From ykanai at berkeley.edu  Mon Dec  1 02:04:45 2008
From: ykanai at berkeley.edu (Yosuke Kanai)
Date: Sun, 30 Nov 2008 17:04:45 -0800
Subject: [Pw_forum] problem with TPSS
	(Tao-Perdew-Staroverov-Scuseria)meta-GGA for silicon
References: <818240.29415.qm@web65705.mail.ac4.yahoo.com>
Message-ID: <006e01c95350$d02f7530$5d01a8c0@YKANAI>

Hi Rafael

When we implemented TPSS in CP code (not PWSCF) at Princeton few years ago, 
we did some comparisons including bulk-Si to
all-electron gaussian-type calculations. Have a look at APPENDIX in the 
following paper if interested.


Journal of Chemical Physics, Volume 125, Issue 23, pp. 234104-234104-8 
(2006)
"Testing the TPSS meta-GGA XC functional in calculations of transition 
states and reaction barriers"
Yosuke Kanai, Xiaofei Wang, Annabella Sellonia, and Roberto Car.

Take care,

Yosuke


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

Yosuke Kanai, Ph.D.

Berkeley Nanosciences and Nanoengineering Institute

University of California, Berkeley

325 Birge Hall
Email : ykanai at berkeley.edu
Phone : (510)-643-1157

----- Original Message ----- 
From: "Rafael Dias Menezes" <rdmeneze at yahoo.com.br>
To: "PWSCF Forum" <pw_forum at pwscf.org>
Sent: Friday, November 28, 2008 10:26 AM
Subject: Re: [Pw_forum] problem with TPSS 
(Tao-Perdew-Staroverov-Scuseria)meta-GGA for silicon


Hi everybody,

thank you  for the help.

That's hug

Rafael Dias


--- Em sex, 28/11/08, Gabriele Sclauzero <sclauzer at sissa.it> escreveu:

> De: Gabriele Sclauzero <sclauzer at sissa.it>
> Assunto: Re: [Pw_forum] problem with TPSS (Tao-Perdew-Staroverov-Scuseria) 
> meta-GGA for silicon
> Para: "PWSCF Forum" <pw_forum at pwscf.org>
> Data: Sexta-feira, 28 de Novembro de 2008, 12:39
> Ari P Seitsonen wrote:
> >
> > Dear Rafael,
> >
> >   Adding to Axel's comment; you might experience
> the problem of
> > "non-spherical" atom in Si since in the free
> atom you have two
> > p-electrons to put on three degenerate (spin-up)
> states. Thus there will
> > be a fight (= usually no convergence) which one of
> p_x, p_y and p_z will
> > get them if tried straightforwardly. What one can try
> is to modify the
> > cell slightly making it non-cubic,
>
> This solution is nice, I'll try it someday. Anyway, the
> pw.x flag:
>
> nosym=.true.
>
> could do the job in this case (and it is often useful for
> computing atoms or molecules in
> supercells).
> You can even fix occupations in the more problematic cases,
> by setting:
>
> occupations = 'from_input'
>
> and specifying the desired occupations at the end of the
> namelists.
>
> NB: works only with gamma point
>
> Hope this helps,
>
> regards
>
> GS
>
> >>>
> >>>
> >>
> >>
> >>
> >
> >
> >
> ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
> -- 
>
> La legge n. 133 uccide l'Universit? e la Ricerca
> italiana!
>
> Save Italian Brains!
> (http://saveitalianbrains.wordpress.com/)
>
> o ------------------------------------------------ o
> | Gabriele Sclauzero, PhD Student                  |
> | c/o:   SISSA & CNR-INFM Democritos,              |
> |        via Beirut 2-4, 34014 Trieste (Italy)     |
> | email: sclauzer at sissa.it                         |
> | phone: +39 040 3787 511                          |
> | skype: gurlonotturno                             |
> o ------------------------------------------------ o
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      Veja quais s?o os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com
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From manoj at phys.ufl.edu  Mon Dec  1 18:31:57 2008
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Mon, 1 Dec 2008 12:31:57 -0500 (EST)
Subject: [Pw_forum] complex band
In-Reply-To: <Pine.GSO.4.21.0811301437520.27070-100000@neptune.phys.ufl.edu>
Message-ID: <Pine.GSO.4.21.0812011230240.26211-100000@neptune.phys.ufl.edu>

Dear Alexander, 
 Dont worry about the previous mail, I figured it out :)

-manoj 
On Sun, 30 Nov 2008, Manoj Srivastava wrote:

> Dear Alexander, 
>  Thank you very much for your answer. It has started making sense, but
> unfortunately not a whole lot. I think I need to have complete
> understanding of this subroutine in order to have the bigger picture. In
> the other e-mail, copied and pasted as below - 
> > the expression -
> > norm2=(((il+xyk(1,ik))*bg(1,1)+(jl+xyk(2,ik))*bg(1,2))**2+ &
> >             ((il+xyk(1,ik))*bg(2,1)+(jl+xyk(2,ik))*bg(2,2))**2)* &
> >
> > i believe is  |G+k|^2. How do you get above expression in the code for
> > this? 
> norm2 is indeed |G_perp+k_perp|^2, where G_perp=il*b_1+jl*b_2 and 2d
> vector 
> k_perp=xyk(1,ik)*b_1+xyk(2,ik)*b_2 and you indeed select out those 
> G_perp+k_perp which satisfy (G_perp+k_perp)^2<Ecut2d.
> 
> Why is K_perp in terms of b_1 and b_2? You can ofcourse take it
> like that but is there any specific reason to do that? If we look at the
> Fourier transform of wavefunction psi(r)=sum_{G}\psi(G)exp(i(K+G).r).
> here in this expression do we always take K in terms of G. I dont think
> so, K can be a label, which might be in terms of G vectors but not
> necessarily. What do you think? 
> In the input file where we enter k_x and k_y, do we enter  these  in
> terms of b1 and b2? or somewhere later in the code it gets multiplied with
> b1 and b2, if yes where? I am having tough time figuring it out :( 
> Thanks for help. 
> 
> Regards, 
> Manoj Srivastava
> Department of Physics,
> University of Florida, Gainesville
> 
> 
>  On Fri, 28 Nov 2008,
> Alexander wrote:
> 
> > Dear Manoj
> > Ngper is the total number of g_perp=G_perp+k_perp with |g_perp|^2<E_cut 
> > which are arranged into the shells. Each shell contains g_perp having the same 
> > norm which is very useful because many calculations with g_perp depend only 
> > on their norms. The number of shells is ngpsh. gnsh(ngpsh) is the norm for 
> > each shell, ninsh(ngpsh)  is the number of g_perp in the shell.
> > The array nshell is the auxiliary array used further to arrange the g_perp 
> > vectors in the shells.
> > 
> > Hope this helps you,
> > regards, Alexander 
> > 
> > and ngpsh is the number of shells 
> > 
> > On Thursday 27 November 2008 00:26, Manoj Srivastava wrote:
> > > Dear Alexander, PWSCF users and developers,
> > >  I have a technical question in one of the subroutines used to calculate
> > > complex band. The subroutine 'init_gper.f90' under PWCOND directory is
> > > used to calculate number of G perpendicular vectors within the energy
> > > cutoff by using [k_{\perp}+G_{\perp}]^2.le.E_{cut}. I understand the
> > > counting of Gper, but i dont understand how do they construct the Gper
> > > vectors. For example what is 'ngpsh'? It is defined as 'no. of shells for
> > > G', but i really dont understand what this is. I dont understand after
> > > line 50 of the code in init_gper.f90.  Mainly what does the following
> > > piece of code do
> > >
> > >           do i=1,nrx
> > > 	  do j=1,nry
> > >            icount=0
> > >           do iw=1, ngpsh
> > >            if (abs(norm2-gnorm2(iw)).gt.eps) then
> > >              icount=icount+1
> > >            else
> > >              nshell(i,j)=iw
> > >            endif
> > >          enddo
> > >          if (icount.eq.ngpsh) then
> > >            ngpsh=ngpsh+1
> > >            gnorm2(ngpsh)=norm2
> > >            nshell(i,j)=ngpsh
> > >          endif
> > >       endif
> > >       enddo
> > >       enddo
> > > I understand it is not a good way of asking question, but I am completely
> > > lost. Any help will be appreciated.
> > >
> > > Regards,
> > > Manoj
> > >
> > > _______________________________________________
> > > 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
> > 
> 
> 


From h-lee at cw.jp.nec.com  Tue Dec  2 01:42:08 2008
From: h-lee at cw.jp.nec.com (Hosik Lee)
Date: Tue, 2 Dec 2008 09:42:08 +0900
Subject: [Pw_forum] SO interaction and Noncollinear magnetism
Message-ID: <5344CACE9AF14565956D8B4AEB58A1B4@nsl.ad.nec.co.jp>

Dear Pwscf users,

 

Hello everyone. I have a question about SO interaction and Noncollinear
magnetism calculation using espresso-3.2.3. It seems that the SO interaction
is included in the pseudo-potential and the noncollinear magnetism can be
characterized with spinor diagonalization. These two is implemented in the
version 3.2.3. Is there any paper which uses these two? I can find those
which use one of them. If I got any answer, I will highly appreciate you. 

 

Best regards,

 

========================================
Dr. Hosik Lee
R&D Unit Central Res. Labs.
Nano Electronics Research Laboratories,
NEC Corporation
34 Miyukigaoka, Tsukuba, 305-8501 JAPAN
Tel +81-29-850-1540 Fax +81-29-856-6136
e-mail:  h-lee at cw.jp.nec.com
=========================================
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From jiri.houska at polymtl.ca  Tue Dec  2 04:54:55 2008
From: jiri.houska at polymtl.ca (Jiri Houska)
Date: Mon, 01 Dec 2008 22:54:55 -0500
Subject: [Pw_forum] smearing at zero K
Message-ID: <1228190095.4934b18f7d39a@www.imp.polymtl.ca>

Hello,
a simple question, but I want to be sure about that: when running a wavefunction
optimization for a metal at zero K, should the result be the same with (1)
occupations smearing & practically-zero degauss and with (2) occupations fixed?

(I understand that using of smearing improves speed of the convergence, but that
is not the question.)

Thanks,
Jiri Houska
Ecole Polytechnique de Montreal



From jjr19 at uakron.edu  Tue Dec  2 16:36:50 2008
From: jjr19 at uakron.edu (J. J. Ramsey)
Date: Tue, 2 Dec 2008 07:36:50 -0800 (PST)
Subject: [Pw_forum] "charge is wrong" error in semiconductor slab calculation
Message-ID: <681353.68805.qm@web50903.mail.re2.yahoo.com>

I'm doing a slab calculation somewhat similar to that in Phys. Rev. B 77, 165323 (2008), except that (1) the geometry is simplified down to 10 atoms and (2) the goal is to relax the positions of the pseudohydrogens used to passivate the bottom of the slab while keeping all other atoms fixed. It's partly a dummy problem to shake out the kinks in doing a simulation in Quantum Espresso. Here is the input file:

&CONTROL
    title = "Finding positions of pseudohydrogens",
    calculation= "relax",
    prefix = findPseudoInitPos_PWscf,
    pseudo_dir = "Pseudopotentials/"
/
&SYSTEM
    ibrav = 8,
    a = 3.92232131524178,
    b = 3.92232131524178,
    c = 22.207375,
    nat = 10,
    ntyp = 4,
    ecutwfc = 40
/
&ELECTRONS
    conv_thr = 1D-6
/
&IONS
    bfgs_ndim         = 3,
    pot_extrapolation = "second_order",
    wfc_extrapolation = "second_order",
/
ATOMIC_SPECIES
Ga 69.723 Ga.pz-bhs.UPF
In 114.818 In.pz-n-bhs.UPF
As 74.92160 As.pz-bhs.UPF 
H* 1.25 01_25-H-tm.fhi.UPF
ATOMIC_POSITIONS angstrom
H* 0 0.980580328810445 0 1 1 1
H* 0 2.94174098643133 0 1 1 1
Ga 0 0 0.693375 0 0 0
As 1.96116065762089 0 2.080125 0 0 0
Ga 1.96116065762089 1.96116065762089 3.466875 0 0 0
As 0 1.96116065762089 4.853625 0 0 0
In 0 0 6.240375 0 0 0
As 1.96116065762089 0 7.732125 0 0 0
In 1.96116065762089 1.96116065762089 9.223875 0 0 0
As 0 1.96116065762089 10.715625 0 0 0
K_POINTS automatic
4 4 1 1 1 1

The error that I get is
WARNING: integrated charge=    34.15000000, expected=    34.50000000

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from electrons : error #         1
     charge is wrong
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

This happened at the first iteration.

The pseudopotentials for Ga, In, and As are from the pseudopotential tables, and I tested them by using them to find the lattice constants of GaAs and InAs, which were found to be about 5.547 and 5.967 angstroms, respectively, which appears reasonable. The pseudopotential for pseudohydrogen was generated from fhi98pp from this input file,

 1.25  0  1  3  0.00 : z  nc  nv iexc rnlc 
    1  0   1.25      : n  l   f 
0  t                 : lmax  s_pp_def 
0  0.00  0.00  t     : lt  rct  et  s_pp_type

and converted to UPF with the fhi2upf utility.

Input, output, and pseudopotential for pseudohydrogen are attached in the job-stuff.tgz tarball.

Any ideas as to what's wrong?


      
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From smeza at uas.uasnet.mx  Tue Dec  2 19:17:21 2008
From: smeza at uas.uasnet.mx (Salvador Meza Aguilar)
Date: Tue, 02 Dec 2008 11:17:21 -0700
Subject: [Pw_forum] MnPd Bulk
Message-ID: <49357BB1.6040500@uas.uasnet.mx>




I'm investigating the magnetic properties of MnPd ordered alloys
on Co(001) and Co(111) fcc, using PWscf version 3.2

I have some questions about the obtained results.

I try to find the values reported in the following paper:
Journal of Alloys and Compounds 415, 31-37 (2006), in the table IV,
the values for magnetic moments for Mn and Pd atoms in each
magnetic configuration. I found dead magnetic moments for each
magnetic configuration. I have several results with MnPd on Co 
substrate; with
non zero magnetic moments for Mn and Pd atoms.

Which is the problem? I attach the input files.


-- 
-----------------------------------------------------------------
Dr. Salvador MEZA AGUILAR
Escuela de Ciencias Fisico-Matematicas
Universidad Autonoma de Sinaloa
Av. de las Americas y Blvd. Universitarios
Ciudad Universitaria
80010 Culiacan Sinaloa
Mexico
Tel./Fax +52 6677 15 64 12 ext 114
Tel./Fax +52 6677 16 11 54 ext 114
e-mail: smeza at uas.uasnet.mx
-----------------------------------------------------------------

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From eyvaz_isaev at yahoo.com  Tue Dec  2 19:48:10 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 2 Dec 2008 10:48:10 -0800 (PST)
Subject: [Pw_forum] MnPd Bulk
In-Reply-To: <49357BB1.6040500@uas.uasnet.mx>
Message-ID: <60570.67017.qm@web65709.mail.ac4.yahoo.com>

Hi,

Mn and Pd are quite interesting metals. You can find a magnetic moment on Pd atoms depending on its local environment and slightly larger lattice parameters. 
This has a sense as you used GGA (PBE) base pseudopotentials which tend to give larger lattice parameter 
inducing magnetism for Pd atoms, at least. You can carry out calculations with LDA-based PsPs.
Try also usin the same lattice parameters as in the paper you cited.

Hope this helps.

Bests,
Eyvaz.

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


--- On Tue, 12/2/08, Salvador Meza Aguilar <smeza at uas.uasnet.mx> wrote:

> From: Salvador Meza Aguilar <smeza at uas.uasnet.mx>
> Subject: [Pw_forum] MnPd Bulk
> To: pw_forum at pwscf.org, "DEMANGEAT Claude" <demangea at fresnel.u-strasbg.fr>, "Bernard M'Passi Mabiala" <mpassi_b at yahoo.com>
> Date: Tuesday, December 2, 2008, 9:17 PM
> I'm investigating the magnetic properties of MnPd
> ordered alloys
> on Co(001) and Co(111) fcc, using PWscf version 3.2
> 
> I have some questions about the obtained results.
> 
> I try to find the values reported in the following paper:
> Journal of Alloys and Compounds 415, 31-37 (2006), in the
> table IV,
> the values for magnetic moments for Mn and Pd atoms in each
> magnetic configuration. I found dead magnetic moments for
> each
> magnetic configuration. I have several results with MnPd on
> Co substrate; with
> non zero magnetic moments for Mn and Pd atoms.
> 
> Which is the problem? I attach the input files.
> 
> 
> --
> -----------------------------------------------------------------
> Dr. Salvador MEZA AGUILAR
> Escuela de Ciencias Fisico-Matematicas
> Universidad Autonoma de Sinaloa
> Av. de las Americas y Blvd. Universitarios
> Ciudad Universitaria
> 80010 Culiacan Sinaloa
> Mexico
> Tel./Fax +52 6677 15 64 12 ext 114
> Tel./Fax +52 6677 16 11 54 ext 114
> e-mail: smeza at uas.uasnet.mx
> -----------------------------------------------------------------
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From stewart at cnf.cornell.edu  Tue Dec  2 20:03:02 2008
From: stewart at cnf.cornell.edu (Derek Stewart)
Date: Tue, 02 Dec 2008 14:03:02 -0500
Subject: [Pw_forum] MnPd Bulk
In-Reply-To: <60570.67017.qm@web65709.mail.ac4.yahoo.com>
References: <60570.67017.qm@web65709.mail.ac4.yahoo.com>
Message-ID: <20081202190302.19811.qmail@mail.spidergraphics.com>

Hi Salvador, 

I agree with Eyvaz that you need to be very careful about the 
pseudopotential you choose for palladium. 

I did some calculations examing potential magnetism in palladium nanowires.  
For some pseudopotentials, they predict that the standard non-magnetic fcc 
crystal should have a magnetic ground state.  Some other groups have also 
observed this problem using other techniques (localized orbitals, Siesta I 
believe). 

If you are interested in more details on the pseudopotentials, see the 
article "Magnetism in coaxial palladium nanowires", J. Appl. Phys. 101, 
09D503 (2007)  http://dx.doi.org/10.1063/1.2672303 

Best regards, 

Derek 

 

Eyvaz Isaev writes: 

> Hi, 
> 
> Mn and Pd are quite interesting metals. You can find a magnetic moment on Pd atoms depending on its local environment and slightly larger lattice parameters. 
> This has a sense as you used GGA (PBE) base pseudopotentials which tend to give larger lattice parameter 
> inducing magnetism for Pd atoms, at least. You can carry out calculations with LDA-based PsPs.
> Try also usin the same lattice parameters as in the paper you cited. 
> 
> Hope this helps. 
> 
> Bests,
> Eyvaz. 
> 
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev, 
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
> Condensed Matter Theory Group, Uppsala University, Sweden 
> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com 
> 
> 
> --- On Tue, 12/2/08, Salvador Meza Aguilar <smeza at uas.uasnet.mx> wrote: 
> 
>> From: Salvador Meza Aguilar <smeza at uas.uasnet.mx>
>> Subject: [Pw_forum] MnPd Bulk
>> To: pw_forum at pwscf.org, "DEMANGEAT Claude" <demangea at fresnel.u-strasbg.fr>, "Bernard M'Passi Mabiala" <mpassi_b at yahoo.com>
>> Date: Tuesday, December 2, 2008, 9:17 PM
>> I'm investigating the magnetic properties of MnPd
>> ordered alloys
>> on Co(001) and Co(111) fcc, using PWscf version 3.2 
>> 
>> I have some questions about the obtained results. 
>> 
>> I try to find the values reported in the following paper:
>> Journal of Alloys and Compounds 415, 31-37 (2006), in the
>> table IV,
>> the values for magnetic moments for Mn and Pd atoms in each
>> magnetic configuration. I found dead magnetic moments for
>> each
>> magnetic configuration. I have several results with MnPd on
>> Co substrate; with
>> non zero magnetic moments for Mn and Pd atoms. 
>> 
>> Which is the problem? I attach the input files. 
>> 
>> 
>> --
>> -----------------------------------------------------------------
>> Dr. Salvador MEZA AGUILAR
>> Escuela de Ciencias Fisico-Matematicas
>> Universidad Autonoma de Sinaloa
>> Av. de las Americas y Blvd. Universitarios
>> Ciudad Universitaria
>> 80010 Culiacan Sinaloa
>> Mexico
>> Tel./Fax +52 6677 15 64 12 ext 114
>> Tel./Fax +52 6677 16 11 54 ext 114
>> e-mail: smeza at uas.uasnet.mx
>> ----------------------------------------------------------------- 
>> 
>> _______________________________________________
>> 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 
> 
 


################################
Derek Stewart, Ph. D.
Scientific Computation Associate
http://www.people.cornell.edu/pages/das248/
250 Duffield Hall
Cornell Nanoscale Facility (CNF)
Ithaca, NY 14853
stewart (at) cnf.cornell.edu
(607) 255-2856

From eyvaz_isaev at yahoo.com  Tue Dec  2 21:47:11 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 2 Dec 2008 12:47:11 -0800 (PST)
Subject: [Pw_forum] "charge is wrong" error in semiconductor slab
	calculation
In-Reply-To: <681353.68805.qm@web50903.mail.re2.yahoo.com>
Message-ID: <165093.99937.qm@web65713.mail.ac4.yahoo.com>

Hi, 

I will try to repeat my own reply as it was sent only to the first address. That seems to be quite strange, because I used "Reply".

>     ibrav = 8,
>     a = 3.92232131524178,
>     b = 3.92232131524178,
>     c = 22.207375,

Why you use orthorhombic lattice instead of simple tetragonal (ibrav=6) as a=b?

This problem was discussed before many times (you could search in the forum archive):
Most likely you have a metallic system though you claim that you have a semiconducting slab.
So, you should include "occupations" and related keywords, otherwise you have a semiconducting system that causes the charge deficiency due to insufficient bands number.

By the way your system might be metallic due to induced states in the band gap as you consider a slab with surfaces.

Please, provide your affiliation, too.

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


--- On Tue, 12/2/08, J. J. Ramsey <jjr19 at uakron.edu> wrote:

> From: J. J. Ramsey <jjr19 at uakron.edu>
> Subject: [Pw_forum] "charge is wrong" error in semiconductor slab calculation
> To: pw_forum at pwscf.org
> Date: Tuesday, December 2, 2008, 6:36 PM
> I'm doing a slab calculation somewhat similar to that in
> Phys. Rev. B 77, 165323 (2008), except that (1) the geometry
> is simplified down to 10 atoms and (2) the goal is to relax
> the positions of the pseudohydrogens used to passivate the
> bottom of the slab while keeping all other atoms fixed.
> It's partly a dummy problem to shake out the kinks in
> doing a simulation in Quantum Espresso. Here is the input
> file:
> 
> &CONTROL
>     title = "Finding positions of
> pseudohydrogens",
>     calculation= "relax",
>     prefix = findPseudoInitPos_PWscf,
>     pseudo_dir = "Pseudopotentials/"
> /
> &SYSTEM
>     ibrav = 8,
>     a = 3.92232131524178,
>     b = 3.92232131524178,
>     c = 22.207375,
>     nat = 10,
>     ntyp = 4,
>     ecutwfc = 40
> /
> &ELECTRONS
>     conv_thr = 1D-6
> /
> &IONS
>     bfgs_ndim         = 3,
>     pot_extrapolation = "second_order",
>     wfc_extrapolation = "second_order",
> /
> ATOMIC_SPECIES
> Ga 69.723 Ga.pz-bhs.UPF
> In 114.818 In.pz-n-bhs.UPF
> As 74.92160 As.pz-bhs.UPF 
> H* 1.25 01_25-H-tm.fhi.UPF
> ATOMIC_POSITIONS angstrom
> H* 0 0.980580328810445 0 1 1 1
> H* 0 2.94174098643133 0 1 1 1
> Ga 0 0 0.693375 0 0 0
> As 1.96116065762089 0 2.080125 0 0 0
> Ga 1.96116065762089 1.96116065762089 3.466875 0 0 0
> As 0 1.96116065762089 4.853625 0 0 0
> In 0 0 6.240375 0 0 0
> As 1.96116065762089 0 7.732125 0 0 0
> In 1.96116065762089 1.96116065762089 9.223875 0 0 0
> As 0 1.96116065762089 10.715625 0 0 0
> K_POINTS automatic
> 4 4 1 1 1 1
> 
> The error that I get is
> WARNING: integrated charge=    34.15000000, expected=   
> 34.50000000
> 
> 
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from electrons : error #         1
>      charge is wrong
> 
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
>      stopping ...
> 
> This happened at the first iteration.
> 
> The pseudopotentials for Ga, In, and As are from the
> pseudopotential tables, and I tested them by using them to
> find the lattice constants of GaAs and InAs, which were
> found to be about 5.547 and 5.967 angstroms, respectively,
> which appears reasonable. The pseudopotential for
> pseudohydrogen was generated from fhi98pp from this input
> file,
> 
>  1.25  0  1  3  0.00 : z  nc  nv iexc rnlc 
>     1  0   1.25      : n  l   f 
> 0  t                 : lmax  s_pp_def 
> 0  0.00  0.00  t     : lt  rct  et  s_pp_type
> 
> and converted to UPF with the fhi2upf utility.
> 
> Input, output, and pseudopotential for pseudohydrogen are
> attached in the job-stuff.tgz tarball.
> 
> Any ideas as to what's wrong?
> 
> 
>       _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From eyvaz_isaev at yahoo.com  Wed Dec  3 00:20:32 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 2 Dec 2008 15:20:32 -0800 (PST)
Subject: [Pw_forum] MnPd Bulk
In-Reply-To: <20081202190302.19811.qmail@mail.spidergraphics.com>
Message-ID: <789156.64028.qm@web65711.mail.ac4.yahoo.com>

Hi Derek,

--- On Tue, 12/2/08, Derek Stewart <stewart at cnf.cornell.edu> wrote:

> Some other groups have also observed this problem using > other techniques (localized orbitals, Siesta I believe). 
 
Another example is so-called Exact Muffin-Tin Orbitals (EMTO) code which is based on Green's functions.
Of course, the physics should not depend on a particular choice of the method to solve the Kohn-Sham equations, if it is developed (and programmed) correctly. 
In this particular case with Pd (you know, of course) the problem is connected to location of the Fermi level in the electronic DOS with quite high N(E_F), in the vicinity of the Stoner criterion IxN(F_F)>1 with I is being intra-atomic exchange integral almost independent on crystalline structure and atom type. If one slightly changes (enlarges) the lattice parameter then the criterion is fulfilled and Pd becomes magnetic.

The only difference might be for so called DMFT-codes, but it is beyond DFT.

Bests,
Eyvaz.
 
> 
>  
> 
> Eyvaz Isaev writes: 
> 
> > Hi, 
> > 
> > Mn and Pd are quite interesting metals. You can find a
> magnetic moment on Pd atoms depending on its local
> environment and slightly larger lattice parameters. 
> > This has a sense as you used GGA (PBE) base
> pseudopotentials which tend to give larger lattice parameter
> 
> > inducing magnetism for Pd atoms, at least. You can
> carry out calculations with LDA-based PsPs.
> > Try also usin the same lattice parameters as in the
> paper you cited. 
> > 
> > Hope this helps. 
> > 
> > Bests,
> > Eyvaz. 
> > 
> >
> -------------------------------------------------------------------
> > Prof. Eyvaz Isaev, 
> > Theoretical Physics Department, Moscow State Institute
> of Steel & Alloys, Russia, 
> > Department of Physics, Chemistry, and Biology (IFM),
> Linkoping University, Sweden 
> > Condensed Matter Theory Group, Uppsala University,
> Sweden 
> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se,
> eyvaz_isaev at yahoo.com 
> > 
> > 
> > --- On Tue, 12/2/08, Salvador Meza Aguilar
> <smeza at uas.uasnet.mx> wrote: 
> > 
> >> From: Salvador Meza Aguilar
> <smeza at uas.uasnet.mx>
> >> Subject: [Pw_forum] MnPd Bulk
> >> To: pw_forum at pwscf.org, "DEMANGEAT
> Claude" <demangea at fresnel.u-strasbg.fr>,
> "Bernard M'Passi Mabiala"
> <mpassi_b at yahoo.com>
> >> Date: Tuesday, December 2, 2008, 9:17 PM
> >> I'm investigating the magnetic properties of
> MnPd
> >> ordered alloys
> >> on Co(001) and Co(111) fcc, using PWscf version
> 3.2 
> >> 
> >> I have some questions about the obtained results. 
> >> 
> >> I try to find the values reported in the following
> paper:
> >> Journal of Alloys and Compounds 415, 31-37 (2006),
> in the
> >> table IV,
> >> the values for magnetic moments for Mn and Pd
> atoms in each
> >> magnetic configuration. I found dead magnetic
> moments for
> >> each
> >> magnetic configuration. I have several results
> with MnPd on
> >> Co substrate; with
> >> non zero magnetic moments for Mn and Pd atoms. 
> >> 
> >> Which is the problem? I attach the input files. 
> >> 
> >> 
> >> --
> >>
> -----------------------------------------------------------------
> >> Dr. Salvador MEZA AGUILAR
> >> Escuela de Ciencias Fisico-Matematicas
> >> Universidad Autonoma de Sinaloa
> >> Av. de las Americas y Blvd. Universitarios
> >> Ciudad Universitaria
> >> 80010 Culiacan Sinaloa
> >> Mexico
> >> Tel./Fax +52 6677 15 64 12 ext 114
> >> Tel./Fax +52 6677 16 11 54 ext 114
> >> e-mail: smeza at uas.uasnet.mx
> >>
> -----------------------------------------------------------------
> 
> >> 
> >> _______________________________________________
> >> 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 
> > 
>  
> 
> 
> ################################
> Derek Stewart, Ph. D.
> Scientific Computation Associate
> http://www.people.cornell.edu/pages/das248/
> 250 Duffield Hall
> Cornell Nanoscale Facility (CNF)
> Ithaca, NY 14853
> stewart (at) cnf.cornell.edu
> (607) 255-2856
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From paulatto at sissa.it  Wed Dec  3 09:32:17 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 03 Dec 2008 09:32:17 +0100
Subject: [Pw_forum] MnPd Bulk
In-Reply-To: <49357BB1.6040500@uas.uasnet.mx>
References: <49357BB1.6040500@uas.uasnet.mx>
Message-ID: <49364411.4040409@sissa.it>

Salvador Meza Aguilar ha scritto:
> Which is the problem? I attach the input files.

It is known that DFT, especially GGA, gives a (wrong) magnetic moment
for Palladium bulk. It is also true that in order to reproduce the
literature results I had to use a smearing smaller than you did (exactly
half was barely sufficient).

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

Due to budget cuts approved by Italian Minister of Finance and Italian
Minister "for" Education, University and Research this may be the last
email you receive from me.

Please send any future correspondence, possibly via pigeon, to
mr. Lorenzo Paulatto
under Roiano Railway Bridge - Pillar 2
34136, Trieste

Donations in food, coins, booze and processor time are warmly welcome.




From mambom1902 at yahoo.com  Wed Dec  3 13:59:24 2008
From: mambom1902 at yahoo.com (loc duong ding)
Date: Wed, 3 Dec 2008 04:59:24 -0800 (PST)
Subject: [Pw_forum] Error while writing to file
Message-ID: <495859.38755.qm@web38807.mail.mud.yahoo.com>

Dear all,

I try to run PWscf in Alpha E45. I got the error:

from davcio : error #??????? 10????? 
error while writing to file

This doesn't happen with another machines.

Sincerely,
---------------------------
Loc Duong Dinh
Carbon Nanotube Research Lab,
Sungkyunkwan University, Suwon, South Korean.?



      
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From paulatto at sissa.it  Wed Dec  3 14:03:55 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 03 Dec 2008 14:03:55 +0100
Subject: [Pw_forum] Error while writing to file
In-Reply-To: <495859.38755.qm@web38807.mail.mud.yahoo.com>
References: <495859.38755.qm@web38807.mail.mud.yahoo.com>
Message-ID: <493683BB.8090408@sissa.it>

loc duong ding ha scritto:
> from davcio : error #        10     
> error while writing to file

It may be: disk is full, outdir does not exist, outdir exists but is not
a directory (i.e. it is a file) or, finally, you have changed the number
changed some parameter in the input (like wf_collect, or the number of
pools) without doing a bit of cleanup in your temporary files.

regards

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

Due to budget cuts approved by Italian Minister of Finance and Italian
Minister "for" Education, University and Research this may be the last
email you receive from me.

Please send any future correspondence, possibly via pigeon, to
mr. Lorenzo Paulatto
under Roiano Railway Bridge - Pillar 2
34136, Trieste

Donations in food, coins, booze and processor time are warmly welcome.




From giannozz at democritos.it  Wed Dec  3 14:13:52 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 03 Dec 2008 14:13:52 +0100
Subject: [Pw_forum] Error while writing to file
In-Reply-To: <493683BB.8090408@sissa.it>
References: <495859.38755.qm@web38807.mail.mud.yahoo.com>
	<493683BB.8090408@sissa.it>
Message-ID: <49368610.1060505@democritos.it>

Lorenzo Paulatto wrote:

> It may be: disk is full, outdir does not exist, outdir exists but is not
> a directory (i.e. it is a file) or, finally, you have changed the number
> changed some parameter in the input (like wf_collect, or the number of
> pools) without doing a bit of cleanup in your temporary files.

it might also be related to the value of parameter DIRECT_IO_FACTOR,
used in PW/diropn.f90:

#if defined(__ALPHA)
#  define DIRECT_IO_FACTOR 2
#else
#  define DIRECT_IO_FACTOR 8
#end
   !
   ! the  record length in direct-access I/O is given by the number of
   ! real*8 words times DIRECT_IO_FACTOR (may depend on the compiler)
   !

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

From giannozz at democritos.it  Wed Dec  3 14:21:57 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 03 Dec 2008 14:21:57 +0100
Subject: [Pw_forum] "charge is wrong" error in semiconductor slab
	calculation
In-Reply-To: <681353.68805.qm@web50903.mail.re2.yahoo.com>
References: <681353.68805.qm@web50903.mail.re2.yahoo.com>
Message-ID: <493687F5.405@democritos.it>

J. J. Ramsey wrote:

> WARNING: integrated charge=    34.15000000, expected=    34.50000000

34.5 electrons? it's a metal.

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

From jjr19 at uakron.edu  Wed Dec  3 14:45:18 2008
From: jjr19 at uakron.edu (J. J. Ramsey)
Date: Wed, 3 Dec 2008 05:45:18 -0800 (PST)
Subject: [Pw_forum] "charge is wrong" error in semiconductor slab
	calculation
References: <165093.99937.qm@web65713.mail.ac4.yahoo.com>
Message-ID: <51261.30307.qm@web50902.mail.re2.yahoo.com>

----- Original Message ----

> From: Eyvaz Isaev <eyvaz_isaev at yahoo.com>
> To: J. J. Ramsey <jjr19 at uakron.edu>; pw_forum at pwscf.org
> Sent: Tuesday, December 2, 2008 3:47:11 PM
> Subject: Re: [Pw_forum] "charge is wrong" error in semiconductor slab calculation
> 
> Hi, 
> 
> I will try to repeat my own reply as it was sent only to the first address. That 
> seems to be quite strange, because I used "Reply".
> 
> >     ibrav = 8,
> >     a = 3.92232131524178,
> >     b = 3.92232131524178,
> >     c = 22.207375,
> 
> Why you use orthorhombic lattice instead of simple tetragonal (ibrav=6) as a=b?

I'll probably need to change my input file anyway to account for surface reconstructions, and in that case a probably won't equal b. It just makes the input file easier to tweak in the future.

> This problem was discussed before many times (you could search in the forum 
> archive):

I did search in the archive, but there were several answers, including possible faults in the geometry. I was a bit uncertain about which of them applied to me.

> So, you should include "occupations" and related keywords, otherwise you have a 
> semiconducting system that causes the charge deficiency due to insufficient 
> bands number.

I used these options:

    occupations = 'smearing',
    degauss = 0.05D0,

This seems to have worked.

> Please, provide your affiliation, too.

University of Akron. Oddly enough, I'm in the Civil Engineering Department, but I and the group of students with which I work are studying quantum dots and their growth.



      

From giannozz at democritos.it  Wed Dec  3 14:58:38 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 03 Dec 2008 14:58:38 +0100
Subject: [Pw_forum] smearing at zero K
In-Reply-To: <1228190095.4934b18f7d39a@www.imp.polymtl.ca>
References: <1228190095.4934b18f7d39a@www.imp.polymtl.ca>
Message-ID: <4936908E.90006@democritos.it>

Jiri Houska wrote:

> when running a wavefunction optimization for a metal
> at zero K, should the result be the same with 
> (1) occupations smearing & practically-zero degauss
 > and with (2) occupations fixed?

no, because fixed occupations means "at each k, occupy
the N lowest states", zero smearing means "occupy all
states starting from the lowest-energy ones and going
to higher energy until you get the correct number of
electrons". For a metal the latter procedure will in
general yield a different number of filled bands for
different k.

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

From wjb19 at psu.edu  Wed Dec  3 15:03:59 2008
From: wjb19 at psu.edu (WILLIAM J BROUWER)
Date: Wed, 3 Dec 2008 09:03:59 -0500
Subject: [Pw_forum] picking ref energies for GIPAW  PP's
Message-ID: <1228313039l.1192104l.0l@psu.edu>

Hi All;

I apologize if this has come up before, but could someone share some wisdom on
picking
ref energies in constructing GIPAW pseudo potentials? 

I am trying to calculate NMR electric field gradients in a variety of
materials, and while
picking orbitals and cut-off radii is fairly transparent, the energies aren't
(column 5 in &testp). 

I've been adjusting them to reproduce physical items like lattice constants, is
this a sensible
way to proceed, for instance?

thanks so much!

bill brouwer
Penn State Chem 




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From rdmeneze at yahoo.com.br  Wed Dec  3 15:38:28 2008
From: rdmeneze at yahoo.com.br (Rafael Dias Menezes)
Date: Wed, 3 Dec 2008 06:38:28 -0800 (PST)
Subject: [Pw_forum] Error while writing to file
In-Reply-To: <49368610.1060505@democritos.it>
Message-ID: <850393.59576.qm@web65713.mail.ac4.yahoo.com>

Dear Paolo Giannozzi

Your suspicion is correct. 

I'm having the same problem with quantum espresso in a alpha machine running a debian linux.

I already  trace the point that the code breaks down and I put some code to return the error message got by the fortran runtime : "Fortran runtime error: Writing more data than the record size (RECL)". That's in the file davcio.f90, the block of code is the following: 

55:  ELSE IF ( io > 0 ) THEN
56:     !
57:     WRITE( UNIT = unit, REC = nrec, IOSTAT = ios ) vect  ! rafael dias
58:     IF ( ios /= 0 ) THEN
59:  .....	 

Well, I change the #define DIRECT_IO_FACTOR to 8 and the code stop the don't break down more.


thanks, 
Rafael Dias


--- Em qua, 3/12/08, Paolo Giannozzi <xxxxxx at democritos.it> escreveu:

> De: Paolo Giannozzi <xxxxxx at democritos.it>
> ...
> it might also be related to the value of parameter
> DIRECT_IO_FACTOR,
> used in PW/diropn.f90:
> 
> #if defined(__ALPHA)
> #  define DIRECT_IO_FACTOR 2
> #else
> #  define DIRECT_IO_FACTOR 8
> #end
>    !
>    ! the  record length in direct-access I/O is given by
> the number of
>    ! real*8 words times DIRECT_IO_FACTOR (may depend on the
> compiler)
>    !
> 
> 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


      Veja quais s?o os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com

From giannozz at democritos.it  Wed Dec  3 15:40:41 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 03 Dec 2008 15:40:41 +0100
Subject: [Pw_forum] Error while writing to file
In-Reply-To: <850393.59576.qm@web65713.mail.ac4.yahoo.com>
References: <850393.59576.qm@web65713.mail.ac4.yahoo.com>
Message-ID: <49369A69.7080503@democritos.it>

Rafael Dias Menezes wrote:

> Well, I change the #define DIRECT_IO_FACTOR to 8 and
 > the code stop the don't break down more.

and ... what ???
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From jjr19 at uakron.edu  Wed Dec  3 15:49:29 2008
From: jjr19 at uakron.edu (J. J. Ramsey)
Date: Wed, 3 Dec 2008 06:49:29 -0800 (PST)
Subject: [Pw_forum] "charge is wrong" error in semiconductor slab
	calculation
References: <681353.68805.qm@web50903.mail.re2.yahoo.com>
	<493687F5.405@democritos.it>
Message-ID: <205208.12195.qm@web50907.mail.re2.yahoo.com>

----- Original Message ----

> From: Paolo Giannozzi <giannozz at democritos.it>
> To: J. J. Ramsey <jjr19 at uakron.edu>; PWSCF Forum <pw_forum at pwscf.org>
> Sent: Wednesday, December 3, 2008 8:21:57 AM
> Subject: Re: [Pw_forum] "charge is wrong" error in semiconductor slab calculation
> 
> J. J. Ramsey wrote:
> 
> > WARNING: integrated charge=    34.15000000, expected=    34.50000000
> 
> 34.5 electrons? it's a metal.

