 times extended super cells but not for 3 times extended onel. I have made sure that the generated atomic co-ordinates are correct. I have tried fixing all the required parameters like, k points, ecutwfc and nbnd. But still its not working. after doing the scf calculations I do the DOS with occupations=tetrahedra. But the DOS plot for the second case is found to be much different from expected while for all other cases the results match. What can be the probable mistake i am doing? Please suggest.

Padmaja Patnaik

Research Scholar

Dept of Physics

IIT Bombay

Mumbai, India


      
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From padmaja_patnaik at yahoo.co.uk  Sun Jul  4 23:09:42 2010
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Sun, 4 Jul 2010 21:09:42 +0000 (GMT)
Subject: [Pw_forum] Total magnetization and local magnetic moment
Message-ID: <149972.76641.qm@web26108.mail.ukl.yahoo.com>

?Dear all

I am getting some surprising results. I am calculating for a semiconductor doped with a transition metal ( using single impurity atom in a super cell). The total magnetization value obtained is more than one and so also the local moment on the impurity atom. But when i performed calculations with relaxation, the total magnetic moment increases but the local moment goes to almost zero value, which is very surprising. I expect the local magnetic moment to be almost of the same value as the total. I have also checked other atoms in the super cell, all are showing zero local moments but still the total magnetic moment is increased after relaxation. Let me mention here I am taking the total magnetic moment from the scf.out file and local moments from pdos.out file.

Please suggest me how to interpret this result? As per my understanding if a sample is showing ferromagnetic results after adding some impurity then it should be reflected on the local magnetic moment of the impurity atom too. In my results, this is the case before relaxation but not after relaxation, which is quite surprising.

Regards
Padmaja Patnaik

Research Scholar

Dept of Physics

IIT Bombay

Mumbai, India


      
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From wangqj1 at 126.com  Mon Jul  5 02:41:27 2010
From: wangqj1 at 126.com (Q.J.Wang)
Date: Mon, 5 Jul 2010 08:41:27 +0800 (CST)
Subject: [Pw_forum] GW
Message-ID: <4e51d9.851.129a00ce721.Coremail.wangqj1@126.com>

Dear all
     I have a problem about the GW method. In the forum, I found some people said GW allows to address large systems (a few hundreds of atoms).But I don't know where ? We know the course of computing the GW quasi-particle  energies is  the following :
1. pw.x
2. pw4gww.x
3. gww.x
If we want to calculate a large system, we must optimized it first with pw.x which is still time-consuming. So I want to know what makes the GW code can calculate the large system and where it reflects in the course of using GW code ?
 
--

Best regards
 
Q.J.Wang
 
XiangTan University 
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From matteo at umn.edu  Mon Jul  5 05:29:29 2010
From: matteo at umn.edu (Matteo Cococcioni)
Date: Sun, 04 Jul 2010 22:29:29 -0500
Subject: [Pw_forum] LDA+U character
In-Reply-To: <623208.7771.qm@web114405.mail.gq1.yahoo.com>
References: <623208.7771.qm@web114405.mail.gq1.yahoo.com>
Message-ID: <4C315199.30002@umn.edu>


dear Ali,

I will try to answer your questions



ali kazempour wrote:
> Dear All
> I have some questions about LDA+U nature. Does U treate like a  
> perturbation( I know that GW( many body peturbation method) is 
> modified version of LDA+U? if yes why we are allowed to take 
> U=0,1,2,........ up to large values? and why we solve system 
> self-consistent?
>

no, U is not treated as a perturbation. it is more a correction to the 
"standard" DFT energy functional. you can check the relationship between 
+U and GW in the following
reference (probably there are many more):

Anisimov et al, Journal of Physics: Condensed Matter 9, 767 (1997)


> Does U comute with KS-hamiltonian in every U values? I mean  does the 
> order of states remains intact with respect to LDA or they can change?
> and final question:
>

For sure the +U correction to the potential commutes with the 
translation and other symmetries of the crystal.
I think it doesn't commute with the rest of the Hamiltonian (the 
unperturbed DFT one). So if you think to switch on the U from a
U=0 ground state, unless the KS states are already bloch sums of atomic 
orbitals (that would be a very unlikely accident) the +U correction
introduces interactions between them if allowed by symmetry and you are 
going to get a non trivial mixing of them besides a shift in the
eigenvalue. Probably the most significant modifications are going to 
take place for states around the Fermi level that may get more localized.
The ones that are deeper in energy are probably closer to be atomic-like 
already and they will, at most, get a shift in the corresponding 
eigenvalues.

> What is the effect of U on
> 1-empty states in conduction band  (with d-character)
>

pushed up

> 2-half filled states in conduction band(with d-character)
>

depends: see above

> 3-filled- states in conduction band (with d-character)
>

pushed down

> Thanks a lot
>
>
> Ali Kazempour
>
>


hope this helps.

Matteo


>
> Fritz-Haber-Institut fax : ++49-30-8413 4701
> der Max-Planck-Gesellschaft
> Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de
> D-14 195 Berlin-Dahlem / German
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 


From baroni at sissa.it  Mon Jul  5 09:15:14 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 5 Jul 2010 09:15:14 +0200
Subject: [Pw_forum] GW
In-Reply-To: <4e51d9.851.129a00ce721.Coremail.wangqj1@126.com>
References: <4e51d9.851.129a00ce721.Coremail.wangqj1@126.com>
Message-ID: <D6868628-4BB8-4364-8DC1-C9D172D4ACC4@sissa.it>

it only means the the QE implementation of GW is supposed to be (much) faster thatn other competing GW implementation. Of course, this does not imply that GW is any faster than plain DFT calculations (it is actually much slower!). SB

On Jul 5, 2010, at 2:41 AM, Q.J.Wang wrote:

> Dear all
>      I have a problem about the GW method. In the forum, I found some people said GW allows to address large systems (a few hundreds of atoms).But I don't know where ? We know the course of computing the GW quasi-particle  energies is  the following :
> 1. pw.x
> 2. pw4gww.x
> 3. gww.x
> If we want to calculate a large system, we must optimized it first with pw.x which is still time-consuming. So I want to know what makes the GW code can calculate the large system and where it reflects in the course of using GW code ?
>  
> --
> Best regards
>  
> Q.J.Wang
>  
> XiangTan 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

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html







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From sclauzer at sissa.it  Mon Jul  5 10:34:54 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Mon, 5 Jul 2010 10:34:54 +0200
Subject: [Pw_forum] Problem in DOS results
In-Reply-To: <364271.18487.qm@web26102.mail.ukl.yahoo.com>
References: <364271.18487.qm@web26102.mail.ukl.yahoo.com>
Message-ID: <FC6CD37D-AD91-4AC6-81A9-F89D070980A2@sissa.it>

Dear Padmaja,

   are you sure that your calculation has been converged wrt the k-point sampling? I believe that if you build the supercell correctly and change the k-point sampling accordingly you'll get the same DOS. In principle this should hold even if you didn't converge wrt the size of the k-point mesh, though not completely sure that this is true also for tetrahedra method occupations. 

Please post at least the atomic positions, lattice parameters and the content of the K_POINTS input card, otherwise it will be impossible to help you further...

GS

Il giorno 04/lug/2010, alle ore 21.56, Padmaja Patnaik ha scritto:

> Dear all
> 
> I am studying the properties of a compound semiconductor using super cell calculations. I have generated super cells by expanding the lattice constant 2times, 3 times and 4 times in all the directions. My calculations gives correct results for 2 times and 4 times extended super cells but not for 3 times extended onel. I have made sure that the generated atomic co-ordinates are correct. I have tried fixing all the required parameters like, k points, ecutwfc and nbnd. But still its not working. after doing the scf calculations I do the DOS with occupations=tetrahedra. But the DOS plot for the second case is found to be much different from expected while for all other cases the results match. What can be the probable mistake i am doing? Please suggest.
> 
> 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


? Gabriele Sclauzero, EPFL SB ITP CSEA
   PH H2 462, Station 3, CH-1015 Lausanne

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From sclauzer at sissa.it  Mon Jul  5 10:42:34 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Mon, 5 Jul 2010 10:42:34 +0200
Subject: [Pw_forum] Total magnetization and local magnetic moment
In-Reply-To: <149972.76641.qm@web26108.mail.ukl.yahoo.com>
References: <149972.76641.qm@web26108.mail.ukl.yahoo.com>
Message-ID: <422DE4FD-F788-4D7E-87B0-9975E478EA02@sissa.it>


So, have you managed to converge the DOS first?

Again, if don't post some specific information about your system, as the input files, part of the output files and a sketch of your procedure, it's almost impossible to localize the problem.

GS


Il giorno 04/lug/2010, alle ore 23.09, Padmaja Patnaik ha scritto:

>  Dear all
> 
> I am getting some surprising results. I am calculating for a semiconductor doped with a transition metal ( using single impurity atom in a super cell). The total magnetization value obtained is more than one and so also the local moment on the impurity atom. But when i performed calculations with relaxation, the total magnetic moment increases but the local moment goes to almost zero value, which is very surprising. I expect the local magnetic moment to be almost of the same value as the total. I have also checked other atoms in the super cell, all are showing zero local moments but still the total magnetic moment is increased after relaxation. Let me mention here I am taking the total magnetic moment from the scf.out file and local moments from pdos.out file.
> 
> 
> Please suggest me how to interpret this result? As per my understanding if a sample is showing ferromagnetic results after adding some impurity then it should be reflected on the local magnetic moment of the impurity atom too. In my results, this is the case before relaxation but not after relaxation, which is quite surprising.
> 
> 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


? Gabriele Sclauzero, EPFL SB ITP CSEA
   PH H2 462, Station 3, CH-1015 Lausanne

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From masoudnahali at live.com  Mon Jul  5 10:55:21 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Mon, 5 Jul 2010 08:55:21 +0000
Subject: [Pw_forum] graphite surface optimizing problem
Message-ID: <COL114-W147F6600F7FBD86C92902DA1B10@phx.gbl>


Dear Quantum Espresso users

I optimized the graphite bulk and
the layers were completely flat. But when I try to "relax" the graphite
surface (slab 2*2 with 3 monolayer) with 10 angstrom vacuum the layers
become extremely ripple!!! I can not find the problem. Your help would
be a great gift.

input file:

&CONTROL
  calculation  = "relax",
  pseudo_dir   = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
  outdir       = "/home/koa/tmp",
  etot_conv_thr= 1.0D-4,
  forc_conv_thr= 1.0D-3,
  nstep=150,
  /
&SYSTEM
  ibrav     = 4,
  a         = 4.9318,
  b         = 4.9318,
  c         = 16.7029,
  cosab     = -0.5,
  cosac     = 1.0,
  cosbc     = 1.0,
  nat       = 24,
  ntyp      = 1,
  ecutwfc   = 40.D0,
  ecutrho   = 400.D0,
  occupations = 'smearing'
  smearing ='mp', 
  degauss = 0.01,
  nspin = 2,
  starting_magnetization(1)= 1.0,
  /
&ELECTRONS
  conv_thr    = 1.D-6,
  mixing_beta = 0.7D0,
  diagonalization = "david",
/
&IONS
 ion_dynamics="bfgs"
/
ATOMIC_SPECIES
C  12.0107  C.star1s-pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C    0.000000    0.000000    0.000000
C    2.465900    0.000000    0.000000
C    -1.232950    2.135532    0.000000
C    1.232950    2.135532    0.000000
C    0.000000    1.423688    0.000000
C    -1.232950    3.559220    0.000000
C    2.465900    1.423688    0.000000
C    1.232950    3.559220    0.000000
C    0.000000    0.000000    3.351450
C    2.465900    0.000000    3.351450
C    -1.232950    2.135532    3.351450
C    1.232950    2.135532    3.351450
C    1.232950    0.711844    3.351450
C    0.000000    2.847376    3.351450
C    3.698850    0.711844    3.351450
C    2.465900    2.847376    3.351450
C    0.000000    0.000000    6.702900
C    2.465900    0.000000    6.702900
C    -1.232950    2.135532    6.702900
C    1.232950    2.135532    6.702900
C    0.000000    1.423688    6.702900
C    -1.232950    3.559220    6.702900
C    2.465900    1.423688    6.702900
C    1.232950    3.559220    6.702900
K_POINTS {automatic}
4 4 1 1 1 1


out put (optimized positions):

C        0.000000000  -0.000000000  -0.686394528
C        2.465900000  -0.003714144  -0.758610095
C       -1.229733457   2.137389072  -0.758610095
C        1.229733457   2.137389072  -0.758610095
C        0.000000000   1.427474855  -0.213813075
C       -1.229670488   3.557326573  -0.213813075
C        2.465900000   1.423688000  -0.285079086
C        1.229670488   3.557326573  -0.213813075
C       -0.000000000   0.000000000   3.630366631
C        2.465900000  -0.014904710   3.544792504
C       -1.220042143   2.142984355   3.544792504
C        1.220042143   2.142984355   3.544792504
C        1.220249305   0.704511250   3.106073641
C        0.000000000   2.847376000   3.022325711
C        3.711550695   0.704511250   3.106073641
C        2.465900000   2.862041499   3.106073641
C        0.000000000   0.000000000   7.468882932
C        2.465900000   0.008344370   7.466151214
C       -1.240176436   2.131359815   7.466151214
C        1.240176436   2.131359815   7.466151214
C        0.000000000   1.414904155   6.963129179
C       -1.240557033   3.563611923   6.963129179
C        2.465900000   1.423688000   6.961528237
C        1.240557033   3.563611923   6.963129179



Many Thanks
Masoud Nahali
Sharif University of Technology
 		 	   		  
_________________________________________________________________
Hotmail: Free, trusted and rich email service.
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From sd.wang000 at gmail.com  Mon Jul  5 11:10:59 2010
From: sd.wang000 at gmail.com (shudong wang)
Date: Mon, 5 Jul 2010 17:10:59 +0800
Subject: [Pw_forum] About GWW
Message-ID: <AANLkTimhJ6RjIUW2Nw3cIgFgRIhZAC2t4609r2JtwU_Q@mail.gmail.com>

Dear developers:
I use GWW to calculate my 2D unit cell with 2C and 2F atoms,first I have
performed  scf_head.in with pw.x code ,it works well.Then I have a ph
calculation at Gamma with head.x but it appears:

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     task #         0
     from solve_e : error #         1
     called in the wrong case
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
My input file is:

&control
    title='gf'
    calculation='scf',
    restart_mode='from_scratch',
    prefix='gf'
    pseudo_dir = '/home/sdwang/espresso-4.1.2/pseudo',
    outdir='/home/sdwang/gw/tmp'
/
&system
    ibrav = 4, celldm(1)=4.839,celldm(3)=7.023,nat=4, ntyp=2,
    ecutwfc = 60.0,nosym=.false.,
occupations='smearing',degauss=0.01,smearing='gaussian'
/
&electrons
    diagonalization='david',
    conv_thr =  1.0d-10,
    mixing_beta = 0.5,
    startingwfc='random',
/
ATOMIC_SPECIES
 C   12.0  C.pz-vbc.UPF
 F   19.0  F.pz-rrkj.UPF
ATOMIC_POSITIONS (crystal)
C        0.331724716   0.667136313   0.096514182
C        0.665075100   0.333783657   0.069110636
F        0.331574264   0.667153962   0.171629429
F        0.665085920   0.333706069  -0.005994247
K_POINTS (automatic)
9 9 1  0 0 0


phonons of gf at Gamma
 &inputph
  tr2_ph=1.d-4,
  prefix='gf',
  outdir='/home/sdwang/gw/tmp/',
  epsil=.false.,
  amass(1)=12.0,
  amass(2)=19.0
  fildyn='gf.dynG',
  recover=.false.
  trans=.false.
  l_head=.true.
  omega_gauss=20.
  n_gauss=79
  grid_type=2
  niter_ph=1
 /
0.0 0.0 0.0
What is my problem?
Thanks!!
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From padmaja_patnaik at yahoo.co.uk  Mon Jul  5 11:54:09 2010
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Mon, 5 Jul 2010 09:54:09 +0000 (GMT)
Subject: [Pw_forum] Problem in DOS results
In-Reply-To: <mailman.2137.1278320126.1814.pw_forum@pwscf.org>
Message-ID: <778140.61172.qm@web26106.mail.ukl.yahoo.com>

I am calculating for SiC. Below is the datas you have asked for. 

?&system
??? ibrav=1, celldm(1) =16.4824, nat=64, ntyp=2,
??? ecutwfc = 32.0,
??? occupations='smearing', smearing='methfessel-paxton', degauss=0.02

?/
?&electrons
??? mixing_beta = 0.7
?/
ATOMIC_SPECIES
?Si 28.086? Si.pz-vbc.UPF
?C? 12.00?? C.pz-vbc.UPF
ATOMIC_POSITIONS
?Si??? 0.000?? 0.000?? 0.000
?Si??? 0.250?? 0.250?? 0.000
?Si??? 0.250? -0.250?? 0.000
?Si?? -0.250?? 0.250?? 0.000
?Si?? -0.250? -0.250?? 0.000
?Si??? 0.250?? 0.000?? 0.250
?Si??? 0.250?? 0.000? -0.250
?Si?? -0.250?? 0.000?? 0.250
?Si?? -0.250?? 0.000? -0.250
?Si??? 0.000?? 0.250?? 0.250
?Si??? 0.000?? 0.250? -0.250
?Si??? 0.000? -0.250?? 0.250
?Si??? 0.000? -0.250? -0.250
?Si??? 0.500?? 0.000?? 0.000
?Si??? 0.000?? 0.500?? 0.000
?Si??? 0.000?? 0.000?? 0.500
?Si??? 0.500?? 0.250?? 0.250
?Si??? 0.500?? 0.250? -0.250
?Si??? 0.500? -0.250?? 0.250
?Si??? 0.500? -0.250? -0.250
?Si??? 0.250?? 0.500?? 0.250
?Si??? 0.250?? 0.500? -0.250
?Si?? -0.250?? 0.500?? 0.250
?Si?? -0.250?? 0.500? -0.250
?Si??? 0.250?? 0.250?? 0.500
?Si??? 0.250? -0.250?? 0.500
?Si?? -0.250?? 0.250?? 0.500
?Si?? -0.250? -0.250?? 0.500
?Si??? 0.500?? 0.500?? 0.000
?Si??? 0.500?? 0.000?? 0.500
?Si??? 0.000?? 0.500?? 0.500
?Si??? 0.500?? 0.500?? 0.500
?C???? 0.125?? 0.125?? 0.125
?C??? -0.125? -0.125?? 0.125
?C???? 0.375? -0.125?? 0.125
?C??? -0.375?? 0.125?? 0.125
?C??? -0.125?? 0.375?? 0.125
?C???? 0.125? -0.375?? 0.125
?C???? 0.125?? 0.125? -0.375
?C??? -0.125? -0.125? -0.375
?C???? 0.375?? 0.375?? 0.125
?C??? -0.375? -0.375?? 0.125
?C???? 0.375? -0.125? -0.375
?C??? -0.375?? 0.125? -0.375
?C??? -0.125?? 0.375? -0.375
?C???? 0.125? -0.375? -0.375
?C???? 0.375?? 0.375? -0.375
?C??? -0.375? -0.375? -0.375
?C??? -0.125?? 0.125?? 0.125
?C???? 0.375?? 0.125?? 0.125
?C??? -0.125? -0.375?? 0.125
?C??? -0.125?? 0.125? -0.375
?C???? 0.375? -0.375?? 0.125
?C???? 0.375?? 0.125? -0.375
?C??? -0.125? -0.375? -0.375
?C???? 0.375? -0.375? -0.375
?C???? 0.125? -0.125? -0.125
?C??? -0.375? -0.125? -0.125
?C???? 0.125?? 0.375? -0.125
?C???? 0.125? -0.125?? 0.375
?C??? -0.375?? 0.375? -0.125
?C??? -0.375? -0.125?? 0.375
?C???? 0.125?? 0.375?? 0.375
?C??? -0.375?? 0.375?? 0.375
K_POINTS {automatic}
?2 2 2 0 0 0

I have repeated runs for different smearing, different k_points also.
?Sending you one of the input files.


---------------------------------------------------------------------

Message: 1
Date: Mon, 5 Jul 2010 10:34:54 +0200
From: Gabriele Sclauzero <sclauzer at sissa.it>
Subject: Re: [Pw_forum] Problem in DOS results
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <FC6CD37D-AD91-4AC6-81A9-F89D070980A2 at sissa.it>
Content-Type: text/plain; charset="iso-8859-1"

Dear Padmaja,

???are you sure that your calculation has been converged wrt the k-point sampling? I believe that if you build the supercell correctly and change the k-point sampling accordingly you'll get the same DOS. In principle this should hold even if you didn't converge wrt the size of the k-point mesh, though not completely sure that this is true also for tetrahedra method occupations. 

Please post at least the atomic positions, lattice parameters and the content of the K_POINTS input card, otherwise it will be impossible to help you further...

GS

Il giorno 04/lug/2010, alle ore 21.56, Padmaja Patnaik ha scritto:

> Dear all
> 
> I am studying the properties of a compound semiconductor using super cell calculations. I have generated super cells by expanding the lattice constant 2times, 3 times and 4 times in all the directions. My calculations gives correct results for 2 times and 4 times extended super cells but not for 3 times extended onel. I have made sure that the generated atomic co-ordinates are correct. I have tried fixing all the required parameters like, k points, ecutwfc and nbnd. But still its not working. after doing the scf calculations I do the DOS with occupations=tetrahedra. But the DOS plot for the second case is found to be much different from expected while for all other cases the results match. What can be the probable mistake i am doing? Please suggest.
> 
> 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


? Gabriele Sclauzero, EPFL SB ITP CSEA
???PH H2 462, Station 3, CH-1015 Lausanne

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Message: 2
Date: Mon, 5 Jul 2010 10:42:34 +0200
From: Gabriele Sclauzero <sclauzer at sissa.it>
Subject: Re: [Pw_forum] Total magnetization and local magnetic moment
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <422DE4FD-F788-4D7E-87B0-9975E478EA02 at sissa.it>
Content-Type: text/plain; charset="iso-8859-1"


So, have you managed to converge the DOS first?

Again, if don't post some specific information about your system, as the input files, part of the output files and a sketch of your procedure, it's almost impossible to localize the problem.

GS


Il giorno 04/lug/2010, alle ore 23.09, Padmaja Patnaik ha scritto:

>? Dear all
> 
> I am getting some surprising results. I am calculating for a semiconductor doped with a transition metal ( using single impurity atom in a super cell). The total magnetization value obtained is more than one and so also the local moment on the impurity atom. But when i performed calculations with relaxation, the total magnetic moment increases but the local moment goes to almost zero value, which is very surprising. I expect the local magnetic moment to be almost of the same value as the total. I have also checked other atoms in the super cell, all are showing zero local moments but still the total magnetic moment is increased after relaxation. Let me mention here I am taking the total magnetic moment from the scf.out file and local moments from pdos.out file.
> 
> 
> Please suggest me how to interpret this result? As per my understanding if a sample is showing ferromagnetic results after adding some impurity then it should be reflected on the local magnetic moment of the impurity atom too. In my results, this is the case before relaxation but not after relaxation, which is quite surprising.
> 
> 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





      
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From weibingzhangavh at gmail.com  Mon Jul  5 12:01:31 2010
From: weibingzhangavh at gmail.com (Wei-Bing Zhang)
Date: Mon, 5 Jul 2010 12:01:31 +0200
Subject: [Pw_forum] How to control the convergence of hybrid functional
	calculations
Message-ID: <AANLkTil-uX_djPHztKZpX6zIPbhSnwO8QnDmQuidS-5n@mail.gmail.com>

Dear all


I am trying to optimize the lattice parameters of Pd with PBE0 and HSE
using QE 4.2. As done in lda/gga, I try to get the total energies with
different lattice parameters and then fit them using EOS. However, I
found the calculations can converge quickly at some lattice parameters
(6.2 6.4 6.6 7.2 7.4) but fail to converge at others(6.8 7.0 7.6). I
have let the calculations run more than 3 days and the calculations
still did not converge.  I know hybrid functional calculations are
very expensive but 3 days should be long enough for a single point
energy calculations.  I think there should be something wrong in my
calculations.

Does anyone have the similar experience with me?  The input files are
attached below. If I have missed something or there is something wrong
in it, please point out.

Thanks very much. Any suggestion about hybrid functional calculations
will be highly appreciated.

Best

Wei-Bing Zhang
------------------------------------------
 &control

    calculation='scf'

    restart_mode='from_scratch',

    tprnfor = .true.

    prefix='pbe0.6.8',

    pseudo_dir = '/afs/ipp/home/w/weibingz/code/espresso-4.2/pseudo/',

    outdir='/p5/batch/weibingz/temp/'

 /

 &system

    ibrav=2, celldm(1) =6.8, nat=  1, ntyp= 1,

    degauss=0.02,

    smearing='mp',

    occupations='smearing',

    input_dft='pbe0', nqx1 = 1, nqx2 = 1, nqx3 = 1,

    x_gamma_extrapolation = .TRUE.

    ecutwfc = 50

 /

 &electrons

    conv_thr =  1.0d-8

    mixing_beta = 0.7

 /

ATOMIC_SPECIES

 Pd 106.42   Pd.UPF

ATOMIC_POSITIONS

 Pd 0.00 0.00 0.00

K_POINTS AUTOMATIC

14 14 14 1 1 1


-- 
----------------------------------------------------------------------
Dr. Wei-Bing Zhang
Fritz-Haber-Institut der Max-Planck-Gesellschaft
Faradayweg 4-6,D-14195 Berlin-Dahlem / Germany
Phone : ++49-30-8413 4830
Fax   : ++49-30-8413 4701
E-mail: zhangwei at fhi-berlin.mpg.de, weibingzhangavh at gmail.com
----------------------------------------------------------------------

From padmaja_patnaik at yahoo.co.uk  Mon Jul  5 12:05:54 2010
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Mon, 5 Jul 2010 10:05:54 +0000 (GMT)
Subject: [Pw_forum] Total magnetization and local magnetic moment
In-Reply-To: <mailman.2137.1278320126.1814.pw_forum@pwscf.org>
Message-ID: <322092.98137.qm@web26101.mail.ukl.yahoo.com>

I have proceeded with the supercell which is giving correct DOS. Here is the value of total magnetizatin from the scf.out file without relaxation.

!??? total energy????????????? = -1494.09037638 Ry
???? Harris-Foulkes estimate?? = -1494.09037639 Ry
???? estimated scf accuracy??? <??????? 6.7E-09 Ry

???? The total energy is the sum of the following terms:

???? one-electron contribution =?? 257.19918198 Ry
???? hartree contribution????? =?? 202.08158140 Ry
???? xc contribution?????????? =? -548.49776710 Ry
???? ewald contribution??????? = -1404.85946098 Ry
???? smearing contrib. (-TS)?? =??? -0.01391169 Ry

???? total magnetization?????? =???? 1.02 Bohr mag/cell
???? absolute magnetization??? =???? 1.12 Bohr mag/cell

???? convergence has been achieved in? 17 iterations
------------------------------------------------------------------------
Here is the portion of the file *.pdos.out? without relaxation

?Atom #?? 1: total charge =? 14.3653, s =? 2.4622, p =? 6.8403, d =? 5.0628,
???????????????? spin up????? =?? 7.7466, s =? 1.2349, p =? 3.4229, d =? 3.0889,
???????????????? spin down??? =?? 6.6187, s =? 1.2274, p =? 3.4174, d =? 1.9739,
???????????????? polarization =?? 1.1279, s =? 0.0075, p =? 0.0054, d =? 1.1150,
???? Atom #?? 2: total charge =?? 2.9244, s =? 0.8587, p =? 2.0656, d =? 0.0000,
???????????????? spin up????? =?? 1.4798, s =? 0.4351, p =? 1.0446, d =? 0.0000,
???????????????? spin down??? =?? 1.4446, s =? 0.4236, p =? 1.0210, d =? 0.0000,
???????????????? polarization =?? 0.0352, s =? 0.0115, p =? 0.0236, d =? 0.0000,
???? Atom #?? 3: total charge =?? 2.9244, s =? 0.8587, p =? 2.0656, d =? 0.0000,
???????????????? spin up????? =?? 1.4798, s =? 0.4351, p =? 1.0446, d =? 0.0000,
???????????????? spin down??? =?? 1.4446, s =? 0.4236, p =? 1.0210, d =? 0.0000,
???????????????? polarization =?? 0.0352, s =? 0.0115, p =? 0.0236, d =? 0.0000,
-----------------------------------------------------------------------------------------------------------------
As you can see atom number 1(this is the impurity) is showing a local magnetic moment. Now, below i add portions of the same two files from with relaxation calculations.
!??? total energy????????????? = -1494.15610974 Ry
???? Harris-Foulkes estimate?? = -1494.15610974 Ry
???? estimated scf accuracy??? <??????? 1.9E-10 Ry

???? The total energy is the sum of the following terms:

???? one-electron contribution =?? 270.52901167 Ry
???? hartree contribution????? =?? 195.52169853 Ry
???? xc contribution?????????? =? -548.43270406 Ry
???? ewald contribution??????? = -1411.76028316 Ry
???? smearing contrib. (-TS)?? =??? -0.01383273 Ry

???? total magnetization?????? =???? 1.13 Bohr mag/cell
???? absolute magnetization??? =???? 1.26 Bohr mag/cell

???? convergence has been achieved in?? 9 iterations


------------------------------------------------------------------------------------------------------------
Atom #?? 1: total charge =? 19.3947, s =? 2.5253, p =? 7.6414, d =? 9.2280,
???????????????? spin up????? =?? 9.7222, s =? 1.2688, p =? 3.8289, d =? 4.6245,
???????????????? spin down??? =?? 9.6725, s =? 1.2566, p =? 3.8125, d =? 4.6035,
???????????????? polarization =?? 0.0496, s =? 0.0122, p =? 0.0164, d =? 0.0210,
???? Atom #?? 2: total charge =?? 3.0599, s =? 0.9045, p =? 2.1555, d =? 0.0000,
???????????????? spin up????? =?? 1.5315, s =? 0.4527, p =? 1.0787, d =? 0.0000,
???????????????? spin down??? =?? 1.5285, s =? 0.4517, p =? 1.0767, d =? 0.0000,
???????????????? polarization =?? 0.0030, s =? 0.0010, p =? 0.0020, d =? 0.0000,
???? Atom #?? 3: total charge =?? 3.0599, s =? 0.9045, p =? 2.1555, d =? 0.0000,
???????????????? spin up????? =?? 1.5315, s =? 0.4527, p =? 1.0787, d =? 0.0000,
???????????????? spin down??? =?? 1.5285, s =? 0.4517, p =? 1.0767, d =? 0.0000,
???????????????? polarization =?? 0.0030, s =? 0.0010, p =? 0.0020, d =? 0.0000,
----------------------------------------------------------------------------------------------------------------------
Here as you can see the total magnetization increases but the atom number 1 (impurity) is showing zero local magnetic moment.
I hope i made the problem more clear this time.

Regards

Message: 2
Date: Mon, 5 Jul 2010 10:42:34 +0200
From: Gabriele Sclauzero <sclauzer at sissa.it>
Subject: Re: [Pw_forum] Total magnetization and local magnetic moment
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <422DE4FD-F788-4D7E-87B0-9975E478EA02 at sissa.it>
Content-Type: text/plain; charset="iso-8859-1"


So, have you managed to converge the DOS first?

Again, if don't post some specific information about your system, as the input files, part of the output files and a sketch of your procedure, it's almost impossible to localize the problem.

GS


Il giorno 04/lug/2010, alle ore 23.09, Padmaja Patnaik ha scritto:

>? Dear all
> 
> I am getting some surprising results. I am calculating for a semiconductor doped with a transition metal ( using single impurity atom in a super cell). The total magnetization value obtained is more than one and so also the local moment on the impurity atom. But when i performed calculations with relaxation, the total magnetic moment increases but the local moment goes to almost zero value, which is very surprising. I expect the local magnetic moment to be almost of the same value as the total. I have also checked other atoms in the super cell, all are showing zero local moments but still the total magnetic moment is increased after relaxation. Let me mention here I am taking the total magnetic moment from the scf.out file and local moments from pdos.out file.
> 
> 
> Please suggest me how to interpret this result? As per my understanding if a sample is showing ferromagnetic results after adding some impurity then it should be reflected on the local magnetic moment of the impurity atom too. In my results, this is the case before relaxation but not after relaxation, which is quite surprising.
> 
> 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


? Gabriele Sclauzero, EPFL SB ITP CSEA
???PH H2 462, Station 3, CH-1015 Lausanne

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------------------------------

Message: 3
Date: Mon, 5 Jul 2010 08:55:21 +0000
From: Masoud Nahali <masoudnahali at live.com>
Subject: [Pw_forum] graphite surface optimizing problem
To: Quantum Espresso <pw_forum at pwscf.org>
Message-ID: <COL114-W147F6600F7FBD86C92902DA1B10 at phx.gbl>
Content-Type: text/plain; charset="windows-1256"


Dear Quantum Espresso users

I optimized the graphite bulk and
the layers were completely flat. But when I try to "relax" the graphite
surface (slab 2*2 with 3 monolayer) with 10 angstrom vacuum the layers
become extremely ripple!!! I can not find the problem. Your help would
be a great gift.

input file:

&CONTROL
? calculation? = "relax",
? pseudo_dir???= "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
? outdir? ? ???= "/home/koa/tmp",
? etot_conv_thr= 1.0D-4,
? forc_conv_thr= 1.0D-3,
? nstep=150,
? /
&SYSTEM
? ibrav? ???= 4,
? a? ? ? ???= 4.9318,
? b? ? ? ???= 4.9318,
? c? ? ? ???= 16.7029,
? cosab? ???= -0.5,
? cosac? ???= 1.0,
? cosbc? ???= 1.0,
? nat? ? ???= 24,
? ntyp? ? ? = 1,
? ecutwfc???= 40.D0,
? ecutrho???= 400.D0,
? occupations = 'smearing'
? smearing ='mp', 
? degauss = 0.01,
? nspin = 2,
? starting_magnetization(1)= 1.0,
? /
&ELECTRONS
? conv_thr? ? = 1.D-6,
? mixing_beta = 0.7D0,
? diagonalization = "david",
/
&IONS
 ion_dynamics="bfgs"
/
ATOMIC_SPECIES
C? 12.0107? C.star1s-pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C? ? 0.000000? ? 0.000000? ? 0.000000
C? ? 2.465900? ? 0.000000? ? 0.000000
C? ? -1.232950? ? 2.135532? ? 0.000000
C? ? 1.232950? ? 2.135532? ? 0.000000
C? ? 0.000000? ? 1.423688? ? 0.000000
C? ? -1.232950? ? 3.559220? ? 0.000000
C? ? 2.465900? ? 1.423688? ? 0.000000
C? ? 1.232950? ? 3.559220? ? 0.000000
C? ? 0.000000? ? 0.000000? ? 3.351450
C? ? 2.465900? ? 0.000000? ? 3.351450
C? ? -1.232950? ? 2.135532? ? 3.351450
C? ? 1.232950? ? 2.135532? ? 3.351450
C? ? 1.232950? ? 0.711844? ? 3.351450
C? ? 0.000000? ? 2.847376? ? 3.351450
C? ? 3.698850? ? 0.711844? ? 3.351450
C? ? 2.465900? ? 2.847376? ? 3.351450
C? ? 0.000000? ? 0.000000? ? 6.702900
C? ? 2.465900? ? 0.000000? ? 6.702900
C? ? -1.232950? ? 2.135532? ? 6.702900
C? ? 1.232950? ? 2.135532? ? 6.702900
C? ? 0.000000? ? 1.423688? ? 6.702900
C? ? -1.232950? ? 3.559220? ? 6.702900
C? ? 2.465900? ? 1.423688? ? 6.702900
C? ? 1.232950? ? 3.559220? ? 6.702900
K_POINTS {automatic}
4 4 1 1 1 1


out put (optimized positions):

C? ? ? ? 0.000000000? -0.000000000? -0.686394528
C? ? ? ? 2.465900000? -0.003714144? -0.758610095
C? ? ???-1.229733457???2.137389072? -0.758610095
C? ? ? ? 1.229733457???2.137389072? -0.758610095
C? ? ? ? 0.000000000???1.427474855? -0.213813075
C? ? ???-1.229670488???3.557326573? -0.213813075
C? ? ? ? 2.465900000???1.423688000? -0.285079086
C? ? ? ? 1.229670488???3.557326573? -0.213813075
C? ? ???-0.000000000???0.000000000???3.630366631
C? ? ? ? 2.465900000? -0.014904710???3.544792504
C? ? ???-1.220042143???2.142984355???3.544792504
C? ? ? ? 1.220042143???2.142984355???3.544792504
C? ? ? ? 1.220249305???0.704511250???3.106073641
C? ? ? ? 0.000000000???2.847376000???3.022325711
C? ? ? ? 3.711550695???0.704511250???3.106073641
C? ? ? ? 2.465900000???2.862041499???3.106073641
C? ? ? ? 0.000000000???0.000000000???7.468882932
C? ? ? ? 2.465900000???0.008344370???7.466151214
C? ? ???-1.240176436???2.131359815???7.466151214
C? ? ? ? 1.240176436???2.131359815???7.466151214
C? ? ? ? 0.000000000???1.414904155???6.963129179
C? ? ???-1.240557033???3.563611923???6.963129179
C? ? ? ? 2.465900000???1.423688000???6.961528237
C? ? ? ? 1.240557033???3.563611923???6.963129179



Many Thanks
Masoud Nahali
Sharif University of Technology
 ??? ???????? ?????? ??? ? 
_________________________________________________________________
Hotmail: Free, trusted and rich email service.
https://signup.live.com/signup.aspx?id=60969
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------------------------------

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From giuseppe.mattioli at mlib.ism.cnr.it  Mon Jul  5 11:35:16 2010
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Mon, 5 Jul 2010 11:35:16 +0200
Subject: [Pw_forum] How to control the convergence of hybrid functional
	calculations
In-Reply-To: <AANLkTil-uX_djPHztKZpX6zIPbhSnwO8QnDmQuidS-5n@mail.gmail.com>
References: <AANLkTil-uX_djPHztKZpX6zIPbhSnwO8QnDmQuidS-5n@mail.gmail.com>
Message-ID: <201007051135.16657.giuseppe.mattioli@mlib.ism.cnr.it>

Dear Wei-Bing
I do not claim a real expertise about HF-DFT calculations, but it seems to me 
that you should use a more dense grid of q-points (the nqx values) when 
dealing with your metallic system. Of course your calculation will become 
quite heavier... Moreover, have you checked, at least at a GGA level, that 50 
Ry are enough for your Pd pseudo?
Yours

Giuseppe

On Monday 05 July 2010 12:01:31 Wei-Bing Zhang wrote:
> Dear all
>
>
> I am trying to optimize the lattice parameters of Pd with PBE0 and HSE
> using QE 4.2. As done in lda/gga, I try to get the total energies with
> different lattice parameters and then fit them using EOS. However, I
> found the calculations can converge quickly at some lattice parameters
> (6.2 6.4 6.6 7.2 7.4) but fail to converge at others(6.8 7.0 7.6). I
> have let the calculations run more than 3 days and the calculations
> still did not converge.  I know hybrid functional calculations are
> very expensive but 3 days should be long enough for a single point
> energy calculations.  I think there should be something wrong in my
> calculations.
>
> Does anyone have the similar experience with me?  The input files are
> attached below. If I have missed something or there is something wrong
> in it, please point out.
>
> Thanks very much. Any suggestion about hybrid functional calculations
> will be highly appreciated.
>
> Best
>
> Wei-Bing Zhang
> ------------------------------------------
>  &control
>
>     calculation='scf'
>
>     restart_mode='from_scratch',
>
>     tprnfor = .true.
>
>     prefix='pbe0.6.8',
>
>     pseudo_dir = '/afs/ipp/home/w/weibingz/code/espresso-4.2/pseudo/',
>
>     outdir='/p5/batch/weibingz/temp/'
>
>  /
>
>  &system
>
>     ibrav=2, celldm(1) =6.8, nat=  1, ntyp= 1,
>
>     degauss=0.02,
>
>     smearing='mp',
>
>     occupations='smearing',
>
>     input_dft='pbe0', nqx1 = 1, nqx2 = 1, nqx3 = 1,
>
>     x_gamma_extrapolation = .TRUE.
>
>     ecutwfc = 50
>
>  /
>
>  &electrons
>
>     conv_thr =  1.0d-8
>
>     mixing_beta = 0.7
>
>  /
>
> ATOMIC_SPECIES
>
>  Pd 106.42   Pd.UPF
>
> ATOMIC_POSITIONS
>
>  Pd 0.00 0.00 0.00
>
> K_POINTS AUTOMATIC
>
> 14 14 14 1 1 1



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From sclauzer at sissa.it  Mon Jul  5 12:39:24 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Mon, 05 Jul 2010 12:39:24 +0200
Subject: [Pw_forum] Problem in DOS results
In-Reply-To: <778140.61172.qm@web26106.mail.ukl.yahoo.com>
References: <778140.61172.qm@web26106.mail.ukl.yahoo.com>
Message-ID: <4C31B65C.3070007@sissa.it>


On 07/05/2010 11:54 AM, Padmaja Patnaik wrote:
> I am calculating for SiC. Below is the datas you have asked for.
>

You are lucky since I'm also studying SiC right now.

What is this supposed to be? Cubic 3C-SiC I guess? If so, I think that 
your atomic structure is wrong. There are some C atoms in the wrong 
place. If you look at it (with xcrysden, for instance), you will see 
that some tetrahedra around the carbon are upwards down. I mean, the 
should be all oriented in one direction.

Please check again your structure.

GS

>
> &system
>     ibrav=1, celldm(1) =16.4824, nat=64, ntyp=2,
>     ecutwfc = 32.0,
>     occupations='smearing', smearing='methfessel-paxton', degauss=0.02
>
>  /
> &electrons
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Si 28.086  Si.pz-vbc.UPF
>  C  12.00   C.pz-vbc.UPF
> ATOMIC_POSITIONS
>  Si    0.000   0.000   0.000
>  Si    0.250   0.250   0.000
>  Si    0.250  -0.250   0.000
>  Si   -0.250   0.250   0.000
>  Si   -0.250  -0.250   0.000
>  Si    0.250   0.000   0.250
>  Si    0.250   0.000  -0.250
>  Si   -0.250   0.000   0.250
>  Si   -0.250   0.000  -0.250
>  Si    0.000   0.250   0.250
>  Si    0.000   0.250  -0.250
>  Si    0.000  -0.250   0.250
>  Si    0.000  -0.250  -0.250
>  Si    0.500   0.000   0.000
>  Si    0.000   0.500   0.000
>  Si    0.000   0.000   0.500
>  Si    0.500   0.250   0.250
>  Si    0.500   0.250  -0.250
>  Si    0.500  -0.250   0.250
>  Si    0.500  -0.250  -0.250
>  Si    0.250   0.500   0.250
>  Si    0.250   0.500  -0.250
>  Si   -0.250   0.500   0.250
>  Si   -0.250   0.500  -0.250
>  Si    0.250   0.250   0.500
>  Si    0.250  -0.250   0.500
>  Si   -0.250   0.250   0.500
>  Si   -0.250  -0.250   0.500
>  Si    0.500   0.500   0.000
>  Si    0.500   0.000   0.500
>  Si    0.000   0.500   0.500
>  Si    0.500   0.500   0.500
>  C     0.125   0.125   0.125
>  C    -0.125  -0.125   0.125
>  C     0.375  -0.125   0.125
>  C    -0.375   0.125   0.125
>  C    -0.125   0.375   0.125
>  C     0.125  -0.375   0.125
>  C     0.125   0.125  -0.375
>  C    -0.125  -0.125  -0.375
>  C     0.375   0.375   0.125
>  C    -0.375  -0.375   0.125
>  C     0.375  -0.125  -0.375
>  C    -0.375   0.125  -0.375
>  C    -0.125   0.375  -0.375
>  C     0.125  -0.375  -0.375
>  C     0.375   0.375  -0.375
>  C    -0.375  -0.375  -0.375
>  C    -0.125   0.125   0.125
>  C     0.375   0.125   0.125
>  C    -0.125  -0.375   0.125
>  C    -0.125   0.125  -0.375
>  C     0.375  -0.375   0.125
>  C     0.375   0.125  -0.375
>  C    -0.125  -0.375  -0.375
>  C     0.375  -0.375  -0.375
>  C     0.125  -0.125  -0.125
>  C    -0.375  -0.125  -0.125
>  C     0.125   0.375  -0.125
>  C     0.125  -0.125   0.375
>  C    -0.375   0.375  -0.125
>  C    -0.375  -0.125   0.375
>  C     0.125   0.375   0.375
>  C    -0.375   0.375   0.375
> K_POINTS {automatic}
>  2 2 2 0 0 0
>
> I have repeated runs for different smearing, different k_points also.
>  Sending you one of the input files.
>
>
>     ---------------------------------------------------------------------
>
>     Message: 1
>     Date: Mon, 5 Jul 2010 10:34:54 +0200
>     From: Gabriele Sclauzero <sclauzer at sissa.it
>     </mc/compose?to=sclauzer at sissa.it>>
>     Subject: Re: [Pw_forum] Problem in DOS results
>     To: PWSCF Forum <pw_forum at pwscf.org
>     </mc/compose?to=pw_forum at pwscf.org>>
>     Message-ID: <FC6CD37D-AD91-4AC6-81A9-F89D070980A2 at sissa.it
>     </mc/compose?to=FC6CD37D-AD91-4AC6-81A9-F89D070980A2 at sissa.it>>
>     Content-Type: text/plain; charset="iso-8859-1"
>
>     Dear Padmaja,
>
>        are you sure that your calculation has been converged wrt the
>     k-point sampling? I believe that if you build the supercell
>     correctly and change the k-point sampling accordingly you'll get
>     the same DOS. In principle this should hold even if you didn't
>     converge wrt the size of the k-point mesh, though not completely
>     sure that this is true also for tetrahedra method occupations.
>
>     Please post at least the atomic positions, lattice parameters and
>     the content of the K_POINTS input card, otherwise it will be
>     impossible to help you further...
>
>     GS
>
>     Il giorno 04/lug/2010, alle ore 21.56, Padmaja Patnaik ha scritto:
>
>     > Dear all
>     >
>     > I am studying the properties of a compound semiconductor using
>     super cell calculations. I have generated super cells by expanding
>     the lattice constant 2times, 3 times and 4 times in all the
>     directions. My calculations gives correct results for 2 times and
>     4 times extended super cells but not for 3 times extended onel. I
>     have made sure that the generated atomic co-ordinates are correct.
>     I have tried fixing all the required parameters like, k points,
>     ecutwfc and nbnd. But still its not working. after doing the scf
>     calculations I do the DOS with occupations=tetrahedra. But the DOS
>     plot for the second case is found to be much different from
>     expected while for all other cases the results match. What can be
>     the probable mistake i am doing? Please suggest.
>     >
>     > Padmaja Patnaik
>     > Research Scholar
>     > Dept of Physics
>     > IIT Bombay
>     > Mumbai, India
>


-- 

Gabriele Sclauzero, EPFL SB ITP CSEA
PH H2 462, Station 3, CH-1015 Lausanne

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From sclauzer at sissa.it  Mon Jul  5 12:43:52 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Mon, 05 Jul 2010 12:43:52 +0200
Subject: [Pw_forum] Total magnetization and local magnetic moment
In-Reply-To: <322092.98137.qm@web26101.mail.ukl.yahoo.com>
References: <322092.98137.qm@web26101.mail.ukl.yahoo.com>
Message-ID: <4C31B768.80500@sissa.it>

On 07/05/2010 12:05 PM, Padmaja Patnaik wrote:
> I have proceeded with the supercell which is giving correct DOS. Here 
> is the value of total magnetizatin from the scf.out file without 
> relaxation.
>
> !    total energy              = -1494.09037638 Ry
>      Harris-Foulkes estimate   = -1494.09037639 Ry
>      estimated scf accuracy <        6.7E-09 Ry
>
>      The total energy is the sum of the following terms:
>
>      one-electron contribution =   257.19918198 Ry
>      hartree contribution      =   202.08158140 Ry
>      xc contribution           =  -548.49776710 Ry
>      ewald contribution        = -1404.85946098 Ry
>      smearing contrib. (-TS)   =    -0.01391169 Ry
>
>      total magnetization       =     1.02 Bohr mag/cell
>      absolute magnetization    =     1.12 Bohr mag/cell
>
>      convergence has been achieved in  17 iterations
> ------------------------------------------------------------------------
> Here is the portion of the file *.pdos.out  without relaxation
>
>  Atom #   1: total charge =  14.3653, s =  2.4622, p =  6.8403, d =  
> 5.0628,
>                  spin up      =   7.7466, s =  1.2349, p =  3.4229, d 
> =  3.0889,
>                  spin down    =   6.6187, s =  1.2274, p =  3.4174, d 
> =  1.9739,
>                  polarization =   1.1279, s =  0.0075, p =  0.0054, d 
> =  1.1150,
>      Atom #   2: total charge =   2.9244, s =  0.8587, p =  2.0656, d 
> =  0.0000,
>                  spin up      =   1.4798, s =  0.4351, p =  1.0446, d 
> =  0.0000,
>                  spin down    =   1.4446, s =  0.4236, p =  1.0210, d 
> =  0.0000,
>                  polarization =   0.0352, s =  0.0115, p =  0.0236, d 
> =  0.0000,
>      Atom #   3: total charge =   2.9244, s =  0.8587, p =  2.0656, d 
> =  0.0000,
>                  spin up      =   1.4798, s =  0.4351, p =  1.0446, d 
> =  0.0000,
>                  spin down    =   1.4446, s =  0.4236, p =  1.0210, d 
> =  0.0000,
>                  polarization =   0.0352, s =  0.0115, p =  0.0236, d 
> =  0.0000,
> -----------------------------------------------------------------------------------------------------------------
> As you can see atom number 1(this is the impurity) is showing a local 
> magnetic moment. Now, below i add portions of the same two files from 
> with relaxation calculations.
> !    total energy              = -1494.15610974 Ry
>      Harris-Foulkes estimate   = -1494.15610974 Ry
>      estimated scf accuracy <        1.9E-10 Ry
>
>      The total energy is the sum of the following terms:
>
>      one-electron contribution =   270.52901167 Ry
>      hartree contribution      =   195.52169853 Ry
>      xc contribution           =  -548.43270406 Ry
>      ewald contribution        = -1411.76028316 Ry
>      smearing contrib. (-TS)   =    -0.01383273 Ry
>
>      total magnetization       =     1.13 Bohr mag/cell
>      absolute magnetization    =     1.26 Bohr mag/cell
>
>      convergence has been achieved in   9 iterations
>
>


It looks like your impurity (Ge, I guess) acquires a lot of charge upon 
relaxing the structure, so that the d electrons get filled and you lose 
the local moment. This may be a real description or some spurious effect 
due to orbitals overlap (though it's unlikely if these are very 
localized 3d electrons).

About the total magnetization, well I don't know. It may come from 
neighboring atoms if they have donated some charge to the impurity.

HTH

GS

> ------------------------------------------------------------------------------------------------------------
> Atom #   1: total charge =  19.3947, s =  2.5253, p =  7.6414, d =  
> 9.2280,
>                  spin up      =   9.7222, s =  1.2688, p =  3.8289, d 
> =  4.6245,
>                  spin down    =   9.6725, s =  1.2566, p =  3.8125, d 
> =  4.6035,
>                  polarization =   0.0496, s =  0.0122, p =  0.0164, d 
> =  0.0210,
>      Atom #   2: total charge =   3.0599, s =  0.9045, p =  2.1555, d 
> =  0.0000,
>                  spin up      =   1.5315, s =  0.4527, p =  1.0787, d 
> =  0.0000,
>                  spin down    =   1.5285, s =  0.4517, p =  1.0767, d 
> =  0.0000,
>                  polarization =   0.0030, s =  0.0010, p =  0.0020, d 
> =  0.0000,
>      Atom #   3: total charge =   3.0599, s =  0.9045, p =  2.1555, d 
> =  0.0000,
>                  spin up      =   1.5315, s =  0.4527, p =  1.0787, d 
> =  0.0000,
>                  spin down    =   1.5285, s =  0.4517, p =  1.0767, d 
> =  0.0000,
>                  polarization =   0.0030, s =  0.0010, p =  0.0020, d 
> =  0.0000,
> ----------------------------------------------------------------------------------------------------------------------
> Here as you can see the total magnetization increases but the atom 
> number 1 (impurity) is showing zero local magnetic moment.
> I hope i made the problem more clear this time.
>
> Regards
>


-- 

Gabriele Sclauzero, EPFL SB ITP CSEA
PH H2 462, Station 3, CH-1015 Lausanne

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From weibingzhangavh at gmail.com  Mon Jul  5 13:56:33 2010
From: weibingzhangavh at gmail.com (Wei-Bing Zhang)
Date: Mon, 5 Jul 2010 13:56:33 +0200
Subject: [Pw_forum] How to control the convergence of hybrid functional
	calculations
Message-ID: <AANLkTimAO-MtkXEomD5URrp0DCmFoNW2Uei7HXsNPQcv@mail.gmail.com>

Dear Giuseppe

Thanks very much for your reply and valuable suggestions. I will do
further test calculations w.r.t q-points and cut-off energy of plane
wave.  The present problem is that the calculations at some lattice
parameter did not converge even using 1x1x1 q-points. In my opinion,
the calculations with denser q-points and lager cut-off energy should
be more difficult to get electronic S.C.F. Am I right ? Any suggestion
about how to get SCF using hybrid functional?

Thanks and Best wishes

Wei-Bing

-- 
----------------------------------------------------------------------
Dr. Wei-Bing Zhang
Fritz-Haber-Institut der Max-Planck-Gesellschaft
Faradayweg 4-6,D-14195 Berlin-Dahlem / Germany
Phone : ++49-30-8413 4830
Fax   : ++49-30-8413 4701
E-mail: zhangwei at fhi-berlin.mpg.de, weibingzhangavh at gmail.com
----------------------------------------------------------------------

From giannozz at democritos.it  Mon Jul  5 14:11:52 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 5 Jul 2010 14:11:52 +0200
Subject: [Pw_forum] How to control the convergence of hybrid functional
	calculations
In-Reply-To: <AANLkTimAO-MtkXEomD5URrp0DCmFoNW2Uei7HXsNPQcv@mail.gmail.com>
References: <AANLkTimAO-MtkXEomD5URrp0DCmFoNW2Uei7HXsNPQcv@mail.gmail.com>
Message-ID: <850B9A4A-03EA-45E2-99CD-FD445566FBD6@democritos.it>


On Jul 5, 2010, at 13:56 , Wei-Bing Zhang wrote:

> In my opinion, the calculations with denser q-points and larger
> cut-off energy should be more difficult to get electronic S.C.F.
> Am I right ?

I don't think so. It may take more time, but not necessarly
more scf iterations

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From kirtinandan07 at gmail.com  Mon Jul  5 14:37:22 2010
From: kirtinandan07 at gmail.com (vicky singh)
Date: Mon, 5 Jul 2010 18:07:22 +0530
Subject: [Pw_forum] problem with nbnd
Message-ID: <AANLkTik82HvGw0deXYdvtWiC6D414CKHjGkQnhdblVe-@mail.gmail.com>

Hi
i am studying trying to relax the structure of Ni - Al system super cell
with 40 atoms. what i understood till now is that if we don't specify nbnd
it takes the defalt value. To test this i performed relax calculation with
pure Ni with 1 atom first with out specifing any nbnd value then with nbnd =
10.  the results were 6.66 equilibrium latt_parameter -2.62 kbar pressure
and fermi energy 14.1765 for default nbnd and 6.66 equilibrium
latt_parameter -2.5 kbar pressure and fermi energy 14.1765 for nbnd =10.
there is slight change in the pressure value. why?

similar calculation i performed for the larger structure of Ni - Al system
super cell with 40 atoms input file attached. but there is significant
variation in the results. I have considered nbnd = 195 because i have 35 Ni
and rest Al atoms.

*condition  (1)*
*INPUT*
&SYSTEM
nspin = 2,  starting_magnetization(1)=0.7
nbnd = 195
*OUTPUT*
          total   stress  (Ry/bohr**3)                   (kbar)     P=
3.59
   0.00002296   0.00000000   0.00000000          3.38      0.00      0.00
   0.00000000   0.00002296   0.00000000          0.00      3.38      0.00
   0.00000000   0.00000000   0.00002739          0.00      0.00      4.03

     the Fermi energy is    13.5287 ev
!    total energy              =   -3027.65131607 Ry
     Harris-Foulkes estimate   =   -3027.65131529 Ry
     estimated scf accuracy    <       0.00000010 Ry

     The total energy is the sum of the following terms:

     one-electron contribution =   -1562.85025157 Ry
     hartree contribution      =    1281.18429645 Ry
     xc contribution           =   -1063.08426181 Ry
     ewald contribution        =   -1682.87860135 Ry
     smearing contrib. (-TS)   =      -0.02249780 Ry

     total magnetization       =    16.07 Bohr mag/cell
     absolute magnetization    =    19.19 Bohr mag/cell

ATOMIC_POSITIONS (crystal)
Ni       0.000000000   0.000000000   0.003462687
Ni       0.500000000   0.500000000   0.003077321
Ni       0.500000000   0.000000000   0.052355136
Ni       0.000000000   0.500000000   0.052355136
Ni       0.000000000   0.000000000   0.101475754
Ni       0.500000000   0.500000000   0.101664051
Ni       0.500000000   0.000000000   0.150808385
Ni       0.000000000   0.500000000   0.150808385
Ni       0.000000000   0.000000000   0.200000000
Ni       0.500000000   0.500000000   0.200000000

*condition  (2)*
*INPUT*
&SYSTEM
nspin = 2,  starting_magnetization(1)=0.7

*OUTPUT*
         total   stress  (Ry/bohr**3)                   (kbar)     P=
2.93
   0.00001834   0.00000000   0.00000000          2.70      0.00      0.00
   0.00000000   0.00001834   0.00000000          0.00      2.70      0.00
   0.00000000   0.00000000   0.00002317          0.00      0.00      3.41
     the Fermi energy is    13.5289 ev

!    total energy              =   -3027.65133623 Ry
     Harris-Foulkes estimate   =   -3027.65132967 Ry
     estimated scf accuracy    <       0.00000007 Ry

     The total energy is the sum of the following terms:

     one-electron contribution =   -1577.38934683 Ry
     hartree contribution      =    1288.44897083 Ry
     xc contribution           =   -1063.08376215 Ry
     ewald contribution        =   -1675.60469092 Ry
     smearing contrib. (-TS)   =      -0.02250718 Ry

     total magnetization       =    16.06 Bohr mag/cell
     absolute magnetization    =    19.18 Bohr mag/cell
ATOMIC_POSITIONS (crystal)
Ni       0.000000000   0.000000000   0.003594618
Ni       0.500000000   0.500000000   0.003232516
Ni       0.500000000   0.000000000   0.052460864
Ni       0.000000000   0.500000000   0.052460864
Ni       0.000000000   0.000000000   0.101507073
Ni       0.500000000   0.500000000   0.101682285
Ni       0.500000000   0.000000000   0.150774629
Ni       0.000000000   0.500000000   0.150774629
Ni       0.000000000   0.000000000   0.200000000
Ni       0.500000000   0.500000000   0.200000000
Ni       0.500000000   0.000000000   0.249225371
Ni       0.000000000   0.500000000   0.249225371
Ni       0.000000000   0.000000000   0.298492927

there is significant variation in the stress, energy and the final
coordinate of the atoms. i am not able to understand why it is getting size
dependent. can anybody please help.

vicky singh

research student
Bangalore
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From giannozz at democritos.it  Mon Jul  5 17:12:20 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 5 Jul 2010 17:12:20 +0200
Subject: [Pw_forum] Hubbard U in the version 4.2
In-Reply-To: <AANLkTil-yllVI_JjKaX739rFySdT2X2hEN5dLoQPKWS6@mail.gmail.com>
References: <AANLkTil-yllVI_JjKaX739rFySdT2X2hEN5dLoQPKWS6@mail.gmail.com>
Message-ID: <7FDCE5F5-DFF7-4A4C-845A-9C7BB4BC7C90@democritos.it>


On Jul 1, 2010, at 23:45 , hanghui chen wrote:

>  My previous email which reports a possible bug in the version 4.2  
> is pending
> because the attached input and output files are too large.

messages "waiting for moderator approval" are automatically canceled  
after
one day. Please follow the suggestions by Gabriele. If the problem  
persists,
resend your post

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From weibingzhangavh at gmail.com  Mon Jul  5 17:13:38 2010
From: weibingzhangavh at gmail.com (Wei-Bing Zhang)
Date: Mon, 5 Jul 2010 17:13:38 +0200
Subject: [Pw_forum] How to control the convergence of hybrid functional
	calculations
Message-ID: <AANLkTimI0JhlHiNH4yWFBnJJoc8Oh7TVuGKXW3MbzEWE@mail.gmail.com>

Dear Giuseppe and Paolo

Thanks very much for your reply

I will try to increase the Q-points in calculations. Do you think this
will give a help to convergence?? if so, could you explain this for me
clearly ?  And which parameter will determinate the convergence
actually?

Thanks again and Best Wishes


Wei-Bing


-- 
----------------------------------------------------------------------
Dr. Wei-Bing Zhang
Fritz-Haber-Institut der Max-Planck-Gesellschaft
Faradayweg 4-6,D-14195 Berlin-Dahlem / Germany
Phone : ++49-30-8413 4830
Fax   : ++49-30-8413 4701
E-mail: zhangwei at fhi-berlin.mpg.de, weibingzhangavh at gmail.com
----------------------------------------------------------------------

From sclauzer at sissa.it  Mon Jul  5 17:28:53 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Mon, 5 Jul 2010 17:28:53 +0200
Subject: [Pw_forum] Hubbard U in the version 4.2
In-Reply-To: <7FDCE5F5-DFF7-4A4C-845A-9C7BB4BC7C90@democritos.it>
References: <AANLkTil-yllVI_JjKaX739rFySdT2X2hEN5dLoQPKWS6@mail.gmail.com>
	<7FDCE5F5-DFF7-4A4C-845A-9C7BB4BC7C90@democritos.it>
Message-ID: <A874FF4E-0588-4C00-A43E-199E3AEC020F@sissa.it>

I think that the thread should be considered closed: Mr Hanghui Chen wrote me personally to say that it was a problem with libraries.

Since this happened to me more than once (I mean that a thread started as a public one in the forum ended as a private communication), I would like every forum thread having an head and a tail, so that if someone will look into the archives will have a clear idea if there was a real problem or not with that feature in that version of the code.


GS

Il giorno 05/lug/2010, alle ore 17.12, Paolo Giannozzi ha scritto:

> 
> On Jul 1, 2010, at 23:45 , hanghui chen wrote:
> 
>> My previous email which reports a possible bug in the version 4.2  
>> is pending
>> because the attached input and output files are too large.
> 
> messages "waiting for moderator approval" are automatically canceled  
> after
> one day. Please follow the suggestions by Gabriele. If the problem  
> persists,
> resend your post
> 
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of 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


? Gabriele Sclauzero, EPFL SB ITP CSEA
   PH H2 462, Station 3, CH-1015 Lausanne

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From masoudnahali at live.com  Mon Jul  5 20:19:19 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Mon, 5 Jul 2010 18:19:19 +0000
Subject: [Pw_forum] Is the Graphite surface flate?
Message-ID: <COL114-W485EB4FCB4B3CF6013F592A1B10@phx.gbl>


Dear Quantum Espresso users

I optimized the graphite bulk and the
 layers were completely flat. But when I try to "relax" the graphite 
surface (slab 2*2 with 3 monolayer) with 10 angstrom vacuum all the layers 
become extremely ripple!!! I can not find the problem. May it related to the number of layers? anyhow the number of layers is like the bulk. Your help would 
be a great gift.

input file:

&CONTROL
  
calculation  = "relax",
  pseudo_dir   = 
"/home/koa/soft/qe4.2/espresso-4.2/pseudo",
  outdir       = 
"/home/koa/tmp",
  etot_conv_thr= 1.0D-4,
  forc_conv_thr= 1.0D-3,
 
 nstep=150,
  /
&SYSTEM
  ibrav     = 4,
  a         = 
4.9318,
  b         = 4.9318,
  c         = 16.7029,
  
cosab     = -0.5,
  cosac     = 1.0,
  cosbc     = 1.0,
  
nat       = 24,
  ntyp      = 1,
  ecutwfc   = 40.D0,
  
ecutrho   = 400.D0,
  occupations = 'smearing'
  smearing ='mp', 
 
 degauss = 0.01,
  nspin = 2,
  starting_magnetization(1)= 1.0,
 
 /
&ELECTRONS
  conv_thr    = 1.D-6,
  mixing_beta = 0.7D0,
 
 diagonalization = "david",
/
&IONS
 ion_dynamics="bfgs"
/
ATOMIC_SPECIES
C 
 12.0107  C.star1s-pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C   
 0.000000    0.000000    0.000000
C    2.465900    0.000000    
0.000000
C    -1.232950    2.135532    0.000000
C    1.232950    
2.135532    0.000000
C    0.000000    1.423688    0.000000
C    
-1.232950    3.559220    0.000000
C    2.465900    1.423688    
0.000000
C    1.232950    3.559220    0.000000
C    0.000000    
0.000000    3.351450
C    2.465900    0.000000    3.351450
C    
-1.232950    2.135532    3.351450
C    1.232950    2.135532    
3.351450
C    1.232950    0.711844    3.351450
C    0.000000    
2.847376    3.351450
C    3.698850    0.711844    3.351450
C    
2.465900    2.847376    3.351450
C    0.000000    0.000000    
6.702900
C    2.465900    0.000000    6.702900
C    -1.232950    
2.135532    6.702900
C    1.232950    2.135532    6.702900
C    
0.000000    1.423688    6.702900
C    -1.232950    3.559220    
6.702900
C    2.465900    1.423688    6.702900
C    1.232950    
3.559220    6.702900
K_POINTS {automatic}
4 4 1 1 1 1


out
 put (optimized positions):

C        0.000000000  
-0.000000000  -0.686394528
C        2.465900000  -0.003714144  
-0.758610095
C       -1.229733457   2.137389072  -0.758610095
C       
 1.229733457   2.137389072  -0.758610095
C        0.000000000   
1.427474855  -0.213813075
C       -1.229670488   3.557326573  
-0.213813075
C        2.465900000   1.423688000  -0.285079086
C       
 1.229670488   3.557326573  -0.213813075
C       -0.000000000   
0.000000000   3.630366631
C        2.465900000  -0.014904710   
3.544792504
C       -1.220042143   2.142984355   3.544792504
C       
 1.220042143   2.142984355   3.544792504
C        1.220249305   
0.704511250   3.106073641
C        0.000000000   2.847376000   
3.022325711
C        3.711550695   0.704511250   3.106073641
C       
 2.465900000   2.862041499   3.106073641
C        0.000000000   
0.000000000   7.468882932
C        2.465900000   0.008344370   
7.466151214
C       -1.240176436   2.131359815   7.466151214
C       
 1.240176436   2.131359815   7.466151214
C        0.000000000   
1.414904155   6.963129179
C       -1.240557033   3.563611923   
6.963129179
C        2.465900000   1.423688000   6.961528237
C       
 1.240557033   3.563611923   6.963129179



Many Thanks
Masoud Nahali
Sharif
 University of Technology
 		 	   		  
_________________________________________________________________
Hotmail: Trusted email with Microsoft?s powerful SPAM protection.
https://signup.live.com/signup.aspx?id=60969
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From hqzhou at nju.edu.cn  Tue Jul  6 06:00:17 2010
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Tue, 6 Jul 2010 12:00:17 +0800
Subject: [Pw_forum] Distributing phonon calculations to different machines
Message-ID: <765B4C21072C43D09F65EB033CA2816E@solarflare>

dear developers,

Please clarify what directory should be copied for distributing phonon calculations
to different machines,  _ph{prefix}.phsave or _ph0{prefix}.phsave? The former is 
described in the manual INPUT_PH.html, the latter is used in the GRID_example. 
Although there is no _ph{prefix}.phsave existed after the preparatory run with 
start_irr=0 and last_irr=0, using the former works OK at the cost of redundant 
calculations. 

     Representation #  1 mode #   1
 
     Self-consistent Calculation
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from davcio : error #        25
     error while reading from file
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
     stopping ...
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From limch at ihpc.a-star.edu.sg  Tue Jul  6 06:08:29 2010
From: limch at ihpc.a-star.edu.sg (Lim Chiang Huay, Freda)
Date: Tue, 6 Jul 2010 12:08:29 +0800
Subject: [Pw_forum] How to compute polarization in the (111) direction?
Message-ID: <EA1C6ED4FAC4B144B5AB82AC0041E8B91FF3DC774C@shared-svc-exch.shared-svc.local>

Hi all,

May I know if it is possible for PWscf to compute the polarization in the (111) direction using Berry's phase calculation?

I understand that gdir=1, 2, 3 is available for the directions of the 1st , 2nd  and 3rd reciprocal lattice vectors. What about directions such as (110) and (111)?


Freda Lim
Institute of High Performance Computing
1 Fusionopolis Way, #16-16 Connexis
Singapore 138632
Email: limch at ihpc.a-star.edu.sg<mailto:limch at ihpc.a-star.edu.sg>


________________________________
This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.
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From hqzhou at nju.edu.cn  Tue Jul  6 06:13:12 2010
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Tue, 6 Jul 2010 12:13:12 +0800
Subject: [Pw_forum] Distributing phonon calculations to different
	machines
References: <765B4C21072C43D09F65EB033CA2816E@solarflare>
Message-ID: <06C591EB5EF54E149F166DF90EA58755@solarflare>

Sorry, I sent an unfinished message.

When using _ph0{prefix}.phsave, I got the error message shown in the previous
message.

Here is the snippet of my script for distributing lsf tasks:

......
nq=`sed -n '2p' ./${system}_q${nq1}${nq2}${nq3}.dyn0`
 
for ((i=1; i<=$nq; i++))
do
    if test ! -d $TMP_DIR/${system}/q${i} ; then
        mkdir $TMP_DIR/${system}/q${i}
        cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
    fi
    if test ! -d $TMP_DIR/${system}/q${i}/_ph0${system}.phsave ; then
        mkdir $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
        cp -r $TMP_DIR/${system}/_ph0${system}.phsave/* $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
    fi
done
 
for ((i=1; i<=$nq; i++))
do
cat > ${system}_q${i}.in << EOF
phonons of ${system}
 &inputph
  tr2_ph = 1.0d-13,
  alpha_mix(1) = 0.2,
  prefix = '${system}',
  ldisp = .true.,
  recover = .true.
  nq1 = ${nq1}, nq2 = ${nq2}, nq3 = ${nq3}
  start_q = $i, last_q = $i
  outdir = '$TMP_DIR/${system}/q${i}',
  fildyn = '${system}_q${nq1}${nq2}${nq3}.dyn'
......
EOF
$ECHO "calculation of q point $i"
bsub -a intelmpi -n $processes \
     -R "span[ptile=8]" \
     -J ${r}q${i}anda \
     -oo ${system}_q${i}.out \
     -eo ${system}_q${i}.err \
     $PH_COMMAND -input ./${system}_q${i}.in
done


Huiqun Zhou
@Earth Sciences, Nanjing University, China
  ----- Original Message ----- 
  From: Huiqun Zhou 
  To: pw_forum at pwscf.org 
  Sent: Tuesday, July 06, 2010 12:00 PM
  Subject: [Pw_forum] Distributing phonon calculations to different machines


  dear developers,

  Please clarify what directory should be copied for distributing phonon calculations
  to different machines,  _ph{prefix}.phsave or _ph0{prefix}.phsave? The former is 
  described in the manual INPUT_PH.html, the latter is used in the GRID_example. 
  Although there is no _ph{prefix}.phsave existed after the preparatory run with 
  start_irr=0 and last_irr=0, using the former works OK at the cost of redundant 
  calculations. 

       Representation #  1 mode #   1
   
       Self-consistent Calculation
   
   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
       from davcio : error #        25
       error while reading from file
   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   
       stopping ...


------------------------------------------------------------------------------


  _______________________________________________
  Pw_forum mailing list
  Pw_forum at pwscf.org
  http://www.democritos.it/mailman/listinfo/pw_forum
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From sclauzer at sissa.it  Tue Jul  6 09:56:22 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 06 Jul 2010 09:56:22 +0200
Subject: [Pw_forum] How to compute polarization in the (111) direction?
In-Reply-To: <EA1C6ED4FAC4B144B5AB82AC0041E8B91FF3DC774C@shared-svc-exch.shared-svc.local>
References: <EA1C6ED4FAC4B144B5AB82AC0041E8B91FF3DC774C@shared-svc-exch.shared-svc.local>
Message-ID: <4C32E1A6.4040609@sissa.it>

On 07/06/2010 06:08 AM, Lim Chiang Huay, Freda wrote:
>
> Hi all,
>
> May I know if it is possible for PWscf to compute the polarization in 
> the (111) direction using Berry's phase calculation?
>
> I understand that gdir=1, 2, 3 is available for the directions of the 
> 1^st , 2^nd  and 3^rd reciprocal lattice vectors. What about 
> directions such as (110) and (111)?
>

Just rotate the crystal such that the (111) direction is along one of 
the three cartesian axes. You'll have to use a supercell, but since the 
Miller indexes are very low I think that it will not be too large.

HTH

GS

> Freda Lim
>
> Institute of High Performance Computing
>
> 1 Fusionopolis Way, #16-16 Connexis
>
> Singapore 138632
>
> Email: limch at ihpc.a-star.edu.sg <mailto:limch at ihpc.a-star.edu.sg>
>
>
> ------------------------------------------------------------------------
> This email is confidential and may be privileged. If you are not the 
> intended recipient, please delete it and notify us immediately. Please 
> do not copy or use it for any purpose, or disclose its contents to any 
> other person. Thank you.
>
>
> _______________________________________________
> 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

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From sclauzer at sissa.it  Tue Jul  6 10:07:25 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 06 Jul 2010 10:07:25 +0200
Subject: [Pw_forum] Is the Graphite surface flate?
In-Reply-To: <COL114-W485EB4FCB4B3CF6013F592A1B10@phx.gbl>
References: <COL114-W485EB4FCB4B3CF6013F592A1B10@phx.gbl>
Message-ID: <4C32E43D.40003@sissa.it>

On 07/05/2010 08:19 PM, Masoud Nahali wrote:
> Dear Quantum Espresso users
>
> I optimized the graphite bulk and the layers were completely flat. But 
> when I try to "relax" the graphite surface (slab 2*2 with 3 monolayer) 
> with 10 angstrom vacuum all the layers become extremely ripple!!! I 
> can not find the problem. May it related to the number of layers? 
> anyhow the number of layers is like the bulk. Your help would be a 
> great gift.
> __
Are you using the experimental or the theoretical value for the in-plane 
(graphene) C-C distance? I guess that the PBE value is larger than the 
experimental one, so that if you start from the experimental C-C 
distance in the graphene layer and let everything relax, then the atoms 
would like to go towards the theoretical equilibrium distance and this 
may cause the rippled structure.
Secondly, I don't know if you can pretend that the innermost layer is 
graphite bulk-like, having only three layers in total.


HTH

GS

-- 

Gabriele Sclauzero, EPFL SB ITP CSEA
PH H2 462, Station 3, CH-1015 Lausanne

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From dalcorso at sissa.it  Tue Jul  6 10:09:11 2010
From: dalcorso at sissa.it (Dal Corso Andrea)
Date: Tue, 06 Jul 2010 10:09:11 +0200
Subject: [Pw_forum] Is the Graphite surface flate?
In-Reply-To: <COL114-W485EB4FCB4B3CF6013F592A1B10@phx.gbl>
References: <COL114-W485EB4FCB4B3CF6013F592A1B10@phx.gbl>
Message-ID: <1278403751.3282.1.camel@dhcp-098.cm.sissa.it>

On Mon, 2010-07-05 at 18:19 +0000, Masoud Nahali wrote:
> Dear Quantum Espresso users
> 
> I optimized the graphite bulk and the layers were completely flat. But
> when I try to "relax" the graphite surface (slab 2*2 with 3 monolayer)
> with 10 angstrom vacuum all the layers become extremely ripple!!! I
> can not find the problem. May it related to the number of layers?
> anyhow the number of layers is like the bulk. Your help would be a
> great gift.
> 
> input file:
> 
> &CONTROL
>   calculation  = "relax",
>   pseudo_dir   = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
>   outdir       = "/home/koa/tmp",
>   etot_conv_thr= 1.0D-4,
>   forc_conv_thr= 1.0D-3,
>   nstep=150,
>   /
> &SYSTEM
>   ibrav     = 4,
>   a         = 4.9318,
>   b         = 4.9318,
>   c         = 16.7029,
>   cosab     = -0.5,
>   cosac     = 1.0,
>   cosbc     = 1.0,
>   nat       = 24,
>   ntyp      = 1,
>   ecutwfc   = 40.D0,
>   ecutrho   = 400.D0,
>   occupations = 'smearing'
>   smearing ='mp', 
>   degauss = 0.01,
>   nspin = 2,
>   starting_magnetization(1)= 1.0,
>   /
> &ELECTRONS
>   conv_thr    = 1.D-6,
>   mixing_beta = 0.7D0,
>   diagonalization = "david",
> /
> &IONS
>  ion_dynamics="bfgs"
> /
> ATOMIC_SPECIES
> C  12.0107  C.star1s-pbe-rrkjus.UPF

Check the pseudopotential. This is a PP with a core hole for special
purposes not for standard simulations.

HTH,

Andrea


> ATOMIC_POSITIONS {angstrom}
> C    0.000000    0.000000    0.000000
> C    2.465900    0.000000    0.000000
> C    -1.232950    2.135532    0.000000
> C    1.232950    2.135532    0.000000
> C    0.000000    1.423688    0.000000
> C    -1.232950    3.559220    0.000000
> C    2.465900    1.423688    0.000000
> C    1.232950    3.559220    0.000000
> C    0.000000    0.000000    3.351450
> C    2.465900    0.000000    3.351450
> C    -1.232950    2.135532    3.351450
> C    1.232950    2.135532    3.351450
> C    1.232950    0.711844    3.351450
> C    0.000000    2.847376    3.351450
> C    3.698850    0.711844    3.351450
> C    2.465900    2.847376    3.351450
> C    0.000000    0.000000    6.702900
> C    2.465900    0.000000    6.702900
> C    -1.232950    2.135532    6.702900
> C    1.232950    2.135532    6.702900
> C    0.000000    1.423688    6.702900
> C    -1.232950    3.559220    6.702900
> C    2.465900    1.423688    6.702900
> C    1.232950    3.559220    6.702900
> K_POINTS {automatic}
> 4 4 1 1 1 1
> 
> 
> out put (optimized positions):
> 
> C        0.000000000  -0.000000000  -0.686394528
> C        2.465900000  -0.003714144  -0.758610095
> C       -1.229733457   2.137389072  -0.758610095
> C        1.229733457   2.137389072  -0.758610095
> C        0.000000000   1.427474855  -0.213813075
> C       -1.229670488   3.557326573  -0.213813075
> C        2.465900000   1.423688000  -0.285079086
> C        1.229670488   3.557326573  -0.213813075
> C       -0.000000000   0.000000000   3.630366631
> C        2.465900000  -0.014904710   3.544792504
> C       -1.220042143   2.142984355   3.544792504
> C        1.220042143   2.142984355   3.544792504
> C        1.220249305   0.704511250   3.106073641
> C        0.000000000   2.847376000   3.022325711
> C        3.711550695   0.704511250   3.106073641
> C        2.465900000   2.862041499   3.106073641
> C        0.000000000   0.000000000   7.468882932
> C        2.465900000   0.008344370   7.466151214
> C       -1.240176436   2.131359815   7.466151214
> C        1.240176436   2.131359815   7.466151214
> C        0.000000000   1.414904155   6.963129179
> C       -1.240557033   3.563611923   6.963129179
> C        2.465900000   1.423688000   6.961528237
> C        1.240557033   3.563611923   6.963129179
> 
> 
> 
> Many Thanks
> Masoud Nahali
> Sharif University of Technology
> 
> 
> ______________________________________________________________________
> Hotmail: Trusted email with Microsoft?s powerful SPAM protection. Sign
> up now.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
34151 Trieste (Italy)               e-mail: dalcorso at sissa.it



From dalcorso at sissa.it  Tue Jul  6 10:14:53 2010
From: dalcorso at sissa.it (Dal Corso Andrea)
Date: Tue, 06 Jul 2010 10:14:53 +0200
Subject: [Pw_forum] Distributing phonon calculations to
	different	machines
In-Reply-To: <06C591EB5EF54E149F166DF90EA58755@solarflare>
References: <765B4C21072C43D09F65EB033CA2816E@solarflare>
	<06C591EB5EF54E149F166DF90EA58755@solarflare>
Message-ID: <1278404093.3282.6.camel@dhcp-098.cm.sissa.it>

On Tue, 2010-07-06 at 12:13 +0800, Huiqun Zhou wrote:
> Sorry, I sent an unfinished message.
>  
> When using _ph0{prefix}.phsave, I got the error message shown in the
> previous
> message.
>  
> Here is the snippet of my script for distributing lsf tasks:
>  
> ......
> nq=`sed -n '2p' ./${system}_q${nq1}${nq2}${nq3}.dyn0`
>  
> for ((i=1; i<=$nq; i++))
> do
>     if test ! -d $TMP_DIR/${system}/q${i} ; then
>         mkdir $TMP_DIR/${system}/q${i}
>         cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
>     fi
>     if test ! -d $TMP_DIR/${system}/q${i}/_ph0${system}.phsave ; then
>         mkdir $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
>         cp -r $TMP_DIR/${system}/_ph0${system}.phsave/*
> $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
>     fi
> done
>  
> for ((i=1; i<=$nq; i++))
> do
> cat > ${system}_q${i}.in << EOF
> phonons of ${system}
>  &inputph
>   tr2_ph = 1.0d-13,
>   alpha_mix(1) = 0.2,
>   prefix = '${system}',
>   ldisp = .true.,
>   recover = .true.
>   nq1 = ${nq1}, nq2 = ${nq2}, nq3 = ${nq3}
>   start_q = $i, last_q = $i
>   outdir = '$TMP_DIR/${system}/q${i}',
>   fildyn = '${system}_q${nq1}${nq2}${nq3}.dyn'
> ......
> EOF
> $ECHO "calculation of q point $i"
> bsub -a intelmpi -n $processes \
>      -R "span[ptile=8]" \
>      -J ${r}q${i}anda \
>      -oo ${system}_q${i}.out \
>      -eo ${system}_q${i}.err \
>      $PH_COMMAND -input ./${system}_q${i}.in
> done
> 
>  
> Huiqun Zhou
> @Earth Sciences, Nanjing University, China
>         ----- Original Message ----- 
>         From: Huiqun Zhou 
>         To: pw_forum at pwscf.org 
>         Sent: Tuesday, July 06, 2010 12:00 PM
>         Subject: [Pw_forum] Distributing phonon calculations to
>         different machines
>         
>         
>         dear developers,
>          
>         Please clarify what directory should be copied
>         for distributing phonon calculations
>         to different machines,  _ph{prefix}.phsave
>         or _ph0{prefix}.phsave? The former is 
>         described in the manual INPUT_PH.html, the latter is used in
>         the GRID_example. 
>         Although there is no _ph{prefix}.phsave existed after the
>         preparatory run with 
>         start_irr=0 and last_irr=0, using the former works OK at the
>         cost of redundant 
>         calculations. 
>          
>              Representation #  1 mode #   1
>          
>              Self-consistent Calculation
>          
>          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>         %%%%%%%%%%%%%%%%%
>              from davcio : error #        25
>              error while reading from file
>          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>         %%%%%%%%%%%%%%%%%
>          
>              stopping ...

Thank you for the message. I will correct the INPUT_PH documentation.
The correct directory is _ph0{prefix}.phsave.

This message usually means that you have not copied all the required
files. Did you copy all the files produced by pw.x?

HTH,

Andrea



>         
>         ______________________________________________________________
>         
>         _______________________________________________
>         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
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
34151 Trieste (Italy)               e-mail: dalcorso at sissa.it



From giuseppe.mattioli at mlib.ism.cnr.it  Tue Jul  6 09:22:16 2010
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Tue, 6 Jul 2010 09:22:16 +0200
Subject: [Pw_forum] Is the Graphite surface flate?
In-Reply-To: <COL114-W485EB4FCB4B3CF6013F592A1B10@phx.gbl>
References: <COL114-W485EB4FCB4B3CF6013F592A1B10@phx.gbl>
Message-ID: <201007060922.16376.giuseppe.mattioli@mlib.ism.cnr.it>

Dear Masoud
apart from the pseudo problem issued by Andrea, you could try the keyword
london=.true.
It adds a Van der Waals contribution to total energy and it is likely to 
improve the interlayer interactions in your system.
Hope this helps
Giuseppe 
 
On Monday 05 July 2010 20:19:19 Masoud Nahali wrote:
> Dear Quantum Espresso users
>
> I optimized the graphite bulk and the
>  layers were completely flat. But when I try to "relax" the graphite
> surface (slab 2*2 with 3 monolayer) with 10 angstrom vacuum all the layers
> become extremely ripple!!! I can not find the problem. May it related to
> the number of layers? anyhow the number of layers is like the bulk. Your
> help would be a great gift.
>
> input file:
>
> &CONTROL
>
> calculation  = "relax",
>   pseudo_dir   =
> "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
>   outdir       =
> "/home/koa/tmp",
>   etot_conv_thr= 1.0D-4,
>   forc_conv_thr= 1.0D-3,
>
>  nstep=150,
>   /
> &SYSTEM
>   ibrav     = 4,
>   a         =
> 4.9318,
>   b         = 4.9318,
>   c         = 16.7029,
>
> cosab     = -0.5,
>   cosac     = 1.0,
>   cosbc     = 1.0,
>
> nat       = 24,
>   ntyp      = 1,
>   ecutwfc   = 40.D0,
>
> ecutrho   = 400.D0,
>   occupations = 'smearing'
>   smearing ='mp',
>
>  degauss = 0.01,
>   nspin = 2,
>   starting_magnetization(1)= 1.0,
>
>  /
> &ELECTRONS
>   conv_thr    = 1.D-6,
>   mixing_beta = 0.7D0,
>
>  diagonalization = "david",
> /
> &IONS
>  ion_dynamics="bfgs"
> /
> ATOMIC_SPECIES
> C
>  12.0107  C.star1s-pbe-rrkjus.UPF
> ATOMIC_POSITIONS {angstrom}
> C
>  0.000000    0.000000    0.000000
> C    2.465900    0.000000
> 0.000000
> C    -1.232950    2.135532    0.000000
> C    1.232950
> 2.135532    0.000000
> C    0.000000    1.423688    0.000000
> C
> -1.232950    3.559220    0.000000
> C    2.465900    1.423688
> 0.000000
> C    1.232950    3.559220    0.000000
> C    0.000000
> 0.000000    3.351450
> C    2.465900    0.000000    3.351450
> C
> -1.232950    2.135532    3.351450
> C    1.232950    2.135532
> 3.351450
> C    1.232950    0.711844    3.351450
> C    0.000000
> 2.847376    3.351450
> C    3.698850    0.711844    3.351450
> C
> 2.465900    2.847376    3.351450
> C    0.000000    0.000000
> 6.702900
> C    2.465900    0.000000    6.702900
> C    -1.232950
> 2.135532    6.702900
> C    1.232950    2.135532    6.702900
> C
> 0.000000    1.423688    6.702900
> C    -1.232950    3.559220
> 6.702900
> C    2.465900    1.423688    6.702900
> C    1.232950
> 3.559220    6.702900
> K_POINTS {automatic}
> 4 4 1 1 1 1
>
>
> out
>  put (optimized positions):
>
> C        0.000000000
> -0.000000000  -0.686394528
> C        2.465900000  -0.003714144
> -0.758610095
> C       -1.229733457   2.137389072  -0.758610095
> C
>  1.229733457   2.137389072  -0.758610095
> C        0.000000000
> 1.427474855  -0.213813075
> C       -1.229670488   3.557326573
> -0.213813075
> C        2.465900000   1.423688000  -0.285079086
> C
>  1.229670488   3.557326573  -0.213813075
> C       -0.000000000
> 0.000000000   3.630366631
> C        2.465900000  -0.014904710
> 3.544792504
> C       -1.220042143   2.142984355   3.544792504
> C
>  1.220042143   2.142984355   3.544792504
> C        1.220249305
> 0.704511250   3.106073641
> C        0.000000000   2.847376000
> 3.022325711
> C        3.711550695   0.704511250   3.106073641
> C
>  2.465900000   2.862041499   3.106073641
> C        0.000000000
> 0.000000000   7.468882932
> C        2.465900000   0.008344370
> 7.466151214
> C       -1.240176436   2.131359815   7.466151214
> C
>  1.240176436   2.131359815   7.466151214
> C        0.000000000
> 1.414904155   6.963129179
> C       -1.240557033   3.563611923
> 6.963129179
> C        2.465900000   1.423688000   6.961528237
> C
>  1.240557033   3.563611923   6.963129179
>
>
>
> Many Thanks
> Masoud Nahali
> Sharif
>  University of Technology
>
> _________________________________________________________________
> Hotmail: Trusted email with Microsoft?s powerful SPAM protection.
> https://signup.live.com/signup.aspx?id=60969



-- 
********************************************************
- 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 00016 - Monterotondo Stazione (RM) ? ? ? ? ?
? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ?
? ?E-mail: <giuseppe.mattioli at ism.cnr.it>

From padmaja_patnaik at yahoo.co.uk  Tue Jul  6 11:34:14 2010
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Tue, 6 Jul 2010 09:34:14 +0000 (GMT)
Subject: [Pw_forum] Total magnetization and local magnetic moment
In-Reply-To: <mailman.2145.1278326633.1814.pw_forum@pwscf.org>
Message-ID: <193141.47226.qm@web26107.mail.ukl.yahoo.com>

First of all thanks a lot for your suggestions. 
As you mentioned that the super cell atomic positions are not correct then why the code is not giving error? 

Coming to the magnetic moment querry, as you said the d electrons get filled and thus loosing the magnetic moment. But then one can expect that the moment may be trasffered to some other atom in the cell. But this also in not true in my result. Can this error be because i am doing the scf calculations for gamma point only and then the DOS calculations for 2*2*2 k points mesh? This is the only thing coming to my mind where i can be wrong. Is the difference in k point mesh give such a big difference in the magnetization value, total magnetization is > 1 and local moment is zero? 

Please suggest.
Regards

Padmaja Patnaik

Research Scholar

Dept of Physics

IIT Bombay

Mumbai, India

-

------------------------------

Message: 3
Date: Mon, 05 Jul 2010 12:43:52 +0200
From: Gabriele Sclauzero <sclauzer at sissa.it>
Subject: Re: [Pw_forum] Total magnetization and local magnetic moment
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <4C31B768.80500 at sissa.it>
Content-Type: text/plain; charset="iso-8859-1"

On 07/05/2010 12:05 PM, Padmaja Patnaik wrote:
> I have proceeded with the supercell which is giving correct DOS. Here 
> is the value of total magnetizatin from the scf.out file without 
> relaxation.
>
> !? ? total energy? ? ? ? ? ? ? = -1494.09037638 Ry
>? ? ? Harris-Foulkes estimate???= -1494.09037639 Ry
>? ? ? estimated scf accuracy <? ? ? ? 6.7E-09 Ry
>
>? ? ? The total energy is the sum of the following terms:
>
>? ? ? one-electron contribution =???257.19918198 Ry
>? ? ? hartree contribution? ? ? =???202.08158140 Ry
>? ? ? xc contribution? ? ? ? ???=? -548.49776710 Ry
>? ? ? ewald contribution? ? ? ? = -1404.85946098 Ry
>? ? ? smearing contrib. (-TS)???=? ? -0.01391169 Ry
>
>? ? ? total magnetization? ? ???=? ???1.02 Bohr mag/cell
>? ? ? absolute magnetization? ? =? ???1.12 Bohr mag/cell
>
>? ? ? convergence has been achieved in? 17 iterations
> ------------------------------------------------------------------------
> Here is the portion of the file *.pdos.out? without relaxation
>
>? Atom #???1: total charge =? 14.3653, s =? 2.4622, p =? 6.8403, d =? 
> 5.0628,
>? ? ? ? ? ? ? ? ? spin up? ? ? =???7.7466, s =? 1.2349, p =? 3.4229, d 
> =? 3.0889,
>? ? ? ? ? ? ? ? ? spin down? ? =???6.6187, s =? 1.2274, p =? 3.4174, d 
> =? 1.9739,
>? ? ? ? ? ? ? ? ? polarization =???1.1279, s =? 0.0075, p =? 0.0054, d 
> =? 1.1150,
>? ? ? Atom #???2: total charge =???2.9244, s =? 0.8587, p =? 2.0656, d 
> =? 0.0000,
>? ? ? ? ? ? ? ? ? spin up? ? ? =???1.4798, s =? 0.4351, p =? 1.0446, d 
> =? 0.0000,
>? ? ? ? ? ? ? ? ? spin down? ? =???1.4446, s =? 0.4236, p =? 1.0210, d 
> =? 0.0000,
>? ? ? ? ? ? ? ? ? polarization =???0.0352, s =? 0.0115, p =? 0.0236, d 
> =? 0.0000,
>? ? ? Atom #???3: total charge =???2.9244, s =? 0.8587, p =? 2.0656, d 
> =? 0.0000,
>? ? ? ? ? ? ? ? ? spin up? ? ? =???1.4798, s =? 0.4351, p =? 1.0446, d 
> =? 0.0000,
>? ? ? ? ? ? ? ? ? spin down? ? =???1.4446, s =? 0.4236, p =? 1.0210, d 
> =? 0.0000,
>? ? ? ? ? ? ? ? ? polarization =???0.0352, s =? 0.0115, p =? 0.0236, d 
> =? 0.0000,
> -----------------------------------------------------------------------------------------------------------------
> As you can see atom number 1(this is the impurity) is showing a local 
> magnetic moment. Now, below i add portions of the same two files from 
> with relaxation calculations.
> !? ? total energy? ? ? ? ? ? ? = -1494.15610974 Ry
>? ? ? Harris-Foulkes estimate???= -1494.15610974 Ry
>? ? ? estimated scf accuracy <? ? ? ? 1.9E-10 Ry
>
>? ? ? The total energy is the sum of the following terms:
>
>? ? ? one-electron contribution =???270.52901167 Ry
>? ? ? hartree contribution? ? ? =???195.52169853 Ry
>? ? ? xc contribution? ? ? ? ???=? -548.43270406 Ry
>? ? ? ewald contribution? ? ? ? = -1411.76028316 Ry
>? ? ? smearing contrib. (-TS)???=? ? -0.01383273 Ry
>
>? ? ? total magnetization? ? ???=? ???1.13 Bohr mag/cell
>? ? ? absolute magnetization? ? =? ???1.26 Bohr mag/cell
>
>? ? ? convergence has been achieved in???9 iterations
>
>


It looks like your impurity (Ge, I guess) acquires a lot of charge upon 
relaxing the structure, so that the d electrons get filled and you lose 
the local moment. This may be a real description or some spurious effect 
due to orbitals overlap (though it's unlikely if these are very 
localized 3d electrons).

About the total magnetization, well I don't know. It may come from 
neighboring atoms if they have donated some charge to the impurity.

HTH

GS

> ------------------------------------------------------------------------------------------------------------
> Atom #???1: total charge =? 19.3947, s =? 2.5253, p =? 7.6414, d =? 
> 9.2280,
>? ? ? ? ? ? ? ? ? spin up? ? ? =???9.7222, s =? 1.2688, p =? 3.8289, d 
> =? 4.6245,
>? ? ? ? ? ? ? ? ? spin down? ? =???9.6725, s =? 1.2566, p =? 3.8125, d 
> =? 4.6035,
>? ? ? ? ? ? ? ? ? polarization =???0.0496, s =? 0.0122, p =? 0.0164, d 
> =? 0.0210,
>? ? ? Atom #???2: total charge =???3.0599, s =? 0.9045, p =? 2.1555, d 
> =? 0.0000,
>? ? ? ? ? ? ? ? ? spin up? ? ? =???1.5315, s =? 0.4527, p =? 1.0787, d 
> =? 0.0000,
>? ? ? ? ? ? ? ? ? spin down? ? =???1.5285, s =? 0.4517, p =? 1.0767, d 
> =? 0.0000,
>? ? ? ? ? ? ? ? ? polarization =???0.0030, s =? 0.0010, p =? 0.0020, d 
> =? 0.0000,
>? ? ? Atom #???3: total charge =???3.0599, s =? 0.9045, p =? 2.1555, d 
> =? 0.0000,
>? ? ? ? ? ? ? ? ? spin up? ? ? =???1.5315, s =? 0.4527, p =? 1.0787, d 
> =? 0.0000,
>? ? ? ? ? ? ? ? ? spin down? ? =???1.5285, s =? 0.4517, p =? 1.0767, d 
> =? 0.0000,
>? ? ? ? ? ? ? ? ? polarization =???0.0030, s =? 0.0010, p =? 0.0020, d 
> =? 0.0000,
> ----------------------------------------------------------------------------------------------------------------------
> Here as you can see the total magnetization increases but the atom 
> number 1 (impurity) is showing zero local magnetic moment.
> I hope i made the problem more clear this time.
>
> Regards
>


-- 

Gabriele Sclauzero, EPFL SB ITP CSEA
PH H2 462, Station 3, CH-1015 Lausanne

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From hqzhou at nju.edu.cn  Tue Jul  6 11:55:13 2010
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Tue, 6 Jul 2010 17:55:13 +0800
Subject: [Pw_forum] Distributing phonon calculations todifferent	machines
References: <765B4C21072C43D09F65EB033CA2816E@solarflare><06C591EB5EF54E149F166DF90EA58755@solarflare>
	<1278404093.3282.6.camel@dhcp-098.cm.sissa.it>
Message-ID: <190836FFFC0F494F881E7F2641CC260D@solarflare>

Thanks, Andrea.

As indicated in the script below, I have copied all files and directories 
created
by pw.x run.

if test ! -d $TMP_DIR/${system}/q${i} ; then
         mkdir $TMP_DIR/${system}/q${i}
         cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
fi

BTW, could you please describe more in detail about the newly added 
information
in INPUT_PH.html for distributing phonon calculations to cluster? If I set 
wf_collect
to true, there should be no relation in nproc and npool between pw.x run and 
later
two ph.x runs, right? Taking AlAs in the GRID_example as example, If I want 
to use
server with 8 CPU core to do calculations for each one q point (8 servers in 
total),
what are the values of images and pools?


Huiqun Zhou
@Earth Sciences, Nanjing University, China

----- Original Message ----- 
From: "Dal Corso Andrea" <dalcorso at sissa.it>
To: "PWSCF Forum" <pw_forum at pwscf.org>
Sent: Tuesday, July 06, 2010 4:14 PM
Subject: Re: [Pw_forum] Distributing phonon calculations todifferent 
machines


> On Tue, 2010-07-06 at 12:13 +0800, Huiqun Zhou wrote:
>> Sorry, I sent an unfinished message.
>>
>> When using _ph0{prefix}.phsave, I got the error message shown in the
>> previous
>> message.
>>
>> Here is the snippet of my script for distributing lsf tasks:
>>
>> ......
>> nq=`sed -n '2p' ./${system}_q${nq1}${nq2}${nq3}.dyn0`
>>
>> for ((i=1; i<=$nq; i++))
>> do
>>     if test ! -d $TMP_DIR/${system}/q${i} ; then
>>         mkdir $TMP_DIR/${system}/q${i}
>>         cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
>>     fi
>>     if test ! -d $TMP_DIR/${system}/q${i}/_ph0${system}.phsave ; then
>>         mkdir $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
>>         cp -r $TMP_DIR/${system}/_ph0${system}.phsave/*
>> $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
>>     fi
>> done
>>
>> for ((i=1; i<=$nq; i++))
>> do
>> cat > ${system}_q${i}.in << EOF
>> phonons of ${system}
>>  &inputph
>>   tr2_ph = 1.0d-13,
>>   alpha_mix(1) = 0.2,
>>   prefix = '${system}',
>>   ldisp = .true.,
>>   recover = .true.
>>   nq1 = ${nq1}, nq2 = ${nq2}, nq3 = ${nq3}
>>   start_q = $i, last_q = $i
>>   outdir = '$TMP_DIR/${system}/q${i}',
>>   fildyn = '${system}_q${nq1}${nq2}${nq3}.dyn'
>> ......
>> EOF
>> $ECHO "calculation of q point $i"
>> bsub -a intelmpi -n $processes \
>>      -R "span[ptile=8]" \
>>      -J ${r}q${i}anda \
>>      -oo ${system}_q${i}.out \
>>      -eo ${system}_q${i}.err \
>>      $PH_COMMAND -input ./${system}_q${i}.in
>> done
>>
>>
>> Huiqun Zhou
>> @Earth Sciences, Nanjing University, China
>>         ----- Original Message ----- 
>>         From: Huiqun Zhou
>>         To: pw_forum at pwscf.org
>>         Sent: Tuesday, July 06, 2010 12:00 PM
>>         Subject: [Pw_forum] Distributing phonon calculations to
>>         different machines
>>
>>
>>         dear developers,
>>
>>         Please clarify what directory should be copied
>>         for distributing phonon calculations
>>         to different machines,  _ph{prefix}.phsave
>>         or _ph0{prefix}.phsave? The former is
>>         described in the manual INPUT_PH.html, the latter is used in
>>         the GRID_example.
>>         Although there is no _ph{prefix}.phsave existed after the
>>         preparatory run with
>>         start_irr=0 and last_irr=0, using the former works OK at the
>>         cost of redundant
>>         calculations.
>>
>>              Representation #  1 mode #   1
>>
>>              Self-consistent Calculation
>>
>>          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>         %%%%%%%%%%%%%%%%%
>>              from davcio : error #        25
>>              error while reading from file
>>          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>         %%%%%%%%%%%%%%%%%
>>
>>              stopping ...
>
> Thank you for the message. I will correct the INPUT_PH documentation.
> The correct directory is _ph0{prefix}.phsave.
>
> This message usually means that you have not copied all the required
> files. Did you copy all the files produced by pw.x?
>
> HTH,
>
> Andrea
>
>
>
>>
>>         ______________________________________________________________
>>
>>         _______________________________________________
>>         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
> -- 
> Andrea Dal Corso                    Tel. 0039-040-3787428
> SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
> 34151 Trieste (Italy)               e-mail: dalcorso at sissa.it
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 



From sclauzer at sissa.it  Tue Jul  6 12:08:42 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 06 Jul 2010 12:08:42 +0200
Subject: [Pw_forum] Total magnetization and local magnetic moment
In-Reply-To: <193141.47226.qm@web26107.mail.ukl.yahoo.com>
References: <193141.47226.qm@web26107.mail.ukl.yahoo.com>
Message-ID: <4C3300AA.5040509@sissa.it>

On 07/06/2010 11:34 AM, Padmaja Patnaik wrote:
> First of all thanks a lot for your suggestions.
> As you mentioned that the super cell atomic positions are not correct 
> then why the code is not giving error?
>

I said "not correct" in the sense that they do not describe any polytype 
of SiC. I was meaning that your atomic structure does not represent 
3C-SiC. The code does not know what kind of system you want to describe 
since it cannot read into your mind and say "hey, stop! this is not the 
system you have in mind!".

It gives however an error message when atoms are (almost) overlapping, 
since this would lead it into serious troubles when computing the energy 
and the potential.

Then I don't know if with the other supercells you entered the atomic 
positions correctly or not, but if those describe correctly 3C-SiC, then 
of course you'll find different results compared to this supercell.

>
> Coming to the magnetic moment querry, as you said the d electrons get 
> filled and thus loosing the magnetic moment. But then one can expect 
> that the moment may be trasffered to some other atom in the cell. But 
> this also in not true in my result. Can this error be because i am 
> doing the scf calculations for gamma point only and then the DOS 
> calculations for 2*2*2 k points mesh? This is the only thing coming to 
> my mind where i can be wrong. Is the difference in k point mesh give 
> such a big difference in the magnetization value, total magnetization 
> is > 1 and local moment is zero?
>

It is important to converge total energy (and magnetization, for 
spin-polarized systems) in the first place. Then you may need more 
k-points in the following nscf calculation in order to converge the DOS 
(also depending on the smearing you choose for projwfc).


HTH

GS

> Please suggest.
> Regards
>
> Padmaja Patnaik
> Research Scholar
> Dept of Physics
> IIT Bombay
> Mumbai, India
>


-- 

Gabriele Sclauzero, EPFL SB ITP CSEA
PH H2 462, Station 3, CH-1015 Lausanne

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From 1009ukumar at gmail.com  Tue Jul  6 12:13:00 2010
From: 1009ukumar at gmail.com (sonu kumar)
Date: Tue, 6 Jul 2010 15:43:00 +0530
Subject: [Pw_forum] Zone centre phonons in ZrO2 ?
Message-ID: <AANLkTimjV1m5fOrGuaKLfbq-97ttA4uc1YyKynKKHj2u@mail.gmail.com>

Dear all Quantum Espresso users and developers,

I am not able to reproduce the zone cente phonons in ZrO2 calculated
in PRL 78, 21, 1997.

My results, without LO-TO splitting(can be calculated, once accoustical
mode=0 cm-1 ) are:

T1u: 14.27 cm-1 <---------not zero
T1u: 219.6 cm-1
T2g: 550.35cm-1

 I am not able to make the accoustical mode=0 cm-1.
 Although  the born charges and dielectric constants are
 ok with relative error~1%.


Input files:-----------------------------------------------

scf file:
&control
    calculation='scf',             ! relax,self consistent calc.
    verbosity='high',
    restart_mode='from_scratch',   ! 'from_scratch',
    prefix='ZrO2',
    wf_collect=.true.,                    ! collect wave func in ./ZrO2.save
    tstress=.true.,
    tprnfor=.true.,
    nstep=100,                             ! default=50
    dt=20,                                      !10,      ! default=20
    etot_conv_thr=1.0D-5,          ! default=1.0D-4
    forc_conv_thr=1.0D-5,          !1.0D-4,  default=1.0D-3
    pseudo_dir = './',
    outdir='./',
 /

 &system
    ibrav = 2,
    celldm(1)=9.67
    nat=3, ntyp=2,
    ! nbnd=                              ! can calculate itself
    ecutwfc=30,                      !50,    !in Ry, no default,
initially=60
    ecutrho=350,                    !350 !300, ! 8*50=400
    !    nr1=14,
    !    nr2=14,
    !    nr3=14,
    !    nr1s=14,
    !    nr2s=14,
    !    nr3s=14,
    !    nosym=.true.,
    nspin=1,                           ! 1,2,4, "noncolin=.true."
    !    input_dft=                    ! read from PP files.
 /

 &electrons
    mixing_beta = 0.2,              ! 0.7
    conv_thr = 1.0d-12,            ! default=1.0d-06, ! 1.0d-12,1.0d-8
    diagonalization=cg              ! 'cg',!'cg', 'david', !

 /

ATOMIC_SPECIES
 Zr   0.0000 Zr.pbe-nsp-van.UPF
 O    0.0000 O.pbe-van_ak.UPF

ATOMIC_POSITIONS (crystal)
Zr 0.0  0.0  0.0
O  0.25 0.25 0.25
O  0.75 0.75 0.75

K_POINTS (automatic)
3 3 3 0 0 0                             !8 8 8 0 0
0

ph file:----------------------------
 &inputph
  tr2_ph=1.0d-14,             !1.0d-14,     ! threshold for self
consistency=1.0d-12(default)
  alpha_mix(1)=0.2,         ! default=0.7
  prefix='ZrO2',
  iverbosity=1,
  epsil=.true.,
  trans=.true.,                   ! default=true ,
  asr=.true.,
  zue=.true.,                     ! eff charges
  amass(1)=91.22400,
  amass(2)=15.99940,
  outdir='./',
  fildyn='ZrO2.dynG',       ! file where the dyn matrix is written

 /
0.0 0.0 0.0

Effect of  convergences (plane waves, k point sampling, augmentation
functions)
is checked. Forces are zero  and press~1 kbar.

Bulk mod~233 GPa, expt~267Gpa => error~13 %.

Also,in above paper LDA pp was used, but i used USPP.

So in nutshell:---
        i think USPP has to be modified or norm conserving pp should be
used.

I need your comments over this.

Thanks!!

With Regards,
Sonu Kumar

Phd Student
Physics Department
Indian Institute of Technology
Delhi-110016, India
web:-http://www.iitd.ac.in/
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From giannozz at democritos.it  Tue Jul  6 12:24:58 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 6 Jul 2010 12:24:58 +0200
Subject: [Pw_forum] Zone centre phonons in ZrO2 ?
In-Reply-To: <AANLkTimjV1m5fOrGuaKLfbq-97ttA4uc1YyKynKKHj2u@mail.gmail.com>
References: <AANLkTimjV1m5fOrGuaKLfbq-97ttA4uc1YyKynKKHj2u@mail.gmail.com>
Message-ID: <65F96F1D-7F6E-433D-A766-8C262603FA60@democritos.it>


On Jul 6, 2010, at 12:13 , sonu kumar wrote:

>  I am not able to make the accoustical mode=0 cm-1.

nor is anybody else:
http://www.quantum-espresso.org/user_guide/ 
node61.html#SECTION000128020000000000000

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From sd.wang000 at gmail.com  Tue Jul  6 12:56:17 2010
From: sd.wang000 at gmail.com (shudong wang)
Date: Tue, 6 Jul 2010 18:56:17 +0800
Subject: [Pw_forum] GWW of bulk silicon
Message-ID: <AANLkTin_sxmu-G6TIp4_A4KtbuXnRHCMplPcaij0A48S@mail.gmail.com>

Dear all:
I have performed GWW calculation of bulk silicon with PWSCF V4.2. In the
output file there is no the file named 'band.dat'. How can I get the
quasiparticle energy gap??Or which output file include this information
about quasiparticle  energy?

Thanks!
S  D  Wang
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From masoudnahali at live.com  Tue Jul  6 13:09:28 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Tue, 6 Jul 2010 11:09:28 +0000
Subject: [Pw_forum] Is the Graphite surface flat ?
In-Reply-To: <mailman.2189.1278404783.1814.pw_forum@pwscf.org>
References: <mailman.2189.1278404783.1814.pw_forum@pwscf.org>
Message-ID: <COL114-W11C8F81C93C5CC18590BC2A1B20@phx.gbl>


Dear pwscf users

answer to the comments:
(many thanks for your kind attention and help but I could not solve the problem)

to G. Scluuzero: I have used the experimental C-C distance but then I have vc-relaxed the bulk cell and found the new positions. After vc-relax I have used 
these coordinates to "relax" the atoms in the cell with vacuum. Also the innermost layer is not graphite-like and is rippled.  

to D. C. Andera: this pseudopotential reproduces the experimental cell parameter of the bulk correctly and exactly. the predicted cell parameter in z-direction (c) by the other pseudopotentials is not so exact and sometimes, a difference about 1 angstrom compared to experimental value appears.

to G. Mattioli:
london=.true. closes the atoms in the different layers to each other in the relax calculation and did not solve the problem.

Now I am trying to relax a 5-layer sample and see the result. but it has not completed yet. really I do not know the surface of graphite is "ripple" in the nature (experimentally) or not? I appreciate your help.

> On 07/05/2010 08:19 PM, Masoud Nahali wrote:
> > Dear Quantum Espresso users
> >
> > I optimized the graphite bulk and the layers were completely flat. But 
> > when I try to "relax" the graphite surface (slab 2*2 with 3 monolayer) 
> > with 10 angstrom vacuum all the layers become extremely ripple!!! I 
> > can not find the problem. May it related to the number of layers? 
> > anyhow the number of layers is like the bulk. Your help would be a 
> > great gift.
G. Scluuzero:
> > __
> Are you using the experimental or the theoretical value for the in-plane 
> (graphene) C-C distance? I guess that the PBE value is larger than the 
> experimental one, so that if you start from the experimental C-C 
> distance in the graphene layer and let everything relax, then the atoms 
> would like to go towards the theoretical equilibrium distance and this 
> may cause the rippled structure.
> Secondly, I don't know if you can pretend that the innermost layer is 
> graphite bulk-like, having only three layers in total.

Dal Corso Andrea :

> Check the pseudopotential. This is a PP with a core hole for special
> purposes not for standard simulations.

 
 Giuseppe Mattioli :
> Dear Masoud
> apart from the pseudo problem issued by Andrea, you could try the keyword
> london=.true.
> It adds a Van der Waals contribution to total energy and it is likely to 
> improve the interlayer interactions in your system.
> Hope this helps
> Giuseppe 

input file:

&CONTROL
  
calculation  = "relax",
  pseudo_dir   = 
"/home/koa/soft/qe4.2/espresso-4.2/pseudo",
  outdir       = 
"/home/koa/tmp",
  etot_conv_thr= 1.0D-4,
  forc_conv_thr= 1.0D-3,
 
 nstep=150,
  /
&SYSTEM
  ibrav     = 4,
  a         = 
4.9318,
  b         = 4.9318,
  c         = 16.7029,
  
cosab     = -0.5,
  cosac     = 1.0,
  cosbc     = 1.0,
  
nat       = 24,
  ntyp      = 1,
  ecutwfc   = 40.D0,
  
ecutrho   = 400.D0,
  occupations = 'smearing'
  smearing ='mp', 
 
 degauss = 0.01,
  nspin = 2,
  starting_magnetization(1)= 1.0,
 
 /
&ELECTRONS
  conv_thr    = 1.D-6,
  mixing_beta = 0.7D0,
 
 diagonalization = "david",
/
&IONS
 ion_dynamics="bfgs"
/
ATOMIC_SPECIES
C 
 12.0107  C.star1s-pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C   
 0.000000    0.000000    0.000000
C    2.465900    0.000000    
0.000000
C    -1.232950    2.135532    0.000000
C    1.232950    
2.135532    0.000000
C    0.000000    1.423688    0.000000
C    
-1.232950    3.559220    0.000000
C    2.465900    1.423688    
0.000000
C    1.232950    3.559220    0.000000
C    0.000000    
0.000000    3.351450
C    2.465900    0.000000    3.351450
C    
-1.232950    2.135532    3.351450
C    1.232950    2.135532    
3.351450
C    1.232950    0.711844    3.351450
C    0.000000    
2.847376    3.351450
C    3.698850    0.711844    3.351450
C    
2.465900    2.847376    3.351450
C    0.000000    0.000000    
6.702900
C    2.465900    0.000000    6.702900
C    -1.232950    
2.135532    6.702900
C    1.232950    2.135532    6.702900
C    
0.000000    1.423688    6.702900
C    -1.232950    3.559220    
6.702900
C    2.465900    1.423688    6.702900
C    1.232950    
3.559220    6.702900
K_POINTS {automatic}
4 4 1 1 1 1


out
 put (optimized positions):

C        0.000000000  
-0.000000000  -0.686394528
C        2.465900000  -0.003714144  
-0.758610095
C       -1.229733457   2.137389072  -0.758610095
C       
 1.229733457   2.137389072  -0.758610095
C        0.000000000   
1.427474855  -0.213813075
C       -1.229670488   3.557326573  
-0.213813075
C        2.465900000   1.423688000  -0.285079086
C       
 1.229670488   3.557326573  -0.213813075
C       -0.000000000   
0.000000000   3.630366631
C        2.465900000  -0.014904710   
3.544792504
C       -1.220042143   2.142984355   3.544792504
C       
 1.220042143   2.142984355   3.544792504
C        1.220249305   
0.704511250   3.106073641
C        0.000000000   2.847376000   
3.022325711
C        3.711550695   0.704511250   3.106073641
C       
 2.465900000   2.862041499   3.106073641
C        0.000000000   
0.000000000   7.468882932
C        2.465900000   0.008344370   
7.466151214
C       -1.240176436   2.131359815   7.466151214
C       
 1.240176436   2.131359815   7.466151214
C        0.000000000   
1.414904155   6.963129179
C       -1.240557033   3.563611923   
6.963129179
C        2.465900000   1.423688000   6.961528237
C       
 1.240557033   3.563611923   6.963129179



Many Thanks
Masoud Nahali
Sharif
 University of Technology

 		 	   		  
_________________________________________________________________
Hotmail: Free, trusted and rich email service.
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From marzari at MIT.EDU  Tue Jul  6 13:17:38 2010
From: marzari at MIT.EDU (Nicola Marzari)
Date: Tue, 06 Jul 2010 12:17:38 +0100
Subject: [Pw_forum] Is the Graphite surface flat ?
In-Reply-To: <COL114-W11C8F81C93C5CC18590BC2A1B20@phx.gbl>
References: <mailman.2189.1278404783.1814.pw_forum@pwscf.org>
	<COL114-W11C8F81C93C5CC18590BC2A1B20@phx.gbl>
Message-ID: <4C3310D2.5060406@mit.edu>

Masoud Nahali wrote:
>
> *to D. C. Andera: *this pseudopotential reproduces the experimental 
> cell parameter of the bulk correctly and exactly. the predicted cell 
> parameter in z-direction (c) by the other pseudopotentials is not so 
> exact and sometimes, a difference about 1 angstrom compared to 
> experimental value appears.


Dear Masoud,

Andrea Dal Corso has told you that the pseudopotential you are
using is not to be used for standard simulations (it has an artificial
hole in the core, for spectroscopic calculation).

It seemed a perfect, and perfectly clear, answer. Change the 
pseudopotential,
and repeat the calculations. Compare yourself e.g. with Mounet et al,
Phys Rev B (2005) - use the same pseudo, and see if you get *exactly* the
same results.

                nicola



-- 
---------------------------------------------------------------------
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 


From giuseppe.mattioli at mlib.ism.cnr.it  Tue Jul  6 12:22:00 2010
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Tue, 6 Jul 2010 12:22:00 +0200
Subject: [Pw_forum] Is the Graphite surface flat ?
In-Reply-To: <COL114-W11C8F81C93C5CC18590BC2A1B20@phx.gbl>
References: <mailman.2189.1278404783.1814.pw_forum@pwscf.org>
	<COL114-W11C8F81C93C5CC18590BC2A1B20@phx.gbl>
Message-ID: <201007061222.00613.giuseppe.mattioli@mlib.ism.cnr.it>

Dear Masoud

> this pseudopotential reproduces the experimental cell
> parameter of the bulk correctly and exactly. the predicted cell parameter
> in z-direction (c) by the other pseudopotentials is not so exact and
> sometimes, a difference about 1 angstrom compared to experimental value
> appears.

I do not know if you catch the point... You are using a pseudopotential which 
contains a core hole into the C 1s shell. it CAN NOT be used to simulate in a 
proper way the graphite bulk! You will collect (actually, have collected...) 
weird results! You have luckily obtained a better interlayer distance because 
DFT generally fails when dealing with graphite, where the layers are not 
connected by covalent bonds. So, if you use a proper C pseudopotential, you 
achieve poor results for the c parameter in a vc-relax calculation.

> london=.true. closes the atoms in the different layers to each other in the
> relax calculation and did not solve the problem.

Have you tryed to perform a vc-relax calculation of the graphite bulk by using 
a standard pseudopotential (us or nc, as you like) and by switching on the 
london=.true. keyword and, after that, to perform a relax calculation with 
the same pseudo and at the cell a and b parameters you found in the previous 
vc-run in order to optimize your tri-layer graphite slab?

hth

Giuseppe


On Tuesday 06 July 2010 13:09:28 Masoud Nahali wrote:
> Dear pwscf users
>
> answer to the comments:
> (many thanks for your kind attention and help but I could not solve the
> problem)
>
> to G. Scluuzero: I have used the experimental C-C distance but then I have
> vc-relaxed the bulk cell and found the new positions. After vc-relax I have
> used these coordinates to "relax" the atoms in the cell with vacuum. Also
> the innermost layer is not graphite-like and is rippled.
>
> to D. C. Andera: this pseudopotential reproduces the experimental cell
> parameter of the bulk correctly and exactly. the predicted cell parameter
> in z-direction (c) by the other pseudopotentials is not so exact and
> sometimes, a difference about 1 angstrom compared to experimental value
> appears.
>
> to G. Mattioli:
> london=.true. closes the atoms in the different layers to each other in the
> relax calculation and did not solve the problem.
>
> Now I am trying to relax a 5-layer sample and see the result. but it has
> not completed yet. really I do not know the surface of graphite is "ripple"
> in the nature (experimentally) or not? I appreciate your help.
>
> > On 07/05/2010 08:19 PM, Masoud Nahali wrote:
> > > Dear Quantum Espresso users
> > >
> > > I optimized the graphite bulk and the layers were completely flat. But
> > > when I try to "relax" the graphite surface (slab 2*2 with 3 monolayer)
> > > with 10 angstrom vacuum all the layers become extremely ripple!!! I
> > > can not find the problem. May it related to the number of layers?
> > > anyhow the number of layers is like the bulk. Your help would be a
> > > great gift.
>
> G. Scluuzero:
> > > __
> >
> > Are you using the experimental or the theoretical value for the in-plane
> > (graphene) C-C distance? I guess that the PBE value is larger than the
> > experimental one, so that if you start from the experimental C-C
> > distance in the graphene layer and let everything relax, then the atoms
> > would like to go towards the theoretical equilibrium distance and this
> > may cause the rippled structure.
> > Secondly, I don't know if you can pretend that the innermost layer is
> > graphite bulk-like, having only three layers in total.
>
> Dal Corso Andrea :
> > Check the pseudopotential. This is a PP with a core hole for special
> > purposes not for standard simulations.
>
>  Giuseppe Mattioli :
> > Dear Masoud
> > apart from the pseudo problem issued by Andrea, you could try the keyword
> > london=.true.
> > It adds a Van der Waals contribution to total energy and it is likely to
> > improve the interlayer interactions in your system.
> > Hope this helps
> > Giuseppe
>
> input file:
>
> &CONTROL
>
> calculation  = "relax",
>   pseudo_dir   =
> "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
>   outdir       =
> "/home/koa/tmp",
>   etot_conv_thr= 1.0D-4,
>   forc_conv_thr= 1.0D-3,
>
>  nstep=150,
>   /
> &SYSTEM
>   ibrav     = 4,
>   a         =
> 4.9318,
>   b         = 4.9318,
>   c         = 16.7029,
>
> cosab     = -0.5,
>   cosac     = 1.0,
>   cosbc     = 1.0,
>
> nat       = 24,
>   ntyp      = 1,
>   ecutwfc   = 40.D0,
>
> ecutrho   = 400.D0,
>   occupations = 'smearing'
>   smearing ='mp',
>
>  degauss = 0.01,
>   nspin = 2,
>   starting_magnetization(1)= 1.0,
>
>  /
> &ELECTRONS
>   conv_thr    = 1.D-6,
>   mixing_beta = 0.7D0,
>
>  diagonalization = "david",
> /
> &IONS
>  ion_dynamics="bfgs"
> /
> ATOMIC_SPECIES
> C
>  12.0107  C.star1s-pbe-rrkjus.UPF
> ATOMIC_POSITIONS {angstrom}
> C
>  0.000000    0.000000    0.000000
> C    2.465900    0.000000
> 0.000000
> C    -1.232950    2.135532    0.000000
> C    1.232950
> 2.135532    0.000000
> C    0.000000    1.423688    0.000000
> C
> -1.232950    3.559220    0.000000
> C    2.465900    1.423688
> 0.000000
> C    1.232950    3.559220    0.000000
> C    0.000000
> 0.000000    3.351450
> C    2.465900    0.000000    3.351450
> C
> -1.232950    2.135532    3.351450
> C    1.232950    2.135532
> 3.351450
> C    1.232950    0.711844    3.351450
> C    0.000000
> 2.847376    3.351450
> C    3.698850    0.711844    3.351450
> C
> 2.465900    2.847376    3.351450
> C    0.000000    0.000000
> 6.702900
> C    2.465900    0.000000    6.702900
> C    -1.232950
> 2.135532    6.702900
> C    1.232950    2.135532    6.702900
> C
> 0.000000    1.423688    6.702900
> C    -1.232950    3.559220
> 6.702900
> C    2.465900    1.423688    6.702900
> C    1.232950
> 3.559220    6.702900
> K_POINTS {automatic}
> 4 4 1 1 1 1
>
>
> out
>  put (optimized positions):
>
> C        0.000000000
> -0.000000000  -0.686394528
> C        2.465900000  -0.003714144
> -0.758610095
> C       -1.229733457   2.137389072  -0.758610095
> C
>  1.229733457   2.137389072  -0.758610095
> C        0.000000000
> 1.427474855  -0.213813075
> C       -1.229670488   3.557326573
> -0.213813075
> C        2.465900000   1.423688000  -0.285079086
> C
>  1.229670488   3.557326573  -0.213813075
> C       -0.000000000
> 0.000000000   3.630366631
> C        2.465900000  -0.014904710
> 3.544792504
> C       -1.220042143   2.142984355   3.544792504
> C
>  1.220042143   2.142984355   3.544792504
> C        1.220249305
> 0.704511250   3.106073641
> C        0.000000000   2.847376000
> 3.022325711
> C        3.711550695   0.704511250   3.106073641
> C
>  2.465900000   2.862041499   3.106073641
> C        0.000000000
> 0.000000000   7.468882932
> C        2.465900000   0.008344370
> 7.466151214
> C       -1.240176436   2.131359815   7.466151214
> C
>  1.240176436   2.131359815   7.466151214
> C        0.000000000
> 1.414904155   6.963129179
> C       -1.240557033   3.563611923
> 6.963129179
> C        2.465900000   1.423688000   6.961528237
> C
>  1.240557033   3.563611923   6.963129179
>
>
>
> Many Thanks
> Masoud Nahali
> Sharif
>  University of Technology
>
>
> _________________________________________________________________
> Hotmail: Free, trusted and rich email service.
> https://signup.live.com/signup.aspx?id=60969



-- 
********************************************************
- 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 ? ? ? ? ? ? ? ?
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? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ?
? ?E-mail: <giuseppe.mattioli at ism.cnr.it>

From 1009ukumar at gmail.com  Tue Jul  6 14:30:05 2010
From: 1009ukumar at gmail.com (sonu kumar)
Date: Tue, 6 Jul 2010 18:00:05 +0530
Subject: [Pw_forum] Zone centre phonons in ZrO2 ?
Message-ID: <AANLkTinxQzf8qV6EL64Jy1cJEAZNi9RXjZTE0ULnZgAX@mail.gmail.com>

>nor is anybody else:
>http://www.quantum-espresso.org/user_guide/<http://www.quantum-espresso.org/user_guide/>
>node61.html#
>SECTION000128020000000000000

i mean, how can i reduce 14.27 cm-1 near to zero.


Sonu Kumar

Phd Student
Physics Department
Indian Institute of Technology
Delhi-110016, India
web:-http://www.iitd.ac.in/
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From 1009ukumar at gmail.com  Tue Jul  6 14:57:35 2010
From: 1009ukumar at gmail.com (sonu kumar)
Date: Tue, 6 Jul 2010 18:27:35 +0530
Subject: [Pw_forum] Zone centre phonons in ZrO2 ?
In-Reply-To: <AANLkTinxQzf8qV6EL64Jy1cJEAZNi9RXjZTE0ULnZgAX@mail.gmail.com>
References: <AANLkTinxQzf8qV6EL64Jy1cJEAZNi9RXjZTE0ULnZgAX@mail.gmail.com>
Message-ID: <AANLkTikq_WyCZl_YOdVqT0notaVC-OiOaf2xjYy1Khpq@mail.gmail.com>

Dear Sir and QE users,

Thank you very much for your reply. please  ignore my previous mail.

>nor is anybody else:
>http://www.quantum-espresso.org/user_guide/<http://www.quantum-espresso.org/user_guide/>
>node61.html#
>SECTION000128020000000000000

i mean, how can i reduce 14.27 cm-1 near to zero, since i have
done all the convergence tests.

With Kind Regards,
Sonu Kumar

Phd Student
Physics Department
Indian Institute of Technology
Delhi-110016, India
web:-http://www.iitd.ac.in/
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From invite+pkihuu5_ at facebookmail.com  Tue Jul  6 16:17:31 2010
From: invite+pkihuu5_ at facebookmail.com (=?UTF-8?B?w4FsdmFybyBTYW50b3MgQWx2ZXM=?=)
Date: Tue, 6 Jul 2010 07:17:31 -0700
Subject: [Pw_forum] Um convite especial
Message-ID: <7be7505591b9d22451d4475a9632ad2b@www.facebook.com>

Ol? Pw,

Criei um perfil no Facebook com minhas fotos, v?deos e eventos e quero adicionar-lhe aos amigos para que voc? possa ver meu perfil. Primeiro, voc? precisa cadastrar-se no Facebook! Uma vez cadastrado, voc? tamb?m poder? criar seu pr?prio perfil.

Obrigada,
?lvaro

Para se cadastrar no Facebook, clique no link abaixo:
http://www.facebook.com/p.php?i=1693588522&k=ZYL63V65W3TFZJLAUC46T5PQT4GAZU21&r

J? possui uma conta? Adicionar este endere?o de e-mail ? sua conta:
http://www.facebook.com/n/?merge_accounts.php&e=pw_forum%40pwscf.org&c=9102c15d798fdaefa5251573c51f7a28

=======================================
pw_forum at pwscf.org foi convidado a participar do Facebook por ?lvaro Santos Alves. Caso n?o queira receber este tipo de e-mail do Facebook no futuro, clique no link a seguir para cancelar o recebimento. 
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From kazempoor2000 at yahoo.com  Tue Jul  6 20:55:23 2010
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Tue, 6 Jul 2010 11:55:23 -0700 (PDT)
Subject: [Pw_forum] LDA+U character
In-Reply-To: <4C315199.30002@umn.edu>
Message-ID: <498376.26774.qm@web114418.mail.gq1.yahoo.com>

Dear Matteo
Thanks?many for your reply. But my special case is for the defect states (has d-character? )in TiO2 that is in resonance with conduction band and is filled with 2 electrons. When I increased the U from 1 to 4 I saw that the defect state bieng pushed up instead lowering of this state as we expected from theory of LDA+U. Is it true? Moreover?for another defect state that is empty and is above conduction band I saw it? being peshed down in contrast with LDA+U expection. But when I perform GW@ GGA+U I see that the behavior is reversed in which empty states?being pushed up while filled state is?pushing down. what does it mean??is it rational?
thanks a lot

Ali Kazempour



Fritz-Haber-Institut fax : ++49-30-8413 4701
der Max-Planck-Gesellschaft
Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de
D-14 195 Berlin-Dahlem / German

--- On Sun, 7/4/10, Matteo Cococcioni <matteo at umn.edu> wrote:


From: Matteo Cococcioni <matteo at umn.edu>
Subject: Re: [Pw_forum] LDA+U character
To: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Sunday, July 4, 2010, 8:29 PM



dear Ali,

I will try to answer your questions



ali kazempour wrote:
> Dear All
> I have some questions about LDA+U nature. Does U treate like a? 
> perturbation( I know that GW( many body peturbation method) is 
> modified version of LDA+U? if yes why we are allowed to take 
> U=0,1,2,........ up to large values? and why we solve system 
> self-consistent?
>

no, U is not treated as a perturbation. it is more a correction to the 
"standard" DFT energy functional. you can check the relationship between 
+U and GW in the following
reference (probably there are many more):

Anisimov et al, Journal of Physics: Condensed Matter 9, 767 (1997)


> Does U comute with KS-hamiltonian in every U values? I mean? does the 
> order of states remains intact with respect to LDA or they can change?
> and final question:
>

For sure the +U correction to the potential commutes with the 
translation and other symmetries of the crystal.
I think it doesn't commute with the rest of the Hamiltonian (the 
unperturbed DFT one). So if you think to switch on the U from a
U=0 ground state, unless the KS states are already bloch sums of atomic 
orbitals (that would be a very unlikely accident) the +U correction
introduces interactions between them if allowed by symmetry and you are 
going to get a non trivial mixing of them besides a shift in the
eigenvalue. Probably the most significant modifications are going to 
take place for states around the Fermi level that may get more localized.
The ones that are deeper in energy are probably closer to be atomic-like 
already and they will, at most, get a shift in the corresponding 
eigenvalues.

> What is the effect of U on
> 1-empty states in conduction band? (with d-character)
>

pushed up

> 2-half filled states in conduction band(with d-character)
>

depends: see above

> 3-filled- states in conduction band (with d-character)
>

pushed down

> Thanks a lot
>
>
> Ali Kazempour
>
>


hope this helps.

Matteo


>
> Fritz-Haber-Institut fax : ++49-30-8413 4701
> der Max-Planck-Gesellschaft
> Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de
> D-14 195 Berlin-Dahlem / German
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
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From matteo at umn.edu  Tue Jul  6 21:49:17 2010
From: matteo at umn.edu (Matteo Cococcioni)
Date: Tue, 06 Jul 2010 14:49:17 -0500
Subject: [Pw_forum] LDA+U character
In-Reply-To: <498376.26774.qm@web114418.mail.gq1.yahoo.com>
References: <498376.26774.qm@web114418.mail.gq1.yahoo.com>
Message-ID: <4C3388BD.70707@umn.edu>


Hi Ali,

it's difficult to predict what is going to happen during the 
calculation. Maybe with a finite U the system prefers to occupy a state 
that was originally empty
and viceversa. or this could be a local minimum. There are few things 
you could try:
1) start the LDA+U run from an LDA one (e.g. reading potential and 
wavefunctions) instead of beginning from scratch
2) try to constrain the eigenvalue of the occupation matrices to be 1 or 
0 or equal to the value you want and see if the system "likes" the solution
3) as in 1 or 2 keeping occupation fixed for a few iterations and see if 
the system readjusts tself in the solution you suggest.
Of course at the end you will need to compare the total energies of all 
these solutions.
unfortunately with lda+U it's not uncommon that the system gets trapped 
in local minima of the energy.

good luck!

Matteo



ali kazempour wrote:
> Dear Matteo
> Thanks many for your reply. But my special case is for the defect 
> states (has d-character  )in TiO2 that is in resonance with conduction 
> band and is filled with 2 electrons. When I increased the U from 1 to 
> 4 I saw that the defect state bieng pushed up instead lowering of this 
> state as we expected from theory of LDA+U. Is it true? Moreover for 
> another defect state that is empty and is above conduction band I saw 
> it  being peshed down in contrast with LDA+U expection. But when I 
> perform GW@ GGA+U I see that the behavior is reversed in which empty 
> states being pushed up while filled state is pushing down. what does 
> it mean? is it rational?
> thanks a lot
>
> Ali Kazempour
>
>
>
> Fritz-Haber-Institut fax : ++49-30-8413 4701
> der Max-Planck-Gesellschaft
> Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de
> D-14 195 Berlin-Dahlem / German
>
> --- On *Sun, 7/4/10, Matteo Cococcioni /<matteo at umn.edu>/* wrote:
>
>
>     From: Matteo Cococcioni <matteo at umn.edu>
>     Subject: Re: [Pw_forum] LDA+U character
>     To: "PWSCF Forum" <pw_forum at pwscf.org>
>     Date: Sunday, July 4, 2010, 8:29 PM
>
>
>     dear Ali,
>
>     I will try to answer your questions
>
>
>
>     ali kazempour wrote:
>     > Dear All
>     > I have some questions about LDA+U nature. Does U treate like a 
>     > perturbation( I know that GW( many body peturbation method) is
>     > modified version of LDA+U? if yes why we are allowed to take
>     > U=0,1,2,........ up to large values? and why we solve system
>     > self-consistent?
>     >
>
>     no, U is not treated as a perturbation. it is more a correction to
>     the
>     "standard" DFT energy functional. you can check the relationship
>     between
>     +U and GW in the following
>     reference (probably there are many more):
>
>     Anisimov et al, Journal of Physics: Condensed Matter 9, 767 (1997)
>
>
>     > Does U comute with KS-hamiltonian in every U values? I mean 
>     does the
>     > order of states remains intact with respect to LDA or they can
>     change?
>     > and final question:
>     >
>
>     For sure the +U correction to the potential commutes with the
>     translation and other symmetries of the crystal.
>     I think it doesn't commute with the rest of the Hamiltonian (the
>     unperturbed DFT one). So if you think to switch on the U from a
>     U=0 ground state, unless the KS states are already bloch sums of
>     atomic
>     orbitals (that would be a very unlikely accident) the +U correction
>     introduces interactions between them if allowed by symmetry and
>     you are
>     going to get a non trivial mixing of them besides a shift in the
>     eigenvalue. Probably the most significant modifications are going to
>     take place for states around the Fermi level that may get more
>     localized.
>     The ones that are deeper in energy are probably closer to be
>     atomic-like
>     already and they will, at most, get a shift in the corresponding
>     eigenvalues.
>
>     > What is the effect of U on
>     > 1-empty states in conduction band  (with d-character)
>     >
>
>     pushed up
>
>     > 2-half filled states in conduction band(with d-character)
>     >
>
>     depends: see above
>
>     > 3-filled- states in conduction band (with d-character)
>     >
>
>     pushed down
>
>     > Thanks a lot
>     >
>     >
>     > Ali Kazempour
>     >
>     >
>
>
>     hope this helps.
>
>     Matteo
>
>
>     >
>     > Fritz-Haber-Institut fax : ++49-30-8413 4701
>     > der Max-Planck-Gesellschaft
>     > Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de
>     <http://us.mc1144.mail.yahoo.com/mc/compose?to=kazempou at fhi-berlin.mpg.de>
>     > D-14 195 Berlin-Dahlem / German
>     >
>     >
>     >
>     ------------------------------------------------------------------------
>     >
>     > _______________________________________________
>     > Pw_forum mailing list
>     > Pw_forum at pwscf.org
>     <http://us.mc1144.mail.yahoo.com/mc/compose?to=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
>     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org
>     <http://us.mc1144.mail.yahoo.com/mc/compose?to=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
>   


-- 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 


From b.janesko at tcu.edu  Tue Jul  6 22:45:11 2010
From: b.janesko at tcu.edu (Janesko, Benjamin)
Date: Tue, 6 Jul 2010 15:45:11 -0500
Subject: [Pw_forum] Cannot reproduce standard CO/Au(111)
	adsorption	energy
In-Reply-To: <mailman.1873.1277617410.1814.pw_forum@pwscf.org>
References: <mailman.1873.1277617410.1814.pw_forum@pwscf.org>
Message-ID: <E4D0B34D82B12643A3BC9058CC4B3CC6B97078D460@FSMAILCL1.tcu.edu>

> On Jun 25, 2010, at 19:34 , Janesko, Benjamin wrote:
> 
> > Everything looks reasonable in XCrysDen
> 
> and what is the C-Au or O-Au distance? it seems to me that the CO
> molecule is very far away from the gold surface. If so, it is normal to
> find very small binding energies
> 
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine

I've rerun from a different starting geometry, and it only partially solved the problem. The optimum C-Au distance is now 2.24 Angstrom, and the new CO-Au(111) adsorption energy is -0.003978 Rydberg = -0.055 eV. Again, this is much smaller than the PBE CO/Au adsorption energy -0.26 eV from Quantum Espresso calculations reported in PRB 77, 085414 (2008). I've done some potential energy surface scans with rigid CO and Au groups, and haven't seen anything helpful. I've attached my CO/Au(111) input file below. Any further explanations of how my calculations differ from the above reference would be appreciated. Thanks again. 