Interesting. Without the pseudohydrogens, there are only 32 (valence) electrons.



      

From giannozz at democritos.it  Wed Dec  3 16:04:04 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 03 Dec 2008 16:04:04 +0100
Subject: [Pw_forum] "charge is wrong" error in semiconductor
	slab	calculation
In-Reply-To: <205208.12195.qm@web50907.mail.re2.yahoo.com>
References: <681353.68805.qm@web50903.mail.re2.yahoo.com>	<493687F5.405@democritos.it>
	<205208.12195.qm@web50907.mail.re2.yahoo.com>
Message-ID: <49369FE4.50007@democritos.it>

J. J. Ramsey wrote:

> Interesting. Without the pseudohydrogens, there are only 32 (valence) electrons.

since the pseudohydrogens have charge 1.25, you get by default
32+2*1.25=34.5 electrons. If you want a different number of
electrons, you have to specify it in variable "nelec"

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

From eyvaz_isaev at yahoo.com  Wed Dec  3 16:33:21 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Wed, 3 Dec 2008 07:33:21 -0800 (PST)
Subject: [Pw_forum] "charge is wrong" error in semiconductor slab
	calculation
In-Reply-To: <205208.12195.qm@web50907.mail.re2.yahoo.com>
Message-ID: <632082.77590.qm@web65711.mail.ac4.yahoo.com>

Hi, 

The simplest way is looking at scf-output file, find a line like this

number of electrons = 26.00

and then you could ask yourself why I have 34.5 electrons.

So, checking (reading) your output file is a good idea, anyway.

Bests,
Eyvaz.  

--- On Wed, 12/3/08, J. J. Ramsey <jjr19 at uakron.edu> wrote:
> > > WARNING: integrated charge=    34.15000000,
> expected=    34.50000000
> > 
> > 34.5 electrons? it's a metal.
> 
> Interesting. Without the pseudohydrogens, there are only 32
> (valence) electrons.
> 
> 
> 
>       
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From jjr19 at uakron.edu  Wed Dec  3 17:02:47 2008
From: jjr19 at uakron.edu (J. J. Ramsey)
Date: Wed, 3 Dec 2008 08:02:47 -0800 (PST)
Subject: [Pw_forum] "charge is wrong" error in semiconductor slab
	calculation
References: <632082.77590.qm@web65711.mail.ac4.yahoo.com>
Message-ID: <795126.3150.qm@web50905.mail.re2.yahoo.com>

----- Original Message ----

> From: Eyvaz Isaev <eyvaz_isaev at yahoo.com>
> To: PWSCF Forum <pw_forum at pwscf.org>
> Sent: Wednesday, December 3, 2008 10:33:21 AM
> Subject: Re: [Pw_forum] "charge is wrong" error in semiconductor slab calculation
> 
> Hi, 
> 
> The simplest way is looking at scf-output file, find a line like this
> 
> number of electrons = 26.00
> 
> and then you could ask yourself why I have 34.5 electrons.

The output file reads

number of electrons       =        34.50

so I'm fine there. Each Ga and In atom contributes 3 electrons, each As atom contributes 5, and each pseudohydrogen contributes 1.25, and if you do the math, you get 34.5 electrons. My main concern is that I'm doing something naive with the pseudohydrogens.



      

From marcello.rosini at unimore.it  Thu Dec  4 09:04:09 2008
From: marcello.rosini at unimore.it (Marcello Rosini)
Date: Thu, 04 Dec 2008 09:04:09 +0100
Subject: [Pw_forum] "charge is wrong" error in semiconductor slab
	calculation
In-Reply-To: <mailman.1.1228376793.27176.pw_forum@pwscf.org>
References: <mailman.1.1228376793.27176.pw_forum@pwscf.org>
Message-ID: <49378EF9.7090404@unimore.it>

The problem is that the bottom surface should mimic the infinite bulk 
and saturating with pseudoH is the best way to achieve this purpose.
I suggest you to saturate also the top surface with pseudoH, this will 
made the system recover the right number of electrons.
Marcello

pw_forum-request at pwscf.org wrote:
> Today's Topics:
>
>    1. Re: "charge is wrong" error in semiconductor slab	calculation
>       (J. J. Ramsey)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 3 Dec 2008 08:02:47 -0800 (PST)
> From: "J. J. Ramsey" <jjr19 at uakron.edu>
> Subject: Re: [Pw_forum] "charge is wrong" error in semiconductor slab
> 	calculation
> To: pw_forum at pwscf.org
> Message-ID: <795126.3150.qm at web50905.mail.re2.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
>
> ----- Original Message ----
>
>   
>> From: Eyvaz Isaev <eyvaz_isaev at yahoo.com>
>> To: PWSCF Forum <pw_forum at pwscf.org>
>> Sent: Wednesday, December 3, 2008 10:33:21 AM
>> Subject: Re: [Pw_forum] "charge is wrong" error in semiconductor slab calculation
>>
>> Hi, 
>>
>> The simplest way is looking at scf-output file, find a line like this
>>
>> number of electrons = 26.00
>>
>> and then you could ask yourself why I have 34.5 electrons.
>>     
>
> The output file reads
>
> number of electrons       =        34.50
>
> so I'm fine there. Each Ga and In atom contributes 3 electrons, each As atom contributes 5, and each pseudohydrogen contributes 1.25, and if you do the math, you get 34.5 electrons. My main concern is that I'm doing something naive with the pseudohydrogens.
>
>
>
>       
>
>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 18, Issue 6
> ***************************************
>   

From valeryweber at hotmail.com  Thu Dec  4 15:10:26 2008
From: valeryweber at hotmail.com (Valery Weber)
Date: Thu, 4 Dec 2008 14:10:26 +0000
Subject: [Pw_forum]  pseudo files for gipaw
In-Reply-To: <49378EF9.7090404@unimore.it>
References: <mailman.1.1228376793.27176.pw_forum@pwscf.org>
	<49378EF9.7090404@unimore.it>
Message-ID: <BAY124-W160EE6BDB64077525261A0BD020@phx.gbl>


Dear All

I would like to ask if some one of you would kindly send me
the pseudo files used by gipaw for the H, C, N and O atoms 
(the X.pbe-tm-gipaw.UPF or X.blyp-tm-gipaw.UPF would be perfect).

Scincerly,

Valery Weber
Institut of Physical Chemistry 
University of Zuirch



_________________________________________________________________
D?couvrez la nouvelle g?n?ration des servives de Windows Live
http://get.live.com
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From jjr19 at uakron.edu  Thu Dec  4 15:16:01 2008
From: jjr19 at uakron.edu (J. J. Ramsey)
Date: Thu, 4 Dec 2008 06:16:01 -0800 (PST)
Subject: [Pw_forum] "charge is wrong" error in semiconductor slab
	calculation
References: <mailman.1.1228376793.27176.pw_forum@pwscf.org>
	<49378EF9.7090404@unimore.it>
Message-ID: <603519.67193.qm@web50904.mail.re2.yahoo.com>

----- Original Message ----

> From: Marcello Rosini <marcello.rosini at unimore.it>
> To: pw_forum at pwscf.org
> Sent: Thursday, December 4, 2008 3:04:09 AM
> Subject: Re: [Pw_forum] "charge is wrong" error in semiconductor slab calculation
> 
> The problem is that the bottom surface should mimic the infinite bulk 
> and saturating with pseudoH is the best way to achieve this purpose.
> I suggest you to saturate also the top surface with pseudoH, this will 
> made the system recover the right number of electrons.

I think I'm OK with having a fractional number of electrons, so long as that is a normal outcome of using pseudohydrogens for passivation. I think I understand now what you meant in your article [Phys. Rev. B 77, 165323 (2008)] about the smearing of 0.02 Ry to account for metallization.

BTW, when you made your pseudopotential for pseudohydrogen, did it have any projectors at all, or did you let the maximum angular momentum be zero?



      

From ceresoli at MIT.EDU  Thu Dec  4 22:41:18 2008
From: ceresoli at MIT.EDU (Davide Ceresoli)
Date: Thu, 4 Dec 2008 16:41:18 -0500 (EST)
Subject: [Pw_forum] pseudo files for gipaw
In-Reply-To: <BAY124-W160EE6BDB64077525261A0BD020@phx.gbl>
References: <mailman.1.1228376793.27176.pw_forum@pwscf.org>
	<49378EF9.7090404@unimore.it>
	<BAY124-W160EE6BDB64077525261A0BD020@phx.gbl>
Message-ID: <Pine.LNX.4.64L.0812041639270.24940@vinegar-pot.mit.edu>

On Thu, 4 Dec 2008, Valery Weber wrote:

>
> Dear All
>
> I would like to ask if some one of you would kindly send me
> the pseudo files used by gipaw for the H, C, N and O atoms
> (the X.pbe-tm-gipaw.UPF or X.blyp-tm-gipaw.UPF would be perfect).
>
> Scincerly,
>
> Valery Weber
> Institut of Physical Chemistry
> University of Zuirch
>
>
Ari Seitsonen kindly generated some GIPAW pseudopotentials.
You can find them at:

     http://www.impmc.jussieu.fr/~software/gipaw/

Davide


+----------------------------------------------------------+
   Davide Ceresoli <ceresoli at mit.edu>
   DMSE 13-4084
   Massachusetts Institute of Technology
   77 Massachusetts Avenue
   Cambridge, MA 02139-4307
   Phone: (617) 253-6026
   Mobile: +39-347-1001570
   Skype: dceresoli
+----------------------------------------------------------+

From willykohn at gmail.com  Fri Dec  5 16:29:34 2008
From: willykohn at gmail.com (willy kohn)
Date: Fri, 5 Dec 2008 10:29:34 -0500
Subject: [Pw_forum] Strange things when calculating bands using pw.x
Message-ID: <8a1b6d820812050729v30c5ecf1nf3cf75ea81d61aba@mail.gmail.com>

Hi, PWSCF users

I met a strange thing when I used pw.x (v 4.0.2) calculating bands of
rutile. When the nbnd is set over 100, the program stuck in some k-points
indefinitely. The program didn't give any error messages but just stopped
response. I'm wondering if somebody has similar experiences and can tell
what happend. The other parameters are as follows:

&control
    calculation = 'bands'
    prefix = 'Rutile'
    pseudo_dir = "./"
    outdir = "./"
    verbosity='high'
    wf_collect=.true.
/
&system
    ibrav=  6,
    celldm(1) = 8.68065, celldm(3) = 0.64409,
    nat=  6, ntyp = 2,
    ecutwfc =80.0, nbnd=160
    nr1=50,nr2=50,nr3=32
/
&electrons
    diagonalization = 'cg'
    mixing_mode = 'plain'
    mixing_beta = 0.7
/
ATOMIC_SPECIES
 Ti  47.867   22-Ti.LDA.fhi.UPF
 O   15.9994  08-O.LDA.fhi.UPF
ATOMIC_POSITIONS crystal
 Ti 0.0000 0.0000 0.0000
 Ti 0.5000 0.5000 0.5000
 O  0.3048 0.3048 0.0000
 O  0.6952 0.6952 0.0000
 O  0.8048 0.1952 0.5000
 O  0.1952 0.8048 0.5000
K_POINTS crystal
  288


Best,

Wei
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From giannozz at democritos.it  Fri Dec  5 16:35:35 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 05 Dec 2008 16:35:35 +0100
Subject: [Pw_forum] Strange things when calculating bands using pw.x
In-Reply-To: <8a1b6d820812050729v30c5ecf1nf3cf75ea81d61aba@mail.gmail.com>
References: <8a1b6d820812050729v30c5ecf1nf3cf75ea81d61aba@mail.gmail.com>
Message-ID: <49394A47.9070707@democritos.it>

willy kohn wrote:

> When the nbnd is set over 100, the program stuck in some 
> k-points indefinitely. The program didn't give any error  
> messages but just stopped response. I'm wondering if somebody 
> has similar experiences and can tell what happend.

on the basis of such a vague description, all one can say is
what is written in the "troubleshooting" section of the user
guide, under "pw.x runs but nothing happens"

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

From willykohn at gmail.com  Fri Dec  5 16:51:54 2008
From: willykohn at gmail.com (willy kohn)
Date: Fri, 5 Dec 2008 10:51:54 -0500
Subject: [Pw_forum] Strange things when calculating bands using pw.x
In-Reply-To: <49394A47.9070707@democritos.it>
References: <8a1b6d820812050729v30c5ecf1nf3cf75ea81d61aba@mail.gmail.com>
	<49394A47.9070707@democritos.it>
Message-ID: <8a1b6d820812050751r58ee405ema1d64ef074255e89@mail.gmail.com>

Hi Paolo:

Thanks a lot for the reply. I tried my best to describe the problem at the
time I wrote the email and I'm still trying to pin down this problem. I just
checked the user's guide and I can add something more in the description. It
happened in both parallel and serial versions with both pgf and gfortran
compilers. Older versions like (3.x.x) could also have the same problem.

Best,

Wei

On Fri, Dec 5, 2008 at 10:35 AM, Paolo Giannozzi <giannozz at democritos.it>wrote:

> willy kohn wrote:
>
> > When the nbnd is set over 100, the program stuck in some
> > k-points indefinitely. The program didn't give any error
> > messages but just stopped response. I'm wondering if somebody
> > has similar experiences and can tell what happend.
>
> on the basis of such a vague description, all one can say is
> what is written in the "troubleshooting" section of the user
> guide, under "pw.x runs but nothing happens"
>
> Paolo
> --
> 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 matteo at umn.edu  Fri Dec  5 16:56:00 2008
From: matteo at umn.edu (Matteo Cococcioni)
Date: Fri, 05 Dec 2008 09:56:00 -0600
Subject: [Pw_forum] resp_mat.f90
Message-ID: <49394F10.4040506@umn.edu>

Dear all,

I have recently realized that the code resp_mat.f90, contained in some 
tutorials on LDA+U calculations (e.g.,
from http://vlab.msi.umn.edu/events/lecture.shtml) and used to compute 
U, has some problems and doesn't work as expected.
I have realized this on a hexagonal system but I'm not sure yet if the 
problem manifests itself also with other crystal structures.

Hoping that not many people were using it I apologize for the 
inconvenient. I also hope to provide a fix in short time.

regards,

Matteo
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From chenweiguang82 at gmail.com  Sat Dec  6 00:57:35 2008
From: chenweiguang82 at gmail.com (Weiguang Chen)
Date: Sat, 6 Dec 2008 07:57:35 +0800
Subject: [Pw_forum] Scf can converge, But Band can not converge
Message-ID: <9e6d976a0812051557r76216d33m65b3fd9c2454b8df@mail.gmail.com>

Hi,
I am a pwscf newbie, i want to get a band structure. Firstly, i have done
the scf calculation,and it can be converged well, but the next step band
calculation, the following information show:
     Band Structure Calculation
     Davidson diagonalization with overlap
     c_bands:  1 eigenvalues not converged
     c_bands:  1 eigenvalues not converged
     c_bands:  1 eigenvalues not converged
     c_bands:  1 eigenvalues not converged
     c_bands:  1 eigenvalues not converged
     c_bands:  1 eigenvalues not converged
     c_bands:  1 eigenvalues not converged
     c_bands:  1 eigenvalues not converged
     c_bands:  1 eigenvalues not converged
     c_bands:  1 eigenvalues not converged
     c_bands:  1 eigenvalues not converged
     c_bands:  1 eigenvalues not converged
     c_bands:  1 eigenvalues not converged
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from davcio : error #        10
     error while reading from file
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

What's the probably problem?How can i do?
Thanks
-- 
Best Wishes
ChenWeiguang
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From ykhuang0731 at gmail.com  Sat Dec  6 07:03:28 2008
From: ykhuang0731 at gmail.com (Yi-Kai Huang)
Date: Sat, 6 Dec 2008 14:03:28 +0800
Subject: [Pw_forum] About band diagram calculation
Message-ID: <2643f0f10812052203p328feb37re83d9fdd872b2018@mail.gmail.com>

Dear all,

I am new to the computation world, and recently I start to calculate
band diagram.
However I have a question, how to know which specific k points
(symmetry points) I should use for some special structures?
Like if I have a rutile or perovskite structure material.

Thanks for the help!

Yi-Kai

From ammar112 at yahoo.com  Sat Dec  6 09:09:54 2008
From: ammar112 at yahoo.com (benamrani ammar)
Date: Sat, 6 Dec 2008 00:09:54 -0800 (PST)
Subject: [Pw_forum] high symmetry points
In-Reply-To: <2643f0f10812052203p328feb37re83d9fdd872b2018@mail.gmail.com>
Message-ID: <582522.83862.qm@web51605.mail.re2.yahoo.com>

Dear Sir...

for plotting band structure for such structure you can first calculate band structure at such special points (we call them high symmetry points).
for your specific points please refer to this useful website: http://www.cryst.ehu.es/
in space group table click on KVEC and then enter the number of your structure for example 225 for FCC OR 221 FOR bcc...PEROVISKE I don't know?.
my greetings
Mr Benamrani Ammar
Optoelectronic Lab.
?S?tif UNiversity
Algeria



      
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From lzh-ming at 163.com  Sat Dec  6 11:37:41 2008
From: lzh-ming at 163.com (lzh-ming)
Date: Sat, 6 Dec 2008 18:37:41 +0800 (CST)
Subject: [Pw_forum] How can I remove the dots on the lines in the band
 structure pictures created by plotband.x?
Message-ID: <12801637.859511228559861417.JavaMail.coremail@bj163app77.163.com>

  
Hello,everyone,
    I have plotted a band structure picture, using plotband.x. But I want to remove the dots on the lines, how can I make it? These dots correspond to the k-points I used for calculations.
    Thanks very much!
 Bests,
li-ming-fan
 
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From eyvaz_isaev at yahoo.com  Sat Dec  6 19:12:31 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sat, 6 Dec 2008 10:12:31 -0800 (PST)
Subject: [Pw_forum] Scf can converge, But Band can not converge
In-Reply-To: <9e6d976a0812051557r76216d33m65b3fd9c2454b8df@mail.gmail.com>
Message-ID: <657313.23077.qm@web65702.mail.ac4.yahoo.com>

Dear Weiguang,

--- On Sat, 12/6/08, Weiguang Chen <chenweiguang82 at gmail.com> wrote:

Actually, there are 2 issues from your question.

1. 
>      c_bands:  1 eigenvalues not converged

This one is harmless, and it is not connected with the message you obtained. For this one please read Users Guide, Troubleshooting.

2. 
>      from davcio : error #        10
>      error while reading from file

As you can see the program  tells you that something is wrong with inut/output files, as corrupted files, full disk. etc. 
So, you can restart your job. If the error still exists, check whether your hard disk is full or you do not share a filname.

Please provide your affiliation.

Bests,
Eyvaz.

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


- 


      

From eyvaz_isaev at yahoo.com  Sat Dec  6 20:53:55 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sat, 6 Dec 2008 11:53:55 -0800 (PST)
Subject: [Pw_forum] About band diagram calculation
In-Reply-To: <2643f0f10812052203p328feb37re83d9fdd872b2018@mail.gmail.com>
Message-ID: <487621.66639.qm@web65708.mail.ac4.yahoo.com>

Dear Yi-Kai,

--- On Sat, 12/6/08, Yi-Kai Huang <ykhuang0731 at gmail.com> wrote:
> 
> I am new to the computation world

Welcome!

> However I have a question, how to know which specific k-points
> (symmetry points) I should use for some special structures?
> Like if I have a rutile or perovskite structure material.
> 

Well, surfing on Bilbao Crystallographic Server is a good idea, as it was suggested. 
Nevertheless, I suggest first you should read some textbooks before (at least, after) doing such kind calculations. The reason is that you should know what is the reciprocal lattice, Brillouin zone, high symmetry points, high symmetry directions, etc. etc.
I can not remember all textbooks in this fields, but there are few very famous and it is worth reading at least one of them.
1. Aschroft & Mermin, Solid State Physics,
2. C. Kittel, Introduction to Solid State Physics
3. Richard Martin, Electronic Structure: Basic Theory and Practical Methods 
4. J. Kohanoff, Electronic Structure calculations for Solids and Molecules 
5. J.Callaway, Energy bands theory
6. H.Jones, Theory of Brilloiun zones and Electronic states in Crystals  
Etc. etc. etc.

Happy reading!

By the way, provide your affiliation if you wish to be answered.
 
Bests,
Eyvaz.

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




> From: Yi-Kai Huang <ykhuang0731 at gmail.com>
> Subject: [Pw_forum] About band diagram calculation
> To: pw_forum at pwscf.org
> Date: Saturday, December 6, 2008, 9:03 AM
> Dear all,
, and recently I start to
> calculate
> band diagram.

> Thanks for the help!
>
> Yi-Kai
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From materialsman at gmail.com  Sat Dec  6 23:48:45 2008
From: materialsman at gmail.com (Alexander Adler)
Date: Sat, 6 Dec 2008 16:48:45 -0600
Subject: [Pw_forum] Band Structure Diagram Error (In2O3)
Message-ID: <173DF02B-5F06-4DD0-B648-175D531EF5E8@gmail.com>

Hello everyone,

I am trying to calculate the band structure for In2O3 (Bixbyite  
structure, Ia-3) using PWSCF.

I am familiar with the examples for Carbon and Silicon and have run  
them successfully; however, this one is giving me trouble. I run the  
self-consistent input first as usual for automatic generation of k- 
points (4x4x4). Then, I run the .nscf calculation and attempt to  
sample the high-symmetry bands:
H: 0.5, -0.5, 0.5
N: 0.25, 0.25, 0.25
P: 0, 0, 0.5

However, I run into the error:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
%%%%%%%
     task #         0
     from d_&_i : error #         1
      some nodes have no k-points
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
%%%%%%%

After extensive searching and manipulation of how the k-points are  
sampled, I cannot determine what is going wrong.

Any advice, links, or suggestions would be greatly appreciated. Thanks  
in advance.

Alexander Adler
Department of Materials Science
Northwestern University
materialsman at gmail.com
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From eyvaz_isaev at yahoo.com  Sun Dec  7 00:18:20 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sat, 6 Dec 2008 15:18:20 -0800 (PST)
Subject: [Pw_forum] Band Structure Diagram Error (In2O3)
In-Reply-To: <173DF02B-5F06-4DD0-B648-175D531EF5E8@gmail.com>
Message-ID: <45286.24997.qm@web65714.mail.ac4.yahoo.com>

Dear Alexander,

I can suggest that you ask a large amount of CPUs. Try reducing 
CPU number.

Bests,
Eyvaz.

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


--- On Sun, 12/7/08, Alexander Adler <materialsman at gmail.com> wrote:

> From: Alexander Adler <materialsman at gmail.com>
> Subject: [Pw_forum] Band Structure Diagram Error (In2O3)
> To: pw_forum at pwscf.org
> Date: Sunday, December 7, 2008, 1:48 AM
> Hello everyone,
> 
> I am trying to calculate the band structure for In2O3
> (Bixbyite structure, Ia-3) using PWSCF.
> 
> I am familiar with the examples for Carbon and Silicon and
> have run them successfully; however, this one is giving me
> trouble. I run the self-consistent input first as usual for
> automatic generation of k-points (4x4x4). Then, I run the
> .nscf calculation and attempt to sample the high-symmetry
> bands:
> H: 0.5, -0.5, 0.5
> N: 0.25, 0.25, 0.25
> P: 0, 0, 0.5
> 
> However, I run into the error:
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     task #         0
>     from d_&_i : error #         1
>      some nodes have no k-points
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
> After extensive searching and manipulation of how the
> k-points are sampled, I cannot determine what is going
> wrong.
> 
> Any advice, links, or suggestions would be greatly
> appreciated. Thanks in advance.
> 
> Alexander Adler
> Department of Materials Science
> Northwestern University
> materialsman at gmail.com_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From wangqj1 at 126.com  Sun Dec  7 07:39:49 2008
From: wangqj1 at 126.com (wangqj1)
Date: Sun, 7 Dec 2008 14:39:49 +0800 (CST)
Subject: [Pw_forum] chdens.x
Message-ID: <14185800.96571228631989057.JavaMail.coremail@bj126app29.126.com>

 Dear all
      I  want to know how to plot the charge or spin density for different orbitals, like 3d, 4s. As the chdens.x can only plots the total charge or spin density. Any advice will be appreciated !
      Best wishes !
Q J Wang

 
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From quantumdft at gmail.com  Sun Dec  7 09:40:01 2008
From: quantumdft at gmail.com (vega lew)
Date: Sun, 7 Dec 2008 16:40:01 +0800
Subject: [Pw_forum] Scf can converge, But Band can not converge
In-Reply-To: <657313.23077.qm@web65702.mail.ac4.yahoo.com>
References: <9e6d976a0812051557r76216d33m65b3fd9c2454b8df@mail.gmail.com>
	<657313.23077.qm@web65702.mail.ac4.yahoo.com>
Message-ID: <412f6c680812070040i29ac519ua5982a91cde4253f@mail.gmail.com>

>      from davcio : error #        10
>      error while reading from file

I used to encounter this problem during the nscf calculation. I solve the
problem by adding the " wf_collect=.true." in the scf input file. Then make
sure the prefix and outdir the same as the scf during the nscf calculations.

hope helps

vega

On Sun, Dec 7, 2008 at 2:12 AM, Eyvaz Isaev <eyvaz_isaev at yahoo.com> wrote:

> Dear Weiguang,
>
> --- On Sat, 12/6/08, Weiguang Chen <chenweiguang82 at gmail.com> wrote:
>
> Actually, there are 2 issues from your question.
>
> 1.
> >      c_bands:  1 eigenvalues not converged
>
> This one is harmless, and it is not connected with the message you
> obtained. For this one please read Users Guide, Troubleshooting.
>
> 2.
> >      from davcio : error #        10
> >      error while reading from file
>
> As you can see the program  tells you that something is wrong with
> inut/output files, as corrupted files, full disk. etc.
> So, you can restart your job. If the error still exists, check whether your
> hard disk is full or you do not share a filname.
>
> Please provide your affiliation.
>
> Bests,
> Eyvaz.
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
> Russia,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
> Sweden
> Condensed Matter Theory Group, Uppsala University, Sweden
> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
> -
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
==================================================================================
Vega Lew ( weijia liu)
PH.D Candidate 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: vegalew at gmail.com
Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing,
Jiangsu, China
******************************************************************************************************************
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From giannozz at democritos.it  Sun Dec  7 09:51:56 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 7 Dec 2008 09:51:56 +0100
Subject: [Pw_forum] Band Structure Diagram Error (In2O3)
In-Reply-To: <173DF02B-5F06-4DD0-B648-175D531EF5E8@gmail.com>
References: <173DF02B-5F06-4DD0-B648-175D531EF5E8@gmail.com>
Message-ID: <B66FE4FE-2739-4F4A-8FA3-959C8DD7A8E9@democritos.it>


On Dec 6, 2008, at 23:48 , Alexander Adler wrote:

>     from d_&_i : error #         1
>      some nodes have no k-points

you are using more pools than k-points

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



From giannozz at democritos.it  Sun Dec  7 09:53:51 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 7 Dec 2008 09:53:51 +0100
Subject: [Pw_forum] chdens.x
In-Reply-To: <14185800.96571228631989057.JavaMail.coremail@bj126app29.126.com>
References: <14185800.96571228631989057.JavaMail.coremail@bj126app29.126.com>
Message-ID: <6031A6B3-0E21-411F-9E3D-6C7D58660151@democritos.it>


On Dec 7, 2008, at 7:39 , wangqj1 wrote:

> I  want to know how to plot the charge or spin density for  
> different orbitals, like 3d, 4s.

there are a number of options for the quantity to be plotted. These  
are selected using
the variable "plot_num". See INPUT_PP.*

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


From lanhaiping at gmail.com  Sun Dec  7 10:33:30 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Sun, 7 Dec 2008 17:33:30 +0800
Subject: [Pw_forum] chdens.x
In-Reply-To: <14185800.96571228631989057.JavaMail.coremail@bj126app29.126.com>
References: <14185800.96571228631989057.JavaMail.coremail@bj126app29.126.com>
Message-ID: <c92002fa0812070133l5ad0a89ke38855e82c1f5210@mail.gmail.com>

these are wavefunctions ..

2008/12/7 wangqj1 <wangqj1 at 126.com>

>  Dear all
>       I  want to know how to plot the charge or spin density for different
> orbitals, like 3d, 4s. As the chdens.x can only plots the total charge or
> spin density. Any advice will be appreciated !
>       Best wishes !
> Q J Wang
>
>
>
>
> ------------------------------
> ????????????????? <http://www.yeah.net>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From chenweiguang82 at gmail.com  Sun Dec  7 11:56:14 2008
From: chenweiguang82 at gmail.com (Weiguang Chen)
Date: Sun, 7 Dec 2008 18:56:14 +0800
Subject: [Pw_forum] Scf can converge, But Band can not converge
In-Reply-To: <412f6c680812070040i29ac519ua5982a91cde4253f@mail.gmail.com>
References: <9e6d976a0812051557r76216d33m65b3fd9c2454b8df@mail.gmail.com>
	<657313.23077.qm@web65702.mail.ac4.yahoo.com>
	<412f6c680812070040i29ac519ua5982a91cde4253f@mail.gmail.com>
Message-ID: <9e6d976a0812070256y24cd0366g5511c631d3d37bde@mail.gmail.com>

Thank you all.
 I have fixed the problem by restarting it completely( create a new
fold) . I guess the temp files are changed in nscf running when I stop
the calculation manually. So PWscf can not find the complete temp
files when I run nscf again.

ChenWeiguang

On Sun, Dec 7, 2008 at 4:40 PM, vega lew <quantumdft at gmail.com> wrote:
>
> >      from davcio : error #        10
> >      error while reading from file
>
> I used to encounter this problem during the nscf calculation. I solve the problem by adding the " wf_collect=.true." in the scf input file. Then make sure the prefix and outdir the same as the scf during the nscf calculations.
>
> hope helps
>
> vega
>
> On Sun, Dec 7, 2008 at 2:12 AM, Eyvaz Isaev <eyvaz_isaev at yahoo.com> wrote:
>>
>> Dear Weiguang,
>>
>> --- On Sat, 12/6/08, Weiguang Chen <chenweiguang82 at gmail.com> wrote:
>>
>> Actually, there are 2 issues from your question.
>>
>> 1.
>> >      c_bands:  1 eigenvalues not converged
>>
>> This one is harmless, and it is not connected with the message you obtained. For this one please read Users Guide, Troubleshooting.
>>
>> 2.
>> >      from davcio : error #        10
>> >      error while reading from file
>>
>> As you can see the program  tells you that something is wrong with inut/output files, as corrupted files, full disk. etc.
>> So, you can restart your job. If the error still exists, check whether your hard disk is full or you do not share a filname.
>>
>> Please provide your affiliation.
>>
>> Bests,
>> Eyvaz.
>>
>> -------------------------------------------------------------------
>> Prof. Eyvaz Isaev,
>> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
>> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden
>> Condensed Matter Theory Group, Uppsala University, Sweden
>> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>>
>>
>> -
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> --
> ==================================================================================
> Vega Lew ( weijia liu)
> PH.D Candidate 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: vegalew 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
>



--
Best Wishes
ChenWeiguang

From materialsman at gmail.com  Sun Dec  7 12:03:34 2008
From: materialsman at gmail.com (Alexander Adler)
Date: Sun, 7 Dec 2008 05:03:34 -0600
Subject: [Pw_forum] Band Structure Diagram Error (In2O3)
Message-ID: <B67B5C87-F352-4622-88EF-02234D01A4A8@gmail.com>


Hello,

I hope I am responding to the digest properly. Please feel free to  
correct me if I'm mistaken.

The odd thing about the band structure diagram error is that I get the  
error even when running on a single processor.

Any thoughts here?

-Alexander Adler
Northwestern University - - Materials Science and Engineering Department



Begin forwarded message:
> Message: 6
> Date: Sat, 6 Dec 2008 15:18:20 -0800 (PST)
> From: Eyvaz Isaev <eyvaz_isaev at yahoo.com>
> Subject: Re: [Pw_forum] Band Structure Diagram Error (In2O3)
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <45286.24997.qm at web65714.mail.ac4.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Alexander,
>
> I can suggest that you ask a large amount of CPUs. Try reducing
> CPU number.
>
> Bests,
> Eyvaz.
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Theoretical Physics Department, Moscow State Institute of Steel &  
> Alloys, Russia,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping  
> University, Sweden
> Condensed Matter Theory Group, Uppsala University, Sweden
> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
> --- On Sun, 12/7/08, Alexander Adler <materialsman at gmail.com> wrote:
>
>> From: Alexander Adler <materialsman at gmail.com>
>> Subject: [Pw_forum] Band Structure Diagram Error (In2O3)
>> To: pw_forum at pwscf.org
>> Date: Sunday, December 7, 2008, 1:48 AM
>> Hello everyone,
>>
>> I am trying to calculate the band structure for In2O3
>> (Bixbyite structure, Ia-3) using PWSCF.
>>
>> I am familiar with the examples for Carbon and Silicon and
>> have run them successfully; however, this one is giving me
>> trouble. I run the self-consistent input first as usual for
>> automatic generation of k-points (4x4x4). Then, I run the
>> .nscf calculation and attempt to sample the high-symmetry
>> bands:
>> H: 0.5, -0.5, 0.5
>> N: 0.25, 0.25, 0.25
>> P: 0, 0, 0.5
>>
>> However, I run into the error:
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
>> %%%%%%%%%%
>>    task #         0
>>    from d_&_i : error #         1
>>     some nodes have no k-points
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
>> %%%%%%%%%%
>>
>> After extensive searching and manipulation of how the
>> k-points are sampled, I cannot determine what is going
>> wrong.
>>
>> Any advice, links, or suggestions would be greatly
>> appreciated. Thanks in advance.
>>
>> Alexander Adler
>> Department of Materials Science
>> Northwestern University
>> materialsman at gmail.com_______________________________________________
>
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From akohlmey at cmm.chem.upenn.edu  Sun Dec  7 13:07:45 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sun, 7 Dec 2008 13:07:45 +0100
Subject: [Pw_forum] Band Structure Diagram Error (In2O3)
In-Reply-To: <B67B5C87-F352-4622-88EF-02234D01A4A8@gmail.com>
References: <B67B5C87-F352-4622-88EF-02234D01A4A8@gmail.com>
Message-ID: <7b6913e90812070407x41521dd0q6aa8ceaa27aa754d@mail.gmail.com>

On 12/7/08, Alexander Adler <materialsman at gmail.com> wrote:
>
> Hello,


hello alexander,

> I hope I am responding to the digest properly. Please feel free to
> correct me if I'm mistaken.
>
> The odd thing about the band structure diagram error is that I get the
> error even when running on a single processor.
>
> Any thoughts here?

please provide information on how to reproduce this
and the parameters of your compile.
i.e. compiler version, cpu type, OS version and architecture.
Q-E version, how compiled. command lines, inputs.

there are three possible reasons,
you are using the code in a way that is incorrect
or not supported, there is a problem with your
compilation, or there is a bug in the code.

cheers,
    axel.
>
> -Alexander Adler
> Northwestern University - - Materials Science and Engineering Department
>
>


-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From lanhaiping at gmail.com  Sun Dec  7 14:22:16 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Sun, 7 Dec 2008 21:22:16 +0800
Subject: [Pw_forum] Scf can converge, But Band can not converge
In-Reply-To: <9e6d976a0812070256y24cd0366g5511c631d3d37bde@mail.gmail.com>
References: <9e6d976a0812051557r76216d33m65b3fd9c2454b8df@mail.gmail.com>
	<657313.23077.qm@web65702.mail.ac4.yahoo.com>
	<412f6c680812070040i29ac519ua5982a91cde4253f@mail.gmail.com>
	<9e6d976a0812070256y24cd0366g5511c631d3d37bde@mail.gmail.com>
Message-ID: <c92002fa0812070522m7c61c185m299b02ee3303854b@mail.gmail.com>

Hi,
you can make confirmation of your guess by checking
the outdir you set in the input file.
And please  give your affiliation.

regards,

On Sun, Dec 7, 2008 at 6:56 PM, Weiguang Chen <chenweiguang82 at gmail.com>wrote:

> Thank you all.
>  I have fixed the problem by restarting it completely( create a new
> fold) . I guess the temp files are changed in nscf running when I stop
> the calculation manually. So PWscf can not find the complete temp
> files when I run nscf again.
>
> ChenWeiguang
>
> On Sun, Dec 7, 2008 at 4:40 PM, vega lew <quantumdft at gmail.com> wrote:
> >
> > >      from davcio : error #        10
> > >      error while reading from file
> >
> > I used to encounter this problem during the nscf calculation. I solve the
> problem by adding the " wf_collect=.true." in the scf input file. Then make
> sure the prefix and outdir the same as the scf during the nscf calculations.
> >
> > hope helps
> >
> > vega
> >
> > On Sun, Dec 7, 2008 at 2:12 AM, Eyvaz Isaev <eyvaz_isaev at yahoo.com>
> wrote:
> >>
> >> Dear Weiguang,
> >>
> >> --- On Sat, 12/6/08, Weiguang Chen <chenweiguang82 at gmail.com> wrote:
> >>
> >> Actually, there are 2 issues from your question.
> >>
> >> 1.
> >> >      c_bands:  1 eigenvalues not converged
> >>
> >> This one is harmless, and it is not connected with the message you
> obtained. For this one please read Users Guide, Troubleshooting.
> >>
> >> 2.
> >> >      from davcio : error #        10
> >> >      error while reading from file
> >>
> >> As you can see the program  tells you that something is wrong with
> inut/output files, as corrupted files, full disk. etc.
> >> So, you can restart your job. If the error still exists, check whether
> your hard disk is full or you do not share a filname.
> >>
> >> Please provide your affiliation.
> >>
> >> Bests,
> >> Eyvaz.
> >>
> >> -------------------------------------------------------------------
> >> Prof. Eyvaz Isaev,
> >> Theoretical Physics Department, Moscow State Institute of Steel &
> Alloys, Russia,
> >> Department of Physics, Chemistry, and Biology (IFM), Linkoping
> University, Sweden
> >> Condensed Matter Theory Group, Uppsala University, Sweden
> >> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
> >>
> >>
> >> -
> >>
> >>
> >>
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> > --
> >
> ==================================================================================
> > Vega Lew ( weijia liu)
> > PH.D Candidate 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: vegalew 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
> >
>
>
>
> --
> Best Wishes
> ChenWeiguang
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From quantumdft at gmail.com  Mon Dec  8 05:22:05 2008
From: quantumdft at gmail.com (vega lew)
Date: Mon, 8 Dec 2008 12:22:05 +0800
Subject: [Pw_forum] I can't view the output file of relax calculation using
	Xcrysden step by step.
Message-ID: <412f6c680812072022s4be10a2aq6cee57b0f5cfb29d@mail.gmail.com>

Dear all,

When I want to visualize the process of the relaxation, I found only last /
initial configuration displayed. I can't visualize the output file step by
step.
Did anyone encounter the same problem using 4.0.3 version of QE?

vega

-- 
==================================================================================
Vega Lew ( weijia liu)
PH.D Candidate 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: vegalew at gmail.com
Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing,
Jiangsu, China
******************************************************************************************************************
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From chenweiguang82 at gmail.com  Mon Dec  8 05:53:05 2008
From: chenweiguang82 at gmail.com (Weiguang Chen)
Date: Mon, 8 Dec 2008 12:53:05 +0800
Subject: [Pw_forum] calculation error about example12
Message-ID: <9e6d976a0812072053t307de8c8w40634b8d9d3772b3@mail.gmail.com>

Hi,

Another puzzle about example12 when I calculate the transmission of
Al-wire, the last several lines of out-file is just as follows:

 E-Ef(ev), T(x2 spins) =    0.2500000   4.0000000
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     from gep_x : error #        38

     error on zggev

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



     stopping ...

p0_24174:  p4_error: : 0

 the input files of example12 is right or not  , and is there any
tricks about transmission calculation?