  - BGJ 

&control
    calculation='relax'
    prefix='coau5-3x3-fcc3',
    pseudo_dir = '/home/bjanesko2/espresso/pseudo//',
    outdir='/tmp/espresso/'
 /
 &system
    ibrav=4,
    celldm(1)=9.439624066,
    celldm(3)=8.0,
    nat=17,
    ntyp=3,
    ecutwfc = 40.0,
    ecutrho = 250.0,
    occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01
 /
 &electrons
    conv_thr=0.0000001
 /
 &ions
   ion_dynamics='bfgs',
   path_thr=0.03
 /
ATOMIC_SPECIES
 Au  196.966  Au.pbe-nd-van.UPF
 C   12.0107  C-pbe-van_ak.UPF
 O   15.9994  O-pbe-van_ak.UPF
ATOMIC_POSITIONS alat
Au      0.000000        0.000000        4.000000  1 1 1
Au      0.500000        0.288675        4.000000  1 1 1
Au      1.000000        0.577350        4.000000  1 1 1
Au      0.333333        0.000000        3.528595  1 1 1
Au      0.833333        0.288675        3.528595  1 1 1
Au      1.333333        0.577350        3.528595  1 1 1
Au      0.666667        0.000000        3.057191  0 0 0
Au      1.166667        0.288675        3.057191  0 0 0
Au      1.666667        0.577350        3.057191  0 0 0
Au      1.000000        0.000000        2.585786  0 0 0
Au      1.500000        0.288675        2.585786  0 0 0
Au      2.000000        0.577350        2.585786  0 0 0
Au      1.333333        0.000000        2.114382  0 0 0
Au      1.833333        0.288675        2.114382  0 0 0
Au      2.333333        0.577350        2.114382  0 0 0
C        0.333333333   0.000000000   4.317809266452 1 1 1
O        0.333333333   0.000000000   4.546726732327 1 1 1
K_POINTS automatic
8 8 1 0 0 0



===================
Benjamin G. Janesko
Assistant Professor
Department of Chemistry
Texas Christian University
Office: SWR 428 
http://personal.tcu.edu/bjanesko/
b.janesko at tcu.edu
Phone: 1-817-257-6202
Fax: 1-817-257-5851 (attn:janesko)
******************

From ttduyle at gmail.com  Tue Jul  6 22:54:04 2010
From: ttduyle at gmail.com (Duy Le)
Date: Tue, 6 Jul 2010 16:54:04 -0400
Subject: [Pw_forum] Cannot reproduce standard CO/Au(111) adsorption
	energy
In-Reply-To: <E4D0B34D82B12643A3BC9058CC4B3CC6B97078D460@FSMAILCL1.tcu.edu>
References: <mailman.1873.1277617410.1814.pw_forum@pwscf.org> 
	<E4D0B34D82B12643A3BC9058CC4B3CC6B97078D460@FSMAILCL1.tcu.edu>
Message-ID: <AANLkTikmEoO4vnXqy_DMQO-jNMjoCxofaixQxSeRtmMv@mail.gmail.com>

How did you evaluate energy of a CO molecule?
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Tue, Jul 6, 2010 at 4:45 PM, Janesko, Benjamin <b.janesko at tcu.edu> wrote:
>> On Jun 25, 2010, at 19:34 , Janesko, Benjamin wrote:
>>
>> > Everything looks reasonable in XCrysDen
>>
>> and what is the C-Au or O-Au distance? it seems to me that the CO
>> molecule is very far away from the gold surface. If so, it is normal to
>> find very small binding energies
>>
>> P.
>> ---
>> Paolo Giannozzi, Dept of Physics, University of Udine
>
> I've rerun from a different starting geometry, and it only partially solved the problem. The optimum C-Au distance is now 2.24 Angstrom, and the new CO-Au(111) adsorption energy is -0.003978 Rydberg = -0.055 eV. Again, this is much smaller than the PBE CO/Au adsorption energy -0.26 eV from Quantum Espresso calculations reported in PRB 77, 085414 (2008). I've done some potential energy surface scans with rigid CO and Au groups, and haven't seen anything helpful. I've attached my CO/Au(111) input file below. Any further explanations of how my calculations differ from the above reference would be appreciated. Thanks again.
>
> ?- BGJ
>
> &control
> ? ?calculation='relax'
> ? ?prefix='coau5-3x3-fcc3',
> ? ?pseudo_dir = '/home/bjanesko2/espresso/pseudo//',
> ? ?outdir='/tmp/espresso/'
> ?/
> ?&system
> ? ?ibrav=4,
> ? ?celldm(1)=9.439624066,
> ? ?celldm(3)=8.0,
> ? ?nat=17,
> ? ?ntyp=3,
> ? ?ecutwfc = 40.0,
> ? ?ecutrho = 250.0,
> ? ?occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01
> ?/
> ?&electrons
> ? ?conv_thr=0.0000001
> ?/
> ?&ions
> ? ion_dynamics='bfgs',
> ? path_thr=0.03
> ?/
> ATOMIC_SPECIES
> ?Au ?196.966 ?Au.pbe-nd-van.UPF
> ?C ? 12.0107 ?C-pbe-van_ak.UPF
> ?O ? 15.9994 ?O-pbe-van_ak.UPF
> ATOMIC_POSITIONS alat
> Au ? ? ?0.000000 ? ? ? ?0.000000 ? ? ? ?4.000000 ?1 1 1
> Au ? ? ?0.500000 ? ? ? ?0.288675 ? ? ? ?4.000000 ?1 1 1
> Au ? ? ?1.000000 ? ? ? ?0.577350 ? ? ? ?4.000000 ?1 1 1
> Au ? ? ?0.333333 ? ? ? ?0.000000 ? ? ? ?3.528595 ?1 1 1
> Au ? ? ?0.833333 ? ? ? ?0.288675 ? ? ? ?3.528595 ?1 1 1
> Au ? ? ?1.333333 ? ? ? ?0.577350 ? ? ? ?3.528595 ?1 1 1
> Au ? ? ?0.666667 ? ? ? ?0.000000 ? ? ? ?3.057191 ?0 0 0
> Au ? ? ?1.166667 ? ? ? ?0.288675 ? ? ? ?3.057191 ?0 0 0
> Au ? ? ?1.666667 ? ? ? ?0.577350 ? ? ? ?3.057191 ?0 0 0
> Au ? ? ?1.000000 ? ? ? ?0.000000 ? ? ? ?2.585786 ?0 0 0
> Au ? ? ?1.500000 ? ? ? ?0.288675 ? ? ? ?2.585786 ?0 0 0
> Au ? ? ?2.000000 ? ? ? ?0.577350 ? ? ? ?2.585786 ?0 0 0
> Au ? ? ?1.333333 ? ? ? ?0.000000 ? ? ? ?2.114382 ?0 0 0
> Au ? ? ?1.833333 ? ? ? ?0.288675 ? ? ? ?2.114382 ?0 0 0
> Au ? ? ?2.333333 ? ? ? ?0.577350 ? ? ? ?2.114382 ?0 0 0
> C ? ? ? ?0.333333333 ? 0.000000000 ? 4.317809266452 1 1 1
> O ? ? ? ?0.333333333 ? 0.000000000 ? 4.546726732327 1 1 1
> K_POINTS automatic
> 8 8 1 0 0 0
>
>
>
> ===================
> Benjamin G. Janesko
> Assistant Professor
> Department of Chemistry
> Texas Christian University
> Office: SWR 428
> http://personal.tcu.edu/bjanesko/
> b.janesko at tcu.edu
> Phone: 1-817-257-6202
> Fax: 1-817-257-5851 (attn:janesko)
> ******************
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From chenhanghuipwscf at gmail.com  Wed Jul  7 04:08:19 2010
From: chenhanghuipwscf at gmail.com (hanghui chen)
Date: Tue, 6 Jul 2010 22:08:19 -0400
Subject: [Pw_forum] GW tutorial
Message-ID: <AANLkTilBT84TZ9YX7vgG7lBsL1qSP5JJ72Dz93RUdlzW@mail.gmail.com>

To QE developers,
     I tried to find some tutorial of GW method in the latest version 4.2
but only found a link http://gww.qe-forge.org/. However, still I could not
find any tutorial on the website gww.qe-forge.org. Anyone could help me?
    Thank you.

Hanghui Chen
Department of Physics
Yale University
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From hqzhou at nju.edu.cn  Wed Jul  7 08:16:55 2010
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Wed, 7 Jul 2010 14:16:55 +0800
Subject: [Pw_forum] Intel Compiler version needed in compiling qe 4.2
Message-ID: <3E2C1B96635548E8AAA1AF69821E83DD@solarflare>

This is just a memo, it may help others.

When I compiled quantum espresso 4.2 by Intel Compilers 10.1.018,
I got an error message about unsupported language features by the 
current compiler. Switching to Intel Compiler 11.1.064, it's OK.

Versions before 4.2 can be compiled by 10.1.018.


Huiqun Zhou
@Earth Sciences, Nanjing University, China
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From sclauzer at sissa.it  Wed Jul  7 09:10:06 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Wed, 7 Jul 2010 09:10:06 +0200
Subject: [Pw_forum] Intel Compiler version needed in compiling qe 4.2
In-Reply-To: <3E2C1B96635548E8AAA1AF69821E83DD@solarflare>
References: <3E2C1B96635548E8AAA1AF69821E83DD@solarflare>
Message-ID: <87E04054-284B-4C88-9487-E962373FD5E6@sissa.it>

Dear Huiqun,

   thanks for having reported this issue, but can you be more precise? Specifically, can you post the error messages from the compiler?

I can tell you that I have recently compiled espresso-4.2 on Linux machines with Intel compilers versions 10.1.025, 11.0.081 and 11.1.056 without any difficulty.


Regads,


GS

Il giorno 07/lug/2010, alle ore 08.16, Huiqun Zhou ha scritto:

> This is just a memo, it may help others.
>  
> When I compiled quantum espresso 4.2 by Intel Compilers 10.1.018,
> I got an error message about unsupported language features by the
> current compiler. Switching to Intel Compiler 11.1.064, it's OK.
>  
> Versions before 4.2 can be compiled by 10.1.018.
>  
>  
> Huiqun Zhou
> @Earth Sciences, Nanjing University, China
> _______________________________________________
> 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

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From padmaja_patnaik at yahoo.co.uk  Wed Jul  7 09:51:56 2010
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Wed, 7 Jul 2010 07:51:56 +0000 (GMT)
Subject: [Pw_forum] Doubt in DOS and PDOS
Message-ID: <226163.19282.qm@web26106.mail.ukl.yahoo.com>

Dear all
I would like to have your suggestions on the following. 
I have calculated DOS and PDOS of a system taking a super cell. Since I have the partial density of states for each atom,  can I integrate over energy upto

Fermi energy  for spin up and spin down separately to get net up and down spins on the atom. The sum will?
give me the total charge on the atom, while the difference will tell you the net magnetic moment of W. 

Regards
Padmaja Patnaik

Research Scholar

Dept of Physics

IIT Bombay

Mumbai, India


      
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From degironc at sissa.it  Wed Jul  7 09:56:26 2010
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 07 Jul 2010 09:56:26 +0200
Subject: [Pw_forum] Doubt in DOS and PDOS
In-Reply-To: <226163.19282.qm@web26106.mail.ukl.yahoo.com>
References: <226163.19282.qm@web26106.mail.ukl.yahoo.com>
Message-ID: <4C34332A.9000907@sissa.it>

correct. and if you look at the end of the standard output produced by 
projwfc.x this is exactly what you find.
stefano

Padmaja Patnaik wrote:
> Dear all
> I would like to have your suggestions on the following. 
> I have calculated DOS and PDOS of a system taking a super cell. Since I have the partial density of states for each atom,  can I integrate over energy upto
>
> Fermi energy  for spin up and spin down separately to get net up and down spins on the atom. The sum will 
> give me the total charge on the atom, while the difference will tell you the net magnetic moment of W. 
>
> 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
>   


From hqzhou at nju.edu.cn  Wed Jul  7 11:58:16 2010
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Wed, 7 Jul 2010 17:58:16 +0800
Subject: [Pw_forum] Intel Compiler version needed in compiling qe 4.2
References: <3E2C1B96635548E8AAA1AF69821E83DD@solarflare>
	<87E04054-284B-4C88-9487-E962373FD5E6@sissa.it>
Message-ID: <DA6211BFFDD24AEC89EC826462D92C9A@solarflare>

Gabriele,

Here are the error messages, it's about format of a module file:

mpiifort -O3 -mcmodel=medium -nomodule -fpp -D__INTEL -D__FFTW3 -D__MPI -D__PARA -I../include -I../iotk/src -I. -c metadyn_io.f90
fortcom: Error: metadyn_io.f90, line 18: The module file cannot be read.  Its format requires a more recent F90 compiler.   [IOTK_MODULE]
  USE iotk_module
------^
fortcom: Error: metadyn_io.f90, line 22: A specification expression object must be a dummy argument, a COMMON block object, or an object accessible through host or use association   [IOTK_ATTLENX]
  CHARACTER(iotk_attlenx) :: attr
------------^
fortcom: Error: metadyn_io.f90, line 22: An automatic object must not appear in the specification part of a module.   [ATTR]
  CHARACTER(iotk_attlenx) :: attr
-----------------------------^
compilation aborted for metadyn_io.f90 (code 1)
make[1]: *** [metadyn_io.o] Error 1
make[1]: Leaving directory `/home/cook/espresso-4.2/Modules'
make: *** [mods] Error 2


Huiqun

  ----- Original Message ----- 
  From: Gabriele Sclauzero 
  To: PWSCF Forum 
  Sent: Wednesday, July 07, 2010 3:10 PM
  Subject: Re: [Pw_forum] Intel Compiler version needed in compiling qe 4.2


  Dear Huiqun,


     thanks for having reported this issue, but can you be more precise? Specifically, can you post the error messages from the compiler?


  I can tell you that I have recently compiled espresso-4.2 on Linux machines with Intel compilers versions 10.1.025, 11.0.081 and 11.1.056 without any difficulty.




  Regads,




  GS


  Il giorno 07/lug/2010, alle ore 08.16, Huiqun Zhou ha scritto:


    This is just a memo, it may help others.

    When I compiled quantum espresso 4.2 by Intel Compilers 10.1.018,
    I got an error message about unsupported language features by the
    current compiler. Switching to Intel Compiler 11.1.064, it's OK.

    Versions before 4.2 can be compiled by 10.1.018.


    Huiqun Zhou
    @Earth Sciences, Nanjing University, China
    _______________________________________________
    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
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From dalcorso at sissa.it  Wed Jul  7 14:06:54 2010
From: dalcorso at sissa.it (Dal Corso Andrea)
Date: Wed, 07 Jul 2010 14:06:54 +0200
Subject: [Pw_forum] Distributing phonon calculations	todifferent	machines
In-Reply-To: <190836FFFC0F494F881E7F2641CC260D@solarflare>
References: <765B4C21072C43D09F65EB033CA2816E@solarflare>
	<06C591EB5EF54E149F166DF90EA58755@solarflare>
	<1278404093.3282.6.camel@dhcp-098.cm.sissa.it>
	<190836FFFC0F494F881E7F2641CC260D@solarflare>
Message-ID: <1278504414.3260.27.camel@dhcp-098.cm.sissa.it>

On Tue, 2010-07-06 at 17:55 +0800, Huiqun Zhou wrote:
> Thanks, Andrea.
> 
> As indicated in the script below, I have copied all files and directories 
> created
> by pw.x run.
> 
> if test ! -d $TMP_DIR/${system}/q${i} ; then
>          mkdir $TMP_DIR/${system}/q${i}
>          cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
> fi
> 

Are the files really there? If all the files are in the directory 
$TMP_DIR/${system}/q${i} there is no reason why the ph.x code stops.
If they are not, I cannot help you. It is not a problem of ph.x.


> BTW, could you please describe more in detail about the newly added 
> information
> in INPUT_PH.html for distributing phonon calculations to cluster? If I set 
> wf_collect
> to true, there should be no relation in nproc and npool between pw.x run and 
> later
> two ph.x runs, right? Taking AlAs in the GRID_example as example, If I want 
> to use
> server with 8 CPU core to do calculations for each one q point (8 servers in 
> total),
> what are the values of images and pools?
> 
> 
You are right, the explanation refer only to the case
wf_collect=.false.. However, image parallelization of ph.x is very
experimental, so be patient. At the moment it divides both q and irreps.
Load balancing on q only is not implemented.  


Andrea 



> Huiqun Zhou
> @Earth Sciences, Nanjing University, China
> 
> ----- Original Message ----- 
> From: "Dal Corso Andrea" <dalcorso at sissa.it>
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Sent: Tuesday, July 06, 2010 4:14 PM
> Subject: Re: [Pw_forum] Distributing phonon calculations todifferent 
> machines
> 
> 
> > On Tue, 2010-07-06 at 12:13 +0800, Huiqun Zhou wrote:
> >> Sorry, I sent an unfinished message.
> >>
> >> When using _ph0{prefix}.phsave, I got the error message shown in the
> >> previous
> >> message.
> >>
> >> Here is the snippet of my script for distributing lsf tasks:
> >>
> >> ......
> >> nq=`sed -n '2p' ./${system}_q${nq1}${nq2}${nq3}.dyn0`
> >>
> >> for ((i=1; i<=$nq; i++))
> >> do
> >>     if test ! -d $TMP_DIR/${system}/q${i} ; then
> >>         mkdir $TMP_DIR/${system}/q${i}
> >>         cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
> >>     fi
> >>     if test ! -d $TMP_DIR/${system}/q${i}/_ph0${system}.phsave ; then
> >>         mkdir $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
> >>         cp -r $TMP_DIR/${system}/_ph0${system}.phsave/*
> >> $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
> >>     fi
> >> done
> >>
> >> for ((i=1; i<=$nq; i++))
> >> do
> >> cat > ${system}_q${i}.in << EOF
> >> phonons of ${system}
> >>  &inputph
> >>   tr2_ph = 1.0d-13,
> >>   alpha_mix(1) = 0.2,
> >>   prefix = '${system}',
> >>   ldisp = .true.,
> >>   recover = .true.
> >>   nq1 = ${nq1}, nq2 = ${nq2}, nq3 = ${nq3}
> >>   start_q = $i, last_q = $i
> >>   outdir = '$TMP_DIR/${system}/q${i}',
> >>   fildyn = '${system}_q${nq1}${nq2}${nq3}.dyn'
> >> ......
> >> EOF
> >> $ECHO "calculation of q point $i"
> >> bsub -a intelmpi -n $processes \
> >>      -R "span[ptile=8]" \
> >>      -J ${r}q${i}anda \
> >>      -oo ${system}_q${i}.out \
> >>      -eo ${system}_q${i}.err \
> >>      $PH_COMMAND -input ./${system}_q${i}.in
> >> done
> >>
> >>
> >> Huiqun Zhou
> >> @Earth Sciences, Nanjing University, China
> >>         ----- Original Message ----- 
> >>         From: Huiqun Zhou
> >>         To: pw_forum at pwscf.org
> >>         Sent: Tuesday, July 06, 2010 12:00 PM
> >>         Subject: [Pw_forum] Distributing phonon calculations to
> >>         different machines
> >>
> >>
> >>         dear developers,
> >>
> >>         Please clarify what directory should be copied
> >>         for distributing phonon calculations
> >>         to different machines,  _ph{prefix}.phsave
> >>         or _ph0{prefix}.phsave? The former is
> >>         described in the manual INPUT_PH.html, the latter is used in
> >>         the GRID_example.
> >>         Although there is no _ph{prefix}.phsave existed after the
> >>         preparatory run with
> >>         start_irr=0 and last_irr=0, using the former works OK at the
> >>         cost of redundant
> >>         calculations.
> >>
> >>              Representation #  1 mode #   1
> >>
> >>              Self-consistent Calculation
> >>
> >>          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >>         %%%%%%%%%%%%%%%%%
> >>              from davcio : error #        25
> >>              error while reading from file
> >>          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >>         %%%%%%%%%%%%%%%%%
> >>
> >>              stopping ...
> >
> > Thank you for the message. I will correct the INPUT_PH documentation.
> > The correct directory is _ph0{prefix}.phsave.
> >
> > This message usually means that you have not copied all the required
> > files. Did you copy all the files produced by pw.x?
> >
> > HTH,
> >
> > Andrea
> >
> >
> >
> >>
> >>         ______________________________________________________________
> >>
> >>         _______________________________________________
> >>         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
> > -- 
> > Andrea Dal Corso                    Tel. 0039-040-3787428
> > SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
> > 34151 Trieste (Italy)               e-mail: dalcorso at sissa.it
> >
> >
> > _______________________________________________
> > 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
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
34151 Trieste (Italy)               e-mail: dalcorso at sissa.it



From giannozz at democritos.it  Wed Jul  7 14:15:22 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 7 Jul 2010 14:15:22 +0200
Subject: [Pw_forum] Intel Compiler version needed in compiling qe 4.2
In-Reply-To: <DA6211BFFDD24AEC89EC826462D92C9A@solarflare>
References: <3E2C1B96635548E8AAA1AF69821E83DD@solarflare>
	<87E04054-284B-4C88-9487-E962373FD5E6@sissa.it>
	<DA6211BFFDD24AEC89EC826462D92C9A@solarflare>
Message-ID: <BEB96C97-B3FE-48CE-9136-8A63517727C6@democritos.it>


On Jul 7, 2010, at 11:58 , Huiqun Zhou wrote:

> Here are the error messages, it's about format of a module file

I have ifort v.10.1.008 and I never saw such an error. Most likely
you have some "leftover" object from a previous compilation.
Remove the iotk directory and recompile.

Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From giannozz at democritos.it  Wed Jul  7 15:32:07 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 7 Jul 2010 15:32:07 +0200
Subject: [Pw_forum] GW tutorial
In-Reply-To: <AANLkTilBT84TZ9YX7vgG7lBsL1qSP5JJ72Dz93RUdlzW@mail.gmail.com>
References: <AANLkTilBT84TZ9YX7vgG7lBsL1qSP5JJ72Dz93RUdlzW@mail.gmail.com>
Message-ID: <A3C1F73B-58B0-4E25-B0F7-D7618D9919D4@democritos.it>


On Jul 7, 2010, at 4:08 , hanghui chen wrote:

>  I could not find any tutorial on the website gww.qe-forge.org

it is currently "missing in action" after the upgrade of the qe-forge
software

> Anyone could help me?

sooner or later the contents of gww.qe-forge.org will resurface.
In the meantime, please search "gww.qe-forge.org" on google
(or whatever search engine you like): at least part of the contents
is in the cached pages

Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From b.janesko at tcu.edu  Wed Jul  7 20:18:12 2010
From: b.janesko at tcu.edu (Janesko, Benjamin)
Date: Wed, 7 Jul 2010 13:18:12 -0500
Subject: [Pw_forum] Cannot reproduce standard CO/Au(111)
In-Reply-To: <mailman.2233.1278449667.1814.pw_forum@pwscf.org>
References: <mailman.2233.1278449667.1814.pw_forum@pwscf.org>
Message-ID: <E4D0B34D82B12643A3BC9058CC4B3CC6B97078D537@FSMAILCL1.tcu.edu>

Duy Lee, 

 Thanks for your reply. I also suspected that CO could be the problem, but I don't see any obvious issues. I put one CO molecule in a big square box (ibrav=1,celldim(1)=40.0), evaluated the energy at the gamma point only, and didn't use Marzari-Vanderbilt screening. All other parameters (ecutwfc,ecutrho,conv_thr) were kept at the values from the slab calculation. The box size seems saturated: increasing it from 20 to 40 au changed the energy by 7*10^(-5) rydberg, which is well below the error in CO-Au binding energy. The C-O bond length was 1.14 Angstrom, which is fairly reasonable for PBE. Any other comments would be appreciated. 

  Best, 

   - BGJ 


From giannozz at democritos.it  Wed Jul  7 22:57:34 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 7 Jul 2010 22:57:34 +0200
Subject: [Pw_forum] Cannot reproduce standard CO/Au(111)
In-Reply-To: <E4D0B34D82B12643A3BC9058CC4B3CC6B97078D537@FSMAILCL1.tcu.edu>
References: <mailman.2233.1278449667.1814.pw_forum@pwscf.org>
	<E4D0B34D82B12643A3BC9058CC4B3CC6B97078D537@FSMAILCL1.tcu.edu>
Message-ID: <EBACBC59-69B9-4C06-B58B-8B1EAE8BEC00@democritos.it>


On Jul 7, 2010, at 20:18 , Janesko, Benjamin wrote:

> Any other comments would be appreciated.


are you sure that you are considering the same adsorption
geometry as in the reference you cited? P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From hqzhou at nju.edu.cn  Thu Jul  8 04:35:48 2010
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Thu, 8 Jul 2010 10:35:48 +0800
Subject: [Pw_forum] Intel Compiler version needed in compiling qe 4.2
References: <3E2C1B96635548E8AAA1AF69821E83DD@solarflare><87E04054-284B-4C88-9487-E962373FD5E6@sissa.it><DA6211BFFDD24AEC89EC826462D92C9A@solarflare>
	<BEB96C97-B3FE-48CE-9136-8A63517727C6@democritos.it>
Message-ID: <92AFA58169794B06B7C4FA74DB077E96@solarflare>

Paolo,

You are right. I don't know when I had an iotk directory created, instead of 
a
soft link to S3DE/iotk. Both "make clean" and "make distclean" failed 
toremove
*.o and *.mod files in the directory.

Sorry to disturb everyone.

huiqun zhou
@earth sciences, nanjing university, china

----- Original Message ----- 
From: "Paolo Giannozzi" <giannozz at democritos.it>
To: "PWSCF Forum" <pw_forum at pwscf.org>
Sent: Wednesday, July 07, 2010 8:15 PM
Subject: Re: [Pw_forum] Intel Compiler version needed in compiling qe 4.2


>
> On Jul 7, 2010, at 11:58 , Huiqun Zhou wrote:
>
>> Here are the error messages, it's about format of a module file
>
> I have ifort v.10.1.008 and I never saw such an error. Most likely
> you have some "leftover" object from a previous compilation.
> Remove the iotk directory and recompile.
>
> Paolo
> ---
> Paolo Giannozzi, Dept of Physics, University of 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 hqzhou at nju.edu.cn  Thu Jul  8 05:11:12 2010
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Thu, 8 Jul 2010 11:11:12 +0800
Subject: [Pw_forum] Distributing phonon calculations	todifferent	machines
References: <765B4C21072C43D09F65EB033CA2816E@solarflare><06C591EB5EF54E149F166DF90EA58755@solarflare><1278404093.3282.6.camel@dhcp-098.cm.sissa.it><190836FFFC0F494F881E7F2641CC260D@solarflare>
	<1278504414.3260.27.camel@dhcp-098.cm.sissa.it>
Message-ID: <EA463310DC694644B6AE0BD8AA9AAD27@solarflare>

Andrea,

I checked the directory, all files are there. See below,

ls /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1/_ph0sill_1.04v0.phsave/
data-file.xml      data-file.xml.2  data-file.xml.5  data-file.xml.8
data-file.xml.1    data-file.xml.3  data-file.xml.6
data-file.xml.1.0  data-file.xml.4  data-file.xml.7

It's a little bit insane, this error only occurred when I compute the
first q point (gamma). ph.x worked fine while calculating other
q points. You can see the script snippet in my second post in this
thread, I had created neccessary directories and copied all needed
files in advance before distributing jobs.

Any ideas?

huiqun zhou
@earth sciences, nanjing university, china

----- Original Message ----- 
From: "Dal Corso Andrea" <dalcorso at sissa.it>
To: "PWSCF Forum" <pw_forum at pwscf.org>
Sent: Wednesday, July 07, 2010 8:06 PM
Subject: Re: [Pw_forum] Distributing phonon calculations todifferent 
machines


> On Tue, 2010-07-06 at 17:55 +0800, Huiqun Zhou wrote:
>> Thanks, Andrea.
>>
>> As indicated in the script below, I have copied all files and directories
>> created
>> by pw.x run.
>>
>> if test ! -d $TMP_DIR/${system}/q${i} ; then
>>          mkdir $TMP_DIR/${system}/q${i}
>>          cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
>> fi
>>
>
> Are the files really there? If all the files are in the directory
> $TMP_DIR/${system}/q${i} there is no reason why the ph.x code stops.
> If they are not, I cannot help you. It is not a problem of ph.x.
>
>
>> BTW, could you please describe more in detail about the newly added
>> information
>> in INPUT_PH.html for distributing phonon calculations to cluster? If I 
>> set
>> wf_collect
>> to true, there should be no relation in nproc and npool between pw.x run 
>> and
>> later
>> two ph.x runs, right? Taking AlAs in the GRID_example as example, If I 
>> want
>> to use
>> server with 8 CPU core to do calculations for each one q point (8 servers 
>> in
>> total),
>> what are the values of images and pools?
>>
>>
> You are right, the explanation refer only to the case
> wf_collect=.false.. However, image parallelization of ph.x is very
> experimental, so be patient. At the moment it divides both q and irreps.
> Load balancing on q only is not implemented.
>
>
> Andrea
>
>
>
>> Huiqun Zhou
>> @Earth Sciences, Nanjing University, China
>>
>> ----- Original Message ----- 
>> From: "Dal Corso Andrea" <dalcorso at sissa.it>
>> To: "PWSCF Forum" <pw_forum at pwscf.org>
>> Sent: Tuesday, July 06, 2010 4:14 PM
>> Subject: Re: [Pw_forum] Distributing phonon calculations todifferent
>> machines
>>
>>
>> > On Tue, 2010-07-06 at 12:13 +0800, Huiqun Zhou wrote:
>> >> Sorry, I sent an unfinished message.
>> >>
>> >> When using _ph0{prefix}.phsave, I got the error message shown in the
>> >> previous
>> >> message.
>> >>
>> >> Here is the snippet of my script for distributing lsf tasks:
>> >>
>> >> ......
>> >> nq=`sed -n '2p' ./${system}_q${nq1}${nq2}${nq3}.dyn0`
>> >>
>> >> for ((i=1; i<=$nq; i++))
>> >> do
>> >>     if test ! -d $TMP_DIR/${system}/q${i} ; then
>> >>         mkdir $TMP_DIR/${system}/q${i}
>> >>         cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
>> >>     fi
>> >>     if test ! -d $TMP_DIR/${system}/q${i}/_ph0${system}.phsave ; then
>> >>         mkdir $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
>> >>         cp -r $TMP_DIR/${system}/_ph0${system}.phsave/*
>> >> $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
>> >>     fi
>> >> done
>> >>
>> >> for ((i=1; i<=$nq; i++))
>> >> do
>> >> cat > ${system}_q${i}.in << EOF
>> >> phonons of ${system}
>> >>  &inputph
>> >>   tr2_ph = 1.0d-13,
>> >>   alpha_mix(1) = 0.2,
>> >>   prefix = '${system}',
>> >>   ldisp = .true.,
>> >>   recover = .true.
>> >>   nq1 = ${nq1}, nq2 = ${nq2}, nq3 = ${nq3}
>> >>   start_q = $i, last_q = $i
>> >>   outdir = '$TMP_DIR/${system}/q${i}',
>> >>   fildyn = '${system}_q${nq1}${nq2}${nq3}.dyn'
>> >> ......
>> >> EOF
>> >> $ECHO "calculation of q point $i"
>> >> bsub -a intelmpi -n $processes \
>> >>      -R "span[ptile=8]" \
>> >>      -J ${r}q${i}anda \
>> >>      -oo ${system}_q${i}.out \
>> >>      -eo ${system}_q${i}.err \
>> >>      $PH_COMMAND -input ./${system}_q${i}.in
>> >> done
>> >>
>> >>
>> >> Huiqun Zhou
>> >> @Earth Sciences, Nanjing University, China
>> >>         ----- Original Message ----- 
>> >>         From: Huiqun Zhou
>> >>         To: pw_forum at pwscf.org
>> >>         Sent: Tuesday, July 06, 2010 12:00 PM
>> >>         Subject: [Pw_forum] Distributing phonon calculations to
>> >>         different machines
>> >>
>> >>
>> >>         dear developers,
>> >>
>> >>         Please clarify what directory should be copied
>> >>         for distributing phonon calculations
>> >>         to different machines,  _ph{prefix}.phsave
>> >>         or _ph0{prefix}.phsave? The former is
>> >>         described in the manual INPUT_PH.html, the latter is used in
>> >>         the GRID_example.
>> >>         Although there is no _ph{prefix}.phsave existed after the
>> >>         preparatory run with
>> >>         start_irr=0 and last_irr=0, using the former works OK at the
>> >>         cost of redundant
>> >>         calculations.
>> >>
>> >>              Representation #  1 mode #   1
>> >>
>> >>              Self-consistent Calculation
>> >>
>> >>          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> >>         %%%%%%%%%%%%%%%%%
>> >>              from davcio : error #        25
>> >>              error while reading from file
>> >>          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> >>         %%%%%%%%%%%%%%%%%
>> >>
>> >>              stopping ...
>> >
>> > Thank you for the message. I will correct the INPUT_PH documentation.
>> > The correct directory is _ph0{prefix}.phsave.
>> >
>> > This message usually means that you have not copied all the required
>> > files. Did you copy all the files produced by pw.x?
>> >
>> > HTH,
>> >
>> > Andrea
>> >
>> >
>> >
>> >>
>> >>         ______________________________________________________________
>> >>
>> >>         _______________________________________________
>> >>         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
>> > -- 
>> > Andrea Dal Corso                    Tel. 0039-040-3787428
>> > SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
>> > 34151 Trieste (Italy)               e-mail: dalcorso at sissa.it
>> >
>> >
>> > _______________________________________________
>> > 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
> -- 
> Andrea Dal Corso                    Tel. 0039-040-3787428
> SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
> 34151 Trieste (Italy)               e-mail: dalcorso at sissa.it
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 



From dalcorso at sissa.it  Thu Jul  8 08:40:53 2010
From: dalcorso at sissa.it (Dal Corso Andrea)
Date: Thu, 08 Jul 2010 08:40:53 +0200
Subject: [Pw_forum] Distributing phonon	calculations	todifferent	machines
In-Reply-To: <EA463310DC694644B6AE0BD8AA9AAD27@solarflare>
References: <765B4C21072C43D09F65EB033CA2816E@solarflare>
	<06C591EB5EF54E149F166DF90EA58755@solarflare>
	<1278404093.3282.6.camel@dhcp-098.cm.sissa.it>
	<190836FFFC0F494F881E7F2641CC260D@solarflare>
	<1278504414.3260.27.camel@dhcp-098.cm.sissa.it>
	<EA463310DC694644B6AE0BD8AA9AAD27@solarflare>
Message-ID: <1278571253.3275.2.camel@dhcp-098.cm.sissa.it>

On Thu, 2010-07-08 at 11:11 +0800, Huiqun Zhou wrote:
> Andrea,
> 
> I checked the directory, all files are there. See below,
> 
> ls /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1/_ph0sill_1.04v0.phsave/
> data-file.xml      data-file.xml.2  data-file.xml.5  data-file.xml.8
> data-file.xml.1    data-file.xml.3  data-file.xml.6
> data-file.xml.1.0  data-file.xml.4  data-file.xml.7
> 

what about the directory /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1 ? 
Are all the files there? and the directory 
/gpfsTMP/hqzhou/tmp/sill_1.04v0/q1/sill_1.04v0.save  ?

Andrea

> It's a little bit insane, this error only occurred when I compute the
> first q point (gamma). ph.x worked fine while calculating other
> q points. You can see the script snippet in my second post in this
> thread, I had created neccessary directories and copied all needed
> files in advance before distributing jobs.
> 
> Any ideas?
> 
> huiqun zhou
> @earth sciences, nanjing university, china
> 
> ----- Original Message ----- 
> From: "Dal Corso Andrea" <dalcorso at sissa.it>
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Sent: Wednesday, July 07, 2010 8:06 PM
> Subject: Re: [Pw_forum] Distributing phonon calculations todifferent 
> machines
> 
> 
> > On Tue, 2010-07-06 at 17:55 +0800, Huiqun Zhou wrote:
> >> Thanks, Andrea.
> >>
> >> As indicated in the script below, I have copied all files and directories
> >> created
> >> by pw.x run.
> >>
> >> if test ! -d $TMP_DIR/${system}/q${i} ; then
> >>          mkdir $TMP_DIR/${system}/q${i}
> >>          cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
> >> fi
> >>
> >
> > Are the files really there? If all the files are in the directory
> > $TMP_DIR/${system}/q${i} there is no reason why the ph.x code stops.
> > If they are not, I cannot help you. It is not a problem of ph.x.
> >
> >
> >> BTW, could you please describe more in detail about the newly added
> >> information
> >> in INPUT_PH.html for distributing phonon calculations to cluster? If I 
> >> set
> >> wf_collect
> >> to true, there should be no relation in nproc and npool between pw.x run 
> >> and
> >> later
> >> two ph.x runs, right? Taking AlAs in the GRID_example as example, If I 
> >> want
> >> to use
> >> server with 8 CPU core to do calculations for each one q point (8 servers 
> >> in
> >> total),
> >> what are the values of images and pools?
> >>
> >>
> > You are right, the explanation refer only to the case
> > wf_collect=.false.. However, image parallelization of ph.x is very
> > experimental, so be patient. At the moment it divides both q and irreps.
> > Load balancing on q only is not implemented.
> >
> >
> > Andrea
> >
> >
> >
> >> Huiqun Zhou
> >> @Earth Sciences, Nanjing University, China
> >>
> >> ----- Original Message ----- 
> >> From: "Dal Corso Andrea" <dalcorso at sissa.it>
> >> To: "PWSCF Forum" <pw_forum at pwscf.org>
> >> Sent: Tuesday, July 06, 2010 4:14 PM
> >> Subject: Re: [Pw_forum] Distributing phonon calculations todifferent
> >> machines
> >>
> >>
> >> > On Tue, 2010-07-06 at 12:13 +0800, Huiqun Zhou wrote:
> >> >> Sorry, I sent an unfinished message.
> >> >>
> >> >> When using _ph0{prefix}.phsave, I got the error message shown in the
> >> >> previous
> >> >> message.
> >> >>
> >> >> Here is the snippet of my script for distributing lsf tasks:
> >> >>
> >> >> ......
> >> >> nq=`sed -n '2p' ./${system}_q${nq1}${nq2}${nq3}.dyn0`
> >> >>
> >> >> for ((i=1; i<=$nq; i++))
> >> >> do
> >> >>     if test ! -d $TMP_DIR/${system}/q${i} ; then
> >> >>         mkdir $TMP_DIR/${system}/q${i}
> >> >>         cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
> >> >>     fi
> >> >>     if test ! -d $TMP_DIR/${system}/q${i}/_ph0${system}.phsave ; then
> >> >>         mkdir $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
> >> >>         cp -r $TMP_DIR/${system}/_ph0${system}.phsave/*
> >> >> $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
> >> >>     fi
> >> >> done
> >> >>
> >> >> for ((i=1; i<=$nq; i++))
> >> >> do
> >> >> cat > ${system}_q${i}.in << EOF
> >> >> phonons of ${system}
> >> >>  &inputph
> >> >>   tr2_ph = 1.0d-13,
> >> >>   alpha_mix(1) = 0.2,
> >> >>   prefix = '${system}',
> >> >>   ldisp = .true.,
> >> >>   recover = .true.
> >> >>   nq1 = ${nq1}, nq2 = ${nq2}, nq3 = ${nq3}
> >> >>   start_q = $i, last_q = $i
> >> >>   outdir = '$TMP_DIR/${system}/q${i}',
> >> >>   fildyn = '${system}_q${nq1}${nq2}${nq3}.dyn'
> >> >> ......
> >> >> EOF
> >> >> $ECHO "calculation of q point $i"
> >> >> bsub -a intelmpi -n $processes \
> >> >>      -R "span[ptile=8]" \
> >> >>      -J ${r}q${i}anda \
> >> >>      -oo ${system}_q${i}.out \
> >> >>      -eo ${system}_q${i}.err \
> >> >>      $PH_COMMAND -input ./${system}_q${i}.in
> >> >> done
> >> >>
> >> >>
> >> >> Huiqun Zhou
> >> >> @Earth Sciences, Nanjing University, China
> >> >>         ----- Original Message ----- 
> >> >>         From: Huiqun Zhou
> >> >>         To: pw_forum at pwscf.org
> >> >>         Sent: Tuesday, July 06, 2010 12:00 PM
> >> >>         Subject: [Pw_forum] Distributing phonon calculations to
> >> >>         different machines
> >> >>
> >> >>
> >> >>         dear developers,
> >> >>
> >> >>         Please clarify what directory should be copied
> >> >>         for distributing phonon calculations
> >> >>         to different machines,  _ph{prefix}.phsave
> >> >>         or _ph0{prefix}.phsave? The former is
> >> >>         described in the manual INPUT_PH.html, the latter is used in
> >> >>         the GRID_example.
> >> >>         Although there is no _ph{prefix}.phsave existed after the
> >> >>         preparatory run with
> >> >>         start_irr=0 and last_irr=0, using the former works OK at the
> >> >>         cost of redundant
> >> >>         calculations.
> >> >>
> >> >>              Representation #  1 mode #   1
> >> >>
> >> >>              Self-consistent Calculation
> >> >>
> >> >>          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >> >>         %%%%%%%%%%%%%%%%%
> >> >>              from davcio : error #        25
> >> >>              error while reading from file
> >> >>          %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >> >>         %%%%%%%%%%%%%%%%%
> >> >>
> >> >>              stopping ...
> >> >
> >> > Thank you for the message. I will correct the INPUT_PH documentation.
> >> > The correct directory is _ph0{prefix}.phsave.
> >> >
> >> > This message usually means that you have not copied all the required
> >> > files. Did you copy all the files produced by pw.x?
> >> >
> >> > HTH,
> >> >
> >> > Andrea
> >> >
> >> >
> >> >
> >> >>
> >> >>         ______________________________________________________________
> >> >>
> >> >>         _______________________________________________
> >> >>         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
> >> > -- 
> >> > Andrea Dal Corso                    Tel. 0039-040-3787428
> >> > SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
> >> > 34151 Trieste (Italy)               e-mail: dalcorso at sissa.it
> >> >
> >> >
> >> > _______________________________________________
> >> > 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
> > -- 
> > Andrea Dal Corso                    Tel. 0039-040-3787428
> > SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
> > 34151 Trieste (Italy)               e-mail: dalcorso at sissa.it
> >
> >
> > _______________________________________________
> > 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
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
34151 Trieste (Italy)               e-mail: dalcorso at sissa.it



From rajanpandey at gmail.com  Thu Jul  8 09:32:43 2010
From: rajanpandey at gmail.com (Rajan Pandey)
Date: Thu, 8 Jul 2010 13:02:43 +0530
Subject: [Pw_forum] Nanoscale Device Modeling Research Positions
Message-ID: <AANLkTinJyUftr-ZWhiTWKzrh9DdQSS4ktnsAYIlfcp7b@mail.gmail.com>

*Nanoscale Device Modeling Research Positions*

*IBM India Semiconductor Research and *

*Development Center, Bangalore, India.*


 The IBM India Semiconductor Research and Development Center invites
applications from outstanding scientists/engineers for multiple positions in
the area of nano science and technology at IBM, Bangalore, India. The
candidates are expected to contribute to the design, theory, and modeling of
next generation semiconductor nanodevices. The research and development work
involves atomistic modeling and Technology-CAD of nano devices.


 *Atomistic/Quantum Effects in Nanodevices :*


 This work involves theoretical understanding of quantum effects in 22 nm
scale devices; these include carrier transport, geometry and material
dependent bandstructure calculations, role of metal and high-k material
interfaces, role of high-k on bandstructure and related phenomena to enable
development of 22 nm scale devices.


 Candidates to be considered for this area are required to have a strong
understanding of semiconductor physics and quantum effects in nanodevices.
The candidates are also expected to have a strong background in devices
physics, electronic structure methods, numerical programming, hands on
experience with ab-initio modeling tools, and computer programming in mixed
language environment.


 *Technology ? CAD : *


 This work involves the improvement and development of an IBM proprietary
tool for the simulation of leading edge semiconductor devices. In
particular, physical and numerical models for carrier transport influenced
by *e.g.*, channel materials, strain, high-k materials, and crystallographic
orientation on device performance will be developed and implemented.


 A comprehensive knowledge of modern device physics is essential to this
position, including both FET and BJT device operation, as well as bulk and
SOI device structures. Also, a good background and understanding of quantum
phenomenon relevant to semiconductor nanodevices is essential.


 *Computer/Software Skills* ? Demonstrated proficiency with C++, C, and Tcl
are required, and experience with team-based large scale software design is
desired. Familiarity with concepts related to numerical solution of PDEs,
and the ability to realize robust numerical implementations of
semiconductor-related physical models in discretized form, are highly
desired. Experience with scientific computation on massively parallel
computer architectures is a plus. Familiarity with the Linux and/or AIX
operating systems, as well as the AFS file system, would be an added plus.


 *Qualifications :*


 Interested applicants for the above regular research positions should have
a Ph.D/MS in Physics, Electrical Engineering, Applied Physics, Computer
Science, or Theoretical Materials Science. Please send your resume to,

kotamurali at in.ibm.com


 *About IBM Semiconductor Research and Development Center :*


 IBM's Semiconductor Research and Development Center is responsible for the
definition and development of industry leading technologies such as Copper
Interconnect, Silicon on Insulator (SOI), High-Performance Logic-Based
Embedded DRAM technologies, and SiGe for RF and analog applications, and
high-k material technologies. SRDC is also the leading organization in
defining the most advanced technologies for the 45 nm and 22 nm nodes,
including research in various aspects of Lithography, strained silicon, and
Magnetic RAM (MRAM). IBM SRDC develops all of IBM?s semiconductor
technologies including SOI, Bulk CMOS, RFCMOS, HV CMOS, SiGe HBT BiCMOS, and
nanodevice technologies. For more information about leadership semiconductor
technologies at IBM, please visit www.ibm.com/chips.


Rajan K. Pandey, Ph.D.

Semiconductor Research & Development Center
India Systems & Technology Engineering Lab
IBM India Pvt. Ltd.
MD3 1F B354
Manyata Embassy  Business Park
Nagawara, Outer Ring Road
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Phone: +91-80-28061262
Email: rajapand at in.ibm.com
Webmail: rajanpandey at gmail.com
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From marsamos at democritos.it  Thu Jul  8 13:07:19 2010
From: marsamos at democritos.it (marsamos at democritos.it)
Date: Thu, 08 Jul 2010 13:07:19 +0200
Subject: [Pw_forum] plumed for ESPRESSO-4.2 available
In-Reply-To: <DC83087E-21EF-4A27-ACF6-99FEF834B482@sissa.it>
References: <20100702145007.szbjy0beqscgg40c@mail.democritos.it>
	<0D6B925C73CB4E1BA5DF2934B90CAB49@solarflare>
	<DC83087E-21EF-4A27-ACF6-99FEF834B482@sissa.it>
Message-ID: <20100708130719.9vpfpv06uwww0sog@mail.democritos.it>

yes indeed. Moreover the Metadynamics that was implemented inside QE 
(not that complete as the one in PLUMED,i .e. less collective variable 
choice) has been eliminated from the current espresso version as it 
wasn't maintained any more.

bests

Layla

Quoting Stefano Baroni <baroni at sissa.it>:

> as far as I understand, plumed is supposed to replave the built-in 
> metadynamics capabilities of QE. the former will hopefully continued 
> to be maintained in the future by a dedicated group of developers, 
> while the latter is probably at a dead end.
> am I correct, Layla?
> see: http://merlino.mi.infn.it/~plumed/PLUMED/Home.html
> SB
>
> On Jul 3, 2010, at 8:10 AM, Huiqun Zhou wrote:
>
>> Layla,
>>
>> Sorry for my ignorance about PLUMED. Could you please explain a little
>> about the differences between metadynamics in PLUMED and that in pwscf?
>>
>> Any reference papers are welcome.
>>
>>
>> Huiqun Zhou
>> @Earth Sciences, Nanjing University, China
>>
>> ----- Original Message -----
>> From: <marsamos at democritos.it>
>> To: <pw_forum at pwscf.org>; <pw_users at pwscf.org>
>> Sent: Friday, July 02, 2010 8:50 PM
>> Subject: [Pw_forum] plumed for ESPRESSO-4.2 available
>>
>>
>>> Dear All, the PLUMED plug-in for metadynamic calculations has been
>>> adapted to Quantum ESPRESSO-4.2 and is available at
>>>
>>> http://qe-forge.org/frs/?group_id=10
>>>
>>> There is also an additional README (README.plumed.xlc_compiler) for
>>> those that uses ibm machines with xlc compiler.
>>>
>>> bests
>>>
>>>
>>> Layla
>>>
>>> --
>>> Dr. L. Martin-Samos
>>> tel. +39 040 3787 429
>>> CNR-DEMOCRITOS and
>>> International School for Advanced Studies (ISAS-SISSA)
>>> via Beirut 2-4
>>> 34151 Trieste Italy
>>>
>>> ----------------------------------------------------------------
>>> This message was sent using IMP, the Internet Messaging Program.
>>>
>>> _______________________________________________
>>> 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
>
> ---
> 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
>
>
>
>
>
>
>
>



-- 
Dr. L. Martin-Samos
tel. +39 040 3787 429
CNR-DEMOCRITOS and
International School for Advanced Studies (ISAS-SISSA)
via Beirut 2-4
34151 Trieste Italy

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.


From masoudnahali at live.com  Thu Jul  8 14:24:16 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Thu, 8 Jul 2010 16:54:16 +0430
Subject: [Pw_forum] Re : Is the Graphite surface flat ?
Message-ID: <AANLkTinWnaW-EQVt7iFwLKpvFfoV9jZ0E8Sm_w2QTScN@mail.gmail.com>

Dear Quantum Espresso Users

I thank Prof. Nicola Marzari and Giuseppe Mattioli for their kind attentions
and helps. I read the paper; it was too useful for me.
Yes, I had a bad mistake in selecting a wrong pseudopotential,


Sincerely Yours
Masoud Nahali
Sharif University of Technology
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From sks.jnc at gmail.com  Thu Jul  8 16:52:48 2010
From: sks.jnc at gmail.com (S. K. S.)
Date: Thu, 8 Jul 2010 16:52:48 +0200
Subject: [Pw_forum] PAW
Message-ID: <AANLkTimLYvj672DAuLVnECHaLJFhVUu8hToXsaL0YnU4@mail.gmail.com>

Dear QE USERS,

I got the following error in the version 4.2 of QE :

Running oxygen test...
 * generating
 * testing
 * testing with spin
done

Generating PAW datasets library
 * Be: (16:35:55)... plotting... done
 * C: (16:35:56)... plotting... done
 * Cl: (16:35:56)...STOP 2
ld1 failed! Aborting...

Is there someone else who also has encountered the same error ?????

Does anyone has PAW data for other elements, for instance, Eu or Sm ?????
Is this possible to use ABINIT PAW inside PWSCF ?????

With best regards,
Saha SK
R&D Assistant
JNCASR
India
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From degironc at sissa.it  Thu Jul  8 17:47:48 2010
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 08 Jul 2010 17:47:48 +0200
Subject: [Pw_forum] PAW
In-Reply-To: <AANLkTimLYvj672DAuLVnECHaLJFhVUu8hToXsaL0YnU4@mail.gmail.com>
References: <AANLkTimLYvj672DAuLVnECHaLJFhVUu8hToXsaL0YnU4@mail.gmail.com>
Message-ID: <4C35F324.6090201@sissa.it>

S. K. S. wrote:
> Dear QE USERS,
>
> I got the following error in the version 4.2 of QE :
>
> Running oxygen test...
>  * generating
>  * testing
>  * testing with spin
> done
>
> Generating PAW datasets library
>  * Be: (16:35:55)... plotting... done
>  * C: (16:35:56)... plotting... done
>  * Cl: (16:35:56)...STOP 2
> ld1 failed! Aborting...
>
> Is there someone else who also has encountered the same error ?????
>
>   
the code now makes additional sanity tests and find that there is a risk 
of producing negative densities ...
increase  rmatch_augfun= 1.6
similarly for Ge.in increase rmatch_augfun= 2.0
> Does anyone has PAW data for other elements, for instance, Eu or Sm ?????
> Is this possible to use ABINIT PAW inside PWSCF ?????
>   
the UPF format of PAW dataset in PWscf is documented.
If someone writes a converter from abinit (or any other code) to UPF it 
should be possible to use them

stefano
> With best regards,
> Saha SK
> R&D Assistant
> JNCASR
> India
>
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From sks.jnc at gmail.com  Thu Jul  8 18:13:28 2010
From: sks.jnc at gmail.com (S. K. S.)
Date: Thu, 8 Jul 2010 18:13:28 +0200
Subject: [Pw_forum] PAW
In-Reply-To: <4C35F324.6090201@sissa.it>
References: <AANLkTimLYvj672DAuLVnECHaLJFhVUu8hToXsaL0YnU4@mail.gmail.com>
	<4C35F324.6090201@sissa.it>
Message-ID: <AANLkTiluK2h_SJaFG5f_yidHZqcxF2AhAqQpbvAkLc9y@mail.gmail.com>

Dear Stefano,

Thanks a lot for your helpful reply. It works fine.
Now the error is  for Li-1s.
 * Li-1s: (18:05:29)...STOP 2
ld1 failed! Aborting...

Should I use  rmatch_augfun= 2.2 in this case ???

In the same way, is it possible to generate Eu PAW using ld1.x ???
With best regards,
Saha SK
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From degironc at sissa.it  Thu Jul  8 18:47:55 2010
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 08 Jul 2010 18:47:55 +0200
Subject: [Pw_forum] PAW
In-Reply-To: <AANLkTiluK2h_SJaFG5f_yidHZqcxF2AhAqQpbvAkLc9y@mail.gmail.com>
References: <AANLkTimLYvj672DAuLVnECHaLJFhVUu8hToXsaL0YnU4@mail.gmail.com>	<4C35F324.6090201@sissa.it>
	<AANLkTiluK2h_SJaFG5f_yidHZqcxF2AhAqQpbvAkLc9y@mail.gmail.com>
Message-ID: <4C36013B.3070706@sissa.it>

S. K. S. wrote:
> Dear Stefano,
>
> Thanks a lot for your helpful reply. It works fine.
> Now the error is  for Li-1s.
>  * Li-1s: (18:05:29)...STOP 2
> ld1 failed! Aborting...
>
> Should I use  rmatch_augfun= 2.2 in this case ???
>   
not really , the error there is another one. I don't know how to solve it.

> In the same way, is it possible to generate Eu PAW using ld1.x ???
>   
as you are experiencing producing a pseudopotential or a PAW dataset is 
a non linear process...
Paolo Giannozzi has recently updated the documentation about 
pseudopotential generation.
I think it would be a good idea to read it carefully.

stefano

> With best regards,
> Saha SK
>
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From giannozz at democritos.it  Thu Jul  8 18:57:46 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 8 Jul 2010 18:57:46 +0200
Subject: [Pw_forum] PAW
In-Reply-To: <4C36013B.3070706@sissa.it>
References: <AANLkTimLYvj672DAuLVnECHaLJFhVUu8hToXsaL0YnU4@mail.gmail.com>	<4C35F324.6090201@sissa.it>
	<AANLkTiluK2h_SJaFG5f_yidHZqcxF2AhAqQpbvAkLc9y@mail.gmail.com>
	<4C36013B.3070706@sissa.it>
Message-ID: <A587A796-4889-435E-8E62-7F1D57888E03@democritos.it>


On Jul 8, 2010, at 18:47 , Stefano de Gironcoli wrote:

> Paolo Giannozzi has recently updated the documentation about
> pseudopotential generation.

unfortunately PG has "started to update" the documentation,
but he is far from having finished...

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From yt203y at yahoo.de  Fri Jul  9 11:00:50 2010
From: yt203y at yahoo.de (Y. Tantirungrotechai)
Date: Fri, 9 Jul 2010 09:00:50 +0000 (GMT)
Subject: [Pw_forum] Postdoc position available at NANOTEC, Thailand
Message-ID: <834953.63638.qm@web25905.mail.ukl.yahoo.com>

Dear all,

A postdoctoral research position focusing on band gap engineering of doped metal oxide for photocatalyst application is immediately available in the nanoscale simulation laboratory, national nanotechnology center (NANOTEC), thailand through NANOTEC Post Doctoral Scholarship Program.

Conditions: 1 year contract with possibility of extension to a second year.
Salary: negotiable based on research experience.

Working place: National Nanotechnology Center (NANOTEC), Thailand (www.nanotec.or.th)

Please see  the atttached pdf file for  further information specific to the position.

Contact person (specific to this position): Dr. Yuthana Tantirungrotechai, Nanoscale simulation laboratory, National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, 130 Thailand Science Park, Paholyothin Rd., Klong Luang, Pathumthani 12120 , Thailand E-mail: yuthana at nanotec.or.th


Yuthana Tantirungrotechai

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From hqzhou at nju.edu.cn  Fri Jul  9 12:24:02 2010
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Fri, 9 Jul 2010 18:24:02 +0800
Subject: [Pw_forum] Distributing phonon	calculations	todifferent	machines
References: <765B4C21072C43D09F65EB033CA2816E@solarflare><06C591EB5EF54E149F166DF90EA58755@solarflare><1278404093.3282.6.camel@dhcp-098.cm.sissa.it><190836FFFC0F494F881E7F2641CC260D@solarflare><1278504414.3260.27.camel@dhcp-098.cm.sissa.it><EA463310DC694644B6AE0BD8AA9AAD27@solarflare>
	<1278571253.3275.2.camel@dhcp-098.cm.sissa.it>
Message-ID: <C9958C27CE744410A6F13D842EAD7FA8@solarflare>

Andrea,

Below are what I have in q1/ directory, it includes everything, I think.

[hqzhou at c01n05 ~]$ ls -l /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1/
total 405184
drwxrwxr-x  2 hqzhou hqzhou    65536 Jul  9 18:17 _ph0sill_1.04v0.phsave
drwxrwxr-x 10 hqzhou hqzhou    65536 Jul  6 07:54 sill_1.04v0.save
-rw-rw-r--  1 hqzhou hqzhou 52060160 Jul  9 18:14 sill_1.04v0.wfc1
-rw-rw-r--  1 hqzhou hqzhou 52224000 Jul  9 18:14 sill_1.04v0.wfc2
-rw-rw-r--  1 hqzhou hqzhou 51773440 Jul  9 18:14 sill_1.04v0.wfc3
-rw-rw-r--  1 hqzhou hqzhou 51814400 Jul  9 18:14 sill_1.04v0.wfc4
-rw-rw-r--  1 hqzhou hqzhou 51855360 Jul  9 18:14 sill_1.04v0.wfc5
-rw-rw-r--  1 hqzhou hqzhou 51363840 Jul  9 18:14 sill_1.04v0.wfc6
-rw-rw-r--  1 hqzhou hqzhou 51896320 Jul  9 18:14 sill_1.04v0.wfc7
-rw-rw-r--  1 hqzhou hqzhou 51609600 Jul  9 18:14 sill_1.04v0.wfc8

Thanks for your help.

huiqun zhou
@earth sciences, nanjing university, china

----- Original Message ----- 
From: "Dal Corso Andrea" <dalcorso at sissa.it>
To: "PWSCF Forum" <pw_forum at pwscf.org>
Sent: Thursday, July 08, 2010 2:40 PM
Subject: Re: [Pw_forum] Distributing phonon calculations todifferent 
machines


> On Thu, 2010-07-08 at 11:11 +0800, Huiqun Zhou wrote:
>> Andrea,
>>
>> I checked the directory, all files are there. See below,
>>
>> ls /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1/_ph0sill_1.04v0.phsave/
>> data-file.xml      data-file.xml.2  data-file.xml.5  data-file.xml.8
>> data-file.xml.1    data-file.xml.3  data-file.xml.6
>> data-file.xml.1.0  data-file.xml.4  data-file.xml.7
>>
>
> what about the directory /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1 ?
> Are all the files there? and the directory
> /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1/sill_1.04v0.save  ?
>
> Andrea
>
>> It's a little bit insane, this error only occurred when I compute the
>> first q point (gamma). ph.x worked fine while calculating other
>> q points. You can see the script snippet in my second post in this
>> thread, I had created neccessary directories and copied all needed
>> files in advance before distributing jobs.
>>
>> Any ideas?
>>
>> huiqun zhou
>> @earth sciences, nanjing university, china
>>
>> ----- Original Message ----- 
>> From: "Dal Corso Andrea" <dalcorso at sissa.it>
>> To: "PWSCF Forum" <pw_forum at pwscf.org>
>> Sent: Wednesday, July 07, 2010 8:06 PM
>> Subject: Re: [Pw_forum] Distributing phonon calculations todifferent
>> machines
>>
>>
>> > On Tue, 2010-07-06 at 17:55 +0800, Huiqun Zhou wrote:
>> >> Thanks, Andrea.
>> >>
>> >> As indicated in the script below, I have copied all files and 
>> >> directories
>> >> created
>> >> by pw.x run.
>> >>
>> >> if test ! -d $TMP_DIR/${system}/q${i} ; then
>> >>          mkdir $TMP_DIR/${system}/q${i}
>> >>          cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
>> >> fi
>> >>
>> >
>> > Are the files really there? If all the files are in the directory
>> > $TMP_DIR/${system}/q${i} there is no reason why the ph.x code stops.
>> > If they are not, I cannot help you. It is not a problem of ph.x.
>> >
>> >
>> >> BTW, could you please describe more in detail about the newly added
>> >> information
>> >> in INPUT_PH.html for distributing phonon calculations to cluster? If I
>> >> set
>> >> wf_collect
>> >> to true, there should be no relation in nproc and npool between pw.x 
>> >> run
>> >> and
>> >> later
>> >> two ph.x runs, right? Taking AlAs in the GRID_example as example, If I
>> >> want
>> >> to use
>> >> server with 8 CPU core to do calculations for each one q point (8 
>> >> servers
>> >> in
>> >> total),
>> >> what are the values of images and pools?
>> >>
>> >>
>> > You are right, the explanation refer only to the case
>> > wf_collect=.false.. However, image parallelization of ph.x is very
>> > experimental, so be patient. At the moment it divides both q and 
>> > irreps.
>> > Load balancing on q only is not implemented.
>> >
>> >
>> > Andrea
>> >
>> >
>> >
>> >> Huiqun Zhou
>> >> @Earth Sciences, Nanjing University, China
>> >>
>> >> ----- Original Message ----- 
>> >> From: "Dal Corso Andrea" <dalcorso at sissa.it>
>> >> To: "PWSCF Forum" <pw_forum at pwscf.org>
>> >> Sent: Tuesday, July 06, 2010 4:14 PM
>> >> Subject: Re: [Pw_forum] Distributing phonon calculations todifferent
>> >> machines
>> >>
>> >>
>> >> > On Tue, 2010-07-06 at 12:13 +0800, Huiqun Zhou wrote:
>> >> >> Sorry, I sent an unfinished message.
>> >> >>
>> >> >> When using _ph0{prefix}.phsave, I got the error message shown in 
>> >> >> the
>> >> >> previous
>> >> >> message.
>> >> >>
>> >> >> Here is the snippet of my script for distributing lsf tasks:
>> >> >>
>> >> >> ......
>> >> >> nq=`sed -n '2p' ./${system}_q${nq1}${nq2}${nq3}.dyn0`
>> >> >>
>> >> >> for ((i=1; i<=$nq; i++))
>> >> >> do
>> >> >>     if test ! -d $TMP_DIR/${system}/q${i} ; then
>> >> >>         mkdir $TMP_DIR/${system}/q${i}
>> >> >>         cp -r $TMP_DIR/${system}/${system}.* 
>> >> >> $TMP_DIR/${system}/q${i}
>> >> >>     fi
>> >> >>     if test ! -d $TMP_DIR/${system}/q${i}/_ph0${system}.phsave ; 
>> >> >> then
>> >> >>         mkdir $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
>> >> >>         cp -r $TMP_DIR/${system}/_ph0${system}.phsave/*
>> >> >> $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
>> >> >>     fi
>> >> >> done
>> >> >>
>> >> >> for ((i=1; i<=$nq; i++))
>> >> >> do
>> >> >> cat > ${system}_q${i}.in << EOF
>> >> >> phonons of ${system}
>> >> >>  &inputph
>> >> >>   tr2_ph = 1.0d-13,
>> >> >>   alpha_mix(1) = 0.2,
>> >> >>   prefix = '${system}',
>> >> >>   ldisp = .true.,
>> >> >>   recover = .true.
>> >> >>   nq1 = ${nq1}, nq2 = ${nq2}, nq3 = ${nq3}
>> >> >>   start_q = $i, last_q = $i
>> >> >>   outdir = '$TMP_DIR/${system}/q${i}',
>> >> >>   fildyn = '${system}_q${nq1}${nq2}${nq3}.dyn'
>> >> >> ......
>> >> >> EOF
>> >> >> $ECHO "calculation of q point $i"
>> >> >> bsub -a intelmpi -n $processes \
>> >> >>      -R "span[ptile=8]" \
>> >> >>      -J ${r}q${i}anda \
>> >> >>      -oo ${system}_q${i}.out \
>> >> >>      -eo ${system}_q${i}.err \
>> >> >>      $PH_COMMAND -input ./${system}_q${i}.in
>> >> >> done
>> >> >>
>> >> >>
>> >> >> Huiqun Zhou
>> >> >> @Earth Sciences, Nanjing University, China
>> >> >>         ----- Original Message ----- 
>> >> >>         From: Huiqun Zhou
>> >> >>         To: pw_forum at pwscf.org
>> >> >>         Sent: Tuesday, July 06, 2010 12:00 PM
>> >> >>         Subject: [Pw_forum] Distributing phonon calculations to
>> >> >>         different machines
>> >> >>
>> >> >>
>> >> >>         dear developers,
>> >> >>
>> >> >>         Please clarify what directory should be copied
>> >> >>         for distributing phonon calculations
>> >> >>         to different machines,  _ph{prefix}.phsave
>> >> >>         or _ph0{prefix}.phsave? The former is
>> >> >>         described in the manual INPUT_PH.html, the latter is used 
>> >> >> in
>> >> >>         the GRID_example.
>> >> >>         Although there is no _ph{prefix}.phsave existed after the
>> >> >>         preparatory run with
>> >> >>         start_irr=0 and last_irr=0, using the former works OK at 
>> >> >> the
>> >> >>         cost of redundant
>> >> >>         calculations.
>> >> >>
>> >> >>              Representation #  1 mode #   1
>> >> >>
>> >> >>              Self-consistent Calculation
>> >> >>
>> >> >> 
>> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> >> >>         %%%%%%%%%%%%%%%%%
>> >> >>              from davcio : error #        25
>> >> >>              error while reading from file
>> >> >> 
>> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> >> >>         %%%%%%%%%%%%%%%%%
>> >> >>
>> >> >>              stopping ...
>> >> >
>> >> > Thank you for the message. I will correct the INPUT_PH 
>> >> > documentation.
>> >> > The correct directory is _ph0{prefix}.phsave.
>> >> >
>> >> > This message usually means that you have not copied all the required
>> >> > files. Did you copy all the files produced by pw.x?
>> >> >
>> >> > HTH,
>> >> >
>> >> > Andrea
>> >> >
>> >> >
>> >> >
>> >> >>
>> >> >> 
>> >> >> ______________________________________________________________
>> >> >>
>> >> >>         _______________________________________________
>> >> >>         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
>> >> > -- 
>> >> > Andrea Dal Corso                    Tel. 0039-040-3787428
>> >> > SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
>> >> > 34151 Trieste (Italy)               e-mail: dalcorso at sissa.it
>> >> >
>> >> >
>> >> > _______________________________________________
>> >> > 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
>> > -- 
>> > Andrea Dal Corso                    Tel. 0039-040-3787428
>> > SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
>> > 34151 Trieste (Italy)               e-mail: dalcorso at sissa.it
>> >
>> >
>> > _______________________________________________
>> > 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
> -- 
> Andrea Dal Corso                    Tel. 0039-040-3787428
> SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
> 34151 Trieste (Italy)               e-mail: dalcorso at sissa.it
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 



From suza.rri at gmail.com  Sun Jul 11 00:07:32 2010
From: suza.rri at gmail.com (Suza W)
Date: Sun, 11 Jul 2010 00:07:32 +0200
Subject: [Pw_forum] SD PSP
Message-ID: <AANLkTin3-Am6klLxcsUDBRpLxO9ALROoeExs3al_9pNr@mail.gmail.com>

Hello All,

Have spin-dependent pesudopotentials (as discussed in Phys. Rev. B 69,
052404, 2004) been incorporated in Quantum Espresso ?
Is it at all justifiable to use a spin-neutral pseudopotential for the
magnetic system ?

Yours sincerely,

 Suza W.
 Ph. D. student
 Institute of Raman Research, India
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From masoudnahali at live.com  Sun Jul 11 09:14:46 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Sun, 11 Jul 2010 11:44:46 +0430
Subject: [Pw_forum] vc-relax time and physical procedure
Message-ID: <AANLkTinfrMpdopsBoLf-37BRqSzvu1vDGbw1U-ETlDVi@mail.gmail.com>

Dear Quantum Espresso Users

I vc-relaxed a (1*1) slab of graphite surface with 3 layers; It takes 20
minutes with parallel running by 4 CPUs. Then I used the exact optimized
cell parameters (obtained from vc-relaxed calculation) to make a (2*2) slab
of graphite with 3 layers and I expected to see the results in a few
minutes. But amazingly it took 17 hours to complete. 48 steps were done in
the calculation for vc-relaxing the cell which have the parameters that had
been optimized before. The cell parameters only change a very bit in the
current vc-relaxing the (2*2) slab. I appreciate if one explain the physical
procedure of vc-relaxing and the reason of the time needed for the
computation.

input file:

CONTROL
  calculation  = "vc-relax",
  pseudo_dir   = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
  outdir       = "/home/koa/tmp",
  etot_conv_thr= 1.0D-4,
  forc_conv_thr= 1.0D-3,
  dt=80,
    /
&SYSTEM
  ibrav     = 4,
  a         = 2.4579,
  b         = 2.4579,
  c         = 16.3069,
  cosab     = -0.5,
  cosac     = 1.0,
  cosbc     = 1.0,
  nat       = 6,
  ntyp      = 1,
  ecutwfc   = 40.D0,
  ecutrho   = 480.D0,
  occupations = 'smearing'
  smearing ='mp',
  degauss = 0.03,
  nspin = 2,
  starting_magnetization(1)= 0.003,
  london=.true.,
  /
&ELECTRONS
  conv_thr    = 1.D-6,
  mixing_beta = 0.7D0,
  diagonalization = "david",
/
&IONS
 ion_dynamics="cg"
/
&CELL
cell_dynamics = 'damp-w',
press = 0.0,
/
ATOMIC_SPECIES
C  12.0107  C.pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
 C                  0.00000000    0.00000000    0.00000000  1 1 0
 C                  0.00000000    1.41908472    0.00000000
 C                  0.00000000    0.00000000    3.15347111
 C                  11.22896342    0.70954236    3.15347111
 C                  0.00000000    0.00000000    6.30694222
 C                  0.00000000    1.41908472    6.30694222
K_POINTS {automatic}
4 4 1 1 1 1 Nahali
SUT
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From member at linkedin.com  Sun Jul 11 22:17:05 2010
From: member at linkedin.com (Timothy Teatro via LinkedIn)
Date: Sun, 11 Jul 2010 13:17:05 -0700 (PDT)
Subject: [Pw_forum] Invitation to connect on LinkedIn
Message-ID: <1165068222.7255337.1278879425573.JavaMail.app@ech3-cdn10.prod>

LinkedIn
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------------------------------------------

veronica,

I'd like to add you to my professional network on LinkedIn.

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Accept invitation from Timothy Teatro
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From 1009ukumar at gmail.com  Mon Jul 12 11:40:52 2010
From: 1009ukumar at gmail.com (sonu kumar)
Date: Mon, 12 Jul 2010 15:10:52 +0530
Subject: [Pw_forum] Thank You : Re: Phonons with non-collinear magnetism ?
	(Dal Corso Andrea)
Message-ID: <AANLkTimKQBJTwzt0Lu8lwcuvN7pk9RmqpsmvwU2in6Ko@mail.gmail.com>

I forgot to say "thank you"

Thank You very much Sir  and Prof.  Andrea Dal Corso.

I am Very very Sorry for this late email.

>What is implemented in PH is written at the beginning of the
>PH/phonon.f90 routine and will be updated when new features will be
>implemented.


  >! ... Presently implemented:
  >! ... dynamical matrix (q/=0)   NC [4], US [4], PAW [4]
  >! ... dynamical matrix (q=0)    NC [5], US [5], PAW [4]
  >! ... dielectric constant       NC [5], US [5], PAW [4]
  >! ... born effective charges    NC [5], US [5], PAW [4]
  >! ... polarizability (iu)       NC [2], US [2]
  >! ... elctron-phonon            NC [3], US [3]
  >! ... electro-optic             NC [1]
  >! ... raman tensor              NC [1]
  >!
  >! NC = norm conserving pseudopotentials
  >! US = ultrasoft pseudopotentials
  >! >PAW = projector augmented-wave
  >! [1] LDA, [2] [1]+GGA, [3] [2]+LSDA/sGGA, [4]
  >[3]+Spin-orbit/nonmagnetic,
  >! [5] [4]+Spin-orbit/magnetic

>Noncollinear at gamma point should work.
>Spin/orbit nonmagnetic should work at gamma and finite q.
>Noncollinear magnetic at finite q is still experimental and there might
>be cases in which it is not working. The phonon interpolation (matdyn in
>particular) is not yet implemented in this case.

>HTH

>Andrea

>Andrea Dal Corso                    Tel. 0039-040-3787428
>SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
>34151 Trieste (Italy)               e-mail: dalcorso at sissa.it



-- 
Sonu Kumar

Phd Student
Physics Department
Indian Institute of Technology
Delhi-110016, India
web:-http://www.iitd.ac.in/
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From rana_nand at yahoo.com  Mon Jul 12 15:33:31 2010
From: rana_nand at yahoo.com (nand)
Date: Mon, 12 Jul 2010 06:33:31 -0700 (PDT)
Subject: [Pw_forum] t and e states of Mn in GaAs
In-Reply-To: <mailman.1.1278488578.30768.pw_forum@pwscf.org>
Message-ID: <636743.59849.qm@web65817.mail.ac4.yahoo.com>

Dear PW Forum,
I have carried out spin dependent DOS and PDOS calculations on Mn dopled GaAs with a 17 atom supercell. From literature i have found that the Mn states get modified in to?three? t and?two? e states in the band gap. Now?I do not know how to extract?information?about these states from my DOS and PDOS plottings. Primariliy i would like to identify these state(bonding and anti bonding)?and their occupancy.?Can some one plz?tell me about these states and any literature available on the web about them.
?
Thanking?in advance.
?
Nand Rana
Research Scholar,
Ranchi University?
India ?


      
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From elie.moujaes at hotmail.co.uk  Mon Jul 12 15:38:13 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Mon, 12 Jul 2010 14:38:13 +0100
Subject: [Pw_forum] Negative pressure during vc-relax
Message-ID: <SNT114-W204F45023A61460D549D8BD3B80@phx.gbl>


Dear All,
 
I am trying to vc-relax a supercell made of 60 Carbon atoms. I have realized that during the iterations, the pressure is getting more negative. For example:
 
Total Force                 Pressure (kbar)
 
3.042645                    -179.66
1.543265                    -189.02
0.871984                    -193.18 
0.686871                    -194.73
0.537735                    -195.49
0.421031                    -195.96
0.366043                    -196.10
 
 
 Is that due to the choice of the pseudopotential, the convergence thresholds or maybe both? I will post a part of the input. Thanks in advance.
 
 

&control
    prefix='GB mgraphene',
    calculation='vc-relax',
    restart_mode='from_scratch',
    pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo/',
    outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/',
    etot_conv_thr = 1.0D-2,
    forc_conv_thr = 1.0D-2,
    tstress = .true.,
    tprnfor = .true.,      
 /
 &system    
    ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =30.0, ecutrho = 120.D0, occupations='smearing', smearing='mp', degauss=0.01
/
 &electrons
    conv_thr=1.D-2,     
    mixing_beta=0.7D0,
    diagonalization='david' 
 /
  &ions
    ion_dynamics = 'bfgs',
   /
  &cell
    cell_dynamics = 'damp-w',
    /
 
CELL_PARAMETERS hexagonal
24.52769   0.00000   0.00000
0.000003   6.614491  0.00000
0.000000   0.000000  10.0000
 
     
ATOMIC_SPECIES
 C  12.0107  C.pz-vbc.UPF
ATOMIC_POSITIONS angstrom
 C   -11.737980    -3.561278     0.000000
 C   -11.057718    -1.211571     0.000000
 C   -12.450000    -7.189838     0.000000
 C   -12.450000    -5.773759     0.000000
 C   -11.329191    -4.926800     0.000000
 C   -10.692399    -2.603942     0.000000
...................
 
As you can see I have used a convergence threshold for electrons of the order of 10^-2 (maybe it should be 10^-5??). The convergence on the forces is 10^-2 which I think is fine. the reason for putting such convergence thresholds is to gain a bit of time especially that i do not think one needs to go further down (than 10^-2  forces wise). Maybe also I am using an inconveninet pseudopotential..Any suggestions...
 
Elie Moujaes
University of Nottingham
Nottingham
NG7 2RD
UK
 		 	   		  
_________________________________________________________________
http://clk.atdmt.com/UKM/go/197222280/direct/01/
We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now
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From giannozz at democritos.it  Mon Jul 12 15:47:27 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 12 Jul 2010 15:47:27 +0200
Subject: [Pw_forum] Negative pressure during vc-relax
In-Reply-To: <SNT114-W204F45023A61460D549D8BD3B80@phx.gbl>
References: <SNT114-W204F45023A61460D549D8BD3B80@phx.gbl>
Message-ID: <4C3B1CEF.1000204@democritos.it>

Elie Moujaes wrote:

> As you can see I have used a convergence threshold for electrons of the 
> order of 10^-2 

way too small

p.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Mon Jul 12 15:48:55 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 12 Jul 2010 15:48:55 +0200
Subject: [Pw_forum] Negative pressure during vc-relax
In-Reply-To: <4C3B1CEF.1000204@democritos.it>
References: <SNT114-W204F45023A61460D549D8BD3B80@phx.gbl>
	<4C3B1CEF.1000204@democritos.it>
Message-ID: <4C3B1D47.7010501@democritos.it>

Paolo Giannozzi wrote:

>> As you can see I have used a convergence threshold for electrons of the 
>> order of 10^-2 
> 
> way too small

I meant: too big, you should use something like the
default (10^{-6})

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From elie.moujaes at hotmail.co.uk  Mon Jul 12 17:21:47 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Mon, 12 Jul 2010 16:21:47 +0100
Subject: [Pw_forum] Negative pressure during vc-relax
In-Reply-To: <4C3B1D47.7010501@democritos.it>
References: <SNT114-W204F45023A61460D549D8BD3B80@phx.gbl>,
	<4C3B1CEF.1000204@democritos.it>, <4C3B1D47.7010501@democritos.it>
Message-ID: <SNT114-W247AA26FB01F7CD88E5819D3B80@phx.gbl>


Dear Profs Gionazzi and Kucukbenli,

 

Thanks very much for your suggestions. I will be revising my input and work accordingly.

 

reagrds

 

Elie Moujaes

University of Nottingham

NG7 2RD 

UK
 
> Date: Mon, 12 Jul 2010 15:48:55 +0200
> From: giannozz at democritos.it
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Negative pressure during vc-relax
> 
> Paolo Giannozzi wrote:
> 
> >> As you can see I have used a convergence threshold for electrons of the 
> >> order of 10^-2 
> > 
> > way too small
> 
> I meant: too big, you should use something like the
> default (10^{-6})
> 
> P.
> -- 
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
_________________________________________________________________
http://clk.atdmt.com/UKM/go/197222280/direct/01/
Do you have a story that started on Hotmail? Tell us now
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From Norbert.Nemec.List at gmx.de  Mon Jul 12 19:24:50 2010
From: Norbert.Nemec.List at gmx.de (Norbert Nemec)
Date: Mon, 12 Jul 2010 19:24:50 +0200
Subject: [Pw_forum] Initial velocities for MD run?
Message-ID: <20100712172450.88740@gmx.net>

Hi there,

is there any way to specify initial velocities for a MD run? From what I see, only thermalization or zero velocites are possible.

Ultimately, I want to do simulate a scattering process of two molecules.

If this is not possible, I would consider implementing it. Does anyone have specific ideas about that?

Greetings,
Norbert
-- 
GMX DSL: Internet-, Telefon- und Handy-Flat ab 19,99 EUR/mtl.  
Bis zu 150 EUR Startguthaben inklusive! http://portal.gmx.net/de/go/dsl

From josepht at chips.ncsu.edu  Mon Jul 12 19:27:15 2010
From: josepht at chips.ncsu.edu (josepht at chips.ncsu.edu)
Date: Mon, 12 Jul 2010 13:27:15 -0400 (EDT)
Subject: [Pw_forum] source of error
In-Reply-To: <55751.152.14.192.32.1277842619.squirrel@chips.ncsu.edu>
References: <55751.152.14.192.32.1277842619.squirrel@chips.ncsu.edu>
Message-ID: <55973.152.14.192.32.1278955635.squirrel@chips.ncsu.edu>

Hello,

I don't see a positive termination of the thread.  Has this been solved?

In your nscf calculation prior to running pw4gww, what was nbnd?  And in your pw4gww
input file, what is num_nbnd_first (size of FCM, corresponding to an FCM energy
cutoff, which is the physical parameter of convergence)?  Reduce num_nbnd_first to
something **below** nbnd.  First try something small, like num_nbnds+10, just to see
if the error goes away.

If this works (you should be able to tell if the error goes away without having to
wait for the job to complete - you will see the line "Out of
matrix_wannier_gamma_big" if the offending grid hurdle is cleared), increase 
num_nbnd_first.  Check for convergence.  If you need so many FCM states (i.e.
approx=nbnd) that the same davcio error is again triggered during tests, you will
have to go back to the nscf calculation and increase nbnd.  Better to start with a
really large value of nbnd, IMO.

Joseph Turnbull
NC State University




>>
>> Dear all
>> Using GWW interface in wannier part(CVS version) I run PW4GWW on its input
>> file m but in the midway I see this error.
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>      task #         9
>>      from davcio : error #        99
>>      error while reading from file
>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>> Where can i find the reason of such error(in which f90 program)?
>>
>>
>> thanks a lot
>>
>>
>>
>> Ali Kazempour
>>
>>
>>
>> Fritz-Haber-Institut fax : ++49-30-8413 4701
>> der Max-Planck-Gesellschaft
>> Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de
>> D-14 195 Berlin-Dahlem / German
>>
>>
>>       _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>



From masoudnahali at live.com  Mon Jul 12 20:24:30 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Mon, 12 Jul 2010 22:54:30 +0430
Subject: [Pw_forum] vc-relax time
Message-ID: <AANLkTimjU0wjc-JXqnSMUXpvcoc1KcCxizemJASloH8j@mail.gmail.com>

Dear Quantum Espresso Users

I vc-relaxed a (1*1) slab of graphite surface with 3 layers; It takes 20
minutes with parallel running by 4 CPUs. Then I used the exact optimized
cell parameters (obtained from vc-relaxed calculation) to make a (2*2) slab
of graphite with 3 layers and I expected to see the results in a few
minutes. But amazingly it took 17 hours to complete. 48 steps were done in
the calculation for vc-relaxing the cell which have the parameters that had
been optimized before. The cell parameters only change a very bit in the
current vc-relaxing the (2*2) slab. I appreciate if one explain the physical
procedure of vc-relaxing and the reason of the time needed for the
computation.

input file:

CONTROL
  calculation  = "vc-relax",
  pseudo_dir   = "/home/koa/soft/qe4.2/
espresso-4.2/pseudo",
  outdir       = "/home/koa/tmp",
  etot_conv_thr= 1.0D-4,
  forc_conv_thr= 1.0D-3,
  dt=80,
    /
&SYSTEM
  ibrav     = 4,
  a         = 2.4579,
  b         = 2.4579,
  c         = 16.3069,
  cosab     = -0.5,
  cosac     = 1.0,
  cosbc     = 1.0,
  nat       = 6,
  ntyp      = 1,
  ecutwfc   = 40.D0,
  ecutrho   = 480.D0,
  occupations = 'smearing'
  smearing ='mp',
  degauss = 0.03,
  nspin = 2,
  starting_magnetization(1)= 0.003,
  london=.true.,
  /
&ELECTRONS
  conv_thr    = 1.D-6,
  mixing_beta = 0.7D0,
  diagonalization = "david",
/
&IONS
 ion_dynamics="cg"
/
&CELL
cell_dynamics = 'damp-w',
press = 0.0,
/
ATOMIC_SPECIES
C  12.0107  C.pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
 C                  0.00000000    0.00000000    0.00000000  1 1 0
 C                  0.00000000    1.41908472    0.00000000
 C                  0.00000000    0.00000000    3.15347111
 C                  11.22896342    0.70954236    3.15347111
 C                  0.00000000    0.00000000    6.30694222
 C                  0.00000000    1.41908472    6.30694222
K_POINTS {automatic}
4 4 1 1 1 1

Sincerely Yours
Masoud Nahali
SUT
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From sks.jnc at gmail.com  Tue Jul 13 01:04:31 2010
From: sks.jnc at gmail.com (S. K. S.)
Date: Tue, 13 Jul 2010 01:04:31 +0200
Subject: [Pw_forum] GGA+U
Message-ID: <AANLkTikvjmPXIdyEO--RY-ZZPR4ZH1yp1dGnYnjYLgEA@mail.gmail.com>

Dear QE Users,

I got the following error while used GGA+U for EuO:

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from set_hubbard_l : error #         1
     pseudopotential not yet inserted
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

Inside source file, I have found that "Eu" is mentioned. However, I do not
understand
the meaning of inserting a pseudopotential.

Thanks in advance for a helpful explanation.

With best regards,

Saha SK
R&D Assistant
JNCASR
Bangalore 560012
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From sclauzer at sissa.it  Tue Jul 13 09:35:19 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 13 Jul 2010 09:35:19 +0200
Subject: [Pw_forum] GGA+U
In-Reply-To: <AANLkTikvjmPXIdyEO--RY-ZZPR4ZH1yp1dGnYnjYLgEA@mail.gmail.com>
References: <AANLkTikvjmPXIdyEO--RY-ZZPR4ZH1yp1dGnYnjYLgEA@mail.gmail.com>
Message-ID: <EF04F553-7F76-4CAD-9662-DAB9C0802FEF@sissa.it>

Dear Saha,

   this question has been asked many times in this forum so far (so many that it could deserve to be included in the FAQ, perhaps), so that you may get your reply by simply browsing in the forum archives. 
Very briefly, the code needs to know which electron manyfold of the "Hubbard" atomic species should be treated with the +U correction and what is the occupation of that electronic shell in the atom. This information has been already hardcoded for the most common elements. Evidently, Eu is not among those. You have to manually modify files set_hubbard_l.f90 and tabd.f90 (in the PW folder) according to what you think reasonable for your case.


Regards,

GS

Il giorno 13/lug/2010, alle ore 01.04, S. K. S. ha scritto:

>   
> 
> Dear QE Users,
> 
> I got the following error while used GGA+U for EuO:
> 
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from set_hubbard_l : error #         1
>      pseudopotential not yet inserted
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
>      stopping ...
> 
> Inside source file, I have found that "Eu" is mentioned. However, I do not understand 
> the meaning of inserting a pseudopotential. 
> 
> Thanks in advance for a helpful explanation.  
> 
> With best regards,
> 
> Saha SK 
> R&D Assistant
> JNCASR
> Bangalore 560012
> 
> _______________________________________________
> 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

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From sclauzer at sissa.it  Tue Jul 13 09:52:15 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 13 Jul 2010 09:52:15 +0200
Subject: [Pw_forum] vc-relax time
In-Reply-To: <AANLkTimjU0wjc-JXqnSMUXpvcoc1KcCxizemJASloH8j@mail.gmail.com>
References: <AANLkTimjU0wjc-JXqnSMUXpvcoc1KcCxizemJASloH8j@mail.gmail.com>
Message-ID: <03BAA7A9-6A95-435B-97AF-1CAC4640449E@sissa.it>

Dear Masoud,

   first I would suggest you to use bfgs as the algorithm for both ions and cell dynamics. Excepted particular cases, it should reach the minimum much faster. 

Also, why do you specify the cell with such an unusual way. You simply need celldm(1) and celldm(3) with ibrav=4 if you want to describe an hexagonal lattice. Other suggestions: your ecutrho looks really large to me, do you really need it. On the other hand, degauss might be too large to describe a spin-polarized system.

Then, are you sure that you have built correctly your supercell? It looks like there are some C-C bonds much shorter that others in the central graphene plane (1.2 instead of 1.4 angs). Please check again your structure. 
In general, you can expect that if you relax the atoms in the supercell some kind of surface-reconstruction may appear, since you leave more freedom to atoms to rearrange in structures with larger periodicity. I don't think this is the case for graphite, but you may find some ripples (as you mentioned in your earlier emails, if I am not wrong) if the C-C bonds are at a distance shorter than the theoretical equilibrium distance (I guess).

HTH

GS


Il giorno 12/lug/2010, alle ore 20.24, Masoud Nahali ha scritto:

> Dear Quantum Espresso Users
> 
> I vc-relaxed a (1*1) slab of graphite surface with 3 layers; It takes 20 minutes with parallel running by 4 CPUs. Then I used the exact optimized cell parameters (obtained from vc-relaxed calculation) to make a (2*2) slab of graphite with 3 layers and I expected to see the results in a few minutes. But amazingly it took 17 hours to complete. 48 steps were done in the calculation for vc-relaxing the cell which have the parameters that had been optimized before. The cell parameters only change a very bit in the current vc-relaxing the (2*2) slab. I appreciate if one explain the physical procedure of vc-relaxing and the reason of the time needed for the computation.
> 
> input file:
> 
> CONTROL
>   calculation  = "vc-relax",
>   pseudo_dir   = "/home/koa/soft/qe4.2/
> espresso-4.2/pseudo",
>   outdir       = "/home/koa/tmp",
>   etot_conv_thr= 1.0D-4,
>   forc_conv_thr= 1.0D-3,
>   dt=80,
>     /
> &SYSTEM
>   ibrav     = 4,
>   a         = 2.4579,
>   b         = 2.4579,
>   c         = 16.3069,
>   cosab     = -0.5,
>   cosac     = 1.0,
>   cosbc     = 1.0,
>   nat       = 6,
>   ntyp      = 1,
>   ecutwfc   = 40.D0,
>   ecutrho   = 480.D0,
>   occupations = 'smearing'
>   smearing ='mp', 
>   degauss = 0.03,
>   nspin = 2,
>   starting_magnetization(1)= 0.003,
>   london=.true.,
>   /
> &ELECTRONS
>   conv_thr    = 1.D-6,
>   mixing_beta = 0.7D0,
>   diagonalization = "david",
> /
> &IONS
>  ion_dynamics="cg"
> /
> &CELL
> cell_dynamics = 'damp-w',
> press = 0.0,
> /
> ATOMIC_SPECIES
> C  12.0107  C.pbe-rrkjus.UPF
> ATOMIC_POSITIONS {angstrom}
>  C                  0.00000000    0.00000000    0.00000000  1 1 0 
>  C                  0.00000000    1.41908472    0.00000000
>  C                  0.00000000    0.00000000    3.15347111
>  C                  11.22896342    0.70954236    3.15347111
>  C                  0.00000000    0.00000000    6.30694222
>  C                  0.00000000    1.41908472    6.30694222
> K_POINTS {automatic}
> 4 4 1 1 1 1 
> 
> Sincerely Yours
> Masoud Nahali
> SUT
> 
> _______________________________________________
> 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

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From julen.azpiroz at gmail.com  Tue Jul 13 11:07:19 2010
From: julen.azpiroz at gmail.com (Julen Ibanez Azpiroz)
Date: Tue, 13 Jul 2010 11:07:19 +0200
Subject: [Pw_forum] Relaxation with Spin-Orbit Coupling
Message-ID: <AANLkTilVg56jene1O5kv-6y-6Ityv-EswBXDzXMqBEH0@mail.gmail.com>

Hello

I would like to make a question to anyone who has experience in using the
spin-orbit coupling (SOC). My problem is as follows:


I relax a structure WITHOUT including SOC by the method damped dynamics:


/
&IONS
 ion_dynamics = "damp",
 pot_extrapolation = "second_order",
 wfc_extrapolation = "second_order",
/
 with the time interval dt=20, and I get a structure where the forces are
<1.0D-4Ry/au. Lets call this structure A.

Now, I include the SOC, and I run an scf calculation with structure A. It
turns out that there are quite big forces, of the order of 0.01Ry/au. The
energy of the unit cell with structure A and SOC included is -207.10202515
Ry.

Then, I try to relax the forces with SOC included with the same method as
before. It relaxes (forces<1.0D-4), but in a structure quite different form
A; lets call this new structure B. The surprising thing is that now, in
structure B, the energy is -207.08231311 Ry, higher than with structure A.
To summarize:

Calculations with SOC included:

          Structure A->  -207.10202515 Ry, forces of the order of 0.01Ry/au
          Structure B->  -207.08231311 Ry, forces <1.0D-4Ry/au

Besides, if I plot the energies of the different structures that go from A
to B when relaxing with SOC included, I see that the energy increases in
each step going from A to B, and the energy of A seems to be in the botttom
of a parabola. So, everything suggests that structure A is the most stable
structure even when SOC is included, except there exist forces. I have
checked the convergence with respect to the cutoff and the k point mesh, and
I have used the same parameters in the calculations without SOC and with
SOC.

I do not know how the forces are calculated when SOC is included, and I do
no know who to trust, the energy or the forces. I will apreciatte very much
any help, thank you in advance


Julen Iba?ez Azpiroz

University of the Basque Country
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From dalcorso at sissa.it  Tue Jul 13 11:17:08 2010
From: dalcorso at sissa.it (Dal Corso Andrea)
Date: Tue, 13 Jul 2010 11:17:08 +0200
Subject: [Pw_forum] Relaxation with Spin-Orbit Coupling
In-Reply-To: <AANLkTilVg56jene1O5kv-6y-6Ityv-EswBXDzXMqBEH0@mail.gmail.com>
References: <AANLkTilVg56jene1O5kv-6y-6Ityv-EswBXDzXMqBEH0@mail.gmail.com>
Message-ID: <1279012628.5185.1.camel@dhcp-098.cm.sissa.it>

Please provide the input. This should not happen.

Andrea




On Tue, 2010-07-13 at 11:07 +0200, Julen Ibanez Azpiroz wrote:
> Hello
> 
> I would like to make a question to anyone who has experience in using
> the spin-orbit coupling (SOC). My problem is as follows:
> 
> 
> I relax a structure WITHOUT including SOC by the method damped
> dynamics:
> 
> 
> /
> &IONS
>  ion_dynamics = "damp",
>  pot_extrapolation = "second_order",
>  wfc_extrapolation = "second_order",
> /
>  with the time interval dt=20, and I get a structure where the forces
> are <1.0D-4Ry/au. Lets call this structure A.
> 
> Now, I include the SOC, and I run an scf calculation with structure A.
> It turns out that there are quite big forces, of the order of
> 0.01Ry/au. The energy of the unit cell with structure A and SOC
> included is -207.10202515 Ry.
> 
> Then, I try to relax the forces with SOC included with the same method
> as before. It relaxes (forces<1.0D-4), but in a structure quite
> different form A; lets call this new structure B. The surprising thing
> is that now, in structure B, the energy is -207.08231311 Ry, higher
> than with structure A. To summarize:
> 
> Calculations with SOC included:
> 
>           Structure A->  -207.10202515 Ry, forces of the order of
> 0.01Ry/au
>           Structure B->  -207.08231311 Ry, forces <1.0D-4Ry/au
> 
> Besides, if I plot the energies of the different structures that go
> from A to B when relaxing with SOC included, I see that the energy
> increases in each step going from A to B, and the energy of A seems to
> be in the botttom of a parabola. So, everything suggests that
> structure A is the most stable structure even when SOC is included,
> except there exist forces. I have checked the convergence with respect
> to the cutoff and the k point mesh, and I have used the same
> parameters in the calculations without SOC and with SOC.
> 
> I do not know how the forces are calculated when SOC is included, and
> I do no know who to trust, the energy or the forces. I will apreciatte
> very much any help, thank you in advance
> 
> 
> Julen Iba?ez Azpiroz
> 
> University of the Basque Country
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
34151 Trieste (Italy)               e-mail: dalcorso at sissa.it



From daijiayu at nudt.edu.cn  Tue Jul 13 11:32:01 2010
From: daijiayu at nudt.edu.cn (jiayudai)
Date: Tue, 13 Jul 2010 17:32:01 +0800
Subject: [Pw_forum] Initial velocities for MD run? (Norbert Nemec)
Message-ID: <JRNHDWXCLYMVKKSKIMNQBSOJGFOG.daijiayu@nudt.edu.cn>



>is there any way to specify initial velocities for a MD run? From what I see, >only thermalization or zero velocites are possible.

If you are using pwscf to do the MD simulations, you can find the initial velocities in "dynamics_modulate.f90" file, where the thermalization is inlcuded. That is to say, the initial velocity has been set according to the Maxwell-Boltzman distribution. If you want to use some other methods, you can change the code.

Jiayu
----------------
-------------------------------------------
Jiayu Dai
Department of Physics
National University of Defense Technology, 
Changsha, 410073, P R China
-----------------------------------------

From davide.ceresoli at materials.ox.ac.uk  Tue Jul 13 11:44:09 2010
From: davide.ceresoli at materials.ox.ac.uk (Davide Ceresoli)
Date: Tue, 13 Jul 2010 10:44:09 +0100
Subject: [Pw_forum] Initial velocities for MD run? (Norbert Nemec)
In-Reply-To: <JRNHDWXCLYMVKKSKIMNQBSOJGFOG.daijiayu@nudt.edu.cn>
References: <JRNHDWXCLYMVKKSKIMNQBSOJGFOG.daijiayu@nudt.edu.cn>
Message-ID: <4C3C3569.9080600@materials.ox.ac.uk>

On 07/13/2010 10:32 AM, jiayudai wrote:
>
>
>> is there any way to specify initial velocities for a MD run? From what I see,>only thermalization or zero velocites are possible.
>
> If you are using pwscf to do the MD simulations, you can find the initial velocities in "dynamics_modulate.f90" file, where the thermalization is inlcuded. That is to say, the initial velocity has been set according to the Maxwell-Boltzman distribution. If you want to use some other methods, you can change the code.
>
> Jiayu
> ----------------
The CPV code has an option to read atomic velocities from input.
However, it has never been clear to me in which units one should
enter the velocities.


Davide


-- 
+----------------------------------------------------------+
   Davide Ceresoli <davide.ceresoli at materials.ox.ac.uk>
   University of Oxford - Department of Materials
   Parks Road, Oxford OX1 3PH, United Kingdom
   Phone: +44-1865-612793
   Mobile:+44-7767-091256, +39-347-1001570
   Skype: dceresoli
+----------------------------------------------------------+

From giuseppe.mattioli at mlib.ism.cnr.it  Tue Jul 13 13:50:33 2010
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Tue, 13 Jul 2010 13:50:33 +0200
Subject: [Pw_forum] GGA+U
In-Reply-To: <EF04F553-7F76-4CAD-9662-DAB9C0802FEF@sissa.it>
References: <AANLkTikvjmPXIdyEO--RY-ZZPR4ZH1yp1dGnYnjYLgEA@mail.gmail.com>
	<EF04F553-7F76-4CAD-9662-DAB9C0802FEF@sissa.it>
Message-ID: <201007131350.33854.giuseppe.mattioli@mlib.ism.cnr.it>

Dear all
I would like to suggest a very simple solution: all the elements could be 
inserted in both the set_hubbard_l.f90 and tabd.f90 files in the most 
straightforward way. If there is anybody who wants something more exotic he 
will change his files by hand.
yours
Giuseppe


On Tuesday 13 July 2010 09:35:19 Gabriele Sclauzero wrote:
> Dear Saha,
>
>    this question has been asked many times in this forum so far (so many
> that it could deserve to be included in the FAQ, perhaps), so that you may
> get your reply by simply browsing in the forum archives. Very briefly, the
> code needs to know which electron manyfold of the "Hubbard" atomic species
> should be treated with the +U correction and what is the occupation of that
> electronic shell in the atom. This information has been already hardcoded
> for the most common elements. Evidently, Eu is not among those. You have to
> manually modify files set_hubbard_l.f90 and tabd.f90 (in the PW folder)
> according to what you think reasonable for your case.
>
>
> Regards,
>
> GS
>
> Il giorno 13/lug/2010, alle ore 01.04, S. K. S. ha scritto:
> > Dear QE Users,
> >
> > I got the following error while used GGA+U for EuO:
> >
> > 
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >%%%%% from set_hubbard_l : error #         1
> >      pseudopotential not yet inserted
> > 
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >%%%%%
> >
> >      stopping ...
> >
> > Inside source file, I have found that "Eu" is mentioned. However, I do
> > not understand the meaning of inserting a pseudopotential.
> >
> > Thanks in advance for a helpful explanation.
> >
> > With best regards,
> >
> > Saha SK
> > R&D Assistant
> > JNCASR
> > Bangalore 560012
> >
> > _______________________________________________
> > 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



-- 
********************************************************
- 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 00016 - Monterotondo Stazione (RM) ? ? ? ? ?
? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ?
? ?E-mail: <giuseppe.mattioli at ism.cnr.it>

From julen.azpiroz at gmail.com  Tue Jul 13 11:59:03 2010
From: julen.azpiroz at gmail.com (Julen Ibanez Azpiroz)
Date: Tue, 13 Jul 2010 11:59:03 +0200
Subject: [Pw_forum] Relaxation with Spin-Orbit Coupling
In-Reply-To: <1279012628.5185.1.camel@dhcp-098.cm.sissa.it>
References: <AANLkTilVg56jene1O5kv-6y-6Ityv-EswBXDzXMqBEH0@mail.gmail.com>
	<1279012628.5185.1.camel@dhcp-098.cm.sissa.it>
Message-ID: <AANLkTik4VqXcMMMD7VSCSqFto650scgfazGpqz5DVz8O@mail.gmail.com>

Hello, thanks for answering,

This is the input:



&control
  calculation='relax',
  dt=10.D0,
  tstress=.true.
  tprnfor=.true.
  verbosity='high',
  restart_mode='from_scratch',
  prefix='si_dt_scalar',
  pseudo_dir='./',
  outdir='/lscratch/azpiroz/relax_sc_pos/'
  forc_conv_thr=1.0D-4 ,
/
&system
  ibrav=12,
  celldm(1)= 7.30868, celldm(2)= 1, celldm(3)= 17.044354, celldm(4)= 0.5,
  nat=26,
  ntyp=2,
  ecutwfc =45,
  noncolin=.true.
  lspinorb=.true.
  occupations='smearing',
  smearing='methfessel-paxton',
  degauss=0.05d0
/
&electrons
  conv_thr=1.0e-6,
  mixing_beta=0.3d0
/
&IONS
 ion_dynamics = "damp",
 pot_extrapolation = "second_order",
 wfc_extrapolation = "second_order",
/
ATOMIC_SPECIES
Si 28.086 Si.rel-pbe-rrkj.UPF
Tl 204.383 Tl.6d_relat_rrkj_nc.UPF
ATOMIC_POSITIONS
Tl        0.000000000  -0.000000003  -5.314678016   0   0   1
Si       -0.500000000  -0.288675141  -4.796768286   0   0   1
Si       -0.500000000  -0.288675106  -4.190720851   0   0   1
Si        0.000000000   0.000000030  -3.983120071   0   0   1
Si        0.000000000   0.000000005  -3.369968660   0   0   1
Si        0.500000000   0.288675142  -3.165727013   0   0   1
Si        0.500000000   0.288675167  -2.553252172   0   0   1
Si       -0.500000000  -0.288675100  -2.348809321   0   0   1
Si       -0.500000000  -0.288675113  -1.736391979   0   0   1
Si        0.000000000   0.000000020  -1.531756523   0   0   1
Si        0.000000000   0.000000029  -0.919281369   0   0   1
Si        0.500000000   0.288675161  -0.714766469   0   0   1
Si        0.500000000   0.288675135  -0.102266533   0   0   1
Si       -0.500000000  -0.288675135   0.102266533   0   0   1
Si       -0.500000000  -0.288675161   0.714766469   0   0   1
Si        0.000000000  -0.000000029   0.919281369   0   0   1
Si        0.000000000  -0.000000020   1.531756523   0   0   1
Si        0.500000000   0.288675113   1.736391979   0   0   1
Si        0.500000000   0.288675100   2.348809321   0   0   1
Si       -0.500000000  -0.288675167   2.553252172   0   0   1
Si       -0.500000000  -0.288675142   3.165727013   0   0   1
Si        0.000000000  -0.000000005   3.369968660   0   0   1
Si        0.000000000  -0.000000030   3.983120071   0   0   1
Si        0.500000000   0.288675106   4.190720851   0   0   1
Si        0.500000000   0.288675141   4.796768286   0   0   1
Tl        0.000000000   0.000000003   5.314678016   0   0   1
K_POINTS {automatic}
16 16 1 0 0 0



This is the structure A, the output gives energy -207.10202515 Ry, but the
forces in the ouput are:


!    total energy              =    -207.10202515 Ry
     Harris-Foulkes estimate   =    -207.10202560 Ry
     estimated scf accuracy    <       0.00000040 Ry

     convergence has been achieved in  19 iterations

     Forces acting on atoms (Ry/au):


     atom   1 type  2   force =     0.00000000    0.00000000   -0.01317569
     atom   2 type  1   force =     0.00000000    0.00000000   -0.00615334
     atom   3 type  1   force =     0.00000000    0.00000000    0.00105593
     atom   4 type  1   force =     0.00000000   -0.00000001   -0.00059280
     atom   5 type  1   force =     0.00000000    0.00000001   -0.00026662
     atom   6 type  1   force =     0.00000000    0.00000000    0.00008699
     atom   7 type  1   force =     0.00000000    0.00000000   -0.00000917
     atom   8 type  1   force =     0.00000000    0.00000000   -0.00002700
     atom   9 type  1   force =     0.00000000    0.00000000    0.00015023
     atom  10 type  1   force =     0.00000000    0.00000000   -0.00013355
     atom  11 type  1   force =     0.00000000    0.00000000    0.00004536
     atom  12 type  1   force =     0.00000000    0.00000000   -0.00005356
     atom  13 type  1   force =     0.00000000    0.00000000    0.00008346
     atom  14 type  1   force =     0.00000000    0.00000000   -0.00008346
     atom  15 type  1   force =     0.00000000    0.00000000    0.00005356
     atom  16 type  1   force =     0.00000000    0.00000000   -0.00004536
     atom  17 type  1   force =     0.00000000    0.00000000    0.00013355
     atom  18 type  1   force =     0.00000000    0.00000000   -0.00015023
     atom  19 type  1   force =     0.00000000    0.00000000    0.00002700
     atom  20 type  1   force =     0.00000000    0.00000000    0.00000917
     atom  21 type  1   force =     0.00000000    0.00000000   -0.00008699
     atom  22 type  1   force =     0.00000000   -0.00000001    0.00026662
     atom  23 type  1   force =     0.00000000    0.00000001    0.00059280
     atom  24 type  1   force =     0.00000000    0.00000000   -0.00105593
     atom  25 type  1   force =     0.00000000    0.00000000    0.00615334
     atom  26 type  2   force =     0.00000000    0.00000000    0.01317569

as I said in the previous email, when SOC was not included the forces were
<1.0D-4Ry/au.

After many cycles it relaxes to structure B:


         1           Tl  tau(  1) = (   0.0000000  -0.0000002  -5.4750706  )
         2           Si  tau(  2) = (  -0.5000000  -0.2886754  -4.9286617  )
         3           Si  tau(  3) = (  -0.5000000  -0.2886751  -4.3089294  )
         4           Si  tau(  4) = (   0.0000000   0.0000001  -4.0900306  )
         5           Si  tau(  5) = (   0.0000000   0.0000005  -3.4646493  )
         6           Si  tau(  6) = (   0.5000000   0.2886757  -3.2486536  )
         7           Si  tau(  7) = (   0.5000000   0.2886753  -2.6244846  )
         8           Si  tau(  8) = (  -0.5000000  -0.2886750  -2.4089562  )
         9           Si  tau(  9) = (  -0.5000000  -0.2886748  -1.7850326  )
        10           Si  tau( 10) = (   0.0000000   0.0000002  -1.5698553  )
        11           Si  tau( 11) = (   0.0000000   0.0000013  -0.9460530  )
        12           Si  tau( 12) = (   0.5000000   0.2886761  -0.7311323  )
        13           Si  tau( 13) = (   0.5000000   0.2886753  -0.1074118  )
        14           Si  tau( 14) = (  -0.5000000  -0.2886753   0.1074118  )
        15           Si  tau( 15) = (  -0.5000000  -0.2886761   0.7311323  )
        16           Si  tau( 16) = (   0.0000000  -0.0000013   0.9460530  )
        17           Si  tau( 17) = (   0.0000000  -0.0000002   1.5698553  )
        18           Si  tau( 18) = (   0.5000000   0.2886748   1.7850326  )
        19           Si  tau( 19) = (   0.5000000   0.2886750   2.4089562  )
        20           Si  tau( 20) = (  -0.5000000  -0.2886753   2.6244846  )
        21           Si  tau( 21) = (  -0.5000000  -0.2886757   3.2486536  )
        22           Si  tau( 22) = (   0.0000000  -0.0000005   3.4646493  )
        23           Si  tau( 23) = (   0.0000000  -0.0000001   4.0900306  )
        24           Si  tau( 24) = (   0.5000000   0.2886751   4.3089294  )
        25           Si  tau( 25) = (   0.5000000   0.2886754   4.9286617  )
        26           Tl  tau( 26) = (   0.0000000   0.0000002   5.4750706  )




were the output says:


!    total energy              =    -207.08193686 Ry
     Harris-Foulkes estimate   =    -207.08193687 Ry
     estimated scf accuracy    <       0.00000002 Ry

    convergence has been achieved in  19 iterations

     Forces acting on atoms (Ry/au):

     atom   1 type  2   force =     0.00000000   -0.00000001   -0.00021452
     atom   2 type  1   force =     0.00000000    0.00000004   -0.00028392
     atom   3 type  1   force =     0.00000000    0.00000004   -0.00036455
     atom   4 type  1   force =     0.00000000   -0.00000001   -0.00029396
     atom   5 type  1   force =     0.00000000   -0.00000002   -0.00029563
     atom   6 type  1   force =     0.00000000   -0.00000008   -0.00028951
     atom   7 type  1   force =     0.00000000    0.00000003   -0.00018682
     atom   8 type  1   force =     0.00000000    0.00000006   -0.00026107
     atom   9 type  1   force =     0.00000000   -0.00000026   -0.00008411
     atom  10 type  1   force =     0.00000000    0.00000037   -0.00018718
     atom  11 type  1   force =     0.00000000   -0.00000073   -0.00001065
     atom  12 type  1   force =     0.00000000    0.00000047   -0.00011851
     atom  13 type  1   force =     0.00000000   -0.00000049    0.00004827
     atom  14 type  1   force =     0.00000000    0.00000049   -0.00004827
     atom  15 type  1   force =     0.00000000   -0.00000047    0.00011851
     atom  16 type  1   force =     0.00000000    0.00000073    0.00001065
     atom  17 type  1   force =     0.00000000   -0.00000037    0.00018718
     atom  18 type  1   force =     0.00000000    0.00000026    0.00008411
     atom  19 type  1   force =     0.00000000   -0.00000006    0.00026107
     atom  20 type  1   force =     0.00000000   -0.00000003    0.00018682
     atom  21 type  1   force =     0.00000000    0.00000008    0.00028951
     atom  22 type  1   force =     0.00000000    0.00000002    0.00029563
     atom  23 type  1   force =     0.00000000    0.00000001    0.00029396
     atom  24 type  1   force =     0.00000000   -0.00000004    0.00036455
     atom  25 type  1   force =     0.00000000   -0.00000004    0.00028392
     atom  26 type  2   force =     0.00000000    0.00000001    0.00021452


This is not forces <1.0D-4Ry/au, but its the most I could converge. The
energy is higher than in the first case. I do not know if it has something
to do with the problem, but the fully relativistic pseudopotentials were
checked in simpler systems giving good results. Thank you in advance

Julen
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From sclauzer at sissa.it  Tue Jul 13 12:07:33 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 13 Jul 2010 12:07:33 +0200
Subject: [Pw_forum] GGA+U
In-Reply-To: <EF04F553-7F76-4CAD-9662-DAB9C0802FEF@sissa.it>
References: <AANLkTikvjmPXIdyEO--RY-ZZPR4ZH1yp1dGnYnjYLgEA@mail.gmail.com>
	<EF04F553-7F76-4CAD-9662-DAB9C0802FEF@sissa.it>
Message-ID: <B4E1CEFE-D90C-4650-ADD8-6F1909EA87AE@sissa.it>


Sorry, I didn't read your mail carefully. Actually the case of Eu is already included in both set_hubbard_l and tabd.

So the problem should be another one.  Which version of QE are you using? If it's not 4.1, please update to 4.2 and try again.

Thanks,

GS

Il giorno 13/lug/2010, alle ore 09.35, Gabriele Sclauzero ha scritto:

> Dear Saha,
> 
>    this question has been asked many times in this forum so far (so many that it could deserve to be included in the FAQ, perhaps), so that you may get your reply by simply browsing in the forum archives. 
> Very briefly, the code needs to know which electron manyfold of the "Hubbard" atomic species should be treated with the +U correction and what is the occupation of that electronic shell in the atom. This information has been already hardcoded for the most common elements. Evidently, Eu is not among those. You have to manually modify files set_hubbard_l.f90 and tabd.f90 (in the PW folder) according to what you think reasonable for your case.
> 
> 
> Regards,
> 
> GS
> 
> Il giorno 13/lug/2010, alle ore 01.04, S. K. S. ha scritto:
> 
>>   
>> 
>> Dear QE Users,
>> 
>> I got the following error while used GGA+U for EuO:
>> 
>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>      from set_hubbard_l : error #         1
>>      pseudopotential not yet inserted
>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> 
>>      stopping ...
>> 
>> Inside source file, I have found that "Eu" is mentioned. However, I do not understand 
>> the meaning of inserting a pseudopotential. 
>> 
>> Thanks in advance for a helpful explanation.  
>> 
>> With best regards,
>> 
>> Saha SK 
>> R&D Assistant
>> JNCASR
>> Bangalore 560012
>> 
>> _______________________________________________
>> 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

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From sclauzer at sissa.it  Tue Jul 13 12:12:41 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 13 Jul 2010 12:12:41 +0200
Subject: [Pw_forum] GGA+U
In-Reply-To: <B4E1CEFE-D90C-4650-ADD8-6F1909EA87AE@sissa.it>
References: <AANLkTikvjmPXIdyEO--RY-ZZPR4ZH1yp1dGnYnjYLgEA@mail.gmail.com>
	<EF04F553-7F76-4CAD-9662-DAB9C0802FEF@sissa.it>
	<B4E1CEFE-D90C-4650-ADD8-6F1909EA87AE@sissa.it>
Message-ID: <50BB577F-F183-41A4-B38F-DAA143121427@sissa.it>


Il giorno 13/lug/2010, alle ore 12.07, Gabriele Sclauzero ha scritto:

> 
> Sorry, I didn't read your mail carefully. Actually the case of Eu is already included in both set_hubbard_l and tabd.
> 
> So the problem should be another one.  Which version of QE are you using? If it's not 4.1, please update to 4.2 and try again.

Sorry, I was actually  meaning "if it's 4.1"...

GS

> 
> Thanks,
> 
> GS
> 
> Il giorno 13/lug/2010, alle ore 09.35, Gabriele Sclauzero ha scritto:
> 
>> Dear Saha,
>> 
>>    this question has been asked many times in this forum so far (so many that it could deserve to be included in the FAQ, perhaps), so that you may get your reply by simply browsing in the forum archives. 
>> Very briefly, the code needs to know which electron manyfold of the "Hubbard" atomic species should be treated with the +U correction and what is the occupation of that electronic shell in the atom. This information has been already hardcoded for the most common elements. Evidently, Eu is not among those. You have to manually modify files set_hubbard_l.f90 and tabd.f90 (in the PW folder) according to what you think reasonable for your case.
>> 
>> 
>> Regards,
>> 
>> GS
>> 
>> Il giorno 13/lug/2010, alle ore 01.04, S. K. S. ha scritto:
>> 
>>>   
>>> 
>>> Dear QE Users,
>>> 
>>> I got the following error while used GGA+U for EuO:
>>> 
>>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>      from set_hubbard_l : error #         1
>>>      pseudopotential not yet inserted
>>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>> 
>>>      stopping ...
>>> 
>>> Inside source file, I have found that "Eu" is mentioned. However, I do not understand 
>>> the meaning of inserting a pseudopotential. 
>>> 
>>> Thanks in advance for a helpful explanation.  
>>> 
>>> With best regards,
>>> 
>>> Saha SK 
>>> R&D Assistant
>>> JNCASR
>>> Bangalore 560012
>>> 
>>> _______________________________________________
>>> 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


? Gabriele Sclauzero, EPFL SB ITP CSEA
   PH H2 462, Station 3, CH-1015 Lausanne

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From dalcorso at sissa.it  Tue Jul 13 12:23:15 2010
From: dalcorso at sissa.it (Dal Corso Andrea)
Date: Tue, 13 Jul 2010 12:23:15 +0200
Subject: [Pw_forum] Relaxation with Spin-Orbit Coupling
In-Reply-To: <AANLkTik4VqXcMMMD7VSCSqFto650scgfazGpqz5DVz8O@mail.gmail.com>
References: <AANLkTilVg56jene1O5kv-6y-6Ityv-EswBXDzXMqBEH0@mail.gmail.com>
	<1279012628.5185.1.camel@dhcp-098.cm.sissa.it>
	<AANLkTik4VqXcMMMD7VSCSqFto650scgfazGpqz5DVz8O@mail.gmail.com>
Message-ID: <1279016595.5185.5.camel@dhcp-098.cm.sissa.it>

Difficult to say. Are you sure about the Tl PP. A ghost in particular
could cause the effects that you report. 

Andrea  


On Tue, 2010-07-13 at 11:59 +0200, Julen Ibanez Azpiroz wrote:
> Hello, thanks for answering,
> 
> This is the input:
> 
> 
> 
> &control
>   calculation='relax',
>   dt=10.D0,
>   tstress=.true.
>   tprnfor=.true.
>   verbosity='high',
>   restart_mode='from_scratch',
>   prefix='si_dt_scalar',
>   pseudo_dir='./',
>   outdir='/lscratch/azpiroz/relax_sc_pos/'
>   forc_conv_thr=1.0D-4 ,
> /
> &system
>   ibrav=12,
>   celldm(1)= 7.30868, celldm(2)= 1, celldm(3)= 17.044354, celldm(4)=
> 0.5,
>   nat=26,
>   ntyp=2,
>   ecutwfc =45,
>   noncolin=.true.
>   lspinorb=.true.
>   occupations='smearing',
>   smearing='methfessel-paxton',
>   degauss=0.05d0
> /
> &electrons
>   conv_thr=1.0e-6,
>   mixing_beta=0.3d0
> /
> &IONS
>  ion_dynamics = "damp",
>  pot_extrapolation = "second_order",
>  wfc_extrapolation = "second_order",
> /
> ATOMIC_SPECIES
> Si 28.086 Si.rel-pbe-rrkj.UPF
> Tl 204.383 Tl.6d_relat_rrkj_nc.UPF
> ATOMIC_POSITIONS
> Tl        0.000000000  -0.000000003  -5.314678016   0   0   1
> Si       -0.500000000  -0.288675141  -4.796768286   0   0   1
> Si       -0.500000000  -0.288675106  -4.190720851   0   0   1
> Si        0.000000000   0.000000030  -3.983120071   0   0   1
> Si        0.000000000   0.000000005  -3.369968660   0   0   1
> Si        0.500000000   0.288675142  -3.165727013   0   0   1
> Si        0.500000000   0.288675167  -2.553252172   0   0   1
> Si       -0.500000000  -0.288675100  -2.348809321   0   0   1
> Si       -0.500000000  -0.288675113  -1.736391979   0   0   1
> Si        0.000000000   0.000000020  -1.531756523   0   0   1
> Si        0.000000000   0.000000029  -0.919281369   0   0   1
> Si        0.500000000   0.288675161  -0.714766469   0   0   1
> Si        0.500000000   0.288675135  -0.102266533   0   0   1
> Si       -0.500000000  -0.288675135   0.102266533   0   0   1
> Si       -0.500000000  -0.288675161   0.714766469   0   0   1
> Si        0.000000000  -0.000000029   0.919281369   0   0   1
> Si        0.000000000  -0.000000020   1.531756523   0   0   1
> Si        0.500000000   0.288675113   1.736391979   0   0   1
> Si        0.500000000   0.288675100   2.348809321   0   0   1
> Si       -0.500000000  -0.288675167   2.553252172   0   0   1
> Si       -0.500000000  -0.288675142   3.165727013   0   0   1
> Si        0.000000000  -0.000000005   3.369968660   0   0   1
> Si        0.000000000  -0.000000030   3.983120071   0   0   1
> Si        0.500000000   0.288675106   4.190720851   0   0   1
> Si        0.500000000   0.288675141   4.796768286   0   0   1
> Tl        0.000000000   0.000000003   5.314678016   0   0   1
> K_POINTS {automatic}
> 16 16 1 0 0 0
> 
> 
> 
> This is the structure A, the output gives energy -207.10202515 Ry, but
> the forces in the ouput are:
> 
> 
> !    total energy              =    -207.10202515 Ry
>      Harris-Foulkes estimate   =    -207.10202560 Ry
>      estimated scf accuracy    <       0.00000040 Ry
> 
>      convergence has been achieved in  19 iterations
> 
>      Forces acting on atoms (Ry/au):
> 
> 
>      atom   1 type  2   force =     0.00000000    0.00000000
> -0.01317569
>      atom   2 type  1   force =     0.00000000    0.00000000
> -0.00615334
>      atom   3 type  1   force =     0.00000000    0.00000000
> 0.00105593
>      atom   4 type  1   force =     0.00000000   -0.00000001
> -0.00059280
>      atom   5 type  1   force =     0.00000000    0.00000001
> -0.00026662
>      atom   6 type  1   force =     0.00000000    0.00000000
> 0.00008699
>      atom   7 type  1   force =     0.00000000    0.00000000
> -0.00000917
>      atom   8 type  1   force =     0.00000000    0.00000000
> -0.00002700
>      atom   9 type  1   force =     0.00000000    0.00000000
> 0.00015023
>      atom  10 type  1   force =     0.00000000    0.00000000
> -0.00013355
>      atom  11 type  1   force =     0.00000000    0.00000000
> 0.00004536
>      atom  12 type  1   force =     0.00000000    0.00000000
> -0.00005356
>      atom  13 type  1   force =     0.00000000    0.00000000
> 0.00008346
>      atom  14 type  1   force =     0.00000000    0.00000000
> -0.00008346
>      atom  15 type  1   force =     0.00000000    0.00000000
> 0.00005356
>      atom  16 type  1   force =     0.00000000    0.00000000
> -0.00004536
>      atom  17 type  1   force =     0.00000000    0.00000000
> 0.00013355
>      atom  18 type  1   force =     0.00000000    0.00000000
> -0.00015023
>      atom  19 type  1   force =     0.00000000    0.00000000
> 0.00002700
>      atom  20 type  1   force =     0.00000000    0.00000000
> 0.00000917
>      atom  21 type  1   force =     0.00000000    0.00000000
> -0.00008699
>      atom  22 type  1   force =     0.00000000   -0.00000001
> 0.00026662
>      atom  23 type  1   force =     0.00000000    0.00000001
> 0.00059280
>      atom  24 type  1   force =     0.00000000    0.00000000
> -0.00105593
>      atom  25 type  1   force =     0.00000000    0.00000000
> 0.00615334
>      atom  26 type  2   force =     0.00000000    0.00000000
> 0.01317569
> 
> as I said in the previous email, when SOC was not included the forces
> were <1.0D-4Ry/au.
> 
> After many cycles it relaxes to structure B:
> 
> 
>          1           Tl  tau(  1) = (   0.0000000  -0.0000002
> -5.4750706  )
>          2           Si  tau(  2) = (  -0.5000000  -0.2886754
> -4.9286617  )
>          3           Si  tau(  3) = (  -0.5000000  -0.2886751
> -4.3089294  )
>          4           Si  tau(  4) = (   0.0000000   0.0000001
> -4.0900306  )
>          5           Si  tau(  5) = (   0.0000000   0.0000005
> -3.4646493  )
>          6           Si  tau(  6) = (   0.5000000   0.2886757
> -3.2486536  )
>          7           Si  tau(  7) = (   0.5000000   0.2886753
> -2.6244846  )
>          8           Si  tau(  8) = (  -0.5000000  -0.2886750
> -2.4089562  )
>          9           Si  tau(  9) = (  -0.5000000  -0.2886748
> -1.7850326  )
>         10           Si  tau( 10) = (   0.0000000   0.0000002
> -1.5698553  )
>         11           Si  tau( 11) = (   0.0000000   0.0000013
> -0.9460530  )
>         12           Si  tau( 12) = (   0.5000000   0.2886761
> -0.7311323  )
>         13           Si  tau( 13) = (   0.5000000   0.2886753
> -0.1074118  )
>         14           Si  tau( 14) = (  -0.5000000  -0.2886753
> 0.1074118  )
>         15           Si  tau( 15) = (  -0.5000000  -0.2886761
> 0.7311323  )
>         16           Si  tau( 16) = (   0.0000000  -0.0000013
> 0.9460530  )
>         17           Si  tau( 17) = (   0.0000000  -0.0000002
> 1.5698553  )
>         18           Si  tau( 18) = (   0.5000000   0.2886748
> 1.7850326  )
>         19           Si  tau( 19) = (   0.5000000   0.2886750
> 2.4089562  )
>         20           Si  tau( 20) = (  -0.5000000  -0.2886753
> 2.6244846  )
>         21           Si  tau( 21) = (  -0.5000000  -0.2886757
> 3.2486536  )
>         22           Si  tau( 22) = (   0.0000000  -0.0000005
> 3.4646493  )
>         23           Si  tau( 23) = (   0.0000000  -0.0000001
> 4.0900306  )
>         24           Si  tau( 24) = (   0.5000000   0.2886751
> 4.3089294  )
>         25           Si  tau( 25) = (   0.5000000   0.2886754
> 4.9286617  )
>         26           Tl  tau( 26) = (   0.0000000   0.0000002
> 5.4750706  )
> 
> 
> 
> 
> were the output says:
> 
> 
> !    total energy              =    -207.08193686 Ry
>      Harris-Foulkes estimate   =    -207.08193687 Ry
>      estimated scf accuracy    <       0.00000002 Ry
> 
>     convergence has been achieved in  19 iterations
> 
>      Forces acting on atoms (Ry/au):
> 
>      atom   1 type  2   force =     0.00000000   -0.00000001
> -0.00021452
>      atom   2 type  1   force =     0.00000000    0.00000004
> -0.00028392
>      atom   3 type  1   force =     0.00000000    0.00000004
> -0.00036455
>      atom   4 type  1   force =     0.00000000   -0.00000001
> -0.00029396
>      atom   5 type  1   force =     0.00000000   -0.00000002
> -0.00029563
>      atom   6 type  1   force =     0.00000000   -0.00000008
> -0.00028951
>      atom   7 type  1   force =     0.00000000    0.00000003
> -0.00018682
>      atom   8 type  1   force =     0.00000000    0.00000006
> -0.00026107
>      atom   9 type  1   force =     0.00000000   -0.00000026
> -0.00008411
>      atom  10 type  1   force =     0.00000000    0.00000037
> -0.00018718
>      atom  11 type  1   force =     0.00000000   -0.00000073
> -0.00001065
>      atom  12 type  1   force =     0.00000000    0.00000047
> -0.00011851
>      atom  13 type  1   force =     0.00000000   -0.00000049
> 0.00004827
>      atom  14 type  1   force =     0.00000000    0.00000049
> -0.00004827
>      atom  15 type  1   force =     0.00000000   -0.00000047
> 0.00011851
>      atom  16 type  1   force =     0.00000000    0.00000073
> 0.00001065
>      atom  17 type  1   force =     0.00000000   -0.00000037
> 0.00018718
>      atom  18 type  1   force =     0.00000000    0.00000026
> 0.00008411
>      atom  19 type  1   force =     0.00000000   -0.00000006
> 0.00026107
>      atom  20 type  1   force =     0.00000000   -0.00000003
> 0.00018682
>      atom  21 type  1   force =     0.00000000    0.00000008
> 0.00028951
>      atom  22 type  1   force =     0.00000000    0.00000002
> 0.00029563
>      atom  23 type  1   force =     0.00000000    0.00000001
> 0.00029396
>      atom  24 type  1   force =     0.00000000   -0.00000004
> 0.00036455
>      atom  25 type  1   force =     0.00000000   -0.00000004
> 0.00028392
>      atom  26 type  2   force =     0.00000000    0.00000001
> 0.00021452
> 
> 
> This is not forces <1.0D-4Ry/au, but its the most I could converge.
> The energy is higher than in the first case. I do not know if it has
> something to do with the problem, but the fully relativistic
> pseudopotentials were checked in simpler systems giving good results.
> Thank you in advance
> 
> Julen
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
34151 Trieste (Italy)               e-mail: dalcorso at sissa.it



From dimpy.sharma at tyndall.ie  Tue Jul 13 12:25:24 2010
From: dimpy.sharma at tyndall.ie (Dimpy Sharma)
Date: Tue, 13 Jul 2010 11:25:24 +0100
Subject: [Pw_forum] Calculation Crashes by running at different processors
	fort he same system.
Message-ID: <D4A761F73683694BBD69D634FF298015533ED6@MAIL.tyndall.ie>


Hello all,

I was running some test calcuations to predict the CPU-time usage at different number of processors, however for the same system I can see that for certain number of processors (like at 4,8,16) the calculations run and finish properly however it crashes at different number of processors by saying the Cholesky decompostion as error message.Can anybodody give me some suggestions?

Thanks in advance.
Dimpy
Dimpy Sharma
ETG-Group
Tyndall National Institute
Cork
Ireland
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From masoudnahali at live.com  Tue Jul 13 12:49:53 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Tue, 13 Jul 2010 15:19:53 +0430
Subject: [Pw_forum] vc-relax time
Message-ID: <AANLkTilAnhIzjqbPiAvK-KuqhH1l_k_j7YWOUGRtlPIS@mail.gmail.com>

  Dear  Gabriele Sclauzero and pwscf Users

   Many thanks for your attentions. The cell dimension and the positions of
the atoms are exactly correct. Yes, indeed the high ecutrho is important for
ultrasoft pseudopotentials. About the rippling : It was my mistake in
selecting a wrong pseudopotential which has a hole. Nicola had explained it
before and accordingly I solved it. The graphite surface is not ripple. When
I use the "max_second=6000 and dt=150" the job completes very fast as the
example of  pwscf. Is the using of such keyboards plausible?
 As I mentioned before I had used the optimized cell parameters of (1*1
slab) for vc-relaxing the (2*2 slab) and I expected to see the results very
soon but the calculation was time consuming while there was only a very very
bit change of the cell dimensions during this 16 hours. There is only 1-3
iterations per each step in the output file and each of them was time
consuming. The job was completed after about 50 steps.

-------------------------------------------------------------------------

> Dear Masoud,
>
>   first I would suggest you to use bfgs as the algorithm for both ions and
> cell dynamics. Excepted particular cases, it should reach the minimum much
> faster.
>
> Also, why do you specify the cell with such an unusual way. You simply need
> celldm(1) and celldm(3) with ibrav=4 if you want to describe an hexagonal
> lattice. Other suggestions: your ecutrho looks really large to me, do you
> really need it. On the other hand, degauss might be too large to describe a
> spin-polarized system.
>
> Then, are you sure that you have built correctly your supercell? It looks
> like there are some C-C bonds much shorter that others in the central
> graphene plane (1.2 instead of 1.4 angs). Please check again your structure.
> In general, you can expect that if you relax the atoms in the supercell
> some kind of surface-reconstruction may appear, since you leave more freedom
> to atoms to rearrange in structures with larger periodicity. I don't think
> this is the case for graphite, but you may find some ripples (as you
> mentioned in your earlier emails, if I am not wrong) if the C-C bonds are at
> a distance shorter than the theoretical equilibrium distance (I guess).
>
> HTH
>
------------------------------------------------------------------------------------------------
 Dear Quantum Espresso Users
>
> I vc-relaxed a (1*1) slab of graphite surface with 3 layers; It takes 20
minutes with parallel running by 4 CPUs. Then I used the exact optimized
cell parameters (obtained from vc-relaxed calculation) to make a (2*2) slab
of graphite with 3 layers and I expected to see the results in a few
minutes. But amazingly it took 17 hours to complete. 48 steps were done in
the calculation for vc-relaxing the cell which have the parameters that had
been optimized before. The cell parameters only change a very bit in the
current vc-relaxing the (2*2) slab. I appreciate if one explain the physical
procedure of vc-relaxing and the reason of the time needed for the
computation.
>
> input file:
>
> CONTROL
>   calculation  = "vc-relax",
>   pseudo_dir   = "/home/koa/soft/qe4.2/
> espresso-4.2/pseudo",
>   outdir       = "/home/koa/tmp",
>   etot_conv_thr= 1.0D-4,
>   forc_conv_thr= 1.0D-3,
>   dt=80,
>     /
> &SYSTEM
>   ibrav     = 4,
>   a         = 2.4579,
>   b         = 2.4579,
>   c         = 16.3069,
>   cosab     = -0.5,
>   cosac     = 1.0,
>   cosbc     = 1.0,
>   nat       = 6,
>   ntyp      = 1,
>   ecutwfc   = 40.D0,
>   ecutrho   = 480.D0,
>   occupations = 'smearing'
>   smearing ='mp',
>   degauss = 0.03,
>   nspin = 2,
>   starting_magnetization(1)= 0.003,
>   london=.true.,
>   /
> &ELECTRONS
>   conv_thr    = 1.D-6,
>   mixing_beta = 0.7D0,
>   diagonalization = "david",
> /
> &IONS
>  ion_dynamics="cg"
> /
> &CELL
> cell_dynamics = 'damp-w',
> press = 0.0,
> /
> ATOMIC_SPECIES
> C  12.0107  C.pbe-rrkjus.UPF
> ATOMIC_POSITIONS {angstrom}
>  C                  0.00000000    0.00000000    0.00000000  1 1 0
>  C                  0.00000000    1.41908472    0.00000000
>  C                  0.00000000    0.00000000    3.15347111
>  C                  11.22896342    0.70954236    3.15347111
>  C                  0.00000000    0.00000000    6.30694222
>  C                  0.00000000    1.41908472    6.30694222
> K_POINTS {automatic}
> 4 4 1 1 1 1
>
 Sincerely Yours
 Masoud Nahali
 SUT
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From sclauzer at sissa.it  Tue Jul 13 13:02:15 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 13 Jul 2010 13:02:15 +0200
Subject: [Pw_forum] vc-relax time
In-Reply-To: <AANLkTilAnhIzjqbPiAvK-KuqhH1l_k_j7YWOUGRtlPIS@mail.gmail.com>
References: <AANLkTilAnhIzjqbPiAvK-KuqhH1l_k_j7YWOUGRtlPIS@mail.gmail.com>
Message-ID: <4C3C47B7.5000708@sissa.it>

On 07/13/2010 12:49 PM, Masoud Nahali wrote:
>   Dear  Gabriele Sclauzero and pwscf Users
>    Many thanks for your attentions. The cell dimension and 
> the positions of the atoms are exactly correct.

Are you completely sure? You can find as an attachment a picture (from 
xcrysden) of the central graphene layer according to the positions given 
in your input. You can now judge if it looks like a honeycomb lattice.

> Yes, indeed the high ecutrho is important for ultrasoft 
> pseudopotentials. About the rippling : It was my mistake in selecting 
> a wrong pseudopotential which has a hole. Nicola had explained it 
> before and accordingly I solved it. The graphite surface is not 
> ripple. When I use the "max_second=6000 and dt=150" the job completes 
> very fast as the example of  pwscf. Is the using of such keyboards 
> plausible?

Please spend some time reading Doc/INPUT_PW to understand the meaning of 
the _keywords_. dt is used only for molecular dynamics runs, not 
relaxations, while max_seconds has nothing to do with how fast your job 
is completed.