 Thanks very much

-- 
Best Wishes
ChenWeiguang

************************************************
#               Chen, Weiguang
#
#    Postgraduate,  Ph. D
#  75 University Road, Physics Buliding  #  218
#  School of Physics & Engineering
#  Zhengzhou University
#  Zhengzhou, Henan 450052  CHINA
#
#  Tel: 86-13203730117
#  E-mail:chenweiguang82 at gmail.com;
#            chenweiguang82 at qq.com
#**********************************************

From giannozz at democritos.it  Mon Dec  8 09:50:51 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 8 Dec 2008 09:50:51 +0100
Subject: [Pw_forum] I can't view the output file of relax calculation
	using Xcrysden step by step.
In-Reply-To: <412f6c680812072022s4be10a2aq6cee57b0f5cfb29d@mail.gmail.com>
References: <412f6c680812072022s4be10a2aq6cee57b0f5cfb29d@mail.gmail.com>
Message-ID: <F1990AD2-3691-4343-879C-6F850471074A@democritos.it>


On Dec 8, 2008, at 5:22 , vega lew wrote:

> When I want to visualize the process of the relaxation, I found  
> only last / initial configuration displayed. I can't visualize the  
> output file step by step.
> Did anyone encounter the same problem using 4.0.3 version of QE?

did you try with a more recent version of xcrysden?

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



From giannozz at democritos.it  Mon Dec  8 09:53:08 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 8 Dec 2008 09:53:08 +0100
Subject: [Pw_forum] calculation error about example12
In-Reply-To: <9e6d976a0812072053t307de8c8w40634b8d9d3772b3@mail.gmail.com>
References: <9e6d976a0812072053t307de8c8w40634b8d9d3772b3@mail.gmail.com>
Message-ID: <10729549-CCE7-435E-8CE0-73371563C8F7@democritos.it>


On Dec 8, 2008, at 5:53 , Weiguang Chen wrote:

>      from gep_x : error #        38
>      error on zggev
>
>  the input files of example12 is right or not

of course it is.

> and is there any tricks about transmission calculation?

you need a working lapack library. Apparently yours doesn't
work very well, at least for that particular routine 'zggev'

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



From quantumdft at gmail.com  Mon Dec  8 10:45:45 2008
From: quantumdft at gmail.com (vega lew)
Date: Mon, 8 Dec 2008 17:45:45 +0800
Subject: [Pw_forum] I can't view the output file of relax calculation
	using Xcrysden step by step.
In-Reply-To: <F1990AD2-3691-4343-879C-6F850471074A@democritos.it>
References: <412f6c680812072022s4be10a2aq6cee57b0f5cfb29d@mail.gmail.com>
	<F1990AD2-3691-4343-879C-6F850471074A@democritos.it>
Message-ID: <412f6c680812080145l41a6aeecieda20547e54a7366@mail.gmail.com>

Dear sir,

I used XCrySDen-1.4.1bin-static. Is this the latest version? If not, could
you please give me the link to it?

thank you for reading.

vega

On Mon, Dec 8, 2008 at 4:50 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Dec 8, 2008, at 5:22 , vega lew wrote:
>
> > When I want to visualize the process of the relaxation, I found
> > only last / initial configuration displayed. I can't visualize the
> > output file step by step.
> > Did anyone encounter the same problem using 4.0.3 version of QE?
>
> did you try with a more recent version of xcrysden?
>
> Paolo
> ---
> 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
>



-- 
==================================================================================
Vega Lew ( weijia liu)
PH.D Candidate 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: vegalew at gmail.com
Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing,
Jiangsu, China
******************************************************************************************************************
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From tone.kokalj at ijs.si  Mon Dec  8 10:51:40 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 08 Dec 2008 10:51:40 +0100
Subject: [Pw_forum] I can't view the output file of relax
	calculation	using Xcrysden step by step.
In-Reply-To: <412f6c680812080145l41a6aeecieda20547e54a7366@mail.gmail.com>
References: <412f6c680812072022s4be10a2aq6cee57b0f5cfb29d@mail.gmail.com>
	<F1990AD2-3691-4343-879C-6F850471074A@democritos.it>
	<412f6c680812080145l41a6aeecieda20547e54a7366@mail.gmail.com>
Message-ID: <1228729900.4368.30.camel@walk.ijs.si>

On Mon, 2008-12-08 at 17:45 +0800, vega lew wrote:
> Dear sir,
> 
> I used XCrySDen-1.4.1bin-static. Is this the latest version? If not,
> could you please give me the link to it?

http://www.xcrysden.org/Download.html

In particular:

http://www.xcrysden.org/download/xc-1.5.17-linux_x86_64-semishared.tar.gz


Regards, Tone
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From akohlmey at cmm.chem.upenn.edu  Mon Dec  8 10:53:15 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 8 Dec 2008 10:53:15 +0100
Subject: [Pw_forum] I can't view the output file of relax calculation
	using Xcrysden step by step.
In-Reply-To: <412f6c680812080145l41a6aeecieda20547e54a7366@mail.gmail.com>
References: <412f6c680812072022s4be10a2aq6cee57b0f5cfb29d@mail.gmail.com>
	<F1990AD2-3691-4343-879C-6F850471074A@democritos.it>
	<412f6c680812080145l41a6aeecieda20547e54a7366@mail.gmail.com>
Message-ID: <7b6913e90812080153o5d6093d3gb470ca97d2ba1b45@mail.gmail.com>

On 12/8/08, vega lew <quantumdft at gmail.com> wrote:
> Dear sir,
>
> I used XCrySDen-1.4.1bin-static. Is this the latest version? If not, could
> you please give me the link to it?

how about checking the xcrysden homepage?
it is a simple as that. in this case you'd find:
http://www.xcrysden.org/News.html#dec05-2008

which will answer your question.

axel.

>
> thank you for reading.
>
> vega
>
> On Mon, Dec 8, 2008 at 4:50 PM, Paolo Giannozzi
> <giannozz at democritos.it>wrote:
>
>>
>> On Dec 8, 2008, at 5:22 , vega lew wrote:
>>
>> > When I want to visualize the process of the relaxation, I found
>> > only last / initial configuration displayed. I can't visualize the
>> > output file step by step.
>> > Did anyone encounter the same problem using 4.0.3 version of QE?
>>
>> did you try with a more recent version of xcrysden?
>>
>> Paolo
>> ---
>> 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
>>
>
>
>
> --
> ==================================================================================
> Vega Lew ( weijia liu)
> PH.D Candidate 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: vegalew at gmail.com
> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing,
> Jiangsu, China
> ******************************************************************************************************************
>


-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From quantumdft at gmail.com  Mon Dec  8 11:20:46 2008
From: quantumdft at gmail.com (vega lew)
Date: Mon, 8 Dec 2008 18:20:46 +0800
Subject: [Pw_forum] I can't view the output file of relax calculation
	using Xcrysden step by step.
In-Reply-To: <7b6913e90812080153o5d6093d3gb470ca97d2ba1b45@mail.gmail.com>
References: <412f6c680812072022s4be10a2aq6cee57b0f5cfb29d@mail.gmail.com>
	<F1990AD2-3691-4343-879C-6F850471074A@democritos.it>
	<412f6c680812080145l41a6aeecieda20547e54a7366@mail.gmail.com>
	<7b6913e90812080153o5d6093d3gb470ca97d2ba1b45@mail.gmail.com>
Message-ID: <412f6c680812080220u74ee289fn994eb6671622b9a4@mail.gmail.com>

Thank you all.
I'll try it immediately.

vega

On Mon, Dec 8, 2008 at 5:53 PM, Axel Kohlmeyer
<akohlmey at cmm.chem.upenn.edu>wrote:

> On 12/8/08, vega lew <quantumdft at gmail.com> wrote:
> > Dear sir,
> >
> > I used XCrySDen-1.4.1bin-static. Is this the latest version? If not,
> could
> > you please give me the link to it?
>
> how about checking the xcrysden homepage?
> it is a simple as that. in this case you'd find:
> http://www.xcrysden.org/News.html#dec05-2008
>
> which will answer your question.
>
> axel.
>
> >
> > thank you for reading.
> >
> > vega
> >
> > On Mon, Dec 8, 2008 at 4:50 PM, Paolo Giannozzi
> > <giannozz at democritos.it>wrote:
> >
> >>
> >> On Dec 8, 2008, at 5:22 , vega lew wrote:
> >>
> >> > When I want to visualize the process of the relaxation, I found
> >> > only last / initial configuration displayed. I can't visualize the
> >> > output file step by step.
> >> > Did anyone encounter the same problem using 4.0.3 version of QE?
> >>
> >> did you try with a more recent version of xcrysden?
> >>
> >> Paolo
> >> ---
> >> 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
> >>
> >
> >
> >
> > --
> >
> ==================================================================================
> > Vega Lew ( weijia liu)
> > PH.D Candidate 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: vegalew at gmail.com
> > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#,
> Nanjing,
> > Jiangsu, China
> >
> ******************************************************************************************************************
> >
>
>
> --
> =======================================================================
> Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>  Center for Molecular Modeling   --   University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
==================================================================================
Vega Lew ( weijia liu)
PH.D Candidate 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: vegalew at gmail.com
Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing,
Jiangsu, China
******************************************************************************************************************
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From lanhaiping at gmail.com  Mon Dec  8 11:52:21 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Mon, 8 Dec 2008 18:52:21 +0800
Subject: [Pw_forum] I can't view the output file of relax calculation
	using Xcrysden step by step.
In-Reply-To: <1228729900.4368.30.camel@walk.ijs.si>
References: <412f6c680812072022s4be10a2aq6cee57b0f5cfb29d@mail.gmail.com>
	<F1990AD2-3691-4343-879C-6F850471074A@democritos.it>
	<412f6c680812080145l41a6aeecieda20547e54a7366@mail.gmail.com>
	<1228729900.4368.30.camel@walk.ijs.si>
Message-ID: <c92002fa0812080252y6965145am5cb2b93d69ba7b7b@mail.gmail.com>

Hi, Tone,
is there any built package for x86-32 configuration ?
i checked it before , and didnot find.
it seems i have some problems to build from  sourecode.

Best,
Hai-Ping

On Mon, Dec 8, 2008 at 5:51 PM, Tone Kokalj <tone.kokalj at ijs.si> wrote:

> On Mon, 2008-12-08 at 17:45 +0800, vega lew wrote:
> > Dear sir,
> >
> > I used XCrySDen-1.4.1bin-static. Is this the latest version? If not,
> > could you please give me the link to it?
>
> http://www.xcrysden.org/Download.html
>
> In particular:
>
> http://www.xcrysden.org/download/xc-1.5.17-linux_x86_64-semishared.tar.gz
>
>
> Regards, Tone
> --
> Tone Kokalj <tone.kokalj at ijs.si>
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
> +386-1-477-3523 // fax:+386-1-477-3822)
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From lzh-ming at 163.com  Mon Dec  8 11:50:37 2008
From: lzh-ming at 163.com (lzh-ming)
Date: Mon, 8 Dec 2008 18:50:37 +0800 (CST)
Subject: [Pw_forum] How can I remove the dots on the lines in a band
 structure picture plotted by plotband.x?
Message-ID: <18707729.802431228733437247.JavaMail.coremail@bj163app19.163.com>

  
Dear all,
  Please help me fix this problem, Thanks very much.
  I have  a band structure picture, using plotband.x. But I want to remove the dots on the lines, how can I make it? These dots correspond to the k-points I used for calculations. 
    Thanks very much! 
Best wishes!
 
li-ming-fan
 

--

Institute of Theoretical Physics,
Lanzhou University, Gansu, China,
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From lanhaiping at gmail.com  Mon Dec  8 13:39:49 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Mon, 8 Dec 2008 20:39:49 +0800
Subject: [Pw_forum] How can I remove the dots on the lines in a band
	structure picture plotted by plotband.x?
In-Reply-To: <18707729.802431228733437247.JavaMail.coremail@bj163app19.163.com>
References: <18707729.802431228733437247.JavaMail.coremail@bj163app19.163.com>
Message-ID: <c92002fa0812080439g3a414ec8m520678d5c3a9558@mail.gmail.com>

Hi,

Repeatedly  submit  your question is not a good idea to
solve your problem.

If you are not farmilar with gnuplot , what i can suggest you is to draw
your bands with other tools, such as
origin , xmgrace et al.

best

2008/12/8 lzh-ming <lzh-ming at 163.com>

>   Dear all,
>   Please help me fix this problem, Thanks very much.
>   I have  a band structure picture, using plotband.x. But I want to remove
> the dots on the lines, how can I make it? These dots correspond to the
> k-points I used for calculations.
>      Thanks very much!
> Best wishes!
>
> li-ming-fan
>
>
> --
> Institute of Theoretical Physics,
> Lanzhou University, Gansu, China,
>
>
> ------------------------------
> [??] 2008??????? <http://popme.163.com/link/003985_1010_7027.html>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From mambom1902 at yahoo.com  Mon Dec  8 13:58:08 2008
From: mambom1902 at yahoo.com (loc duong ding)
Date: Mon, 8 Dec 2008 04:58:08 -0800 (PST)
Subject: [Pw_forum] Interprution of running pw.x
References: <089.c806f4c83f71eb12fcf272811b3af5a0@mcs.anl.gov>
	<098.8455ba104cab2050b6783738f0506b67@mcs.anl.gov>
Message-ID: <392269.71455.qm@web38807.mail.mud.yahoo.com>

Dear,


I?get a strange error when running pw.x. The error is:

?total energy????????????? =? -313.00559496 Ry
???? Harris-Foulkes estimate?? =? -314.62641196 Ry
???? estimated scf accuracy??? <???? 0.04292274 Ry
???? total magnetization?????? =???? 2.00 Bohr mag/cell
???? absolute magnetization??? =???? 3.41 Bohr mag/cell
???? iteration #? 2???? ecut=??? 35.00 Ry???? beta=0.60
mpiexec_master: mpd_uncaught_except_tb handling:
? exceptions.IOError: [Errno 5] Input/output error
??? /opt/mpich2/bin/mpiexec? 1051? handle_cli_stderr_input
??????? sys.stderr.write(msg)
??? /opt/mpich2/bin/mpdlib.py? 762? handle_active_streams
??????? handler(stream,*args)
??? /opt/mpich2/bin/mpiexec? 515? mpiexec
??????? rv = streamHandler.handle_active_streams(timeout=1.0)
??? /opt/mpich2/bin/mpiexec? 1423? ?
??????? mpiexec()


This error interprut the running process. I try to run it again with "restart' option and the error is:

?The initial density is read from file :
???? ./C8OOH_model11_vcrelax.save/charge-density.dat

???? negative rho (up, down):? 0.209E+00 0.219E+00
???? Starting wfc are?? 82 atomic wfcs
???? total cpu time spent up to now is???? 22.03 secs
???? per-process dynamical memory:??? 20.9 Mb
???? Self-consistent Calculation
???? iteration #? 1???? ecut=??? 35.00 Ry???? beta=0.60
rank 3 in job 13? master_34911?? caused collective abort of all ranks
? exit status of rank 3: return code 0


I don't know where the error comes from and how I can solve this problem.
Please help me.

Best regards,
Loc Duong Dinh
SAINT, Sungkyunkwan University, South Korean.



      
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From wangqj1 at 126.com  Mon Dec  8 13:58:19 2008
From: wangqj1 at 126.com (wangqj1)
Date: Mon, 8 Dec 2008 20:58:19 +0800 (CST)
Subject: [Pw_forum] about cpu utilization ratio
Message-ID: <28523634.662681228741099233.JavaMail.coremail@bj126app81.126.com>

 
 Dear all
      My comupter configure as following:
      cpu:Intel Q9550 
      memory: ddr2-1066
      mainboard:P5Q-PRO
But when it works ,I find the %cpu is only about 67% of all the cups ,the max is only 75% ,I want to know why the %cpu is so low ? 
     Any advice will be appreciated !
Best Wishes
Q J Wang
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From frnkhzi at yahoo.com  Mon Dec  8 15:05:50 2008
From: frnkhzi at yahoo.com (fereydoon khazali)
Date: Mon, 8 Dec 2008 06:05:50 -0800 (PST)
Subject: [Pw_forum] example03
Message-ID: <897354.23243.qm@web110810.mail.gq1.yahoo.com>

dear all 
Al is fcc but in example03 seems to be bcc. why?
F. kh
Azad univ. of omidieh , iran


      
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From manoj at phys.ufl.edu  Mon Dec  8 15:17:36 2008
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Mon, 8 Dec 2008 09:17:36 -0500 (EST)
Subject: [Pw_forum] calculation error about example12
In-Reply-To: <9e6d976a0812072053t307de8c8w40634b8d9d3772b3@mail.gmail.com>
Message-ID: <Pine.GSO.4.21.0812080906560.5749-100000@neptune.phys.ufl.edu>

Dear Chenweiguang, 
 The input file of example 12 is correct, at least in the version i am
using. I could run the example perfectly in version 4.0.1. Which version
are you using? Can you run any other examples?

Cheers, 
Manoj

 On Mon, 8 Dec 2008, Weiguang Chen wrote:

> Hi,
> 
> Another puzzle about example12 when I calculate the transmission of
> Al-wire, the last several lines of out-file is just as follows:
> 
>  E-Ef(ev), T(x2 spins) =    0.2500000   4.0000000
>   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
>      from gep_x : error #        38
> 
>      error on zggev
> 
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
> 
> 
>      stopping ...
> 
> p0_24174:  p4_error: : 0
> 
>  the input files of example12 is right or not  , and is there any
> tricks about transmission calculation?
> 
>  Thanks very much
> 
> -- 
> Best Wishes
> ChenWeiguang
> 
> ************************************************
> #               Chen, Weiguang
> #
> #    Postgraduate,  Ph. D
> #  75 University Road, Physics Buliding  #  218
> #  School of Physics & Engineering
> #  Zhengzhou University
> #  Zhengzhou, Henan 450052  CHINA
> #
> #  Tel: 86-13203730117
> #  E-mail:chenweiguang82 at gmail.com;
> #            chenweiguang82 at qq.com
> #**********************************************
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


From lanhaiping at gmail.com  Mon Dec  8 15:40:04 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Mon, 8 Dec 2008 22:40:04 +0800
Subject: [Pw_forum] about cpu utilization ratio
In-Reply-To: <28523634.662681228741099233.JavaMail.coremail@bj126app81.126.com>
References: <28523634.662681228741099233.JavaMail.coremail@bj126app81.126.com>
Message-ID: <c92002fa0812080640h1372c7bet45e6cecdffbb7984@mail.gmail.com>

Hi,
Just with this limited information , no conclusion can be reached.
Without definite works you carried out, no one can give you suggestion or
solution.
regards

2008/12/8 wangqj1 <wangqj1 at 126.com>

>
>  Dear all
>       My comupter configure as following:
>       cpu:Intel Q9550
>       memory: ddr2-1066
>       mainboard:P5Q-PRO
> But when it works ,I find the %cpu is only about 67% of all the cups ,the
> max is only 75% ,I want to know why the %cpu is so low ?
>      Any advice will be appreciated !
> Best Wishes
> Q J Wang
>
>
> ------------------------------
> ????????????????? <http://www.yeah.net>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From giannozz at democritos.it  Mon Dec  8 17:27:50 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 8 Dec 2008 17:27:50 +0100
Subject: [Pw_forum] example03
In-Reply-To: <897354.23243.qm@web110810.mail.gq1.yahoo.com>
References: <897354.23243.qm@web110810.mail.gq1.yahoo.com>
Message-ID: <1D68862A-9CA3-450D-93A9-D5351F3773C6@democritos.it>


On Dec 8, 2008, at 15:05 , fereydoon khazali wrote:

> Al is fcc but in example03 seems to be bcc. why?

examples are not meant to be realistic

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



From eyvaz_isaev at yahoo.com  Mon Dec  8 17:29:24 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 8 Dec 2008 08:29:24 -0800 (PST)
Subject: [Pw_forum] example03
In-Reply-To: <897354.23243.qm@web110810.mail.gq1.yahoo.com>
Message-ID: <797319.85796.qm@web65706.mail.ac4.yahoo.com>

Dear Fereydoon,

Why dou you think Al is bcc in example03? What is your argument for this?
In this example A(001) slab with tetragonal (ibrav=6) symmetry is examined.

Bests,
Eyvaz.

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


--- On Mon, 12/8/08, fereydoon khazali <frnkhzi at yahoo.com> wrote:

> From: fereydoon khazali <frnkhzi at yahoo.com>
> Subject: [Pw_forum] example03
> To: pw_forum at pwscf.org
> Date: Monday, December 8, 2008, 5:05 PM
> dear all 
> Al is fcc but in example03 seems to be bcc. why?
> F. kh
> Azad univ. of omidieh , iran
> 
> 
>       _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From giannozz at democritos.it  Mon Dec  8 17:31:18 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 8 Dec 2008 17:31:18 +0100
Subject: [Pw_forum] Interprution of running pw.x
In-Reply-To: <392269.71455.qm@web38807.mail.mud.yahoo.com>
References: <089.c806f4c83f71eb12fcf272811b3af5a0@mcs.anl.gov>
	<098.8455ba104cab2050b6783738f0506b67@mcs.anl.gov>
	<392269.71455.qm@web38807.mail.mud.yahoo.com>
Message-ID: <55BE3932-5A6A-4DFC-A657-16C3E974B446@democritos.it>


On Dec 8, 2008, at 13:58 , loc duong ding wrote:

> I get a strange error when running pw.x. The error is: [...]
> mpiexec_master: mpd_uncaught_except_tb handling

this falls into the category "strange MPI errors". There
are explanations in the user guide and in the faq.

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



From giannozz at democritos.it  Mon Dec  8 17:36:17 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 8 Dec 2008 17:36:17 +0100
Subject: [Pw_forum] How can I remove the dots on the lines in a band
	structure picture plotted by plotband.x?
In-Reply-To: <18707729.802431228733437247.JavaMail.coremail@bj163app19.163.com>
References: <18707729.802431228733437247.JavaMail.coremail@bj163app19.163.com>
Message-ID: <BECA85EE-77D0-4726-84D7-AAC3CD1061C1@democritos.it>


On Dec 8, 2008, at 11:50 , lzh-ming wrote:

>   I have  a band structure picture, using plotband.x. But I want to  
> remove the dots on the lines, how can I make it? These dots  
> correspond to the k-points I used for calculations.

in the postscript output? remove/comment the lines containing "dot";
or else, comment in the fortran file the line writing "dot", recompile,
re-run

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



From chen_shao_hua197 at yahoo.com.tw  Mon Dec  8 20:04:44 2008
From: chen_shao_hua197 at yahoo.com.tw (=?big5?B?s68gpNa12A==?=)
Date: Tue, 9 Dec 2008 03:04:44 +0800 (CST)
Subject: [Pw_forum] specify correct q-point grid!
Message-ID: <829824.93587.qm@web73012.mail.tp2.yahoo.com>

Dear forum's members,

I do an el-ph calculation.
The error message is
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     task #         0
     from matdyn : error #         1
     specify correct q-point grid!
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

So I examine the  espresso-4.0.3/PH/matdyn.f90
...
IF (dos) THEN
        IF (nk1 < 1 .OR. nk2 < 1 .OR. nk3 < 1) &
             CALL errore  ('matdyn','specify correct q-point grid!',1)
        ntetra = 6 * nk1 * nk2 * nk3
...

And I set

K_POINTS {automatic}
12 12 8 0 0 0           ( in scf.in )

  nq1=3, nq2=3, nq3=2    ( in elph.in )

I don't know why that error message show up and how to solve it ?

Thanks in advance
Max
Candidate of PhD
Physics department, National Taiwan University, Taipei, Taiwan


P.S. cat *.dyn0

   3   3   2
   6
   0.000000000000000E+00   0.000000000000000E+00   0.000000000000000E+00
   0.000000000000000E+00   0.000000000000000E+00  -0.337153960894342E+00
   0.000000000000000E+00   0.338170830884862E+00   0.000000000000000E+00
   0.000000000000000E+00   0.338170830884862E+00  -0.337153960894342E+00
   0.338170830884862E+00   0.338170830884862E+00   0.000000000000000E+00
   0.338170830884862E+00   0.338170830884862E+00  -0.337153960894342E+00





      ______________________________________________________________________________________________________
?????????Yahoo!??????2.0????????????? http://tw.mg0.mail.yahoo.com/dc/landing

From eyvaz_isaev at yahoo.com  Mon Dec  8 22:16:37 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 8 Dec 2008 13:16:37 -0800 (PST)
Subject: [Pw_forum] specify correct q-point grid!
In-Reply-To: <829824.93587.qm@web73012.mail.tp2.yahoo.com>
Message-ID: <215369.16652.qm@web65702.mail.ac4.yahoo.com>

Dear Max,

> IF (dos) THEN
> IF (nk1 < 1 .OR. nk2 < 1 .OR. nk3 < 1)
> & CALL errore ('matdyn','specify correct q-point grid!',1)

You correctly noticed that the error is due these lines. 
Because of that integration of DOS is done using the  tetrahedra method, so, there will be at least 1 tetrahedron with 4 points (vertexes). 

> ntetra = 6 * nk1 * nk2 * nk3 

This line (total number of tetrahedra) is due to the improved tetrahedra method by Bl\"ochl. You can find more in the original paper.

> nq1=3, nq2=3, nq3=2    ( in elph.in )

This q-points are not connected to DOS calculations in matdyn.x, they are for dynamical matrices D_{a,b}^{i,j}(q) calculations which then used to perform FFT to get real space F_{a,b}^{i,j}(R) force constants matrix.

You should use nk1,nk2,nk3 keywords in matdyn.in file for DOS calculations. By the way, most likely you did not specify these keywords which are zeros by default. Namely this one is stated in the abovementioned error.

Hope this helps,
Bests,
Eyvaz.

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


--- On Mon, 12/8/08, ? ?? <chen_shao_hua197 at yahoo.com.tw> wrote:

> From: ? ?? <chen_shao_hua197 at yahoo.com.tw>
> Subject: [Pw_forum] specify correct q-point grid!
> To: "Pwscf" <pw_forum at pwscf.org>
> Date: Monday, December 8, 2008, 10:04 PM
> Dear forum's members,
> 
> I do an el-ph calculation.
> The error message is
> 
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      task #         0
>      from matdyn : error #         1
>      specify correct q-point grid!
> 
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
> So I examine the  espresso-4.0.3/PH/matdyn.f90
> ...
> IF (dos) THEN
>         IF (nk1 < 1 .OR. nk2 < 1 .OR. nk3 < 1)
> &
>              CALL errore  ('matdyn','specify
> correct q-point grid!',1)
>         ntetra = 6 * nk1 * nk2 * nk3
> ...
> 
> And I set
> 
> K_POINTS {automatic}
> 12 12 8 0 0 0           ( in scf.in )
> 
>   nq1=3, nq2=3, nq3=2    ( in elph.in )
> 
> I don't know why that error message show up and how to
> solve it ?
> 
> Thanks in advance
> Max
> Candidate of PhD
> Physics department, National Taiwan University, Taipei,
> Taiwan
> 
> 
> P.S. cat *.dyn0
> 
>    3   3   2
>    6
>    0.000000000000000E+00   0.000000000000000E+00  
> 0.000000000000000E+00
>    0.000000000000000E+00   0.000000000000000E+00 
> -0.337153960894342E+00
>    0.000000000000000E+00   0.338170830884862E+00  
> 0.000000000000000E+00
>    0.000000000000000E+00   0.338170830884862E+00 
> -0.337153960894342E+00
>    0.338170830884862E+00   0.338170830884862E+00  
> 0.000000000000000E+00
>    0.338170830884862E+00   0.338170830884862E+00 
> -0.337153960894342E+00
> 
> 
> 
> 
> 
>      
> ______________________________________________________________________________________________________
> ?????????Yahoo!??????2.0?????????????
> http://tw.mg0.mail.yahoo.com/dc/landing
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From tone.kokalj at ijs.si  Tue Dec  9 01:09:05 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 09 Dec 2008 01:09:05 +0100
Subject: [Pw_forum] I can't view the output file of relax
	calculation	using Xcrysden step by step.
In-Reply-To: <c92002fa0812080252y6965145am5cb2b93d69ba7b7b@mail.gmail.com>
References: <412f6c680812072022s4be10a2aq6cee57b0f5cfb29d@mail.gmail.com>
	<F1990AD2-3691-4343-879C-6F850471074A@democritos.it>
	<412f6c680812080145l41a6aeecieda20547e54a7366@mail.gmail.com>
	<1228729900.4368.30.camel@walk.ijs.si>
	<c92002fa0812080252y6965145am5cb2b93d69ba7b7b@mail.gmail.com>
Message-ID: <1228781345.4759.34.camel@walk.ijs.si>

On Mon, 2008-12-08 at 18:52 +0800, lan haiping wrote:
> Hi, Tone, 
> is there any built package for x86-32 configuration ?

I have just put x83_32 binaries on the download page.
Here are the links:

http://www.xcrysden.org/download/xc-1.5.17-linux_x86-semishared.tar.gz
http://www.xcrysden.org/download/xc-1.5.17-linux_x86-shared.tar.gz

Regards, Tone
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From mambom1902 at yahoo.com  Tue Dec  9 01:30:40 2008
From: mambom1902 at yahoo.com (loc duong ding)
Date: Mon, 8 Dec 2008 16:30:40 -0800 (PST)
Subject: [Pw_forum] Interprution of running pw.x (CRASH file)
Message-ID: <132401.78925.qm@web38808.mail.mud.yahoo.com>

Dear,


The CRASH file content of the error is:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
task # 7
from pzpotrf : error # 68
problems computing cholesky decomposition 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%?
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
task # 7
from pzpotrf : error # 55
problems computing cholesky decomposition 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Best regards,
Loc Duong Dinh
SAINT, Sungkyunkwan University, South Korean.


      
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From lzh-ming at 163.com  Tue Dec  9 06:01:39 2008
From: lzh-ming at 163.com (lzh-ming)
Date: Tue, 9 Dec 2008 13:01:39 +0800 (CST)
Subject: [Pw_forum] How can I remove the dots on the lines in a band
 structure picture plotted by plotband.x?
In-Reply-To: <c92002fa0812080439g3a414ec8m520678d5c3a9558@mail.gmail.com>
References: <c92002fa0812080439g3a414ec8m520678d5c3a9558@mail.gmail.com>
	<18707729.802431228733437247.JavaMail.coremail@bj163app19.163.com>
Message-ID: <15155296.285441228798899043.JavaMail.coremail@bj163app113.163.com>

Hi,lan haiping,
   Thanks for your instruction. I draw my first gnuplot pictrue right yesterday. I tried many ways to fix that problem and make my drawing more optional, but I failed all those ways. 
Gnuplot is really powerful, though requiring writing my own scripts. I'll try to get familiar with it. Thank you very much.
 
li-ming-fan
 
?2008-12-08?"lan haiping" <lanhaiping at gmail.com> ???

Hi,

Repeatedly  submit  your question is not a good idea to 
solve your problem.

If you are not farmilar with gnuplot , what i can suggest you is to draw your bands with other tools, such as 
origin , xmgrace et al.

best


2008/12/8 lzh-ming <lzh-ming at 163.com>

  
Dear all,
  Please help me fix this problem, Thanks very much.
  I have  a band structure picture, using plotband.x. But I want to remove the dots on the lines, how can I make it? These dots correspond to the k-points I used for calculations. 
    Thanks very much! 
Best wishes!
 
li-ming-fan
 

--

Institute of Theoretical Physics,
Lanzhou University, Gansu, China,



[??] 2008???????
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum





-- 
Hai-Ping Lan 
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From paulatto at sissa.it  Tue Dec  9 09:08:04 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 09 Dec 2008 09:08:04 +0100
Subject: [Pw_forum] Strange things when calculating bands using pw.x
In-Reply-To: <8a1b6d820812050729v30c5ecf1nf3cf75ea81d61aba@mail.gmail.com>
References: <8a1b6d820812050729v30c5ecf1nf3cf75ea81d61aba@mail.gmail.com>
Message-ID: <493E2764.8000704@sissa.it>

willy kohn ha scritto:
>     diagonalization = 'cg'
Hi Willy,
have you tried to use the default algorithm (david) instead?

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

Due to budget cuts approved by Italian Minister of Finance and Italian
Minister "for" Education, University and Research this may be the last
email you receive from me.

Please send any future correspondence, possibly via pigeon, to
mr. Lorenzo Paulatto
under Roiano Railway Bridge - Pillar 2
34136, Trieste

Donations in food, coins, booze and processor time are warmly welcome.




From sclauzer at sissa.it  Tue Dec  9 09:16:50 2008
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 09 Dec 2008 09:16:50 +0100
Subject: [Pw_forum] chdens.x
In-Reply-To: <14185800.96571228631989057.JavaMail.coremail@bj126app29.126.com>
References: <14185800.96571228631989057.JavaMail.coremail@bj126app29.126.com>
Message-ID: <493E2972.3010207@sissa.it>

If what you actually need is the density of states projected onto atomic orbitals, you may
use the postprocessing tool called projwfc.x in the PP directory. The related documentatio
is written in INPUT_PROJWFC.txt, in the Doc directory.

GS

wangqj1 wrote:
> Dear all I  want to know how to plot the charge or spin density for different orbitals,
> like 3d, 4s. As the chdens.x can only plots the total charge or spin density. Any
> advice will be appreciated ! Best wishes ! Q J Wang
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________ Pw_forum mailing list 
> Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum

-- 

La legge n. 133 uccide l'Universit? e la Ricerca italiana!

Save Italian Brains! (http://saveitalianbrains.wordpress.com/)

o ------------------------------------------------ o
| Gabriele Sclauzero, PhD Student                  |
| c/o:   SISSA & CNR-INFM Democritos,              |
|        via Beirut 2-4, 34014 Trieste (Italy)     |
| email: sclauzer at sissa.it                         |
| phone: +39 040 3787 511                          |
| skype: gurlonotturno                             |
o ------------------------------------------------ o

From sclauzer at sissa.it  Tue Dec  9 09:26:15 2008
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 09 Dec 2008 09:26:15 +0100
Subject: [Pw_forum] calculation error about example12
In-Reply-To: <9e6d976a0812072053t307de8c8w40634b8d9d3772b3@mail.gmail.com>
References: <9e6d976a0812072053t307de8c8w40634b8d9d3772b3@mail.gmail.com>
Message-ID: <493E2BA7.2080504@sissa.it>

If you give a look into the source code of gep_x subroutine you'll find the answer:

!
!  for some reason the lapack routine does not work if the diagonal elements
!  of the matrices are exactly zero. We tested these routines on
!  pc_ifc, ibmsp and origin.
!

maybe your version of the lapack subroutine is more lousy than usual and you will need to 
increase just a bit the delgep parameter (which will not influence the conductance at the 
significant digits, if it is kept small enough)

GS



Weiguang Chen wrote:
> Hi,
> 
> Another puzzle about example12 when I calculate the transmission of
> Al-wire, the last several lines of out-file is just as follows:
> 
>  E-Ef(ev), T(x2 spins) =    0.2500000   4.0000000
>   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
>      from gep_x : error #        38
> 
>      error on zggev
> 
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
> 
> 
>      stopping ...
> 
> p0_24174:  p4_error: : 0
> 
>  the input files of example12 is right or not  , and is there any
> tricks about transmission calculation?
> 
>  Thanks very much
> 

-- 

La legge n. 133 uccide l'Universit? e la Ricerca italiana!

Save Italian Brains! (http://saveitalianbrains.wordpress.com/)

o ------------------------------------------------ o
| Gabriele Sclauzero, PhD Student                  |
| c/o:   SISSA & CNR-INFM Democritos,              |
|        via Beirut 2-4, 34014 Trieste (Italy)     |
| email: sclauzer at sissa.it                         |
| phone: +39 040 3787 511                          |
| skype: gurlonotturno                             |
o ------------------------------------------------ o

From willykohn at gmail.com  Tue Dec  9 14:52:39 2008
From: willykohn at gmail.com (willy kohn)
Date: Tue, 9 Dec 2008 08:52:39 -0500
Subject: [Pw_forum] Strange things when calculating bands using pw.x
In-Reply-To: <493E2764.8000704@sissa.it>
References: <8a1b6d820812050729v30c5ecf1nf3cf75ea81d61aba@mail.gmail.com>
	<493E2764.8000704@sissa.it>
Message-ID: <8a1b6d820812090552t222884va37d517a2c3968c2@mail.gmail.com>

Hi, Lorenzo:

Yes, but it didn't help, and actually it even didn't work for some k-points
that could go through with cg method.

best,

Wei

On Tue, Dec 9, 2008 at 3:08 AM, Lorenzo Paulatto <paulatto at sissa.it> wrote:

> willy kohn ha scritto:
> >     diagonalization = 'cg'
> Hi Willy,
> have you tried to use the default algorithm (david) instead?
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/<http://people.sissa.it/%7Epaulatto/>
>
> Due to budget cuts approved by Italian Minister of Finance and Italian
> Minister "for" Education, University and Research this may be the last
> email you receive from me.
>
> Please send any future correspondence, possibly via pigeon, to
> mr. Lorenzo Paulatto
> under Roiano Railway Bridge - Pillar 2
> 34136, Trieste
>
> Donations in food, coins, booze and processor time are warmly welcome.
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From giannozz at democritos.it  Tue Dec  9 16:49:18 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 09 Dec 2008 16:49:18 +0100
Subject: [Pw_forum] Interprution of running pw.x (CRASH file)
In-Reply-To: <132401.78925.qm@web38808.mail.mud.yahoo.com>
References: <132401.78925.qm@web38808.mail.mud.yahoo.com>
Message-ID: <493E937E.70401@democritos.it>

loc duong ding wrote:

> The CRASH file content of the error is:

> from pzpotrf : error # 68
> problems computing cholesky decomposition

this falls in the same category of the following:
"pw.x stops with error in cdiaghg or rdiaghg"
http://www.quantum-espresso.org/wiki/index.php/Troubleshooting_(PWscf)#pw.x_stops_with_error_in_cdiaghg_or_rdiaghg
You should also try the "-ndiag 1" option to disable
parallel distributed subspace diagonalization

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

From mambom1902 at yahoo.com  Wed Dec 10 02:49:06 2008
From: mambom1902 at yahoo.com (loc duong ding)
Date: Tue, 9 Dec 2008 17:49:06 -0800 (PST)
Subject: [Pw_forum] Error while writing to file
References: <mailman.342.1228318405.15655.pw_forum@pwscf.org>
Message-ID: <139286.91673.qm@web38803.mail.mud.yahoo.com>





________________________________

From: "pw_forum-request at pwscf.org" <pw_forum-request at pwscf.org>
To: pw_forum at pwscf.org
Sent: Wednesday, December 3, 2008 7:33:25 AM
Subject: Pw_forum Digest, Vol 18, Issue 5

I checked for all this factor. It can not solve the problem. 

>regards

-- 
>Lorenzo Paulatto
>SISSA? &? DEMOCRITOS (Trieste)
>phone: +39 040 3787 511
>skype: paulatz
>www:? http://people.sissa.it/~paulatto/

>Due to budget cuts approved by Italian Minister of Finance and Italian
>Minister "for" Education, University and Research this may be the last
>email you receive from me.

>Please send any future correspondence, possibly via pigeon, to
>mr. Lorenzo Paulatto
>under Roiano Railway Bridge - Pillar 2
>34136, Trieste

>Donations in food, coins, booze and processor time are warmly welcome.





>------------------------------

>Message: 4
>Date: Wed, 03 Dec 2008 14:13:52 +0100
>From: Paolo Giannozzi <giannozz at democritos.it>
>Subject: Re: [Pw_forum] Error while writing to file
>To: PWSCF Forum <pw_forum at pwscf.org>
>Message-ID: <49368610.1060505 at democritos.it>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed

>Lorenzo Paulatto wrote:

>> It may be: disk is full, outdir does not exist, outdir exists but is not
>> a directory (i.e. it is a file) or, finally, you have changed the number
>> changed some parameter in the input (like wf_collect, or the number of
>> pools) without doing a bit of cleanup in your temporary files.

>it might also be related to the value of parameter DIRECT_IO_FACTOR,
>used in PW/diropn.f90:

>#if defined(__ALPHA)
>#? define DIRECT_IO_FACTOR 2
>#else
>#? define DIRECT_IO_FACTOR 8
>#end
? >!
? >! the? record length in direct-access I/O is given by the number of
?> ! real*8 words times DIRECT_IO_FACTOR (may depend on the compiler)
? >!
I had change the DIRECT_IO_FACTOR to 2 but the error has untill happened.