GS
>  As I mentioned before I had used the optimized cell parameters 
> of (1*1 slab) for vc-relaxing the (2*2 slab) and I expected to see the 
> results very soon but the calculation was time consuming while there 
> was only a very very bit change of the cell dimensions during this 16 
> hours. There is only 1-3 iterations per each step in the output file 
> and each of them was time consuming. The job was completed after about 
> 50 steps.
> -------------------------------------------------------------------------
>
>     Dear Masoud,
>
>       first I would suggest you to use bfgs as the algorithm for both
>     ions and cell dynamics. Excepted particular cases, it should reach
>     the minimum much faster.
>
>     Also, why do you specify the cell with such an unusual way. You
>     simply need celldm(1) and celldm(3) with ibrav=4 if you want to
>     describe an hexagonal lattice. Other suggestions: your ecutrho
>     looks really large to me, do you really need it. On the other
>     hand, degauss might be too large to describe a spin-polarized system.
>
>     Then, are you sure that you have built correctly your supercell?
>     It looks like there are some C-C bonds much shorter that others in
>     the central graphene plane (1.2 instead of 1.4 angs). Please check
>     again your structure.
>     In general, you can expect that if you relax the atoms in the
>     supercell some kind of surface-reconstruction may appear, since
>     you leave more freedom to atoms to rearrange in structures with
>     larger periodicity. I don't think this is the case for graphite,
>     but you may find some ripples (as you mentioned in your earlier
>     emails, if I am not wrong) if the C-C bonds are at a distance
>     shorter than the theoretical equilibrium distance (I guess).
>
>     HTH
>
> ------------------------------------------------------------------------------------------------
>  Dear Quantum Espresso Users
> >
> > I vc-relaxed a (1*1) slab of graphite surface with 3 layers; It 
> takes 20 minutes with parallel running by 4 CPUs. Then I used the 
> exact optimized cell parameters (obtained from vc-relaxed calculation) 
> to make a (2*2) slab of graphite with 3 layers and I expected to see 
> the results in a few minutes. But amazingly it took 17 hours to 
> complete. 48 steps were done in the calculation for vc-relaxing the 
> cell which have the parameters that had been optimized before. The 
> cell parameters only change a very bit in the current vc-relaxing the 
> (2*2) slab. I appreciate if one explain the physical procedure of 
> vc-relaxing and the reason of the time needed for the computation.
> >
> > input file:
> >
> > CONTROL
> >   calculation  = "vc-relax",
> >   pseudo_dir   = "/home/koa/soft/qe4.2/
> > espresso-4.2/pseudo",
> >   outdir       = "/home/koa/tmp",
> >   etot_conv_thr= 1.0D-4,
> >   forc_conv_thr= 1.0D-3,
> >   dt=80,
> >     /
> > &SYSTEM
> >   ibrav     = 4,
> >   a         = 2.4579,
> >   b         = 2.4579,
> >   c         = 16.3069,
> >   cosab     = -0.5,
> >   cosac     = 1.0,
> >   cosbc     = 1.0,
> >   nat       = 6,
> >   ntyp      = 1,
> >   ecutwfc   = 40.D0,
> >   ecutrho   = 480.D0,
> >   occupations = 'smearing'
> >   smearing ='mp',
> >   degauss = 0.03,
> >   nspin = 2,
> >   starting_magnetization(1)= 0.003,
> >   london=.true.,
> >   /
> > &ELECTRONS
> >   conv_thr    = 1.D-6,
> >   mixing_beta = 0.7D0,
> >   diagonalization = "david",
> > /
> > &IONS
> >  ion_dynamics="cg"
> > /
> > &CELL
> > cell_dynamics = 'damp-w',
> > press = 0.0,
> > /
> > ATOMIC_SPECIES
> > C  12.0107  C.pbe-rrkjus.UPF
> > ATOMIC_POSITIONS {angstrom}
> >  C                  0.00000000    0.00000000    0.00000000  1 1 0
> >  C                  0.00000000    1.41908472    0.00000000
> >  C                  0.00000000    0.00000000    3.15347111
> >  C                  11.22896342    0.70954236    3.15347111
> >  C                  0.00000000    0.00000000    6.30694222
> >  C                  0.00000000    1.41908472    6.30694222
> > K_POINTS {automatic}
> > 4 4 1 1 1 1
> >
>  Sincerely Yours
>  Masoud Nahali
>  SUT
>
>
> _______________________________________________
> 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

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From masoudnahali at live.com  Tue Jul 13 15:41:00 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Tue, 13 Jul 2010 18:11:00 +0430
Subject: [Pw_forum] vc-relax time
Message-ID: <AANLkTiliB97ORdBpvJKw5uWuSF-50zuAg5s9y-JvKD_1@mail.gmail.com>

 Dear Gabriele and pwscf users


Perfectly I am sure that the positions of atoms is exactly correct. Note
that the input is belong to a (1*1) slab
and indeed you could not see a honeycomb ! but It is easy to see a honeycomb
when you have a (2*2) slab like this:

C        0.000352513   0.001055549   0.000000000
C        2.459305478   0.000933657  -0.008798962
C       -1.229191611   2.130502759  -0.008802160
C        1.229819481   2.130516670  -0.008801637
C        0.000327447   1.420695799  -0.007291549
C       -1.229173562   3.550193436  -0.007292113
C        2.459296954   1.420621766  -0.009715082
C        1.229852979   3.550208684  -0.007292392
C        0.000507119   0.000488868   3.187515573
C        2.459486429   0.000491165   3.187352189
C       -1.228985445   2.130026298   3.187352283
C        1.229997454   2.130026366   3.187352273
C        1.229970852   0.710263879   3.187439366
C        0.000476982   2.839800509   3.187332530
C        3.688943914   0.710263968   3.187439418
C        2.459456202   2.839797012   3.187439363
C        0.000212609   0.000545761   6.403453823
C        2.459191836   0.000545600   6.403451859
C       -1.229278051   2.130084159   6.403451942
C        1.229700861   2.130084205   6.403451921
C        0.000121431   1.420208410   6.403892505
C       -1.229369239   3.549746424   6.403892711
C        2.459100653   1.420208253   6.403888354
C        1.229609673   3.549746469   6.403892772

  a         = 4.9178,
  b         = 4.9178,
  c         = 16.4112,  10 angstrom vacuum


Also,  see the "As.vcs00.in" example in the "VCSexample" folder of quantum
espresso 4.2. In this example a vc-relax calculation
has been performed using the max_seconds and dt keyboard.

Many Thanks

I hope one helps these problems mentioned below.





>Are you completely sure? You can find as an attachment a picture (from
>xcrysden) of the central graphene layer according to the positions given
>in your input. You can now judge if it looks like a honeycomb lattice.

> Yes, indeed the high ecutrho is important for ultrasoft
> pseudopotentials. About the rippling : It was my mistake in selecting
> a wrong pseudopotential which has a hole. Nicola had explained it
> before and accordingly I solved it. The graphite surface is not
> ripple. When I use the "max_second=6000 and dt=150" the job completes
> very fast as the example of  pwscf. Is the using of such keyboards
> plausible?

>Please spend some time reading Doc/INPUT_PW to understand the meaning of
>the _keywords_. dt is used only for molecular dynamics runs, not
>relaxations, while max_seconds has nothing to do with how fast your job
>is completed.


> > Dear  Gabriele Sclauzero and pwscf Users
>
> > Many thanks for your attentions. The cell dimension and the positions of
> >the atoms are exactly correct. Yes, indeed the high ecutrho is important
> for
> >ultrasoft pseudopotentials. About the rippling : It was my mistake in
> >selecting a wrong pseudopotential which has a hole. Nicola had explained
> it
> >before and accordingly I solved it. The graphite surface is not ripple.
> When
> >I use the "max_second=6000 and dt=150" the job completes very fast as the
> >example of  pwscf. Is the using of such keyboards plausible?
>   >As I mentioned before I had used the optimized cell parameters of (1*1
> >slab) for vc-relaxing the (2*2 slab) and I expected to see the results
> very
> >soon but the calculation was time consuming while there was only a very
> very
> >bit change of the cell dimensions during this 16 hours. There is only 1-3
> >iterations per each step in the output file and each of them was time
> >consuming. The job was completed after about 50 steps.
>
> -------------------------------------------------------------------------
>
> > Dear Masoud,
> >
> >   first I would suggest you to use bfgs as the algorithm for both ions
> and
> > cell dynamics. Excepted particular cases, it should reach the minimum
> much
> > faster.
> >
> > Also, why do you specify the cell with such an unusual way. You simply
> need
> > celldm(1) and celldm(3) with ibrav=4 if you want to describe an hexagonal
> > lattice. Other suggestions: your ecutrho looks really large to me, do you
> > really need it. On the other hand, degauss might be too large to describe
> a
> > spin-polarized system.
> >
> > Then, are you sure that you have built correctly your supercell? It looks
> > like there are some C-C bonds much shorter that others in the central
> > graphene plane (1.2 instead of 1.4 angs). Please check again your
> structure.
> > In general, you can expect that if you relax the atoms in the supercell
> > some kind of surface-reconstruction may appear, since you leave more
> freedom
> > to atoms to rearrange in structures with larger periodicity. I don't
> think
> > this is the case for graphite, but you may find some ripples (as you
> > mentioned in your earlier emails, if I am not wrong) if the C-C bonds are
> at
> > a distance shorter than the theoretical equilibrium distance (I guess).
> >
> > HTH
> >
>
> ------------------------------------------------------------------------------------------------
>  Dear Quantum Espresso Users
> >
> > I vc-relaxed a (1*1) slab of graphite surface with 3 layers; It takes 20
> minutes with parallel running by 4 CPUs. Then I used the exact optimized
> cell parameters (obtained from vc-relaxed calculation) to make a (2*2) slab
> of graphite with 3 layers and I expected to see the results in a few
> minutes. But amazingly it took 17 hours to complete. 48 steps were done in
> the calculation for vc-relaxing the cell which have the parameters that had
> been optimized before. The cell parameters only change a very bit in the
> current vc-relaxing the (2*2) slab. I appreciate if one explain the
> physical
> procedure of vc-relaxing and the reason of the time needed for the
> computation.
> >
> > input file:
> >
> > CONTROL
> >   calculation  = "vc-relax",
> >   pseudo_dir   = "/home/koa/soft/qe4.2/
> > espresso-4.2/pseudo",
> >   outdir       = "/home/koa/tmp",
> >   etot_conv_thr= 1.0D-4,
> >   forc_conv_thr= 1.0D-3,
> >   dt=80,
> >     /
> > &SYSTEM
> >   ibrav     = 4,
> >   a         = 2.4579,
> >   b         = 2.4579,
> >   c         = 16.3069,
> >   cosab     = -0.5,
> >   cosac     = 1.0,
> >   cosbc     = 1.0,
> >   nat       = 6,
> >   ntyp      = 1,
> >   ecutwfc   = 40.D0,
> >   ecutrho   = 480.D0,
> >   occupations = 'smearing'
> >   smearing ='mp',
> >   degauss = 0.03,
> >   nspin = 2,
> >   starting_magnetization(1)= 0.003,
> >   london=.true.,
> >   /
> > &ELECTRONS
> >   conv_thr    = 1.D-6,
> >   mixing_beta = 0.7D0,
> >   diagonalization = "david",
> > /
> > &IONS
> >  ion_dynamics="cg"
> > /
> > &CELL
> > cell_dynamics = 'damp-w',
> > press = 0.0,
> > /
> > ATOMIC_SPECIES
> > C  12.0107  C.pbe-rrkjus.UPF
> > ATOMIC_POSITIONS {angstrom}
> >  C                  0.00000000    0.00000000    0.00000000  1 1 0
> >  C                  0.00000000    1.41908472    0.00000000
> >  C                  0.00000000    0.00000000    3.15347111
> >  C                  11.22896342    0.70954236    3.15347111
> >  C                  0.00000000    0.00000000    6.30694222
> >  C                  0.00000000    1.41908472    6.30694222
> > K_POINTS {automatic}
> > 4 4 1 1 1 1
> >
>
>
>
>
>
>
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From matteo at umn.edu  Tue Jul 13 15:54:43 2010
From: matteo at umn.edu (Matteo Cococcioni)
Date: Tue, 13 Jul 2010 08:54:43 -0500
Subject: [Pw_forum] GGA+U
In-Reply-To: <B4E1CEFE-D90C-4650-ADD8-6F1909EA87AE@sissa.it>
References: <AANLkTikvjmPXIdyEO--RY-ZZPR4ZH1yp1dGnYnjYLgEA@mail.gmail.com>	<EF04F553-7F76-4CAD-9662-DAB9C0802FEF@sissa.it>
	<B4E1CEFE-D90C-4650-ADD8-6F1909EA87AE@sissa.it>
Message-ID: <4C3C7023.4030207@umn.edu>


Dear Saha,

maybe the problem is a "formal" one. Open the PP file (maybe you want to 
share it with this community) and make sure
the name of the element is a) present (not sure whether the code would 
stop or not without the name);
b) written exactly 'Eu'. That is what the code has instructions for.

Matteo



Gabriele Sclauzero wrote:
>
> Sorry, I didn't read your mail carefully. Actually the case of Eu is 
> already included in both set_hubbard_l and tabd.
>
> So the problem should be another one.  Which version of QE are you 
> using? If it's not 4.1, please update to 4.2 and try again.
>
> Thanks,
>
> GS
>
> Il giorno 13/lug/2010, alle ore 09.35, Gabriele Sclauzero ha scritto:
>
>> Dear Saha,
>>
>>    this question has been asked many times in this forum so far (so 
>> many that it could deserve to be included in the FAQ, perhaps), so 
>> that you may get your reply by simply browsing in the forum archives. 
>> Very briefly, the code needs to know which electron manyfold of the 
>> "Hubbard" atomic species should be treated with the +U correction and 
>> what is the occupation of that electronic shell in the atom. This 
>> information has been already hardcoded for the most common elements. 
>> Evidently, Eu is not among those. You have to manually modify files 
>> set_hubbard_l.f90 and tabd.f90 (in the PW folder) according to what 
>> you think reasonable for your case.
>>
>>
>> Regards,
>>
>> GS
>>
>> Il giorno 13/lug/2010, alle ore 01.04, S. K. S. ha scritto:
>>
>>>  
>>>
>>> Dear QE Users,
>>>
>>> I got the following error while used GGA+U for EuO:
>>>
>>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>      from set_hubbard_l : error #         1
>>>      pseudopotential not yet inserted
>>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>
>>>      stopping ...
>>>
>>> Inside source file, I have found that "Eu" is mentioned. However, I 
>>> do not understand
>>> the meaning of inserting a pseudopotential.
>>>
>>> Thanks in advance for a helpful explanation. 
>>>
>>> With best regards,
>>>
>>> Saha SK
>>> R&D Assistant
>>> JNCASR
>>> Bangalore 560012
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org <mailto: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 <mailto: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
>   


From giannozz at democritos.it  Tue Jul 13 15:57:27 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 13 Jul 2010 15:57:27 +0200
Subject: [Pw_forum] GGA+U
In-Reply-To: <4C3C7023.4030207@umn.edu>
References: <AANLkTikvjmPXIdyEO--RY-ZZPR4ZH1yp1dGnYnjYLgEA@mail.gmail.com>	<EF04F553-7F76-4CAD-9662-DAB9C0802FEF@sissa.it>	<B4E1CEFE-D90C-4650-ADD8-6F1909EA87AE@sissa.it>
	<4C3C7023.4030207@umn.edu>
Message-ID: <4C3C70C7.4080407@democritos.it>

Matteo Cococcioni wrote:

> make sure the name of the element is a) present (not sure whether 
> the code would stop or not without the name)

I don't think it would stop, but the name of the element is reprinted
on output, so it is easy to verify

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Tue Jul 13 16:03:32 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 13 Jul 2010 16:03:32 +0200
Subject: [Pw_forum] Calculation Crashes by running at different
 processors fort he same system.
In-Reply-To: <D4A761F73683694BBD69D634FF298015533ED6@MAIL.tyndall.ie>
References: <D4A761F73683694BBD69D634FF298015533ED6@MAIL.tyndall.ie>
Message-ID: <4C3C7234.5060202@democritos.it>

Dimpy Sharma wrote:

> for the same system I can see that for certain number of processors
> (like at 4,8,16) the calculations run and finish properly
> however it crashes at different number of processors by saying
> the Cholesky decompostion as error message.

please see this thread:
http://www.democritos.it/pipermail/pw_forum/2010-June/017434.html

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From Norbert.Nemec.List at gmx.de  Tue Jul 13 16:13:35 2010
From: Norbert.Nemec.List at gmx.de (Norbert Nemec)
Date: Tue, 13 Jul 2010 16:13:35 +0200
Subject: [Pw_forum] Initial velocities for MD run? (Norbert Nemec)
In-Reply-To: <4C3C3569.9080600@materials.ox.ac.uk>
References: <JRNHDWXCLYMVKKSKIMNQBSOJGFOG.daijiayu@nudt.edu.cn>
	<4C3C3569.9080600@materials.ox.ac.uk>
Message-ID: <20100713141335.186530@gmx.net>


-------- Original-Nachricht --------
> Datum: Tue, 13 Jul 2010 10:44:09 +0100
> Von: Davide Ceresoli <davide.ceresoli at materials.ox.ac.uk>
>
> The CPV code has an option to read atomic velocities from input.
> However, it has never been clear to me in which units one should
> enter the velocities.

Thanks for the hint. I'll have a look at it.

As for the units: I would go for physical units that are independent of the MD timestep.

B.t.w: May it be that "zero initial velocity" is implemented incorrectly in the code? At the moment, the code sets 'tau_old=tau'. In Verlet, however, the current velocity is defined as '(tau_new-tau_old)/(2*dt)'.

To correctly set an initial velocity v0 in Verlet, the first time step has to be defined by the two conditions:

  tau_new+tau_old = 2*tau + a*dt**2
  tau_new-tau_old = v0*2*dt

eliminating tau_old and getting

  tau_new = tau+a/2*dt**2+v0*dt

Once the first two time steps are known, the algorithm can then continue without velocities as usual.
-- 
GRATIS f?r alle GMX-Mitglieder: Die maxdome Movie-FLAT!
Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

From giannozz at democritos.it  Tue Jul 13 16:21:37 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 13 Jul 2010 16:21:37 +0200
Subject: [Pw_forum] Initial velocities for MD run?
In-Reply-To: <20100712172450.88740@gmx.net>
References: <20100712172450.88740@gmx.net>
Message-ID: <4C3C7671.8020701@democritos.it>

Norbert Nemec wrote:

> is there any way to specify initial velocities for a MD run?

CP or PW? in the latter case, unfortunately it is not possible
right now. Once upon a time I considered implementing it, but
the way dynamics is implemented in PW/dynamics_module.f90 makes
addition of initial velocities not completely obvious.

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Tue Jul 13 16:26:31 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 13 Jul 2010 16:26:31 +0200
Subject: [Pw_forum] SD PSP
In-Reply-To: <AANLkTin3-Am6klLxcsUDBRpLxO9ALROoeExs3al_9pNr@mail.gmail.com>
References: <AANLkTin3-Am6klLxcsUDBRpLxO9ALROoeExs3al_9pNr@mail.gmail.com>
Message-ID: <4C3C7797.3040401@democritos.it>

Suza W wrote:

> Have spin-dependent pesudopotentials (as discussed in Phys. Rev. B 69, 
> 052404, 2004) been incorporated in Quantum Espresso ?

no

> Is it at all justifiable to use a spin-neutral pseudopotential for the 
> magnetic system ?  

With the nonlinear core correction, it should

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From pastore at democritos.it  Tue Jul 13 17:27:46 2010
From: pastore at democritos.it (pastore at democritos.it)
Date: Tue, 13 Jul 2010 17:27:46 +0200
Subject: [Pw_forum] Initial velocities for MD run?
In-Reply-To: <4C3C7671.8020701@democritos.it>
References: <20100712172450.88740@gmx.net> <4C3C7671.8020701@democritos.it>
Message-ID: <20100713172746.dxz7iysdiccss0cs@mail.democritos.it>

Quoting Paolo Giannozzi <giannozz at democritos.it>:
...
> CP or PW? in the latter case, unfortunately it is not possible
> right now. Once upon a time I considered implementing it, but
> the way dynamics is implemented in PW/dynamics_module.f90 makes
> addition of initial velocities not completely obvious.
>

Paolo, I do not see any reason why PW dynamics should continue to be 
based on position Verlet. Shifting to Velocity Verlet should be almost 
trivial (CP is a completely different story due to the orthogonality 
constraint) and there would be the great benefit of a direct control on 
the initial velocities.

Giorgio

--
Giorgio Pastore - Dipartimento di Fisica dell' Universita' - sede di Miramare
                  and IOM-CNR (Democritos)
                  Strada Costiera 11, 34151 Trieste, Italy
  phone :         + 39 040 2240247   fax: + 39 040 224601
  e-mail:         pastore at ts.infn.it


----------------------------------------------------------------
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From giannozz at democritos.it  Tue Jul 13 17:56:06 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 13 Jul 2010 17:56:06 +0200
Subject: [Pw_forum] Initial velocities for MD run?
In-Reply-To: <20100713172746.dxz7iysdiccss0cs@mail.democritos.it>
References: <20100712172450.88740@gmx.net> <4C3C7671.8020701@democritos.it>
	<20100713172746.dxz7iysdiccss0cs@mail.democritos.it>
Message-ID: <4C3C8C96.8020102@democritos.it>

pastore at democritos.it wrote:

> Paolo, I do not see any reason why PW dynamics should continue 
> to be based on position Verlet.

most likely there aren't any, apart from historical reasons
(which are seldom good reasons)

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From Norbert.Nemec.List at gmx.de  Tue Jul 13 18:13:31 2010
From: Norbert.Nemec.List at gmx.de (Norbert Nemec)
Date: Tue, 13 Jul 2010 18:13:31 +0200
Subject: [Pw_forum] Initial velocities for MD run?
In-Reply-To: <20100713172746.dxz7iysdiccss0cs@mail.democritos.it>
References: <20100712172450.88740@gmx.net> <4C3C7671.8020701@democritos.it>
	<20100713172746.dxz7iysdiccss0cs@mail.democritos.it>
Message-ID: <20100713161331.77750@gmx.net>

-------- Original-Nachricht --------
> Datum: Tue, 13 Jul 2010 17:27:46 +0200
> Von: pastore at democritos.it
> Paolo, I do not see any reason why PW dynamics should continue to be 
> based on position Verlet. Shifting to Velocity Verlet should be almost 
> trivial (CP is a completely different story due to the orthogonality 
> constraint) and there would be the great benefit of a direct control on 
> the initial velocities.

As described in my other mail, position Verlet allows a simple implementation of initial velocities. (Including a correction of the currently faulty implementation of zero-velocities.)

I will have a look at it and try to come up with an implementation.
-- 
GRATIS f?r alle GMX-Mitglieder: Die maxdome Movie-FLAT!
Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

From samolyuk at gmail.com  Tue Jul 13 20:29:06 2010
From: samolyuk at gmail.com (German Samolyuk)
Date: Tue, 13 Jul 2010 14:29:06 -0400
Subject: [Pw_forum] Initial velocities for MD run?
In-Reply-To: <20100712172450.88740@gmx.net>
References: <20100712172450.88740@gmx.net>
Message-ID: <AANLkTikCgL7f67GLIohfkJF3WD9a0XXX6nWYLubB1Ge4@mail.gmail.com>

I did it by hands in subroutine dynamics_modyle.
I was calculating cascade in SiC.
If it's interestinf, I've attached function. If you uncomment lines
startsing from ! gds, it will initialise velosity of the particle
number 100
with velocity corresponding to energy 100 eV.
It's not a regular way, but if you need few calculation, it could work.

Best,
German Samolyuk,
ORNL, USA

PS; It's for version 4.1.1

On Mon, Jul 12, 2010 at 1:24 PM, Norbert Nemec
<Norbert.Nemec.List at gmx.de> wrote:
> Hi there,
>
> is there any way to specify initial velocities for a MD run? From what I see, only thermalization or zero velocites are possible.
>
> Ultimately, I want to do simulate a scattering process of two molecules.
>
> If this is not possible, I would consider implementing it. Does anyone have specific ideas about that?
>
> Greetings,
> Norbert
> --
> GMX DSL: Internet-, Telefon- und Handy-Flat ab 19,99 EUR/mtl.
> Bis zu 150 EUR Startguthaben inklusive! http://portal.gmx.net/de/go/dsl
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From kazempoor at ph.iut.ac.ir  Tue Jul 13 22:56:25 2010
From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir)
Date: Wed, 14 Jul 2010 01:26:25 +0430 (IRDT)
Subject: [Pw_forum] DFPT+U
Message-ID: <1417431553.15257.1279054585934.JavaMail.root@mta.iut.ac.ir>

Dear All
which version of espresso can do DFPT+U calculation?
Thanks 

Ali Kazempour
Physics Department, Isfahn University of Technology

From sks.jnc at gmail.com  Wed Jul 14 01:27:54 2010
From: sks.jnc at gmail.com (S. K. S.)
Date: Wed, 14 Jul 2010 01:27:54 +0200
Subject: [Pw_forum] GGA+U
In-Reply-To: <4C3C70C7.4080407@democritos.it>
References: <AANLkTikvjmPXIdyEO--RY-ZZPR4ZH1yp1dGnYnjYLgEA@mail.gmail.com>
	<EF04F553-7F76-4CAD-9662-DAB9C0802FEF@sissa.it>
	<B4E1CEFE-D90C-4650-ADD8-6F1909EA87AE@sissa.it>
	<4C3C7023.4030207@umn.edu> <4C3C70C7.4080407@democritos.it>
Message-ID: <AANLkTilTzQGbhDVX19qt_NIjEqlSSJiCQU_JJViW08nA@mail.gmail.com>

 Dear QE USERS,

 Yes, the code works fine when I change the name
 of element from "eu" to "Eu" inside the pseudopotential file.
 Thank you all for your kind reply.

 One more question : what is Hubbard_alpha ?
  Is this Lagrange multipliers? What is its typical value?
  Is this possible to specify J & U both, in the input file of the newest
version
  of QE code or  is this always U_eff ?

 regards,
 Saha SK
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From chenhanghuipwscf at gmail.com  Wed Jul 14 04:02:47 2010
From: chenhanghuipwscf at gmail.com (hanghui chen)
Date: Tue, 13 Jul 2010 22:02:47 -0400
Subject: [Pw_forum] starting_magnetization
Message-ID: <AANLkTil-3wzIFILXpolaYIl5fiTQ_uS4QHLuZ09U-ASl@mail.gmail.com>

Dear QE developers,
     In the PWscf, there is a constraint on the variable
'starting_magnetization': if 'starting_magnetization>1', then it is set to
be 1; if 'starting_magnetization< -1', then it is set to be -1. Why do we
need such a constraint?
     Thank you.

Hanghui Chen
Department of Physics
Yale Unversity
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From julen.azpiroz at gmail.com  Wed Jul 14 09:32:26 2010
From: julen.azpiroz at gmail.com (Julen Ibanez Azpiroz)
Date: Wed, 14 Jul 2010 09:32:26 +0200
Subject: [Pw_forum] Relaxation with Spin-Orbit Coupling
In-Reply-To: <1279016595.5185.5.camel@dhcp-098.cm.sissa.it>
References: <AANLkTilVg56jene1O5kv-6y-6Ityv-EswBXDzXMqBEH0@mail.gmail.com>
	<1279012628.5185.1.camel@dhcp-098.cm.sissa.it>
	<AANLkTik4VqXcMMMD7VSCSqFto650scgfazGpqz5DVz8O@mail.gmail.com>
	<1279016595.5185.5.camel@dhcp-098.cm.sissa.it>
Message-ID: <AANLkTimWvsN9KXBfKhhWvFvf1kWk1SiJpWb21NOPIlx7@mail.gmail.com>

Hello

Ok, I will check the pseudopotentials, thank you very much for your
suggestion

Julen
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From invite+pkihuu5_ at facebookmail.com  Wed Jul 14 09:40:13 2010
From: invite+pkihuu5_ at facebookmail.com (=?UTF-8?B?THVjYXMgRmVybsOhbmRleiBTZWl2YW5l?=)
Date: Wed, 14 Jul 2010 00:40:13 -0700
Subject: [Pw_forum] =?utf-8?q?Me_gustar=C3=ADa_seguir_en_contacto_contigo_?=
 =?utf-8?q?en_Facebook?=
Message-ID: <1a891a77b6c5ff09bd3982c7a40558f5@www.facebook.com>

Hola, Pwscf:

He creado un perfil en Facebook donde puedo publicar mis fotos, v?deos y eventos, y quiero a?adirte a mis amigos para que puedas verlo. Para ello, necesitas registrarte en Facebook y, despu?s, podr?s crear tambi?n tu propio perfil.

Gracias,
Lucas

Para registrarte en Facebook, sigue este enlace:
http://www.facebook.com/p.php?i=516122321&k=55C423TYTT6BWJEDP13Y2USTZUJ15ZY&r

"?Ya tiene una cuenta? Agregue este correo electr?nico a su cuenta"
http://www.facebook.com/n/?merge_accounts.php&e=pw_forum%40pwscf.org&c=9102c15d798fdaefa5251573c51f7a28

=======================================
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From sclauzer at sissa.it  Wed Jul 14 10:23:03 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Wed, 14 Jul 2010 10:23:03 +0200
Subject: [Pw_forum] t and e states of Mn in GaAs
In-Reply-To: <636743.59849.qm@web65817.mail.ac4.yahoo.com>
References: <636743.59849.qm@web65817.mail.ac4.yahoo.com>
Message-ID: <67D8C78B-6DDA-49AF-A00E-925A7F2FAA3A@sissa.it>

Dear Nand,

   first you should identify the crystal symmetry group. For GaAs it should be the cubic group T_d (-43m), if I'm not wrong. When you consider a supercell with a substitutional impurity things might change, you should check. I suggest you to put the impurity in the origin. You can let pw.x print symmetries and space group of your system by specifying verbosity='high'.

   If the T_d group is detected, then you have to find out which representation each atomic orbital of Mn belongs to. You will have s and d electrons. If Mn is in the origin, the former transforming as the identity representation A1, while the latter according to irrep T (xz, yz and xy) or to the bidimensional irrep E (x^2-y^2 and 3z^2-r^2). 
Plz have a look here: http://www.staff.ncl.ac.uk/j.p.goss/symmetry/Td.html.
If the symmetry group is different, then you can retrieve the corresponding information from the same website. Even if the symmetry downgrades to the smallest group of the cubic family,T (23), the decomposition of above is still valid.

Then you should find the desired information by plotting or integrating the corresponding column in the PDOS file of Mn (see also the header of PP/projwfc.f90).

HTH


GS


Il giorno 12/lug/2010, alle ore 15.33, nand ha scritto:

> Dear PW Forum,
> I have carried out spin dependent DOS and PDOS calculations on Mn dopled GaAs with a 17 atom supercell. From literature i have found that the Mn states get modified in to three  t and two  e states in the band gap. Now I do not know how to extract information about these states from my DOS and PDOS plottings. Primariliy i would like to identify these state(bonding and anti bonding) and their occupancy. Can some one plz tell me about these states and any literature available on the web about them.
>  
> Thanking in advance.
>  
> Nand Rana
> Research Scholar,
> Ranchi University 
> India  
> 
> _______________________________________________
> 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

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From giannozz at democritos.it  Wed Jul 14 11:49:54 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 14 Jul 2010 11:49:54 +0200
Subject: [Pw_forum] DFPT+U
In-Reply-To: <1417431553.15257.1279054585934.JavaMail.root@mta.iut.ac.ir>
References: <1417431553.15257.1279054585934.JavaMail.root@mta.iut.ac.ir>
Message-ID: <4C3D8842.9080801@democritos.it>

kazempoor at ph.iut.ac.ir wrote:

> which version of espresso can do DFPT+U calculation?

some version in the future, I guess

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Wed Jul 14 11:55:07 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 14 Jul 2010 11:55:07 +0200
Subject: [Pw_forum] starting_magnetization
In-Reply-To: <AANLkTil-3wzIFILXpolaYIl5fiTQ_uS4QHLuZ09U-ASl@mail.gmail.com>
References: <AANLkTil-3wzIFILXpolaYIl5fiTQ_uS4QHLuZ09U-ASl@mail.gmail.com>
Message-ID: <4C3D897B.4010008@democritos.it>

hanghui chen wrote:

> there is a constraint on the variable 'starting_magnetization'

starting_magnetization(nt) = +1 (-1) means all atomic states
for atom type nt with spin up (down)

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From matteo at umn.edu  Wed Jul 14 15:21:22 2010
From: matteo at umn.edu (Matteo Cococcioni)
Date: Wed, 14 Jul 2010 08:21:22 -0500
Subject: [Pw_forum] GGA+U
In-Reply-To: <AANLkTilTzQGbhDVX19qt_NIjEqlSSJiCQU_JJViW08nA@mail.gmail.com>
References: <AANLkTikvjmPXIdyEO--RY-ZZPR4ZH1yp1dGnYnjYLgEA@mail.gmail.com>	<EF04F553-7F76-4CAD-9662-DAB9C0802FEF@sissa.it>	<B4E1CEFE-D90C-4650-ADD8-6F1909EA87AE@sissa.it>	<4C3C7023.4030207@umn.edu>
	<4C3C70C7.4080407@democritos.it>
	<AANLkTilTzQGbhDVX19qt_NIjEqlSSJiCQU_JJViW08nA@mail.gmail.com>
Message-ID: <4C3DB9D2.8080802@umn.edu>

S. K. S. wrote:
>
>  Dear QE USERS,
>  
>  Yes, the code works fine when I change the name
>  of element from "eu" to "Eu" inside the pseudopotential file.
>  Thank you all for your kind reply.
>
>  One more question : what is Hubbard_alpha ?
>   Is this Lagrange multipliers? What is its typical value?

yes, it's used to compute U (see PRB 71 035105 (2005))

>   Is this possible to specify J & U both, in the input file of the 
> newest version
>   of QE code or  is this always U_eff ?

always U_eff. the functional with U and J was never implemented on 
official version of the code.

Matteo

>  
>  regards,
>  Saha SK
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 


From matteo at umn.edu  Wed Jul 14 15:22:22 2010
From: matteo at umn.edu (Matteo Cococcioni)
Date: Wed, 14 Jul 2010 08:22:22 -0500
Subject: [Pw_forum] GGA+U
In-Reply-To: <AANLkTilTzQGbhDVX19qt_NIjEqlSSJiCQU_JJViW08nA@mail.gmail.com>
References: <AANLkTikvjmPXIdyEO--RY-ZZPR4ZH1yp1dGnYnjYLgEA@mail.gmail.com>	<EF04F553-7F76-4CAD-9662-DAB9C0802FEF@sissa.it>	<B4E1CEFE-D90C-4650-ADD8-6F1909EA87AE@sissa.it>	<4C3C7023.4030207@umn.edu>
	<4C3C70C7.4080407@democritos.it>
	<AANLkTilTzQGbhDVX19qt_NIjEqlSSJiCQU_JJViW08nA@mail.gmail.com>
Message-ID: <4C3DBA0E.3020303@umn.edu>

S. K. S. wrote:
>
>  Dear QE USERS,
>  
>  Yes, the code works fine when I change the name
>  of element from "eu" to "Eu" inside the pseudopotential file.
>  Thank you all for your kind reply.
>
>  One more question : what is Hubbard_alpha ?
>   Is this Lagrange multipliers? What is its typical value?

typical value: -0.2 to 0.2 in most case should work. center around 0 and 
check linearity of occupations
with alpha.

>   Is this possible to specify J & U both, in the input file of the 
> newest version
>   of QE code or  is this always U_eff ?
>  
>  regards,
>  Saha SK
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 


From Norbert.Nemec.List at gmx.de  Wed Jul 14 17:36:50 2010
From: Norbert.Nemec.List at gmx.de (Norbert Nemec)
Date: Wed, 14 Jul 2010 17:36:50 +0200
Subject: [Pw_forum] constraints: planar and torsion angles
Message-ID: <20100714153650.234150@gmx.net>

Hi there,

in case someone is curious about the commits I just checked in. Apart from some cleanup and some better logging output, I changed the internal handling of angle constraints:

Planar and and torsion angles used to be handled internally by their cosine. This had caused a problem for angles of 0 or 180 degree, where the derivative of the constraint would become zero and the constraint could not be enforced correctly. Specifically, this caused problems for planar benzene molecules that I tried to constrain.

With my change, the constraints are now internally handled as angle, the torsion angle as signed angle. It works beautifully for my test case. I adjusted the metadynamics code, otherwise, no code seems to be affected.

For the user, there should be no difference except in the case that someone would have explicitly specified torsion angles with incorrect sign in the input file. I doubt that anyone would do that...

Greetings,
Norbert
-- 
GMX DSL: Internet-, Telefon- und Handy-Flat ab 19,99 EUR/mtl.  
Bis zu 150 EUR Startguthaben inklusive! http://portal.gmx.net/de/go/dsl

From adehaopan at hotmail.com  Wed Jul 14 19:00:00 2010
From: adehaopan at hotmail.com (HaoPan)
Date: Thu, 15 Jul 2010 01:00:00 +0800
Subject: [Pw_forum] phonon calculations
Message-ID: <SNT117-W1363B5EE2F7FBC7D0412EAB6BA0@phx.gbl>


Dear developer,

I am using the quantum espresso 4.1.2.  The compiler I used is intel 11.1. I am calculating  the phonon frequency to check the zero energy. The phonon calculations are good for semiconductor and insulator. For some metal it is good, like Al, Ag, etc. For others, like Ba, Cu.  The ph.x runing stay at dyn2 or dyn3 until my required time run out. I don't know is the problem common or not.

 I test it on my pc. It can get all dyn*.  Howerver the result is bad. There are negative frequency arond the equilibrium positon. For different metal I tried different pseudo potentials. Some worked some failed. Some of solids I just can not get the right dispersion.  So hopeful I can get the solution from you. Thanks a lot.

best,
Pan Hao 
Tulane University
 		 	   		  
_________________________________________________________________
????????????????
http://cn.bing.com/search?q=%E5%A4%A9%E6%B0%94%E9%A2%84%E6%8A%A5&form=MICHJ2
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From afsaneh.daemi at gmail.com  Wed Jul 14 20:28:28 2010
From: afsaneh.daemi at gmail.com (afsaneh daemi)
Date: Wed, 14 Jul 2010 11:28:28 -0700
Subject: [Pw_forum] afsaneh daemi wants to chat
Message-ID: <AANLkTinPzHQzrkXj_-3-Xhbm059yo3kP9MwuBnViILqJ@mail.gmail.com>

-----------------------------------------------------------------------

afsaneh daemi wants to stay in better touch using some of Google's coolest new
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To get Gmail - a free email account from Google with over 2,800 megabytes of
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From arebol2 at uic.edu  Wed Jul 14 23:03:25 2010
From: arebol2 at uic.edu (=?iso-8859-1?Q?=22Alejandro_R=E9bola=22?=)
Date: Wed, 14 Jul 2010 16:03:25 -0500
Subject: [Pw_forum] Question about vc-relax
Message-ID: <21d812dc53a5e54c5f7861f42b5dc6b7.squirrel@webmail.uic.edu>

Hello everybody,

I'm trying to do a structural optimization for FeSe (tetragonal). I want
pwscf to determine the optimal a and c and also one internal parameter:
the z coordinate for Se. I'm trying to do a vc-relax calculation, but I
get an error, apparently because I'm not including a Cell card. When I ran
over the examples for vc-relax, a Cell card is included. However, in this
case pwscf also changes the angles, and what I want is to keep the cell as
tetragonal and only look for the optimal a, c and z. Does anybody know
what I should do?
Thank you in advance for your help.
Best,

Alejandro

&control
    calculation= "vc-relax",
    pseudo_dir ='/home/alejandro/quantum_espresso/espresso-4.1.3/pseudo1',
outdir='/scratch/alejandro/espresso'
    verbosity = 'high',
    prefix='FeSe',
 /
 &system
    ibrav= 6,
    a=3.7,
    c=5.5,
    nat= 4, ntyp= 2,
    ecutwfc = 60.0, ecutrho = 350.0,
    occupations='smearing', smearing='mp', degauss=0.01,
 /
 &electrons
    mixing_beta = 0.5
 /
 &IONS
   ion_dynamics      = "damp",
   pot_extrapolation = "second_order",
   wfc_extrapolation = "second_order",
 /
ATOMIC_SPECIES
 Fe  1.  Fe.pbe-nd-rrkjus.UPF
 Se  1.  Se.pbe-van.UPF
ATOMIC_POSITIONS crystal
 Fe 0.75  0.25  0.0  0  0  0
 Fe 0.25  0.75  0.0  0  0  0
 Se 0.25  0.25  0.2  0  0  1
 Se 0.75  0.75 -0.2  0  0  1
K_POINTS automatic
 8 8 6 0 0 0





From hande at newton.physics.metu.edu.tr  Thu Jul 15 07:56:14 2010
From: hande at newton.physics.metu.edu.tr (Hande Ustunel)
Date: Thu, 15 Jul 2010 08:56:14 +0300 (EEST)
Subject: [Pw_forum] Question about vc-relax
In-Reply-To: <21d812dc53a5e54c5f7861f42b5dc6b7.squirrel@webmail.uic.edu>
Message-ID: <Pine.LNX.4.44.1007150851160.1804-100000@newton.physics.metu.edu.tr>

Dear Alejandro,

I think cell_dofree under the CELL section would do what you were looking
for. If you would only like to change the lengths of the cell vectors
without changing the angle inbetween them, you could use the option

    cell_dofree='xyz'

The internal parameter on the on the other hand would be spontaneously
relaxed during the geometric optimization to its optimal value obeying the
constrictions you have placed in your input.

Best regards,
Hande 

On Wed, 14 Jul 2010, "Alejandro R?bola" wrote:

> Hello everybody,
> 
> I'm trying to do a structural optimization for FeSe (tetragonal). I want
> pwscf to determine the optimal a and c and also one internal parameter:
> the z coordinate for Se. I'm trying to do a vc-relax calculation, but I
> get an error, apparently because I'm not including a Cell card. When I ran
> over the examples for vc-relax, a Cell card is included. However, in this
> case pwscf also changes the angles, and what I want is to keep the cell as
> tetragonal and only look for the optimal a, c and z. Does anybody know
> what I should do?
> Thank you in advance for your help.
> Best,
> 
> Alejandro
> 
> &control
>     calculation= "vc-relax",
>     pseudo_dir ='/home/alejandro/quantum_espresso/espresso-4.1.3/pseudo1',
> outdir='/scratch/alejandro/espresso'
>     verbosity = 'high',
>     prefix='FeSe',
>  /
>  &system
>     ibrav= 6,
>     a=3.7,
>     c=5.5,
>     nat= 4, ntyp= 2,
>     ecutwfc = 60.0, ecutrho = 350.0,
>     occupations='smearing', smearing='mp', degauss=0.01,
>  /
>  &electrons
>     mixing_beta = 0.5
>  /
>  &IONS
>    ion_dynamics      = "damp",
>    pot_extrapolation = "second_order",
>    wfc_extrapolation = "second_order",
>  /
> ATOMIC_SPECIES
>  Fe  1.  Fe.pbe-nd-rrkjus.UPF
>  Se  1.  Se.pbe-van.UPF
> ATOMIC_POSITIONS crystal
>  Fe 0.75  0.25  0.0  0  0  0
>  Fe 0.25  0.75  0.0  0  0  0
>  Se 0.25  0.25  0.2  0  0  1
>  Se 0.75  0.75 -0.2  0  0  1
> K_POINTS automatic
>  8 8 6 0 0 0
> 
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

-- 
Hande Toffoli
Department of Physics
Office 439
Middle East Technical University
Ankara 06531, Turkey
Tel : +90 312 210 3264
http://www.physics.metu.edu.tr/~hande


From giannozz at democritos.it  Thu Jul 15 08:59:11 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 15 Jul 2010 08:59:11 +0200
Subject: [Pw_forum] constraints: planar and torsion angles
In-Reply-To: <20100714153650.234150@gmx.net>
References: <20100714153650.234150@gmx.net>
Message-ID: <4C3EB1BF.3090006@democritos.it>

Norbert Nemec wrote:

> With my change, the constraints are now internally handled as angle [...]
> It works beautifully for my test case.

good! P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From an.floris at gmail.com  Thu Jul 15 12:14:55 2010
From: an.floris at gmail.com (Andrea Floris)
Date: Thu, 15 Jul 2010 11:14:55 +0100
Subject: [Pw_forum] DFPT+U
Message-ID: <AANLkTilfvTuA8OQz-DNy8jGwH7XUBB0kR-glDK3oVUDn@mail.gmail.com>

Dear Ali,

The DFPT+U has been recently implemented, and I am doing some
calculations on test materials, to see
how it performs. It will be public in the future, both in
norm-conserving and ultrasoft pseudopotentials.

Regards,

Andrea


> which version of espresso can do DFPT+U calculation?

some version in the future, I guess

P.
--
Paolo Giannozzi, Democritos and University of Udine, Italy

-- 
?Dr Andrea Floris
?Research Associate
?King's College London
?Strand, London WC2R 2LS
?United Kingdom
?Phone: +44 (0) 207 848 2064
?Fax? ? : +44 (0) 207 848 2420
?Room: 7.33 Strand Building
?Emails: andrea.floris at kcl.ac.uk, an.floris at gmail.com
?Internet: http://www.kcl.ac.uk/schools/pse/physics/people/research/floris/

From sks.jnc at gmail.com  Thu Jul 15 14:58:03 2010
From: sks.jnc at gmail.com (S. K. S.)
Date: Thu, 15 Jul 2010 14:58:03 +0200
Subject: [Pw_forum] DFPT+U
In-Reply-To: <AANLkTilfvTuA8OQz-DNy8jGwH7XUBB0kR-glDK3oVUDn@mail.gmail.com>
References: <AANLkTilfvTuA8OQz-DNy8jGwH7XUBB0kR-glDK3oVUDn@mail.gmail.com>
Message-ID: <AANLkTimz-l0MfkEUl0MZLOn4jrD4TQXQEouifCn2D2Ly@mail.gmail.com>

  Dear QE USERS,

  It is nice to know that the DFPT+U has been recently implemented.
  I hope, it will be public soon. If not, may I ask a developmental
implementation or
  executables, so that I can also perform some test calculations for my
systems ?
  Sometime carrying out FROZEN PHONON is boring.

  By the way, thanks a lot for the good news.

  Regards,
  Saha SK,
  R&D Assistant,
  JNC, Bangalore


On Thu, Jul 15, 2010 at 12:14 PM, Andrea Floris <an.floris at gmail.com> wrote:

> Dear Ali,
>
> The DFPT+U has been recently implemented, and I am doing some
> calculations on test materials, to see
> how it performs. It will be public in the future, both in
> norm-conserving and ultrasoft pseudopotentials.
>
> Regards,
>
> Andrea
>
>
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From masoudnahali at live.com  Thu Jul 15 15:38:58 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Thu, 15 Jul 2010 18:08:58 +0430
Subject: [Pw_forum] vc-relax and dt
Message-ID: <AANLkTimtFbI-zn8czEJdrlEy-Hsdv-UZ37QZgy8SY5ad@mail.gmail.com>

Dear PWscf Users

Is using and setting the variable "dt" in the vc-relax calculation necessary
or not ? In the forum are many different suggestions. Also, how can one
determine which value of
the variable "max_seconds" is sufficient and safe. when one does not use the
"max_seconds" the vc-relax calculation may takes huge time without changing
the cell
after a specific time.  A comprehensive example for vc-relax calculation
should be very useful.

Many Thanks
Masoud
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From sclauzer at sissa.it  Thu Jul 15 16:34:39 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Thu, 15 Jul 2010 16:34:39 +0200
Subject: [Pw_forum] vc-relax and dt
In-Reply-To: <AANLkTimtFbI-zn8czEJdrlEy-Hsdv-UZ37QZgy8SY5ad@mail.gmail.com>
References: <AANLkTimtFbI-zn8czEJdrlEy-Hsdv-UZ37QZgy8SY5ad@mail.gmail.com>
Message-ID: <0D6E91EA-7C0E-4822-AC8B-0D7A8E654168@sissa.it>


Il giorno 15/lug/2010, alle ore 15.38, Masoud Nahali ha scritto:

> Dear PWscf Users
> 
> Is using and setting the variable "dt" in the vc-relax calculation necessary or not ?

As far as I can understand, it is necessary only if you use damped dynamics. If you use BFGS algorithm (which is the default), it shouldn't.

> In the forum are many different suggestions. Also, how can one determine which value of
> the variable "max_seconds" is sufficient and safe.

Have you read the documentation??? This variable tells the code after which (elapsed) time the calculation should be stopped smoothly. It is needed only if you have some time constraints on how long you can run your job uninterruptedly (for instance, due to walltime restrictions in a supercomputing center). If you set the variable to a value below the walltime the code should stop and save everything before your job gets kicked out. Then you can restart your calculation safely. It does not affect the convergence of your calculation in any way.

> when one does not use the "max_seconds" the vc-relax calculation may takes huge time without changing the cell 
> after a specific time. 

This sound quite strange, the two things should not be related. I could barely believe they are...

> A comprehensive example for vc-relax calculation should be very useful.


Please have a look at examples/{example03,VCSexample} and here:
http://www.quantum-espresso.org/wiki/index.php/QESB09
http://www.fisica.uniud.it/~giannozz/QE-Tutorial/

> 
> Many Thanks
> Masoud
>    
> _______________________________________________
> 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

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From degironc at sissa.it  Thu Jul 15 16:40:59 2010
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 15 Jul 2010 16:40:59 +0200
Subject: [Pw_forum] vc-relax and dt
In-Reply-To: <AANLkTimtFbI-zn8czEJdrlEy-Hsdv-UZ37QZgy8SY5ad@mail.gmail.com>
References: <AANLkTimtFbI-zn8czEJdrlEy-Hsdv-UZ37QZgy8SY5ad@mail.gmail.com>
Message-ID: <4C3F1DFB.5030604@sissa.it>

Masoud Nahali wrote:
> Dear PWscf Users
>
> Is using and setting the variable "dt" in the vc-relax calculation necessary
> or not ? In the forum are many different suggestions.
the value of dt is needed if you perform damped molecular dynamics. it 
is NOT, nor it is necessary to specify the cell mass (wcell) if you 
relax by bfgs . I would use bfgs... which, by the way,  is the default.

>  Also, how can one
> determine which value of
> the variable "max_seconds" is sufficient and safe. when one does not use the
> "max_seconds" the vc-relax calculation may takes huge time without changing
> the cell
> after a specific time. 
max_seconds has nothing to do with vc-relax... it is a variable that can 
be used to instruct the code to stop cleanly after some specified time 
(that should be shorter than the time-limit if the queue you are using) 
so that the calculation can be restarted smoothly.
Please read the corresponding entry in INPUT_PW.html input description.
>  A comprehensive example for vc-relax calculation
> should be very useful.
>   
VCSexample

> Many Thanks
> Masoud
>
>   
stefano
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From baroni at sissa.it  Thu Jul 15 19:55:32 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 15 Jul 2010 19:55:32 +0200
Subject: [Pw_forum] constraints: planar and torsion angles
In-Reply-To: <20100714153650.234150@gmx.net>
References: <20100714153650.234150@gmx.net>
Message-ID: <A0D6DDD1-DCDC-45DC-B554-6AA42C49618D@sissa.it>

thanks - SB

On Jul 14, 2010, at 5:36 PM, Norbert Nemec wrote:

> Hi there,
> 
> in case someone is curious about the commits I just checked in. Apart from some cleanup and some better logging output, I changed the internal handling of angle constraints:
> 
> Planar and and torsion angles used to be handled internally by their cosine. This had caused a problem for angles of 0 or 180 degree, where the derivative of the constraint would become zero and the constraint could not be enforced correctly. Specifically, this caused problems for planar benzene molecules that I tried to constrain.
> 
> With my change, the constraints are now internally handled as angle, the torsion angle as signed angle. It works beautifully for my test case. I adjusted the metadynamics code, otherwise, no code seems to be affected.
> 
> For the user, there should be no difference except in the case that someone would have explicitly specified torsion angles with incorrect sign in the input file. I doubt that anyone would do that...
> 
> Greetings,
> Norbert
> -- 
> GMX DSL: Internet-, Telefon- und Handy-Flat ab 19,99 EUR/mtl.  
> Bis zu 150 EUR Startguthaben inklusive! http://portal.gmx.net/de/go/dsl
> _______________________________________________
> 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







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From masoudnahali at live.com  Thu Jul 15 22:23:45 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Fri, 16 Jul 2010 00:53:45 +0430
Subject: [Pw_forum] vc-relax and dt
Message-ID: <AANLkTilw8g8iiQRBURpb_Y5Jw6ghbvj2esL_MO_0a3_f@mail.gmail.com>

Dear Stefano and Gabriele

Many many thanks for the clear explanations. It was very useful.  the
"max_seconds" variable has implemented in a example which is available in
"VCSexample" folder and I thought that is physically important.

Truly Yours
Masoud Nahali
SUT
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From jiachen at princeton.edu  Fri Jul 16 18:34:33 2010
From: jiachen at princeton.edu (jia chen)
Date: Fri, 16 Jul 2010 12:34:33 -0400
Subject: [Pw_forum] about U value determination in DFT+U calculation
Message-ID: <AANLkTikzO_0g_hLE6Gz-eqIhowP9xU4209lnO5Gu6qvM@mail.gmail.com>

Dear All,

I am doing a calculation to determine U value for DFT+U calculation
following method of Prof Cococcioni by pw 4.2. I did the similar work
several months before and I always could get making sense values, so I
think I can handle this method. But this time, results I obtained are
very wired. Because I am using semi-core pseudopotential which
contains both 3d and 4d atomic orbitals, I wonder if this can cause a
problem. When projecting KS states to atomic orbitals in order to
calculate occupation number, if it is possible that pw code could mess
up 3d and 4d orbitals? In my case, 3d is occupied and 4d should be
empty. If pw code can pick up 3d orbitals without any problem, I made
some mistakes and apologize here. Any suggestion is greatly
appreciate!

Best Wishes
-- 
Jia Chen

Dept of Chemistry
Princeton University
Princeton, NJ 08544

From gianluca.giovannetti at gmail.com  Sat Jul 17 07:27:16 2010
From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti)
Date: Sat, 17 Jul 2010 07:27:16 +0200
Subject: [Pw_forum] GW for large systems
Message-ID: <AANLkTimiJzrbm4OnuGzSDBkY7dgPEAIAS2nGelKUBPL6@mail.gmail.com>

Dear All,

i want to do GW calculations on a large system containing 120 ions.

i would say i can try to run it with the scheme proposed by P. Umari, G.
Stenuit and S. Baroni, *Optimal representation of the polarization
propagator for large-scale GW calculations*, Phys. Rev. B *79* (2009)
201104(R).

do you have some experience about it?

i hope a such calculation can be dealt with this scheme.

is it available the GW scheme mentioned above in some version of Quantum
Espresso?

i have found at the website:

http://gww.qe-forge.org/index.php?page=intro

a good description about how to use it.

is it available with 4.2.1 version?

i thank you in advance.

cheers,

Gianluca Giovannetti
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From masoudnahali at live.com  Sun Jul 18 08:38:42 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Sun, 18 Jul 2010 11:08:42 +0430
Subject: [Pw_forum] c_bands: 4 eigenvalues not converged
Message-ID: <AANLkTimWqjPiUbJBORYV-48SkZYIlTXJozbRHlz8gKex@mail.gmail.com>

Dear PWscf Users


I get the below lines in the first iterations but after the iteration  #  4
or 5 disappears and again in the next steps the story repeats.

 Davidson diagonalization with overlap
c_bands:  1 eigenvalues not converged
c_bands:  4 eigenvalues not converged

As proposed in the manual and forum I tried to ran the Job without
considering symmetry and the number of such lines reduced but did not
disappear completely and
the vc-relax calculation in such way is too time consuming and not completed
yet.
My system is a 3 layers graphite with palladium impurity. I do not know that
I must be worry of encountering such lines or not? Also, May you please say
me the "c_band" is related to my Carbon atoms or not? I appreciate your
help.


 &CONTROL
  calculation  = "vc-relax",
  etot_conv_thr= 1.0D-4,
  forc_conv_thr= 1.0D-3,
       /
&SYSTEM
  ibrav     = 4,
  a         = 4.9178,
  b         = 4.9178,
  c         = 22.8224,
  cosab     = -0.5,
  cosac     = 1.0,
  cosbc     = 1.0,
  nat       = 25,
  ntyp      = 2,
  ecutwfc   = 40.D0,
  ecutrho   = 480.D0,
  occupations = 'smearing'
  smearing ='mp',
  degauss = 0.03,
  nspin = 2,
  starting_magnetization(1)= 0.01,
  starting_magnetization(2)= 0.5,
  london=.true.,
  /
&ELECTRONS
  conv_thr    = 1.D-6,
  mixing_beta = 0.7D0,
  diagonalization = "david",
/
&IONS
 ion_dynamics="bfgs"
/
&CELL
cell_dynamics = 'bfgs',
press = 0.0,
/

Many Thanks
Masoud Nahali
SUT
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From giannozz at democritos.it  Sun Jul 18 11:31:36 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 18 Jul 2010 11:31:36 +0200
Subject: [Pw_forum] c_bands: 4 eigenvalues not converged
In-Reply-To: <AANLkTimWqjPiUbJBORYV-48SkZYIlTXJozbRHlz8gKex@mail.gmail.com>
References: <AANLkTimWqjPiUbJBORYV-48SkZYIlTXJozbRHlz8gKex@mail.gmail.com>
Message-ID: <735F88F5-DCA4-49EB-A9F7-2DE8354FF142@democritos.it>


On Jul 18, 2010, at 8:38 , Masoud Nahali wrote:

> I get the below lines in the first iterations but after the  
> iteration  #  4 or 5 disappears and again in the next steps the  
> story repeats.
>
>  Davidson diagonalization with overlap
> c_bands:  1 eigenvalues not converged
> c_bands:  4 eigenvalues not converged
>
> As proposed in the manual and forum I tried to ran the Job without  
> considering symmetry

where did you read that?

\paragraph{{\em Warning : N eigenvectors not converged}}
This is a warning message that can be safely ignored if it is not
present in the last steps of self-consistency. If it is still present
in the last steps of self-consistency, and if the number of
unconverged eigenvector is a significant part of the total, it may
signal serious trouble in self-consistency (see next point) or
something badly wrong in input data.

> I do not know that I must be worry of encountering such lines or not?

as explained above, you shouldn't.

> Also, May you please say me the "c_band" is related to my Carbon  
> atoms or not?

no: "c_bands" is the routine that issues the message

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From giannozz at democritos.it  Sun Jul 18 11:33:57 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 18 Jul 2010 11:33:57 +0200
Subject: [Pw_forum] c_bands: 4 eigenvalues not converged
In-Reply-To: <735F88F5-DCA4-49EB-A9F7-2DE8354FF142@democritos.it>
References: <AANLkTimWqjPiUbJBORYV-48SkZYIlTXJozbRHlz8gKex@mail.gmail.com>
	<735F88F5-DCA4-49EB-A9F7-2DE8354FF142@democritos.it>
Message-ID: <CD041C1C-4152-455F-BCFC-9BFF192A852F@democritos.it>


On Jul 18, 2010, at 11:31 , Paolo Giannozzi wrote:

>> I do not know that I must be worry of encountering such lines or not?
>
> as explained above, you shouldn't.

I meant: "you shouldn't worry"

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From masoudnahali at live.com  Mon Jul 19 12:33:10 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Mon, 19 Jul 2010 15:03:10 +0430
Subject: [Pw_forum] c_bands: 4 eigenvalues not converged
Message-ID: <AANLkTikNBDiTu_WVvyA0raahUQSzQ96zBK45YpA83e01@mail.gmail.com>

Dear Paolo Giannozzi

Many thanks for your help. I had a mistake and  thought that it is a
significant error of vc-relax.


> > I get the below lines in the first iterations but after the
> > iteration  #  4 or 5 disappears and again in the next steps the
> > story repeats.
> >
> >  Davidson diagonalization with overlap
> > c_bands:  1 eigenvalues not converged
> > c_bands:  4 eigenvalues not converged
> >
> > As proposed in the manual and forum I tried to ran the Job without
> > considering symmetry
>
> where did you read that?
>
> \paragraph{{\em Warning : N eigenvectors not converged}}
> This is a warning message that can be safely ignored if it is not
> present in the last steps of self-consistency. If it is still present
> in the last steps of self-consistency, and if the number of
> unconverged eigenvector is a significant part of the total, it may
> signal serious trouble in self-consistency (see next point) or
> something badly wrong in input data.
>
> > I do not know that I must be worry of encountering such lines or not?
>
> as explained above, you shouldn't.
>
> > Also, May you please say me the "c_band" is related to my Carbon
> > atoms or not?
>
> no: "c_bands" is the routine that issues the message
>
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>     Best Wishes
    Masoud Nahali
    SUT
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From gianluca.giovannetti at gmail.com  Mon Jul 19 14:23:52 2010
From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti)
Date: Mon, 19 Jul 2010 14:23:52 +0200
Subject: [Pw_forum] pseudopotential rare earths
Message-ID: <AANLkTiln9SbLF_kO0UQV5JyjPPeYvNHdtzm3u2k2Jd1H@mail.gmail.com>

Dear All,

i want to look at systems like R-Mo2-O7 R being rare hearths elements.

the physics of the system should be governed by Mo d levels so probably i
can make pseudo-potentials of R even if DFT is not fully working for R.

i wanted to ask to have the inputs file of La (is is present in the web
page) in order to have a look at them.
this would be useful as i`m not really expert in making pseudos.

may i have it? is there someone having it?

do you have good advices to give me before i start to look at this?

thank you in advance.

cheers,

Gianluca Giovannetti
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From sclauzer at sissa.it  Mon Jul 19 15:30:58 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Mon, 19 Jul 2010 15:30:58 +0200
Subject: [Pw_forum] about U value determination in DFT+U calculation
In-Reply-To: <AANLkTikzO_0g_hLE6Gz-eqIhowP9xU4209lnO5Gu6qvM@mail.gmail.com>
References: <AANLkTikzO_0g_hLE6Gz-eqIhowP9xU4209lnO5Gu6qvM@mail.gmail.com>
Message-ID: <4C445392.2070408@sissa.it>

Dear Jia Chen,

  On 07/16/2010 06:34 PM, jia chen wrote:
> Dear All,
>
> I am doing a calculation to determine U value for DFT+U calculation
> following method of Prof Cococcioni by pw 4.2. I did the similar work
> several months before and I always could get making sense values, so I
> think I can handle this method. But this time, results I obtained are
> very wired. Because I am using semi-core pseudopotential which
> contains both 3d and 4d atomic orbitals, I wonder if this can cause a
> problem. When projecting KS states to atomic orbitals in order to
> calculate occupation number, if it is possible that pw code could mess
> up 3d and 4d orbitals? In my case, 3d is occupied and 4d should be
> empty.
If the 4d orbital has the occupation set to zero in the pseudopotential 
(look inside the header of the PP file), then the code should select the 
3d orbitals to build the local occupations needed for DFT+U. Please have 
a look at subroutine PW/offset_atom_wfc.f90 and eventually add some 
debugging printout instruction to be sure that the correct wavefunctions 
are selected (compare with the header of the PP file, the atomic 
wavefunctions should be processed in the same order as listed therein).
If you find still problems, please add more information to your next 
post, otherwise it will be hard to help you further. For instance, if 
you compute the isolated atom with pw.x, how much are the occupations 
written on output when lda_plus_U=.true.? Do they coincide with the 
occupation of the 3d orbital as written in the PP?

Regards,

GS


> If pw code can pick up 3d orbitals without any problem, I made
> some mistakes and apologize here. Any suggestion is greatly
> appreciate!
>
> Best Wishes
>    


-- 

Gabriele Sclauzero, EPFL SB ITP CSEA
PH H2 462, Station 3, CH-1015 Lausanne


From elie.moujaes at hotmail.co.uk  Mon Jul 19 20:29:29 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Mon, 19 Jul 2010 19:29:29 +0100
Subject: [Pw_forum] c_bands: eigenvalues not converged ina bilayer graphene
 calculations with an electric field
Message-ID: <SNT114-W4DAE97601641B808D945AD3BF0@phx.gbl>


I am trying to obtain the DOS (electronic) for a bilayer graphene when a homogeneous electric field is applied but the scf convergence is not being achieved and a lot of messages "c_bands: eigenvalues not converged" are displayed. I checked my input..I cannot see anything wrong..My conv_thresh is small enough..I will display my input and the output will be attached (i stopped the compilation at some point):

 

thanks

 

Elie Moujaes

University of Nottingham

NG7 2RD 

UK

 

The scf input is:

 

  &control
    prefix='bi graphene',
    calculation='scf',
    restart_mode='from_scratch',
    lelfield = .true.,
    pseudo_dir = '/espresso-4.2/pseudo/',
    outdir='/tmp/results_MOUJAES/'
 /
 &system    
    ibrav=  4, celldm(1) =4.608737, celldm(3)=5.330410, nat=4, ntyp= 1,
    ecutwfc = 60.D0, nosym=.true.,occupations='smearing', smearing='XYZ', degauss=0.01
/
 &electrons
    conv_thr=1.D-8,     
    mixing_beta=0.1D0,
    mixing_mode='local-TF'
    efield_cart(1) = 0.0,
    efield_cart(2) = 0.0,
    efield_cart(3) = 0.00275021,
 /
ATOMIC_SPECIES
 C  12.00000  C.pz-rrkjus.UPF
ATOMIC_POSITIONS crystal
 C 0.000000  0.000000  0.000000  
 C 0.000000  0.000000  0.257692 
 C 0.333333  -0.33333  0.000000  
 C -0.333333  0.33333  0.257692  
 
K_POINTS automatic
   20 20 1  0 0 0  
 
Many thanks again..

 

 
 		 	   		  
_________________________________________________________________
http://clk.atdmt.com/UKM/go/197222280/direct/01/
Do you have a story that started on Hotmail? Tell us now
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From eyvaz_isaev at yahoo.com  Mon Jul 19 21:15:10 2010
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 19 Jul 2010 12:15:10 -0700 (PDT)
Subject: [Pw_forum] c_bands: eigenvalues not converged ina bilayer
	graphene calculations with an electric field
In-Reply-To: <SNT114-W4DAE97601641B808D945AD3BF0@phx.gbl>
References: <SNT114-W4DAE97601641B808D945AD3BF0@phx.gbl>
Message-ID: <791731.74022.qm@web65703.mail.ac4.yahoo.com>

Dear Elie,

Have you read a discussion tree about this message in the forum, or even simpler 
- User Guide?

> ecutwfc = 60.D0
> C  12.00000  C.pz-rrkjus.UPF

You vast time with such kind unusually   high cutoff energy with US-type 
pseudopotential for  which is ecutwfc  typically is about 25-30Ry. Besides, you 
should add "ecutrho", 8-10 times of ecutwfc. For more information please see 
User Guide in your QE distribution directory.


>smearing='XYZ'

Is it really used in your  calculations?

Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, 
Sweden 

Theoretical Physics Department, Moscow State Institute of Steel & Alloys, 
Russia, 

isaev at ifm.liu.se, eyvaz_isaev at yahoo.com

 
 
 /
 &system    
    ibrav=  4, celldm(1) =4.608737, celldm(3)=5.330410, nat=4, ntyp= 1,
    ecutwfc = 60.D0, nosym=.true.,occupations='smearing', smearing='XYZ', 
degauss=0.01
/
 &electrons
    conv_thr=1.D-8,     
    mixing_beta=0.1D0,
    mixing_mode='local-TF'
    efield_cart(1) = 0.0,
    efield_cart(2) = 0.0,
    efield_cart(3) = 0.00275021,
 /
ATOMIC_SPECIES
 C  12.00000  C.pz-rrkjus.UPF
ATOMIC_POSITIONS crystal
 C 0.000000  0.000000  0.000000  
 C 0.000000  0.000000  0.257692 
 C 0.333333  -0.33333  0.000000  
 C -0.333333  0.33333  0.257692  
 
K_POINTS automatic
   20 20 1  0 0 0  
 
Many thanks again..
 
 

________________________________
Get a new e-mail account with Hotmail - Free. Sign-up now.


      
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From giannozz at democritos.it  Mon Jul 19 21:33:44 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 19 Jul 2010 21:33:44 +0200
Subject: [Pw_forum] c_bands: eigenvalues not converged ina bilayer
	graphene calculations with an electric field
In-Reply-To: <SNT114-W4DAE97601641B808D945AD3BF0@phx.gbl>
References: <SNT114-W4DAE97601641B808D945AD3BF0@phx.gbl>
Message-ID: <05D65AAE-588C-4CDD-B2C3-151FDB4EF95C@democritos.it>


On Jul 19, 2010, at 20:29 , Elie Moujaes wrote:

> I am trying to obtain the DOS (electronic) for a bilayer graphene
> when a homogeneous electric field is applied but the scf convergence
> is not being achieved

you should first make a calculation without electric field, then turn
the electric field on, reading the initial wavefunctions and charge
density from the previous case. See example 31

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From elie.moujaes at hotmail.co.uk  Mon Jul 19 21:43:57 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Mon, 19 Jul 2010 20:43:57 +0100
Subject: [Pw_forum] c_bands: eigenvalues not converged ina
	bilayer	graphene calculations with an electric field
In-Reply-To: <791731.74022.qm@web65703.mail.ac4.yahoo.com>
References: <SNT114-W4DAE97601641B808D945AD3BF0@phx.gbl>,
	<791731.74022.qm@web65703.mail.ac4.yahoo.com>
Message-ID: <SNT114-W16107D03B07D5C2DD63E68D3BF0@phx.gbl>


Thanks for Professors Eyvaz and Paulo's suggestions and for their time. 