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


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Today's Topics:

? 1. Re: MnPd Bulk (Lorenzo Paulatto)
? 2. Error while writing to file (loc duong ding)
? 3. Re: Error while writing to file (Lorenzo Paulatto)
? 4. Re: Error while writing to file (Paolo Giannozzi)
? 5. Re: "charge is wrong" error in semiconductor slab??? calculation
? ? ? (Paolo Giannozzi)
? 6. Re: "charge is wrong" error in semiconductor slab??? calculation
? ? ? (J. J. Ramsey)
? 7. Re: smearing at zero K (Paolo Giannozzi)
? 8. picking ref energies for GIPAW? PP's (WILLIAM J BROUWER)
? 9. Re: Error while writing to file (Rafael Dias Menezes)
? 10. Re: Error while writing to file (Paolo Giannozzi)
? 11. Re: "charge is wrong" error in semiconductor slab??? calculation
? ? ? (J. J. Ramsey)
? 12. Re: "charge is wrong" error in semiconductor??? slab??? calculation
? ? ? (Paolo Giannozzi)
? 13. Re: "charge is wrong" error in semiconductor slab??? calculation
? ? ? (Eyvaz Isaev)


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

Message: 1
Date: Wed, 03 Dec 2008 09:32:17 +0100
From: Lorenzo Paulatto <paulatto at sissa.it>
Subject: Re: [Pw_forum] MnPd Bulk
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <49364411.4040409 at sissa.it>
Content-Type: text/plain; charset=ISO-8859-15

Salvador Meza Aguilar ha scritto:
> Which is the problem? I attach the input files.

It is known that DFT, especially GGA, gives a (wrong) magnetic moment
for Palladium bulk. It is also true that in order to reproduce the
literature results I had to use a smearing smaller than you did (exactly
half was barely sufficient).

-- 
Lorenzo Paulatto
SISSA? &? DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:? http://people.sissa.it/~paulatto/

Due to budget cuts approved by Italian Minister of Finance and Italian
Minister "for" Education, University and Research this may be the last
email you receive from me.

Please send any future correspondence, possibly via pigeon, to
mr. Lorenzo Paulatto
under Roiano Railway Bridge - Pillar 2
34136, Trieste

Donations in food, coins, booze and processor time are warmly welcome.





????? 
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>------------------------------

>Message: 3
>Date: Wed, 03 Dec 2008 14:03:55 +0100
>From: Lorenzo Paulatto <paulatto at sissa.it>
>Subject: Re: [Pw_forum] Error while writing to file
>To: PWSCF Forum <pw_forum at pwscf.org>
>Message-ID: <493683BB.8090408 at sissa.it>
>Content-Type: text/plain; charset=ISO-8859-15

>loc duong ding ha scritto:
>> from davcio : error #? ? ? ? 10? ? 
>> error while writing to file

>It may be: disk is full, outdir does not exist, outdir exists but is not
>a directory (i.e. it is a file) or, finally, you have changed the number
>changed some parameter in the input (like wf_collect, or the number of
>pools) without doing a bit of cleanup in your temporary files.



      
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From frnkhzi at yahoo.com  Wed Dec 10 06:29:37 2008
From: frnkhzi at yahoo.com (fereydoon khazali)
Date: Tue, 9 Dec 2008 21:29:37 -0800 (PST)
Subject: [Pw_forum] example03
Message-ID: <396885.11145.qm@web110814.mail.gq1.yahoo.com>

Dear Prof. Eyvaz
Thank you very much for your reply.In this example Al seems to be bcc because an Al atom is in position (0.5 0.5 z)but there aren't any atom in (0.0? 0.5? 0.5) ,(0.5? 0.0? 0.5 ) , ... . thanks
F. K.h
Azad univ. omidieh , Iran


      
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From panda.deng.pan at gmail.com  Wed Dec 10 08:10:49 2008
From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=)
Date: Wed, 10 Dec 2008 15:10:49 +0800
Subject: [Pw_forum] (no subject)
Message-ID: <c8dadee0812092310w185227fwde5a3e9e9b567253@mail.gmail.com>

I was running pw.x to repeat the Example01.When I execute the 'pw.x'.
it appear this: 'mpirun must be used to launch all MPI applications'
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From holger.hesske at chem.ethz.ch  Wed Dec 10 08:33:51 2008
From: holger.hesske at chem.ethz.ch (Holger Hesske)
Date: Wed, 10 Dec 2008 08:33:51 +0100
Subject: [Pw_forum] example03
In-Reply-To: <396885.11145.qm@web110814.mail.gq1.yahoo.com>
References: <396885.11145.qm@web110814.mail.gq1.yahoo.com>
Message-ID: <200812100833.52138.holger.hesske@chem.ethz.ch>

Dear fereydoon,

in example 03, the fcc structure is found "like defined" in the 110 direction.
It could not be bcc, even it looks for the first glimpse so, because z-distance 
between two identical layers is not equal x or y distance (so it's not cubic).

Hope this helps,
Greetings form cold and snowy Zurich

Holger


Am Mittwoch 10 Dezember 2008 06:29:37 schrieb fereydoon khazali:
> Dear Prof. Eyvaz
> Thank you very much for your reply.In this example Al seems to be bcc
> because an Al atom is in position (0.5 0.5 z)but there aren't any atom in
> (0.0? 0.5? 0.5) ,(0.5? 0.0? 0.5 ) , ... . thanks F. K.h
> Azad univ. omidieh , Iran

-- 
Dr. Holger Hesske
Inst.f.Chemie-/Bioingenieurwissenschaft.
Wolfgang-Pauli-Str. 10
ETH H?nggerberg, HCI E 134
CH-8093 Z?rich
Tel: +41 (0)44 633 66 19
Fax: +41 (0)44 632 11 63
E-Mail: holger.hesske at chem.ethz.ch 

From paulatto at sissa.it  Wed Dec 10 08:57:28 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 10 Dec 2008 08:57:28 +0100
Subject: [Pw_forum] (no subject)
In-Reply-To: <c8dadee0812092310w185227fwde5a3e9e9b567253@mail.gmail.com>
References: <c8dadee0812092310w185227fwde5a3e9e9b567253@mail.gmail.com>
Message-ID: <493F7668.10209@sissa.it>

?? ha scritto:
> I was running pw.x to repeat the Example01.When I execute the 'pw.x'.
> it appear this: 'mpirun must be used to launch all MPI applications'
Hi ??,
everything is explained in  the file examples/environment_variables: if
you have compiled the parallel version of QE you will have to set the
examples to use mpirun. It's not difficult at all.

regards

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

Due to budget cuts approved by Italian Minister of Finance and Italian
Minister "for" Education, University and Research this may be the last
email you receive from me.

Please send any future correspondence, possibly via pigeon, to
mr. Lorenzo Paulatto
under Roiano Railway Bridge - Pillar 2
34136, Trieste

Donations in food, coins, booze and processor time are warmly welcome.




From giannozz at democritos.it  Wed Dec 10 10:51:23 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 10 Dec 2008 10:51:23 +0100
Subject: [Pw_forum] Error while writing to file
In-Reply-To: <139286.91673.qm@web38803.mail.mud.yahoo.com>
References: <mailman.342.1228318405.15655.pw_forum@pwscf.org>
	<139286.91673.qm@web38803.mail.mud.yahoo.com>
Message-ID: <493F911B.30705@democritos.it>

You sent 182 lines of quoted text and, as far as I understand,
two pieces of (non-)information:

>  >It may be: disk is full, outdir does not exist, outdir exists but is not
>  >a directory (i.e. it is a file) or, finally, you have changed the number
>  >changed some parameter in the input (like wf_collect, or the number of
>  >pools) without doing a bit of cleanup in your temporary files.

> I checked for all this factor. It can not solve the problem.

and

> I had change the DIRECT_IO_FACTOR to 2 but the error has untill happened.

so please
1) would you mind sending messages that do not require half an hour
to be decryopted?
2) if you have STRONG evidence that the problem you encounter is
related to the particular calculation you are executing and NOT
to your compiler/machine/libraries/operating system, please provide
all the information needed to reproduce your calculation

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

From vcuteym at 126.com  Wed Dec 10 18:27:55 2008
From: vcuteym at 126.com (=?gbk?B?0e7Drw==?=)
Date: Thu, 11 Dec 2008 01:27:55 +0800 (CST)
Subject: [Pw_forum] How to change the weight parameter in hybrid functional?
Message-ID: <17284108.1111228930075467.JavaMail.coremail@bj126app55.126.com>

Hi, everyone
The "PBE hybrid functional" is given as: 
Exc(PBE)=a*Ex(HF)+(1-a)*Ex(PBE)+Ec(PBE). There is a weight parameter "a" in the range (0,1), and PBE0 is for a=0.25. How can I change the parameter "a" in the input file of PWSCF code?
"Phys. Rev. Lett. 101, 106802 (2008)" and "Phys. Rev. Lett. 101, 046405 (2008)"
have changed parameter "a" in order to make the bandgap value of some semiconductors agreed with experiment.
thanks
myang
     
Tel:?86-010-6275-7594
Email: vcuteym at 126.com
School of Physics
Peking University
Beijing, 100871
China
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From vormar at gmail.com  Wed Dec 10 20:59:44 2008
From: vormar at gmail.com (Marci)
Date: Wed, 10 Dec 2008 20:59:44 +0100
Subject: [Pw_forum] How to change the weight parameter in hybrid
	functional?
In-Reply-To: <17284108.1111228930075467.JavaMail.coremail@bj126app55.126.com>
References: <17284108.1111228930075467.JavaMail.coremail@bj126app55.126.com>
Message-ID: <34ad5960812101159q1b2ca8d5w70666e28fc48d94a@mail.gmail.com>

Dear Myang,

Ive found an easy but dirty way that should work:
just change variable exx_fraction = 0.25_DP to whatever you want in
row no. 349 of file functionals.f90 in espresso_dir/Modules/ and do a
"make pw" (my espresso version is 4.0.3).
As you can see you need to recompile espresso each time you want to
change the mixing parameter.
A better solution would be to add a new flag to the input parameters.

Yours sincerely,

Marton Voros
--
physicist student @
Department of Atomic Physics
Budapest University of Technology and Economics (BME)
Budafoki ?t 8., H-1111, Budapest, Hungary
vormar_at_gmail_dot_com, vm776_at_hszk_dot_bme_dot_hu

2008/12/10 ?? <vcuteym at 126.com>
>
> Hi, everyone
> The "PBE hybrid functional" is given as:
> Exc(PBE)=a*Ex(HF)+(1-a)*Ex(PBE)+Ec(PBE). There is a weight parameter "a" in the range (0,1), and PBE0 is for a=0.25. How can I change the parameter "a" in the input file of PWSCF code?
> "Phys. Rev. Lett. 101, 106802 (2008)" and "Phys. Rev. Lett. 101, 046405 (2008)"
> have changed parameter "a" in order to make the bandgap value of some semiconductors agreed with experiment.
> thanks
> myang
>
> Tel:?86-010-6275-7594
> Email: vcuteym at 126.com
> School of Physics
> Peking University
> Beijing, 100871
> China

From lanhaiping at gmail.com  Thu Dec 11 00:16:25 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Thu, 11 Dec 2008 07:16:25 +0800
Subject: [Pw_forum] How to change the weight parameter in hybrid
	functional?
In-Reply-To: <34ad5960812101159q1b2ca8d5w70666e28fc48d94a@mail.gmail.com>
References: <17284108.1111228930075467.JavaMail.coremail@bj126app55.126.com>
	<34ad5960812101159q1b2ca8d5w70666e28fc48d94a@mail.gmail.com>
Message-ID: <c92002fa0812101516x313a96d8vc25c0e3fc7037927@mail.gmail.com>

Dear Marci,
Your scheme seems wonderful to be  consistent with  literature.
But my wonder is how to adapt the related pseudopotentials ?

regards,

2008/12/11 Marci <vormar at gmail.com>

> Dear Myang,
>
> Ive found an easy but dirty way that should work:
> just change variable exx_fraction = 0.25_DP to whatever you want in
> row no. 349 of file functionals.f90 in espresso_dir/Modules/ and do a
> "make pw" (my espresso version is 4.0.3).
> As you can see you need to recompile espresso each time you want to
> change the mixing parameter.
> A better solution would be to add a new flag to the input parameters.
>
> Yours sincerely,
>
> Marton Voros
> --
> physicist student @
> Department of Atomic Physics
> Budapest University of Technology and Economics (BME)
> Budafoki ?t 8., H-1111, Budapest, Hungary
> vormar_at_gmail_dot_com, vm776_at_hszk_dot_bme_dot_hu
>
> 2008/12/10 ?? <vcuteym at 126.com>
> >
> > Hi, everyone
> > The "PBE hybrid functional" is given as:
> > Exc(PBE)=a*Ex(HF)+(1-a)*Ex(PBE)+Ec(PBE). There is a weight parameter "a"
> in the range (0,1), and PBE0 is for a=0.25. How can I change the parameter
> "a" in the input file of PWSCF code?
> > "Phys. Rev. Lett. 101, 106802 (2008)" and "Phys. Rev. Lett. 101, 046405
> (2008)"
> > have changed parameter "a" in order to make the bandgap value of some
> semiconductors agreed with experiment.
> > thanks
> > myang
> >
> > Tel:?86-010-6275-7594
> > Email: vcuteym at 126.com
> > School of Physics
> > Peking University
> > Beijing, 100871
> > China
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From vormar at gmail.com  Thu Dec 11 01:26:22 2008
From: vormar at gmail.com (Marci)
Date: Thu, 11 Dec 2008 01:26:22 +0100
Subject: [Pw_forum] How to change the weight parameter in hybrid
	functional?
In-Reply-To: <c92002fa0812101516x313a96d8vc25c0e3fc7037927@mail.gmail.com>
References: <17284108.1111228930075467.JavaMail.coremail@bj126app55.126.com>
	<34ad5960812101159q1b2ca8d5w70666e28fc48d94a@mail.gmail.com>
	<c92002fa0812101516x313a96d8vc25c0e3fc7037927@mail.gmail.com>
Message-ID: <34ad5960812101626i1f948079xc4fc4e80096ddd45@mail.gmail.com>

Dear Ian haiping,

as far as I know, implementing (norm-conserving) pseudopotentials
based on hybrid functionals is not a trivial problem, the main reason
could be the non-locality of the hartree-fock exchange. The accepted
approach is to create pseudopotentials using
the corresponding non-hybrid functional and use it in hybrid
calculations. This is said in the EXX_example readme file. So you
should simply force pwscf to use the hybrid functional by specifying
the "input_dft" parameter.

Yours sincerely,
Marton Voros
--
physicist student @
Department of Atomic Physics
Budapest University of Technology and Economics (BME)
Budafoki ?t 8., H-1111, Budapest, Hungary
vormar_at_gmail_dot_com, vm776_at_hszk_dot_bme_dot_hu

2008/12/11 lan haiping <lanhaiping at gmail.com>:
> Dear Marci,
> Your scheme seems wonderful to be  consistent with  literature.
> But my wonder is how to adapt the related pseudopotentials ?
>
> regards,
>
> 2008/12/11 Marci <vormar at gmail.com>
>>
>> Dear Myang,
>>
>> Ive found an easy but dirty way that should work:
>> just change variable exx_fraction = 0.25_DP to whatever you want in
>> row no. 349 of file functionals.f90 in espresso_dir/Modules/ and do a
>> "make pw" (my espresso version is 4.0.3).
>> As you can see you need to recompile espresso each time you want to
>> change the mixing parameter.
>> A better solution would be to add a new flag to the input parameters.
>>
>> Yours sincerely,
>>
>> Marton Voros
>> --
>> physicist student @
>> Department of Atomic Physics
>> Budapest University of Technology and Economics (BME)
>> Budafoki ?t 8., H-1111, Budapest, Hungary
>> vormar_at_gmail_dot_com, vm776_at_hszk_dot_bme_dot_hu
>>
>> 2008/12/10 ?? <vcuteym at 126.com>
>> >
>> > Hi, everyone
>> > The "PBE hybrid functional" is given as:
>> > Exc(PBE)=a*Ex(HF)+(1-a)*Ex(PBE)+Ec(PBE). There is a weight parameter "a"
>> > in the range (0,1), and PBE0 is for a=0.25. How can I change the parameter
>> > "a" in the input file of PWSCF code?
>> > "Phys. Rev. Lett. 101, 106802 (2008)" and "Phys. Rev. Lett. 101, 046405
>> > (2008)"
>> > have changed parameter "a" in order to make the bandgap value of some
>> > semiconductors agreed with experiment.
>> > thanks
>> > myang
>> >
>> > Tel:?86-010-6275-7594
>> > Email: vcuteym at 126.com
>> > School of Physics
>> > Peking University
>> > Beijing, 100871
>> > China
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> --
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871
> lanhaiping at gmail.com, hplan at pku.edu.cn
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

From rezakalantarinezhad at gmail.com  Thu Dec 11 07:29:18 2008
From: rezakalantarinezhad at gmail.com (Reza Kalantari)
Date: Thu, 11 Dec 2008 09:59:18 +0330
Subject: [Pw_forum] How can I define a Supercell in my simulation?
Message-ID: <fad65060812102229q26462fe1j5204589f5cef6515@mail.gmail.com>

Dear all

I am PhD student and working on simulation of electronic structure of a
carbon nanotube after binding of an external biomolecule to this carbon
nanotube. I know that I should use supercell for this purpose but I don't
know how can I do it?

How can I define a supercell in my simulation?

Have you seen ever such as this simulation by Quantum-Espresso?


Best Regards

Reza Kalantari Nezhad
PhD Student
Mechanical Engineering
Amir Kabir University of Technology (Tehran Polytechnic)
Tehran
Iran
rkalantrari at aut.ac.ir
rezakalantarinezhad at gmail.com



Mobile Phone: 0098-935-2578543
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From giannozz at democritos.it  Thu Dec 11 14:04:06 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 11 Dec 2008 14:04:06 +0100
Subject: [Pw_forum] How can I define a Supercell in my simulation?
In-Reply-To: <fad65060812102229q26462fe1j5204589f5cef6515@mail.gmail.com>
References: <fad65060812102229q26462fe1j5204589f5cef6515@mail.gmail.com>
Message-ID: <C1E5DFBA-C6C9-45C3-B5D5-CAC48C22DB69@democritos.it>

On Dec 11, 2008, at 7:29 , Reza Kalantari wrote:
> I know that I should use supercell for this purpose but I don't  
> know how can I do it?
>
there is no conceptual difference between a so-called "supercell" and
a crystal cell.
> Have you seen ever such as this simulation by Quantum-Espresso?
>
like this? http://web.mit.edu/newsoffice/2006/nanotubes.html

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



From rezakalantarinezhad at gmail.com  Fri Dec 12 08:50:10 2008
From: rezakalantarinezhad at gmail.com (Reza Kalantari)
Date: Fri, 12 Dec 2008 11:20:10 +0330
Subject: [Pw_forum] How can I define a Supercell in my simulation?
In-Reply-To: <C1E5DFBA-C6C9-45C3-B5D5-CAC48C22DB69@democritos.it>
References: <fad65060812102229q26462fe1j5204589f5cef6515@mail.gmail.com>
	<C1E5DFBA-C6C9-45C3-B5D5-CAC48C22DB69@democritos.it>
Message-ID: <fad65060812112350p298de055oc8899ad9a3660735@mail.gmail.com>

Dear Paolo Giannozzi

Thank you so much for your attention. I have seen Marzari's group
simulations on carbon nanotube which were done with Quantum-Espresso but all
examples of Quantum-Espresso on its official website are for periodic mater
so I don't have a sample input file for a non-periodic simulation.
Where can I find an input sample file (pw.x input file) for a non-periodic
simulation?
How should I define
ibrav<file:///E:/PhDThesis/Simulation/QUANTUM-ESPRESSO/Doc/INPUT_PW.html#id2982558>|
celldm<file:///E:/PhDThesis/Simulation/QUANTUM-ESPRESSO/Doc/INPUT_PW.html#id2982665>|
assume_isolated?<file:///E:/PhDThesis/Simulation/QUANTUM-ESPRESSO/Doc/INPUT_PW.html#id2983511>
Should I define
CELL_PARAMETERS<file:///E:/PhDThesis/Simulation/QUANTUM-ESPRESSO/Doc/INPUT_PW.html#id2985370>?
I try to calculate electronic structure of a carbon nanotube when another
biomolecule dock with it. have seen ever such as this by Quantum-Espresso? I
want to know that it's a conceptual barrier to this purpose  with
Quantum-Espresso?
Thank you very much again for you attention. I have started working on this
subject recently so maybe my questions are rudimentary so sorry.

Reza Kalantari-Nezhad
PhD Student
Amir Kabir University of Technology
rezakalantarinezhad at gmail.com
rkalantari at aut.ac.ir

On Thu, Dec 11, 2008 at 4:34 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

> On Dec 11, 2008, at 7:29 , Reza Kalantari wrote:
> > I know that I should use supercell for this purpose but I don't
> > know how can I do it?
> >
> there is no conceptual difference between a so-called "supercell" and
> a crystal cell.
> > Have you seen ever such as this simulation by Quantum-Espresso?
> >
> like this? http://web.mit.edu/newsoffice/2006/nanotubes.html
>
> 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
>



-- 
Eradatmand
Reza Kalantari Nezhad
PhD Student
Mechanical Engineering
Amir Kabir University of Technology (Tehran Polytechnic)
Tehran
Iran


Mobile Phone: 0098-935-2578543
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From lanhaiping at gmail.com  Fri Dec 12 09:28:25 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Fri, 12 Dec 2008 16:28:25 +0800
Subject: [Pw_forum] How can I define a Supercell in my simulation?
In-Reply-To: <fad65060812112350p298de055oc8899ad9a3660735@mail.gmail.com>
References: <fad65060812102229q26462fe1j5204589f5cef6515@mail.gmail.com>
	<C1E5DFBA-C6C9-45C3-B5D5-CAC48C22DB69@democritos.it>
	<fad65060812112350p298de055oc8899ad9a3660735@mail.gmail.com>
Message-ID: <c92002fa0812120028j15fb3120jaba1672d34dce623@mail.gmail.com>

Hi,
QE package performs calculation with periodic cell.
if you want to do non-periodic calculations , you should
set up supercell with  large vacuum seperations between
the periodic images.

With respect to  carbon nanotubes,
you can define ibrav to 6 with certain values for celldm(1) and celldm(3),
such as celldm(1)=47.243171944358878, celldm(3) =0.1704 for zigzag
nanotube.  If you want to simulate finite  carbon nanotubes,  what you need
is to define some value along longitudinal direction.

Regards,

On Fri, Dec 12, 2008 at 3:50 PM, Reza Kalantari <
rezakalantarinezhad at gmail.com> wrote:

> Dear Paolo Giannozzi
>
> Thank you so much for your attention. I have seen Marzari's group
> simulations on carbon nanotube which were done with Quantum-Espresso but all
> examples of Quantum-Espresso on its official website are for periodic mater
> so I don't have a sample input file for a non-periodic simulation.
> Where can I find an input sample file (pw.x input file) for a non-periodic
> simulation?
> How should I define ibrav | celldm | assume_isolated?
> Should I define CELL_PARAMETERS ?
> I try to calculate electronic structure of a carbon nanotube when another
> biomolecule dock with it. have seen ever such as this by Quantum-Espresso? I
> want to know that it's a conceptual barrier to this purpose  with
> Quantum-Espresso?
> Thank you very much again for you attention. I have started working on this
> subject recently so maybe my questions are rudimentary so sorry.
>
> Reza Kalantari-Nezhad
> PhD Student
> Amir Kabir University of Technology
> rezakalantarinezhad at gmail.com
> rkalantari at aut.ac.ir
>
>
> On Thu, Dec 11, 2008 at 4:34 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:
>
>> On Dec 11, 2008, at 7:29 , Reza Kalantari wrote:
>> > I know that I should use supercell for this purpose but I don't
>> > know how can I do it?
>> >
>> there is no conceptual difference between a so-called "supercell" and
>> a crystal cell.
>> > Have you seen ever such as this simulation by Quantum-Espresso?
>> >
>> like this? http://web.mit.edu/newsoffice/2006/nanotubes.html
>>
>> 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
>>
>
>
>
> --
> Eradatmand
> Reza Kalantari Nezhad
> PhD Student
> Mechanical Engineering
> Amir Kabir University of Technology (Tehran Polytechnic)
> Tehran
> Iran
>
>
> Mobile Phone: 0098-935-2578543
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From Giovanni.Cantele at na.infn.it  Fri Dec 12 10:36:36 2008
From: Giovanni.Cantele at na.infn.it (Giovanni Cantele)
Date: Fri, 12 Dec 2008 10:36:36 +0100
Subject: [Pw_forum] How can I define a Supercell in my simulation?
In-Reply-To: <fad65060812112350p298de055oc8899ad9a3660735@mail.gmail.com>
References: <fad65060812102229q26462fe1j5204589f5cef6515@mail.gmail.com>	<C1E5DFBA-C6C9-45C3-B5D5-CAC48C22DB69@democritos.it>
	<fad65060812112350p298de055oc8899ad9a3660735@mail.gmail.com>
Message-ID: <494230A4.3030002@na.infn.it>


> Thank you so much for your attention. I have seen Marzari's group 
> simulations on carbon nanotube which were done with Quantum-Espresso 
> but all examples of Quantum-Espresso on its official website are for 
> periodic mater so I don't have a sample input file for a non-periodic 
> simulation.
A truly non-periodic calculation CANNOT be performed within 
Quantum-Espresso because the code will always assume a three-dimensional 
lattice (according to the value of ibrav you specify in the input file), 
yet the definition of a supercell allows you to calculate all the 
properties (DOS, band structure, phonons, ...) of a non-periodic system 
(molecules, surfaces, nanowires, defects, ....).

The "supercell" input file has the SAME structure of a "standard" input 
file. Some "examples" can be found in the Quantum-Espresso "examples"!   
: example09 (SiH4 molecule), example11 (isolated atom), WorkFct_example 
(surface), and others.

The supercell definition allows you to perform numerical simulations of 
two-, one- and zero-dimensional systems, EVEN IF in all those cases the 
system will be replicated in all directions. See (pag. 18-19) 
http://www.fisica.uniud.it/~giannozz/Corsi/metnum.pdf and (p. 1054) 
Payne et al, Rev. Mod. Phys. 64, just to cite two references.
The basic issue is that if, for example, you want to calculate 
properties of a zero-dimensional system (e.g. a molecule), the unit cell 
parameters must be defined in such a way that vacuum space must separate 
periodic replica. Such space must be enough to prevent such replica from 
interacting. How much depends on your system and the convergence of the 
calculations must be checked. Therefore: supercell size in the i-th 
direction (assumed "non-periodic") = system size in that direction + 
vacuum space

Also consider that, if the i-th direction is a non-periodic one, you 
don't need to use k-point sampling along that direction (so, for a 
molecule, you could use only gamma point).
> Where can I find an input sample file (pw.x input file) for a 
> non-periodic simulation?
see above

> How should I define ibrav 
> <file:///E:/PhDThesis/Simulation/QUANTUM-ESPRESSO/Doc/INPUT_PW.html#id2982558> 
> | celldm 
> <file:///E:/PhDThesis/Simulation/QUANTUM-ESPRESSO/Doc/INPUT_PW.html#id2982665> 
> | assume_isolated? 
> <file:///E:/PhDThesis/Simulation/QUANTUM-ESPRESSO/Doc/INPUT_PW.html#id2983511>
ibrav: it depends on the system, in the case of a molecule one can 
usually specify a cubic lattice (ibrav=1), but some other choices can be 
more efficient if for example the molecule size is not nearly the same 
in all directions. For a nanowire a choice can be a tetragonal lattice 
(ibrav=6), where the "c" axis is the periodicity direction.
celldm: you must define your supercell and choose it accordingly
assume_isolated: not mandatory


> Should I define CELL_PARAMETERS 
> <file:///E:/PhDThesis/Simulation/QUANTUM-ESPRESSO/Doc/INPUT_PW.html#id2985370> 
> ?
As for the "periodic" system, you can either use ibrav /= 0 and 
celldm(1:6) or ibrav=0 and CELL_PARAMETERS
> I try to calculate electronic structure of a carbon nanotube when 
> another biomolecule dock with it. have seen ever such as this by 
> Quantum-Espresso? I want to know that it's a conceptual barrier to 
> this purpose  with Quantum-Espresso? 
No conceptual barrier, just a matter on how large (size, number of atoms 
and electrons) is you system, because the larger it is, the more 
(computationally) expensive is the calculation!

Giovanni


-- 



Dr. Giovanni Cantele
Coherentia CNR-INFM and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario di Monte S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910
Fax:   +39 081 676346
E-mail: giovanni.cantele at cnr.it
        giovanni.cantele at na.infn.it
Web: http://people.na.infn.it/~cantele
Research Group: http://www.nanomat.unina.it


From giannozz at democritos.it  Fri Dec 12 10:51:48 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 12 Dec 2008 10:51:48 +0100
Subject: [Pw_forum] How to change the weight parameter in
	hybrid	functional?
In-Reply-To: <34ad5960812101159q1b2ca8d5w70666e28fc48d94a@mail.gmail.com>
References: <17284108.1111228930075467.JavaMail.coremail@bj126app55.126.com>
	<34ad5960812101159q1b2ca8d5w70666e28fc48d94a@mail.gmail.com>
Message-ID: <49423434.7030707@democritos.it>

Marci wrote:

> A better solution would be to add a new flag to the input parameters.

if one day hybrid calculations with variable exx_fraction  become
common, what you propose will be done for sure. In any event, everybody
can modify the code and add an input variable.  Some instructions  can
be found in the (would-be) developer manual on the quantum-espresso wiki:

http://www.quantum-espresso.org/wiki/index.php/Developer_Manual#Adding_or_modifying_input_variables


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

From iori at theory.polytechnique.fr  Fri Dec 12 14:02:18 2008
From: iori at theory.polytechnique.fr (Federico Iori)
Date: Fri, 12 Dec 2008 14:02:18 +0100
Subject: [Pw_forum] Hybrids in PWscf
Message-ID: <494260DA.1040104@theory.polytechnique.fr>

Dear all,

I would like to ask you some infos about the PBE0 and BLYP in the CVS 
version of pwscf.
I dont want to bother anyone, if the questions I'm gonna ask were 
already  appear somewhere over the rainbow in the forum.

I was wondering to relax my system V2O3 (very nice compound!) using PBE0 
and also B3LYP...but after several iterations i found this error message:



     WARNING: integrated charge=     0.00000000, expected=   457.00000000

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from electrons : error #         1
     charge is wrong
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

 I would like to ask you: why?

i can provide my input file also:

 &CONTROL
        calculation='scf'
        title='scf'
        verbosity='high'
        restart_mode='from_scratch'
        nstep=100
        iprint=1
        tprnfor=.true.
        outdir='./'
        prefix='scf'
        disk_io='default'
        pseudo_dir='/home/fiori/CODES/PW_pseudo/'
/
 &SYSTEM
        ibrav=0
        celldm(1)=0
        nat=80
        ntyp=3
        nbnd=240
        ecutwfc=30.0
        ecutrho=400.0
        !nosym=.TRUE.
        occupations='smearing',
        smearing='gaussian',
        degauss=0.08,
        !input_dft='PBE0',
        input_dft='B3LP',
        nqx1 = 1, nqx2 = 1, nqx3 = 1
/
 &ELECTRONS
        !diagonalization='cg'
        !conv_thr=1.0d-6
        mixing_mode = 'plain'
        mixing_beta=0.06d0
!       startingwfc='file'
!       startingpot='file'
/
 &IONS
        ion_dynamics='bfgs'
        upscale=20.0
/
ATOMIC_SPECIES
        V     50.9415   V.pbe-n-van.UPF
        O     15.9994   O.pbe-van_ak.UPF
        Cr    51.9961   Cr.pbe-sp-van.UPF
ATOMIC_POSITIONS {Bohr}
...

K_POINTS {automatic}
2 2 2 1 1 1
CELL_PARAMETERS
   10.90708       0.000000       17.52666
  -5.453541       9.445809       17.52666
  -5.453541      -9.445809       17.52666




NB: I omitted the coordinates since are 80 atoms just for sake of 
shorteness..anyway if needed i can provide the coordinates in a second mail!

Thanks in adavance,
have a nice day.

federico iori.


-- 
Dr. Federico Iori, PhD!

Laboratoire des Solides Irradi?s,
Ecole Polytechnique - CEA/DSM, CNRS 
91128 Palaiseau, France

www.etsf.polytechnique.fr

phone: +33 (0) 1 69 33 44 85
emails: federico.iori @ polytechnique.edu 
        iori.federico @ unimore.it
http://www.pdmodena.it/
http://www.comune.mo.it


From giannozz at democritos.it  Fri Dec 12 15:03:08 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 12 Dec 2008 15:03:08 +0100
Subject: [Pw_forum] Hybrids in PWscf
In-Reply-To: <494260DA.1040104@theory.polytechnique.fr>
References: <494260DA.1040104@theory.polytechnique.fr>
Message-ID: <49426F1C.2070102@democritos.it>

Federico Iori wrote:

>         calculation='scf'

wasn't it a "relax" calculation?

> NB: I omitted the coordinates since are 80 atoms just for sake of 
> shorteness..anyway if needed i can provide the coordinates in a second mail!

what is needed here is first of all the following:
1) whether this error is reproducible (on the same machine
    or also on different machines), and if so,
2) under which exact conditions this happens (even better:
    under which slightly changed conditions this doesn't happen
    any longer), and
3) whether this problem is present in all Q-E versions or only
    some of them and which ones.
There is no way one can guess where the problem can be without
pieces 1) and 2) of information (or maybe also with them).
Reproducing an 80-atom calculation requires computer and human
resources that may or may not be available (typically they aren't)

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

From iori at theory.polytechnique.fr  Fri Dec 12 15:23:19 2008
From: iori at theory.polytechnique.fr (Federico Iori)
Date: Fri, 12 Dec 2008 15:23:19 +0100
Subject: [Pw_forum] Hybrids in PWscf
In-Reply-To: <49426F1C.2070102@democritos.it>
References: <494260DA.1040104@theory.polytechnique.fr>
	<49426F1C.2070102@democritos.it>
Message-ID: <494273D7.5060104@theory.polytechnique.fr>

Paolo Giannozzi wrote:
> Federico Iori wrote:
>
>   
>>         calculation='scf'
>>     
>
> wasn't it a "relax" calculation?
>   
yes at the beginning was a relax calculation...then when i found this 
error, i decide that maybe was better to start my relaxation from the 
density calculated with the hybrids  through a scf calculation. this is 
the story.
>   
>> NB: I omitted the coordinates since are 80 atoms just for sake of 
>> shorteness..anyway if needed i can provide the coordinates in a second mail!
>>     
>
> what is needed here is first of all the following:
> 1) whether this error is reproducible (on the same machine
>     or also on different machines), and if so,
> 2) under which exact conditions this happens (even better:
>     under which slightly changed conditions this doesn't happen
>     any longer), and
> 3) whether this problem is present in all Q-E versions or only
>     some of them and which ones.
> There is no way one can guess where the problem can be without
> pieces 1) and 2) of information (or maybe also with them).
> Reproducing an 80-atom calculation requires computer and human
> resources that may or may not be available (typically they aren't)
>
> Paolo
>   
ok Paolo. I will provide the information you ask..this calculation is 
terrible..your right in terms of human time and resources and since that 
i was now focusing my attention on some other aspects. But i would like 
to resolve it.
so let me "waste" more cpu time in the following days, and then with the 
infos you ask...i will post again on the forum.

3) concerning this point i forgot to mentino i try only the 4.1CVS 
version...since from what i read on the website, they suggest to use the 
exx option only in the cvs version. but, may i try to compile and use it 
also from other production versions?

thanks!
federico!


-- 
Dr. Federico Iori, PhD!

Laboratoire des Solides Irradi?s,
Ecole Polytechnique - CEA/DSM, CNRS 
91128 Palaiseau, France

www.etsf.polytechnique.fr

phone: +33 (0) 1 69 33 44 85
emails: federico.iori @ polytechnique.edu 
        iori.federico @ unimore.it
http://www.pdmodena.it/
http://www.comune.mo.it


From degironc at sissa.it  Fri Dec 12 15:50:37 2008
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 12 Dec 2008 15:50:37 +0100
Subject: [Pw_forum] Hybrids in PWscf
In-Reply-To: <494260DA.1040104@theory.polytechnique.fr>
References: <494260DA.1040104@theory.polytechnique.fr>
Message-ID: <49427A3D.2090704@sissa.it>

What happens if you do a PBE calculation (no exx)... does the error also 
appears or not ?
stefano

Federico Iori wrote:
> Dear all,
>
> I would like to ask you some infos about the PBE0 and BLYP in the CVS 
> version of pwscf.
> I dont want to bother anyone, if the questions I'm gonna ask were 
> already  appear somewhere over the rainbow in the forum.
>
> I was wondering to relax my system V2O3 (very nice compound!) using PBE0 
> and also B3LYP...but after several iterations i found this error message:
>
>
>
>      WARNING: integrated charge=     0.00000000, expected=   457.00000000
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from electrons : error #         1
>      charge is wrong
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>      stopping ...
>
>  I would like to ask you: why?
>
> i can provide my input file also:
>
>  &CONTROL
>         calculation='scf'
>         title='scf'
>         verbosity='high'
>         restart_mode='from_scratch'
>         nstep=100
>         iprint=1
>         tprnfor=.true.
>         outdir='./'
>         prefix='scf'
>         disk_io='default'
>         pseudo_dir='/home/fiori/CODES/PW_pseudo/'
> /
>  &SYSTEM
>         ibrav=0
>         celldm(1)=0
>         nat=80
>         ntyp=3
>         nbnd=240
>         ecutwfc=30.0
>         ecutrho=400.0
>         !nosym=.TRUE.
>         occupations='smearing',
>         smearing='gaussian',
>         degauss=0.08,
>         !input_dft='PBE0',
>         input_dft='B3LP',
>         nqx1 = 1, nqx2 = 1, nqx3 = 1
> /
>  &ELECTRONS
>         !diagonalization='cg'
>         !conv_thr=1.0d-6
>         mixing_mode = 'plain'
>         mixing_beta=0.06d0
> !       startingwfc='file'
> !       startingpot='file'
> /
>  &IONS
>         ion_dynamics='bfgs'
>         upscale=20.0
> /
> ATOMIC_SPECIES
>         V     50.9415   V.pbe-n-van.UPF
>         O     15.9994   O.pbe-van_ak.UPF
>         Cr    51.9961   Cr.pbe-sp-van.UPF
> ATOMIC_POSITIONS {Bohr}
> ...
>
> K_POINTS {automatic}
> 2 2 2 1 1 1
> CELL_PARAMETERS
>    10.90708       0.000000       17.52666
>   -5.453541       9.445809       17.52666
>   -5.453541      -9.445809       17.52666
>
>
>
>
> NB: I omitted the coordinates since are 80 atoms just for sake of 
> shorteness..anyway if needed i can provide the coordinates in a second mail!
>
> Thanks in adavance,
> have a nice day.
>
> federico iori.
>
>
>   


From iori at theory.polytechnique.fr  Fri Dec 12 15:58:57 2008
From: iori at theory.polytechnique.fr (Federico Iori)
Date: Fri, 12 Dec 2008 15:58:57 +0100
Subject: [Pw_forum] Hybrids in PWscf
In-Reply-To: <49427A3D.2090704@sissa.it>
References: <494260DA.1040104@theory.polytechnique.fr>
	<49427A3D.2090704@sissa.it>
Message-ID: <49427C31.2000008@theory.polytechnique.fr>

Stefano de Gironcoli wrote:
> What happens if you do a PBE calculation (no exx)... does the error also 
> appears or not ?
> stefano
>   
ah no. with PBE calculation everything is fine. absolutely. I did with 
the PBE the scf and relax calculation. no matter for that.

> Federico Iori wrote:
>   
>> Dear all,
>>
>> I would like to ask you some infos about the PBE0 and BLYP in the CVS 
>> version of pwscf.
>> I dont want to bother anyone, if the questions I'm gonna ask were 
>> already  appear somewhere over the rainbow in the forum.
>>
>> I was wondering to relax my system V2O3 (very nice compound!) using PBE0 
>> and also B3LYP...but after several iterations i found this error message:
>>
>>
>>
>>      WARNING: integrated charge=     0.00000000, expected=   457.00000000
>>
>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>      from electrons : error #         1
>>      charge is wrong
>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>>      stopping ...
>>
>>  I would like to ask you: why?
>>
>> i can provide my input file also:
>>
>>  &CONTROL
>>         calculation='scf'
>>         title='scf'
>>         verbosity='high'
>>         restart_mode='from_scratch'
>>         nstep=100
>>         iprint=1
>>         tprnfor=.true.
>>         outdir='./'
>>         prefix='scf'
>>         disk_io='default'
>>         pseudo_dir='/home/fiori/CODES/PW_pseudo/'
>> /
>>  &SYSTEM
>>         ibrav=0
>>         celldm(1)=0
>>         nat=80
>>         ntyp=3
>>         nbnd=240
>>         ecutwfc=30.0
>>         ecutrho=400.0
>>         !nosym=.TRUE.
>>         occupations='smearing',
>>         smearing='gaussian',
>>         degauss=0.08,
>>         !input_dft='PBE0',
>>         input_dft='B3LP',
>>         nqx1 = 1, nqx2 = 1, nqx3 = 1
>> /
>>  &ELECTRONS
>>         !diagonalization='cg'
>>         !conv_thr=1.0d-6
>>         mixing_mode = 'plain'
>>         mixing_beta=0.06d0
>> !       startingwfc='file'
>> !       startingpot='file'
>> /
>>  &IONS
>>         ion_dynamics='bfgs'
>>         upscale=20.0
>> /
>> ATOMIC_SPECIES
>>         V     50.9415   V.pbe-n-van.UPF
>>         O     15.9994   O.pbe-van_ak.UPF
>>         Cr    51.9961   Cr.pbe-sp-van.UPF
>> ATOMIC_POSITIONS {Bohr}
>> ...
>>
>> K_POINTS {automatic}
>> 2 2 2 1 1 1
>> CELL_PARAMETERS
>>    10.90708       0.000000       17.52666
>>   -5.453541       9.445809       17.52666
>>   -5.453541      -9.445809       17.52666
>>
>>
>>
>>
>> NB: I omitted the coordinates since are 80 atoms just for sake of 
>> shorteness..anyway if needed i can provide the coordinates in a second mail!
>>
>> Thanks in adavance,
>> have a nice day.
>>
>> federico iori.
>>
>>
>>   
>>     
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>   


-- 
Dr. Federico Iori, PhD!

Laboratoire des Solides Irradi?s,
Ecole Polytechnique - CEA/DSM, CNRS 
91128 Palaiseau, France

www.etsf.polytechnique.fr

phone: +33 (0) 1 69 33 44 85
emails: federico.iori @ polytechnique.edu 
        iori.federico @ unimore.it
http://www.pdmodena.it/
http://www.comune.mo.it


From giannozz at democritos.it  Fri Dec 12 17:07:59 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 12 Dec 2008 17:07:59 +0100
Subject: [Pw_forum] Hybrids in PWscf
In-Reply-To: <494273D7.5060104@theory.polytechnique.fr>
References: <494260DA.1040104@theory.polytechnique.fr>	<49426F1C.2070102@democritos.it>
	<494273D7.5060104@theory.polytechnique.fr>
Message-ID: <49428C5F.6090907@democritos.it>

Federico Iori wrote:

> 3) concerning this point i forgot to mentino i try only the 4.1CVS 
> version...since from what i read on the website, they suggest to use the 
> exx option only in the cvs version. but, may i try to compile and use it 
> also from other production versions?

the exx option has been around since some time, so what the website
says (where exactly?) might be obsolete. I don;t think there has
been much activity on exx since the release of the stable version,
but I might be wrong.

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

From marc at fq.edu.uy  Fri Dec 12 23:27:32 2008
From: marc at fq.edu.uy (Marc Segovia)
Date: Fri, 12 Dec 2008 20:27:32 -0200
Subject: [Pw_forum] QE with debian
Message-ID: <4942E554.9060507@fq.edu.uy>

Dear all

 We want to install Quantum Espresso in a 32bit machine, with debian, 
there we have ifort, mpif77 ,openmpi and mpich, but we have some troubles.
 Can someone guide us, we are new with parallel implementation, but we 
cannot install serial too.
We try several options like

1)  ./configure
mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW 
-I../include   -I./  -I../Modules  -I../iotk/src -I../PW  -I../PH -c 
iotk_base.f90
--------------------------------------------------------------------------
The Open MPI wrapper compiler was unable to find the specified compiler
gfortran in your PATH.

Note that this compiler was either specified at configure time or in
one of several possible environment variables.
--------------------------------------------------------------------------
make[2]: *** [iotk_base.o] Error 1
make[2]: Leaving directory `/home/marc/espresso-4.0.4/iotk/src'
make[1]: *** [lib+util] Error 2
make[1]: Leaving directory `/home/marc/espresso-4.0.4/iotk'
make: *** [libiotk] Error 2

2) then ./configure MPIF90=mpif77, after exclude some options -nomodule 
-assume byterecyl

ar: iotk_attr+CHARACTER1_0.o: No such file or directory
make[2]: *** [libiotk.a] Error 1
make[2]: Leaving directory `/home/marc/espresso-4.0.4/iotk/src'
make[1]: *** [lib+util] Error 2
make[1]: Leaving directory `/home/marc/espresso-4.0.4/iotk'
make: *** [libiotk] Error 2

3) then ./configure MPIF90=ifort

fortcom: Severe: Too many errors, exiting
compilation aborted for xml_io_base.f90 (code 1)
make[1]: *** [xml_io_base.o] Error 1
make[1]: Leaving directory `/home/marc/espresso-4.0.4/Modules'
make: *** [mods] Error 2




 


From lanhaiping at gmail.com  Sat Dec 13 00:50:03 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Sat, 13 Dec 2008 07:50:03 +0800
Subject: [Pw_forum] QE with debian
In-Reply-To: <4942E554.9060507@fq.edu.uy>
References: <4942E554.9060507@fq.edu.uy>
Message-ID: <c92002fa0812121550w4a95c669l1cb129a6ff2d6670@mail.gmail.com>

you should build mpi with gfortran but without gfortran in your PATH ??

The Open MPI wrapper compiler was unable to find the specified compiler
gfortran in your PATH.

On Sat, Dec 13, 2008 at 6:27 AM, Marc Segovia <marc at fq.edu.uy> wrote:

> Dear all
>
>  We want to install Quantum Espresso in a 32bit machine, with debian,
> there we have ifort, mpif77 ,openmpi and mpich, but we have some troubles.
>  Can someone guide us, we are new with parallel implementation, but we
> cannot install serial too.
> We try several options like
>
> 1)  ./configure
> mpif90 -O2 -assume byterecl -nomodule -fpp -D__INTEL -D__FFTW
> -I../include   -I./  -I../Modules  -I../iotk/src -I../PW  -I../PH -c
> iotk_base.f90
> --------------------------------------------------------------------------
> The Open MPI wrapper compiler was unable to find the specified compiler
> gfortran in your PATH.
>
> Note that this compiler was either specified at configure time or in
> one of several possible environment variables.
> --------------------------------------------------------------------------
> make[2]: *** [iotk_base.o] Error 1
> make[2]: Leaving directory `/home/marc/espresso-4.0.4/iotk/src'
> make[1]: *** [lib+util] Error 2
> make[1]: Leaving directory `/home/marc/espresso-4.0.4/iotk'
> make: *** [libiotk] Error 2
>
> 2) then ./configure MPIF90=mpif77, after exclude some options -nomodule
> -assume byterecyl
>
> ar: iotk_attr+CHARACTER1_0.o: No such file or directory
> make[2]: *** [libiotk.a] Error 1
> make[2]: Leaving directory `/home/marc/espresso-4.0.4/iotk/src'
> make[1]: *** [lib+util] Error 2
> make[1]: Leaving directory `/home/marc/espresso-4.0.4/iotk'
> make: *** [libiotk] Error 2
>
> 3) then ./configure MPIF90=ifort
>
> fortcom: Severe: Too many errors, exiting
> compilation aborted for xml_io_base.f90 (code 1)
> make[1]: *** [xml_io_base.o] Error 1
> make[1]: Leaving directory `/home/marc/espresso-4.0.4/Modules'
> make: *** [mods] Error 2
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From chem.jonathan at gmail.com  Sat Dec 13 12:37:04 2008
From: chem.jonathan at gmail.com (Jonathan Li)
Date: Sat, 13 Dec 2008 03:37:04 -0800
Subject: [Pw_forum] Jonathan Li wants to chat
Message-ID: <16c569cb0812130337r38428c14u@mail.gmail.com>

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

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storage - and chat with Jonathan Li, visit:
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- Instant messaging right inside Gmail
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From giannozz at democritos.it  Sat Dec 13 12:38:13 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 13 Dec 2008 12:38:13 +0100
Subject: [Pw_forum] QE with debian
In-Reply-To: <4942E554.9060507@fq.edu.uy>
References: <4942E554.9060507@fq.edu.uy>
Message-ID: <1AC3938C-1B4E-4233-B7BF-0180E57ECAD5@democritos.it>


On Dec 12, 2008, at 23:27 , Marc Segovia wrote:

>  We want to install Quantum Espresso in a 32bit machine, with debian,
> there we have ifort, mpif77 ,openmpi and mpich, but we have some
> troubles. Can someone guide us

there are rather detailed instructions in the user guide.
You need a working f95 serial compiler to compile for
serial execution, a working f95 parallel compiler using
MPI with working MPI libraries. My guess is that you
have none of them

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



From panda.deng.pan at gmail.com  Sun Dec 14 07:49:53 2008
From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=)
Date: Sun, 14 Dec 2008 14:49:53 +0800
Subject: [Pw_forum] (no subject)
Message-ID: <c8dadee0812132249h35041c55wdb5afa1adf81bcd5@mail.gmail.com>

Dear All,
     I have a question about this input file in example03.
cat > al001.mm.in << EOF
&CONTROL
  calculation = "relax",
 * dt          = 30.D0,*
  pseudo_dir  = "$PSEUDO_DIR",
  outdir      = "$TMP_DIR",
/
&SYSTEM
  ibrav       = 6,
  celldm(1)   = 5.3033D0,
  celldm(3)   = 8.D0,
  nat         = 7,
  ntyp        = 1,
  ecutwfc     = 12.D0,
  occupations = "smearing",
  smearing    = "methfessel-paxton",
  degauss     = 0.05D0,
/
&ELECTRONS
  conv_thr    = 1.D-7,
  mixing_beta = 0.3D0,
/
&IONS
*  ion_dynamics      = "damp",*
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
/

Is the "dt" necessory for the "ion_dynamics=damp" ? And how to determine the
value of "dt"?

Thanks.
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From yay451 at mail.usask.ca  Sun Dec 14 20:24:31 2008
From: yay451 at mail.usask.ca (Yansun Yao)
Date: Sun, 14 Dec 2008 13:24:31 -0600
Subject: [Pw_forum] input/output not consistent for ibrav =0 in subroutine
	readmat (elphon.f90)
Message-ID: <1229282671.49455d6fb1426@webmail.usask.ca>

Dear Quantum-ESPRESSO developers,

    I found if one uses ibrav=0 for phonon calculations, there are 4 extra lines
printed out on the top of dyn file, showing explicitly the cell parameters. For
example,

cubic
   1.008529298   0.000000000   0.000000000
   0.000000000   1.008529298   0.000000000
   0.000000000   0.000000000   1.726604604

   However, the subroutine readmat in elphon.f90 does not have the option
reading/avoiding these lines.  These are the relavent lines I grepped from
elphon.f90:

  REWIND (iudyn)
  READ (iudyn, '(a)') line
  READ (iudyn, '(a)') line
  READ (iudyn, * ) ntyp_, nat_, ibrav_, celldm_
  DO na = 1, nat
     READ (iudyn, * ) i, ityp_, tau_
     IF (na.NE.i.OR.ityp_.NE.ityp (na) ) CALL errore ('readmat', &
          'inconsistent data', 10 + na)
  ENDDO

  I guess we might need to insert some commands here for ibrav=0.

  I hope my understanding here is correct, but please forgive me if I rised a
stupid question.  Recently I updated my Quantum-ESPRESSO to the newest version
from version 2.1.4, so there are some parts become unfamiliar to me.  I guess I
need to update it more often.

  Cheers

Yansun

Yansun Yao
Steacie Institute for Molecular Sciences
National Research Council of Canada
100 Sussex Drive
Ottawa, Ontario K1A 0R6


From marc at fq.edu.uy  Mon Dec 15 00:48:07 2008
From: marc at fq.edu.uy (marc at fq.edu.uy)
Date: Sun, 14 Dec 2008 21:48:07 -0200 (UYST)
Subject: [Pw_forum] QE with debian
In-Reply-To: <1AC3938C-1B4E-4233-B7BF-0180E57ECAD5@democritos.it>
References: <4942E554.9060507@fq.edu.uy>
	<1AC3938C-1B4E-4233-B7BF-0180E57ECAD5@democritos.it>
Message-ID: <1432.190.134.6.125.1229298487.squirrel@webmail.fq.edu.uy>

 You are right, we install gfortran, and i compiles pretty good, many thanks.
 Marc

>
> On Dec 12, 2008, at 23:27 , Marc Segovia wrote:
>
>>  We want to install Quantum Espresso in a 32bit machine, with debian,
>> there we have ifort, mpif77 ,openmpi and mpich, but we have some
>> troubles. Can someone guide us
>
> there are rather detailed instructions in the user guide.
> You need a working f95 serial compiler to compile for
> serial execution, a working f95 parallel compiler using
> MPI with working MPI libraries. My guess is that you
> have none of them
>
> Paolo
> ---
> 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
>



From edu.ogando at ehu.es  Mon Dec 15 13:07:41 2008
From: edu.ogando at ehu.es (edu)
Date: Mon, 15 Dec 2008 13:07:41 +0100
Subject: [Pw_forum] Benchmarks
Message-ID: <200812151307.41294.edu.ogando@ehu.es>

Hi!
	We have made some benchmarks in our Itanium, Opteron, Core2duo and Pentium 
machines with pw.x and ph.x. You can find them here

http://www.ehu.es/SGI/Informes_tf.html

	I hope you can find useful.

Have a nice day,
Edu.

From yuminqian at gmail.com  Mon Dec 15 14:35:51 2008
From: yuminqian at gmail.com (yumin qian)
Date: Mon, 15 Dec 2008 21:35:51 +0800
Subject: [Pw_forum] pseudo potential generation problem
Message-ID: <aa128b2c0812150535ud69a83dr8ff8b6066bf69b9c@mail.gmail.com>

>
> Dear PWSCF users
>
        I  meet a problem in pseudo potential generation using the 'atomic'
package
        I meet various problems such as
      from run_pseudo : error #         1
     Errors in PS-KS equation



      from ld1_readin : error #         1
     unbound states must be empty


     from ld1_readin : error #         1
     only one local channel


       I think all of the problems arise from the wrong setting of
 PseudoPotentialGenerationCards
        my question is  how to set this section to avoid this error .Is
there a general reference about the setting of this section ?
I look into the atomic_doc folder ,but I can not  find the solution .

this is my input file
 &input
        title='Sr',
        zed=38.0,
        rel=0,
        iswitch=3,
        rlderiv=2.50,
        eminld=-4.0,
        emaxld=4.0,
        deld=0.02,
        config='[Kr] 5s2 5p0',
        dft='LDA'
 /
 &inputp
        pseudotype=2,
        lloc=0,
        file_pseudopw='Sr_LDA_TM.UPF',
        nlcc=.true.,
        tm=.true.,
        rcore=1.2,
        rcloc=2.0
 /
2
5P  2  1  0.00  0.00  2.20  3.40  0.00
5S  1  0  2.00  0.50  2.10  2.60  0.00
~

the output gives :
      from ld1_readin : error #         1
     unbound states must be empty


Can anyone help me , many thanks.



-- 
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel:  + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From fratesi at mater.unimib.it  Mon Dec 15 14:43:53 2008
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Mon, 15 Dec 2008 14:43:53 +0100 (CET)
Subject: [Pw_forum] pseudo potential generation problem
In-Reply-To: <aa128b2c0812150535ud69a83dr8ff8b6066bf69b9c@mail.gmail.com>
References: <aa128b2c0812150535ud69a83dr8ff8b6066bf69b9c@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0812151438550.30530@localhost>

Dear Yumin,
try changing
   5S  1  0  2.00  0.50  2.10  2.60  0.00
to
   5S  1  0  2.00  0.00  2.10  2.60  0.00
(a value different from zero means that you are specifying the energy 
for an empty state, which is what you might want to do in order to add a 
second projector for the same state, in that case with charge=0)
Hope this helps,
Guido

On Mon, 15 Dec 2008, yumin qian wrote:

>>
>> Dear PWSCF users
>>
>        I  meet a problem in pseudo potential generation using the 'atomic'
> package
>        I meet various problems such as
>      from run_pseudo : error #         1
>     Errors in PS-KS equation
>
>
>
>      from ld1_readin : error #         1
>     unbound states must be empty
>
>
>     from ld1_readin : error #         1
>     only one local channel
>
>
>       I think all of the problems arise from the wrong setting of
> PseudoPotentialGenerationCards
>        my question is  how to set this section to avoid this error .Is
> there a general reference about the setting of this section ?
> I look into the atomic_doc folder ,but I can not  find the solution .
>
> this is my input file
> &input
>        title='Sr',
>        zed=38.0,
>        rel=0,
>        iswitch=3,
>        rlderiv=2.50,
>        eminld=-4.0,
>        emaxld=4.0,
>        deld=0.02,
>        config='[Kr] 5s2 5p0',
>        dft='LDA'
> /
> &inputp
>        pseudotype=2,
>        lloc=0,
>        file_pseudopw='Sr_LDA_TM.UPF',
>        nlcc=.true.,
>        tm=.true.,
>        rcore=1.2,
>        rcloc=2.0
> /
> 2
> 5P  2  1  0.00  0.00  2.20  3.40  0.00
> 5S  1  0  2.00  0.50  2.10  2.60  0.00
> ~
>
> the output gives :
>      from ld1_readin : error #         1
>     unbound states must be empty
>
>
> Can anyone help me , many thanks.
>
>
>
>

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy


From yuminqian at gmail.com  Mon Dec 15 15:04:37 2008
From: yuminqian at gmail.com (yumin qian)
Date: Mon, 15 Dec 2008 22:04:37 +0800
Subject: [Pw_forum] pseudo potential generation problem
In-Reply-To: <Pine.LNX.4.64.0812151438550.30530@localhost>
References: <aa128b2c0812150535ud69a83dr8ff8b6066bf69b9c@mail.gmail.com>
	<Pine.LNX.4.64.0812151438550.30530@localhost>
Message-ID: <aa128b2c0812150604m1f34026cibc49945a1a4a9682@mail.gmail.com>

Thanks for your help , I did it following your suggestion ,and the output
gives

     task #         0
     from run_pseudo : error #         1
     Errors in PS-KS equation
I don't know  what cause this error.
thank you
2008/12/15 Guido Fratesi <fratesi at mater.unimib.it>

> Dear Yumin,
> try changing
>   5S  1  0  2.00  0.50  2.10  2.60  0.00
> to
>   5S  1  0  2.00  0.00  2.10  2.60  0.00
> (a value different from zero means that you are specifying the energy
> for an empty state, which is what you might want to do in order to add a
> second projector for the same state, in that case with charge=0)
> Hope this helps,
> Guido
>
> On Mon, 15 Dec 2008, yumin qian wrote:
>
> >>
> >> Dear PWSCF users
> >>
> >        I  meet a problem in pseudo potential generation using the
> 'atomic'
> > package
> >        I meet various problems such as
> >      from run_pseudo : error #         1
> >     Errors in PS-KS equation
> >
> >
> >
> >      from ld1_readin : error #         1
> >     unbound states must be empty
> >
> >
> >     from ld1_readin : error #         1
> >     only one local channel
> >
> >
> >       I think all of the problems arise from the wrong setting of
> > PseudoPotentialGenerationCards
> >        my question is  how to set this section to avoid this error .Is
> > there a general reference about the setting of this section ?
> > I look into the atomic_doc folder ,but I can not  find the solution .
> >
> > this is my input file
> > &input
> >        title='Sr',
> >        zed=38.0,
> >        rel=0,
> >        iswitch=3,
> >        rlderiv=2.50,
> >        eminld=-4.0,
> >        emaxld=4.0,
> >        deld=0.02,
> >        config='[Kr] 5s2 5p0',
> >        dft='LDA'
> > /
> > &inputp
> >        pseudotype=2,
> >        lloc=0,
> >        file_pseudopw='Sr_LDA_TM.UPF',
> >        nlcc=.true.,
> >        tm=.true.,
> >        rcore=1.2,
> >        rcloc=2.0
> > /
> > 2
> > 5P  2  1  0.00  0.00  2.20  3.40  0.00
> > 5S  1  0  2.00  0.50  2.10  2.60  0.00
> > ~
> >
> > the output gives :
> >      from ld1_readin : error #         1
> >     unbound states must be empty
> >
> >
> > Can anyone help me , many thanks.
> >
> >
> >
> >
>
> --
> Guido Fratesi
>
> Dipartimento di Scienza dei Materiali
> Universita` degli Studi di Milano-Bicocca
> via Cozzi 53, 20125 Milano, Italy
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel:  + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From giannozz at democritos.it  Mon Dec 15 15:35:52 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 15 Dec 2008 15:35:52 +0100
Subject: [Pw_forum] pseudo potential generation problem
In-Reply-To: <aa128b2c0812150604m1f34026cibc49945a1a4a9682@mail.gmail.com>
References: <aa128b2c0812150535ud69a83dr8ff8b6066bf69b9c@mail.gmail.com>	<Pine.LNX.4.64.0812151438550.30530@localhost>
	<aa128b2c0812150604m1f34026cibc49945a1a4a9682@mail.gmail.com>
Message-ID: <49466B48.1010007@democritos.it>

yumin qian wrote:

>      from run_pseudo : error #         1
>      Errors in PS-KS equation
> I don't know  what cause this error.

nor do I, but what I know for sure that it is quite difficult
to get a pseudopotential right even with reasonable generation
parameters. With unreasonable parameters like these:

> 5P  2  1  0.00  0.00  2.20  3.40  0.00
> 5S  1  0  2.00  0.50  2.10  2.60  0.00

it is close to impossible.
[ Rc=2.10 and 2.20 are unreasonably small for orbitals whose maximum
  is located at 3.6690 and 4.8303 a.u. respectively; 2.60 and 3.40 are
  for UltraSoft pseudization and are ignored with option iswitch=2,
  i.e. Norm Conserving pseudization with multiple projectors per
  angular momentum; in this case equivalent to iswitch=1, since there
  is just one projector per angular momentum above.]
In general, it is close to impossible to produce a pseudopotential
without some understanding of how the generation procedure works,
and some care in preparing input data (for which a rather detailed
documentation exists)

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

From yuminqian at gmail.com  Mon Dec 15 15:47:27 2008
From: yuminqian at gmail.com (yumin qian)
Date: Mon, 15 Dec 2008 22:47:27 +0800
Subject: [Pw_forum] pseudo potential generation problem
In-Reply-To: <49466B48.1010007@democritos.it>
References: <aa128b2c0812150535ud69a83dr8ff8b6066bf69b9c@mail.gmail.com>
	<Pine.LNX.4.64.0812151438550.30530@localhost>
	<aa128b2c0812150604m1f34026cibc49945a1a4a9682@mail.gmail.com>
	<49466B48.1010007@democritos.it>
Message-ID: <aa128b2c0812150647v68a42950x9e47659afe6aa856@mail.gmail.com>

Thanks for you reply ,I am reading the notes of pseudopotential generation
in the atomic_doc folder
  I thank I need some detailed understanding about pseudopotential
generation ,
 Many Thanks It's very kind of you .

2008/12/15 Paolo Giannozzi <giannozz at democritos.it>

> yumin qian wrote:
>
> >      from run_pseudo : error #         1
> >      Errors in PS-KS equation
> > I don't know  what cause this error.
>
> nor do I, but what I know for sure that it is quite difficult
> to get a pseudopotential right even with reasonable generation
> parameters. With unreasonable parameters like these:
>
> > 5P  2  1  0.00  0.00  2.20  3.40  0.00
> > 5S  1  0  2.00  0.50  2.10  2.60  0.00
>
> it is close to impossible.
> [ Rc=2.10 and 2.20 are unreasonably small for orbitals whose maximum
>  is located at 3.6690 and 4.8303 a.u. respectively; 2.60 and 3.40 are
>  for UltraSoft pseudization and are ignored with option iswitch=2,
>  i.e. Norm Conserving pseudization with multiple projectors per
>  angular momentum; in this case equivalent to iswitch=1, since there
>  is just one projector per angular momentum above.]
> In general, it is close to impossible to produce a pseudopotential
> without some understanding of how the generation procedure works,
> and some care in preparing input data (for which a rather detailed
> documentation exists)
>
> Paolo
> --
> 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
>



-- 
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel:  + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From akohlmey at cmm.chem.upenn.edu  Mon Dec 15 16:44:43 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 15 Dec 2008 10:44:43 -0500 (EST)
Subject: [Pw_forum] (no subject)
In-Reply-To: <c8dadee0812132249h35041c55wdb5afa1adf81bcd5@mail.gmail.com>
References: <c8dadee0812132249h35041c55wdb5afa1adf81bcd5@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0812151040130.2391@localhost.localdomain>

On Sun, 14 Dec 2008, ???? wrote:

???> Dear All,

dear <insert name here>,

???> Is the "dt" necessory for the "ion_dynamics=damp" ? And how to 

yes. of course! just look up what damped dynamics does
and you'll understand.

???> determine the value of "dt"?

same thing. the optimal value of dt depends on the mass of
the atoms and the strength of their interactions, or to be
more precise the fastest motion in the system. there should
be some helpful discussions on the topic in the mailing list
archives. ... and have you checked the wiki?

cheers,
    axel.

???> 
???> Thanks.
???> 


p.s.: please follow the policy of this mailing list and
provide your name and affiliation in your posts. thanks.

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From afsaneh.daemi at gmail.com  Mon Dec 15 18:48:34 2008
From: afsaneh.daemi at gmail.com (afsaneh daemi)
Date: Mon, 15 Dec 2008 21:18:34 +0330
Subject: [Pw_forum] LDA+U
Message-ID: <373015a50812150948w6be39d66iee8b6566a4575389@mail.gmail.com>

Dear Professors,
                   may I ask you about systems in which we can use LDA? I
hear that LDA will not be able to interpret systems containing Van der Waals
interactions. Should it be considered using the LDA+U for these systems?
Sincerely Yours
Afsaneh Daemi
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From giannozz at democritos.it  Mon Dec 15 18:50:32 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 15 Dec 2008 18:50:32 +0100
Subject: [Pw_forum] LDA+U
In-Reply-To: <373015a50812150948w6be39d66iee8b6566a4575389@mail.gmail.com>
References: <373015a50812150948w6be39d66iee8b6566a4575389@mail.gmail.com>
Message-ID: <494698E8.4060503@democritos.it>

afsaneh daemi wrote:

> I hear that LDA will not be able to interpret systems containing  
> Van der Waals interactions. Should it be considered using the  
> LDA+U for these systems?

definitely not. LDA+U is for strongly correlated systems.

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

From jjr19 at uakron.edu  Mon Dec 15 22:32:05 2008
From: jjr19 at uakron.edu (J. J. Ramsey)
Date: Mon, 15 Dec 2008 13:32:05 -0800 (PST)
Subject: [Pw_forum] Question on how PWscf handles fractional electrons of
	pseudohydrogens
Message-ID: <731573.35121.qm@web50907.mail.re2.yahoo.com>

Simple question, I guess ...

If I have a system containing pseudohydrogens each with 1.25 valence electrons, will PWscf set the calculations up so that each pseudohydrogen contributes two Kohn-Sham orbitals, one with occupancy 1 and the other with occupation 0.25?



      

From m.abbasnejad at gmail.com  Tue Dec 16 08:11:53 2008
From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad)
Date: Tue, 16 Dec 2008 10:41:53 +0330
Subject: [Pw_forum] pw2casino
Message-ID: <7699a1950812152311u6a6dd26an10eeba8a7563711f@mail.gmail.com>

Hi,
I have a question about pw2casino:
How can I run pw2casino?
please answer me,( *m.abbasnejad at gmail.com )* <m.abbasnejad at gmail.com>
Kind regards,
-- 
--------------------------------------------------------------------------------

Mohaddeseh Abbasnejad,
Room No. 323, Department of Physics,
University of Tehran, End of north Karegar Ave.,
Tehran, P.O.Box: 14395-547- IRAN
Tel. No.: +98 21 6111 8634  & Fax No.: +98 21 8800 4781
E-Mail:    *m.abbasnejad at gmail.com * <m.abbasnejad at gmail.com>
Website:  *http://physics.ut.ac.ir <http://physics.ut.ac.ir%20>
*
--------------------------------------------------------------------------------
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From paulatto at sissa.it  Tue Dec 16 09:03:29 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 16 Dec 2008 09:03:29 +0100
Subject: [Pw_forum] Question on how PWscf handles fractional electrons
 of	pseudohydrogens
In-Reply-To: <731573.35121.qm@web50907.mail.re2.yahoo.com>
References: <731573.35121.qm@web50907.mail.re2.yahoo.com>
Message-ID: <494760D1.3050302@sissa.it>

J. J. Ramsey ha scritto:
> If I have a system containing pseudohydrogens each with 1.25 valence electrons, will PWscf set the calculations up so that each pseudohydrogen contributes two Kohn-Sham orbitals, one with occupancy 1 and the other with occupation 0.25?
>   
Dear J.J.,
Unless you have a multiple of 4 hydrogens, the system shall be metallic.
What will QE with the occupations do depends on what you require in the
input file.

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/



From giannozz at democritos.it  Tue Dec 16 09:05:42 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 16 Dec 2008 09:05:42 +0100
Subject: [Pw_forum] pw2casino
In-Reply-To: <7699a1950812152311u6a6dd26an10eeba8a7563711f@mail.gmail.com>
References: <7699a1950812152311u6a6dd26an10eeba8a7563711f@mail.gmail.com>
Message-ID: <49476156.4010304@democritos.it>

mohaddeseh abbasnejad wrote:

> How can I run pw2casino?

like all other postprocessing codes:
pw2casino.x
&inputpp
   outdir='...', prefix='...'
/

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

From zhaohscas at yahoo.com.cn  Tue Dec 16 11:40:28 2008
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Tue, 16 Dec 2008 18:40:28 +0800
Subject: [Pw_forum] Question on the tools used to visualize the point
	defects, such as vacancy and interstitial configurations.
In-Reply-To: <494760D1.3050302@sissa.it>
References: <731573.35121.qm@web50907.mail.re2.yahoo.com>
	<494760D1.3050302@sissa.it>
Message-ID: <942197838.20081216184028@yahoo.com.cn>

Hi all,

I'm currently want to visualize the point defects, such as vacancy and interstitial configurations in ZnO according to the Kr?ger-Vink Notation.  But I find that the though the perfect crystal structure is easy to construct, the ones with specific defects are more difficult to visualize.  Would you give me some hints on the tools used to visualize the point defects, such as vacancy and interstitial configurations?

Regards,
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn> 
Xinjiang Technical Institute of Physics and Chemistry
Chinese Academy of Sciences 
GnuPG DSA: 0xD108493
2008-12-16

__________________________________________________
?????????????????????????????
http://cn.mail.yahoo.com


From xuzp at MIT.EDU  Tue Dec 16 11:36:47 2008
From: xuzp at MIT.EDU (Zhiping Xu)
Date: Tue, 16 Dec 2008 05:36:47 -0500
Subject: [Pw_forum] In consistence between plotnum = 7/10 (PP.x)
In-Reply-To: <49476156.4010304@democritos.it>
References: <7699a1950812152311u6a6dd26an10eeba8a7563711f@mail.gmail.com>
	<49476156.4010304@democritos.it>
Message-ID: <20081216053647.4t3mgzrws7pwkk0s@webmail.mit.edu>

Hi all:
  I performed projected DOS calculation for the valence and conduction bands
using two different approaches:
(1) plotnum = 7, kpoint = 0 (Gamma point), kband around nelectrons/2
(2) plotnum = 10, by setting Emin and Emax contaning most part of the band

  The second method gives reasonable results, while the first one is shifted by
1 band. Any idea on this? Thanks.
Best,
Zhiping




From sclauzer at sissa.it  Tue Dec 16 12:14:04 2008
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 16 Dec 2008 12:14:04 +0100
Subject: [Pw_forum] In consistence between plotnum = 7/10 (PP.x)
In-Reply-To: <20081216053647.4t3mgzrws7pwkk0s@webmail.mit.edu>
References: <7699a1950812152311u6a6dd26an10eeba8a7563711f@mail.gmail.com>	<49476156.4010304@democritos.it>
	<20081216053647.4t3mgzrws7pwkk0s@webmail.mit.edu>
Message-ID: <49478D7C.8050307@sissa.it>

Dear Zhiping
Zhiping Xu wrote:
> Hi all:
>   I performed projected DOS calculation for the valence and conduction bands
> using two different approaches:
> (1) plotnum = 7, kpoint = 0 (Gamma point), kband around nelectrons/2

If the gamma point is the first k-point in the list (check pw.x output) you should specify 
kpoint = 1, NOT kpoint = 0. In principle you should get an error message if you actually 
used the an invalid kpoint index.

from PP/local_dos.f90:

   if ( (iflag == 0) .and. ( kpoint < 1 .or. kpoint > nks ) ) &
        call errore ('local_dos', 'wrong kpoint specified', 1)

Regards

Gabriele


> (2) plotnum = 10, by setting Emin and Emax contaning most part of the band
> 
>   The second method gives reasonable results, while the first one is shifted by
> 1 band. Any idea on this? Thanks.
> Best,
> Zhiping
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

-- 

La legge n. 133 uccide l'Universit? e la Ricerca italiana!

Save Italian Brains! (http://saveitalianbrains.wordpress.com/)

o ------------------------------------------------ o
| Gabriele Sclauzero, PhD Student                  |
| c/o:   SISSA & CNR-INFM Democritos,              |
|        via Beirut 2-4, 34014 Trieste (Italy)     |
| email: sclauzer at sissa.it                         |
| phone: +39 040 3787 511                          |
| skype: gurlonotturno                             |
o ------------------------------------------------ o

From meghdad_saeedian at yahoo.com  Tue Dec 16 13:19:25 2008
From: meghdad_saeedian at yahoo.com (meghdad saeedian)
Date: Tue, 16 Dec 2008 04:19:25 -0800 (PST)
Subject: [Pw_forum] eliminating symmetry for pw2casino
Message-ID: <66683.46657.qm@web31406.mail.mud.yahoo.com>

Hi,
I have a question:
How can I run scf without symmetry?
I mean: how should I make the required file?
Best regards,
Saeedian



      
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From sclauzer at sissa.it  Tue Dec 16 13:38:16 2008
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 16 Dec 2008 13:38:16 +0100
Subject: [Pw_forum] eliminating symmetry for pw2casino
In-Reply-To: <66683.46657.qm@web31406.mail.mud.yahoo.com>
References: <66683.46657.qm@web31406.mail.mud.yahoo.com>
Message-ID: <4947A138.4030202@sissa.it>

Hi,

meghdad saeedian wrote:
> Hi,
> I have a question:
> How can I run scf without symmetry?

nosym=.TRUE. in the namelist &control should do the job.
Be careful when chosing the k-point grid (see warnings in Doc/INPUT_PW.txt).

> I mean: how should I make the required file?

I hope I've actually understood your question...

regards,

GS

> Best regards,
> Saeedian
> 
> 
> 
>       
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 

La legge n. 133 uccide l'Universit? e la Ricerca italiana!

Save Italian Brains! (http://saveitalianbrains.wordpress.com/)

o ------------------------------------------------ o
| Gabriele Sclauzero, PhD Student                  |
| c/o:   SISSA & CNR-INFM Democritos,              |
|        via Beirut 2-4, 34014 Trieste (Italy)     |
| email: sclauzer at sissa.it                         |
| phone: +39 040 3787 511                          |
| skype: gurlonotturno                             |
o ------------------------------------------------ o

From sclauzer at sissa.it  Tue Dec 16 13:48:55 2008
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 16 Dec 2008 13:48:55 +0100
Subject: [Pw_forum] eliminating symmetry for pw2casino
In-Reply-To: <4947A138.4030202@sissa.it>
References: <66683.46657.qm@web31406.mail.mud.yahoo.com>
	<4947A138.4030202@sissa.it>
Message-ID: <4947A3B7.30603@sissa.it>



Gabriele Sclauzero wrote:
> Hi,
> 
> meghdad saeedian wrote:
>> Hi,
>> I have a question:
>> How can I run scf without symmetry?
> 
> nosym=.TRUE. in the namelist &control should do the job.

Sorry, it goes in the &system namelist

GS

> Be careful when chosing the k-point grid (see warnings in Doc/INPUT_PW.txt).
> 
>> I mean: how should I make the required file?
> 
> I hope I've actually understood your question...
> 
> regards,
> 
> GS
> 
>> Best regards,
>> Saeedian
>>
>>
>>
>>       
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
> 

-- 

La legge n. 133 uccide l'Universit? e la Ricerca italiana!

Save Italian Brains! (http://saveitalianbrains.wordpress.com/)

o ------------------------------------------------ o
| Gabriele Sclauzero, PhD Student                  |
| c/o:   SISSA & CNR-INFM Democritos,              |
|        via Beirut 2-4, 34014 Trieste (Italy)     |
| email: sclauzer at sissa.it                         |
| phone: +39 040 3787 511                          |
| skype: gurlonotturno                             |
o ------------------------------------------------ o

From giannozz at democritos.it  Tue Dec 16 14:02:36 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 16 Dec 2008 14:02:36 +0100
Subject: [Pw_forum] Question on the tools used to visualize the point
 defects, such as vacancy and interstitial configurations.
In-Reply-To: <942197838.20081216184028@yahoo.com.cn>
References: <731573.35121.qm@web50907.mail.re2.yahoo.com>	<494760D1.3050302@sissa.it>
	<942197838.20081216184028@yahoo.com.cn>
Message-ID: <4947A6EC.6090201@democritos.it>

Hongsheng Zhao wrote:

> I'm currently want to visualize the point defects, 
> such as vacancy and interstitial configurations 
> But I find that the though the perfect crystal structure 
> is easy to construct, the ones with specific defects are
> more difficult to visualize.

would you please better explain what is your problem?
"construct" or "visualize"? tools that visualize crystals
(like xcrysden) will visualize defects as well

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

From tone.kokalj at ijs.si  Tue Dec 16 14:11:22 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 16 Dec 2008 14:11:22 +0100
Subject: [Pw_forum] Question on the tools used to visualize the
	point	defects, such as vacancy and interstitial configurations.
In-Reply-To: <942197838.20081216184028@yahoo.com.cn>
References: <731573.35121.qm@web50907.mail.re2.yahoo.com>
	<494760D1.3050302@sissa.it>  <942197838.20081216184028@yahoo.com.cn>
Message-ID: <1229433082.23916.25.camel@walk.ijs.si>

On Tue, 2008-12-16 at 18:40 +0800, Hongsheng Zhao wrote:
>  Would you give me some hints on the tools
>  used to visualize the point defects, such as vacancy and 
> interstitial configurations?

xcrysden has a possibility to render "vacancies". Here comes the recipe
(after you open you particular structure):

1. turn on the molecular surfaces, menu: Display->Molecular surfaces
2. click the menu: Modify->Molecular surface settings (new window will
appear)
3. on the new window, select "Surface Type=Gap analysis", and press
"Update" button
4. Optionally you may also change the "Function type" to some other
function, which will render vacancies slightly different. Play with all
paremeters on that window as long as you are not satisfied.

( short info about molecular surfaces in xcrysden:
http://www.xcrysden.org/doc/modify.html#molecular-surface )

Regards, Tone

-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From xuzp at MIT.EDU  Tue Dec 16 14:40:35 2008
From: xuzp at MIT.EDU (Zhiping Xu)
Date: Tue, 16 Dec 2008 08:40:35 -0500
Subject: [Pw_forum] In consistence between plotnum = 7/10 (PP.x)
In-Reply-To: <49478D7C.8050307@sissa.it>
References: <7699a1950812152311u6a6dd26an10eeba8a7563711f@mail.gmail.com>
	<49476156.4010304@democritos.it>
	<20081216053647.4t3mgzrws7pwkk0s@webmail.mit.edu>
	<49478D7C.8050307@sissa.it>
Message-ID: <1229434835.15821.39.camel@lamm-3.mit.edu>

Sorry, that a typo in the previous email
it should be kpoint = 1 (Gamma point)
thank you Gabriele
On Tue, 2008-12-16 at 12:14 +0100, Gabriele Sclauzero wrote:
> Dear Zhiping
> Zhiping Xu wrote:
> > Hi all:
> >   I performed projected DOS calculation for the valence and conduction bands
> > using two different approaches:
> > (1) plotnum = 7, kpoint = 0 (Gamma point), kband around nelectrons/2
> 
> If the gamma point is the first k-point in the list (check pw.x output) you should specify 
> kpoint = 1, NOT kpoint = 0. In principle you should get an error message if you actually 
> used the an invalid kpoint index.
> 
> from PP/local_dos.f90:
> 
>    if ( (iflag == 0) .and. ( kpoint < 1 .or. kpoint > nks ) ) &
>         call errore ('local_dos', 'wrong kpoint specified', 1)
> 
> Regards
> 
> Gabriele
> 
> 
> > (2) plotnum = 10, by setting Emin and Emax contaning most part of the band
> > 
> >   The second method gives reasonable results, while the first one is shifted by
> > 1 band. Any idea on this? Thanks.
> > Best,
> > Zhiping
> > 
> > 
> > 
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> > 
> 


From jjr19 at uakron.edu  Tue Dec 16 14:45:42 2008
From: jjr19 at uakron.edu (J. J. Ramsey)
Date: Tue, 16 Dec 2008 05:45:42 -0800 (PST)
Subject: [Pw_forum] Question on how PWscf handles fractional electrons
	of pseudohydrogens
References: <731573.35121.qm@web50907.mail.re2.yahoo.com>
	<494760D1.3050302@sissa.it>
Message-ID: <53091.75082.qm@web50907.mail.re2.yahoo.com>

----- Original Message ----

> From: Lorenzo Paulatto <paulatto at sissa.it>
> To: PWSCF Forum <pw_forum at pwscf.org>
> Sent: Tuesday, December 16, 2008 3:03:29 AM
> Subject: Re: [Pw_forum] Question on how PWscf handles fractional electrons of pseudohydrogens
> 
> J. J. Ramsey ha scritto:
> > If I have a system containing pseudohydrogens each with 1.25 valence 
> electrons, will PWscf set the calculations up so that each pseudohydrogen 
> contributes two Kohn-Sham orbitals, one with occupancy 1 and the other with 
> occupation 0.25?
> >  
> Dear J.J.,
> Unless you have a multiple of 4 hydrogens, the system shall be metallic.
> What will QE with the occupations do depends on what you require in the
> input file.