 

Regards
 


Date: Mon, 19 Jul 2010 12:15:10 -0700
From: eyvaz_isaev at yahoo.com
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] c_bands: eigenvalues not converged ina bilayer graphene calculations with an electric field




Dear Elie,

Have you read a discussion tree about this message in the forum, or even simpler - User Guide?

> ecutwfc = 60.D0 
> C  12.00000  C.pz-rrkjus.UPF

You vast time with such kind unusually   high cutoff energy with US-type pseudopotential for  which is ecutwfc  typically is about 25-30Ry. Besides, you should add "ecutrho", 8-10 times of ecutwfc. For more information please see User Guide in your QE distribution directory.


>smearing='XYZ'

Is it really used in your  calculations?

Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


 
 
 /
 &system    
    ibrav=  4, celldm(1) =4.608737, celldm(3)=5.330410, nat=4, ntyp= 1,
    ecutwfc = 60.D0, nosym=.true.,occupations='smearing', smearing='XYZ', degauss=0.01
/
 &electrons
    conv_thr=1.D-8,     
    mixing_beta=0.1D0,
    mixing_mode='local-TF'
    efield_cart(1) = 0.0,
    efield_cart(2) = 0.0,
    efield_cart(3) = 0.00275021,
 /
ATOMIC_SPECIES
 C  12.00000  C.pz-rrkjus.UPF
ATOMIC_POSITIONS crystal
 C 0.000000  0.000000  0.000000  
 C 0.000000  0.000000  0.257692 
 C 0.333333  -0.33333  0.000000  
 C -0.333333  0.33333  0.257692  
 
K_POINTS automatic
   20 20 1  0 0 0  
 Many thanks again..
 
 



Get a new e-mail account with Hotmail - Free. Sign-up now.
 		 	   		  
_________________________________________________________________
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From jiachen at princeton.edu  Mon Jul 19 23:13:33 2010
From: jiachen at princeton.edu (jia chen)
Date: Mon, 19 Jul 2010 17:13:33 -0400
Subject: [Pw_forum] about U value determination in DFT+U calculation
Message-ID: <AANLkTinC9nvzZGFXOalfoIIne-b_2V0boZWsAJ5ktepb@mail.gmail.com>

Dear Gabriele Sclauzero,

Thank you so much for your help. I did an atomic calculation according to
your suggestion using that pseudo-potential. Sadly, the occupation number is
not correct.
first step
atom    1   Tr[ns(na)]=   7.0000000
and after optimization
atom    1   Tr[ns(na)]=   0.0748899

The pseudo-potential I got from website of QE named
Co.pbe-sp-mt_gipaw.UPF<http://www.pwscf.org/pseudo/1.3/UPF/Co.pbe-sp-mt_gipaw.UPF>
<http://www.pwscf.org/pseudo/1.3/UPF/Co.pbe-sp-mt_gipaw.UPF>and header of
this pseudo-potential is copied below

<PP_HEADER>
   0                   Version Number
  Co                   Element
   NC                  Norm - Conserving pseudopotential
    F                  Nonlinear Core Correction
 SLA  PW   PBX  PBC    PBE  Exchange-Correlation functional
   17.00000000000      Z valence
 -287.58146877626      Total energy
      0.000      0.000 Suggested cutoff for wfc and rho
    2                  Max angular momentum component
 1193                  Number of points in mesh
    6    2             Number of Wavefunctions, Number of Projectors
 Wavefunctions         nl  l   occ
                       3S  0  2.00
                       4S  0  0.00
                       3P  1  6.00
                       4P  1  0.00
                       3D  2  7.00
                       4D  2  0.00
</PP_HEADER>

According to your post, I don't think it can be any problem, but atomic
calculation I did is not correct. Can you give me further help about what
can go wrong? I looked inside offset_atom_wfc.f90, but I have no idea how to
check if pw picks right atomic wavefunction.... Can you give me some hints
about that? Thank you so much!

Bests
-- 
Jia Chen

Dept of Chemistry
Princeton University
Princeton, NJ 08544
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From lpadro at gatech.edu  Tue Jul 20 05:20:39 2010
From: lpadro at gatech.edu (Luz Padro)
Date: Mon, 19 Jul 2010 23:20:39 -0400
Subject: [Pw_forum] Two-electric fields method for Raman spectroscopy
Message-ID: <AANLkTilymYYeDX81MW1tnaAwG9QeqJ24zlaJesXYw_e9@mail.gmail.com>

Dear QE users,

I have checked the following thread in the Quantum Espresso forum:

http://www.democritos.it/pipermail/pw_forum/2007-May/006479.html

At the moment, it is not clear to me if the method to compute the atomic
forces under the influence of two different force fields using the CP.X code
has been actually implemented for non-cubic crystalline systems. Or is it
the case that the method described in "Infrared and Raman Spectra of
Disordered Materials from First Principles", Diamond and Related Materials
14, 1255 (2005)" is only applicable to cubic lattices?

Thanks for your help,
lpadro,
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From lpadro at gatech.edu  Tue Jul 20 05:27:50 2010
From: lpadro at gatech.edu (Luz Padro)
Date: Mon, 19 Jul 2010 23:27:50 -0400
Subject: [Pw_forum] Fwd: Two-electric fields method for Raman spectroscopy
In-Reply-To: <AANLkTilymYYeDX81MW1tnaAwG9QeqJ24zlaJesXYw_e9@mail.gmail.com>
References: <AANLkTilymYYeDX81MW1tnaAwG9QeqJ24zlaJesXYw_e9@mail.gmail.com>
Message-ID: <AANLkTinvWG8ZuVZlqaW7JZHZ0j3pvOdiAHNnv79WaJKE@mail.gmail.com>

Dear QE users,

I have checked the following thread in the Quantum Espresso forum:

http://www.democritos.it/pipermail/pw_forum/2007-May/006479.html

At the moment, it is not clear to me if the method to compute the atomic
forces under the influence of two different force fields using the CP.X code
has been actually implemented for non-cubic crystalline systems. Or is it
the case that the method described in "Infrared and Raman Spectra of
Disordered Materials from First Principles", Diamond and Related Materials
14, 1255 (2005)" is only applicable to cubic lattices?

Thanks for your help,
lpadro,
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From vitruss at gmail.com  Tue Jul 20 06:39:16 2010
From: vitruss at gmail.com (Vit)
Date: Tue, 20 Jul 2010 11:39:16 +0700
Subject: [Pw_forum] Hardware configuration for QE
Message-ID: <op.vf4kjoipijpzuf@arch.che.intra.net>

Dear, QE users!
We are planing to buy new cluster hardware for our lab purposes. The plan is to have 64 physical cores.
I have a bunch of questions regarding this:

1. Which network is preferable? Is Gbit enough? or Infiniband does the best?
2. Is it critical to have fast drives for local tmp filesystem on Gbit ethernet? Or it's considered better to have one common tmp through Infiniband and get rid of HDD's on nodes?
3. What is the amount of RAM recommended per 1 core in a node?

With best regards,
Koroteev Victor
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From kirtinandan07 at gmail.com  Tue Jul 20 07:27:11 2010
From: kirtinandan07 at gmail.com (vicky singh)
Date: Tue, 20 Jul 2010 10:57:11 +0530
Subject: [Pw_forum] how does the quantum espresso scale with increasing the
	number of nodes.
Message-ID: <AANLkTimQFPfsIhYBwyOy1CrtICPEN-M-hR_R6HOmEDwO@mail.gmail.com>

Hi
Can anybody let me know how does the quantum espresso scale with increasing
the number of nodes or number of processors. we have to establish a
computational facility. this information is required to know.
thanks
vicky singh
research student
Bangalore
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From kirtinandan07 at gmail.com  Tue Jul 20 07:58:00 2010
From: kirtinandan07 at gmail.com (vicky singh)
Date: Tue, 20 Jul 2010 11:28:00 +0530
Subject: [Pw_forum] how does the quantum espresso scale with increasing the
	number of nodes.
Message-ID: <AANLkTilwel-AJBqFbcGrEeP_wnv5GuoBrn1b3M8JWzBP@mail.gmail.com>

Hi
Can anybody let me know how does the quantum espresso scale with increasing
the number of nodes or number of processors. we have to establish a
computational facility. this information is required to know.

I ran QE simulation with 40 atoms with 8 nodes and 12 nodes. the system got
relaxed in 2 days 11 hrs with 8 nodes but it could nod relax even in 3 days
with 12 nodes. i could not understand why.

thanks in advance

vicky singh
research student
Bangalore
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From giannozz at democritos.it  Tue Jul 20 09:47:29 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 20 Jul 2010 09:47:29 +0200
Subject: [Pw_forum] how does the quantum espresso scale with increasing
 the	number of nodes.
In-Reply-To: <AANLkTilwel-AJBqFbcGrEeP_wnv5GuoBrn1b3M8JWzBP@mail.gmail.com>
References: <AANLkTilwel-AJBqFbcGrEeP_wnv5GuoBrn1b3M8JWzBP@mail.gmail.com>
Message-ID: <4C455491.2010809@democritos.it>

vicky singh wrote:

> Can anybody let me know how does the quantum espresso scale with 
> increasing the number of nodes or number of processors. 

short answer: it depends. Please read the documentation, in
particular sec.3 of the userguide; sec.5 of J.Phys. Condens.
Matter 21, 395502 (2009); the following slides:
http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_para.pdf

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From sclauzer at sissa.it  Tue Jul 20 11:24:17 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 20 Jul 2010 11:24:17 +0200
Subject: [Pw_forum] about U value determination in DFT+U calculation
In-Reply-To: <AANLkTinC9nvzZGFXOalfoIIne-b_2V0boZWsAJ5ktepb@mail.gmail.com>
References: <AANLkTinC9nvzZGFXOalfoIIne-b_2V0boZWsAJ5ktepb@mail.gmail.com>
Message-ID: <4C456B41.7090808@sissa.it>

Dear Jia Chen,

    do you really need to use this specific pseudopotential? It looks 
like it was built for specific purposes (XPS calculations) and has some 
non-standard features (in my opinion at least). Specifically, it has 
more wavefunctions than beta projectors and moreover the 3d channel is 
treated as local (I don't if and how this may affect transferability).
However the 3D wavefunction is present and has occupation greater than 
zero (contrary to the 4D wfc), so I can't see the reason why the code 
should give such result. I will have a look at it, but in the meanwhile 
I suggest you to try also one of the other PBE  PPs for Co which are 
present on the QE website.


GS

On 07/19/2010 11:13 PM, jia chen wrote:
> Dear Gabriele Sclauzero,
>
> Thank you so much for your help. I did an atomic calculation according 
> to your suggestion using that pseudo-potential. Sadly, the occupation 
> number is not correct.
> first step
> atom    1   Tr[ns(na)]=   7.0000000
> and after optimization
> atom    1   Tr[ns(na)]=   0.0748899
>
> The pseudo-potential I got from website of QE named 
> Co.pbe-sp-mt_gipaw.UPF 
> <http://www.pwscf.org/pseudo/1.3/UPF/Co.pbe-sp-mt_gipaw.UPF>
> and header of this pseudo-potential is copied below
> <PP_HEADER>
>     0                   Version Number
>    Co                   Element
>     NC                  Norm - Conserving pseudopotential
>      F                  Nonlinear Core Correction
>   SLA  PW   PBX  PBC    PBE  Exchange-Correlation functional
>     17.00000000000      Z valence
>   -287.58146877626      Total energy
>        0.000      0.000 Suggested cutoff for wfc and rho
>      2                  Max angular momentum component
>   1193                  Number of points in mesh
>      6    2             Number of Wavefunctions, Number of Projectors
>   Wavefunctions         nl  l   occ
>                         3S  0  2.00
>                         4S  0  0.00
>                         3P  1  6.00
>                         4P  1  0.00
>                         3D  2  7.00
>                         4D  2  0.00
> </PP_HEADER>
>    
> According to your post, I don't think it can be any problem, but 
> atomic calculation I did is not correct. Can you give me further help 
> about what can go wrong? I looked inside offset_atom_wfc.f90, but I 
> have no idea how to check if pw picks right atomic wavefunction.... 
> Can you give me some hints about that? Thank you so much!
>
> Bests
> -- 
> Jia Chen
>
> Dept of Chemistry
> Princeton University
> Princeton, NJ 08544
>
>
> _______________________________________________
> 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

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From sclauzer at sissa.it  Tue Jul 20 12:31:10 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 20 Jul 2010 12:31:10 +0200
Subject: [Pw_forum] about U value determination in DFT+U calculation
In-Reply-To: <4C456B41.7090808@sissa.it>
References: <AANLkTinC9nvzZGFXOalfoIIne-b_2V0boZWsAJ5ktepb@mail.gmail.com>
	<4C456B41.7090808@sissa.it>
Message-ID: <4C457AEE.9090107@sissa.it>

On 07/20/2010 11:24 AM, Gabriele Sclauzero wrote:
> Dear Jia Chen,
>
>    do you really need to use this specific pseudopotential? It looks 
> like it was built for specific purposes (XPS calculations) and has 
> some non-standard features (in my opinion at least). Specifically, it 
> has more wavefunctions than beta projectors and moreover the 3d 
> channel is treated as local (I don't if and how this may affect 
> transferability).
> However the 3D wavefunction is present and has occupation greater than 
> zero (contrary to the 4D wfc), so I can't see the reason why the code 
> should give such result. 

Actually I realized that the subroutine checks if the occupation is 
greater OR equal to zero, so that in your case the 4D wavefunction is 
actually selected, because it is listed after the 3D.

You can solve this problem by changing the following line (in 
offset_atom_wfc.f90)
    IF ( upf(nt)%lchi(n) == Hubbard_l(nt) ) offset(na) = counter
into
    IF ( upf(nt)%oc(n) > 0.D0 .AND. upf(nt)%lchi(n) == Hubbard_l(nt) ) 
offset(na) = counter

I don't know if this fix does fit the general logic of DFT+U and 
deserves to be included permanently in the code: maybe it does, since in 
most cases one puts the +U correction to (partly) occupied electronic 
manifolds. At least so far I haven't seen anyone applying it to empty 
shells... does anyone have a clue/hint about that?

GS


> I will have a look at it, but in the meanwhile I suggest you to try 
> also one of the other PBE  PPs for Co which are present on the QE website.
>
>
> GS
>
> On 07/19/2010 11:13 PM, jia chen wrote:
>> Dear Gabriele Sclauzero,
>>
>> Thank you so much for your help. I did an atomic calculation 
>> according to your suggestion using that pseudo-potential. Sadly, the 
>> occupation number is not correct.
>> first step
>> atom    1   Tr[ns(na)]=   7.0000000
>> and after optimization
>> atom    1   Tr[ns(na)]=   0.0748899
>>
>> The pseudo-potential I got from website of QE named 
>> Co.pbe-sp-mt_gipaw.UPF 
>> <http://www.pwscf.org/pseudo/1.3/UPF/Co.pbe-sp-mt_gipaw.UPF>
>> and header of this pseudo-potential is copied below
>> <PP_HEADER>
>>     0                   Version Number
>>    Co                   Element
>>     NC                  Norm - Conserving pseudopotential
>>      F                  Nonlinear Core Correction
>>   SLA  PW   PBX  PBC    PBE  Exchange-Correlation functional
>>     17.00000000000      Z valence
>>   -287.58146877626      Total energy
>>        0.000      0.000 Suggested cutoff for wfc and rho
>>      2                  Max angular momentum component
>>   1193                  Number of points in mesh
>>      6    2             Number of Wavefunctions, Number of Projectors
>>   Wavefunctions         nl  l   occ
>>                         3S  0  2.00
>>                         4S  0  0.00
>>                         3P  1  6.00
>>                         4P  1  0.00
>>                         3D  2  7.00
>>                         4D  2  0.00
>> </PP_HEADER>
>>    
>> According to your post, I don't think it can be any problem, but 
>> atomic calculation I did is not correct. Can you give me further help 
>> about what can go wrong? I looked inside offset_atom_wfc.f90, but I 
>> have no idea how to check if pw picks right atomic wavefunction.... 
>> Can you give me some hints about that? Thank you so much!
>>
>> Bests
>> -- 
>> Jia Chen
>>
>> Dept of Chemistry
>> Princeton University
>> Princeton, NJ 08544
>>
>>
>> _______________________________________________
>> 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

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From dimpy.sharma at tyndall.ie  Tue Jul 20 15:41:15 2010
From: dimpy.sharma at tyndall.ie (Dimpy Sharma)
Date: Tue, 20 Jul 2010 14:41:15 +0100
Subject: [Pw_forum] Predicting the cpu time usage for bigger system withour
	doing the simulation
Message-ID: <D4A761F73683694BBD69D634FF298015533EEB@MAIL.tyndall.ie>

Hi Quantum espresso users.
I would like to predict an approximate CPU time usage to finish one scf calculation in quantum espresso for a system with 5 supercells. I have the CPU time usage for the same sytem with one supercell.So are there  any possible ways to predict the time needed for more number of supercell (for the same system) required in quantum espresso,without doing the simulations.Can I calcuate it from the following method 
Tscf= NiterTiter + Tinit
 
Thanks and Regards.
 
Dimpy
Dimpy Sharma
ETG-Group
Tyndall National Institute
Cork
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From Michael at ihpc.a-star.edu.sg  Tue Jul 20 16:15:18 2010
From: Michael at ihpc.a-star.edu.sg (Michael Sullivan)
Date: Tue, 20 Jul 2010 22:15:18 +0800
Subject: [Pw_forum] Predicting the cpu time usage for bigger system
 withour	doing the simulation
In-Reply-To: <D4A761F73683694BBD69D634FF298015533EEB@MAIL.tyndall.ie>
References: <D4A761F73683694BBD69D634FF298015533EEB@MAIL.tyndall.ie>
Message-ID: <EA1C6ED4FAC4B144B5AB82AC0041E8B91FF403AA63@shared-svc-exch.shared-svc.local>

Dimpy:

DFT usually scales as N^3 so I'd guess that it will take 5**3=125 times longer than the small system. You would probably gain somewhere due to fewer k-Points, etc. but that's my rough estimate.

Others may have other comments that I welcome...

Mike
michael at ihpc.a-star.edu.sg<mailto:michael at ihpc.a-star.edu.sg>
http://www.sullivan.sg/


From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Dimpy Sharma
Sent: Tuesday, July 20, 2010 9:41 PM
To: pw_forum at pwscf.org
Subject: [Pw_forum] Predicting the cpu time usage for bigger system withour doing the simulation

Hi Quantum espresso users.
I would like to predict an approximate CPU time usage to finish one scf calculation in quantum espresso for a system with 5 supercells. I have the CPU time usage for the same sytem with one supercell.So are there  any possible ways to predict the time needed for more number of supercell (for the same system) required in quantum espresso,without doing the simulations.Can I calcuate it from the following method
Tscf= NiterTiter + Tinit

Thanks and Regards.

Dimpy

Dimpy Sharma

ETG-Group

Tyndall National Institute

Cork

________________________________
This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.
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From daniel.forrer at unipd.it  Tue Jul 20 17:18:11 2010
From: daniel.forrer at unipd.it (Daniel Forrer)
Date: Tue, 20 Jul 2010 17:18:11 +0200
Subject: [Pw_forum] strange behavior of npool + nscf output
Message-ID: <AANLkTinUZzl8JMbG9ofYZDXoklHnWX_WHIz4Hkp8SNP1@mail.gmail.com>

Dear all,
in the output file of the nscf run, using npool > 1
the line of the type:
"Computing kpt #:    xx"
are printed only for a few k-points, precisely from kpt=1 to kpt=(total
kpt)/npool
we checked that the nscf run computes actually the whole set of k-points, so
that it is only a matter of the textual output.

kind regards

Daniel Forrer (Universit? di Padova)
Luca Sementa (IPCF-CNR Pisa)
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From sclauzer at sissa.it  Tue Jul 20 17:34:02 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 20 Jul 2010 17:34:02 +0200
Subject: [Pw_forum] strange behavior of npool + nscf output
In-Reply-To: <AANLkTinUZzl8JMbG9ofYZDXoklHnWX_WHIz4Hkp8SNP1@mail.gmail.com>
References: <AANLkTinUZzl8JMbG9ofYZDXoklHnWX_WHIz4Hkp8SNP1@mail.gmail.com>
Message-ID: <80A63ACB-80BD-4FAD-8B82-9ABC4D327D11@sissa.it>


Have you set verbosity='high' in the input? If so, I think this is the expected behavior of the code. When running in parallel, however, I suspect that only the IO node prints this information, so that's why you don't see this printout for all the k-points but only for those assigned to the first pool. Anyway, this should not affect the results in any way.

HTH

GS

Il giorno 20/lug/2010, alle ore 17.18, Daniel Forrer ha scritto:

> Dear all,
> in the output file of the nscf run, using npool > 1
> the line of the type:
> "Computing kpt #:    xx"
> are printed only for a few k-points, precisely from kpt=1 to kpt=(total kpt)/npool
> we checked that the nscf run computes actually the whole set of k-points, so that it is only a matter of the textual output.
> 
> kind regards
> 
> Daniel Forrer (Universit? di Padova)
> Luca Sementa (IPCF-CNR Pisa)
> _______________________________________________
> 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

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From daniel.forrer at unipd.it  Tue Jul 20 18:04:16 2010
From: daniel.forrer at unipd.it (Daniel Forrer)
Date: Tue, 20 Jul 2010 18:04:16 +0200
Subject: [Pw_forum] strange behavior of npool + nscf output
In-Reply-To: <80A63ACB-80BD-4FAD-8B82-9ABC4D327D11@sissa.it>
References: <AANLkTinUZzl8JMbG9ofYZDXoklHnWX_WHIz4Hkp8SNP1@mail.gmail.com>
	<80A63ACB-80BD-4FAD-8B82-9ABC4D327D11@sissa.it>
Message-ID: <AANLkTimwW9ybL0-fGd9gLQgYr2LqqR6yG5S4SnFJdIiN@mail.gmail.com>

Dear Gabriele,
thank you for your prompt answer.
Indeed, we set verbosity = 'high'.
It was a little confusing to us that this line was present only for a subset
of k-points.

regards
Daniel and Luca



2010/7/20 Gabriele Sclauzero <sclauzer at sissa.it>

>
> Have you set verbosity='high' in the input? If so, I think this is the
> expected behavior of the code. When running in parallel, however, I suspect
> that only the IO node prints this information, so that's why you don't see
> this printout for all the k-points but only for those assigned to the first
> pool. Anyway, this should not affect the results in any way.
>
> HTH
>
> GS
>
> Il giorno 20/lug/2010, alle ore 17.18, Daniel Forrer ha scritto:
>
> Dear all,
> in the output file of the nscf run, using npool > 1
> the line of the type:
> "Computing kpt #:    xx"
> are printed only for a few k-points, precisely from kpt=1 to kpt=(total
> kpt)/npool
> we checked that the nscf run computes actually the whole set of k-points,
> so that it is only a matter of the textual output.
>
> kind regards
>
> Daniel Forrer (Universit? di Padova)
> Luca Sementa (IPCF-CNR Pisa)
> _______________________________________________
> 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
>
>


-- 
 ----------------------------------

  Daniel Forrer
  Dipartimento di Scienze Chimiche
  Universit? degli Studi di Padova
  V. Marzolo 1, Padova
  mail   daniel.forrer at unipd.it
  tel.   +39 049 8275166

 ----------------------------------
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From jjhaver at purdue.edu  Tue Jul 20 23:45:27 2010
From: jjhaver at purdue.edu (Janam)
Date: Tue, 20 Jul 2010 17:45:27 -0400
Subject: [Pw_forum] Si bandgap using hybrid functionals
Message-ID: <4C4618F7.9000009@purdue.edu>

Hi,

I'm trying to get the right band gap (~1.12 eV) for Silicon using hybrid 
functions. I'm using espresso 4.2. Unfortunately, the band gap doesn't 
seem to be affected by using the hybrid functionals.

For example, when I use Si.pb-rrkj.UPF (no hybrid functional), I get a 
band gap of 0.633eV. When I use the same pseudopotential with B3LYP, I 
get a band gap of 0.583.

I've posting my scf input file below. Any help/advice would be greatly 
appreciated

&control
    prefix='si-pbe-b3lyp',
    pseudo_dir='/home/nanohub/janam/QuantumEspresso/Si/pseudo'
    outdir ='/home/nanohub/janam/QuantumEspresso/Si/tmp',
    tstress = .true.,
    tprnfor = .true.,
 /
 &system   
    ibrav=  2, celldm(1) =10.35, nat=  2, ntyp= 1,
    ecutwfc = 80.0, input_dft="b3lyp",
 /
 &electrons
    conv_thr=1E-7
 /
ATOMIC_SPECIES
 Si  28.086  Si.pbe-rrkj.UPF
ATOMIC_POSITIONS
 Si 0.00 0.00 0.00
 Si 0.25 0.25 0.25
K_POINTS automatic
   8 8 8 0 0 0

Sincerely
---
Janam Jhaveri
School of Electrical and Computer Engineering
Purdue University
C# (765)-409-1948


From psavita at crlindia.com  Wed Jul 21 06:50:45 2010
From: psavita at crlindia.com (psavita at crlindia.com)
Date: Wed, 21 Jul 2010 10:20:45 +0530
Subject: [Pw_forum] Pw_forum Digest, Vol 37,
 Issue 46 : Re: Predicting the cpu time usage for bigger system
 withour doing the simulation
In-Reply-To: <mailman.2670.1279635348.1814.pw_forum@pwscf.org>
References: <mailman.2670.1279635348.1814.pw_forum@pwscf.org>
Message-ID: <OF17043521.DACB341B-ON65257767.001A9EA7-65257767.001A9EA9@crlindia.com>

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From Michael at ihpc.a-star.edu.sg  Wed Jul 21 07:23:15 2010
From: Michael at ihpc.a-star.edu.sg (Michael Sullivan)
Date: Wed, 21 Jul 2010 13:23:15 +0800
Subject: [Pw_forum] Predicting the cpu time usage for bigger system
 withour	doing the simulation
In-Reply-To: <OF17043521.DACB341B-ON65257767.001A9EA7-65257767.001A9EA9@crlindia.com>
References: <mailman.2670.1279635348.1814.pw_forum@pwscf.org>
	<OF17043521.DACB341B-ON65257767.001A9EA7-65257767.001A9EA9@crlindia.com>
Message-ID: <EA1C6ED4FAC4B144B5AB82AC0041E8B91FF403AB62@shared-svc-exch.shared-svc.local>

Hi,

I chose N=5 because the original post referred to 5 supercells. If your system is twice as big it will be 2**3, or 8 times bigger.

For the second part of your message, I don't have a good way to know in advance how it's going to perform. Usually I run some tests and build up experience.

If I understand you clearly, I would guess you're running out of memory when you run on a smaller number of nodes. If you're using pools for k-point parallelization, the memory doesn't scale.

Mike
michael at ihpc.a-star.edu.sg<mailto:michael at ihpc.a-star.edu.sg>
http://www.sullivan.sg/

From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of psavita at crlindia.com
Sent: Wednesday, July 21, 2010 12:51 PM
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] Pw_forum Digest, Vol 37, Issue 46 : Re: Predicting the cpu time usage for bigger system withour doing the simulation

Hello Mike,

"DFT usually scales as N^3 so I'd guess that it will take 5**3=125 times longer than the small system. You would probably gain somewhere due to fewer k-Points, etc. but that's my rough estimate."

Regarding your above comment, may I know how you choose N=5, is it just an example?
I have similar related question.
Is it possible to know the most appropriate compute resources for running a simulation without actually carrying out the same? My experience on a cluster is that by specifying a smaller number of nodes than the demand often results into node failure. Can this be avoided?

Thanks in advance for any clarification.

Regards,
Savita Pundlik
Applications Group : Computational Materials Simulations
Computational Research Laboratories Ltd.,
Taco House, Damle Path, Off Law College Road
Pune - 411004, India.


________________________________
This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.
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From psavita at crlindia.com  Wed Jul 21 07:56:32 2010
From: psavita at crlindia.com (psavita at crlindia.com)
Date: Wed, 21 Jul 2010 11:26:32 +0530
Subject: [Pw_forum] Predicting the cpu time usage for bigger system
 withour doing the simulation
In-Reply-To: <mailman.2689.1279689811.1814.pw_forum@pwscf.org>
References: <mailman.2689.1279689811.1814.pw_forum@pwscf.org>
Message-ID: <OF0925A836.B82E91F0-ON65257767.0020A489-65257767.0020A48B@crlindia.com>

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From sclauzer at sissa.it  Wed Jul 21 09:28:51 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Wed, 21 Jul 2010 09:28:51 +0200
Subject: [Pw_forum] strange behavior of npool + nscf output
In-Reply-To: <AANLkTimwW9ybL0-fGd9gLQgYr2LqqR6yG5S4SnFJdIiN@mail.gmail.com>
References: <AANLkTinUZzl8JMbG9ofYZDXoklHnWX_WHIz4Hkp8SNP1@mail.gmail.com>	<80A63ACB-80BD-4FAD-8B82-9ABC4D327D11@sissa.it>
	<AANLkTimwW9ybL0-fGd9gLQgYr2LqqR6yG5S4SnFJdIiN@mail.gmail.com>
Message-ID: <4C46A1B3.9070608@sissa.it>

On 07/20/2010 06:04 PM, Daniel Forrer wrote:
> Dear Gabriele,
> thank you for your prompt answer.
> Indeed, we set verbosity = 'high'.
> It was a little confusing to us that this line was present only for a 
> subset of k-points.

I see. You are right, maybe this kind of printout should be modified in 
order to take into account the case with npool > 1, for the sake of 
completeness (and to avoid confusing users).

Regards,

Gabriele

>
> regards
> Daniel and Luca
>
>
>
> 2010/7/20 Gabriele Sclauzero <sclauzer at sissa.it 
> <mailto:sclauzer at sissa.it>>
>
>
>     Have you set verbosity='high' in the input? If so, I think this is
>     the expected behavior of the code. When running in parallel,
>     however, I suspect that only the IO node prints this information,
>     so that's why you don't see this printout for all the k-points but
>     only for those assigned to the first pool. Anyway, this should not
>     affect the results in any way.
>
>     HTH
>
>     GS
>
>     Il giorno 20/lug/2010, alle ore 17.18, Daniel Forrer ha scritto:
>
>>     Dear all,
>>     in the output file of the nscf run, using npool > 1
>>     the line of the type:
>>     "Computing kpt #:    xx"
>>     are printed only for a few k-points, precisely from kpt=1 to
>>     kpt=(total kpt)/npool
>>     we checked that the nscf run computes actually the whole set of
>>     k-points, so that it is only a matter of the textual output.
>>
>>     kind regards
>>
>>     Daniel Forrer (Universit? di Padova)
>>     Luca Sementa (IPCF-CNR Pisa)
>>     _______________________________________________
>>     Pw_forum mailing list
>>     Pw_forum at pwscf.org <mailto: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 <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> -- 
>  ----------------------------------
>
>   Daniel Forrer
>   Dipartimento di Scienze Chimiche
>   Universit? degli Studi di Padova
>   V. Marzolo 1, Padova
>   mail daniel.forrer at unipd.it <mailto:daniel.forrer at unipd.it>
>   tel.   +39 049 8275166
>
>  ----------------------------------
>
>
> _______________________________________________
> 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

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From masoudnahali at live.com  Wed Jul 21 10:59:15 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Wed, 21 Jul 2010 13:29:15 +0430
Subject: [Pw_forum] Sym.Ops
Message-ID: <AANLkTiloyAn2kZ4OdhuMsMuH6iPmhezWoGcwYe1YhD30@mail.gmail.com>

Dear PWscf Users

For the graphite bulk, in the output file I see "24 Sym.Ops." but for the
graphite surface (a slab with 10 angstrom vacuum) I see "6 Sym.Ops." . Is
this plausible and correct ?
I appreciate your help.

Many Thanks
Masoud Nahali
SUT
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From kirtinandan07 at gmail.com  Wed Jul 21 11:50:38 2010
From: kirtinandan07 at gmail.com (vicky singh)
Date: Wed, 21 Jul 2010 15:20:38 +0530
Subject: [Pw_forum] how does the quantum espresso scale with increasing
	the number of nodes.
In-Reply-To: <4C455491.2010809@democritos.it>
References: <AANLkTilwel-AJBqFbcGrEeP_wnv5GuoBrn1b3M8JWzBP@mail.gmail.com>
	<4C455491.2010809@democritos.it>
Message-ID: <AANLkTimmSZu8D-oEXhPqd7kXT4PrJeGfQ3o1F7ln2edW@mail.gmail.com>

Dear prof Giannozzi

sorry to disturb you but i want to ask one question. the same work raran QE
simulation with 40 atoms with 8 nodes and 12 nodes. the system got relaxed
in 2 days 11 hrs with 8 nodes but it could nod relax even in 3 days with 12
nodes. even it got relaxed with 16 nodes in 2 days 11 hrs but not relax in 6
days with 32 nodes.

can u help me out.

with regards


vicky singh
research student
Bangalore



On Tue, Jul 20, 2010 at 1:17 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

> vicky singh wrote:
>
> > Can anybody let me know how does the quantum espresso scale with
> > increasing the number of nodes or number of processors.
>
> short answer: it depends. Please read the documentation, in
> particular sec.3 of the userguide; sec.5 of J.Phys. Condens.
> Matter 21, 395502 (2009); the following slides:
> http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_para.pdf<http://www.fisica.uniud.it/%7Egiannozz/QE-Tutorial/tutorial_para.pdf>
>
> P.
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From sclauzer at sissa.it  Wed Jul 21 12:41:51 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Wed, 21 Jul 2010 12:41:51 +0200
Subject: [Pw_forum] Sym.Ops
In-Reply-To: <AANLkTiloyAn2kZ4OdhuMsMuH6iPmhezWoGcwYe1YhD30@mail.gmail.com>
References: <AANLkTiloyAn2kZ4OdhuMsMuH6iPmhezWoGcwYe1YhD30@mail.gmail.com>
Message-ID: <4C46CEEF.5070700@sissa.it>

On 07/21/2010 10:59 AM, Masoud Nahali wrote:
> Dear PWscf Users
>
> For the graphite bulk, in the output file I see "24 Sym.Ops." but for 
> the graphite surface (a slab with 10 angstrom vacuum) I see "6 
> Sym.Ops." . Is this plausible and correct ?

The symmetry operations are determined correctly in the code. The 
symmetry group that you get for a graphite slab depends on which type of 
graphite you consider  (i.e. hexagonal or Bernal) and how you build your 
slab. If your system has a mirror plane coinciding with z=0 (assuming z 
to be the stacking direction), then you will get 24 operations for an 
hexagonal graphite slab and 12 for a Bernal graphite slab (which is the 
maximum of the symmetry operations possible for each of the two systems).
To get more information about the symmetry on the output you can specify 
verbosity='high'.


HTH

GS


> I appreciate your help.
>
> Many Thanks
> Masoud Nahali
> SUT
>
>
> _______________________________________________
> 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

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From siyouber at yahoo.fr  Wed Jul 21 18:53:04 2010
From: siyouber at yahoo.fr (Bertrand SITAMTZE)
Date: Wed, 21 Jul 2010 16:53:04 +0000 (GMT)
Subject: [Pw_forum] Postprocessing code for MSD
Message-ID: <517598.85636.qm@web26501.mail.ukl.yahoo.com>

Dear all,

Last time? I posted on the calculation of Means Squared Displacement(MSD) through QE output? I didn't got satisfactory reactions. I tried to do it, but it was not succesfull.

Please could somebody give me a hint on how to postprocess the output files to get the MSD of each atom after molecular dynamic runs?

Is there any available code for this purpose? I have? the? same? problem with the calculation of Pair Correlation Function.


Thanks very much for your help.


************************
Bertrand SITAMTZE
Laboratory of Material Sciences
Department? of Physics
University of Yaounde I-Cameroon
****************************




      
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From adehaopan at hotmail.com  Wed Jul 21 20:54:16 2010
From: adehaopan at hotmail.com (HaoPan)
Date: Thu, 22 Jul 2010 02:54:16 +0800
Subject: [Pw_forum] ph.x faiedlbecause of the diagonalization
Message-ID: <SNT117-W13936EB17E352AEF3C16C2B6A10@phx.gbl>


Hi, everyone,

Is there anybody know the ph.x diagonalization crash?  I have searched the Archives saw someone 
had the same problem. But there is no solution.  I used the interactive mpirun to calculate the 
phonon, the crash happened at dyn2. 

     task #         0
     from cdiaghg : error #        33  (or 29,  51,etc)
     diagonalization (ZHEGV*) failed

Is that the problem of parallization? Should I compile QE again? 

Sincerely,
Pan Hao
 		 	   		  
_________________________________________________________________
MSN????????????????25???????????2010?????????
http://kaba.msn.com.cn/?k=1
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From hqzhou at nju.edu.cn  Thu Jul 22 03:48:59 2010
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Thu, 22 Jul 2010 09:48:59 +0800
Subject: [Pw_forum] how does the quantum espresso scale with
	increasingthe number of nodes.
References: <AANLkTilwel-AJBqFbcGrEeP_wnv5GuoBrn1b3M8JWzBP@mail.gmail.com><4C455491.2010809@democritos.it>
	<AANLkTimmSZu8D-oEXhPqd7kXT4PrJeGfQ3o1F7ln2edW@mail.gmail.com>
Message-ID: <705686E36D194AEEA60A4E228573BB34@solarflare>

vicky,

If by node you mean a compute node with 4 or 8 CPU cores, I'm afraid you
used too much compute resource. I had ever successfully optimized a spin 
polarized structure with 56 atoms by vc-relax on one compute node with 8 
CPU cores within several hours. Although you didn't mention what system 
you are calculating, I strongly recommend you try to run on one or two nodes 
to see how much wall time it'll take.

Efficiency of parallel computing depends on many things, one of which is the
system size. Usually you need to do simpler calculations to determine how
many cpu cores are optimal for your job. 


huiqun zhou
@earth sciences, nanjing University, china

  ----- Original Message ----- 
  From: vicky singh 
  To: PWSCF Forum 
  Sent: Wednesday, July 21, 2010 5:50 PM
  Subject: Re: [Pw_forum] how does the quantum espresso scale with increasingthe number of nodes.


  Dear prof Giannozzi

  sorry to disturb you but i want to ask one question. the same work raran QE simulation with 40 atoms with 8 nodes and 12 nodes. the system got relaxed in 2 days 11 hrs with 8 nodes but it could nod relax even in 3 days with 12 nodes. even it got relaxed with 16 nodes in 2 days 11 hrs but not relax in 6 days with 32 nodes.

  can u help me out.

  with regards 




  vicky singh
  research student
  Bangalore




  On Tue, Jul 20, 2010 at 1:17 PM, Paolo Giannozzi <giannozz at democritos.it> wrote:

    vicky singh wrote:

    > Can anybody let me know how does the quantum espresso scale with
    > increasing the number of nodes or number of processors.


    short answer: it depends. Please read the documentation, in
    particular sec.3 of the userguide; sec.5 of J.Phys. Condens.
    Matter 21, 395502 (2009); the following slides:
    http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_para.pdf

    P.
    --
    Paolo Giannozzi, Democritos and University of Udine, Italy

    _______________________________________________
    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
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From mambom1902 at yahoo.com  Thu Jul 22 05:16:48 2010
From: mambom1902 at yahoo.com (loc duong ding)
Date: Wed, 21 Jul 2010 20:16:48 -0700 (PDT)
Subject: [Pw_forum] band structure of graphene-size effect of unit cell
Message-ID: <474391.9869.qm@web38803.mail.mud.yahoo.com>

Dear all,

I have?a problem when I calculate?band structure of graphene. The band structure 
of graphene calculated by unit of 2 atoms and 8 atoms is different.?the gap at 
gama point as well as M point?are totally different. 


In general case, unit of?2 atoms and?unit of 8 atoms both create graphene 
strucutre. I can not unserstand why?they are different? Is my understanding is 
wrong? 


I know this is the general question but I hope I can receive?helpful 
instructions. 


I aprreciate all?ypur helps.?
?
Sincerely,-----------------------------------------------
Loc Duong Dinh
Ms-Ph.D Student
Sungkyunkwan Advanced Institute of Nanotechnology,
Sungkyunkwan University,
Suwon, 440-746, Korea 
Email: mambom1902 at yahoo.com, ddloc at skku.edu 


      

From nkxirainbow at gmail.com  Thu Jul 22 05:27:41 2010
From: nkxirainbow at gmail.com (xirainbow)
Date: Thu, 22 Jul 2010 11:27:41 +0800
Subject: [Pw_forum] band structure of graphene-size effect of unit cell
In-Reply-To: <474391.9869.qm@web38803.mail.mud.yahoo.com>
References: <474391.9869.qm@web38803.mail.mud.yahoo.com>
Message-ID: <AANLkTin0TzrPbT4OqzijhYR7QAAziuewh8yz6CEtpTDE@mail.gmail.com>

Dear Loc Duong Dinh?
The band structure must be different between 2 and 8 atoms in every unit
cell.
The coordinate of M point of 2 atoms is different from that of 8 atoms, for
the length of primitive vectors are different.
Furtheremore, there are 8 valence electrons in 2 atoms' unit cell. However,
there are 32 velence electrons in 8 atoms' unit cell.
I think you can refer to textbook of solid state physics for more
imformation.
On Thu, Jul 22, 2010 at 11:16 AM, loc duong ding <mambom1902 at yahoo.com>wrote:

> Dear all,
>
> I have a problem when I calculate band structure of graphene. The band
> structure
> of graphene calculated by unit of 2 atoms and 8 atoms is different. the gap
> at
> gama point as well as M point are totally different.
>
>
> In general case, unit of 2 atoms and unit of 8 atoms both create graphene
> strucutre. I can not unserstand why they are different? Is my understanding
> is
> wrong?
>
>
> I know this is the general question but I hope I can receive helpful
> instructions.
>
>
> I aprreciate all ypur helps.
>
> Sincerely,-----------------------------------------------
> Loc Duong Dinh
> Ms-Ph.D Student
> Sungkyunkwan Advanced Institute of Nanotechnology,
> Sungkyunkwan University,
> Suwon, 440-746, Korea
> Email: mambom1902 at yahoo.com, ddloc at skku.edu
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
____________________________________
Hui Wang
School of physics, Nankai University, Tianjin, China
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From sclauzer at sissa.it  Thu Jul 22 09:33:28 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Thu, 22 Jul 2010 09:33:28 +0200
Subject: [Pw_forum] how does the quantum espresso scale with increasing
	the number of nodes.
In-Reply-To: <AANLkTimmSZu8D-oEXhPqd7kXT4PrJeGfQ3o1F7ln2edW@mail.gmail.com>
References: <AANLkTilwel-AJBqFbcGrEeP_wnv5GuoBrn1b3M8JWzBP@mail.gmail.com>
	<4C455491.2010809@democritos.it>
	<AANLkTimmSZu8D-oEXhPqd7kXT4PrJeGfQ3o1F7ln2edW@mail.gmail.com>
Message-ID: <782078AE-CD2E-4FB5-8770-04B08E1045B2@sissa.it>


Just a personal remark: I don't think it's a good idea to test scaling of pw using a relaxation run. You may just need to perform a few iterations of the scf cycle (set electron_maxstep=5, for instance). Forces and stresses require usually less time than a complete scf loop, but you may test them after one single scf loop with a reduced threshold (e.g. conv_thr=1.D-4). No need to perform a full relaxation for testing scaling, in my opinion. It looks such a waste a cpu time...

Another suggestion is to look carefully and try to understand the timings at the end of the run. You can get an idea on which parts of the code devour more cpu time and how those scale with number of processors for your system (by looking at fft_scatter you may have an idea on how time is spent in interprocess communication for the parallel FFT, for instance). Then you have to consider the best way to scale (i.e. choose npool, ndiag, ntg, consider if it's worth using hybrid MPI/OpenMP parallelization, etc.).

HTH

GS

Il giorno 21/lug/2010, alle ore 11.50, vicky singh ha scritto:

> Dear prof Giannozzi
> 
> sorry to disturb you but i want to ask one question. the same work raran QE simulation with 40 atoms with 8 nodes and 12 nodes. the system got relaxed in 2 days 11 hrs with 8 nodes but it could nod relax even in 3 days with 12 nodes. even it got relaxed with 16 nodes in 2 days 11 hrs but not relax in 6 days with 32 nodes.
> 
> can u help me out.
> 
> with regards 
> 
> 
> vicky singh
> research student
> Bangalore
> 
> 
> 
> On Tue, Jul 20, 2010 at 1:17 PM, Paolo Giannozzi <giannozz at democritos.it> wrote:
> vicky singh wrote:
> 
> > Can anybody let me know how does the quantum espresso scale with
> > increasing the number of nodes or number of processors.
> 
> short answer: it depends. Please read the documentation, in
> particular sec.3 of the userguide; sec.5 of J.Phys. Condens.
> Matter 21, 395502 (2009); the following slides:
> http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_para.pdf
> 
> P.
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> 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


? Gabriele Sclauzero, EPFL SB ITP CSEA
   PH H2 462, Station 3, CH-1015 Lausanne

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From sclauzer at sissa.it  Thu Jul 22 09:42:46 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Thu, 22 Jul 2010 09:42:46 +0200
Subject: [Pw_forum] band structure of graphene-size effect of unit cell
In-Reply-To: <474391.9869.qm@web38803.mail.mud.yahoo.com>
References: <474391.9869.qm@web38803.mail.mud.yahoo.com>
Message-ID: <F28C70B4-C78D-48EA-A3FC-D8DE875497D8@sissa.it>

Dear Loc Duong Dinh,

   have you haver heard about "refolding" of the band structure (in the context of supercells)? If not, first have a look at some good electronic structure textbook. 
The band structure is actually the same, but in practice you are visualizing it in a different way. Try to compute the (fully converged) DOS for the two different unit cells and compare them (with appropriate weights). What do you see?


GS

Il giorno 22/lug/2010, alle ore 05.16, loc duong ding ha scritto:

> Dear all,
> 
> I have a problem when I calculate band structure of graphene. The band structure 
> of graphene calculated by unit of 2 atoms and 8 atoms is different. the gap at 
> gama point as well as M point are totally different. 
> 
> 
> In general case, unit of 2 atoms and unit of 8 atoms both create graphene 
> strucutre. I can not unserstand why they are different? Is my understanding is 
> wrong? 
> 
> 
> I know this is the general question but I hope I can receive helpful 
> instructions. 
> 
> 
> I aprreciate all ypur helps. 
>  
> Sincerely,-----------------------------------------------
> Loc Duong Dinh
> Ms-Ph.D Student
> Sungkyunkwan Advanced Institute of Nanotechnology,
> Sungkyunkwan University,
> Suwon, 440-746, Korea 
> Email: mambom1902 at yahoo.com, ddloc at skku.edu 
> 
> 
> 
> _______________________________________________
> 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

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From wangweiphysics at yahoo.com.cn  Fri Jul 23 07:15:20 2010
From: wangweiphysics at yahoo.com.cn (wangwei)
Date: Fri, 23 Jul 2010 13:15:20 +0800 (CST)
Subject: [Pw_forum] how can I plot phonon dispersion and the a2F(omega) vs.
	omega function curve?
Message-ID: <267005.75643.qm@web15204.mail.cnb.yahoo.com>

Dear sir,

I want to calulate phonon properties, including ?phonon dispersion, dos, el-ph 
coupling, and a2F(omega), 

now I have?4 questions (the version I used is 4.04):

1. What is the meaning of the files named a2F.dos.1,..., a2Fdos.10?

2. What is the meaning of the files named a2Fmatdyn51,...,matdyn60?

3. how can I plot phonon dispersion using the file of case.freq?

4. which file can be used to plot a2F(omega) vs. omega function curve and how to 
plot it?


Thanks for any reply!

Best wishes!

wangwei
Huaibei Normal University


      


From a.nourmohammadi at yahoo.com  Fri Jul 23 07:28:04 2010
From: a.nourmohammadi at yahoo.com (Amene Nouri)
Date: Thu, 22 Jul 2010 22:28:04 -0700 (PDT)
Subject: [Pw_forum] different k point in scf and nscf
Message-ID: <209256.92276.qm@web59416.mail.ac4.yahoo.com>

















Hello all
In scf calculation we choose a k point for sampling Brilouin Zone for example n1*n1*n1.
In next step in nscf calculations we choose another k point for example n2*n2*n2.
Do not we use the results of scf calculation in nscf calculation?
why k points can be different?
which results of scf calculation is used in nscf step?
Thanks in advance.



      
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From rana_nand at yahoo.com  Fri Jul 23 07:47:39 2010
From: rana_nand at yahoo.com (nand)
Date: Thu, 22 Jul 2010 22:47:39 -0700 (PDT)
Subject: [Pw_forum] How to integrate a particular PDOS column
In-Reply-To: <mailman.2474.1279095786.1814.pw_forum@pwscf.org>
References: <mailman.2474.1279095786.1814.pw_forum@pwscf.org>
Message-ID: <736956.92343.qm@web65806.mail.ac4.yahoo.com>

Dear      Dr Sclauzero and PW users,
Thanks for replying on my last query. Now i would like to know (as a new user) 
how to integrate a particular column of PDOS file . Is there a tool for that or 
is done using ones own program.
Thanking you in advance.

Nand Rana
Ranchi University.
India



      
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From nkxirainbow at gmail.com  Fri Jul 23 08:22:24 2010
From: nkxirainbow at gmail.com (xirainbow)
Date: Fri, 23 Jul 2010 14:22:24 +0800
Subject: [Pw_forum] different k point in scf and nscf
In-Reply-To: <209256.92276.qm@web59416.mail.ac4.yahoo.com>
References: <209256.92276.qm@web59416.mail.ac4.yahoo.com>
Message-ID: <AANLkTinGvWyb_8VPNrQWqqzAprEazdm4FyOSo1v2Geel@mail.gmail.com>

Dear Amene Nouri :
Usually, the k-mesh used in nscf is bigger than that in scf.
In scf calculation, the difference between input and output electron density
must be less than a small value.
However, the electron density obtained in scf is used and maintained in nscf
calculation. That means electron density in nscf calculation is  not
self-consisent.
As mentioned above, nscf is not not self-consisent. Therefore, nscf can save
a lot of time.

If your calculation is converged, the nscf and scf would give the same
result.

On Fri, Jul 23, 2010 at 1:28 PM, Amene Nouri <a.nourmohammadi at yahoo.com>wrote:

>
>
>
>    Hello all
> In scf calculation we choose a k point for sampling Brilouin Zone for
> example n1*n1*n1.
> In next step in nscf calculations we choose another k point for example
> n2*n2*n2.
> Do not we use the results of scf calculation in nscf calculation?
> why k points can be different?
> which results of scf calculation is used in nscf step?
>
> Thanks in advance.
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
____________________________________
Hui Wang
School of physics, Nankai University, Tianjin, China
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From 1009ukumar at gmail.com  Fri Jul 23 08:45:25 2010
From: 1009ukumar at gmail.com (sonu kumar)
Date: Fri, 23 Jul 2010 12:15:25 +0530
Subject: [Pw_forum] Is restart of phonon calculations reliable?
Message-ID: <AANLkTimAkT0XVgnegQ063wToEx2qDvUYmMF1XdyyfK5k@mail.gmail.com>

Dear all Quantum Espresso Users,

Is restart of phonon calculations due to power failure/ system shutdown etc.

is reliable?

It happened with me after running a program for two days. Should i restart
or start again?

Thank you !

With Kind Regards,
Sonu Kumar

Phd Student
Physics Department
Indian Institute of Technology
Delhi-110016, India
web:-http://www.iitd.ac.in/
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From dekura at sci.ehime-u.ac.jp  Fri Jul 23 08:56:05 2010
From: dekura at sci.ehime-u.ac.jp (Haruhiko Dekura)
Date: Fri, 23 Jul 2010 15:56:05 +0900
Subject: [Pw_forum] How to integrate a particular PDOS column
In-Reply-To: <736956.92343.qm@web65806.mail.ac4.yahoo.com>
References: <mailman.2474.1279095786.1814.pw_forum@pwscf.org>
	<736956.92343.qm@web65806.mail.ac4.yahoo.com>
Message-ID: <BC471F52-561B-4B6B-BE4C-574EDC791FD6@sci.ehime-u.ac.jp>

Dear Nand

You can integrate each PDOS files to obtain the total PDOS for selecting orbitals by using sumpdos.x. 

Below is the output of help message from sumpdos.x; 

./sumpdos.x -h
----------------------------------------
USAGE: sumpdos [-h] [-f <filein>] [<file1> ... <fileN>]
  Sum the pdos from the file specified in input and write the sum 
  to stdout
     -h           : write this manual
     -f <filein>  : takes the list of pdos files from <filein> 
                    (one per line) instead of command line
     <fileM>      : the M-th pdos file
---------------------------------------------

And see also user-guide. 



Hope this helps. 
Haruhiko Dekura

On 2010/07/23, at 14:47, nand wrote:

> Dear      Dr Sclauzero and PW users,
> Thanks for replying on my last query. Now i would like to know (as a new user) how to integrate a particular column of PDOS file . Is there a tool for that or is done using ones own program.
> Thanking you in advance.
> 
> Nand Rana
> Ranchi University.
> India 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From dekura at cmp.sanken.osaka-u.ac.jp  Fri Jul 23 08:37:22 2010
From: dekura at cmp.sanken.osaka-u.ac.jp (Haruhiko Dekura)
Date: Fri, 23 Jul 2010 15:37:22 +0900
Subject: [Pw_forum] How to integrate a particular PDOS column
In-Reply-To: <736956.92343.qm@web65806.mail.ac4.yahoo.com>
References: <mailman.2474.1279095786.1814.pw_forum@pwscf.org>
	<736956.92343.qm@web65806.mail.ac4.yahoo.com>
Message-ID: <9C9073ED-BFC1-443F-A90D-73C099C6BD20@cmp.sanken.osaka-u.ac.jp>

Dear Nand

You can integrate each PDOS files to obtain the total PDOS for selecting orbitals by using sumpdos.x. 

Below is the output of help message from sumpdos.x; 

./sumpdos.x -h
----------------------------------------
USAGE: sumpdos [-h] [-f <filein>] [<file1> ... <fileN>]
  Sum the pdos from the file specified in input and write the sum 
  to stdout
     -h           : write this manual
     -f <filein>  : takes the list of pdos files from <filein> 
                    (one per line) instead of command line
     <fileM>      : the M-th pdos file
---------------------------------------------

And see also user-guide. 



Hope this helps. 
Haruhiko Dekura



On 2010/07/23, at 14:47, nand wrote:

> Dear      Dr Sclauzero and PW users,
> Thanks for replying on my last query. Now i would like to know (as a new user) how to integrate a particular column of PDOS file . Is there a tool for that or is done using ones own program.
> Thanking you in advance.
> 
> Nand Rana
> Ranchi University.
> India 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From bipulrr at gmail.com  Fri Jul 23 09:28:55 2010
From: bipulrr at gmail.com (Bipul Rakshit)
Date: Fri, 23 Jul 2010 12:58:55 +0530
Subject: [Pw_forum] Is restart of phonon calculations reliable?
In-Reply-To: <AANLkTimAkT0XVgnegQ063wToEx2qDvUYmMF1XdyyfK5k@mail.gmail.com>
References: <AANLkTimAkT0XVgnegQ063wToEx2qDvUYmMF1XdyyfK5k@mail.gmail.com>
Message-ID: <AANLkTi=uekUkYrqz7fgkHUtfNrcgn+QVEYZU4kz=edLT@mail.gmail.com>

yes u can use recover option to restart and it gives the same result, as yr
continuous job.

recover generally restart the calculation from the last scf step, but
sometime it shows some error. So it is always better to start the
calculation from the beginning of scf steps. To do this just type

rm OUT/_ph*

where OUT is your directory, where your output data's are stored. (outdir =
'./OUT',)

Remember just remove the files not the whole directory

On Fri, Jul 23, 2010 at 12:15 PM, sonu kumar <1009ukumar at gmail.com> wrote:

> Dear all Quantum Espresso Users,
>
> Is restart of phonon calculations due to power failure/ system shutdown
> etc.
> is reliable?
>
> It happened with me after running a program for two days. Should i restart
> or start again?
>
> Thank you !
>
> With Kind 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
>
>


-- 
Dr. Bipul Rakshit
Research Associate,
S N Bose Centre for Basic Sciences,
Salt Lake,
Kolkata 700 098
India
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From dekura at sci.ehime-u.ac.jp  Fri Jul 23 09:32:37 2010
From: dekura at sci.ehime-u.ac.jp (Haruhiko Dekura)
Date: Fri, 23 Jul 2010 16:32:37 +0900
Subject: [Pw_forum] how can I plot phonon dispersion and the a2F(omega)
	vs. omega function curve?
In-Reply-To: <267005.75643.qm@web15204.mail.cnb.yahoo.com>
References: <267005.75643.qm@web15204.mail.cnb.yahoo.com>
Message-ID: <9CE6BACE-E560-4180-97AA-B4AC3C331955@sci.ehime-u.ac.jp>

Dear wangwei


> What is the meaning of the files named a2F.dos.1,..., a2Fdos.10?

alpha^2F: alpha^2 means electron-phonon coupling strength, and F means phonon density of states. 
Normally, we call this function as "Eliashberg function" in metallic system. In the formulation of a^2F, you see the delta functions and it's to be treated by Gaussian in espresso, and then we should have the smearing width of broadening. The number attached with a2F.dos.* correspond to the each width.  
a2Fdos file shows the a^2F as the function of  phonon frequency. 

> which file can be used to plot a2F(omega) vs. omega function curve and how to 
> plot it?

The best one is depending on the accuracy in your calculations.
I'would say, check the convergency of lambda with respect to the number of k-points in el-ph calculation, Gaussian smearing width, as well as typical checks before el-ph calculation (the convergency of phonon frequency and total electronic energy against Ecut and k-poins, smearing width...and so on.)

As for the plotting, you can select whatever you want to use, such as gnuplot. 



Best Regards. 
Haruhiko Dekura
       


On 2010/07/23, at 14:15, wangwei wrote:

> Dear sir,
> 
> I want to calulate phonon properties, including  phonon dispersion, dos, el-ph 
> coupling, and a2F(omega), 
> 
> now I have 4 questions (the version I used is 4.04):
> 
> 1. What is the meaning of the files named a2F.dos.1,..., a2Fdos.10?
> 
> 2. What is the meaning of the files named a2Fmatdyn51,...,matdyn60?
> 
> 3. how can I plot phonon dispersion using the file of case.freq?
> 
> 4. which file can be used to plot a2F(omega) vs. omega function curve and how to 
> plot it?
> 
> 
> Thanks for any reply!
> 
> Best wishes!
> 
> wangwei
> Huaibei Normal University
> 
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From dekura at sci.ehime-u.ac.jp  Fri Jul 23 09:55:55 2010
From: dekura at sci.ehime-u.ac.jp (Haruhiko Dekura)
Date: Fri, 23 Jul 2010 16:55:55 +0900
Subject: [Pw_forum] how can I plot phonon dispersion and the a2F(omega)
	vs. omega function curve?
In-Reply-To: <267005.75643.qm@web15204.mail.cnb.yahoo.com>
References: <267005.75643.qm@web15204.mail.cnb.yahoo.com>
Message-ID: <A593B711-B902-4B13-8FF6-F8F42B9229F4@sci.ehime-u.ac.jp>

Dear Wangwei

> 3. how can I plot phonon dispersion using the file of case.freq?

As for me, (may be not so good way), I use gnuplot after a little modifying *.freq file. 
If you can read python script, my junk program may help you. ( but, may be it is dirty for you, sorry. )

I attach a sample with this mail. 


--------------------------- 

 
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usage: 

(1) plotBAND.py < MgO.phband.freq.out

and then, you see "band.out".

launch gnuplot, and 

(2) type "plot band.out"  

You should modify it to be appropriate figure. 


Hope this helps. 
and, if you find better way, please let me know : -)    


Haruhiko Dekura




From sclauzer at sissa.it  Fri Jul 23 10:08:50 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Fri, 23 Jul 2010 10:08:50 +0200
Subject: [Pw_forum] How to integrate a particular PDOS column
In-Reply-To: <9C9073ED-BFC1-443F-A90D-73C099C6BD20@cmp.sanken.osaka-u.ac.jp>
References: <mailman.2474.1279095786.1814.pw_forum@pwscf.org>	<736956.92343.qm@web65806.mail.ac4.yahoo.com>
	<9C9073ED-BFC1-443F-A90D-73C099C6BD20@cmp.sanken.osaka-u.ac.jp>
Message-ID: <4C494E12.2000605@sissa.it>

On 07/23/2010 08:37 AM, Haruhiko Dekura wrote:
> Dear Nand
>
> You can integrate each PDOS files to obtain the total PDOS for 
> selecting orbitals by using sumpdos.x.
>
> Below is the output of help message from sumpdos.x;
>
> ./sumpdos.x -h
> ----------------------------------------
> USAGE: sumpdos [-h] [-f <filein>] [<file1> ... <fileN>]
>   Sum the pdos from the file specified in input and write the sum
>   to stdout
>      -h           : write this manual
>      -f <filein>  : takes the list of pdos files from <filein>
>                     (one per line) instead of command line
> <fileM>      : the M-th pdos file
> ---------------------------------------------
>
> And see also user-guide.

This utility is meant for summing the PDOS from several files 
(corresponding to different atoms) in order to get a single PDOS, but 
does not compute any integral of the PDOS, so I don't think that's what 
Nand needs.

>
>
>
> Hope this helps.
> Haruhiko Dekura
>
>
>
> On 2010/07/23, at 14:47, nand wrote:
>
>> Dear      Dr Sclauzero and PW users,
>> Thanks for replying on my last query. Now i would like to know (as a 
>> new user) how to integrate a particular column of PDOS file . Is 
>> there a tool for that or is done using ones own program.

I think there's no such utility in the QE package, but if the energy 
grid is dense enough you can use the very simple rectangle method 
(that's what is used in PP/dos.f90 for integrating the DOS, for instance).
You can test the accuracy by looking how the integral converges when the 
energy step is reduced, obviously (should be O(deltae^2) ).
If you want something more precise you may need to refer to some 
numerical analysis textbook or to the old good Numerical Recipes, that 
used to be available online, for instance.

GS

>> Thanking you in advance.
>>
>> Nand Rana
>> Ranchi University.
>> India
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org <mailto: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
>    


-- 

Gabriele Sclauzero, EPFL SB ITP CSEA
PH H2 462, Station 3, CH-1015 Lausanne

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From dekura at cmp.sanken.osaka-u.ac.jp  Fri Jul 23 10:39:01 2010
From: dekura at cmp.sanken.osaka-u.ac.jp (Haruhiko Dekura)
Date: Fri, 23 Jul 2010 17:39:01 +0900
Subject: [Pw_forum] How to integrate a particular PDOS column
In-Reply-To: <4C494E12.2000605@sissa.it>
References: <mailman.2474.1279095786.1814.pw_forum@pwscf.org>	<736956.92343.qm@web65806.mail.ac4.yahoo.com>
	<9C9073ED-BFC1-443F-A90D-73C099C6BD20@cmp.sanken.osaka-u.ac.jp>
	<4C494E12.2000605@sissa.it>
Message-ID: <36BBFED5-4AD1-43FB-BD87-D68401BDA2F7@cmp.sanken.osaka-u.ac.jp>

Dear Gabriele 
On 2010/07/23, at 17:08, Gabriele Sclauzero wrote:

>> 
> 
> This utility is meant for summing the PDOS from several files (corresponding to different atoms) in order to get a single PDOS, but does not compute any integral of the PDOS, so I don't think that's what Nand needs.
> 
Now I understand what Nand really ask, by your pointing. I think you are right. 
Thank you very much. 

and, sorry for Nand.  


Best Regards. 
Haruhiko Dekura


>> 
>> On 2010/07/23, at 14:47, nand wrote:
>> 
>>> Dear      Dr Sclauzero and PW users,
>>> Thanks for replying on my last query. Now i would like to know (as a new user) how to integrate a particular column of PDOS file . Is there a tool for that or is done using ones own program.
> 
> I think there's no such utility in the QE package, but if the energy grid is dense enough you can use the very simple rectangle method (that's what is used in PP/dos.f90 for integrating the DOS, for instance). 
> You can test the accuracy by looking how the integral converges when the energy step is reduced, obviously (should be O(deltae^2) ).
> If you want something more precise you may need to refer to some numerical analysis textbook or to the old good Numerical Recipes, that used to be available online, for instance.
> 
> GS
> 
>>> Thanking you in advance.
>>> 
>>> Nand Rana
>>> Ranchi University.
>>> India 
>>> 
>>> _______________________________________________
>>> 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
>>   
> 
> 
> -- 
> 
> 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

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From eyvaz_isaev at yahoo.com  Fri Jul 23 10:50:49 2010
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 23 Jul 2010 01:50:49 -0700 (PDT)
Subject: [Pw_forum] how can I plot phonon dispersion and the a2F(omega)
	vs. omega function curve?
In-Reply-To: <267005.75643.qm@web15204.mail.cnb.yahoo.com>
References: <267005.75643.qm@web15204.mail.cnb.yahoo.com>
Message-ID: <654933.92649.qm@web65708.mail.ac4.yahoo.com>

Hi,

To plot phonon dispersion relations use PlotPhon utility (see your QE 4.2 case).
You can gain more info from your phonon calculations if you look at also QHA 
directory.
 
Bests,
Eyvaz.

 -------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, 
Sweden 

Theoretical Physics Department, Moscow State Institute of Steel & Alloys, 
Russia, 

isaev at ifm.liu.se, eyvaz_isaev at yahoo.com



----- Original Message ----
From: wangwei <wangweiphysics at yahoo.com.cn>
To: pw_forum at pwscf.org
Sent: Fri, July 23, 2010 7:15:20 AM
Subject: [Pw_forum] how can I plot phonon dispersion and the a2F(omega) vs. 
omega function curve?

Dear sir,

I want to calulate phonon properties, including  phonon dispersion, dos, el-ph 
coupling, and a2F(omega), 

now I have 4 questions (the version I used is 4.04):

1. What is the meaning of the files named a2F.dos.1,..., a2Fdos.10?

2. What is the meaning of the files named a2Fmatdyn51,...,matdyn60?

3. how can I plot phonon dispersion using the file of case.freq?

4. which file can be used to plot a2F(omega) vs. omega function curve and how to 

plot it?


Thanks for any reply!

Best wishes!

wangwei
Huaibei Normal University


      

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum



      


From rana_nand at yahoo.com  Fri Jul 23 11:04:13 2010
From: rana_nand at yahoo.com (nand)
Date: Fri, 23 Jul 2010 02:04:13 -0700 (PDT)
Subject: [Pw_forum] How to integrate a particular PDOS column
In-Reply-To: <mailman.1.1279870236.31524.pw_forum@pwscf.org>
References: <mailman.1.1279870236.31524.pw_forum@pwscf.org>
Message-ID: <33395.29953.qm@web65803.mail.ac4.yahoo.com>

Dear Haruhiko and users,
Thanks for your reply. The sumpdos.x program can sum the up and down spin ldos 
columns from different pdos files. How ever i will like to integrate a 
particular column in a pdos file that stands for pdos of a particular m value of 
the given atom (for example the header of the column would be pdosup(E)).
Thanking you again
 
Dear Nand

You can integrate each PDOS files to obtain the total PDOS for selecting 
orbitals by using sumpdos.x. 


Below is the output of help message from sumpdos.x; 

./sumpdos.x -h
----------------------------------------
USAGE: sumpdos [-h] [-f <filein>] [<file1> ... <fileN>]
  Sum the pdos from the file specified in input and write the sum 
  to stdout
     -h           : write this manual
     -f <filein>  : takes the list of pdos files from <filein> 
                    (one per line) instead of command line
     <fileM>      : the M-th pdos file
---------------------------------------------

And see also user-guide. 



Hope this helps. 
Haruhiko Dekura



On 2010/07/23, at 14:47, nand wrote:

> Dear      Dr Sclauzero and PW users,
> Thanks for replying on my last query. Now i would like to know (as a new user) 
>how to integrate a particular column of PDOS file . Is there a tool for that or 
>is done using ones own program.
> Thanking you in advance.
> 
> Nand Rana
> Ranchi University.
> India 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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------------------------------

Message: 2
Date: Fri, 23 Jul 2010 12:58:55 +0530
From: Bipul Rakshit <bipulrr at gmail.com>
Subject: Re: [Pw_forum] Is restart of phonon calculations reliable?
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
    <AANLkTi=uekUkYrqz7fgkHUtfNrcgn+QVEYZU4kz=edLT at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

yes u can use recover option to restart and it gives the same result, as yr
continuous job.

recover generally restart the calculation from the last scf step, but
sometime it shows some error. So it is always better to start the
calculation from the beginning of scf steps. To do this just type

rm OUT/_ph*

where OUT is your directory, where your output data's are stored. (outdir =
'./OUT',)

Remember just remove the files not the whole directory

On Fri, Jul 23, 2010 at 12:15 PM, sonu kumar <1009ukumar at gmail.com> wrote:

> Dear all Quantum Espresso Users,
>
> Is restart of phonon calculations due to power failure/ system shutdown
> etc.
> is reliable?
>
> It happened with me after running a program for two days. Should i restart
> or start again?
>
> Thank you !
>
> With Kind 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
>
>


-- 
Dr. Bipul Rakshit
Research Associate,
S N Bose Centre for Basic Sciences,
Salt Lake,
Kolkata 700 098
India
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------------------------------

_______________________________________________
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Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


End of Pw_forum Digest, Vol 37, Issue 52
****************************************



      
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From modaresi.mohsen at gmail.com  Fri Jul 23 15:12:40 2010
From: modaresi.mohsen at gmail.com (mohsen modaresi)
Date: Fri, 23 Jul 2010 17:42:40 +0430
Subject: [Pw_forum] band structure of graphene-size effect of unit cell
In-Reply-To: <474391.9869.qm@web38803.mail.mud.yahoo.com>
References: <474391.9869.qm@web38803.mail.mud.yahoo.com>
Message-ID: <AANLkTinou-yADs9hWo56gPefw+8LQdoPBctt-aJRUCzy@mail.gmail.com>

Dear loc duong ding
Band structure are different (becuse primitive cells in real and so in
inverse space are different) but the DOS in this two case must be the
same chek it.
Mohsen Modarresi
Ferdowsi University of Mashhad, Iran.