Actually, I do have a multiple of 4 pseudohydrogens, 250 electrons total. I did set the "occupations" variable to "smearing", though.



      

From zucco at dipteris.unige.it  Tue Dec 16 14:52:39 2008
From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini)
Date: Tue, 16 Dec 2008 14:52:39 +0100
Subject: [Pw_forum] Error in compilation QE-4.1CVS
Message-ID: <4F182518-6A61-4379-945F-78E6BC61EA0D@dipteris.unige.it>

Hello to all,
I'm trying to compile QE 4.1CVS (2008-12-02) using mpich libraries  
detecting this error:

/sh/binaries/mpich/bin/mpif90 -ftrace=full -O3 -cpp -D__INTEL -D__FFTW  
-D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I/sh/binaries/ 
mpich/include -I./  -I../Modules  -I../iotk/src -I../PW  -I../PH -c  
allocate_fft.f90
In file allocate_fft.f90:22

   USE gcoarse,   ONLY : nr1c,nr2c,nr3c,nrxxc,ngmc, nlc, nlcm
                                                             1
Fatal Error: Can't open module file 'gcoarse.mod' at (1) for reading:  
No such file or directory
make[1]: *** [allocate_fft.o] Error 1
make: *** [pw] Error 2

But the file gcoarse.mod is present, indeed.

The serial compilation it'ok. And also v4.0.4 enabling parallel  
computation it is ok.

Does any of you has found the same behavior?

m.


*******************************************************
Marino Vetuschi Zuccolini
zucco at dipteris.unige.it
Researcher / Geochemist
Laboratory of Geochemistry

DIPartimento per lo studio della TErra e delle sue RISorse -  
Universit?  di Genova
Tel. ++39 010 3538136 Fax. ++39 010 352169
Corso Europa 26, 16132 - Genova - Italy



From sclauzer at sissa.it  Tue Dec 16 15:48:57 2008
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 16 Dec 2008 15:48:57 +0100
Subject: [Pw_forum] In consistence between plotnum = 7/10 (PP.x)
In-Reply-To: <1229434835.15821.39.camel@lamm-3.mit.edu>
References: <7699a1950812152311u6a6dd26an10eeba8a7563711f@mail.gmail.com>	<49476156.4010304@democritos.it>	<20081216053647.4t3mgzrws7pwkk0s@webmail.mit.edu>	<49478D7C.8050307@sissa.it>
	<1229434835.15821.39.camel@lamm-3.mit.edu>
Message-ID: <4947BFD9.7000601@sissa.it>

Even if you specified the correct kpoint index, you would not get the same result from 
plotnum=7 and plotnum=10 (unless you're using the gamma point as the only kpoint). The 
first kind of plot gives the charge density of the KS eigenstate corresponding to the 
kpoint and band you specify on input, while the second sums up the charge of all KS 
eigenstates for which the corresponding eigenvalue lies in the energy window [emin,emax].

GS

Zhiping Xu wrote:
> Sorry, that a typo in the previous email
> it should be kpoint = 1 (Gamma point)
> thank you Gabriele
> On Tue, 2008-12-16 at 12:14 +0100, Gabriele Sclauzero wrote:
>> Dear Zhiping
>> Zhiping Xu wrote:
>>> Hi all:
>>>   I performed projected DOS calculation for the valence and conduction bands
>>> using two different approaches:
>>> (1) plotnum = 7, kpoint = 0 (Gamma point), kband around nelectrons/2
>> If the gamma point is the first k-point in the list (check pw.x output) you should specify 
>> kpoint = 1, NOT kpoint = 0. In principle you should get an error message if you actually 
>> used the an invalid kpoint index.
>>
>> from PP/local_dos.f90:
>>
>>    if ( (iflag == 0) .and. ( kpoint < 1 .or. kpoint > nks ) ) &
>>         call errore ('local_dos', 'wrong kpoint specified', 1)
>>
>> Regards
>>
>> Gabriele
>>
>>
>>> (2) plotnum = 10, by setting Emin and Emax contaning most part of the band
>>>
>>>   The second method gives reasonable results, while the first one is shifted by
>>> 1 band. Any idea on this? Thanks.
>>> Best,
>>> Zhiping
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
> 

-- 

La legge n. 133 uccide l'Universit? e la Ricerca italiana!

Save Italian Brains! (http://saveitalianbrains.wordpress.com/)

o ------------------------------------------------ o
| Gabriele Sclauzero, PhD Student                  |
| c/o:   SISSA & CNR-INFM Democritos,              |
|        via Beirut 2-4, 34014 Trieste (Italy)     |
| email: sclauzer at sissa.it                         |
| phone: +39 040 3787 511                          |
| skype: gurlonotturno                             |
o ------------------------------------------------ o

From jjr19 at uakron.edu  Tue Dec 16 16:18:20 2008
From: jjr19 at uakron.edu (J. J. Ramsey)
Date: Tue, 16 Dec 2008 07:18:20 -0800 (PST)
Subject: [Pw_forum] Error in compilation QE-4.1CVS
References: <4F182518-6A61-4379-945F-78E6BC61EA0D@dipteris.unige.it>
Message-ID: <152296.22023.qm@web50911.mail.re2.yahoo.com>

----- Original Message ----

> From: Marino Vetuschi Zuccolini <zucco at dipteris.unige.it>
> To: PWSCF Forum <pw_forum at pwscf.org>
> Sent: Tuesday, December 16, 2008 8:52:39 AM
> Subject: [Pw_forum] Error in compilation QE-4.1CVS
> 
> Hello to all,
> I'm trying to compile QE 4.1CVS (2008-12-02) using mpich libraries  
> detecting this error:
> 
> /sh/binaries/mpich/bin/mpif90 -ftrace=full -O3 -cpp -D__INTEL -D__FFTW  
> -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I/sh/binaries/ 
> mpich/include -I./  -I../Modules  -I../iotk/src -I../PW  -I../PH -c  
> allocate_fft.f90
> In file allocate_fft.f90:22
> 
>    USE gcoarse,   ONLY : nr1c,nr2c,nr3c,nrxxc,ngmc, nlc, nlcm
>                                                              1
> Fatal Error: Can't open module file 'gcoarse.mod' at (1) for reading:  
> No such file or directory
> make[1]: *** [allocate_fft.o] Error 1
> make: *** [pw] Error 2
> 
> But the file gcoarse.mod is present, indeed.
> 
> The serial compilation it'ok. And also v4.0.4 enabling parallel  
> computation it is ok.
> 
> Does any of you has found the same behavior?

Not with QE 4.1CVS (since I haven't tried it), but I've seen similar behavior when a .mod file was neither in the current directory nor a directory in the path for including files. Maybe there needs to be another "-I" flag pointing to the directory containing gcoarse.mod.


      

From giannozz at democritos.it  Tue Dec 16 16:43:50 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 16 Dec 2008 16:43:50 +0100
Subject: [Pw_forum] Error in compilation QE-4.1CVS
In-Reply-To: <4F182518-6A61-4379-945F-78E6BC61EA0D@dipteris.unige.it>
References: <4F182518-6A61-4379-945F-78E6BC61EA0D@dipteris.unige.it>
Message-ID: <4947CCB6.9070802@democritos.it>

Marino Vetuschi Zuccolini wrote:

> Fatal Error: Can't open module file 'gcoarse.mod' at (1) for reading:  
> No such file or directory [...]
> But the file gcoarse.mod is present, indeed.

you should re-run "./configure", or at least, add "-I../EE"
to MODFLAGS in make.sys

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

From eyvaz_isaev at yahoo.com  Wed Dec 17 02:23:23 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 16 Dec 2008 17:23:23 -0800 (PST)
Subject: [Pw_forum] Variable cell
Message-ID: <20112.17779.qm@web65716.mail.ac4.yahoo.com>

Dear developers and users,

I am quite agree there is no time to submit any question, it is time to be prepared to incoming X-Mas.

Nevertheless, sorry, one question. I am doing variable-cell calculations by means of damp-w option. 
Initial choice for the lattice is ibrav=12, i.e. simple monoclinic. As far as I know the (Wentzcovitch) method should not change the cell shape (i.e. basis vectors will not change their symmetry). As it is mentioned in the original paper "... eliminate symmetry breaking"

But it seems to be not the case for a mononclinic cell, as initial basis vectors are:

a1 = 1     0   0
a2 = 0.0340004 0.999671 0
a3 = 0     0   0.999225

then right after the first step (i.e. damp-w starts) these vectors become

a1 = 0.999348118 -0.000624697 0.
a2 = 0.029359585 0.999030676  0
a3 = 0       0    0.998400159

I expected basis vectors will keep the original symmetry, though a1 seems to be changed. For tetragonal symmetry there is no such kind problem.

I have just tested it using v.4.0.4, the same result.

It would be very nice if someone can explain me why this happens for a monoclinic cell. May be there is some misunderstanding of mine side.

Bests,
Eyvaz.

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


      

From degironc at sissa.it  Wed Dec 17 13:20:04 2008
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 17 Dec 2008 13:20:04 +0100
Subject: [Pw_forum] Variable cell
In-Reply-To: <20112.17779.qm@web65716.mail.ac4.yahoo.com>
References: <20112.17779.qm@web65716.mail.ac4.yahoo.com>
Message-ID: <4948EE74.3080704@sissa.it>

how many symmetry operations are found by the code  ?
stefano

Eyvaz Isaev wrote:
> Dear developers and users,
>
> I am quite agree there is no time to submit any question, it is time to be prepared to incoming X-Mas.
>
> Nevertheless, sorry, one question. I am doing variable-cell calculations by means of damp-w option. 
> Initial choice for the lattice is ibrav=12, i.e. simple monoclinic. As far as I know the (Wentzcovitch) method should not change the cell shape (i.e. basis vectors will not change their symmetry). As it is mentioned in the original paper "... eliminate symmetry breaking"
>
> But it seems to be not the case for a mononclinic cell, as initial basis vectors are:
>
> a1 = 1     0   0
> a2 = 0.0340004 0.999671 0
> a3 = 0     0   0.999225
>
> then right after the first step (i.e. damp-w starts) these vectors become
>
> a1 = 0.999348118 -0.000624697 0.
> a2 = 0.029359585 0.999030676  0
> a3 = 0       0    0.998400159
>
> I expected basis vectors will keep the original symmetry, though a1 seems to be changed. For tetragonal symmetry there is no such kind problem.
>
> I have just tested it using v.4.0.4, the same result.
>
> It would be very nice if someone can explain me why this happens for a monoclinic cell. May be there is some misunderstanding of mine side.
>
> Bests,
> Eyvaz.
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev, 
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
> Condensed Matter Theory Group, Uppsala University, Sweden 
> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
>       
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From niuli1978 at yahoo.com.cn  Thu Dec 18 07:58:29 2008
From: niuli1978 at yahoo.com.cn (li niu)
Date: Thu, 18 Dec 2008 14:58:29 +0800 (CST)
Subject: [Pw_forum] calculation about isotope substitution
Message-ID: <421023.89746.qm@web15002.mail.cnb.yahoo.com>

Dear Pwscf user,
?
I'm a PWSCF user from China. I want to calculate the influence of isotope substitution on the phonon modes. But I don?t know how to implement it?Any help will be appreciated.
?
So many thanks in advance!
?
Best Regards,

Li Niu
Ph.D. Candidate,
Center for Composite Materials,
Harbin Institute of Technology,
Harbin, Heilongjiang, 150080, China


      ___________________________________________________________ 
  ????????????????? 
http://card.mail.cn.yahoo.com/
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From degironc at sissa.it  Thu Dec 18 08:34:23 2008
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 18 Dec 2008 08:34:23 +0100
Subject: [Pw_forum] calculation about isotope substitution
In-Reply-To: <421023.89746.qm@web15002.mail.cnb.yahoo.com>
References: <421023.89746.qm@web15002.mail.cnb.yahoo.com>
Message-ID: <4949FCFF.3020607@sissa.it>

change mass in the imput of the phonon code....
more specifically you can generate the interatomic force constants for 
the (electronically perfect) system and then use code matdyn to generate 
a supercell and asssign different masses to different atoms (look at the 
amass and readtau variable in the input of matdyn) to study the isotopic 
effect.
stefano

li niu wrote:
>
> Dear Pwscf user,
>
>  
>
> I'm a PWSCF user from China. I want to calculate the influence of 
> isotope substitution on the phonon modes. But I don?t know how to 
> implement it?Any help will be appreciated.
>
>  
>
> So many thanks in advance!
>
>  
>
> Best Regards,
>
> Li Niu
>
> Ph.D. Candidate,
>
> Center for Composite Materials,
>
> Harbin Institute of Technology,
>
> Harbin, Heilongjiang, 150080, China
>
>
> ------------------------------------------------------------------------
> ????????????????? 
> <http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/> 
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From lfhuang at theory.issp.ac.cn  Thu Dec 18 09:03:43 2008
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Thu, 18 Dec 2008 16:03:43 +0800
Subject: [Pw_forum] =?utf-8?q?calculation_about_isotope_substitution?=
Message-ID: <20081218080343.21579.qmail@ms.hfcas.ac.cn>

Dear Li Niu:
   Isotopes of one given element have the same chemical properties that is to say the same electronic structure,
so the electrons of the isotopes are the same from each other, and the only thing different is the MASS of the 
atom.So you only need to give the corresponding mass of the isotopic atom which you want to substitute.
In addition, are you calculating critical superconducting temperature? If you are, and your system is compound,
then you can calculate the isotope effect of every type of atom by this substitution, the formula of which is:
-d(logTc)/d(logm), 
you can refer to the paper for details:
Matteo Calandra and Francesco Mauri, "Theoretical Explanation of Superconductivity in C6Ca" PRL 95 237002(2005)

Yours Sincerely
L.F.Huang

> Date: Thu, 18 Dec 2008 14:58:29 +0800 (CST)
> From: li niu 
> Subject: [Pw_forum] calculation about isotope substitution
> To: pw_forum at pwscf.org
> Message-ID: 
> Content-Type: text/plain; charset="utf-8"
> 
> Dear Pwscf user,
> ?
> I'm a PWSCF user from China. I want to calculate the influence of isotope substitution on the phonon modes. But I don?t know how to implement it?Any help will be appreciated.
> ?
> So many thanks in advance!
> ?
> Best Regards,
> 
> Li Niu
> Ph.D. Candidate,
> Center for Composite Materials,
> Harbin Institute of Technology,
> Harbin, Heilongjiang, 150080, China

------
======================================================================
L.F.Huang(???) lfhuang at theory.issp.ac.cn
======================================================================
Add: Research Laboratory for Computational Materials Sciences,
Instutue of Solid State Physics,the Chinese Academy of Sciences,
P.O.Box 1129, Hefei 230031, P.R.China
Tel: 86-551-5591464-328(office)
Fax: 86-551-5591434
Web: http://theory.issp.ac.cn (website of our theory group)
http://www.issp.ac.cn    (website of our institute)
======================================================================


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From panda.deng.pan at gmail.com  Thu Dec 18 10:23:10 2008
From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=)
Date: Thu, 18 Dec 2008 17:23:10 +0800
Subject: [Pw_forum] Outputs about project
Message-ID: <c8dadee0812180123v2110e97h95bba74ae639b920@mail.gmail.com>

Dear All:

  I'm beginner of PWscf.I had run the example08,and I don't know how
to determine which orbital to let the projfwc.x to output.If I want
the p orbital in example08.
  I searched for this and only got  this "the order of m components of
Y_{lm} is determined by routine "ylmr2"".But I do not know where the
"ylmr2" is.It do not show in the inputfile of projwfc.
  Tanks a lot.Have a nice day.

Pan Deng

Nanjing University

From sclauzer at sissa.it  Thu Dec 18 10:32:29 2008
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Thu, 18 Dec 2008 10:32:29 +0100
Subject: [Pw_forum] Outputs about project
In-Reply-To: <c8dadee0812180123v2110e97h95bba74ae639b920@mail.gmail.com>
References: <c8dadee0812180123v2110e97h95bba74ae639b920@mail.gmail.com>
Message-ID: <494A18AD.2050007@sissa.it>


?? wrote:
> Dear All:
> 
>   I'm beginner of PWscf.I had run the example08,and I don't know how
> to determine which orbital to let the projfwc.x to output.If I want
> the p orbital in example08.
>   I searched for this and only got  this "the order of m components of
> Y_{lm} is determined by routine "ylmr2"".But I do not know where the
> "ylmr2" is.It do not show in the inputfile of projwfc.

I think you can find many posts on this topic in the Forum archives. Anyway, a possible 
answer to your question has been reported at the link

http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions#What_is_the_order_of_Ylm_components_in_projected_DOS_.2F_projection_of_atomic_wavefunctions.3F

but maybe it could be more clear to you if you give a look at the header of the 
PP/projwfc.f90 file in the QE distribution.

Regards

GS



>   Tanks a lot.Have a nice day.
> 
> Pan Deng
> 
> Nanjing University
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

-- 

La legge n. 133 uccide l'Universit? e la Ricerca italiana!

Save Italian Brains! (http://saveitalianbrains.wordpress.com/)

o ------------------------------------------------ o
| Gabriele Sclauzero, PhD Student                  |
| c/o:   SISSA & CNR-INFM Democritos,              |
|        via Beirut 2-4, 34014 Trieste (Italy)     |
| email: sclauzer at sissa.it                         |
| phone: +39 040 3787 511                          |
| skype: gurlonotturno                             |
o ------------------------------------------------ o

From thmason24 at yahoo.com  Thu Dec 18 17:00:04 2008
From: thmason24 at yahoo.com (Timothy Mason)
Date: Thu, 18 Dec 2008 08:00:04 -0800 (PST)
Subject: [Pw_forum] VC-relax questions
Message-ID: <51154.79554.qm@web81806.mail.mud.yahoo.com>

Gentlemen and ladies,? 

I have some rookie questions about VC-relax.??? I've pasted the input file and greps of Total energy, Total Forces and stresses below.?? Its the same problem of oscillations that has been posted before. ? Here are my questions.

1).?? how can it be that? while the forces and stresses are oscillating the total energy continues to decrease albeit slowly??? Am I really relaxing fine but just have a long way to go?
2)??? I've read many posts suggestioning an MD run to determine an effective dt but I don't think I understand.??? I run molecular dynamics and look for the oscillation period of the total forces??????? Then use a dt equal to some fraction of the period?
3)??? I've seen conflicting suggestions on whether the default cell mass is a good guess.????? any further thoughts on this?
4)?? I'm starting off with "! no symmetries" and hoping to relax to a point where I find symmetries.??? is VC-relax even appropriate for this application?

thanks in advance!

Tim Mason
Graduate student physics
University of Missouri St. Louis

!??? total energy????????????? =? -130.99725337 Ry
!??? total energy????????????? =? -130.99742389 Ry
!??? total energy????????????? =? -130.99765896 Ry
!??? total energy????????????? =? -130.99788028 Ry
!??? total energy????????????? =? -130.99814044 Ry
!??? total energy????????????? =? -130.99838484 Ry
!??? total energy????????????? =? -130.99862662 Ry
!??? total energy????????????? =? -130.99883535 Ry
!??? total energy????????????? =? -130.99906028 Ry
!??? total energy????????????? =? -130.99921630 Ry
!??? total energy????????????? =? -130.99942817 Ry
!??? total energy????????????? =? -130.99962083 Ry
!??? total energy????????????? =? -130.99984032 Ry
!??? total energy????????????? =? -131.00005894 Ry
!??? total energy????????????? =? -131.00027167 Ry
!??? total energy????????????? =? -131.00032697 Ry
!??? total energy????????????? =? -131.00055195 Ry
!??? total energy????????????? =? -131.00075005 Ry
!??? total energy????????????? =? -131.00092926 Ry
!??? total energy????????????? =? -131.00110579 Ry
!??? total energy????????????? =? -131.00128893 Ry
!??? total energy????????????? =? -131.00152437 Ry
!??? total energy????????????? =? -131.00176666 Ry
!??? total energy????????????? =? -131.00201744 Ry
!??? total energy????????????? =? -131.00222657 Ry

???? Total force =???? 0.025775???? Total SCF correction =???? 0.000281
???? Total force =???? 0.020098???? Total SCF correction =???? 0.000361
???? Total force =???? 0.015661???? Total SCF correction =???? 0.000081
???? Total force =???? 0.016340???? Total SCF correction =???? 0.000253
???? Total force =???? 0.012358???? Total SCF correction =???? 0.000853
???? Total force =???? 0.012918???? Total SCF correction =???? 0.000221
???? Total force =???? 0.011349???? Total SCF correction =???? 0.000287
???? Total force =???? 0.013804???? Total SCF correction =???? 0.000249
???? Total force =???? 0.012754???? Total SCF correction =???? 0.000124
???? Total force =???? 0.016969???? Total SCF correction =???? 0.000230
???? Total force =???? 0.011474???? Total SCF correction =???? 0.000262
???? Total force =???? 0.013177???? Total SCF correction =???? 0.000210
???? Total force =???? 0.010928???? Total SCF correction =???? 0.000265
???? Total force =???? 0.009784???? Total SCF correction =???? 0.000097
???? Total force =???? 0.010154???? Total SCF correction =???? 0.000534
???? Total force =???? 0.023392???? Total SCF correction =???? 0.000539
???? Total force =???? 0.018644???? Total SCF correction =???? 0.000303
???? Total force =???? 0.013266???? Total SCF correction =???? 0.000284
???? Total force =???? 0.012565???? Total SCF correction =???? 0.000137
???? Total force =???? 0.011408???? Total SCF correction =???? 0.000406
???? Total force =???? 0.013103???? Total SCF correction =???? 0.000212
???? Total force =???? 0.011107???? Total SCF correction =???? 0.000195
???? Total force =???? 0.009844???? Total SCF correction =???? 0.000492
???? Total force =???? 0.010155???? Total SCF correction =???? 0.000692
???? Total force =???? 0.014920???? Total SCF correction =???? 0.000309

???????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 0.85
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 1.09
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 1.44
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.07
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.36
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.74
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.96
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.95
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.92
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 3.35
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 3.21
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 3.13
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.91
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.85
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.61
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 1.46
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 1.75
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.29
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.03
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 1.97
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.01
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.26
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.44
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.66
????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=??? 2.59

&CONTROL
calculation = "vc-relax",
prefix = 'n1',
tprnfor = .TRUE.
pseudo_dir = '/home/tim/PWSCF/PSPS',
outdir='/home/tim/tmp'
etot_conv_thr = 1.0D-5,
forc_conv_thr = 0.0004,
dt = 20
nstep = 100
/

&SYSTEM
ibrav = 0, nat = 15, ntyp = 5,
ecutwfc = 40
ecutrho = 480
celldm(1) = 1.889725989
/

&ELECTRONS
mixing_mode = 'plain',
mixing_beta = 0.7,
conv_thr = 1.0D-7,
/


&IONS
ion_dynamics? = 'damp',
ion_damping? = 0.1,
ion_positions = 'from_input',
pot_extrapolation = "second_order",
wfc_extrapolation = "second_order",
upscale = 100,
/

&CELL
press = 0.0,
cell_dynamics = 'damp-w'
/

ATOMIC_SPECIES
Li 1.0 Li.pbe-n-van.UPF
Ca 1.0 Ca.pbe-nsp-van.UPF
N 1.0 N.pbe-rrkjus.UPF
H 1.0 H.pbe-rrkjus.UPF
B 1.0 B.pbe-n-van.UPF

CELL_PARAMETERS
11.03225111 0.49197118 -0.92807585
-0.15038487 5.49373010 -0.38883048
3.04894498 0.25407718 4.19633759

ATOMIC_POSITIONS {crystal}
Li 0.144228066000 0.155479905000 0.105275909000
Ca 0.911201719000 0.659605393000 0.179405853000
?N 0.954182418000 0.066667349000 0.203452528000
?H 0.879987796000 0.160521652000 0.398773311000
?H 0.949093887000 0.150685763000 0.033727675000
?H 0.590246767000 0.244749224000 0.483311768000
?H 0.563997731000 0.067035740000 0.225636766000
?H 0.437455407000 0.306433941000 0.454794956000
?H 0.611216941000 0.379448807000 0.154202770000
?H 0.231109967000 0.728337975000 0.002905585000
?H 0.397236924000 0.644804127000 -0.037067236000
?H 0.288752224000 0.877300760000 0.238936122000
?H 0.231627436000 0.575300194000 0.301639728000
?B 0.550495441000 0.249323405000 0.329678852000
?B 0.288025902000 0.707564656000 0.123296526000

K_POINTS automatic
4 4 4 0 0 0


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From adams_mejl at hotmail.com  Fri Dec 19 01:08:03 2008
From: adams_mejl at hotmail.com (Adam Jacobsson)
Date: Fri, 19 Dec 2008 01:08:03 +0100
Subject: [Pw_forum] Effective Charges and US-PP
Message-ID: <COL103-W75D164C9E1C0011AB5844AE4F00@phx.gbl>


Hi everyone!

I'm doing some phonon calculations with espresso right now. The available pseudo potentials for the atoms in the material I'm interested in are of the US kind so I was thinking about how to get the correct LO/TO splitting. As a test I run a calculation with .epsil. true for BaTiO3 using US PP and got a quite good agreement for the effective charges with the litterature (Zhong, King-Smith and Vanderbilt 1993) .

Is that a coincidence given the information from http://www.pwscf.org/pseudo.html?

Best,
Adam Jacobsson,
Diploma student
The theoretical magnetism group
Uppsala University



_________________________________________________________________
Var sommaren f?r kort? H?r hittar du solen!
http://resor.se.msn.com/
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From eyvaz_isaev at yahoo.com  Fri Dec 19 02:05:59 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 18 Dec 2008 17:05:59 -0800 (PST)
Subject: [Pw_forum] Effective Charges and US-PP
In-Reply-To: <COL103-W75D164C9E1C0011AB5844AE4F00@phx.gbl>
Message-ID: <474269.54490.qm@web65710.mail.ac4.yahoo.com>

Hi Jacob,

What is your particular problem with US-PP ans Born charges? 
There will be no problem with such kind calculations using US-PP.

Bests,
EYvaz.

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


--- On Fri, 12/19/08, Adam Jacobsson <adams_mejl at hotmail.com> wrote:

> From: Adam Jacobsson <adams_mejl at hotmail.com>
> Subject: [Pw_forum] Effective Charges and US-PP
> To: pw_forum at pwscf.org
> Date: Friday, December 19, 2008, 3:08 AM
> Hi everyone!
> 
> I'm doing some phonon calculations with espresso right
> now. The available pseudo potentials for the atoms in the
> material I'm interested in are of the US kind so I was
> thinking about how to get the correct LO/TO splitting. As a
> test I run a calculation with .epsil. true for BaTiO3 using
> US PP and got a quite good agreement for the effective
> charges with the litterature (Zhong, King-Smith and
> Vanderbilt 1993) .
> 
> Is that a coincidence given the information from
> http://www.pwscf.org/pseudo.html?
> 
> Best,
> Adam Jacobsson,
> Diploma student
> The theoretical magnetism group
> Uppsala University
> 
> 
> 
> _________________________________________________________________
> Var sommaren f?r kort? H?r hittar du solen!
> http://resor.se.msn.com/_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From niuli1978 at yahoo.com.cn  Fri Dec 19 02:09:27 2008
From: niuli1978 at yahoo.com.cn (li niu)
Date: Fri, 19 Dec 2008 09:09:27 +0800 (CST)
Subject: [Pw_forum] calculation about isotope substitution
In-Reply-To: <mailman.708.1229616010.15655.pw_forum@pwscf.org>
Message-ID: <844996.27646.qm@web15001.mail.cnb.yahoo.com>

Dear Stefano de Gironcoli and L.F.Huang,

  Thank you so much for your help and quick reply. I understand your mean and I will do it right now. Thanks again for your kind help.

Wishing you a sparkling Christmas and bright happy New Year!

Best Regards,

Li Niu
Ph.D. Candidate,
Center for Composite Materials,
Harbin Institute of Technology,
Harbin, Heilongjiang, 150080, China



      ___________________________________________________________ 
  ????????????????? 
http://card.mail.cn.yahoo.com/

From njuxuyuehua at gmail.com  Fri Dec 19 14:55:57 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 19 Dec 2008 21:55:57 +0800
Subject: [Pw_forum] error in the phonon calculation! (the 19th phonon
	problem)
Message-ID: <aca2feb20812190555n1aa2626bredac4c5f9978de2c@mail.gmail.com>

hi all :
    i face a problem during calculation phonon at G point process. the
error  is following :

  Representation # 19 mode #  19
     Self-consistent Calculation
      iter #   1 total cpu time :  3876.6 secs   av.it.:   3.9
      thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.412E-07
      iter #   2 total cpu time :  3896.1 secs   av.it.:  10.3
      thresh= 0.203E-04 alpha_mix =  0.700 |ddv_scf|^2 =  0.891E-09
      iter #   3 total cpu time :  3918.1 secs   av.it.:  12.9
      thresh= 0.298E-05 alpha_mix =  0.700 |ddv_scf|^2 =  0.155E-08
      iter #   4 total cpu time :  3939.5 secs   av.it.:  11.9
      thresh= 0.394E-05 alpha_mix =  0.700 |ddv_scf|^2 =  0.415E-11
     kpoint   7 ibnd  17 solve_linter: root not converged  NaN
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from broyden : error #         3
     factorization
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from broyden : error #         3
     factorization
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from broyden : error #         3
     factorization
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
the error is in the 19th phonon calculation ,before is OK.
SO i do not know what happened. i need your help.

-- 
Xu Yuehua
physics Department of Nanjing university
China
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From degironc at sissa.it  Fri Dec 19 15:47:12 2008
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 19 Dec 2008 15:47:12 +0100
Subject: [Pw_forum] Effective Charges and US-PP
In-Reply-To: <COL103-W75D164C9E1C0011AB5844AE4F00@phx.gbl>
References: <COL103-W75D164C9E1C0011AB5844AE4F00@phx.gbl>
Message-ID: <494BB3F0.40605@sissa.it>

Dear Adam Jacobsson,
  in fact,  effectve charges with USPP are implemented in the QE.
  stefano de Gironcoli

Adam Jacobsson wrote:
> Hi everyone!
>
> I'm doing some phonon calculations with espresso right now. The 
> available pseudo potentials for the atoms in the material I'm 
> interested in are of the US kind so I was thinking about how to get 
> the correct LO/TO splitting. As a test I run a calculation with 
> .epsil. true for BaTiO3 using US PP and got a quite good agreement for 
> the effective charges with the litterature (Zhong, King-Smith and 
> Vanderbilt 1993) .
>
> Is that a coincidence given the information from 
> http://www.pwscf.org/pseudo.html?
>
> Best,
> Adam Jacobsson,
> Diploma student
> The theoretical magnetism group
> Uppsala University
>
>
>
> ------------------------------------------------------------------------
> Best?ll bl?ck f?re 19 f?r leverans n?sta vardag inkClub 
> <http://www.inkclub.com/msn8>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From adams_mejl at hotmail.com  Fri Dec 19 17:29:25 2008
From: adams_mejl at hotmail.com (Adam Jacobsson)
Date: Fri, 19 Dec 2008 17:29:25 +0100
Subject: [Pw_forum] Effective Charges and US-PP
In-Reply-To: <494BB3F0.40605@sissa.it>
References: <COL103-W75D164C9E1C0011AB5844AE4F00@phx.gbl>
	<494BB3F0.40605@sissa.it>
Message-ID: <COL103-W63218513CD854955ABA3A7E4F00@phx.gbl>


Hi,
 
Thanks to Stefano and Eyvaz for clarifying the status of the code! 
 
God Jul!
Adam> Date: Fri, 19 Dec 2008 15:47:12 +0100> From: degironc at sissa.it> To: pw_forum at pwscf.org> Subject: Re: [Pw_forum] Effective Charges and US-PP> > Dear Adam Jacobsson,> in fact, effectve charges with USPP are implemented in the QE.> stefano de Gironcoli> > Adam Jacobsson wrote:> > Hi everyone!> >> > I'm doing some phonon calculations with espresso right now. The > > available pseudo potentials for the atoms in the material I'm > > interested in are of the US kind so I was thinking about how to get > > the correct LO/TO splitting. As a test I run a calculation with > > .epsil. true for BaTiO3 using US PP and got a quite good agreement for > > the effective charges with the litterature (Zhong, King-Smith and > > Vanderbilt 1993) .> >> > Is that a coincidence given the information from > > http://www.pwscf.org/pseudo.html?> >> > Best,> > Adam Jacobsson,> > Diploma student> > The theoretical magnetism group> > Uppsala University> >> >> >> > ------------------------------------------------------------------------> > Best?ll bl?ck f?re 19 f?r leverans n?sta vardag inkClub > > <http://www.inkclub.com/msn8>> > ------------------------------------------------------------------------> >> > _______________________________________________> > 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
_________________________________________________________________
Var sommaren f?r kort? H?r hittar du solen!
http://resor.se.msn.com/
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From giannozz at democritos.it  Fri Dec 19 18:52:22 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 19 Dec 2008 18:52:22 +0100
Subject: [Pw_forum] Effective Charges and US-PP
In-Reply-To: <COL103-W75D164C9E1C0011AB5844AE4F00@phx.gbl>
References: <COL103-W75D164C9E1C0011AB5844AE4F00@phx.gbl>
Message-ID: <200812191852.22869.giannozz@democritos.it>

On Friday 19 December 2008 01:08, Adam Jacobsson wrote:

> Is that a coincidence given the information from
> http://www.pwscf.org/pseudo.html?

since some time the contents of www.pwscf.org is no
longer updated, only www.quantum-espresso.org is updated.
Sorry about that, sooner or later this will be fixed for good.

Paolo
-- 
Paolo Giannozzi, Democritos and Udine University

From padmaja_patnaik at yahoo.co.uk  Sat Dec 20 13:03:56 2008
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Sat, 20 Dec 2008 12:03:56 +0000 (GMT)
Subject: [Pw_forum] Finding atomic positions
Message-ID: <947366.15880.qm@web25407.mail.ukl.yahoo.com>

Dear all
?
Can anybody suggest me on the following. I want to do the calculations considering a bulk of the material means involving more number of atoms. How to find the atomic positions? Is their any code available for it?
?
Thanx and regards

Padmaja Patnaik
Research Scholar
Dept of Physics
IIT Bombay
Mumbai, India


      
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From davidfarrell2008 at u.northwestern.edu  Sat Dec 20 15:51:36 2008
From: davidfarrell2008 at u.northwestern.edu (David Farrell)
Date: Sat, 20 Dec 2008 08:51:36 -0600
Subject: [Pw_forum] compile problem on BG/P
Message-ID: <C2713E86-97BF-4CCA-85EC-AD13AEBBC199@u.northwestern.edu>

Hi All,

I am trying to compile pw & cp on a BG/P, using a slightly modified  
version of the included makefile (just added the correct path to the  
ESSL library), and upon compiling things go fine until the linking  
phase, when I get the following errors:

../Modules/berry_phase.o: In function `__berry_phase_NMOD_indi_of_ig':
berry_phase.f90:(.text+0xc4): undefined reference to `ln_ind'
berry_phase.f90:(.text+0xec): undefined reference to `ln_ind'
berry_phase.f90:(.text+0x164): undefined reference to `ln_ind'
berry_phase.f90:(.text+0x180): undefined reference to `ln_ind'
berry_phase.f90:(.text+0x19c): undefined reference to `ln_ind'
../Modules/berry_phase.o:berry_phase.f90:(.text+0x1e8): more undefined  
references to `ln_ind' follow
../Modules/berry_phase.o: In function `__berry_phase_NMOD_ln_setup':
berry_phase.f90:(.text+0x1334): undefined reference to `ln_alloc'
berry_phase.f90:(.text+0x1380): undefined reference to `ln_set'
berry_phase.f90:(.text+0x139c): undefined reference to `ln_activate'
../Modules/berry_phase.o: In function `__berry_phase_NMOD_ln_closeup':
berry_phase.f90:(.text+0x1400): undefined reference to `ln_dealloc'
../Modules/check_stop.o: In function `__check_stop_NMOD_check_stop_now':
check_stop.f90:(.text+0x120): undefined reference to `cclock'
../Modules/check_stop.o: In function  
`__check_stop_NMOD_check_stop_init':
check_stop.f90:(.text+0x970): undefined reference to `cclock'
../Modules/clocks.o: In function `start_clock':
(.text+0x260): undefined reference to `scnds'
../Modules/clocks.o: In function `start_clock':
(.text+0x2f8): undefined reference to `cclock'
../Modules/clocks.o: In function `start_clock':
(.text+0x324): undefined reference to `scnds'
../Modules/clocks.o: In function `stop_clock':
(.text+0x52c): undefined reference to `scnds'
../Modules/clocks.o: In function `stop_clock':
(.text+0x590): undefined reference to `cclock'
../Modules/clocks.o: In function `print_this_clock':
(.text+0x87c): undefined reference to `scnds'
../Modules/clocks.o: In function `print_this_clock':
(.text+0x890): undefined reference to `cclock'
../Modules/clocks.o: In function `get_clock':
(.text+0x12b0): undefined reference to `scnds'
../Modules/clocks.o: In function `get_clock':
(.text+0x1328): undefined reference to `scnds'
../Modules/xml_io_base.o: In function  
`__xml_io_base_NMOD_create_directory':
xml_io_base.f90:(.text+0xdbec): undefined reference to `c_mkdir'
../Modules/zhpev_drv.o: In function `__zhpev_module_NMOD_pzsteqr':
zhpev_drv.f90:(.text+0x2cbc): undefined reference to `cclock'
libpw.a(electrons.o): In function `electrons':
electrons.f90:(.text+0x1f0): undefined reference to `memstat'
libpw.a(input.o): In function `verify_tmpdir':
(.text+0xa508): undefined reference to `c_mkdir'
libpw.a(orthoatwfc.o): In function `orthoatwfc':
orthoatwfc.f90:(.text+0x80): undefined reference to `scnds'
libpw.a(new_ns.o): In function `new_ns':
new_ns.f90:(.text+0x10c): undefined reference to `scnds'
make[1]: *** [pw.x] Error 1
make[1]: Leaving directory `/gpfs/home/defarr/Quantum_Espresso/ 
espresso-4.0.4/PW'
make: *** [pw] Error 2


Based on an older post on the pw_forum list, I removed berry_phase.o  
and replaced it with an empty file, and that got rid of the first set  
of errors (the post said that module wasn't used... is that correct?)

However, the other errors remained.

Any ideas?

Thanks,

Dave


David E. Farrell
Post-Doctoral Fellow
Department of Materials Science and Engineering
Northwestern University
email: d-farrell2 at northwestern.edu

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From giannozz at democritos.it  Sat Dec 20 21:33:46 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 20 Dec 2008 21:33:46 +0100
Subject: [Pw_forum] compile problem on BG/P
In-Reply-To: <C2713E86-97BF-4CCA-85EC-AD13AEBBC199@u.northwestern.edu>
References: <C2713E86-97BF-4CCA-85EC-AD13AEBBC199@u.northwestern.edu>
Message-ID: <200812202133.46703.giannozz@democritos.it>

On Saturday 20 December 2008 15:51, David Farrell wrote:

> berry_phase.f90:(.text+0xc4): undefined reference to `ln_ind'
> berry_phase.f90:(.text+0x1334): undefined reference to `ln_alloc'
> berry_phase.f90:(.text+0x1380): undefined reference to `ln_set'
> berry_phase.f90:(.text+0x139c): undefined reference to `ln_activate'
> berry_phase.f90:(.text+0x1400): undefined reference to `ln_dealloc'
> check_stop.f90:(.text+0x120): undefined reference to `cclock'
> electrons.f90:(.text+0x1f0): undefined reference to `memstat'
> (.text+0xa508): undefined reference to `c_mkdir'
> orthoatwfc.f90:(.text+0x80): undefined reference to `scnds'

> Any ideas?

hint:  what do they have in common?  they are all C functions. 