From jiachen at princeton.edu  Fri Jul 23 18:02:37 2010
From: jiachen at princeton.edu (jia chen)
Date: Fri, 23 Jul 2010 12:02:37 -0400
Subject: [Pw_forum] about U value determination in DFT+U calculation
Message-ID: <AANLkTimJqrgwtTHeVHmGVNYp_DXf2K2G74MbLWUV7NQi@mail.gmail.com>

Dear?Gabriele Sclauzero,

Thank you so much for you help, it took me a while to test and to do
calculations. Now, I think, at least, pw can choose 3d instead of 4d
without any problem. Now I can get U values and other properties which
are reasonable even though different from results calculated from
ultrasoft pseudo-potential. I really appreciate your help.

Just one thing I would like to make sure. If offset_atom_wfc.f90 is
the only place we need to change something, I am not familiar with pw
code, I still not 100% sure everything is all rigorous right now. One
thing I noticed is that the initial guess is not correct, because the
occupation number after the first step is always 0, anyway, it is not
a big problem as long as we can get correct ground state. Thank you in
advance.

Bests
Jia

--
Jia Chen

Dept of Chemistry
Princeton University
Princeton, NJ 08544

From sclauzer at sissa.it  Fri Jul 23 18:29:20 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Fri, 23 Jul 2010 18:29:20 +0200
Subject: [Pw_forum] about U value determination in DFT+U calculation
In-Reply-To: <AANLkTimJqrgwtTHeVHmGVNYp_DXf2K2G74MbLWUV7NQi@mail.gmail.com>
References: <AANLkTimJqrgwtTHeVHmGVNYp_DXf2K2G74MbLWUV7NQi@mail.gmail.com>
Message-ID: <AF65A27C-F4A6-4FAA-875A-2B9B8490D7BD@sissa.it>


Il giorno 23/lug/2010, alle ore 18.02, jia chen ha scritto:

> Dear Gabriele Sclauzero,
> 
> Thank you so much for you help, it took me a while to test and to do
> calculations. Now, I think, at least, pw can choose 3d instead of 4d
> without any problem. Now I can get U values and other properties which
> are reasonable even though different from results calculated from
> ultrasoft pseudo-potential. I really appreciate your help.

Yes, you will get different results because the two PP have been generated with different atomic configurations. About the TM PP, it looks strange to me that if you sum the occupations you get 15, while Z=17. Maybe is one of those special PPs used for XPS calculations.

> 
> Just one thing I would like to make sure. If offset_atom_wfc.f90 is
> the only place we need to change something, I am not familiar with pw
> code, I still not 100% sure everything is all rigorous right now.

I think it's OK like that. The "index" of the atomic wavefunctions is calculated only once at the beginning of the run.

> One
> thing I noticed is that the initial guess is not correct, because the
> occupation number after the first step is always 0, anyway, it is not
> a big problem as long as we can get correct ground state. Thank you in
> advance.

Occupations can fluctuate during self consistency because the charge and the wavefunctions do. The case of the isolated atom is quite "unstable" (and difficult to converge in general, you may need to fix occupations of the KS levels from input). The initial guess is built according to the (experimental) occupations of the electronic states in the isolated atom (and on the starting magnetization on that atom, for spin polarized calculations)


Regards,

GS

> 
> Bests
> Jia
> 
> --
> Jia Chen
> 
> Dept of Chemistry
> Princeton University
> Princeton, NJ 08544
> _______________________________________________
> 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

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From karthik.guda at gmail.com  Fri Jul 23 21:20:20 2010
From: karthik.guda at gmail.com (Guda Karthik)
Date: Fri, 23 Jul 2010 15:20:20 -0400
Subject: [Pw_forum] Slab calculation in pwscf
Message-ID: <AANLkTi=bw=cOO1CJsRTGaMarmyBU91AGTdvpk_Tf41rL@mail.gmail.com>

Hi all,
>


   I am trying to do some slab calculations using pw.x . I made a supercell
in the direction normal to the surface I am interested in, and made the
lattice vector much larger than the actual supercell length to avoid
interaction between two periodic images. Is this the way to do in pwscf? or
is there an option where one could do a non periodic calculation by
specifying the dimension and setting the k-points in the direction normal to
the surface to zero (this information I could not find in the manual)?
Please reply.

regards,
Karthik
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From mohnish.iitk at gmail.com  Sat Jul 24 05:52:09 2010
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Sat, 24 Jul 2010 09:22:09 +0530
Subject: [Pw_forum] Slab calculation in pwscf
In-Reply-To: <AANLkTi=bw=cOO1CJsRTGaMarmyBU91AGTdvpk_Tf41rL@mail.gmail.com>
References: <AANLkTi=bw=cOO1CJsRTGaMarmyBU91AGTdvpk_Tf41rL@mail.gmail.com>
Message-ID: <AANLkTinm9tWC8XQHgbDTWv7XKCcp6H13tGyvYvwB3HkS@mail.gmail.com>

Dear Karthik,
                     To my knowledge most of the DFT codes use *periodic
boundary condition*, the same case is with PWSCF. For supercell calculation
you have to take the size of the supercell large enough so that there is no
interaction between slabs. And will be glad if you mention your affiliation
so that we can know whom are interacting with.

On Sat, Jul 24, 2010 at 12:50 AM, Guda Karthik <karthik.guda at gmail.com>wrote:

>
>
> Hi all,
>>
>
>
>    I am trying to do some slab calculations using pw.x . I made a supercell
> in the direction normal to the surface I am interested in, and made the
> lattice vector much larger than the actual supercell length to avoid
> interaction between two periodic images. Is this the way to do in pwscf? or
> is there an option where one could do a non periodic calculation by
> specifying the dimension and setting the k-points in the direction normal to
> the surface to zero (this information I could not find in the manual)?
> Please reply.
>
> regards,
> Karthik
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Regards,
MOHNISH,
-----------------------------------------------------------------
Mohnish Pandey
Y6927262,5th Year dual degree student,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
+919235721300
-----------------------------------------------------------------
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From a.nourmohammadi at yahoo.com  Sat Jul 24 07:23:51 2010
From: a.nourmohammadi at yahoo.com (Amene Nouri)
Date: Fri, 23 Jul 2010 22:23:51 -0700 (PDT)
Subject: [Pw_forum] different k point in scf and nscf
Message-ID: <887848.32174.qm@web59406.mail.ac4.yahoo.com>






Dear xirainbow
Thanks for explaining. Do you mean that in nscf step the calculation starts fom the density obtained in scf step and the eigenvalues are calculated just in one iteration, or there are iterations in nscf too?
?
I appreciate your help.


      
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From nkxirainbow at gmail.com  Sat Jul 24 09:06:01 2010
From: nkxirainbow at gmail.com (xirainbow)
Date: Sat, 24 Jul 2010 15:06:01 +0800
Subject: [Pw_forum] different k point in scf and nscf
In-Reply-To: <887848.32174.qm@web59406.mail.ac4.yahoo.com>
References: <887848.32174.qm@web59406.mail.ac4.yahoo.com>
Message-ID: <AANLkTikPMPrNoK11LHHoZorQ2pTmHb5MLfiWTBHfUSP6@mail.gmail.com>

Dear Amene Nouri :

      Do you mean that in nscf step the calculation starts fom the density
> obtained in scf step and the eigenvalues are calculated just in one
> iteration?
>
Yes, I think so.

____________________________________
Hui Wang
School of physics, Nankai University, Tianjin, China
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From baroni at sissa.it  Sat Jul 24 15:13:28 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Sat, 24 Jul 2010 15:13:28 +0200
Subject: [Pw_forum] different k point in scf and nscf
In-Reply-To: <887848.32174.qm@web59406.mail.ac4.yahoo.com>
References: <887848.32174.qm@web59406.mail.ac4.yahoo.com>
Message-ID: <750FD7B1-3C3B-4B86-BECD-C569BEF27F08@sissa.it>

the "n" in "nscf" stands for "not" (self consistent) ...
pw.x acutally does some iterations for nscf, as well, but just to refine wavefuntions at fixed potential, not to refine the potential (as done in a self-consistent calculation)
S.

On Jul 24, 2010, at 7:23 AM, Amene Nouri wrote:

> 
> Dear xirainbow
> Thanks for explaining. Do you mean that in nscf step the calculation starts fom the density obtained in scf step and the eigenvalues are calculated just in one iteration, or there are iterations in nscf too?
>  
> I appreciate your help.
> 
> _______________________________________________
> 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







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From sd.wang000 at gmail.com  Sat Jul 24 16:32:38 2010
From: sd.wang000 at gmail.com (shudong wang)
Date: Sat, 24 Jul 2010 22:32:38 +0800
Subject: [Pw_forum] TDDFT
Message-ID: <AANLkTikCnPuZKsjc6=8ZY4mzKFGv6bPJwrsH4r0DNPHQ@mail.gmail.com>

Dear developers:
I want to know how can I use TDDFT in pwscf,or when it can be used?
Thanks!
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From weylfang at gmail.com  Sun Jul 25 07:29:01 2010
From: weylfang at gmail.com (Weyl Fang)
Date: Sun, 25 Jul 2010 13:29:01 +0800
Subject: [Pw_forum] starting_magnetization problem
Message-ID: <4C4BCB9D.2040100@gmail.com>

Dear all,

Recently i want to do a spin polarization calculation. After I read the
pw.x input file description, i know if i set the tot_magnetization to
unspecified the amount of electronic magnetization is determined during
the self-consistent cycle. So i set the tot_magnetization to
unspecified. But when i execute pw.x, i get a error message some
starting_magnetization MUST be set. But i get the message" If you fix
the magnetization with "tot_magnetization", you should not specify
starting_magnetization." from the pw.x input file description. If i
still should specify the starting_magnetization? And If i want the
amount of electronic magnetization determined during the self-consistent
cycle, how should i specify the starting_magnetization?

Thanks for your help!

Weyl

===========================================================================

Weyl FANG
Graduate student in Chemical Engineering
State Key Laboratory of Materials-oriented Chemical Engineering
College of Chemistry and Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
****************************************************************************************************************
Email: weylfang at gmail.com
Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China
********************************************************************* *******************************************



From hqzhou at nju.edu.cn  Sun Jul 25 09:11:14 2010
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Sun, 25 Jul 2010 15:11:14 +0800
Subject: [Pw_forum] starting_magnetization problem
References: <4C4BCB9D.2040100@gmail.com>
Message-ID: <92222650104D438D820AC98BE3172008@solarflare>

The manual is a little bit misleading. It just says implicitly: don't
let both tot_magnetization and starting_magnetization appear in
your input file simutanously, they are mutual exclusive. For your
purpose, you just need to define starting_magnetization and don't
bother yourself with defining tot_magnetization = -1 in the input,
which is not allowed according to your practice although it should
be OK logically.

huiqun zhou
@earth sciences, nanjing university, china

----- Original Message ----- 
From: "Weyl Fang" <weylfang at gmail.com>
To: <pw_forum at pwscf.org>
Sent: Sunday, July 25, 2010 1:29 PM
Subject: [Pw_forum] starting_magnetization problem


> Dear all,
>
> Recently i want to do a spin polarization calculation. After I read the
> pw.x input file description, i know if i set the tot_magnetization to
> unspecified the amount of electronic magnetization is determined during
> the self-consistent cycle. So i set the tot_magnetization to
> unspecified. But when i execute pw.x, i get a error message some
> starting_magnetization MUST be set. But i get the message" If you fix
> the magnetization with "tot_magnetization", you should not specify
> starting_magnetization." from the pw.x input file description. If i
> still should specify the starting_magnetization? And If i want the
> amount of electronic magnetization determined during the self-consistent
> cycle, how should i specify the starting_magnetization?
>
> Thanks for your help!
>
> Weyl
>
> ===========================================================================
>
> Weyl FANG
> Graduate student in Chemical Engineering
> State Key Laboratory of Materials-oriented Chemical Engineering
> College of Chemistry and Chemical Engineering
> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
> ****************************************************************************************************************
> Email: weylfang at gmail.com
> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, 
> Nanjing, Jiangsu, China
> ********************************************************************* 
> *******************************************
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 



From didi5158 at gmail.com  Sun Jul 25 09:28:47 2010
From: didi5158 at gmail.com (Wang Di)
Date: Sun, 25 Jul 2010 15:28:47 +0800
Subject: [Pw_forum] (no subject)
Message-ID: <AANLkTikvdNK3ynns1cw3oy3rvTgU4oWk83nTs6s_+=dn@mail.gmail.com>

Dear All:
      I plan to calculate the phonon of the crystal structure with hexagonal
lattice. It spend me one day  to build the crystal structure which was
confirmed by Xcrysden. According the experiences of previous e-mails about
phonon calculate, the "relax " process of the crystal structure was needed,
then I  vc-relaxed the crystal structure and hoped to get a  approving
structure in a few hours. But the calculation had took more than 40
thousands second after 14 steps and stopped with the error : too many C-
bond were not converged.

input file:
&CONTROL
                 calculation = 'vc-relax' ,
                      outdir = '/root/espresso-4.2/work/Dean/LSAFB/temp/' ,
                      wfcdir = '/root/espresso-4.2/work/Dean/LSAFB/wftemp/'
,
                  pseudo_dir = '/root/espresso-4.2/work/Dean/LSAFB/pp/' ,
                      prefix = 'LSAF' ,
                 lkpoint_dir = .true. ,
               etot_conv_thr = 1.0D-5 ,
               forc_conv_thr = 1.0D-4 ,
                       nstep = 100 ,
                     tstress = .true. ,
                     tprnfor = .true. ,
                          dt = 20 ,
                    dipfield = .true. ,
 /
 &SYSTEM
                       ibrav = 4,
                   celldm(1) = 5.0716,
                   celldm(3) = 2.0093,
                         nat = 18,
                        ntyp = 4,
                     ecutwfc = 80 ,
                 occupations = 'smearing' ,
                     degauss = 0.02 ,
                    smearing = 'gaussian' ,
 /
 &ELECTRONS
            electron_maxstep = 100,
                    conv_thr = 1.0D-12 ,
                 mixing_mode = 'plain' ,
                 mixing_beta = 0.7D ,
 /
 &IONS
                ion_dynamics = 'bfgs' ,
           pot_extrapolation = 'second_order' ,
           wfc_extrapolation = 'second_order' ,
                     upscale = 10D ,
                   bfgs_ndim = 1 ,
            trust_radius_max = 0.8D0 ,
            trust_radius_min = 1.0D-3 ,
            trust_radius_ini = 0.5D ,
 /
ATOMIC_SPECIES
   Li    6.94100  Li.pbe-n-van.UPF
   Al   26.98154  Al.pbe-sp-van.UPF
   Sr   87.62000  Sr.pbe-nsp-van.UPF
    F   18.99840  F.pbe-n-van.UPF
ATOMIC_POSITIONS alat
   Sr      0.000000000    0.000000000    0.000000000
   Sr      0.000000000    0.000000000    1.004630000
   Li      0.500000000    0.288650000    1.500000000
   Li      0.000000000    0.577370000    0.502310000
   Al      0.500500000    0.288650000    0.502320000
   Al      0.000000000    0.577380000    1.506900000
    F      0.371500000    0.028400000    0.298380000
    F      0.789650000    0.307530000    0.298380000
    F      0.338850000    0.530090000    0.298380000
    F      0.661150000    0.530090000    0.706260000
    F      0.628500000    0.028400000    0.706260000
    F      0.210350000    0.307530000    0.706260000
    F      0.128500000    0.837620000    1.710890000
    F     -0.289650000    0.558500000    1.710890000
    F      0.161150000    0.335930000    1.710890100
    F     -0.161150000    0.335930000    1.303010000
    F     -0.128500000    0.837620000    1.303010000
    F      0.289650000    0.558500000    1.303010000
K_POINTS automatic
  8 8 8   1 1 1

I appreciate if one give me some advises to resolve the problem and the
reason.

Best regards

Wang Di
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From weylfang at gmail.com  Sun Jul 25 09:38:30 2010
From: weylfang at gmail.com (Weyl Fang)
Date: Sun, 25 Jul 2010 15:38:30 +0800
Subject: [Pw_forum] starting_magnetization problem
In-Reply-To: <mailman.1.1280042624.17723.pw_forum@pwscf.org>
References: <mailman.1.1280042624.17723.pw_forum@pwscf.org>
Message-ID: <4C4BE9F6.5060102@gmail.com>

Dear Zhou

Thank you very much for your kindly reply. I will follow your suggestion 
to do some test.
Thanks again!

Weyl


? 2010/7/25 15:23, pw_forum-request at pwscf.org ??:
> Message: 3
> Date: Sun, 25 Jul 2010 13:29:01 +0800
> From: Weyl Fang<weylfang at gmail.com>
> Subject: [Pw_forum] starting_magnetization problem
> To: pw_forum at pwscf.org
> Message-ID:<4C4BCB9D.2040100 at gmail.com>
> Content-Type: text/plain; charset=GB2312
>
> Dear all,
>
> Recently i want to do a spin polarization calculation. After I read the
> pw.x input file description, i know if i set the tot_magnetization to
> unspecified the amount of electronic magnetization is determined during
> the self-consistent cycle. So i set the tot_magnetization to
> unspecified. But when i execute pw.x, i get a error message some
> starting_magnetization MUST be set. But i get the message" If you fix
> the magnetization with "tot_magnetization", you should not specify
> starting_magnetization." from the pw.x input file description. If i
> still should specify the starting_magnetization? And If i want the
> amount of electronic magnetization determined during the self-consistent
> cycle, how should i specify the starting_magnetization?
>
> Thanks for your help!
>
> Weyl
>
> ===========================================================================
>
> Weyl FANG
> Graduate student in Chemical Engineering
> State Key Laboratory of Materials-oriented Chemical Engineering
> College of Chemistry and Chemical Engineering
> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
> ****************************************************************************************************************
> Email: weylfang at gmail.com
> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China
> ********************************************************************* *******************************************
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 25 Jul 2010 15:11:14 +0800
> From: "Huiqun Zhou"<hqzhou at nju.edu.cn>
> Subject: Re: [Pw_forum] starting_magnetization problem
> To: "PWSCF Forum"<pw_forum at pwscf.org>
> Message-ID:<92222650104D438D820AC98BE3172008 at solarflare>
> Content-Type: text/plain; format=flowed; charset="ISO-8859-1";
> 	reply-type=original
>
> The manual is a little bit misleading. It just says implicitly: don't
> let both tot_magnetization and starting_magnetization appear in
> your input file simutanously, they are mutual exclusive. For your
> purpose, you just need to define starting_magnetization and don't
> bother yourself with defining tot_magnetization = -1 in the input,
> which is not allowed according to your practice although it should
> be OK logically.
>
> huiqun zhou
> @earth sciences, nanjing university, china
>
> ----- Original Message -----
> From: "Weyl Fang"<weylfang at gmail.com>
> To:<pw_forum at pwscf.org>
> Sent: Sunday, July 25, 2010 1:29 PM
> Subject: [Pw_forum] starting_magnetization problem
>
>
>    
>> Dear all,
>>
>> Recently i want to do a spin polarization calculation. After I read the
>> pw.x input file description, i know if i set the tot_magnetization to
>> unspecified the amount of electronic magnetization is determined during
>> the self-consistent cycle. So i set the tot_magnetization to
>> unspecified. But when i execute pw.x, i get a error message some
>> starting_magnetization MUST be set. But i get the message" If you fix
>> the magnetization with "tot_magnetization", you should not specify
>> starting_magnetization." from the pw.x input file description. If i
>> still should specify the starting_magnetization? And If i want the
>> amount of electronic magnetization determined during the self-consistent
>> cycle, how should i specify the starting_magnetization?
>>
>> Thanks for your help!
>>
>> Weyl
>>
>> ===========================================================================
>>
>> Weyl FANG
>> Graduate student in Chemical Engineering
>> State Key Laboratory of Materials-oriented Chemical Engineering
>> College of Chemistry and Chemical Engineering
>> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
>> ****************************************************************************************************************
>> Email: weylfang at gmail.com
>> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#,
>> Nanjing, Jiangsu, China
>> *********************************************************************
>> *******************************************
>>
>>
>> _______________________________________________
>> 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
>
>
> End of Pw_forum Digest, Vol 37, Issue 56
> ****************************************
>    


-- 
===========================================================================
Weyl FANG
Graduate student in Chemical Engineering
State Key Laboratory of Materials-oriented Chemical Engineering
College of Chemistry and Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
****************************************************************************************************************
Email: weylfang at gmail.com
Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China
********************************************************************* *******************************************


From baroni at sissa.it  Sun Jul 25 10:59:39 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Sun, 25 Jul 2010 10:59:39 +0200
Subject: [Pw_forum] TDDFT
In-Reply-To: <AANLkTikCnPuZKsjc6=8ZY4mzKFGv6bPJwrsH4r0DNPHQ@mail.gmail.com>
References: <AANLkTikCnPuZKsjc6=8ZY4mzKFGv6bPJwrsH4r0DNPHQ@mail.gmail.com>
Message-ID: <33921343-1CF0-4ED9-8925-FB0E09CA46EB@sissa.it>

The next major release of QE (foreseen to be distributed  2010 Q4) will contain both a real-time  and a spectral Liouville-Lanczos implementation of TDDFT. SB

On Jul 24, 2010, at 4:32 PM, shudong wang wrote:

> Dear developers:
> I want to know how can I use TDDFT in pwscf,or when it can be used?
> Thanks!
> _______________________________________________
> 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







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From haoweipeng at gmail.com  Mon Jul 26 05:13:24 2010
From: haoweipeng at gmail.com (Haowei Peng)
Date: Sun, 25 Jul 2010 22:13:24 -0500
Subject: [Pw_forum] Is there a tutorial for generating a PAW pseudopotential
Message-ID: <AANLkTikoh65jEZsutvJcw0nMcmVgeRuNX_mSj+BESXm2@mail.gmail.com>

Hi everyone,

I am looking for a tutorial about generating a PAW pseudopotential, any
comments?
Thanks a lot.

-- 
Haowei Peng
Northwestern University
Department of Physics & Astronomy
2145 Sheridan Rd.
Evanston, IL 60208-3112
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From sclauzer at sissa.it  Mon Jul 26 09:56:19 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Mon, 26 Jul 2010 09:56:19 +0200
Subject: [Pw_forum] starting_magnetization problem
In-Reply-To: <4C4BCB9D.2040100@gmail.com>
References: <4C4BCB9D.2040100@gmail.com>
Message-ID: <4C4D3FA3.8070606@sissa.it>

On 07/25/2010 07:29 AM, Weyl Fang wrote:
> Dear all,
>
> Recently i want to do a spin polarization calculation.

For a metal or an insulator?

> After I read the
> pw.x input file description, i know if i set the tot_magnetization to
> unspecified the amount of electronic magnetization is determined during
> the self-consistent cycle. So i set the tot_magnetization to
> unspecified. But when i execute pw.x, i get a error message some
> starting_magnetization MUST be set. But i get the message" If you fix
> the magnetization with "tot_magnetization", you should not specify
> starting_magnetization."

So, do you really want to fix the total magnetization of the system or 
do you want it to reach its ground state magnetization?


> from the pw.x input file description. If i
> still should specify the starting_magnetization?

If you are using the broadening of the occupations, I think you should. 
If you want to fix the total magnetization in this case you should use 
constrained_magnetization, not tot_magnetization method (which still 
might work, but probably will not be able to reach self-consistency).

> And If i want the
> amount of electronic magnetization determined during the self-consistent
> cycle, how should i specify the starting_magnetization?
>    

It dipends on your system. In many cases any reasonable value between -1 
and 1 is good. If you can guess a value close to that of the ground 
state then the code will reach self-consistency faster. In complicated 
systems you may get stuck in some local minimum if the 
starting_magnetization is too "wrong".

HTH

GS

> Thanks for your help!
>
> Weyl
>
> ===========================================================================
>
> Weyl FANG
> Graduate student in Chemical Engineering
> State Key Laboratory of Materials-oriented Chemical Engineering
> College of Chemistry and Chemical Engineering
> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
> ****************************************************************************************************************
> Email: weylfang at gmail.com
> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China
> ********************************************************************* *******************************************
>
>
> _______________________________________________
> 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


From sclauzer at sissa.it  Mon Jul 26 10:07:18 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Mon, 26 Jul 2010 10:07:18 +0200
Subject: [Pw_forum] Si bandgap using hybrid functionals
In-Reply-To: <4C4618F7.9000009@purdue.edu>
References: <4C4618F7.9000009@purdue.edu>
Message-ID: <4C4D4236.9030704@sissa.it>

On 07/20/2010 11:45 PM, Janam wrote:
> Hi,
>
> I'm trying to get the right band gap (~1.12 eV) for Silicon using hybrid
> functions. I'm using espresso 4.2. Unfortunately, the band gap doesn't
> seem to be affected by using the hybrid functionals.
>
> For example, when I use Si.pb-rrkj.UPF (no hybrid functional), I get a
> band gap of 0.633eV. When I use the same pseudopotential with B3LYP, I
> get a band gap of 0.583.
>    

I think you are not using the exact exchange method in the correct way. 
At the moment there are no pseudopotentials built upon exact exchange 
calculations, so that one uses the non-hybrid PP _corresponding_ to the 
hybrid functional.
For instance, you can use PBE PPs with PBE0 hybrid functional, but you 
CANNOT use PZ PPs with the PBE0 hybrid. For the same reason I guess that 
you need to use BLYP PPs with the B3LYP hybrid.
In your example below you are mixing a PBE PP with the B3LYP hybrid. I 
think this is wrong because it leads to an unconsistency.
Try with input_dft='pbe0', you should see the opening of the Si band gap.

At least, this is my (little) understanding so far...

HTH

GS

> I've posting my scf input file below. Any help/advice would be greatly
> appreciated
>
> &control
>      prefix='si-pbe-b3lyp',
>      pseudo_dir='/home/nanohub/janam/QuantumEspresso/Si/pseudo'
>      outdir ='/home/nanohub/janam/QuantumEspresso/Si/tmp',
>      tstress = .true.,
>      tprnfor = .true.,
>   /
>   &system
>      ibrav=  2, celldm(1) =10.35, nat=  2, ntyp= 1,
>      ecutwfc = 80.0, input_dft="b3lyp",
>   /
>   &electrons
>      conv_thr=1E-7
>   /
> ATOMIC_SPECIES
>   Si  28.086  Si.pbe-rrkj.UPF
> ATOMIC_POSITIONS
>   Si 0.00 0.00 0.00
>   Si 0.25 0.25 0.25
> K_POINTS automatic
>     8 8 8 0 0 0
>
> Sincerely
> ---
> Janam Jhaveri
> School of Electrical and Computer Engineering
> Purdue University
> C# (765)-409-1948
>
> _______________________________________________
> 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


From a.nourmohammadi at yahoo.com  Mon Jul 26 13:25:32 2010
From: a.nourmohammadi at yahoo.com (Amene Nouri)
Date: Mon, 26 Jul 2010 04:25:32 -0700 (PDT)
Subject: [Pw_forum] EXX error
Message-ID: <851238.82722.qm@web59407.mail.ac4.yahoo.com>






Thank you professor Stefano Baroni.
?
I want to use HSE functional. I have followed instructions in EXX-example.
make clean
add -DEXX to DFLAGS
make pw
but when I run EXX-example?I encounter error # 19.
What does it mean??
Do you think the error is coneccted to the?compilation?
What is my mistake?
?
any suggestion will be appreciated.




      
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From marsamos at democritos.it  Mon Jul 26 17:29:43 2010
From: marsamos at democritos.it (marsamos at democritos.it)
Date: Mon, 26 Jul 2010 17:29:43 +0200
Subject: [Pw_forum] Hand's on Workshop annoucement: nanoexcite2010
Message-ID: <20100726172943.sbqzny0j8c8o080o@mail.democritos.it>

   SISSA and CNR-IOM-DEMOCRITOS are organizing a Hand's on Workshop on 
electronic excitations, nanoexcite2010. During the workshop advanced 
concepts of Time Dependent Density Functional Theory, GW and 
Bethe-Salpeter Equation will be introduced. Short theoretical lectures 
will be followed by extensive hands-on classes. Participants will have 
the opportunity of testing on realistic systems the theoretical tools 
by using several public codes and their respective dedicated tutorials. 
The codes that will be used are

    * PWscf
    * Yambo
    * Sax
    * Real-Time TDDFT
    * TDFTPT
    * GWL

   Participants are expected to have a strong background in Density 
Functional Theory and long experience with Quantum ESPRESSO. The 
Workshop will be held at SISSA (Trieste, Italy) from October 18th to 
22th. For further information and subscription please see 
http://www.democritos.it/nanoexcite2010

bests

Layla

-- 
Dr. L. Martin-Samos
tel. +39 040 3787 429
CNR-DEMOCRITOS and
International School for Advanced Studies (ISAS-SISSA)
via Beirut 2-4
34151 Trieste Italy

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From gianluca.giovannetti at gmail.com  Mon Jul 26 17:34:13 2010
From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti)
Date: Mon, 26 Jul 2010 17:34:13 +0200
Subject: [Pw_forum] occupancies of atomic orbitals
Message-ID: <AANLkTinXw8icky2gd_7vixGdN7N5Vq1xJoVrxooXhhFo@mail.gmail.com>

Dear All,

i have made self-consistent for my system (FeSe).

Printing out the density matrix in LDA+U within U=0 at Fe sites i believe i
can get the occupancies of d atomic orbitals.

For example in the output i get (non spin polarized calculations):
-----------------------------------------------------------------------------------------------------------
atom  4  spin  1
eigenvalues:  0.7294836 0.7306191 0.7326025 0.7629065 0.8283887
 eigenvectors
 1   0.0000000  0.0000000 -1.0000000  0.0000000  0.0000000
 2   0.0000000 -1.0000000  0.0000000  0.0000000  0.0000000
 3  -0.0087135  0.0000000  0.0000000  0.9999620  0.0000000
 4   0.0000000  0.0000000  0.0000000  0.0000000 -1.0000000
 5  -0.9999620  0.0000000  0.0000000 -0.0087135  0.0000000
 occupations
 0.828  0.000  0.000  0.001  0.000
 0.000  0.731  0.000  0.000  0.000
 0.000  0.000  0.729  0.000  0.000
 0.001  0.000  0.000  0.733  0.000
 0.000  0.000  0.000  0.000  0.763
-----------------------------------------------------------------------------------------------------------

looking at the eigenvalues i can say for the occupancies n of d orbital
states:

   z2-r2         xz            yz             x2-y2        xy
n 0.8283887 0.7306191 0.7294836 0.7326025 0.7629065

is this correct?

thank you in advance.

Gianluca Giovannetti
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From marsamos at democritos.it  Mon Jul 26 19:14:21 2010
From: marsamos at democritos.it (marsamos at democritos.it)
Date: Mon, 26 Jul 2010 19:14:21 +0200
Subject: [Pw_forum] EXX error
In-Reply-To: <851238.82722.qm@web59407.mail.ac4.yahoo.com>
References: <851238.82722.qm@web59407.mail.ac4.yahoo.com>
Message-ID: <20100726191421.4jdhhsf2wws0s8c4@mail.democritos.it>

Dear Amene, did the job generate some .out file? if yes can you send it?

bests

Layla

Quoting Amene Nouri <a.nourmohammadi at yahoo.com>:

>
>
>
>
>
> Thank you professor Stefano Baroni.
> ?
> I want to use HSE functional. I have followed instructions in EXX-example.
> make clean
> add -DEXX to DFLAGS
> make pw
> but when I run EXX-example?I encounter error # 19.
> What does it mean??
> Do you think the error is coneccted to the?compilation?
> What is my mistake?
> ?
> any suggestion will be appreciated.
>
>
>
>
>



-- 
Dr. L. Martin-Samos
tel. +39 040 3787 429
CNR-DEMOCRITOS and
International School for Advanced Studies (ISAS-SISSA)
via Beirut 2-4
34151 Trieste Italy

----------------------------------------------------------------
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From didi5158 at gmail.com  Tue Jul 27 07:56:44 2010
From: didi5158 at gmail.com (Wang Di)
Date: Tue, 27 Jul 2010 13:56:44 +0800
Subject: [Pw_forum] anybody know how to calculate the properties of a unit
	in melting or in solution?
Message-ID: <AANLkTimmG7JiNe3YUzsX9BUXGAGygUNAao+QREGmsJQd@mail.gmail.com>

hello everyone:
       recently, I wish to use the first principle to calculate the
properties of a unit in melting state or in solution. Does anybody knows how
to do it and provides some advises or references. Thanks for your help.!

Wang Di
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From o.sedelnikova at gmail.com  Tue Jul 27 12:42:53 2010
From: o.sedelnikova at gmail.com (Olga Sedelnikova)
Date: Tue, 27 Jul 2010 17:42:53 +0700
Subject: [Pw_forum] problem with vc-relax
Message-ID: <AANLkTima_ph8H7dStLRGQRCVXniUv50Veh2x8WnQwE3-@mail.gmail.com>

Dear All,
I have a problem with 'vc-relax' option for graphene. I have used david and
cg diagonalization proceedures, different types of smearing and ion and cell
dynamics but all calculations were crashed.
One of my input file:

&CONTROL
     calculation = 'vc-relax',
     prefix = 'graphene',
     restart_mode='from_scratch'
     tstress=.true.,
     tprnfor=.true.,
     nstep=45,
      etot_conv_thr = 1.0E-4 ,
      forc_conv_thr = 1.0D-3 ,
      max_seconds = 36000 ,
      dt = 100,
   /
&SYSTEM
     ibrav = 4,
     celldm(1)= 4.64833
     celldm(3)=5.447621
               nat = 2,
               ntyp = 1,
               ecutwfc = 18.0,
               nbnd =8,
     occupations='smearing'
     smearing = 'mv'
     degauss = 0.005
       /
&ELECTRONS
     conv_thr = 1.0d-7
     electron_maxstep = 70
     diagonalization='cg'
   /
&IONS
     ion_dynamics='damp'
/
&CELL
    cell_dynamics = 'damp-w' ,
    press=0.00 ,
    wmass=0.0015 ,
/

ATOMIC_SPECIES
     C   12.01100 C.pz-vbc.UPF
ATOMIC_POSITIONS crystal
    C      0.00000000    0.00000000    0.50000000
    C      0.33333333    0.66666666    0.50000000
K_POINTS {automatic}
   6 6 6 0 0 0
Inthis cause:

from electrons : error #         1
     charge is wrong
Maybe somebody has already dealed with this problem and can advice the
correct options for graphene.
Any suggestion will be appreciated.

-- 
Best wishes,
Olga Sedelnikova
Nikolaev Institute of Inorganic Chemistry of SB RAS
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From skgupta.physics at gmail.com  Tue Jul 27 12:55:11 2010
From: skgupta.physics at gmail.com (Sanjeev Kumar Gupta)
Date: Tue, 27 Jul 2010 12:55:11 +0200
Subject: [Pw_forum] problem with vc-relax
In-Reply-To: <AANLkTima_ph8H7dStLRGQRCVXniUv50Veh2x8WnQwE3-@mail.gmail.com>
References: <AANLkTima_ph8H7dStLRGQRCVXniUv50Veh2x8WnQwE3-@mail.gmail.com>
Message-ID: <AANLkTi=HMJArf=8Lj12Ppqgoew2qojgthNLeGoFESjwB@mail.gmail.com>

Please visit this achieve
http://www.democritos.it/pipermail/pw_forum/2006-August/004713.html, and
http://www.democritos.it/pipermail/pw_forum/2008-December/010853.html,
you may find the solution.
Best Regards
Sanjeev

Dept. of Physics
Bhavnagar University
Gujarat

On 27 July 2010 12:42, Olga Sedelnikova <o.sedelnikova at gmail.com> wrote:

> Dear All,
> I have a problem with 'vc-relax' option for graphene. I have used david
> and cg diagonalization proceedures, different types of smearing and ion and
> cell dynamics but all calculations were crashed.
> One of my input file:
>
> &CONTROL
>      calculation = 'vc-relax',
>      prefix = 'graphene',
>      restart_mode='from_scratch'
>      tstress=.true.,
>      tprnfor=.true.,
>      nstep=45,
>       etot_conv_thr = 1.0E-4 ,
>       forc_conv_thr = 1.0D-3 ,
>       max_seconds = 36000 ,
>       dt = 100,
>    /
> &SYSTEM
>      ibrav = 4,
>      celldm(1)= 4.64833
>      celldm(3)=5.447621
>                nat = 2,
>                ntyp = 1,
>                ecutwfc = 18.0,
>                nbnd =8,
>      occupations='smearing'
>      smearing = 'mv'
>      degauss = 0.005
>        /
> &ELECTRONS
>      conv_thr = 1.0d-7
>      electron_maxstep = 70
>      diagonalization='cg'
>    /
> &IONS
>      ion_dynamics='damp'
> /
> &CELL
>     cell_dynamics = 'damp-w' ,
>     press=0.00 ,
>     wmass=0.0015 ,
> /
>
> ATOMIC_SPECIES
>      C   12.01100 C.pz-vbc.UPF
> ATOMIC_POSITIONS crystal
>     C      0.00000000    0.00000000    0.50000000
>     C      0.33333333    0.66666666    0.50000000
> K_POINTS {automatic}
>    6 6 6 0 0 0
> Inthis cause:
>
> from electrons : error #         1
>      charge is wrong
> Maybe somebody has already dealed with this problem and can advice the
> correct options for graphene.
> Any suggestion will be appreciated.
>
> --
> Best wishes,
> Olga Sedelnikova
> Nikolaev Institute of Inorganic Chemistry of SB RAS
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
With Kind Regards,
Sanjeev K. Gupta
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From matteo at umn.edu  Tue Jul 27 16:21:22 2010
From: matteo at umn.edu (Matteo Cococcioni)
Date: Tue, 27 Jul 2010 09:21:22 -0500
Subject: [Pw_forum] occupancies of atomic orbitals
In-Reply-To: <AANLkTinXw8icky2gd_7vixGdN7N5Vq1xJoVrxooXhhFo@mail.gmail.com>
References: <AANLkTinXw8icky2gd_7vixGdN7N5Vq1xJoVrxooXhhFo@mail.gmail.com>
Message-ID: <AANLkTinDsmsx0_zWO00_+=VaE5X+tBuW4otJ=mWLEXxR@mail.gmail.com>

Hi Gianluca,

I think your interpretation is correct. In fact the occupation matrix is
almost diagonal...

Matteo

On Mon, Jul 26, 2010 at 10:34 AM, Gianluca Giovannetti <
gianluca.giovannetti at gmail.com> wrote:

> Dear All,
>
> i have made self-consistent for my system (FeSe).
>
> Printing out the density matrix in LDA+U within U=0 at Fe sites i believe i
> can get the occupancies of d atomic orbitals.
>
> For example in the output i get (non spin polarized calculations):
>
> -----------------------------------------------------------------------------------------------------------
> atom  4  spin  1
> eigenvalues:  0.7294836 0.7306191 0.7326025 0.7629065 0.8283887
>  eigenvectors
>  1   0.0000000  0.0000000 -1.0000000  0.0000000  0.0000000
>  2   0.0000000 -1.0000000  0.0000000  0.0000000  0.0000000
>  3  -0.0087135  0.0000000  0.0000000  0.9999620  0.0000000
>  4   0.0000000  0.0000000  0.0000000  0.0000000 -1.0000000
>  5  -0.9999620  0.0000000  0.0000000 -0.0087135  0.0000000
>  occupations
>  0.828  0.000  0.000  0.001  0.000
>  0.000  0.731  0.000  0.000  0.000
>  0.000  0.000  0.729  0.000  0.000
>  0.001  0.000  0.000  0.733  0.000
>  0.000  0.000  0.000  0.000  0.763
>
> -----------------------------------------------------------------------------------------------------------
>
> looking at the eigenvalues i can say for the occupancies n of d orbital
> states:
>
>    z2-r2         xz            yz             x2-y2        xy
> n 0.8283887 0.7306191 0.7294836 0.7326025 0.7629065
>
> is this correct?
>
> thank you in advance.
>
> Gianluca Giovannetti
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From marsamos at democritos.it  Tue Jul 27 16:31:58 2010
From: marsamos at democritos.it (marsamos at democritos.it)
Date: Tue, 27 Jul 2010 16:31:58 +0200
Subject: [Pw_forum] GW for large systems
In-Reply-To: <AANLkTimiJzrbm4OnuGzSDBkY7dgPEAIAS2nGelKUBPL6@mail.gmail.com>
References: <AANLkTimiJzrbm4OnuGzSDBkY7dgPEAIAS2nGelKUBPL6@mail.gmail.com>
Message-ID: <20100727163158.i7n02v6k0s40o008@mail.democritos.it>

Dear Gianluca, yes the Umari's et al GW is available in espresso-4.2 
just make gww to compile the module (GWW). 120 ions if bulk are 
accessible by traditional GWs schemes so for sure you can afford 
comfortably the calculation with GWW.

bests

Layla

Quoting Gianluca Giovannetti <gianluca.giovannetti at gmail.com>:

> Dear All,
>
> i want to do GW calculations on a large system containing 120 ions.
>
> i would say i can try to run it with the scheme proposed by P. Umari, G.
> Stenuit and S. Baroni, *Optimal representation of the polarization
> propagator for large-scale GW calculations*, Phys. Rev. B *79* (2009)
> 201104(R).
>
> do you have some experience about it?
>
> i hope a such calculation can be dealt with this scheme.
>
> is it available the GW scheme mentioned above in some version of Quantum
> Espresso?
>
> i have found at the website:
>
> http://gww.qe-forge.org/index.php?page=intro
>
> a good description about how to use it.
>
> is it available with 4.2.1 version?
>
> i thank you in advance.
>
> cheers,
>
> Gianluca Giovannetti
>



-- 
Dr. L. Martin-Samos
tel. +39 040 3787 429
CNR-DEMOCRITOS and
International School for Advanced Studies (ISAS-SISSA)
via Beirut 2-4
34151 Trieste Italy

----------------------------------------------------------------
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From lcqsigi at gmail.com  Tue Jul 27 17:47:57 2010
From: lcqsigi at gmail.com (S. Sanchez)
Date: Tue, 27 Jul 2010 11:47:57 -0400
Subject: [Pw_forum] Units of Raman Tensor
Message-ID: <AANLkTikR7S_9CVc7kpuuJSNt5O3c2xpCiEdXnJ5v+kq+@mail.gmail.com>

Dear QE users,

I have a question regarding the Raman Tensor units. I have seen in the QE
forum that units of the Raman Tensor resulting from the use of ph.x code are
given in: "A^2" (Angstroms^2).

Question: do these units results after a multiplication of the third-order
rank tensors (dchi/dr, where "r" indicates atomic displacement) by their
respective normal-mode displacements? Or do the units of "A^2" correspond
only to the dchi/dr tensor?

My question arises given the fact that the dchi/dr tensor can be obtained as
the third order derivative of the Energy (in units of Ry or Ha) with respect
to the atomic displacement (bohr) and two times the electric field (e/bohr).

dchi/dr=d^3E/(dr*de1*de2)
where E is the Energy; r the displacement, e1 and e2 the electric fields.
Replacing the above-mentioned units, I can only get units of Ha*bohr
((Ry/2)*bohr); where e^2=1 for Hartree or e^2=2 for Rydberg.

Thanks for your help,
S. Sanchez
Researcher
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From 1009ukumar at gmail.com  Tue Jul 27 18:48:34 2010
From: 1009ukumar at gmail.com (sonu kumar)
Date: Tue, 27 Jul 2010 22:18:34 +0530
Subject: [Pw_forum] How to find the charge density corresponding to AE and
	Pseudo states in atomic code?
Message-ID: <AANLkTi=Svu07X3Wv8aT7Lyhv0NUOZfm7vhKgA6dQYzcd@mail.gmail.com>

Dear All Quantum Espresso users,

How can i find out :

1) all electron charge density corresponding  to core and valence states

2) pseudo charge density corresponding to pseudized core(nlcc) and
valence(or/and semicore) states

using "atomic" code  in Quantum Espresso?

I am not an experienced QE user.

With Kind Regards,

Sonu Kumar
Phd Student
Physics Department
Indian Institute of Technology
Delhi-110016, India
web:-http://www.iitd.ac.in/
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From o.sedelnikova at gmail.com  Wed Jul 28 08:09:20 2010
From: o.sedelnikova at gmail.com (Olga Sedelnikova)
Date: Wed, 28 Jul 2010 13:09:20 +0700
Subject: [Pw_forum] problem with vc-relax
Message-ID: <AANLkTi=rp9S10tCLXmGp62P5tHq7BtY-P1f1juFWJs+b@mail.gmail.com>

 Dear Sanjeev,


The problem is not with wrong charge. The error "charge is wrong" appeared
only for current options (smearing='mv', dynamics='damp', cg
diagonalization). If I use other physically appropriate options I will
obtain other errors: problem with davidson diagonalization, too small
trust_radius for bfgs method and sometimes error from efirmig.f90 "internal
error, cannot braket Ef". I have checked the dynamics of unit cell during
vc-relaxation by XCrySDen and found that interlayer distance and bond length
in graphite decreased  to ~ 2 and 1.2   Angstroms correspondingly. For
graphene calculations the unit cell was compressed along the z-axis and C-C
bond length decreased. However the "relax" calculation is fine.

Can anybody recommend the right options for "vc-relax" calculation of
graphite?

Thank you,

Olga Sedelnikova
Nikolaev Institute of Inorganic Chemistry of SB RAS



> Please visit this achieve
> http://www.democritos.it/pipermail/pw_forum/2006-August/004713.html, and
> http://www.democritos.it/pipermail/pw_forum/2008-December/010853.html,
> you may find the solution.
> Best Regards
> Sanjeev
>
> Dept. of Physics
> Bhavnagar University
> Gujarat
>
>
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From merlin.meheut at lmtg.obs-mip.fr  Wed Jul 28 11:44:27 2010
From: merlin.meheut at lmtg.obs-mip.fr (Merlin Meheut)
Date: Wed, 28 Jul 2010 11:44:27 +0200
Subject: [Pw_forum] Ni.pbe-sp-mt_gipaw.UPF
Message-ID: <4C4FFBFB.6030206@lmtg.obs-mip.fr>

Dear PWSCF users,

I would like to compute fcc Nickel metal using the pseudopotential 
Ni.pbe-sp-mt_gipaw.UPF, available on your website.
I do not need the GIPAW part, but I have been said that this should not 
be an issue. However, using an input very
similar to example02, the calculation fails by "not recognizing the 
pseudo":

-------------------------------------------------------
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 

      from read_pseudo_gipaw : error #         1
      UPF/GIPAW in unknown format
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

      stopping ...
--------------------------------------------------------

I use Quantum Espresso version 4.1.2.

Below is my input file (which works with pseudo Ni.pbe-nd-rrkjus.UPF 
<http://www.quantum-espresso.org/pseudo/1.3/UPF/Ni.pbe-nd-rrkjus.UPF>) :

&control
            disk_io = 'default' ,
     pseudo_dir     = '$PBS_O_WORKDIR',
     outdir         = '/tmpdir/$PBS_O_LOGNAME/',
     tprnfor        = .true.,
     tstress        = .true.,
     calculation    = 'scf'
     prefix         = 'ni',
     verbosity      = 'high',
  /
&system
     ibrav=2, celldm(1) =6.65, nat=  1, ntyp= 1,
     nspin=2,
     starting_magnetization(1)=0.5,
     degauss=0.02,
     smearing='mp',
     occupations='smearing',
     ecutwfc =27.0
     ecutrho =300.0
  /
&electrons
     conv_thr =  1.0d-8
     mixing_beta = 0.7
  /
ATOMIC_SPECIES
  Ni  58.6934  Ni.pbe-sp-mt_gipaw.UPF
ATOMIC_POSITIONS
  Ni 0.00 0.00 0.00
K_POINTS AUTOMATIC
8 8 8 1 1 1

Thanks for any help,

Merlin Meheut

-- 
Merlin M?heut
Maitre de conf?rences
LMTG- Universit? Paul Sabatier Toulouse 3
14 avenue Edoaurd Belin
31400 Toulouse
tel: (+33)5 61 33 26 21
Fax: (+33) 5 61 33 25 60
Mobile: (+33) 6 34 67 57 02


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From Ari.P.Seitsonen at iki.fi  Wed Jul 28 12:16:27 2010
From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen)
Date: Wed, 28 Jul 2010 12:16:27 +0200 (CEST)
Subject: [Pw_forum] Ni.pbe-sp-mt_gipaw.UPF
In-Reply-To: <4C4FFBFB.6030206@lmtg.obs-mip.fr>
References: <4C4FFBFB.6030206@lmtg.obs-mip.fr>
Message-ID: <alpine.LNX.2.00.1007281209050.28489@pcihpc19.uzh.ch>


Dear Merlin,

   You can either

  1) remove the whole GIPAW part from the pseudo potential,
  2) modify the pseudo potential file:

<PP_PAW_FORMAT_VERSION>
    0.10000000000E+00
</PP_PAW_FORMAT_VERSION>

and

<PP_GIPAW_FORMAT_VERSION>
0.1
</PP_GIPAW_FORMAT_VERSION>

   The version 4.1.2 of the code wants an integer in the latter case, so 
you can modify the "0.1" into "1",

  3) or you modify the source code in Modules/read_upf_v1.f90 so that it 
accepts this syntax also.

   Sorry for the confusion (I am partially guilty for it). Please tell if 
this doesn't solve your problem.

     Greetings from Zurich,

        apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
   Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
   Physikalisch-Chemisches Institut der Universitaet Zuerich
   Tel: +41 44 63 54 497  /  Mobile: +41 79 71 90 935

On Wed, 28 Jul 2010, Merlin Meheut wrote:

> Dear PWSCF users,
> 
> I would like to compute fcc Nickel metal using the pseudopotential
> Ni.pbe-sp-mt_gipaw.UPF, available on your website.
> I do not need the GIPAW part, but I have been said that this should not be
> an issue. However, using an input very
> similar to example02, the calculation fails by "not recognizing the pseudo":
> 
> -------------------------------------------------------
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%
> ???? from read_pseudo_gipaw : error #???????? 1
> ???? UPF/GIPAW in unknown format
> ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%
> 
> ???? stopping ...
> --------------------------------------------------------
> 
> I use Quantum Espresso version 4.1.2.
> 
> Below is my input file (which works with pseudo Ni.pbe-nd-rrkjus.UPF) :
> 
> &control
> ?????????? disk_io = 'default' ,
> ??? pseudo_dir???? = '$PBS_O_WORKDIR',
> ??? outdir???????? = '/tmpdir/$PBS_O_LOGNAME/',
> ??? tprnfor??????? = .true.,
> ??? tstress??????? = .true.,
> ??? calculation??? = 'scf'
> ??? prefix???????? = 'ni',
> ??? verbosity????? = 'high',
> ?/
> &system
> ??? ibrav=2, celldm(1) =6.65, nat=? 1, ntyp= 1,
> ??? nspin=2,
> ??? starting_magnetization(1)=0.5,
> ??? degauss=0.02,
> ??? smearing='mp',
> ??? occupations='smearing',
> ??? ecutwfc =27.0
> ??? ecutrho =300.0
> ?/
> &electrons
> ??? conv_thr =? 1.0d-8
> ??? mixing_beta = 0.7
> ?/
> ATOMIC_SPECIES
> ?Ni? 58.6934? Ni.pbe-sp-mt_gipaw.UPF
> ATOMIC_POSITIONS
> ?Ni 0.00 0.00 0.00
> K_POINTS AUTOMATIC
> 8 8 8 1 1 1
> 
> Thanks for any help,
> 
> Merlin Meheut
> 
> -- 
> Merlin M?heut
> Maitre de conf?rences 
> LMTG- Universit? Paul Sabatier Toulouse 3
> 14 avenue Edoaurd Belin
> 31400 Toulouse
> tel: (+33)5 61 33 26 21
> Fax: (+33) 5 61 33 25 60
> Mobile: (+33) 6 34 67 57 02
> 
> 
>

From eyvaz_isaev at yahoo.com  Wed Jul 28 15:36:36 2010
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Wed, 28 Jul 2010 06:36:36 -0700 (PDT)
Subject: [Pw_forum] problem with vc-relax
In-Reply-To: <AANLkTima_ph8H7dStLRGQRCVXniUv50Veh2x8WnQwE3-@mail.gmail.com>
References: <AANLkTima_ph8H7dStLRGQRCVXniUv50Veh2x8WnQwE3-@mail.gmail.com>
Message-ID: <846523.52444.qm@web65713.mail.ac4.yahoo.com>

Dear Olga,

I could not reproduce the error you report using different  pw.x versions. 
They  finished by the error message (QE 4.2, compiler gfortran on Ubuntu 9.4 on 
my laptop, serial):
 
      from scale_h : error #         1
     Not enough space allocated for radial FFT: try restarting with a larger 
cell_factor.

Usually,   that means unreasonable lattice parameters. Say, one of them  is much  
larger than expected. In fact, this turned out to be dependent on  ecutwfc and 
pseudopotential type. The error persists for norm-conserving  type pseudo you 
used. But using US pseudo for C, and the cutoff energy  30Ry (360 for ecutrho) , 
no  problem arises. 

Besides, for Norm-conserving type pseudo for C 18Ry seems to be  extremely low. 
You can play around ecutwfc, upscale and cell_factor parameters. 

If you like, you can fix c-axis, do relax, and using a set of c-axis parameter  
find the minimum. 

 
Last, if you study a graphene sheet why you used 6 6 6? The correct one seems to 
be 6 6 1.

Bests,
Eyvaz.
 -------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, 
Sweden 

Theoretical Physics Department, Moscow State Institute of Steel & Alloys, 
Russia, 

isaev at ifm.liu.se, eyvaz_isaev at yahoo.com




________________________________
From: Olga Sedelnikova <o.sedelnikova at gmail.com>
To: pw_forum at pwscf.org
Sent: Tue, July 27, 2010 12:42:53 PM
Subject: [Pw_forum] problem with vc-relax


Dear All,
I have a problem with 'vc-relax' option for graphene. I have used david and cg 
diagonalization proceedures, different types of smearing and ion and cell 
dynamics but all calculations were crashed. 
One of my input file:
 
&CONTROL
     calculation = 'vc-relax',
     prefix = 'graphene',
     restart_mode='from_scratch'
     tstress=.true.,
     tprnfor=.true.,
     nstep=45,
      etot_conv_thr = 1.0E-4 ,
      forc_conv_thr = 1.0D-3 ,
      max_seconds = 36000 ,
      dt = 100,
   /
&SYSTEM
     ibrav = 4,
     celldm(1)= 4.64833
     celldm(3)=5.447621
               nat = 2, 
               ntyp = 1, 
               ecutwfc = 18.0,
               nbnd =8, 
     occupations='smearing'
     smearing = 'mv'
     degauss = 0.005
       /
&ELECTRONS
     conv_thr = 1.0d-7
     electron_maxstep = 70
     diagonalization='cg'
   /
&IONS
     ion_dynamics='damp'
/
&CELL
    cell_dynamics = 'damp-w' ,
    press=0.00 ,
    wmass=0.0015 ,
/
  
ATOMIC_SPECIES
     C   12.01100 C.pz-vbc.UPF
ATOMIC_POSITIONS crystal 
    C      0.00000000    0.00000000    0.50000000
    C      0.33333333    0.66666666    0.50000000
K_POINTS {automatic}
   6 6 6 0 0 0

Inthis cause: 
     
from electrons : error #         1
     charge is wrong

Maybe somebody has already dealed with this problem and can advice the correct 
options for graphene.
Any suggestion will be appreciated.

-- 
Best wishes,
Olga Sedelnikova
Nikolaev Institute of Inorganic Chemistry of SB RAS



      
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From pnyawere at gmail.com  Wed Jul 28 16:30:46 2010
From: pnyawere at gmail.com (Phillip Nyawere)
Date: Wed, 28 Jul 2010 16:30:46 +0200
Subject: [Pw_forum] problem with vc-relax
In-Reply-To: <AANLkTima_ph8H7dStLRGQRCVXniUv50Veh2x8WnQwE3-@mail.gmail.com>
References: <AANLkTima_ph8H7dStLRGQRCVXniUv50Veh2x8WnQwE3-@mail.gmail.com>
Message-ID: <AANLkTik3WmBz0Hm5KeiCAQNcnjRsQ-6QjRbo8P6Uyat9@mail.gmail.com>

Try cell_dynamics='bfgs' and not 'damp'
Success

On Tue, Jul 27, 2010 at 12:42 PM, Olga Sedelnikova
<o.sedelnikova at gmail.com>wrote:

> Dear All,
> I have a problem with 'vc-relax' option for graphene. I have used david
> and cg diagonalization proceedures, different types of smearing and ion and
> cell dynamics but all calculations were crashed.
> One of my input file:
>
> &CONTROL
>      calculation = 'vc-relax',
>      prefix = 'graphene',
>      restart_mode='from_scratch'
>      tstress=.true.,
>      tprnfor=.true.,
>      nstep=45,
>       etot_conv_thr = 1.0E-4 ,
>       forc_conv_thr = 1.0D-3 ,
>       max_seconds = 36000 ,
>       dt = 100,
>    /
> &SYSTEM
>      ibrav = 4,
>      celldm(1)= 4.64833
>      celldm(3)=5.447621
>                nat = 2,
>                ntyp = 1,
>                ecutwfc = 18.0,
>                nbnd =8,
>      occupations='smearing'
>      smearing = 'mv'
>      degauss = 0.005
>        /
> &ELECTRONS
>      conv_thr = 1.0d-7
>      electron_maxstep = 70
>      diagonalization='cg'
>    /
> &IONS
>      ion_dynamics='damp'
> /
> &CELL
>     cell_dynamics = 'damp-w' ,
>     press=0.00 ,
>     wmass=0.0015 ,
> /
>
> ATOMIC_SPECIES
>      C   12.01100 C.pz-vbc.UPF
> ATOMIC_POSITIONS crystal
>     C      0.00000000    0.00000000    0.50000000
>     C      0.33333333    0.66666666    0.50000000
> K_POINTS {automatic}
>    6 6 6 0 0 0
> Inthis cause:
>
> from electrons : error #         1
>      charge is wrong
> Maybe somebody has already dealed with this problem and can advice the
> correct options for graphene.
> Any suggestion will be appreciated.
>
> --
> Best wishes,
> Olga Sedelnikova
> Nikolaev Institute of Inorganic Chemistry of SB RAS
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Phillip W. Otieno Nyawere,
Kabarak University,
Dept of Physics & Mathematics,
P.O Box Private Bag - 20157,
Kabarak, Kenya.
Tel +254728342054
pnyawere at gmail.com, potieno at kabarak.ac.ke

The battle belongs to the Lord.
CURRENTLY IN CAPE TOWN, SOUTH AFRICA
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From kazempoor2000 at yahoo.com  Wed Jul 28 16:42:08 2010
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Wed, 28 Jul 2010 07:42:08 -0700 (PDT)
Subject: [Pw_forum] GWW with occupied states only
Message-ID: <323063.45928.qm@web114407.mail.gq1.yahoo.com>

Dear All
Does anyone know that recent version of GWW that works with just occupied state is implemented now or not?
Thanks a lot

Ali Kazempour







Fritz-Haber-Institut              fax   : ++49-30-8413 4701

der Max-Planck-Gesellschaft

Faradayweg 4-6                    e-mail: kazempou at fhi-berlin.mpg.de

D-14 195 Berlin-Dahlem / German


      
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From masoudnahali at live.com  Wed Jul 28 16:54:42 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Wed, 28 Jul 2010 19:24:42 +0430
Subject: [Pw_forum] problem with vc-relax
Message-ID: <AANLkTimPRvNgXy8DYaWhuxivZsxND=ZTyRzD3hJvq300@mail.gmail.com>

Dear Olga Sedelnikova


At first please use the C.pbe-rrkjus.UPF as the pseudopotential. This is
well tested by Nicola Marzari , Phys. Rev. B 71, 205214 (2005), and also I
have tested it. The paper of Nicola is very useful.  please be careful that
it is an ultra soft pseudopotential and you should select ecutrho 10X
greater than ecutwfc. Don't be worry about the cell size in the Z-direction
since it is due to london interactions and may not be predicted well by DFT.
But you can use ?london=.true.? to improve the results. For both
ion_dynamics and cell_dynamics I have used ?bfgs?. I am sure that you will
get better results. Please examine and don't hesitates to inform me about
the problem.

Best wishes

Masoud Nahali

SUT




> The problem is not with wrong charge. The error "charge is wrong" appeared
> only for current options (smearing='mv', dynamics='damp', cg
> diagonalization). If I use other physically appropriate options I will
> obtain other errors: problem with davidson diagonalization, too small
> trust_radius for bfgs method and sometimes error from efirmig.f90 "internal
> error, cannot braket Ef". I have checked the dynamics of unit cell during
> vc-relaxation by XCrySDen and found that interlayer distance and bond
> length
> in graphite decreased  to ~ 2 and 1.2   Angstroms correspondingly. For
> graphene calculations the unit cell was compressed along the z-axis and C-C
> bond length decreased. However the "relax" calculation is fine.
>
> Can anybody recommend the right options for "vc-relax" calculation of
> graphite?
>
> Thank you,
>
> Olga Sedelnikova
> Nikolaev Institute of Inorganic Chemistry of SB RAS
>
>
>
> > Please visit this achieve
> > http://www.democritos.it/pipermail/pw_forum/2006-August/004713.html, and
> > http://www.democritos.it/pipermail/pw_forum/2008-December/010853.html,
> > you may find the solution.
> > Best Regards
> > Sanjeev
> >
> > Dept. of Physics
> > Bhavnagar University
> > Gujarat
> >
> >
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>
> ------------------------------
>
> Message: 2
> Date: Wed, 28 Jul 2010 11:44:27 +0200
> From: Merlin Meheut <merlin.meheut at lmtg.obs-mip.fr>
> Subject: [Pw_forum] Ni.pbe-sp-mt_gipaw.UPF
> To: pw_forum at pwscf.org
> Message-ID: <4C4FFBFB.6030206 at lmtg.obs-mip.fr>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear PWSCF users,
>
> I would like to compute fcc Nickel metal using the pseudopotential
> Ni.pbe-sp-mt_gipaw.UPF, available on your website.
> I do not need the GIPAW part, but I have been said that this should not
> be an issue. However, using an input very
> similar to example02, the calculation fails by "not recognizing the
> pseudo":
>
> -------------------------------------------------------
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>      from read_pseudo_gipaw : error #         1
>      UPF/GIPAW in unknown format
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>      stopping ...
> --------------------------------------------------------
>
> I use Quantum Espresso version 4.1.2.
>
> Below is my input file (which works with pseudo Ni.pbe-nd-rrkjus.UPF
> <http://www.quantum-espresso.org/pseudo/1.3/UPF/Ni.pbe-nd-rrkjus.UPF>) :
>
> &control
>            disk_io = 'default' ,
>     pseudo_dir     = '$PBS_O_WORKDIR',
>     outdir         = '/tmpdir/$PBS_O_LOGNAME/',
>     tprnfor        = .true.,
>     tstress        = .true.,
>     calculation    = 'scf'
>     prefix         = 'ni',
>     verbosity      = 'high',
>  /
> &system
>     ibrav=2, celldm(1) =6.65, nat=  1, ntyp= 1,
>     nspin=2,
>     starting_magnetization(1)=0.5,
>     degauss=0.02,
>     smearing='mp',
>     occupations='smearing',
>     ecutwfc =27.0
>     ecutrho =300.0
>  /
> &electrons
>     conv_thr =  1.0d-8
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Ni  58.6934  Ni.pbe-sp-mt_gipaw.UPF
> ATOMIC_POSITIONS
>  Ni 0.00 0.00 0.00
> K_POINTS AUTOMATIC
> 8 8 8 1 1 1
>
> Thanks for any help,
>
> Merlin Meheut
>
> --
> Merlin M?heut
> Maitre de conf?rences
> LMTG- Universit? Paul Sabatier Toulouse 3
> 14 avenue Edoaurd Belin
> 31400 Toulouse
> tel: (+33)5 61 33 26 21
> Fax: (+33) 5 61 33 25 60
> Mobile: (+33) 6 34 67 57 02
>
>
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>
> ------------------------------
>
> Message: 3
> Date: Wed, 28 Jul 2010 12:16:27 +0200 (CEST)
> From: Ari P Seitsonen <Ari.P.Seitsonen at iki.fi>
> Subject: Re: [Pw_forum] Ni.pbe-sp-mt_gipaw.UPF
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <alpine.LNX.2.00.1007281209050.28489 at pcihpc19.uzh.ch>
> Content-Type: text/plain; charset="iso-8859-15"
>
>
> Dear Merlin,
>
>   You can either
>
>  1) remove the whole GIPAW part from the pseudo potential,
>  2) modify the pseudo potential file:
>
> <PP_PAW_FORMAT_VERSION>
>    0.10000000000E+00
> </PP_PAW_FORMAT_VERSION>
>
> and
>
> <PP_GIPAW_FORMAT_VERSION>
> 0.1
> </PP_GIPAW_FORMAT_VERSION>
>
>   The version 4.1.2 of the code wants an integer in the latter case, so
> you can modify the "0.1" into "1",
>
>  3) or you modify the source code in Modules/read_upf_v1.f90 so that it
> accepts this syntax also.
>
>   Sorry for the confusion (I am partially guilty for it). Please tell if
> this doesn't solve your problem.
>
>     Greetings from Zurich,
>
>        apsi
>
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>   Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/<http://www.iki.fi/%7Eapsi/>
>   Physikalisch-Chemisches Institut der Universitaet Zuerich
>   Tel: +41 44 63 54 497  /  Mobile: +41 79 71 90 935
>
> On Wed, 28 Jul 2010, Merlin Meheut wrote:
>
> > Dear PWSCF users,
> >
> > I would like to compute fcc Nickel metal using the pseudopotential
> > Ni.pbe-sp-mt_gipaw.UPF, available on your website.
> > I do not need the GIPAW part, but I have been said that this should not
> be
> > an issue. However, using an input very
> > similar to example02, the calculation fails by "not recognizing the
> pseudo":
> >
> > -------------------------------------------------------
> >
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > %%%
> > ???? from read_pseudo_gipaw : error #???????? 1
> > ???? UPF/GIPAW in unknown format
> >
> ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > %%%%
> >
> > ???? stopping ...
> > --------------------------------------------------------
> >
> > I use Quantum Espresso version 4.1.2.
> >
> > Below is my input file (which works with pseudo Ni.pbe-nd-rrkjus.UPF) :
> >
> > &control
> > ?????????? disk_io = 'default' ,
> > ??? pseudo_dir???? = '$PBS_O_WORKDIR',
> > ??? outdir???????? = '/tmpdir/$PBS_O_LOGNAME/',
> > ??? tprnfor??????? = .true.,
> > ??? tstress??????? = .true.,
> > ??? calculation??? = 'scf'
> > ??? prefix???????? = 'ni',
> > ??? verbosity????? = 'high',
> > ?/
> > &system
> > ??? ibrav=2, celldm(1) =6.65, nat=? 1, ntyp= 1,
> > ??? nspin=2,
> > ??? starting_magnetization(1)=0.5,
> > ??? degauss=0.02,
> > ??? smearing='mp',
> > ??? occupations='smearing',
> > ??? ecutwfc =27.0
> > ??? ecutrho =300.0
> > ?/
> > &electrons
> > ??? conv_thr =? 1.0d-8
> > ??? mixing_beta = 0.7
> > ?/
> > ATOMIC_SPECIES
> > ?Ni? 58.6934? Ni.pbe-sp-mt_gipaw.UPF
> > ATOMIC_POSITIONS
> > ?Ni 0.00 0.00 0.00
> > K_POINTS AUTOMATIC
> > 8 8 8 1 1 1
> >
> > Thanks for any help,
> >
> > Merlin Meheut
> >
> > --
> > Merlin M?heut
> > Maitre de conf?rences
> > LMTG- Universit? Paul Sabatier Toulouse 3
> > 14 avenue Edoaurd Belin
> > 31400 Toulouse
> > tel: (+33)5 61 33 26 21
> > Fax: (+33) 5 61 33 25 60
> > Mobile: (+33) 6 34 67 57 02
> >
> >
> >
>
> ------------------------------
>
> Message: 4
> Date: Wed, 28 Jul 2010 06:36:36 -0700 (PDT)
> From: Eyvaz Isaev <eyvaz_isaev at yahoo.com>
> Subject: Re: [Pw_forum] problem with vc-relax
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <846523.52444.qm at web65713.mail.ac4.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Olga,
>
> I could not reproduce the error you report using different  pw.x versions.
> They  finished by the error message (QE 4.2, compiler gfortran on Ubuntu
> 9.4 on
> my laptop, serial):
>
>      from scale_h : error #         1
>     Not enough space allocated for radial FFT: try restarting with a larger
> cell_factor.
>
> Usually,   that means unreasonable lattice parameters. Say, one of them  is
> much
> larger than expected. In fact, this turned out to be dependent on  ecutwfc
> and
> pseudopotential type. The error persists for norm-conserving  type pseudo
> you
> used. But using US pseudo for C, and the cutoff energy  30Ry (360 for
> ecutrho) ,
> no  problem arises.
>
> Besides, for Norm-conserving type pseudo for C 18Ry seems to be  extremely
> low.
> You can play around ecutwfc, upscale and cell_factor parameters.
>
> If you like, you can fix c-axis, do relax, and using a set of c-axis
> parameter
> find the minimum.
>
>
> Last, if you study a graphene sheet why you used 6 6 6? The correct one
> seems to
> be 6 6 1.
>
> Bests,
> Eyvaz.
>  -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
> Sweden
>
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
> Russia,
>
> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
>
>
> ________________________________
> From: Olga Sedelnikova <o.sedelnikova at gmail.com>
> To: pw_forum at pwscf.org
> Sent: Tue, July 27, 2010 12:42:53 PM
> Subject: [Pw_forum] problem with vc-relax
>
>
> Dear All,
> I have a problem with 'vc-relax' option for graphene. I have used david and
> cg
> diagonalization proceedures, different types of smearing and ion and cell
> dynamics but all calculations were crashed.
> One of my input file:
>
> &CONTROL
>     calculation = 'vc-relax',
>     prefix = 'graphene',
>     restart_mode='from_scratch'
>     tstress=.true.,
>     tprnfor=.true.,
>     nstep=45,
>      etot_conv_thr = 1.0E-4 ,
>      forc_conv_thr = 1.0D-3 ,
>      max_seconds = 36000 ,
>      dt = 100,
>   /
> &SYSTEM
>     ibrav = 4,
>     celldm(1)= 4.64833
>     celldm(3)=5.447621
>               nat = 2,
>               ntyp = 1,
>               ecutwfc = 18.0,
>               nbnd =8,
>     occupations='smearing'
>     smearing = 'mv'
>     degauss = 0.005
>       /
> &ELECTRONS
>     conv_thr = 1.0d-7
>     electron_maxstep = 70
>     diagonalization='cg'
>   /
> &IONS
>     ion_dynamics='damp'
> /
> &CELL
>    cell_dynamics = 'damp-w' ,
>    press=0.00 ,
>    wmass=0.0015 ,
> /
>
> ATOMIC_SPECIES
>     C   12.01100 C.pz-vbc.UPF
> ATOMIC_POSITIONS crystal
>    C      0.00000000    0.00000000    0.50000000
>    C      0.33333333    0.66666666    0.50000000
> K_POINTS {automatic}
>   6 6 6 0 0 0
>
> Inthis cause:
>
> from electrons : error #         1
>     charge is wrong
>
> Maybe somebody has already dealed with this problem and can advice the
> correct
> options for graphene.
> Any suggestion will be appreciated.
>
> --
> Best wishes,
> Olga Sedelnikova
> Nikolaev Institute of Inorganic Chemistry of SB RAS
>
>
>
>
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> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 37, Issue 60
> ****************************************
>
>
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From baroni at sissa.it  Wed Jul 28 17:33:13 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 28 Jul 2010 17:33:13 +0200
Subject: [Pw_forum] GWW with occupied states only
In-Reply-To: <323063.45928.qm@web114407.mail.gq1.yahoo.com>
References: <323063.45928.qm@web114407.mail.gq1.yahoo.com>
Message-ID: <4CA31880-9133-4448-AA1D-6C13178FAE83@sissa.it>

not yet in the public domain
SB

On Jul 28, 2010, at 4:42 PM, ali kazempour wrote:

> Dear All
> Does anyone know that recent version of GWW that works with just occupied state is implemented now or not?
> Thanks a lot
> 
> Ali Kazempour
> 
> 
> 
> Fritz-Haber-Institut fax : ++49-30-8413 4701
> der Max-Planck-Gesellschaft
> Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de
> D-14 195 Berlin-Dahlem / German
> 
> _______________________________________________
> 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







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From adehaopan at hotmail.com  Wed Jul 28 17:33:21 2010
From: adehaopan at hotmail.com (HaoPan)
Date: Wed, 28 Jul 2010 23:33:21 +0800
Subject: [Pw_forum] Fourier interpolation
Message-ID: <SNT117-W101BC51D627FFA6735C37FB6A80@phx.gbl>


Hi, everyone,



On each q point I got, the phone frequencies are positive. But after the Fourier interpolation process, There

exist negative frequencies. I check the some special q points using ph.x, there are no negative frequencies. I

know the dynamical matrices for metal are not smooth function of q, but how do I fix it to get the right

dispersion curves? Thanks a lot.