Modify include/c_defs.h as needed: "configure" recognizes the 
correct one, unfortunately for the front-end, not necessarily for
the BG itself

Paolo
-- 
Paolo Giannozzi, Democritos and Udine University 

From zhaohscas at yahoo.com.cn  Sun Dec 21 12:49:45 2008
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Sun, 21 Dec 2008 19:49:45 +0800
Subject: [Pw_forum] ab initio vs. first principles.
Message-ID: <153533741.20081221194945@yahoo.com.cn>

Hi all,

Some times we say ab initio, sometimes first principles.  Actually,
I find in many case people use them to explain one another.  But the fact may be not the case, who can give some hints on the differences between ab initio and first principles? 

Regards,
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn> 
Xinjiang Technical Institute of Physics and Chemistry
Chinese Academy of Sciences 
GnuPG DSA: 0xD108493
2008-12-21

__________________________________________________
?????????????????????????????
http://cn.mail.yahoo.com


From zhaohscas at yahoo.com.cn  Sun Dec 21 13:34:44 2008
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Sun, 21 Dec 2008 20:34:44 +0800
Subject: [Pw_forum] ab initio vs. first principles.
In-Reply-To: <20081221070825.315smxls68kg40gs@webmail.seas.upenn.edu>
References: <153533741.20081221194945@yahoo.com.cn>
	<20081221070825.315smxls68kg40gs@webmail.seas.upenn.edu>
Message-ID: <337361456.20081221203444@yahoo.com.cn>

On Sunday, December 21, 2008 at 20:08, migliore at seas.upenn.edu wrote:
> Hello

> In (computational) physics and chemistry the two expressions are used
> interchangeably to indicate calculations that start directly at the  
> level of established laws (or principles) of physics and do not make  
> any assumption, such as concerning models and/or fitting parameters.

Thanks a lot.
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn> 
Xinjiang Technical Institute of Physics and Chemistry
Chinese Academy of Sciences 
GnuPG DSA: 0xD108493
2008-12-21


From eyvaz_isaev at yahoo.com  Sun Dec 21 17:43:38 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sun, 21 Dec 2008 08:43:38 -0800 (PST)
Subject: [Pw_forum] ab initio vs. first principles.
In-Reply-To: <153533741.20081221194945@yahoo.com.cn>
Message-ID: <855379.91972.qm@web65707.mail.ac4.yahoo.com>

Dear Hongsheng,

You can find the answer in 
 
http://en.wikipedia.org/wiki/Ab_initio

Below is what is described on the webpage:


From baroni at sissa.it  Sun Dec 21 21:32:38 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Sun, 21 Dec 2008 21:32:38 +0100
Subject: [Pw_forum] ab initio vs. first principles.
In-Reply-To: <153533741.20081221194945@yahoo.com.cn>
References: <153533741.20081221194945@yahoo.com.cn>
Message-ID: <CC7B5012-ACBD-43DC-BAA3-3360D61D5251@sissa.it>

none - sb

On Dec 21, 2008, at 12:49 PM, Hongsheng Zhao wrote:

> Hi all,
>
> Some times we say ab initio, sometimes first principles.  Actually,
> I find in many case people use them to explain one another.  But the  
> fact may be not the case, who can give some hints on the differences  
> between ab initio and first principles?
>
> Regards,
> -- 
> Hongsheng Zhao <zhaohscas at yahoo.com.cn>
> Xinjiang Technical Institute of Physics and Chemistry
> Chinese Academy of Sciences
> GnuPG DSA: 0xD108493
> 2008-12-21
>
> __________________________________________________
> ?????????????????????????????
> http://cn.mail.yahoo.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://www.sissa.it/~baroni / [+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 leommj at usp.br  Mon Dec 22 02:47:17 2008
From: leommj at usp.br (Leonardo Matheus)
Date: Sun, 21 Dec 2008 23:47:17 -0200
Subject: [Pw_forum] ab initio vs. first principles.
In-Reply-To: <337361456.20081221203444@yahoo.com.cn>
References: <153533741.20081221194945@yahoo.com.cn>
	<20081221070825.315smxls68kg40gs@webmail.seas.upenn.edu>
	<337361456.20081221203444@yahoo.com.cn>
Message-ID: <c09ad1e50812211747i762dafa5l116ce18ca8e037d9@mail.gmail.com>

A small doubt that I had while following this discussion, please someone
correct-me if I'm wrong:
Is the following definition right?

"[in ab-initio calculations we] do not make any assumption, such as
> concerning models and/or fitting parameters."
>


I'm saying this because we use, for example, the homogeneous electron gas
model for LDA calculations, nonetheless it is still "ab-initio".
I think that it's not the use of parameters or models that define a first
principles method, but from where those parameters were taken.
If your parameters came from experimental values, it's somewhat empirical
(or semi-empirical at least), if you used just theoretical values (even if
using a simplified model) it can be called ab-initio.

Is this right?

This can even create some discussion if some new functionals can be called
"ab-initio" or not...

Leonardo Matheus
IF-USP / Brazil
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From davidfarrell2008 at u.northwestern.edu  Mon Dec 22 03:09:19 2008
From: davidfarrell2008 at u.northwestern.edu (David Farrell)
Date: Sun, 21 Dec 2008 20:09:19 -0600
Subject: [Pw_forum] ab initio vs. first principles.
In-Reply-To: <c09ad1e50812211747i762dafa5l116ce18ca8e037d9@mail.gmail.com>
References: <153533741.20081221194945@yahoo.com.cn>
	<20081221070825.315smxls68kg40gs@webmail.seas.upenn.edu>
	<337361456.20081221203444@yahoo.com.cn>
	<c09ad1e50812211747i762dafa5l116ce18ca8e037d9@mail.gmail.com>
Message-ID: <0A153D78-432B-4A2C-99FE-8750D9460772@u.northwestern.edu>

I also had a similar question in my head for a while about the  
ubiquitous use of ab initio == quantum mechanical model in materials  
science and physics literature (nanomechanics as well, for what it's  
worth). Mostly because some of the techniques include things that are  
definitely approximations or involve some sort of parameterization.  
Now, compared to empirical potentials, DFT, Hartree-Fock and even many  
Tight Binding approaches are certainly 'ab initio' because of how and  
where the approximations are made... and this seems to be the  
justification for using 'ab initio' in this manner. Besides, it sounds  
cool when written or said... a reason whose influence probably  
shouldn't be underestimated.

Dave

On Dec 21, 2008, at 7:47 PM, Leonardo Matheus wrote:

> A small doubt that I had while following this discussion, please  
> someone correct-me if I'm wrong:
> Is the following definition right?
>
> "[in ab-initio calculations we] do not make any assumption, such as  
> concerning models and/or fitting parameters."
>
>
> I'm saying this because we use, for example, the homogeneous  
> electron gas model for LDA calculations, nonetheless it is still "ab- 
> initio".
> I think that it's not the use of parameters or models that define a  
> first principles method, but from where those parameters were taken.
> If your parameters came from experimental values, it's somewhat  
> empirical (or semi-empirical at least), if you used just theoretical  
> values (even if using a simplified model) it can be called ab-initio.
>
> Is this right?
>
> This can even create some discussion if some new functionals can be  
> called "ab-initio" or not...
>
> Leonardo Matheus
> IF-USP / Brazil
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

David E. Farrell
Post-Doctoral Fellow
Department of Materials Science and Engineering
Northwestern University
email: d-farrell2 at northwestern.edu

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From davidfarrell2008 at u.northwestern.edu  Mon Dec 22 03:30:33 2008
From: davidfarrell2008 at u.northwestern.edu (David Farrell)
Date: Sun, 21 Dec 2008 20:30:33 -0600
Subject: [Pw_forum] compile problem on BG/P
In-Reply-To: <200812202133.46703.giannozz@democritos.it>
References: <C2713E86-97BF-4CCA-85EC-AD13AEBBC199@u.northwestern.edu>
	<200812202133.46703.giannozz@democritos.it>
Message-ID: <1BC96B38-9A14-4647-90C0-AB1507C4C7E7@u.northwestern.edu>

After fiddling with c_defs.h, I was able to get it to compile without  
errors.

For those interested, here it is:

/* include/c_defs.h.  Generated by configure.  */
/*
Copyright (C) 2006 Quantum-ESPRESSO group
This file is distributed under the terms of the
GNU General Public License. See the file `License'
in the root directory of the present distribution,
or http://www.gnu.org/copyleft/gpl.txt .
*/

/* File c_defs.h.in is used by configure to generate c_defs.h
    Variables that configure defines should be #undef-ined in
    include/c_defs.h.in !!! */

/* fortran-to-C naming convention, for functions with and without
    underscores in the name (some compilers treat them differently) */

#define F77_FUNC(name,NAME) name
#define F77_FUNC_(name,NAME) name

/* do we have the mallinfo structure (see clib/memstat.c) ? */

#define HAVE_MALLINFO 1





On Dec 20, 2008, at 2:33 PM, Paolo Giannozzi wrote:

> On Saturday 20 December 2008 15:51, David Farrell wrote:
>
>> berry_phase.f90:(.text+0xc4): undefined reference to `ln_ind'
>> berry_phase.f90:(.text+0x1334): undefined reference to `ln_alloc'
>> berry_phase.f90:(.text+0x1380): undefined reference to `ln_set'
>> berry_phase.f90:(.text+0x139c): undefined reference to `ln_activate'
>> berry_phase.f90:(.text+0x1400): undefined reference to `ln_dealloc'
>> check_stop.f90:(.text+0x120): undefined reference to `cclock'
>> electrons.f90:(.text+0x1f0): undefined reference to `memstat'
>> (.text+0xa508): undefined reference to `c_mkdir'
>> orthoatwfc.f90:(.text+0x80): undefined reference to `scnds'
>
>> Any ideas?
>
> hint:  what do they have in common?  they are all C functions.
>
> Modify include/c_defs.h as needed: "configure" recognizes the
> correct one, unfortunately for the front-end, not necessarily for
> the BG itself
>
> Paolo
> -- 
> Paolo Giannozzi, Democritos and Udine University
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

David E. Farrell
Post-Doctoral Fellow
Department of Materials Science and Engineering
Northwestern University
email: d-farrell2 at northwestern.edu

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From zl.liu.caep at gmail.com  Mon Dec 22 05:20:07 2008
From: zl.liu.caep at gmail.com (Zhong-Li Liu)
Date: Mon, 22 Dec 2008 12:20:07 +0800
Subject: [Pw_forum] compile problem on BG/P
In-Reply-To: <1BC96B38-9A14-4647-90C0-AB1507C4C7E7@u.northwestern.edu>
References: <C2713E86-97BF-4CCA-85EC-AD13AEBBC199@u.northwestern.edu>
	<200812202133.46703.giannozz@democritos.it>
	<1BC96B38-9A14-4647-90C0-AB1507C4C7E7@u.northwestern.edu>
Message-ID: <8cdd828c0812212020t36762495o30e3d2b0dff6788f@mail.gmail.com>

Dear Dave,

    I have also some problems in compiling pw.x and ph.x using ESSL libs on
PPC . Could you attach a copy of your make.sys file?
Thanks a lot!


2008/12/22 David Farrell <davidfarrell2008 at u.northwestern.edu>

> After fiddling with c_defs.h, I was able to get it to compile without
> errors.
>
>
>
> --
PhD. student of IAMP,  Sichuan University, China
E-mail: zl.liu.caep at gmail.com
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From zhaohscas at yahoo.com.cn  Mon Dec 22 05:43:55 2008
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Mon, 22 Dec 2008 12:43:55 +0800
Subject: [Pw_forum] ab initio vs. first principles.
In-Reply-To: <CC7B5012-ACBD-43DC-BAA3-3360D61D5251@sissa.it>
References: <153533741.20081221194945@yahoo.com.cn>
	<CC7B5012-ACBD-43DC-BAA3-3360D61D5251@sissa.it>
Message-ID: <1322426672.20081222124355@yahoo.com.cn>

On Monday, December 22, 2008 at 4:32, baroni at sissa.it wrote:
> none - sb

Thanks all the helps and discussions here.  I've got it by and large.
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn> 
Xinjiang Technical Institute of Physics and Chemistry
Chinese Academy of Sciences 
GnuPG DSA: 0xD108493
2008-12-22


From jameslipd at gmail.com  Mon Dec 22 08:10:28 2008
From: jameslipd at gmail.com (Jiaye, Li)
Date: Mon, 22 Dec 2008 15:10:28 +0800
Subject: [Pw_forum] =?utf-8?q?PWscf_calculation_problem_=EF=BC=88mpi_and_s?=
	=?utf-8?b?ZXJpYWzvvIk=?=
Message-ID: <b5d787260812212310i6074932bq83d3d0f5799da4fc@mail.gmail.com>

Dear users

I installed pwscf on the RH.Linux with 2G memory(2 CPUs and 4 processes).
MPICH1.2.7,Ifort,lapack-3.1.1, BLAS and fftw-3.2 have been successfully
installed, too. The subsequent installation process of PWscf report no
error. All the example tests are successful. In addition, I selected a
surface slab model to make another couples of test. I met some problems:
1. I typed " mpirun -np 4 ~/bin/pw.x <IO.inp |tee IO.out &" , then I
followed the content of output file closely, finding it stops after the
lines:

     number of k points=    4  gaussian broad. (Ry)=  0.0200     ngauss =
0
                       cart. coord. in units 2pi/a_0
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.5000000
        k(    2) = (   0.0000000   0.0000000  -1.0872780), wk =   0.5000000
        k(    3) = (   0.0000000  -1.0872780  -1.0872780), wk =   0.5000000
        k(    4) = (   0.0000000  -1.0872780   0.0000000), wk =   0.5000000
     G cutoff =17198.9000  (1997991 G-vectors)     FFT grid: (270,125,125)
     G cutoff = 2293.1867  (  97139 G-vectors)  smooth grid: ( 96, 45, 45)
     Largest allocated arrays     est. size (Mb)     dimensions
        Kohn-Sham Wavefunctions        14.87 Mb     (   3074, 317)
        NL pseudopotentials            27.02 Mb     (   3074, 576)
        Each V/rho on FFT grid         16.48 Mb     (1080000)
        Each G-vector array             3.81 Mb     ( 499499)
        G-vector shells                 0.70 Mb     (  91837)
     Largest temporary arrays     est. size (Mb)     dimensions
        Auxiliary wavefunctions        59.48 Mb     (   3074,1268)
        Each subspace H/S matrix       24.53 Mb     (   1268,1268)
        Each <psi_i|beta_j> matrix      2.79 Mb     (    576, 317)
        Arrays for rho mixing         131.84 Mb     (1080000,   8)

but pw.x process is still occupying 4x25 % cpu and 10 % MEM. I wait for
hours and there are no further new contents read from the output file. I
don't know whether it is the overflow of the memery? Could anybody help me
with these problems? Thanks.

Attached file is the make.sys of the PWscf.



-- 
Sincerely

Jiaye Li



==============================================
Li, Jiaye

M.S. in designing and developing novel materials

Research experience:
*ALD precursor. ie. Metal complexes
*Surface modification. ie. Indium tin oxide, SiO2
*Gas storage and adsorption. ie. Ionic Liquids

Skills:
*ab-initial method, DFT simulation and Force Field simulation

Please contact me at:
1. jameslipd at gmail.com  or
2. jameslibd at gmail.com

==============================================
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From amigliore at cmm.upenn.edu  Mon Dec 22 09:39:36 2008
From: amigliore at cmm.upenn.edu (Agostino Migliore)
Date: Mon, 22 Dec 2008 03:39:36 -0500 (EST)
Subject: [Pw_forum] ab initio vs. first principles
Message-ID: <1509.87.10.173.183.1229935176.squirrel@cmm.upenn.edu>

Hello

By itself, "ab initio", as directly derived and used from Latin, excludes
models and parametrization. Other thing is that, in general, we cannot
exactly describe a physical system, thus making use of approximations, so
of models. In the general use of computational physics and chemistry, the
expression includes models where empirical or semiempirical parameters are
not employed, so that a system is represented in a simplified way (->
model) while still resting on physics principles. One could argue on the
meaning of those approximations and the resulting "ab initio" nature of
the approach, thus also falling on linguistics arguments. I think it is
better to leave the expression with the meaning it acquired from the
general use (which is now its proper meaning in the proper computational
context). By rigorously speaking, my sentence reported below is right with
reference to the original meaning of "ab initio", and also agrees with its
acceptation in the computational world, once the "and" in "model and
fitting parameters" is interpreted as a logical AND.

Best regards,
Agostino Migliore

> A small doubt that I had while following this discussion, please someone
> correct-me if I'm wrong:
> Is the following definition right?

>> "[in ab-initio calculations we] do not make any assumption, such as
>> concerning models and/or fitting parameters."

> I'm saying this because we use, for example, the homogeneous electron gas
> model for LDA calculations, nonetheless it is still "ab-initio".
> I think that it's not the use of parameters or models that define a first
> principles method, but from where those parameters were taken.
> If your parameters came from experimental values, it's somewhat empirical
> (or semi-empirical at least), if you used just theoretical values (even
> if using a simplified model) it can be called ab-initio.


From baroni at sissa.it  Mon Dec 22 09:49:39 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 22 Dec 2008 09:49:39 +0100
Subject: [Pw_forum] ab initio vs. first principles.
In-Reply-To: <c09ad1e50812211747i762dafa5l116ce18ca8e037d9@mail.gmail.com>
References: <153533741.20081221194945@yahoo.com.cn>
	<20081221070825.315smxls68kg40gs@webmail.seas.upenn.edu>
	<337361456.20081221203444@yahoo.com.cn>
	<c09ad1e50812211747i762dafa5l116ce18ca8e037d9@mail.gmail.com>
Message-ID: <9A990E19-FE4D-498D-8A17-DF5C27FCA9BD@sissa.it>

yep!
(although quantum chemists may disagree to some extent)
SB

On Dec 22, 2008, at 2:47 AM, Leonardo Matheus wrote:

> A small doubt that I had while following this discussion, please  
> someone correct-me if I'm wrong:
> Is the following definition right?
>
> "[in ab-initio calculations we] do not make any assumption, such as  
> concerning models and/or fitting parameters."
>
>
> I'm saying this because we use, for example, the homogeneous  
> electron gas model for LDA calculations, nonetheless it is still "ab- 
> initio".
> I think that it's not the use of parameters or models that define a  
> first principles method, but from where those parameters were taken.
> If your parameters came from experimental values, it's somewhat  
> empirical (or semi-empirical at least), if you used just theoretical  
> values (even if using a simplified model) it can be called ab-initio.
>
> Is this right?
>
> This can even create some discussion if some new functionals can be  
> called "ab-initio" or not...
>
> Leonardo Matheus
> IF-USP / Brazil
> _______________________________________________
> 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://www.sissa.it/~baroni / [+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 giannozz at democritos.it  Mon Dec 22 10:02:16 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 22 Dec 2008 10:02:16 +0100
Subject: [Pw_forum] compile problem on BG/P
In-Reply-To: <8cdd828c0812212020t36762495o30e3d2b0dff6788f@mail.gmail.com>
References: <C2713E86-97BF-4CCA-85EC-AD13AEBBC199@u.northwestern.edu>	<200812202133.46703.giannozz@democritos.it>	<1BC96B38-9A14-4647-90C0-AB1507C4C7E7@u.northwestern.edu>
	<8cdd828c0812212020t36762495o30e3d2b0dff6788f@mail.gmail.com>
Message-ID: <494F5798.4040902@democritos.it>

Zhong-Li Liu wrote:

> I have also some problems in compiling pw.x and ph.x using ESSL libs 
> on PPC . Could you attach a copy of your make.sys file?

a make.sys for a BG/P machine is likely useless on any other
machine. Which compilation problem do you have? recent versions
of q-e should work on ibm machines of all kinds

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

From lataprem29 at gmail.com  Mon Dec 22 11:35:50 2008
From: lataprem29 at gmail.com (premlata pandit)
Date: Mon, 22 Dec 2008 16:05:50 +0530
Subject: [Pw_forum] about phonon calculation
Message-ID: <6f289440812220235j129d5c1bj9263c7e4b810efdd@mail.gmail.com>

Dear Pwscf users,
Here I am sending you the input file of Li2S (large band gap semi-conductor)
for scf and phonon calculations. I have some queries regarding this

1. For electronic calculation i am using 8x8x8 k-points which results in
only 60 points. Is it enough to do correct electronic calculations?
With these 60 points only, I calculated the bulk mobulus and the equilibrium
lattice constants, which matches well with the experiment and other
theoritical results.

2. For phonon calculation, I didnt get the LO-TO splitting. Can you please
tell me what more parameters i will use to get the splitting.
I set epsil .true., but it gives the error

     from phq_readin : error #         1
     no elec. field with metals

Any suggestion is highly apperciable

li2s.scf.in

&CONTROL
               calculation = 'scf' ,
              restart_mode = 'from_scratch' ,
                    outdir = './OUT',
                pseudo_dir = '/root/bipul/espresso-4.0.1/pseudo/Li2S',
                   prefix = 'Li2S',
             etot_conv_thr = 1.0d-5 ,
             forc_conv_thr = 1.0d-4 ,
                   tstress = .true. ,
                   tprnfor = .true. ,
                        dt = 80
 /
 &SYSTEM
                     ibrav = 2,
                 celldm(1) =  10.72700,
                       nat = 3,
                      ntyp = 2 ,
                   ecutwfc = 32,
                   ecutrho = 600,
                  occupations = 'smearing' ,
                    smearing = 'methfessel-paxton',
                   degauss = 0.01
 /
 &ELECTRONS
               mixing_beta = 0.5 ,
            conv_thr =  1.0d-8
           diagonalization = 'david' ,
 /
 &IONS
 /
ATOMIC_SPECIES
 S   32.066  S.pw91-van_ak.UPF
 Li  6.914   Li.pw91-s-van_ak.UPF
ATOMIC_POSITIONS (crystal)
S  0.0 0.0 0.0
Li 0.25 0.25 0.25
Li 0.75 0.75 0.75
K_POINTS automatic
  8 8 8 1 1 1

li2s.ph.in

phonons of Li2S
 &inputph
 ! recover =.true.,
  tr2_ph=1.0d-12,
  alpha_mix(1)=0.6,
  prefix='Li2S',
 ! fildvscf='li2sdv',
  amass(1)=32.066,
  amass(2)=6.941,
  outdir='./OUT',
  fildyn='li2s.dyn',
 ! elph=.true.,
 ! trans=.true.,
  ldisp=.true.
  nq1=4, nq2=4, nq3=4
 /


-- 
Premlata Pandit
Ph.d. student,
Barkatullah university,
Bhopal 462026,
MP, India
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From giannozz at democritos.it  Mon Dec 22 11:46:48 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 22 Dec 2008 11:46:48 +0100
Subject: [Pw_forum]
 =?utf-8?q?PWscf_calculation_problem_=EF=BC=88mpi_and_s?=
 =?utf-8?b?ZXJpYWzvvIk=?=
In-Reply-To: <b5d787260812212310i6074932bq83d3d0f5799da4fc@mail.gmail.com>
References: <b5d787260812212310i6074932bq83d3d0f5799da4fc@mail.gmail.com>
Message-ID: <494F7018.6020109@democritos.it>

Jiaye, Li wrote:

>  I wait for hours and there are no further new contents read from the
> output file. I don't know whether it is the overflow of the memery?

while you wait, you could have a look at the "Troubleshooting" section:
http://www.quantum-espresso.org/wiki/index.php/Troubleshooting_(PWscf)
in particular item 1.15 "pw.x runs but nothing happens";
and also to the "Running on parallel machine" section:
http://www.quantum-espresso.org/wiki/index.php/Running_on_parallel_machines
You could also remove output redirection (in case of trouble, it tends
to eat error messages); run a smaller calculation; try serial execution;
etc. etc.

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

From jameslipd at gmail.com  Mon Dec 22 13:19:40 2008
From: jameslipd at gmail.com (Jiaye, Li)
Date: Mon, 22 Dec 2008 20:19:40 +0800
Subject: [Pw_forum] Slab relaxation
In-Reply-To: <b5d787260811200540i1d433aeg84904586e669cd29@mail.gmail.com>
References: <b5d787260811200540i1d433aeg84904586e669cd29@mail.gmail.com>
Message-ID: <b5d787260812220419h8c2e33au65235148c04a9f3d@mail.gmail.com>

Dear Eyvaz

Thanks. Now I rewrite the input file according to example03.

On Thu, Nov 20, 2008 at 9:40 PM, Jiaye, Li <jameslipd at gmail.com> wrote:

> Dear All
>
> I met with a problem when I am trying to relax the geometry of MgO (001)
> slab, the error message occured:
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      task #         0
>      from  system_checkin      : error #         1
>       ecutwfc out of range
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Therefore pw.x didn't work. But the test of the examples reported no
> problem. I cannot figure out what's wrong with it, could anybody help me?
> Thanks in advance.
>
> This is my input file:
> &CONTROL
>  calculation = "relax" ,
>  pseudo_dir = "/home/blade/jamesli/source/pwscf/espresso-4.0.3/pseudo" ,
>  outdir = "/home/blade/temp-pwscf" ,
>  etot_conv_thr = 1.D-4 ,
>  forc_conv_thr = 1.D-3 ,
>  nstep = 200 ,
> /
> &SYSTEM
>  ibrav = 6 ,
>  A = 4.2112 ,
>  B = 4.2112 ,
>  C = 17.1056 ,
>  cosAB = 0 ,
>  cosBC = 0 ,
>  cosAC = 0 ,
>  nat = 8,
>  ntyp = 2,
>  occupations = "tetrahedra" ,
>  nspin = 2 ,
> /
> &ELECTRONS
>  electron_maxstep = 100,
>  conv_thr = 1.D-6 ,
> /
> ATOMIC_SPECIES
> Mg  24.3050   Mg.pw91-np-van.UPF
> O   15.9994   O.pw91-van_ak.UPF
> ATOMIC_POSITIONS
> Mg    0.00000   0.50000   0.12309 1 1 1
> Mg    0.00000   0.00000   0.00000 0 0 0
> Mg    0.50000   0.50000   0.00000 0 0 0
> Mg    0.50000   0.00000   0.12309 1 1 1
> O     0.50000   0.00000   0.00000 0 0 0
> O     0.50000   0.50000   0.12309 1 1 1
> O     0.00000   0.00000   0.12309 1 1 1
> O     0.00000   0.50000   0.00000 0 0 0
> K_POINTS {automatic}
> 2 2 1 0 0 0
>
>
> --
> Sincerely
>
> Jiaye Li
>
>
>
> ==============================================
> Li, Jiaye
>
> M.S. in designing and developing novel materials
>
> Research experience:
> *ALD precursor. ie. Metal complexes
> *Surface modification. ie. Indium tin oxide, SiO2
> *Gas storage and adsorption. ie. Ionic Liquids
>
> Skills:
> *ab-initial method, DFT simulation and Force Field simulation
>
> Please contact me at:
> 1. jameslipd at gmail.com  or
> 2. jameslibd at gmail.com
>
> ==============================================
>



-- 
Sincerely

Jiaye Li



==============================================
Li, Jiaye

M.S. in designing and developing novel materials

Research experience:
*ALD precursor. ie. Metal complexes
*Surface modification. ie. Indium tin oxide, SiO2
*Gas storage and adsorption. ie. Ionic Liquids

Skills:
*ab-initial method, DFT simulation and Force Field simulation

Please contact me at:
1. jameslipd at gmail.com  or
2. jameslibd at gmail.com

==============================================
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From adams_mejl at hotmail.com  Mon Dec 22 21:19:22 2008
From: adams_mejl at hotmail.com (Adam Jacobsson)
Date: Mon, 22 Dec 2008 21:19:22 +0100
Subject: [Pw_forum] about phonon calculation
In-Reply-To: <6f289440812220235j129d5c1bj9263c7e4b810efdd@mail.gmail.com>
References: <6f289440812220235j129d5c1bj9263c7e4b810efdd@mail.gmail.com>
Message-ID: <COL103-W33AC4ED1D16DF23261BF80E4EF0@phx.gbl>


Hi! 
 
Regarding k-points: The program will use symmetry to reduce the amount of used k-points as much as possible, i.e. those found in the irreducible BZ. Those might just be 60 in your case.   
 
Regarding phonons: You need to change occupation from smearing. That one is appropriate for metals but not for insulators. Use 'fixed' instead. Check the documentation for details. 
 
Best,
Adam Jacobsson



Date: Mon, 22 Dec 2008 16:05:50 +0530From: lataprem29 at gmail.comTo: pw_forum at pwscf.orgSubject: [Pw_forum] about phonon calculationDear Pwscf users,Here I am sending you the input file of Li2S (large band gap semi-conductor) for scf and phonon calculations. I have some queries regarding this1. For electronic calculation i am using 8x8x8 k-points which results in only 60 points. Is it enough to do correct electronic calculations?With these 60 points only, I calculated the bulk mobulus and the equilibrium lattice constants, which matches well with the experiment and other theoritical results.2. For phonon calculation, I didnt get the LO-TO splitting. Can you please tell me what more parameters i will use to get the splitting. I set epsil .true., but it gives the error       from phq_readin : error #         1     no elec. field with metalsAny suggestion is highly apperciable li2s.scf.in&CONTROL               calculation = 'scf' ,              restart_mode = 'from_scratch' ,                    outdir = './OUT',                pseudo_dir = '/root/bipul/espresso-4.0.1/pseudo/Li2S',                   prefix = 'Li2S',             etot_conv_thr = 1.0d-5 ,             forc_conv_thr = 1.0d-4 ,                   tstress = .true. ,                   tprnfor = .true. ,                        dt = 80 / &SYSTEM                     ibrav = 2,                 celldm(1) =  10.72700,                       nat = 3,                      ntyp = 2 ,                   ecutwfc = 32,                   ecutrho = 600,                  occupations = 'smearing' ,                    smearing = 'methfessel-paxton',                   degauss = 0.01 / &ELECTRONS               mixing_beta = 0.5 ,            conv_thr =  1.0d-8           diagonalization = 'david' , / &IONS /ATOMIC_SPECIES S   32.066  S.pw91-van_ak.UPF Li  6.914   Li.pw91-s-van_ak.UPFATOMIC_POSITIONS (crystal)S  0.0 0.0 0.0Li 0.25 0.25 0.25Li 0.75 0.75 0.75K_POINTS automatic  8 8 8 1 1 1li2s.ph.inphonons of Li2S &inputph ! recover =.true.,  tr2_ph=1.0d-12,  alpha_mix(1)=0.6,  prefix='Li2S', ! fildvscf='li2sdv',  amass(1)=32.066,  amass(2)=6.941,  outdir='./OUT',  fildyn='li2s.dyn', ! elph=.true., ! trans=.true.,  ldisp=.true.  nq1=4, nq2=4, nq3=4 /-- Premlata PanditPh.d. student,Barkatullah university,Bhopal 462026,MP, India 
_________________________________________________________________
Hetaste modetipsen & h?rligaste sk?nhetstesterna!
http://salongk.msn.se/
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From adams_mejl at hotmail.com  Mon Dec 22 21:37:19 2008
From: adams_mejl at hotmail.com (Adam Jacobsson)
Date: Mon, 22 Dec 2008 21:37:19 +0100
Subject: [Pw_forum] about phonon calculation
In-Reply-To: <COL103-W33AC4ED1D16DF23261BF80E4EF0@phx.gbl>
References: <6f289440812220235j129d5c1bj9263c7e4b810efdd@mail.gmail.com>
	<COL103-W33AC4ED1D16DF23261BF80E4EF0@phx.gbl>
Message-ID: <COL103-W29E29C3A095DAD2B996679E4EF0@phx.gbl>


Hi!
 
Sorry, didn't notice that your material was a semiconductor. Check occupation anyway. 
 
Best,
Adam Jacobsson



From: adams_mejl at hotmail.comTo: pw_forum at pwscf.orgDate: Mon, 22 Dec 2008 21:19:22 +0100Subject: Re: [Pw_forum] about phonon calculation

Hi!  Regarding k-points: The program will use symmetry to reduce the amount of used k-points as much as possible, i.e. those found in the irreducible BZ. Those might just be 60 in your case.    Regarding phonons: You need to change occupation from smearing. That one is appropriate for metals but not for insulators. Use 'fixed' instead. Check the documentation for details.  Best,Adam Jacobsson



Date: Mon, 22 Dec 2008 16:05:50 +0530From: lataprem29 at gmail.comTo: pw_forum at pwscf.orgSubject: [Pw_forum] about phonon calculationDear Pwscf users,Here I am sending you the input file of Li2S (large band gap semi-conductor) for scf and phonon calculations. I have some queries regarding this1. For electronic calculation i am using 8x8x8 k-points which results in only 60 points. Is it enough to do correct electronic calculations?With these 60 points only, I calculated the bulk mobulus and the equilibrium lattice constants, which matches well with the experiment and other theoritical results.2. For phonon calculation, I didnt get the LO-TO splitting. Can you please tell me what more parameters i will use to get the splitting. I set epsil .true., but it gives the error       from phq_readin : error #         1     no elec. field with metalsAny suggestion is highly apperciable li2s.scf.in&CONTROL               calculation = 'scf' ,              restart_mode = 'from_scratch' ,                    outdir = './OUT',                pseudo_dir = '/root/bipul/espresso-4.0.1/pseudo/Li2S',                   prefix = 'Li2S',             etot_conv_thr = 1.0d-5 ,             forc_conv_thr = 1.0d-4 ,                   tstress = .true. ,                   tprnfor = .true. ,                        dt = 80 / &SYSTEM                     ibrav = 2,                 celldm(1) =  10.72700,                       nat = 3,                      ntyp = 2 ,                   ecutwfc = 32,                   ecutrho = 600,                  occupations = 'smearing' ,                    smearing = 'methfessel-paxton',                   degauss = 0.01 / &ELECTRONS               mixing_beta = 0.5 ,            conv_thr =  1.0d-8           diagonalization = 'david' , / &IONS /ATOMIC_SPECIES S   32.066  S.pw91-van_ak.UPF Li  6.914   Li.pw91-s-van_ak.UPFATOMIC_POSITIONS (crystal)S  0.0 0.0 0.0Li 0.25 0.25 0.25Li 0.75 0.75 0.75K_POINTS automatic  8 8 8 1 1 1li2s.ph.inphonons of Li2S &inputph ! recover =.true.,  tr2_ph=1.0d-12,  alpha_mix(1)=0.6,  prefix='Li2S', ! fildvscf='li2sdv',  amass(1)=32.066,  amass(2)=6.941,  outdir='./OUT',  fildyn='li2s.dyn', ! elph=.true., ! trans=.true.,  ldisp=.true.  nq1=4, nq2=4, nq3=4 /-- Premlata PanditPh.d. student,Barkatullah university,Bhopal 462026,MP, India 



L?gg till karta och v?gbeskrivning f?r din fest. Visa v?gen! 
_________________________________________________________________
H?stst?da med nya dammsugarp?sar.
http://www.inkclub.com/msn9
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From zl.liu.caep at gmail.com  Wed Dec 24 13:54:36 2008
From: zl.liu.caep at gmail.com (Zhong-Li Liu)
Date: Wed, 24 Dec 2008 20:54:36 +0800
Subject: [Pw_forum] Problems in compiling pw.x and ph.x using XLF and ESSL
	on IBM-PPC
Message-ID: <8cdd828c0812240454g2b2b7b4fla783ec9d921f16ab@mail.gmail.com>

Dear Paolo,

  I can successfully configure before make using "./configure
--disable-parallel" during the compilation of 4.0.4 version, and make is
also sucessful without error messages. The compiler is XLF  and lib is ESSL.
But when I ran the examples using pw.x and ph.x,
complaints always appear saying:

"      from  cfft3d  : error #         1
       no scalar fft driver specified

      stopping ..."

Before I have consulted you about this, and following your suggestions and
the previous mail-list's disscussions  I set

DFLAGS         =  -D__ESSL
FDFLAGS        =  -D__ESSL

then the pw.x is ok, but ph.x complains "Segmentation Fault".

The above is  for the serial version, in the following I list the parallel
version problems.

The configure can not recognize my parallel environment, so I modified
make.sys which is also attached. The compilation is also
ok, but when running ph.x it complained :

" ** On entry to ZHPEV  parameter number  1 had an illegal value"

After searching the mail-list, I found you have said it may be because the
appearance sequence of ESSL and lapack libs. So
I have tried reversed the sequence of the two libs, but the error message
still appears.

So could you find some missettings of the compilation parameters and
something wrong? Please do me a favour. Thank you very
much.

Best wishes,

Z. Liu


N.B. The linux system is SUSE for ppc machine.



>2008/12/22 Paolo Giannozzi <giannozz at democritos.it>>- Hide quoted text -

>Zhong-Li Liu wrote:

> I have also some problems in compiling pw.x and ph.x using ESSL libs
> on PPC . Could you attach a copy of your make.sys file?

>a make.sys for a BG/P machine is likely useless on any other
>machine. Which compilation problem do you have? recent versions
>of q-e should work on ibm machines of all kinds

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

-- 
PhD. student of IAMP,  Sichuan University, China
E-mail: zl.liu.caep at gmail.com
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From davidfarrell2008 at u.northwestern.edu  Wed Dec 24 19:16:29 2008
From: davidfarrell2008 at u.northwestern.edu (David Farrell)
Date: Wed, 24 Dec 2008 12:16:29 -0600
Subject: [Pw_forum] compiled pw, cp on a BG/P - scf.in test hangs
Message-ID: <20F197A1-7563-42A1-BA08-9374E74B8C88@u.northwestern.edu>

Hi All,

So I was able to get pw and cp to compile on the BG/P, but when I try  
and test out pw using the scf.in test, the code hangs at the following  
(regardless of number of procs, time, etc)

launched as follows:

Program PWSCF     v.4.0.4  starts ...
      Today is 24Dec2008 at 12: 7:44

      Parallel version (MPI)

      Number of processors in use:       1

      For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials  
or PAW

      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

(hangs here until killed)

Any ideas what could cause this? Maybe a missed option someplace? I  
don't get any useful information sent to stderr.

Thanks and happy holidays,

Dave



David E. Farrell
Post-Doctoral Fellow
Department of Materials Science and Engineering
Northwestern University
email: d-farrell2 at northwestern.edu

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From jjr19 at uakron.edu  Wed Dec 24 19:30:15 2008
From: jjr19 at uakron.edu (J. J. Ramsey)
Date: Wed, 24 Dec 2008 10:30:15 -0800 (PST)
Subject: [Pw_forum] compiled pw, cp on a BG/P - scf.in test hangs
References: <20F197A1-7563-42A1-BA08-9374E74B8C88@u.northwestern.edu>
Message-ID: <759729.93620.qm@web50911.mail.re2.yahoo.com>

______________________________

So I was able to get pw and cp to compile on the BG/P, but when I try and test out pw using the scf.in test, the code hangs at the following (regardless of number of procs, time, etc)

launched as follows: 

Program PWSCF     v.4.0.4  starts ...
     Today is 24Dec2008 at 12: 7:44 

     Parallel version (MPI)

     Number of processors in use:       1

     For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW

     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

(hangs here until killed)

Any ideas what could cause this? Maybe a missed option someplace? I don't get any useful information sent to stderr

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

My guess is that something goofy happened with input redirection. If you haven't done it already, try running the test as "mpirun-or-exec ./pw.x -in scf.in > scf.out", and see what you get.

(BTW, I've noticed that on a cluster that I've used, running the "check-pw.x.j" within a batch job works fine even though input redirection in the script uses the "<" operator, but when running mpirun.lsf directly from the batch script, I need the "-in" option. Go figure.)



      

From davidfarrell2008 at u.northwestern.edu  Thu Dec 25 00:55:16 2008
From: davidfarrell2008 at u.northwestern.edu (David Farrell)
Date: Wed, 24 Dec 2008 17:55:16 -0600
Subject: [Pw_forum] compiled pw, cp on a BG/P - scf.in test hangs
In-Reply-To: <759729.93620.qm@web50911.mail.re2.yahoo.com>
References: <20F197A1-7563-42A1-BA08-9374E74B8C88@u.northwestern.edu>
	<759729.93620.qm@web50911.mail.re2.yahoo.com>
Message-ID: <70B4B170-EF38-4A18-B950-E3534CEE7A4A@u.northwestern.edu>

Looks like a combination of not having the pseudo_dir set and the  
passing of the input data was the problem.

Thanks!