Sincerely,

Pan Hao

Tulane University 		 	   		  
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From baroni at sissa.it  Wed Jul 28 17:49:28 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 28 Jul 2010 17:49:28 +0200
Subject: [Pw_forum] Fourier interpolation
In-Reply-To: <SNT117-W101BC51D627FFA6735C37FB6A80@phx.gbl>
References: <SNT117-W101BC51D627FFA6735C37FB6A80@phx.gbl>
Message-ID: <5670438B-7E3A-460B-AFBA-3A26E56641AB@sissa.it>

the kpoint grid you are using may be too coarse
dynamical matrices in metals are indeed smooth functions of k, unless you have Kohn anomalies
SB

On Jul 28, 2010, at 5:33 PM, HaoPan wrote:

> Hi, everyone,
> 
> On each q point I got, the phone frequencies are positive. But after the Fourier interpolation process, There
> exist negative frequencies. I check the some special q points using ph.x, there are no negative frequencies. I
> know the dynamical matrices for metal are not smooth function of q, but how do I fix it to get the right
> dispersion curves? Thanks a lot.
> 
> Sincerely,
> Pan Hao
> Tulane 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

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html







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From o.sedelnikova at gmail.com  Thu Jul 29 06:24:07 2010
From: o.sedelnikova at gmail.com (Olga Sedelnikova)
Date: Thu, 29 Jul 2010 11:24:07 +0700
Subject: [Pw_forum] problem with vc-relax
Message-ID: <AANLkTimntB6BgFAHJgkme_1seyMr+t9d4gUOQXTcjbbd@mail.gmail.com>

Dear All,

I have improved the cutoff energy (30 Ry) and used C.pbe-rrkjus.UPF.
 All calculations of graphite and graphene were successful for damp and bfgs
dynamics.
Thank you very much for your kind help!

-- 
Best wishes,
Olga Sedelnikova
Nikolaev Institute of Inorganic Chemistry of SB RAS
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From abmus911 at yahoo.ie  Thu Jul 29 10:15:54 2010
From: abmus911 at yahoo.ie (bayo mus)
Date: Thu, 29 Jul 2010 08:15:54 +0000 (GMT)
Subject: [Pw_forum] My Research
Message-ID: <755615.74464.qm@web29606.mail.ird.yahoo.com>

Dear QE users
?I am very new in the use of QE and I need to know all what exactly QE can do 
?for compounds comprising of many elements?e.g. NaAlSi3O8 (like optical 
properties, elastic properties or structural properties e.t.c.) so that i can 
channel my research and devote my studies on that. Please i wil appreciate ur 
quick and favourable reply. ?

Musari Abolore
University Of Agriculture
Nigeria

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From merlin.meheut at lmtg.obs-mip.fr  Thu Jul 29 11:36:25 2010
From: merlin.meheut at lmtg.obs-mip.fr (Merlin Meheut)
Date: Thu, 29 Jul 2010 11:36:25 +0200
Subject: [Pw_forum] Ni.pbe-sp-mt_gipaw.UPF: one pseudopotential for two
 oxidation states?
In-Reply-To: <alpine.LNX.2.00.1007281209050.28489@pcihpc19.uzh.ch>
References: <4C4FFBFB.6030206@lmtg.obs-mip.fr>
	<alpine.LNX.2.00.1007281209050.28489@pcihpc19.uzh.ch>
Message-ID: <4C514B99.2070908@lmtg.obs-mip.fr>

Dear Ari,

Thank you very much for your answer. I was indeed able to use this 
pseudopotential. The problem is, for Ni metal, the pressure converges at 
about -275kbar for the experimental structure, which is rather large and 
different from the other pseudopotential available,  
Ni.pbe-nd-rrkjus.UPF (which gives around +5kbars). My guess is that this 
is related to the configuration: the "Ni2+" configuration used in  
Ni.pbe-sp-mt_gipaw.UPF is adapted to computation of NiO or other 
compounds with Ni ion, but not to Ni metal, whereas Ni.pbe-nd-rrkjus.UPF 
takes the 4s1 3d9 neutral configuration.

Said otherwise, I would be very interrested in a pseudopotential 
transferable from Ni metal to compounds where Ni is ionic. I will give a 
try at generating it, but would be very interrested in some hints on 
this matter.

Thanks again,

Merlin Meheut



Le 28/07/2010 12:16, Ari P Seitsonen a ?crit :
>
> Dear Merlin,
>
>   You can either
>
>  1) remove the whole GIPAW part from the pseudo potential,
>  2) modify the pseudo potential file:
>
> <PP_PAW_FORMAT_VERSION>
>    0.10000000000E+00
> </PP_PAW_FORMAT_VERSION>
>
> and
>
> <PP_GIPAW_FORMAT_VERSION>
> 0.1
> </PP_GIPAW_FORMAT_VERSION>
>
>   The version 4.1.2 of the code wants an integer in the latter case, 
> so you can modify the "0.1" into "1",
>
>  3) or you modify the source code in Modules/read_upf_v1.f90 so that 
> it accepts this syntax also.
>
>   Sorry for the confusion (I am partially guilty for it). Please tell 
> if this doesn't solve your problem.
>
>     Greetings from Zurich,
>
>        apsi
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- 
>
>   Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
>   Physikalisch-Chemisches Institut der Universitaet Zuerich
>   Tel: +41 44 63 54 497  /  Mobile: +41 79 71 90 935
>
> On Wed, 28 Jul 2010, Merlin Meheut wrote:
>
>> Dear PWSCF users,
>>
>> I would like to compute fcc Nickel metal using the pseudopotential
>> Ni.pbe-sp-mt_gipaw.UPF, available on your website.
>> I do not need the GIPAW part, but I have been said that this should 
>> not be
>> an issue. However, using an input very
>> similar to example02, the calculation fails by "not recognizing the 
>> pseudo":
>>
>> -------------------------------------------------------
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
>>
>> %%%
>>      from read_pseudo_gipaw : error #         1
>>      UPF/GIPAW in unknown format
>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
>>
>> %%%%
>>
>>      stopping ...
>> --------------------------------------------------------
>>
>> I use Quantum Espresso version 4.1.2.
>>
>> Below is my input file (which works with pseudo Ni.pbe-nd-rrkjus.UPF) :
>>
>> &control
>>            disk_io = 'default' ,
>>     pseudo_dir     = '$PBS_O_WORKDIR',
>>     outdir         = '/tmpdir/$PBS_O_LOGNAME/',
>>     tprnfor        = .true.,
>>     tstress        = .true.,
>>     calculation    = 'scf'
>>     prefix         = 'ni',
>>     verbosity      = 'high',
>>  /
>> &system
>>     ibrav=2, celldm(1) =6.65, nat=  1, ntyp= 1,
>>     nspin=2,
>>     starting_magnetization(1)=0.5,
>>     degauss=0.02,
>>     smearing='mp',
>>     occupations='smearing',
>>     ecutwfc =27.0
>>     ecutrho =300.0
>>  /
>> &electrons
>>     conv_thr =  1.0d-8
>>     mixing_beta = 0.7
>>  /
>> ATOMIC_SPECIES
>>  Ni  58.6934  Ni.pbe-sp-mt_gipaw.UPF
>> ATOMIC_POSITIONS
>>  Ni 0.00 0.00 0.00
>> K_POINTS AUTOMATIC
>> 8 8 8 1 1 1
>>
>> Thanks for any help,
>>
>> Merlin Meheut
>>
>> -- 
>> Merlin M?heut
>> Maitre de conf?rences LMTG- Universit? Paul Sabatier Toulouse 3
>> 14 avenue Edoaurd Belin
>> 31400 Toulouse
>> tel: (+33)5 61 33 26 21
>> Fax: (+33) 5 61 33 25 60
>> Mobile: (+33) 6 34 67 57 02
>>
>>
>>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>    


-- 
Merlin M?heut
Maitre de conf?rences
LMTG- Universit? Paul Sabatier Toulouse 3
14 avenue Edoaurd Belin
31400 Toulouse
tel: (+33)5 61 33 26 21
Fax: (+33) 5 61 33 25 60
Mobile: (+33) 6 34 67 57 02


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From a.nourmohammadi at yahoo.com  Thu Jul 29 13:19:17 2010
From: a.nourmohammadi at yahoo.com (Amene Nouri)
Date: Thu, 29 Jul 2010 04:19:17 -0700 (PDT)
Subject: [Pw_forum] EXX error
Message-ID: <767736.37760.qm@web59402.mail.ac4.yahoo.com>

Hello all
?
after "make clean" I added the option to -DEXX to DFLAGS and the " make all "
I recieved the followig warrnings during compile:

..................................................................................................
: warning #5117: Bad # preprocessor line
: warning #5117: Bad # preprocessor line
: warning #5117: Bad # preprocessor line
: warning #5117: Bad # preprocessor line
: warning #5117: Bad # preprocessor line
: warning #5117: Bad # preprocessor line
iotk_stream.spp(54): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value.?? [VAL]
subroutine iotk_stream_read_LOGICAL1(unit,header,val,setpos,getpos,noval,ierr)
-------------------------------------------------^
iotk_stream.spp(54): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value.?? [VAL]
subroutine iotk_stream_read_INTEGER1(unit,header,val,setpos,getpos,noval,ierr)
-------------------------------------------------^
iotk_stream.spp(54): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value.?? [VAL]
subroutine iotk_stream_read_REAL1(unit,header,val,setpos,getpos,noval,ierr)
----------------------------------------------^
iotk_stream.spp(54): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value.?? [VAL]
subroutine iotk_stream_read_REAL2(unit,header,val,setpos,getpos,noval,ierr)
----------------------------------------------^
iotk_stream.spp(54): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value.?? [VAL]
subroutine iotk_stream_read_COMPLEX1(unit,header,val,setpos,getpos,noval,ierr)
-------------------------------------------------^
iotk_stream.spp(54): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value.?? [VAL]
subroutine iotk_stream_read_COMPLEX2(unit,header,val,setpos,getpos,noval,ierr)
-------------------------------------------------^
iotk_stream.spp(54): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value.?? [VAL]
subroutine iotk_stream_read_CHARACTER1(unit,header,val,setpos,getpos,noval,ierr)
---------------------------------------------------^
: warning #5117: Bad # preprocessor line
: warning #5117: Bad # preprocessor line
: warning #5117: Bad # preprocessor line
: warning #5117: Bad # preprocessor line
: warning #5117: Bad # preprocessor line
: warning #5117: Bad # preprocessor line
ar: creating libiotk.a
ar: creating libqemod.a
ar: creating mglib.a
ar: creating clib.a
ar: creating flib.a
ar: creating ptools.a
ar: creating libee.a
ar: creating libpw.a
ar: creating libph.a
ar: creating libcp.a
ar: creating minpacklib.a
ar: creating libpw4gww.a
..................................................................................................
The run the rests the results were not very different from resources. 
?
But the example EXX-example: it did not run
for example the output?? was:

................................................................
???? Program PWSCF v.4.2??????? starts on 29Jul2010 at 12:51:46 
???? This program is part of the open-source Quantum ESPRESSO suite
???? for quantum simulation of materials; please acknowledge
???????? "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
????????? URL http://www.quantum-espresso.org", 
???? in publications or presentations arising from this work. More details at
???? http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
???? Current dimensions of program PWSCF are:
???? Max number of different atomic species (ntypx) = 10
???? Max number of k-points (npk) =? 40000
???? Max angular momentum in pseudopotentials (lmaxx) =? 3
???? Waiting for input...
?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
???? from? read_namelists? : error #??????? 19
????? reading namelist system 
?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
???? stopping ...
......................................................................................................
?
Another problem is that I want to use openmp.
I set PARA-PREFIX env OMP_NUM_THREADS=2 as is in the userguid, but just one of cores is used.
What the problem is?



      
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From eyvaz_isaev at yahoo.com  Thu Jul 29 14:42:08 2010
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 29 Jul 2010 05:42:08 -0700 (PDT)
Subject: [Pw_forum] My Research
In-Reply-To: <755615.74464.qm@web29606.mail.ird.yahoo.com>
References: <755615.74464.qm@web29606.mail.ird.yahoo.com>
Message-ID: <280566.46153.qm@web65704.mail.ac4.yahoo.com>

Dear Bayo,




________________________________
From: bayo mus <abmus911 at yahoo.ie>


> I am very new in the use of QE 

Welcome!

>and I need to know all what exactly QE can do  for compounds comprising of many 
>elements e.g. >NaAlSi3O8 (like optical properties, elastic properties or 
>structural properties e.t.c.) so that i can channel >my research and devote my 
>studies on that. Please i wil appreciate ur quick and favourable reply.  
 
Please read the User Guide in /Doc of your QE distribution, then download  
examples-tar from QE website, then try and fail. First try simple and well known 
systems to understand what and how you are doing. This will save time, too. 


Bests,
Eyvaz.
 -------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, 
Sweden 

Theoretical Physics Department, Moscow State Institute of Steel & Alloys, 
Russia, 

isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


      
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From ma at nano.ku.dk  Thu Jul 29 14:12:57 2010
From: ma at nano.ku.dk (Martin Andersson)
Date: Thu, 29 Jul 2010 14:12:57 +0200 (CEST)
Subject: [Pw_forum] input for d3.x
Message-ID: <2889b02f55eb673602ce7084329328ea.squirrel@hermes.fys.ku.dk>

Hi all,

I was trying to find information on how to use the d3.x program. I have
successully calculated frequencies, ir and raman intensities for my test
system, a CO2 molecule. I would like to try and calculate anharmonic
effects on linewidths using d3.x but can't seem to get it to work. If
anyone could point me in the right direction I would be grateful.

Thanks,
Martin Andersson,
NanoGeoScience,
University of Copenhagen

From lily_physics at yahoo.com.sg  Thu Jul 29 15:30:54 2010
From: lily_physics at yahoo.com.sg (Lily Anh)
Date: Thu, 29 Jul 2010 21:30:54 +0800 (SGT)
Subject: [Pw_forum] Temperature and Pressure control in FPMD simulation
Message-ID: <769195.66076.qm@web76110.mail.sg1.yahoo.com>

Dear all,
?
I planned to do a NPT simulation with FPMD code. I adopted Nose thermostat for both ions and fictious electrons. However, in the output files, it says electronic and ionic temperature are not controlled.?Do not know why.?

?
The input file:
&control????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? calculation = 'fpmd',???????????????????????????????????????????????????????????????????????????????????????????????????? 
??? restart_mode = 'from_scratch',??????????????????????????????????????????????????????????????????????????????????????????? 
??? ndr = 50,???????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? ndw = -1,???????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? nstep? = 100000,????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? iprint = 10,????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? isave? = 100,???????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? tstress = .TRUE.,???????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? tprnfor = .TRUE.,???????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? dt??? = 5.0d0,??????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? etot_conv_thr = 1.d-8,??????????????????????????????????????????????????????????????????????????????????????????????????? 
??? prefix = 'h2-h2o',??????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? pseudo_dir = '/pseudo/',????????????????????????????????????????????????????????????????????? 
??? outdir="/tmp2/'?????????????????????????????????????????????????????????????????????????? 
/???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
?&system????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? ibrav = 14,?????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? celldm(1)? =15.32039374349225306466,????????????????????????????????????????????????????????????????????????????????????? 
??? celldm(2) = 1.0,????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? celldm(3) = .72241957765936451549,??????????????????????????????????????????????????????????????????????????????????????? 
??? celldm(4) = 0.0,????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? celldm(5) = 0.0,????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? celldm(6) = 0.0,????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? nat = 80,???????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? ntyp = 2,???????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? ecutwfc = 80.0,?????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? ecfixed = 78.0,?????????????????????????????????????????????????????????????????????????????????????????????????????????? 
?/??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
?&electrons?????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? emass = 100.d0,?????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? emass_cutoff = 2.5d0,???????????????????????????????????????????????????????????????????????????????????????????????????? 
??? orthogonalization = 'ortho',????????????????????????????????????????????????????????????????????????????????????????????? 
??? ortho_eps = 5.d-8,??????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? ortho_max = 100,????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? electron_dynamics = 'sd',???????????????????????????????????????????????????????????????????????????????????????????????? 
??? electron_velocities = 'zero',???????????????????????????????????????????????????????????????????????????????????????????? 
??? electron_temperature = 'nose',??????????????????????????????????????????????????????????????????????????????????????????? 
?/??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
?&ions??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? ion_dynamics = 'sd',????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? ion_radius(1) = 0.8d0,??????????????????????????????????????????????????????????????????????????????????????????????????? 
??? ion_radius(2) = 0.5d0,??????????????????????????????????????????????????????????????????????????????????????????????????? 
??? ion_velocities = 'zero',????????????????????????????????????????????????????????????????????????????????????????????????? 
??? ion_temperature = 'nose'????????????????????????????????????????????????????????????????????????????????????????????????? 
??? tempw=300,??????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
?/??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
?&cell??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? cell_dynamics = 'damp-pr',??????????????????????????????????????????????????????????????????????????????????????????????? 
??? cell_velocities = 'zero',???????????????????????????????????????????????????????????????????????????????????????????????? 
??? press = 200.0d0,????????????????????????????????????????????????????????????????????????????????????????????????????????? 
??? wmass = 70000.0d0???????????????????????????????????????????????????????????????????????????????????????????????????????? 
?/??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
ATOMIC_SPECIES??????????????????????????????????????????????????????????????????????????????????????????????????????????????? 
?O 15.9994 O.pbe-mt.upf?????????????????????????????????????????????????????????????????????????????????????????????????????? 
?H 1.00794 H.pbe-vbc.UPF????????????????????????????????????????????????????????????????????????????????????????????????????? 
ATOMIC_POSITIONS (crystal)??????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.12402 0.12402 0???????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.12402 0.62402 0???????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.62402 0.12402 0???????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.62402 0.62402 0???????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.37598 0.37598 0.5?????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.37598 0.87598 0.5?????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.87598 0.37598 0.5?????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.87598 0.87598 0.5?????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.12598 0.37402 0.25????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.12598 0.87402 0.25????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.62598 0.37402 0.25????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.62598 0.87402 0.25????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.37402 0.12598 0.75????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.37402 0.62598 0.75????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.87402 0.12598 0.75????????????????????????????????????????????????????????????????????????????????????????????????? 
O?????? 0.87402 0.62598 0.75????????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.12256 0.02125 0.10225?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.12256 0.52125 0.10225?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.62256 0.02125 0.10225?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.62256 0.52125 0.10225?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.09972 0.13926 0.45107?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.09972 0.63926 0.45107?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.59972 0.13926 0.45107?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.59972 0.63926 0.45107?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.37744 0.47875 0.60225?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.37744 0.97875 0.60225?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.87744 0.47875 0.60225?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.87744 0.97875 0.60225?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.40028 0.36074 0.95107?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.40028 0.86074 0.95107?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.90028 0.36074 0.95107?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.90028 0.86074 0.95107?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.22875 0.37256 0.35225?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.22875 0.87256 0.35225?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.72875 0.37256 0.35225?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.72875 0.87256 0.35225?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.11074 0.34972 0.70107?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.11074 0.84972 0.70107?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.61074 0.34972 0.70107?????????????????????????????????????????????????????????????????????????????????????????????? 
H?????? 0.61074 0.84972 0.70107
H?????? 0.27125 0.12744 0.85225
H?????? 0.27125 0.62744 0.85225
H?????? 0.77125 0.12744 0.85225
H?????? 0.77125 0.62744 0.85225
H?????? 0.38926 0.15028 0.20107
H?????? 0.38926 0.65028 0.20107
H?????? 0.88926 0.15028 0.20107
H?????? 0.88926 0.65028 0.20107
H?????? 0.12744 0.27125 0.14775
H?????? 0.12744 0.77125 0.14775
H?????? 0.62744 0.27125 0.14775
H?????? 0.62744 0.77125 0.14775
H?????? 0.15028 0.38926 0.79893
H?????? 0.15028 0.88926 0.79893
H?????? 0.65028 0.38926 0.79893
H?????? 0.65028 0.88926 0.79893
H?????? 0.37256 0.22875 0.64775
H?????? 0.37256 0.72875 0.64775
H?????? 0.87256 0.22875 0.64775
H?????? 0.87256 0.72875 0.64775
H?????? 0.34972 0.11074 0.29893
H?????? 0.34972 0.61074 0.29893
H?????? 0.84972 0.11074 0.29893
H?????? 0.84972 0.61074 0.29893
H?????? 0.02125 0.12256 0.89775
H?????? 0.02125 0.62256 0.89775
H?????? 0.52125 0.12256 0.89775
H?????? 0.52125 0.62256 0.89775
H?????? 0.13926 0.09972 0.54893
H?????? 0.13926 0.59972 0.54893
H?????? 0.63926 0.09972 0.54893
H?????? 0.63926 0.59972 0.54893
H?????? 0.47875 0.37744 0.39775
H?????? 0.47875 0.87744 0.39775
H?????? 0.97875 0.37744 0.39775
H?????? 0.97875 0.87744 0.39775
H?????? 0.36074 0.40028 0.04893
H?????? 0.36074 0.90028 0.04893
H?????? 0.86074 0.40028 0.04893
H?????? 0.86074 0.90028 0.04893

And the averaged physical quantities from output file:
????????????????????? accomulated????? this run
?? ekinc???????? :??????? 0.00655?????? 0.00655 (AU)
?? ekin????????? :????? 216.67593???? 216.67593 (AU)
?? epot????????? :???? -497.28571??? -497.28571 (AU)
?? total energy? :???? -293.97401??? -293.97401 (AU)
?? temperature?? :??????? 0.02392?????? 0.02392 (K )
?? enthalpy????? :???? -274.59255??? -274.59255 (AU)
?? econs???????? :???? -274.58884??? -274.58884 (AU)
?? pressure????? :??????? 0.10872?????? 0.10872 (Gpa)
?? volume??????? :???? 2851.11076??? 2851.11076 (AU)

?
Also, the averaged temperaure and pressure are far away from the target value set in the input file. Could someone please give me some clue?
?
Thanks and Regards
Lily (PhD candidate)
Nanyang Technological University
Singapore


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From juanlopez415 at gmail.com  Thu Jul 29 15:33:43 2010
From: juanlopez415 at gmail.com (Juan Manuel Lopez)
Date: Thu, 29 Jul 2010 09:33:43 -0400
Subject: [Pw_forum] Full relativistic pseudopotential for Fe (Iron)
Message-ID: <AANLkTimbHoqi9ij0D6MAQasTvghKtsekjBNxQU2-qYjU@mail.gmail.com>

Dear all,

Somebody has a full relativistic pseudopotential for Fe?

-- 
Best regards,
--------------------------------------
Juan M. Lopez Encarnacion
Research associate, Institute of Physics, Universidad Aut?noma de Santo
Domingo, Dominican Republic
Graduate Student Doctoral Program in Chemical Physics, University of Puerto
Rico, Rio Piedras Campus
P.O.Box 23343
San Juan, PR 00931-3343
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From juanlopez415 at gmail.com  Thu Jul 29 15:35:36 2010
From: juanlopez415 at gmail.com (Juan Manuel Lopez)
Date: Thu, 29 Jul 2010 09:35:36 -0400
Subject: [Pw_forum] Full relativistic pseudopotential for Fe (Iron)
In-Reply-To: <AANLkTimbHoqi9ij0D6MAQasTvghKtsekjBNxQU2-qYjU@mail.gmail.com>
References: <AANLkTimbHoqi9ij0D6MAQasTvghKtsekjBNxQU2-qYjU@mail.gmail.com>
Message-ID: <AANLkTimqOsrrRJuezNEsPKQYZ-1hQcr1VSFCRR2gpXyy@mail.gmail.com>

Dear all,

Somebody has a full relativistic pesudopotential for Sc-Zn serie?




-- 
Best regards,
--------------------------------------
Juan M. Lopez Encarnacion
Research associate, Institute of Physics, Universidad Aut?noma de Santo
Domingo, Dominican Republic
Graduate Student Doctoral Program in Chemical Physics, University of Puerto
Rico, Rio Piedras Campus
P.O.Box 23343
San Juan, PR 00931-3343
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From giannozz at democritos.it  Thu Jul 29 16:48:26 2010
From: giannozz at democritos.it (giannozz at democritos.it)
Date: Thu, 29 Jul 2010 16:48:26 +0200
Subject: [Pw_forum] Temperature and Pressure control in FPMD simulation
In-Reply-To: <769195.66076.qm@web76110.mail.sg1.yahoo.com>
References: <769195.66076.qm@web76110.mail.sg1.yahoo.com>
Message-ID: <20100729164826.csjf23zh8ggcoo0c@mail.democritos.it>

Quoting Lily Anh <lily_physics at yahoo.com.sg>:
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????
> ??? calculation ='fpmd'

this is old and has been replaced by 'cp'.

P.

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From giannozz at democritos.it  Thu Jul 29 16:49:43 2010
From: giannozz at democritos.it (giannozz at democritos.it)
Date: Thu, 29 Jul 2010 16:49:43 +0200
Subject: [Pw_forum] input for d3.x
In-Reply-To: <2889b02f55eb673602ce7084329328ea.squirrel@hermes.fys.ku.dk>
References: <2889b02f55eb673602ce7084329328ea.squirrel@hermes.fys.ku.dk>
Message-ID: <20100729164943.1pm1q1g00ws444c0@mail.democritos.it>

Quoting Martin Andersson <ma at nano.ku.dk>:

> I was trying to find information on how to use the d3.x program

see examples/example14. There isn't much more than this available

Paolo

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From giannozz at democritos.it  Thu Jul 29 16:54:23 2010
From: giannozz at democritos.it (giannozz at democritos.it)
Date: Thu, 29 Jul 2010 16:54:23 +0200
Subject: [Pw_forum] EXX error
In-Reply-To: <767736.37760.qm@web59402.mail.ac4.yahoo.com>
References: <767736.37760.qm@web59402.mail.ac4.yahoo.com>
Message-ID: <20100729165423.qoabam8ggc8ks0w8@mail.democritos.it>

Quoting Amene Nouri <a.nourmohammadi at yahoo.com>:

> : warning #5117: Bad # preprocessor line

not sure why this message is issued, but it is harmless

> iotk_stream.spp(54): warning #6843: A dummy argument with an explicit 
> INTENT(OUT) declaration is not given an explicit value.?? [VAL]
> subroutine

as above

> ???? from? read_namelists? : error #??????? 19
> ????? reading namelist system

I don't see the message

     EXPERIMENTAL VERSION WITH EXACT EXCHANGE

You are likely running the non-EXX version with EXX input data.

> Another problem is that I want to use openmp.


you need to compile with openmp enabled. For recent versions:
   ./configure --enable-openmp
should do the job

P.

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From giannozz at democritos.it  Thu Jul 29 16:57:16 2010
From: giannozz at democritos.it (giannozz at democritos.it)
Date: Thu, 29 Jul 2010 16:57:16 +0200
Subject: [Pw_forum] Ni.pbe-sp-mt_gipaw.UPF: one pseudopotential for
	two	oxidation states?
In-Reply-To: <4C514B99.2070908@lmtg.obs-mip.fr>
References: <4C4FFBFB.6030206@lmtg.obs-mip.fr>
	<alpine.LNX.2.00.1007281209050.28489@pcihpc19.uzh.ch>
	<4C514B99.2070908@lmtg.obs-mip.fr>
Message-ID: <20100729165716.ci4burlog00gs4wc@mail.democritos.it>

Quoting Merlin Meheut <merlin.meheut at lmtg.obs-mip.fr>:

> Said otherwise, I would be very interested in a pseudopotential 
> transferable from Ni metal to compounds where Ni is ionic. I will 
> give a try at generating it, but would be very interested in some 
> hints on this matter.

good luck. In my opinion, you should put 3s and 3p semicore states in 
valence. Ni.pbe-sp-mt_gipaw.UPF does that, by the way, if the
naming is correct; Ni.pbe-nd-rrkjus.UPF doesn't

Paolo

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From giannozz at democritos.it  Thu Jul 29 16:58:20 2010
From: giannozz at democritos.it (giannozz at democritos.it)
Date: Thu, 29 Jul 2010 16:58:20 +0200
Subject: [Pw_forum] Is there a tutorial for generating a
	PAW	pseudopotential
In-Reply-To: <AANLkTikoh65jEZsutvJcw0nMcmVgeRuNX_mSj+BESXm2@mail.gmail.com>
References: <AANLkTikoh65jEZsutvJcw0nMcmVgeRuNX_mSj+BESXm2@mail.gmail.com>
Message-ID: <20100729165820.3fat0bnpyc0k0ogs@mail.democritos.it>

Quoting Haowei Peng <haoweipeng at gmail.com>:

> I am looking for a tutorial about generating a PAW pseudopotential, any
> comments?

if you find one, please let us know!

Paolo

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From giannozz at democritos.it  Thu Jul 29 17:10:34 2010
From: giannozz at democritos.it (giannozz at democritos.it)
Date: Thu, 29 Jul 2010 17:10:34 +0200
Subject: [Pw_forum] Units of Raman Tensor
In-Reply-To: <AANLkTikR7S_9CVc7kpuuJSNt5O3c2xpCiEdXnJ5v+kq+@mail.gmail.com>
References: <AANLkTikR7S_9CVc7kpuuJSNt5O3c2xpCiEdXnJ5v+kq+@mail.gmail.com>
Message-ID: <20100729171034.whwkscptkwwk84ss@mail.democritos.it>

Quoting "S. Sanchez" <lcqsigi at gmail.com>:

> My question arises given the fact that the dchi/dr tensor can be obtained as
> the third order derivative of the Energy (in units of Ry or Ha) with respect
> to the atomic displacement (bohr) and two times the electric field (e/bohr).
>
> dchi/dr=d^3E/(dr*de1*de2)
> where E is the Energy; r the displacement, e1 and e2 the electric fields.

I don't have here my notes, but e^2/8\pi (e=electric field)
is an energy density, i.e. energy per unit volume, so 
dchi/dr=d^3E/(dr*de1*de2) has the dimension of r^2.

P.

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From giannozz at democritos.it  Thu Jul 29 17:15:02 2010
From: giannozz at democritos.it (giannozz at democritos.it)
Date: Thu, 29 Jul 2010 17:15:02 +0200
Subject: [Pw_forum] Fourier interpolation
In-Reply-To: <SNT117-W101BC51D627FFA6735C37FB6A80@phx.gbl>
References: <SNT117-W101BC51D627FFA6735C37FB6A80@phx.gbl>
Message-ID: <20100729171502.ah3aajbbe4ogoww8@mail.democritos.it>

Quoting HaoPan <adehaopan at hotmail.com>:

> On each q point I got, the phone frequencies are positive. But after 
> the Fourier interpolation process, There exist negative frequencies.

hard to say what is happening. When you re-generate phonon from
the force constant matrix, you should find exactly the same phonon
frequencies for the wave-vector grid used to generate force constants
in real space. If not, something has gone wrong in the generation
of interatomic force constants

Paolo

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From baroni at sissa.it  Thu Jul 29 18:35:59 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 29 Jul 2010 18:35:59 +0200
Subject: [Pw_forum] input for d3.x
In-Reply-To: <2889b02f55eb673602ce7084329328ea.squirrel@hermes.fys.ku.dk>
References: <2889b02f55eb673602ce7084329328ea.squirrel@hermes.fys.ku.dk>
Message-ID: <114ABC40-589B-47BA-A6E9-E6005B33C417@sissa.it>

Hi! To my understending, vibronic linewidths in any finite system (such as the CO2) cannot have anything to do with anharmonic effects. In an infinite system, the anharmonic contribution to a phonon linewidth is due to the (anharmonic) coupling between a state of interest and a *continuuum* of quasi-degenerate harmonic states. In the symple case of a Raman or IR line, the state of interest is a zone-center (IR or Raman) active mode, while the continuum is made by pairs of acoustic modes of opposite momenta and frequencies whose sum is equal to the frequency of the optic mode.  In a molecule, all the harmonic modes are discrete, so that no coupling among them can cause any broadening. SB

On Jul 29, 2010, at 2:12 PM, Martin Andersson wrote:

> Hi all,
> 
> I was trying to find information on how to use the d3.x program. I have
> successully calculated frequencies, ir and raman intensities for my test
> system, a CO2 molecule. I would like to try and calculate anharmonic
> effects on linewidths using d3.x but can't seem to get it to work. If
> anyone could point me in the right direction I would be grateful.
> 
> Thanks,
> Martin Andersson,
> NanoGeoScience,
> University of Copenhagen
> _______________________________________________
> 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







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From payam.norouzzadeh at gmail.com  Thu Jul 29 19:31:37 2010
From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh)
Date: Thu, 29 Jul 2010 22:01:37 +0430
Subject: [Pw_forum] Pseudopotential for Europium
Message-ID: <AANLkTikoZVPoPpY+e8ueHES9qBuC=zF5yYuipR=7tX3q@mail.gmail.com>

Dear Quantum-Espresso users

Does anyone have a pseudopotential for element Europium(Eu) ?

Breg,Payam Norouzzadeh
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From adehaopan at hotmail.com  Thu Jul 29 21:49:32 2010
From: adehaopan at hotmail.com (HaoPan)
Date: Fri, 30 Jul 2010 03:49:32 +0800
Subject: [Pw_forum] Fourier interpolation
Message-ID: <SNT117-W111B57CB1E1212D5A742AB6A90@phx.gbl>


Dear Baroni,

The kpoint grid I chose is 60*60*60.     
    nk1=60, nk2=60, nk3=60,

I think that is fine enough. Because the q point grid is just 6*6*6. 
For metal, the frequencies of the gamma point are  alway not zero (some small negative value) . 
Some may cause the frequencies around the gamma point negative. But even all q points I got are 
positive, there exit negative frequencies after the matdyn.x calculation. I don't know why.

Sincerely,
Pan Hao
Tulane University


the kpoint grid you are using may be too coarse
dynamical matrices in metals are indeed smooth functions of k, unless you have Kohn anomalies
SB

On Jul 28, 2010, at 5:33 PM, HaoPan wrote:

> Hi, everyone,
> 
> On each q point I got, the phone frequencies are positive. But after the Fourier interpolation process, There
> exist negative frequencies. I check the some special q points using ph.x, there are no negative frequencies. I
> know the dynamical matrices for metal are not smooth function of q, but how do I fix it to get the right
> dispersion curves? Thanks a lot.
> 
> Sincerely,
> Pan Hao
> Tulane University _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
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From adehaopan at hotmail.com  Thu Jul 29 22:00:23 2010
From: adehaopan at hotmail.com (HaoPan)
Date: Fri, 30 Jul 2010 04:00:23 +0800
Subject: [Pw_forum] Fourier interpolation
In-Reply-To: <SNT117-W1303C3E4566E0A684A10D9B6A90@phx.gbl>
References: <SNT117-W1303C3E4566E0A684A10D9B6A90@phx.gbl>
Message-ID: <SNT117-W25305AAC1D48B284A1F958B6A90@phx.gbl>





Dear Paolo, 

The re-generated phonon from the force constant matrix are negative. 
  0.177215  0.000000  0.000000
  -45.4648  -45.4648  119.2232  626.1196  626.1196  645.7030

comparing to the frequency got by ph.x 

   q = (    0.177215000   0.000000000   0.000000000 ) 

 **************************************************************************
     omega( 1) =       0.431524 [THz] =      14.394177 [cm-1]
 (  0.000000  0.000000  0.129619 -0.022092  0.597312 -0.371775 ) 
 (  0.000000  0.000000  0.118762  0.048530  0.686479  0.000000 ) 
     omega( 2) =       0.431524 [THz] =      14.394177 [cm-1]
 ( -0.000000  0.000000 -0.693560  0.118207  0.111631 -0.069481 ) 
 ( -0.000000 -0.000000 -0.635471 -0.259673  0.128295 -0.000000 ) 
     omega( 3) =       3.535384 [THz] =     117.928499 [cm-1]
 ( -0.661130 -0.445106  0.000000  0.000000  0.000000 -0.000000 ) 
 ( -0.247111 -0.551111  0.000000  0.000000  0.000000  0.000000 ) 
     omega( 4) =      18.715499 [THz] =     624.285984 [cm-1]
 ( -0.000000 -0.000000  0.000000 -0.000000 -0.106238  0.066124 ) 
 (  0.000000  0.000000 -0.000000 -0.000000  0.992140  0.000000 ) 
     omega( 5) =      18.715499 [THz] =     624.285984 [cm-1]
 ( -0.000000 -0.000000 -0.110727  0.058294  0.000000 -0.000000 ) 
 (  0.000000  0.000000  0.989559  0.071511  0.000000 -0.000000 ) 
     omega( 6) =      19.507679 [THz] =     650.710441 [cm-1]
 (  0.080574  0.054886 -0.000000 -0.000000 -0.000000 -0.000000 ) 
 ( -0.402244 -0.910327  0.000000  0.000000  0.000000  0.000000 ) 
 **************************************************************************

Maybe something wrong in the generation of interatomic force constant, but how to check it? Thanks a lot.

Sincerely,
Pan Hao 
Tulane University 







  
Quoting HaoPan <adehaopan at hotmail.com>:

> On each q point I got, the phone frequencies are positive. But after 
> the Fourier interpolation process, There exist negative frequencies.

hard to say what is happening. When you re-generate phonon from
the force constant matrix, you should find exactly the same phonon
frequencies for the wave-vector grid used to generate force constants
in real space. If not, something has gone wrong in the generation
of interatomic force constants

Paolo
 		 	   		  
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From eyvaz_isaev at yahoo.com  Thu Jul 29 22:43:05 2010
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 29 Jul 2010 13:43:05 -0700 (PDT)
Subject: [Pw_forum] Fourier interpolation
In-Reply-To: <SNT117-W111B57CB1E1212D5A742AB6A90@phx.gbl>
References: <SNT117-W111B57CB1E1212D5A742AB6A90@phx.gbl>
Message-ID: <983348.48638.qm@web65704.mail.ac4.yahoo.com>

Dear Hao,


> The kpoint grid I chose is 60*60*60.     

I suppose you vast time with such kind incredibly large k-mesh.

Try increasing nq's for phonon calculations (ph.in). Play around 
cutoff energy and the threshold parameter for phonons.

What is the accuracy of your q2r.x (FFT) run?

Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, 
Sweden 

Theoretical Physics Department, Moscow State Institute of Steel & Alloys, 
Russia, 

isaev at ifm.liu.se, eyvaz_isaev at yahoo.com




________________________________
From: HaoPan <adehaopan at hotmail.com>
To: pw_forum at pwscf.org
Sent: Thu, July 29, 2010 9:49:32 PM
Subject: [Pw_forum] Fourier interpolation

 
Dear Baroni,

The kpoint grid I chose is 60*60*60.     
    nk1=60, nk2=60, nk3=60,

I think that is fine enough. Because the q point grid is just 6*6*6. 
For metal, the frequencies of the gamma point are  alway not zero (some small 
negative value) . 

Some may cause the frequencies around the gamma point negative. But even all q 
points I got are 

positive, there exit negative frequencies after the matdyn.x calculation. I 
don't know why.

Sincerely,
Pan Hao
Tulane University


the kpoint grid you are using may be too coarse
dynamical matrices in metals are indeed smooth functions of k, unless you have 
Kohn anomalies
SB

On Jul 28, 2010, at 5:33 PM, HaoPan wrote:

> Hi, everyone,
> 
> On each q point I got, the phone frequencies are positive. But after the 
>Fourier interpolation process, There
> exist negative frequencies. I check the some special q points using ph.x, there 
>are no negative frequencies. I
> know the dynamical matrices for metal are not smooth function of q, but how do 
>I fix it to get the right
> dispersion curves? Thanks a lot.
> 
> Sincerely,
> Pan Hao
> Tulane University _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



      
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From mohnish.iitk at gmail.com  Fri Jul 30 08:59:32 2010
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Fri, 30 Jul 2010 12:29:32 +0530
Subject: [Pw_forum] calculation for antiferromagnetic MnO
Message-ID: <AANLkTi=eJ-Abwcy9tjDvD2iftUZi6_Jjv9eHVzLshotP@mail.gmail.com>

Dear users,
                  I want to do calculation for MnO antiferromagnetic system.
I want to know how to start the calculation for this antiferromagnetic
system, i.e. should the magnetization be conserved to be in
antiferromagnetic state? And how to build the cell for this rocksalt
structure so that structure is antiferromagnetic.

-- 
Regards,
MOHNISH,
-----------------------------------------------------------------
Mohnish Pandey
Y6927262,5th Year dual degree student,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
+919235721300
-----------------------------------------------------------------
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From matteo at umn.edu  Fri Jul 30 10:29:10 2010
From: matteo at umn.edu (Matteo Cococcioni)
Date: Fri, 30 Jul 2010 03:29:10 -0500
Subject: [Pw_forum] calculation for antiferromagnetic MnO
In-Reply-To: <AANLkTi=eJ-Abwcy9tjDvD2iftUZi6_Jjv9eHVzLshotP@mail.gmail.com>
References: <AANLkTi=eJ-Abwcy9tjDvD2iftUZi6_Jjv9eHVzLshotP@mail.gmail.com>
Message-ID: <AANLkTinsFtdzAQ2xvbXPyt0tmRc_KxsJPExXAfto=tLG@mail.gmail.com>

Dear Mohnish

I would recommend you to figure this out yourself first.
Then, if you want to verify your results you can go on
quantum-espresso.organd look for the tutorials
for the school held in Santa Barbara in 2009. you will find an example about
NiO (and maybe FeO, I don't remember)
that are materials with the same structure and AF order of MnO.

Matteo


On Fri, Jul 30, 2010 at 1:59 AM, mohnish pandey <mohnish.iitk at gmail.com>wrote:

> Dear users,
>                   I want to do calculation for MnO antiferromagnetic
> system. I want to know how to start the calculation for this
> antiferromagnetic system, i.e. should the magnetization be conserved to be
> in antiferromagnetic state? And how to build the cell for this rocksalt
> structure so that structure is antiferromagnetic.
>
> --
> Regards,
> MOHNISH,
> -----------------------------------------------------------------
> Mohnish Pandey
> Y6927262,5th Year dual degree student,
> Department of Chemical Engineering,
> IIT KANPUR, UP, INDIA
> +919235721300
> -----------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From mohnish.iitk at gmail.com  Fri Jul 30 12:42:05 2010
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Fri, 30 Jul 2010 16:12:05 +0530
Subject: [Pw_forum] calculation for antiferromagnetic MnO
In-Reply-To: <AANLkTinsFtdzAQ2xvbXPyt0tmRc_KxsJPExXAfto=tLG@mail.gmail.com>
References: <AANLkTi=eJ-Abwcy9tjDvD2iftUZi6_Jjv9eHVzLshotP@mail.gmail.com>
	<AANLkTinsFtdzAQ2xvbXPyt0tmRc_KxsJPExXAfto=tLG@mail.gmail.com>
Message-ID: <AANLkTin4o8x75Fx-uVZMhS67PQ8t-uvAaDBC72eMbb9P@mail.gmail.com>

Thank you so much Prof. Matteo, in fact I also wanted to do that myself but
I was not able to get the starting point but know I believe I can do that...

On Fri, Jul 30, 2010 at 1:59 PM, Matteo Cococcioni <matteo at umn.edu> wrote:

> Dear Mohnish
>
> I would recommend you to figure this out yourself first.
> Then, if you want to verify your results you can go on
> quantum-espresso.org and look for the tutorials
> for the school held in Santa Barbara in 2009. you will find an example
> about NiO (and maybe FeO, I don't remember)
> that are materials with the same structure and AF order of MnO.
>
> Matteo
>
>
> On Fri, Jul 30, 2010 at 1:59 AM, mohnish pandey <mohnish.iitk at gmail.com>wrote:
>
>> Dear users,
>>                   I want to do calculation for MnO antiferromagnetic
>> system. I want to know how to start the calculation for this
>> antiferromagnetic system, i.e. should the magnetization be conserved to be
>> in antiferromagnetic state? And how to build the cell for this rocksalt
>> structure so that structure is antiferromagnetic.
>>
>> --
>> Regards,
>> MOHNISH,
>> -----------------------------------------------------------------
>> Mohnish Pandey
>> Y6927262,5th Year dual degree student,
>> Department of Chemical Engineering,
>> IIT KANPUR, UP, INDIA
>> +919235721300
>> -----------------------------------------------------------------
>>
>> _______________________________________________
>> 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
>
>


-- 
Regards,
MOHNISH,
-----------------------------------------------------------------
Mohnish Pandey
Y6927262,5th Year dual degree student,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
+919235721300
-----------------------------------------------------------------
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From quantumdft at gmail.com  Fri Jul 30 14:49:11 2010
From: quantumdft at gmail.com (vega lew)
Date: Fri, 30 Jul 2010 20:49:11 +0800
Subject: [Pw_forum] Acknowledgment to this forum
Message-ID: <4C52CA47.2040509@gmail.com>

  Dear developers,

My first paper published as communication (**DOI=10.1039/B920128A) in 
PCCP today.
The link is http://pubs.rsc.org/en/Content/ArticleLanding/2010/CP/B920128A

During the preliminary stage of my study in this paper, I learned a lot 
from this forum. With the help from many scientists in this forum, I 
have built a small cluster, understood some basic problems about 
calculation and done my own scientific study etc. I want to say 'thank 
you' to everybody who replied my questions and provided very helpful 
information to me.

And I also express my gratitude to this forum in the acknowledgment part 
of my communication.

thank you again

best wishes,

vega

-- 

================================================
Vega Lew ( weijia liu)
Graduate student
State Key Laboratory of Materials-oriented Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, China
***************************************************************
Email: vegalew at gmail.com
Office: Room A705, Technical Innovation Building,
Xinmofan Road 5#, Nanjing, China
***************************************************************

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From elie.moujaes at hotmail.co.uk  Fri Jul 30 15:35:46 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Fri, 30 Jul 2010 14:35:46 +0100
Subject: [Pw_forum] STOP ERROR reading file header
Message-ID: <SNT114-W5716A01A1E5ADF4DCB750FD3AA0@phx.gbl>


Dear All, I am doing calculations for the band structure of bilayer graphene in the presence of an electric field. I reached the stage where the .DAT file was produced. However when i executed the plotband.x common using /espresso-4.2/bin/plotband.x  and input"ed" the .DAT I got the error:

 

STOP ERROR reading file header.

 

When I checked the .DAT file I realized that the header is strange as it contains four stars (****) and looked like that:

 

&plot nbnd=  12, nks=**** /
            0.000000  0.000000  0.000000
 -18.176 -18.014  -6.915  -5.899  -1.571  -1.571  -1.546  -1.546   4.547   5.693
   6.616   9.569
            0.000000  0.010497  0.000000
 -18.174 -18.012  -6.913  -5.896  -1.579  -1.576  -1.554  -1.550   4.550   5.696
   6.619   9.571
            0.000000  0.020995  0.000000
 -18.168 -18.006  -6.905  -5.889  -1.603  -1.589  -1.578  -1.564   4.558   5.704
   6.626   9.578
            0.000000  0.031492  0.000000
 -18.158 -17.997  -6.893  -5.878  -1.643  -1.611  -1.618  -1.586   4.571   5.717
   6.639   9.589
            0.000000  0.041989  0.000000

...................
 
I tried to re-execute the bands.x command several times but in vain as the 4 stars re-appeared everytime. Does anyone know why is this occuring and how to treat it?
 
Thanks
 
Elie A. M.
School of physics and astronomy
University of Nottingham
NG7 2RD
UK 		 	   		  
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From eyvaz_isaev at yahoo.com  Fri Jul 30 16:15:52 2010
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 30 Jul 2010 07:15:52 -0700 (PDT)
Subject: [Pw_forum] STOP ERROR reading file header
In-Reply-To: <SNT114-W5716A01A1E5ADF4DCB750FD3AA0@phx.gbl>
References: <SNT114-W5716A01A1E5ADF4DCB750FD3AA0@phx.gbl>
Message-ID: <122321.44697.qm@web65708.mail.ac4.yahoo.com>

Dear Eli, 

First, are you familiar with Fortran? If not, please learn about formatted 
input/output. 


The stars mean you use more than 9999 k-points that seems to be quite 
unreasonable.  Use less k-points.

Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, 
Sweden 

Theoretical Physics Department, Moscow State Institute of Steel & Alloys, 
Russia, 

isaev at ifm.liu.se, eyvaz_isaev at yahoo.com




________________________________
From: Elie Moujaes <elie.moujaes at hotmail.co.uk>
To: pw_forum at pwscf.org
Sent: Fri, July 30, 2010 3:35:46 PM
Subject: [Pw_forum] STOP ERROR reading file header

 Dear All, I am doing calculations for the band structure of bilayer graphene in 
the presence of an electric field. I reached the stage where the .DAT file was 
produced. However when i executed the plotband.x common using 
/espresso-4.2/bin/plotband.x  and input"ed" the .DAT I got the error:
 
STOP ERROR reading file header.
 
When I checked the .DAT file I realized that the header is strange as it 
contains four stars (****) and looked like that:
 

&plot nbnd=  12, nks=**** /
            0.000000  0.000000  0.000000
 -18.176 -18.014  -6.915  -5.899  -1.571  -1.571  -1.546  -1.546   4.547   5.693
   6.616   9.569
            0.000000  0.010497  0.000000
 -18.174 -18.012  -6.913  -5.896  -1.579  -1.576  -1.554  -1.550   4.550   5.696
   6.619   9.571
            0.000000  0.020995  0.000000
 -18.168 -18.006  -6.905  -5.889  -1.603  -1.589  -1.578  -1.564   4.558   5.704
   6.626   9.578
            0.000000  0.031492  0.000000
 -18.158 -17.997  -6.893  -5.878  -1.643  -1.611  -1.618  -1.586   4.571   5.717
   6.639   9.589
            0.000000  0.041989  0.000000

...................
 
I tried to re-execute the bands.x command several times but in vain as the 4 
stars re-appeared everytime. Does anyone know why is this occuring and how to 
treat it?
 
Thanks
 
Elie A. M.
School of physics and astronomy
University of Nottingham
NG7 2RD
UK


      
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From elie.moujaes at hotmail.co.uk  Fri Jul 30 16:27:15 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Fri, 30 Jul 2010 15:27:15 +0100
Subject: [Pw_forum] STOP ERROR reading file header
In-Reply-To: <SNT114-W5716A01A1E5ADF4DCB750FD3AA0@phx.gbl>
References: <SNT114-W5716A01A1E5ADF4DCB750FD3AA0@phx.gbl>
Message-ID: <SNT114-W6459D08C769DB63886B2C6D3AA0@phx.gbl>


Thanks all for your help.

 

It was a silly question from my part. I apologize.

 

Reagrds

 

Elie A M

 


 


From: elie.moujaes at hotmail.co.uk
To: pw_forum at pwscf.org
Subject: STOP ERROR reading file header
Date: Fri, 30 Jul 2010 14:35:46 +0100




Dear All, I am doing calculations for the band structure of bilayer graphene in the presence of an electric field. I reached the stage where the .DAT file was produced. However when i executed the plotband.x common using /espresso-4.2/bin/plotband.x  and input"ed" the .DAT I got the error:
 
STOP ERROR reading file header.
 
When I checked the .DAT file I realized that the header is strange as it contains four stars (****) and looked like that:
 

&plot nbnd=  12, nks=**** /
            0.000000  0.000000  0.000000
 -18.176 -18.014  -6.915  -5.899  -1.571  -1.571  -1.546  -1.546   4.547   5.693
   6.616   9.569
            0.000000  0.010497  0.000000
 -18.174 -18.012  -6.913  -5.896  -1.579  -1.576  -1.554  -1.550   4.550   5.696
   6.619   9.571
            0.000000  0.020995  0.000000
 -18.168 -18.006  -6.905  -5.889  -1.603  -1.589  -1.578  -1.564   4.558   5.704
   6.626   9.578
            0.000000  0.031492  0.000000
 -18.158 -17.997  -6.893  -5.878  -1.643  -1.611  -1.618  -1.586   4.571   5.717
   6.639   9.589
            0.000000  0.041989  0.000000

...................
 
I tried to re-execute the bands.x command several times but in vain as the 4 stars re-appeared everytime. Does anyone know why is this occuring and how to treat it?
 
Thanks
 
Elie A. M.
School of physics and astronomy
University of Nottingham
NG7 2RD
UK 		 	   		  
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From baroni at sissa.it  Fri Jul 30 18:08:30 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 30 Jul 2010 18:08:30 +0200
Subject: [Pw_forum] Acknowledgment to this forum
In-Reply-To: <4C52CA47.2040509@gmail.com>
References: <4C52CA47.2040509@gmail.com>
Message-ID: <5A25F69A-49E1-4A24-94F1-3CB0EEEF3ED8@sissa.it>

Vega: congratulations for your publication!
I am really really moved by your nice words.
Thank you for being with us, and best wishes for a brlliant and long scientific career.
Stefano B

On Jul 30, 2010, at 2:49 PM, vega lew wrote:

> Dear developers,
> 
> My first paper published as communication (DOI=10.1039/B920128A) in PCCP today. 
> The link is http://pubs.rsc.org/en/Content/ArticleLanding/2010/CP/B920128A
> 
> During the preliminary stage of my study in this paper, I learned a lot from this forum. With the help from many scientists in this forum, I have built a small cluster, understood some basic problems about calculation and done my own scientific study etc. I want to say 'thank you' to everybody who replied my questions and provided very helpful information to me.
> 
> And I also express my gratitude to this forum in the acknowledgment part of my communication.
> 
> thank you again
> 
> best wishes,
> 
> vega
> 
> -- 
> ================================================
> Vega Lew ( weijia liu)
> Graduate student
> State Key Laboratory of Materials-oriented Chemical Engineering
> Nanjing University of Technology, 210009, Nanjing, China
> ***************************************************************
> Email: vegalew at gmail.com
> Office: Room A705, Technical Innovation Building,
> Xinmofan Road 5#, Nanjing, China
> ***************************************************************
> 
> _______________________________________________
> 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







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From quantumdft at gmail.com  Fri Jul 30 19:13:56 2010
From: quantumdft at gmail.com (vega lew)
Date: Sat, 31 Jul 2010 01:13:56 +0800
Subject: [Pw_forum] Acknowledgment to this forum
In-Reply-To: <5A25F69A-49E1-4A24-94F1-3CB0EEEF3ED8@sissa.it>
References: <4C52CA47.2040509@gmail.com>
	<5A25F69A-49E1-4A24-94F1-3CB0EEEF3ED8@sissa.it>
Message-ID: <AANLkTinfz1X+zqsTP9CE1V797JbkAHnXMKwkd=35-of2@mail.gmail.com>

Dear sir,

I could remember in the days when I joined this forum. At that time, I know
nothing about how to build a cluster, how to compile and run QE in parallel
and even how to do a scientific research. It is Axel Kohlmeyer, you and
other scientist in this forum to tell me how to use QE and do my own
research.

I still remember the word that you lecture me.
For example, "i would trust more a colleague next dore (whom, at least I
could tease and ask questions) than a journal, ANY journal, no matter its
impact factor, publishing company, title ...";
"what is good for a system may be totally wrong for another, unless you know
exactly WHY it is good in one case and you are sure that the same argument
holds for the second. this only YOU can say, after sweating quite a lot to
understand by yourself, which, I understand, you are not quite prepared to
do";
"it sounds like somebody led you to believe that the purpose of science is
to publish in high-impact journals. are you sure this is really the case?";
and "If I were to describe in one sentence what makes the difference between
modern science and ancient knowledge systems, it is the role played in the
former by the "doubt": never trust a truth unless you can give by yourself a
correct answer to a legitimate question. and reproducibly so." etc.

It has been more than two years since I joined this forum. I found someone
who used to be very active had been leave here for something more important,
such as Axel Kohlmeyer, Eyvaz Isaev and so on. I am always laying their help
by my heart. You and your team is still here to develop the QE. I really
appreciate everything you did, which makes our investigation possible.

I think many users like me are not the proper person the contribute to the
codes or the forum, because my background is not physics. But I think what I
could do is to use Q-E to find something interest and useful and make Q-E
more well-known.

Hope Q-E and this forum become better and better.

best wishes,

vega

On Sat, Jul 31, 2010 at 12:08 AM, Stefano Baroni <baroni at sissa.it> wrote:

> Vega: congratulations for your publication!
> I am really really moved by your nice words.
> Thank you for being with us, and best wishes for a brlliant and long
> scientific career.
> Stefano B
>
> On Jul 30, 2010, at 2:49 PM, vega lew wrote:
>
>  Dear developers,
>
> My first paper published as communication (**DOI=10.1039/B920128A) in PCCP
> today.
> The link is http://pubs.rsc.org/en/Content/ArticleLanding/2010/CP/B920128A
>
> During the preliminary stage of my study in this paper, I learned a lot
> from this forum. With the help from many scientists in this forum, I have
> built a small cluster, understood some basic problems about calculation and
> done my own scientific study etc. I want to say 'thank you' to everybody who
> replied my questions and provided very helpful information to me.
>
> And I also express my gratitude to this forum in the acknowledgment part of
> my communication.
>
> thank you again
>
> best wishes,
>
> vega
>
> --
>
> ================================================
> Vega Lew ( weijia liu)
> Graduate student
> State Key Laboratory of Materials-oriented Chemical Engineering
> Nanjing University of Technology, 210009, Nanjing, China
> ***************************************************************
> Email: vegalew at gmail.com
> Office: Room A705, Technical Innovation Building,
> Xinmofan Road 5#, Nanjing, China
> ***************************************************************
>   _______________________________________________
> 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
>
>
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
==================================================================================
Vega Lew ( weijia liu)
Graduate student
State Key Laboratory of Materials-oriented Chemical Engineering
College of Chemistry and Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
******************************************************************************************************************
Email: vegalew at gmail.com
Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing,
Jiangsu, China
******************************************************************************************************************
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From padmaja_patnaik at yahoo.co.uk  Fri Jul 30 20:03:58 2010
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Fri, 30 Jul 2010 18:03:58 +0000 (GMT)
Subject: [Pw_forum] error in running examples
Message-ID: <831703.10400.qm@web26108.mail.ukl.yahoo.com>

Dear all

I am trying to run espresso on a 64 bit parallel
machine, four processors, with Ubuntu-8.04. Few of the examples are not
running successfully, like example 11, 12 and 13. It stops
automatically giving the following error message.
--------------------------------------------------------------------------------- 
cleaning /home/padmaja/tmp... done
? running self-consistent calculation for Al atom...2
Error condition encountered during test: exit status = 2
Aborting
--------------------------------------------------------------------------------- ??????????? 
I
have tried with different version of the code like, 4.0.3, 4.0.5,
4.1.1, 4.1.3 and 4.2.1. No error in the configure and make all
messages. 
Please suggest.
Regards

Padmaja Patnaik

Research Scholar

Dept of Physics

IIT Bombay

Mumbai, India


      
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From eyvaz_isaev at yahoo.com  Fri Jul 30 20:16:40 2010
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 30 Jul 2010 11:16:40 -0700 (PDT)
Subject: [Pw_forum] error in running examples
In-Reply-To: <831703.10400.qm@web26108.mail.ukl.yahoo.com>
References: <831703.10400.qm@web26108.mail.ukl.yahoo.com>
Message-ID: <678276.13413.qm@web65701.mail.ac4.yahoo.com>

Dear Padmaja,

It is hard to conclude anything based on your message. Can you please have a 
look at your output files for the failed runs and see what is the error message?

Bests,
Eyvaz.

 -------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, 
Sweden 

Theoretical Physics Department, Moscow State Institute of Steel & Alloys, 
Russia, 

isaev at ifm.liu.se, eyvaz_isaev at yahoo.com




________________________________
From: Padmaja Patnaik <padmaja_patnaik at yahoo.co.uk>
To: pw_forum at pwscf.org
Sent: Fri, July 30, 2010 8:03:58 PM
Subject: [Pw_forum] error in running examples


Dear all

I am trying to run espresso on a 64 bit parallel machine, four processors, with 
Ubuntu-8.04. Few of the examples are not running successfully, like example 11, 
12 and 13. It stops automatically giving the following error message.
---------------------------------------------------------------------------------
 
cleaning /home/padmaja/tmp... done
  running self-consistent calculation for Al atom...2
Error condition encountered during test: exit status = 2
Aborting
---------------------------------------------------------------------------------
             

I have tried with different version of the code like, 4.0.3, 4.0.5, 4.1.1, 4.1.3 
and 4.2.1. No error in the configure and make all messages. 

Please suggest.
Regards

Padmaja Patnaik
Research Scholar
Dept of Physics
IIT Bombay
Mumbai, India 



      
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From lcqsigi at gmail.com  Fri Jul 30 20:47:11 2010
From: lcqsigi at gmail.com (S. Sanchez)
Date: Fri, 30 Jul 2010 11:47:11 -0700
Subject: [Pw_forum] Raman Spectrum using CP.X
Message-ID: <AANLkTinqjYKeWf4N=EGrua=O2mwdDeTSGRj8YVFTLGAz@mail.gmail.com>

Dear QE users,

I have checked the following thread in the Quantum Espresso forum:

*http://www.democritos.it/pipermail/pw_forum/2007-May/006479.html*<http://www.democritos.it/pipermail/pw_forum/2007-May/006479.html>

At the moment, it is not clear to me if the method to compute the atomic
forces under the influence of two force fields using the CP.X code
has been actually implemented for non-cubic lattices. Or is it
the case that the method is only applicable to cubic lattices?

Thanks,
S. Sanchez
Researcher
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From 1009ukumar at gmail.com  Sat Jul 31 07:41:07 2010
From: 1009ukumar at gmail.com (sonu kumar)
Date: Sat, 31 Jul 2010 11:11:07 +0530
Subject: [Pw_forum] Fourier interpolation
Message-ID: <AANLkTinqHrsnyBuLLU42gqo+JCNZf6o1xqVkm7Hm2+w=@mail.gmail.com>

*Dear Prof. **Eyvaz Isaev and QE users,*
*
*
*> Play around cutoff energy and the threshold parameter for phonons.

*
*where is the cutoff energy parameter related to phonon calculations?*
*
*
*i couldn't find it in the manual for ph.x. Only "tr2_ph"  theshold **parameter
is *
*there in addition to "eth_rps" and "eth_ns" **parameters for Raman
calculations.*
*
*
*i am sorry if am wrong.*
*Thank you very much.*
*
*
*With Kind Regards,*
*Sonu Kumar*
*Phd Student
Physics Department
IIT Delhi
*
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From eyvaz_isaev at yahoo.com  Sat Jul 31 11:20:31 2010
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sat, 31 Jul 2010 02:20:31 -0700 (PDT)
Subject: [Pw_forum] Fourier interpolation
In-Reply-To: <AANLkTinqHrsnyBuLLU42gqo+JCNZf6o1xqVkm7Hm2+w=@mail.gmail.com>
References: <AANLkTinqHrsnyBuLLU42gqo+JCNZf6o1xqVkm7Hm2+w=@mail.gmail.com>
Message-ID: <463491.96241.qm@web65710.mail.ac4.yahoo.com>

Dear Sonu,

Of course, there is no cutoff energy  in phonon input file. But the second order 
derivatives to define  phonons are  related to the charge density and its first 
order derivative. So,  phonons are dependent on the cutoff energy. In its turn, 
the cutoff energy is connected to a Pseudo-type used.  


Yes, I meant tr2_ph parameter. 

Bests,
Eyvaz.

 -------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, 
Sweden 

Theoretical Physics Department, Moscow State Institute of Steel & Alloys, 
Russia, 

isaev at ifm.liu.se, eyvaz_isaev at yahoo.com




________________________________
From: sonu kumar <1009ukumar at gmail.com>
To: pw_forum at pwscf.org
Sent: Sat, July 31, 2010 7:41:07 AM
Subject: Re: [Pw_forum] Fourier interpolation

Dear Prof. Eyvaz Isaev and QE users,
> Play around cutoff energy and the threshold parameter for phonons.


where is the cutoff energy parameter related to phonon calculations?

i couldn't find it in the manual for ph.x. Only "tr2_ph"  theshold parameter is 
there in addition to "eth_rps" and "eth_ns" parameters for Raman calculations.

i am sorry if am wrong.
Thank you very much.

With Kind Regards,
Sonu Kumar
Phd Student
Physics Department
IIT Delhi


      
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