On Dec 24, 2008, at 12:30 PM, J. J. Ramsey wrote:

> ______________________________
>
> So I was able to get pw and cp to compile on the BG/P, but when I  
> try and test out pw using the scf.in test, the code hangs at the  
> following (regardless of number of procs, time, etc)
>
> launched as follows:
>
> Program PWSCF     v.4.0.4  starts ...
>     Today is 24Dec2008 at 12: 7:44
>
>     Parallel version (MPI)
>
>     Number of processors in use:       1
>
>     For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials  
> or PAW
>
>     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
>
> (hangs here until killed)
>
> Any ideas what could cause this? Maybe a missed option someplace? I  
> don't get any useful information sent to stderr
>
> -----------------------------
>
> My guess is that something goofy happened with input redirection. If  
> you haven't done it already, try running the test as "mpirun-or- 
> exec ./pw.x -in scf.in > scf.out", and see what you get.
>
> (BTW, I've noticed that on a cluster that I've used, running the  
> "check-pw.x.j" within a batch job works fine even though input  
> redirection in the script uses the "<" operator, but when running  
> mpirun.lsf directly from the batch script, I need the "-in" option.  
> Go figure.)
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

David E. Farrell
Post-Doctoral Fellow
Department of Materials Science and Engineering
Northwestern University
email: d-farrell2 at northwestern.edu

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From mansourehp at gmail.com  Thu Dec 25 06:42:52 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Thu, 25 Dec 2008 09:12:52 +0330
Subject: [Pw_forum] LDA+U
Message-ID: <cbe1626b0812242142n11a52226q261c68edeccc59c@mail.gmail.com>

Dear all
In a LDA+U calculation how can I set starting_ns_eigenvalue.
Thanks in advance for your attention
Mansoureh
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From rezaebraahimi at yahoo.com  Thu Dec 25 17:30:16 2008
From: rezaebraahimi at yahoo.com (Reza Ebraahimi)
Date: Thu, 25 Dec 2008 08:30:16 -0800 (PST)
Subject: [Pw_forum] ASR
Message-ID: <223810.3767.qm@web59814.mail.ac4.yahoo.com>

Hi 
can anyone refer me to some literature about history of acoustic sum rules? i mean when was it proposed for the first time? and it's versions known here as "simple" and "crystal"? 
Thank You


      
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From 041019019 at fudan.edu.cn  Thu Dec 25 19:29:59 2008
From: 041019019 at fudan.edu.cn (Wang Qinjing)
Date: Fri, 26 Dec 2008 02:29:59 +0800
Subject: [Pw_forum] segmentation fault when using pwcond.x
Message-ID: <001601c966be$cb080690$3f7c620a@fduphy778548b0>

Dear all:

I am using pwcond.x to calculating the transimission of a system. The pwcond.x is compiled by openmpi 1.1.4. The pwcond.x was tested and confirmed get the same results as the example 12.

I wrote the input file just follow the example 12. The necessary files from the scf calculation is in the directory ./outdir. The input file is as follows:

--------------
 &inputcond
    outdir='./outdir',
    prefixl='lead',
    prefixs='scattering',
    tran_file='trans.file',
    ikind = 1,
    energy0=3.d0,
    denergy=0.d0,
    ewind=4.d0,
    epsproj=1.d-2,
    nz1 = 1,
 /
    1
    0.0  0.0  1.0
18
  3.0
  2.7
  2.5
  1.6
  1.0
  0.9
  0.1
  0.0
 -0.1
 -0.25
 -1.15
 -1.45
 -1.9
 -3.0
 -4.0
 -5.0
 -6.0
 -6.2
---------------------

After I typed the command "pwcond.x < cond.in ", the last line of the standard out is as follows:

-----------------------
        k(    1) = (   0.0000000   0.0000000), wk =   1.0000000

 ngper, shell number =          537         108
Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
Failing at addr:0x98f7e70da0
[0] func:/opt/mpi/ifort/openmpi-1.1.4/lib/libopal.so.0 [0x2a9588366a]
[1] func:/lib64/tls/libpthread.so.0 [0x31c8e0c420]
[2] func:pwcond.x(local_1_+0x110e) [0x478778]
[3] func:pwcond.x(local_+0xab6) [0x474fdc]
[4] func:pwcond.x(do_cond_+0x8ed) [0x45a565]
[5] func:pwcond.x(MAIN__+0x48) [0x4584b4]
[6] func:pwcond.x(main+0x2a) [0x44c2a2]
[7] func:/lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x31c851c4bb]
[8] func:pwcond.x(free+0x52) [0x44c1ea]
*** End of error message ***
Segmentation fault
-----------------------

What may the problem be?

Thank you in advance.

Yours Wang




------------------------------------
??????????????
Wang Qinjing, Physics Department, 
Fudan University
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From baroni at sissa.it  Thu Dec 25 22:02:08 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 25 Dec 2008 22:02:08 +0100
Subject: [Pw_forum] ASR
In-Reply-To: <223810.3767.qm@web59814.mail.ac4.yahoo.com>
References: <223810.3767.qm@web59814.mail.ac4.yahoo.com>
Message-ID: <452F56B8-2771-4BB7-B5DD-D24180F4775F@sissa.it>

On Dec 25, 2008, at 5:30 PM, Reza Ebraahimi wrote:

> Hi

Hi

> can anyone refer me to some literature about history of acoustic sum  
> rules? i mean when was it proposed for the first time?

Pick, Cohen, Martin, Phys. Rev. B 1, 910 - 920 (1970)

> and it's versions known here as "simple" and "crystal"?

"simple" only deals with q->0 frequencies, and modifies the q=0  
dynamical matrix so as to impose that the sum of the eigenvalues  
vanishes (this can be achieved by subtracting T/N from the diagonal  
elements, where T is the trace and N the dimension); "crystal" would  
do something more sophisticated on the interatomic force constants, so  
as to enforce continuity in the q->0 limit. do not know if the details  
have ever been written anywhere

> Thank You

you are most welcome. you would be even more so if you took the time  
of signing your posts to this forum, including your accademic  
affiliation.

Best wishes

Stefano Baroni

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -  
Trieste
http://www.sissa.it/~baroni / [+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 jameslipd at gmail.com  Fri Dec 26 04:31:51 2008
From: jameslipd at gmail.com (Jiaye, Li)
Date: Fri, 26 Dec 2008 11:31:51 +0800
Subject: [Pw_forum] Problem on pp.x
Message-ID: <b5d787260812251931r6192904eo27079f7dccb53333@mail.gmail.com>

Dear all

I installed parallel version of pwscf on my FC10. I am going to calculate
the workfunction of a surface, the first step via pw.x is done successfully,
but pp.x seems doesn't work, it reports errors:

     Program POST-PROC v.4.0.3  starts ...
     Today is 26Dec2008 at 19:12:45
     Parallel version (MPI)
     Number of processors in use:       1
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from postproc : error #       225
     reading inputpp namelist
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
[0] MPI Abort by user Aborting program !
[0] Aborting program!
Could anybody help me with me? At the first glance, it seems to be the error
of MPI, however, there is no problem with pw.x. So I am confused.

-- 
Sincerely

Jiaye Li



==============================================
Li, Jiaye

M.S. in designing and developing novel materials

Research experience:
*ALD precursor. ie. Metal complexes
*Surface modification. ie. Indium tin oxide, SiO2
*Gas storage and adsorption. ie. Ionic Liquids

Skills:
*ab-initial method, DFT simulation and Force Field simulation

Please contact me at:
1. jameslipd at gmail.com  or
2. jameslibd at gmail.com

==============================================
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From jameslipd at gmail.com  Fri Dec 26 04:48:58 2008
From: jameslipd at gmail.com (Jiaye, Li)
Date: Fri, 26 Dec 2008 11:48:58 +0800
Subject: [Pw_forum] Problem on pp.x
In-Reply-To: <b5d787260812251931r6192904eo27079f7dccb53333@mail.gmail.com>
References: <b5d787260812251931r6192904eo27079f7dccb53333@mail.gmail.com>
Message-ID: <b5d787260812251948q33f3495bg672250a81b7328fd@mail.gmail.com>

I tried like this: mpirun -np 2 ~/bin/pp.x input.inp output.out. But there
is no reponce after that command. It seems it wasnot running at all.

On Fri, Dec 26, 2008 at 11:31 AM, Jiaye, Li <jameslipd at gmail.com> wrote:

> Dear all
>
> I installed parallel version of pwscf on my FC10. I am going to calculate
> the workfunction of a surface, the first step via pw.x is done successfully,
> but pp.x seems doesn't work, it reports errors:
>
>      Program POST-PROC v.4.0.3  starts ...
>      Today is 26Dec2008 at 19:12:45
>      Parallel version (MPI)
>      Number of processors in use:       1
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from postproc : error #       225
>      reading inputpp namelist
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      stopping ...
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
> Could anybody help me with me? At the first glance, it seems to be the
> error of MPI, however, there is no problem with pw.x. So I am confused.
>
> --
> Sincerely
>
> Jiaye Li
>
>
>
> ==============================================
> Li, Jiaye
>
> M.S. in designing and developing novel materials
>
> Research experience:
> *ALD precursor. ie. Metal complexes
> *Surface modification. ie. Indium tin oxide, SiO2
> *Gas storage and adsorption. ie. Ionic Liquids
>
> Skills:
> *ab-initial method, DFT simulation and Force Field simulation
>
> Please contact me at:
> 1. jameslipd at gmail.com  or
> 2. jameslibd at gmail.com
>
> ==============================================
>



-- 
Sincerely

Jiaye Li



==============================================
Li, Jiaye

M.S. in designing and developing novel materials

Research experience:
*ALD precursor. ie. Metal complexes
*Surface modification. ie. Indium tin oxide, SiO2
*Gas storage and adsorption. ie. Ionic Liquids

Skills:
*ab-initial method, DFT simulation and Force Field simulation

Please contact me at:
1. jameslipd at gmail.com  or
2. jameslibd at gmail.com

==============================================
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From lanhaiping at gmail.com  Fri Dec 26 07:29:26 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Fri, 26 Dec 2008 14:29:26 +0800
Subject: [Pw_forum] Problem on pp.x
In-Reply-To: <b5d787260812251948q33f3495bg672250a81b7328fd@mail.gmail.com>
References: <b5d787260812251931r6192904eo27079f7dccb53333@mail.gmail.com>
	<b5d787260812251948q33f3495bg672250a81b7328fd@mail.gmail.com>
Message-ID: <c92002fa0812252229h72d03176lc07b63d7d56cbe69@mail.gmail.com>

Hi,
     reading inputpp namelist

donot you notice this output ?
you must make a mistake in your input file.

regards
On Fri, Dec 26, 2008 at 11:48 AM, Jiaye, Li <jameslipd at gmail.com> wrote:

> I tried like this: mpirun -np 2 ~/bin/pp.x input.inp output.out. But there
> is no reponce after that command. It seems it wasnot running at all.
>
>
> On Fri, Dec 26, 2008 at 11:31 AM, Jiaye, Li <jameslipd at gmail.com> wrote:
>
>> Dear all
>>
>> I installed parallel version of pwscf on my FC10. I am going to calculate
>> the workfunction of a surface, the first step via pw.x is done successfully,
>> but pp.x seems doesn't work, it reports errors:
>>
>>      Program POST-PROC v.4.0.3  starts ...
>>      Today is 26Dec2008 at 19:12:45
>>      Parallel version (MPI)
>>      Number of processors in use:       1
>>
>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>      from postproc : error #       225
>>      reading inputpp namelist
>>
>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>      stopping ...
>> [0] MPI Abort by user Aborting program !
>> [0] Aborting program!
>> Could anybody help me with me? At the first glance, it seems to be the
>> error of MPI, however, there is no problem with pw.x. So I am confused.
>>
>> --
>> Sincerely
>>
>> Jiaye Li
>>
>>
>>
>> ==============================================
>> Li, Jiaye
>>
>> M.S. in designing and developing novel materials
>>
>> Research experience:
>> *ALD precursor. ie. Metal complexes
>> *Surface modification. ie. Indium tin oxide, SiO2
>> *Gas storage and adsorption. ie. Ionic Liquids
>>
>> Skills:
>> *ab-initial method, DFT simulation and Force Field simulation
>>
>> Please contact me at:
>> 1. jameslipd at gmail.com  or
>> 2. jameslibd at gmail.com
>>
>> ==============================================
>>
>
>
>
> --
> Sincerely
>
> Jiaye Li
>
>
>
> ==============================================
> Li, Jiaye
>
> M.S. in designing and developing novel materials
>
> Research experience:
> *ALD precursor. ie. Metal complexes
> *Surface modification. ie. Indium tin oxide, SiO2
> *Gas storage and adsorption. ie. Ionic Liquids
>
> Skills:
> *ab-initial method, DFT simulation and Force Field simulation
>
> Please contact me at:
> 1. jameslipd at gmail.com  or
> 2. jameslibd at gmail.com
>
> ==============================================
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From jameslipd at gmail.com  Fri Dec 26 09:52:32 2008
From: jameslipd at gmail.com (Jiaye, Li)
Date: Fri, 26 Dec 2008 16:52:32 +0800
Subject: [Pw_forum]  Problem on pp.x
Message-ID: <b5d787260812260052u78581743j9ec17c0a8c67ad58@mail.gmail.com>

Hi


I am a new user of pwscf. At present I want to calculate the work function
of a surface slab. What confused me is where I am able to start, but I
happen to find that in the source directory where there is an example
(WorkFct_example) concerning that issue. I studied on it and modify the
input files accordingly. The first step for calculating via pw.x is ok. But
performing the second step via pp.x meets some problem. this is my input
file for pp.x:

 &inputPP
   outdir='/home/blade/jamesli/test/tmp',                       # temp files
   plot_num=11                          # the V_bare + V_H potential
   filplot = 'IO-O.pot'                 # the quantity selected by plot_num
/
 &plot
   iflag= 3,                                    # 3D plot
   output_format=3                              # format suitable for
XCRYSDEN  (1D, 2D, 3D)
/
I made a little changes in accord to the corresponding file in the pwscf
source directory. I tested the example in WorkFct_example, and it worked
well. I really don't know why it doesn't work for the present work. My
surface direction is along x axis, is that the root of problem? Could you
help me more about it?

-- 
Sincerely

Jiaye Li



==============================================
Li, Jiaye

M.S. in designing and developing novel materials

Research experience:
*ALD precursor. ie. Metal complexes
*Surface modification. ie. Indium tin oxide, SiO2
*Gas storage and adsorption. ie. Ionic Liquids

Skills:
*ab-initial method, DFT simulation and Force Field simulation

Please contact me at:
1. jameslipd at gmail.com  or
2. jameslibd at gmail.com

==============================================
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From lanhaiping at gmail.com  Fri Dec 26 09:57:15 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Fri, 26 Dec 2008 16:57:15 +0800
Subject: [Pw_forum] Problem on pp.x
In-Reply-To: <b5d787260812260052u78581743j9ec17c0a8c67ad58@mail.gmail.com>
References: <b5d787260812260052u78581743j9ec17c0a8c67ad58@mail.gmail.com>
Message-ID: <c92002fa0812260057p2f6b4120r2d1b94fac55c5b9@mail.gmail.com>

Then, what is your problem ?

regards,

On Fri, Dec 26, 2008 at 4:52 PM, Jiaye, Li <jameslipd at gmail.com> wrote:

> Hi
>
>
> I am a new user of pwscf. At present I want to calculate the work function
> of a surface slab. What confused me is where I am able to start, but I
> happen to find that in the source directory where there is an example
> (WorkFct_example) concerning that issue. I studied on it and modify the
> input files accordingly. The first step for calculating via pw.x is ok. But
> performing the second step via pp.x meets some problem. this is my input
> file for pp.x:
>
>  &inputPP
>    outdir='/home/blade/jamesli/test/tmp',                       # temp
> files
>    plot_num=11                          # the V_bare + V_H potential
>    filplot = 'IO-O.pot'                 # the quantity selected by plot_num
> /
>  &plot
>    iflag= 3,                                    # 3D plot
>    output_format=3                              # format suitable for
> XCRYSDEN  (1D, 2D, 3D)
> /
> I made a little changes in accord to the corresponding file in the pwscf
> source directory. I tested the example in WorkFct_example, and it worked
> well. I really don't know why it doesn't work for the present work. My
> surface direction is along x axis, is that the root of problem? Could you
> help me more about it?
>
> --
> Sincerely
>
> Jiaye Li
>
>
>
> ==============================================
> Li, Jiaye
>
> M.S. in designing and developing novel materials
>
> Research experience:
> *ALD precursor. ie. Metal complexes
> *Surface modification. ie. Indium tin oxide, SiO2
> *Gas storage and adsorption. ie. Ionic Liquids
>
> Skills:
> *ab-initial method, DFT simulation and Force Field simulation
>
> Please contact me at:
> 1. jameslipd at gmail.com  or
> 2. jameslibd at gmail.com
>
> ==============================================
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From jameslipd at gmail.com  Fri Dec 26 10:41:31 2008
From: jameslipd at gmail.com (Jiaye, Li)
Date: Fri, 26 Dec 2008 17:41:31 +0800
Subject: [Pw_forum]  Workfunction from slab calculations?
Message-ID: <b5d787260812260141g19de72d0kac31d592849f8165@mail.gmail.com>

Hi Georg

Was your problem solved? I wonder why you used plot_num = 1, rather than 11?

-- 
Sincerely

Jiaye Li



==============================================
Li, Jiaye

M.S. in designing and developing novel materials

Research experience:
*ALD precursor. ie. Metal complexes
*Surface modification. ie. Indium tin oxide, SiO2
*Gas storage and adsorption. ie. Ionic Liquids

Skills:
*ab-initial method, DFT simulation and Force Field simulation

Please contact me at:
1. jameslipd at gmail.com  or
2. jameslibd at gmail.com

==============================================
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From smogunov at sissa.it  Fri Dec 26 11:15:12 2008
From: smogunov at sissa.it (Alexander Smogunov)
Date: Fri, 26 Dec 2008 11:15:12 +0100
Subject: [Pw_forum] segmentation fault when using pwcond.x
In-Reply-To: <001601c966be$cb080690$3f7c620a@fduphy778548b0>
References: <001601c966be$cb080690$3f7c620a@fduphy778548b0>
Message-ID: <200812261115.12957.smogunov@sissa.it>

Dear Wang
Try to replace the subroutine PWCOND/init_orbitals.f90
by the one from espresso-4.0.3 distribution. 
This might fix the problem.
regards, Alexander

On Thursday 25 December 2008 19:29, Wang Qinjing wrote:
> Dear all:
>
> I am using pwcond.x to calculating the transimission of a system. The
> pwcond.x is compiled by openmpi 1.1.4. The pwcond.x was tested and
> confirmed get the same results as the example 12.
>
> I wrote the input file just follow the example 12. The necessary files from
> the scf calculation is in the directory ./outdir. The input file is as
> follows:
>
> --------------
>  &inputcond
>     outdir='./outdir',
>     prefixl='lead',
>     prefixs='scattering',
>     tran_file='trans.file',
>     ikind = 1,
>     energy0=3.d0,
>     denergy=0.d0,
>     ewind=4.d0,
>     epsproj=1.d-2,
>     nz1 = 1,
>  /
>     1
>     0.0  0.0  1.0
> 18
>   3.0
>   2.7
>   2.5
>   1.6
>   1.0
>   0.9
>   0.1
>   0.0
>  -0.1
>  -0.25
>  -1.15
>  -1.45
>  -1.9
>  -3.0
>  -4.0
>  -5.0
>  -6.0
>  -6.2
> ---------------------
>
> After I typed the command "pwcond.x < cond.in ", the last line of the
> standard out is as follows:
>
> -----------------------
>         k(    1) = (   0.0000000   0.0000000), wk =   1.0000000
>
>  ngper, shell number =          537         108
> Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
> Failing at addr:0x98f7e70da0
> [0] func:/opt/mpi/ifort/openmpi-1.1.4/lib/libopal.so.0 [0x2a9588366a]
> [1] func:/lib64/tls/libpthread.so.0 [0x31c8e0c420]
> [2] func:pwcond.x(local_1_+0x110e) [0x478778]
> [3] func:pwcond.x(local_+0xab6) [0x474fdc]
> [4] func:pwcond.x(do_cond_+0x8ed) [0x45a565]
> [5] func:pwcond.x(MAIN__+0x48) [0x4584b4]
> [6] func:pwcond.x(main+0x2a) [0x44c2a2]
> [7] func:/lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x31c851c4bb]
> [8] func:pwcond.x(free+0x52) [0x44c1ea]
> *** End of error message ***
> Segmentation fault
> -----------------------
>
> What may the problem be?
>
> Thank you in advance.
>
> Yours Wang
>
>
>
>
> ------------------------------------
> ????????????????????????????
> Wang Qinjing, Physics Department,
> Fudan University

From luotengf at msu.edu  Fri Dec 26 19:28:12 2008
From: luotengf at msu.edu (Tengfei Luo)
Date: Fri, 26 Dec 2008 13:28:12 -0500
Subject: [Pw_forum] need QHA code
Message-ID: <32918BBEE2BE4B00ADD17C030E997BB9@WIN1DV2EQQQRS7>

Hi, all:
I'm looking for a copy of the QHA code. I found the post from Eyvaz, but I could not download it. Could anyone please direct me where to download it or just send me a copy? I would greatly appreciate it!

Happy holiday!

Tengfei Luo
Mechanical Engineering
Michigan State University
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From eyvaz_isaev at yahoo.com  Fri Dec 26 21:30:22 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 26 Dec 2008 12:30:22 -0800 (PST)
Subject: [Pw_forum] need QHA code
In-Reply-To: <32918BBEE2BE4B00ADD17C030E997BB9@WIN1DV2EQQQRS7>
Message-ID: <793818.1251.qm@web65712.mail.ac4.yahoo.com>

Hi,

I will send it to you. As a new Year Gift!

Bests,
Eyvaz.

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


--- On Fri, 12/26/08, Tengfei Luo <luotengf at msu.edu> wrote:

> From: Tengfei Luo <luotengf at msu.edu>
> Subject: [Pw_forum] need QHA code
> To: pw_forum at pwscf.org
> Date: Friday, December 26, 2008, 9:28 PM
> Hi, all:
> I'm looking for a copy of the QHA code. I found the
> post from Eyvaz, but I could not download it. Could anyone
> please direct me where to download it or just send me a
> copy? I would greatly appreciate it!
> 
> Happy holiday!
> 
> Tengfei Luo
> Mechanical Engineering
> Michigan State University
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From luotengf at msu.edu  Fri Dec 26 21:32:02 2008
From: luotengf at msu.edu (Tengfei Luo)
Date: Fri, 26 Dec 2008 15:32:02 -0500
Subject: [Pw_forum] need QHA code
In-Reply-To: <793818.1251.qm@web65712.mail.ac4.yahoo.com>
References: <793818.1251.qm@web65712.mail.ac4.yahoo.com>
Message-ID: <789AE5F6FDBE4E658145F14DFF9C2865@WIN1DV2EQQQRS7>

Thank you very much!

Tengfei

----- Original Message ----- 
From: "Eyvaz Isaev" <eyvaz_isaev at yahoo.com>
To: "PWSCF Forum" <pw_forum at pwscf.org>
Sent: Friday, December 26, 2008 3:30 PM
Subject: Re: [Pw_forum] need QHA code


> Hi,
>
> I will send it to you. As a new Year Gift!
>
> Bests,
> Eyvaz.
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, 
> Russia,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, 
> Sweden
> Condensed Matter Theory Group, Uppsala University, Sweden
> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
> --- On Fri, 12/26/08, Tengfei Luo <luotengf at msu.edu> wrote:
>
>> From: Tengfei Luo <luotengf at msu.edu>
>> Subject: [Pw_forum] need QHA code
>> To: pw_forum at pwscf.org
>> Date: Friday, December 26, 2008, 9:28 PM
>> Hi, all:
>> I'm looking for a copy of the QHA code. I found the
>> post from Eyvaz, but I could not download it. Could anyone
>> please direct me where to download it or just send me a
>> copy? I would greatly appreciate it!
>>
>> Happy holiday!
>>
>> Tengfei Luo
>> Mechanical Engineering
>> Michigan State University
>> _______________________________________________
>> 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
> 


From pganesh at ciw.edu  Fri Dec 26 22:05:55 2008
From: pganesh at ciw.edu (P. Ganesh)
Date: Fri, 26 Dec 2008 16:05:55 -0500
Subject: [Pw_forum] question on optimization
In-Reply-To: <793818.1251.qm@web65712.mail.ac4.yahoo.com>
References: <793818.1251.qm@web65712.mail.ac4.yahoo.com>
Message-ID: <49554733.7020806@ciw.edu>


Hi,

I was wondering if it possible to do a constrained structural 
optimization using 'pwscf' of a monoclinic structure whereby
the 'a' and 'b' in-plane lattices are kept fixed, while the 'c' axis 
(i.e. mod(c), and angles alpha and beta) alone is allowed to relax.

Wish you all happy holidays.

Thanks,
Ganesh

From adams_mejl at hotmail.com  Sat Dec 27 00:31:46 2008
From: adams_mejl at hotmail.com (Adam Jacobsson)
Date: Sat, 27 Dec 2008 00:31:46 +0100
Subject: [Pw_forum] dynmat.x
Message-ID: <COL103-W21C71A35E17C019FDC2454E4EB0@phx.gbl>


Hi!
 
I have a small trouble with the dynmat.x program. When I try to run the program for the gamma point it complains that I have not supplied a direction for q and that the TO-LO splitting therefore not will be available. '
 
I thought that setting the setting q(i)=0 for i = 1,2,3 was to supply a direction for q? 
 
Best Regards,
Adam JAcobsson 
_________________________________________________________________
Var sommaren f?r kort? H?r hittar du solen!
http://resor.se.msn.com/
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From adams_mejl at hotmail.com  Sat Dec 27 00:40:15 2008
From: adams_mejl at hotmail.com (Adam Jacobsson)
Date: Sat, 27 Dec 2008 00:40:15 +0100
Subject: [Pw_forum] dynmat.x
In-Reply-To: <COL103-W21C71A35E17C019FDC2454E4EB0@phx.gbl>
References: <COL103-W21C71A35E17C019FDC2454E4EB0@phx.gbl>
Message-ID: <COL103-W4468958887B34377243A79E4EB0@phx.gbl>


Hi again!
 
My first thought was that the program wanted the direction from where to approach the gamma point as a limit. Is that the case?
 
Best Regards,
Adam  



From: adams_mejl at hotmail.comTo: pw_forum at pwscf.orgDate: Sat, 27 Dec 2008 00:31:46 +0100Subject: [Pw_forum] dynmat.x

Hi! I have a small trouble with the dynmat.x program. When I try to run the program for the gamma point it complains that I have not supplied a direction for q and that the TO-LO splitting therefore not will be available. ' I thought that setting the setting q(i)=0 for i = 1,2,3 was to supply a direction for q?  Best Regards,Adam JAcobsson 



Best?ll bl?ck f?re 19 f?r leverans n?sta vardag inkClub
_________________________________________________________________
Senaste sportnyheterna & rykande f?rska resultat!
http://sport.msn.se/
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From padmaja_patnaik at yahoo.co.uk  Sat Dec 27 03:25:03 2008
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Sat, 27 Dec 2008 02:25:03 +0000 (GMT)
Subject: [Pw_forum] Code for atomic positions of a supercell
Message-ID: <589797.40445.qm@web25408.mail.ukl.yahoo.com>


Hi All

I need to find out the atomic positions of a supercell. can anybody suggest me a code for that purpose?

Regards
Padmaja Patnaik

Research Scholar

Dept of Physics

IIT Bombay

Mumbai, India


      
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From manoj at phys.ufl.edu  Sat Dec 27 04:26:19 2008
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Fri, 26 Dec 2008 22:26:19 -0500 (EST)
Subject: [Pw_forum] complex band
Message-ID: <Pine.GSO.4.21.0812262202420.19061-100000@neptune.phys.ufl.edu>

Dear Alexander and PWSCF users, 
 I have two questions about complex band code based on the Choi and Ihm
paper(PRB 59,2167,(1999)) 
 1. At the expressions where we have to use non local potential
W((k+G)_{\perp},tau-z-d), i can see the code only uses
W((k+G)_{\perp},tau-z). I guess this is because of periodicity of nonlocal
potential in the z direction. Am i right?
 
 2. This question is about determining the coefficients of the
wavefunctions. As we can see from equations (17) for the local part of the
potential it has N*2*N_2d number of unknown cofficients. Now using the
boundary conditions, that the wavefunction and its derivative should be
continuous between the slabs, we can determine (N-1)*2*N_2d unknownns,
which leaves 2*N_2d no. of coefficients to be determined later. The same
thing applies for the solutions of nonlocal part of the potential in
equation (24). Thus the number of linearly independent solution for the
nonlocal part is 2*N_2d. we use Bloch's condition to determine these
unknown coeffiecints. This is where my question is. When we are trying to
construct the general solution as in  equation (39), the local part has
number of unknown coeffieints 2*N_2d, which is fine. But the nonlocal part
has C_{\alpha,l,m} number of unknown coefficients, which is not equal to
2*N_2d. My question is why? Are we somehow combining the coefficients of
local part with nonlocal part? 
Any help will be appreciated. 
Happy Holidays!

Manoj Srivastava
Graduate Student 
Department of Physics 
University of Florida, Gainesville, Fl 32601 


From njuxuyuehua at gmail.com  Sat Dec 27 05:35:13 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Sat, 27 Dec 2008 12:35:13 +0800
Subject: [Pw_forum] error :kpoint 7 ibnd 17 solve_linter: root not converged
	NaN
Message-ID: <aca2feb20812262035h527e4f0i6516e506010a8de@mail.gmail.com>

error in the phonon calculation! (the 19th phonon problem)????
hi all :
my system is a excited state, my aim is to get the phonon phonon at G point
at this state,but i face
the error  is following in the 19 phonon calculation ?

  Representation # 19 mode #  19
     Self-consistent Calculation
      iter #   1 total cpu time :  3876.6 secs   av.it.:   3.9
      thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.412E-07
      iter #   2 total cpu time :  3896.1 secs   av.it.:  10.3
      thresh= 0.203E-04 alpha_mix =  0.700 |ddv_scf|^2 =  0.891E-09
      iter #   3 total cpu time :  3918.1 secs   av.it.:  12.9
      thresh= 0.298E-05 alpha_mix =  0.700 |ddv_scf|^2 =  0.155E-08
      iter #   4 total cpu time :  3939.5 secs   av.it.:  11.9
      thresh= 0.394E-05 alpha_mix =  0.700 |ddv_scf|^2 =  0.415E-11
     kpoint   7 ibnd  17 solve_linter: root not converged  NaN
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from broyden : error #         3
     factorization
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from broyden : error #         3
     factorization
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from broyden : error #         3
     factorization
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
the error is in the 19th phonon calculation ,before is OK.
SO i do not know what happened. i need your help.

-- 
Xu Yuehua
physics Department of Nanjing university
China
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From lataprem29 at gmail.com  Sat Dec 27 10:14:46 2008
From: lataprem29 at gmail.com (premlata pandit)
Date: Sat, 27 Dec 2008 14:44:46 +0530
Subject: [Pw_forum] unknown softening of phonon modes
In-Reply-To: <6f289440812270106w578e6b1ag3e55ff1c9235ce60@mail.gmail.com>
References: <6f289440812270106w578e6b1ag3e55ff1c9235ce60@mail.gmail.com>
Message-ID: <6f289440812270114q7d830c59xebe8fe67513d2169@mail.gmail.com>

Dear Pwscf users,
I have done the phonon calculation of Li2S using 4x4x4 (8-q-points) using
this code. In this mail I am sending the scf file and the ph.in file and
also the PDC obtained in
0.0 0.0 0.0 to 1.0 0.0 0.0
direction, (our results and the reported previous results JPCM 3 (1991)
1055-1064)

In our calculated PDC we are getting good agreement at gamma points. But
when we draw in the whole brillouin zone we are getting an unwanted
softening of optical and also one of the acoustic mode in the midway of G-X
direction.
Can anybody comment on this.
It will be really helpful for my PhD work.
Regards
 &CONTROL
               calculation = 'scf' ,
              restart_mode = 'from_scratch' ,
                    outdir = './OUT',
             pseudo_dir = '/root/bipul/espresso-4.0.1/pseudo/Li2S',
             prefix = 'Li2S',
             etot_conv_thr = 1.0d-5 ,
             forc_conv_thr = 1.0d-4 ,
                   tstress = .true. ,
                   tprnfor = .true. ,
 /
 &SYSTEM
                     ibrav = 2,
                 celldm(1) =  10.78750,
                       nat = 3,
                      ntyp = 2 ,
                   ecutwfc = 32,
                   ecutrho = 600,
                  occupations = 'fixed' ,
                  smearing = 'methfessel-paxton',
 !                  degauss = 0.01
 /
 &ELECTRONS
               mixing_beta = 0.5 ,
            conv_thr =  1.0d-8
           diagonalization = 'david' ,
 /
 &IONS
 /
ATOMIC_SPECIES
 S   32.066  S.pw91-van_ak.UPF
 Li  6.914   Li.pw91-s-van_ak.UPF
ATOMIC_POSITIONS (crystal)
S  0.0 0.0 0.0
Li 0.25 0.25 0.25
Li 0.75 0.75 0.75
K_POINTS automatic
   8  8  8 1 1 1



phonons of Li2S
 &inputph
  recover =.true.,
  tr2_ph=1.0d-14,
  alpha_mix(1)=0.4,
  prefix='Li2S',
  amass(1)=32.066,
  amass(2)=6.941,
  outdir='./OUT',
  fildyn='li2s.dyn',
  epsil= .true.,
  trans= .true.,
! ldisp=.true.
 nq1=4, nq2=4, nq3=4
 /
~

~


-- 
Premlata Pandit
Ph.d. student,
Barkatullah university,
Bhopal 462026,
MP, India
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From eyvaz_isaev at yahoo.com  Sat Dec 27 14:14:43 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sat, 27 Dec 2008 05:14:43 -0800 (PST)
Subject: [Pw_forum] dynmat.x
In-Reply-To: <COL103-W4468958887B34377243A79E4EB0@phx.gbl>
Message-ID: <796321.82196.qm@web65715.mail.ac4.yahoo.com>

Hi Adam, 

Most likely, you mean matdyn.x, but not dynmat.x.

If you mean a message like "TO-LO splitting at q=0 will be absent!"
then you should note that there is a message about missing of Z_star (Born effective charge) that really makes TO_LO calculations impossible.
But this is the case for a metallic system, not semiconducting or insulating. 
Simply the program tells you have no Z_star (as you have a metallic system), and TO-LO calculations are omitted.

If you have a metallic system this message is harmless. 

Bests,
Eyvaz.

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


--- On Sat, 12/27/08, Adam Jacobsson <adams_mejl at hotmail.com> wrote:

> From: Adam Jacobsson <adams_mejl at hotmail.com>
> Subject: Re: [Pw_forum] dynmat.x
> To: pw_forum at pwscf.org
> Date: Saturday, December 27, 2008, 2:40 AM
> Hi again!
>  
> My first thought was that the program wanted the direction
> from where to approach the gamma point as a limit. Is that
> the case?
>  
> Best Regards,
> Adam  
> 
> 
> 
> From: adams_mejl at hotmail.comTo: pw_forum at pwscf.orgDate:
> Sat, 27 Dec 2008 00:31:46 +0100Subject: [Pw_forum] dynmat.x
> 
> Hi! I have a small trouble with the dynmat.x program. When
> I try to run the program for the gamma point it complains
> that I have not supplied a direction for q and that the
> TO-LO splitting therefore not will be available. ' I
> thought that setting the setting q(i)=0 for i = 1,2,3 was to
> supply a direction for q?  Best Regards,Adam JAcobsson 
> 
> 
> 
> Best?ll bl?ck f?re 19 f?r leverans n?sta vardag
> inkClub
> _________________________________________________________________
> Senaste sportnyheterna & rykande f?rska resultat!
> http://sport.msn.se/_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From bipulrr at gmail.com  Sat Dec 27 14:53:10 2008
From: bipulrr at gmail.com (Bipul Rakshit)
Date: Sat, 27 Dec 2008 19:23:10 +0530
Subject: [Pw_forum] q-points for antifluorite structure
Message-ID: <3a749910812270553s75e05f5fy751442391078dd9b@mail.gmail.com>

Dear users,
I am doing phonon calculation of anti-fluorite structure of Li2S. I just
want to ask what q-points I have to put in matdyn.in file to get a smooth
PDC curve.

In Li2S.ph.in file I am using 4x4x4 grid with 8 q-points

   0.000000000000000E+00   0.000000000000000E+00   0.000000000000000E+00
  -0.250000000000000E+00   0.250000000000000E+00  -0.250000000000000E+00
   0.500000000000000E+00  -0.500000000000000E+00   0.500000000000000E+00
   0.000000000000000E+00   0.500000000000000E+00   0.000000000000000E+00
   0.750000000000000E+00  -0.250000000000000E+00   0.750000000000000E+00
   0.500000000000000E+00   0.000000000000000E+00   0.500000000000000E+00
   0.000000000000000E+00  -0.100000000000000E+01   0.000000000000000E+00
  -0.500000000000000E+00  -0.100000000000000E+01   0.000000000000000E+00

So for PDC curve how can i take the high symmetry directions
-- 
Bipul Rakshit
PhD Student,
Barkatullah University,
Bhopal 462026,
MP, India
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From eyvaz_isaev at yahoo.com  Sat Dec 27 15:45:25 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sat, 27 Dec 2008 06:45:25 -0800 (PST)
Subject: [Pw_forum] Code for atomic positions of a supercell
In-Reply-To: <589797.40445.qm@web25408.mail.ukl.yahoo.com>
Message-ID: <314207.34651.qm@web65706.mail.ac4.yahoo.com>

Dear Padmaja,

> I need to find out the atomic positions of a supercell. can
> anybody suggest me a code for that purpose?

You do not need any code to do it, all you need is the knowledge of basis vectors and atomic positions in the unit cell, then just extend these positions according R'=R0+J*a+K*b+L*c, where a,b,c are basis vectors, R0 are original atomic positions, J,K,L are translations along a,b,c vectors.

Nevertheless, if you feel this is quite incredible job for you (that is the worst case) have a look at Dario Alfe's webpage 
http://chianti.geol.ucl.ac.uk/~dario/
 download his phonon code  and learn how to get atomic positions in a supercell.

Bests,
Eyvaz.

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


--- On Sat, 12/27/08, Padmaja Patnaik <padmaja_patnaik at yahoo.co.uk> wrote:

> From: Padmaja Patnaik <padmaja_patnaik at yahoo.co.uk>
> Subject: [Pw_forum] Code for atomic positions of a supercell
> To: pw_forum at pwscf.org
> Date: Saturday, December 27, 2008, 5:25 AM
> Hi All
> 
> I need to find out the atomic positions of a supercell. can
> anybody suggest me a code for that purpose?
> 
> 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 eyvaz_isaev at yahoo.com  Sat Dec 27 16:15:16 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sat, 27 Dec 2008 07:15:16 -0800 (PST)
Subject: [Pw_forum] q-points for antifluorite structure
In-Reply-To: <3a749910812270553s75e05f5fy751442391078dd9b@mail.gmail.com>
Message-ID: <756588.2707.qm@web65711.mail.ac4.yahoo.com>

Dear Bipul,

For face centered cubic lattice the high symmetry directions are

G(000)-X[100]-X[110]-G-L(1/2,1/2,1/2)-X(100)-W(1,1/2,0)-L

Note there is no X[100]-X[110] direction, this is only to show that the end points for G-X[100] and G-X[110] directions are the same.

Bests,
Eyvaz.

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


--- On Sat, 12/27/08, Bipul Rakshit <bipulrr at gmail.com> wrote:

> From: Bipul Rakshit <bipulrr at gmail.com>
> Subject: [Pw_forum] q-points for antifluorite structure
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Date: Saturday, December 27, 2008, 4:53 PM
> Dear users,
> I am doing phonon calculation of anti-fluorite structure of
> Li2S. I just
> want to ask what q-points I have to put in matdyn.in file
> to get a smooth
> PDC curve.
> 
> In Li2S.ph.in file I am using 4x4x4 grid with 8 q-points
> 
>    0.000000000000000E+00   0.000000000000000E+00  
> 0.000000000000000E+00
>   -0.250000000000000E+00   0.250000000000000E+00 
> -0.250000000000000E+00
>    0.500000000000000E+00  -0.500000000000000E+00  
> 0.500000000000000E+00
>    0.000000000000000E+00   0.500000000000000E+00  
> 0.000000000000000E+00
>    0.750000000000000E+00  -0.250000000000000E+00  
> 0.750000000000000E+00
>    0.500000000000000E+00   0.000000000000000E+00  
> 0.500000000000000E+00
>    0.000000000000000E+00  -0.100000000000000E+01  
> 0.000000000000000E+00
>   -0.500000000000000E+00  -0.100000000000000E+01  
> 0.000000000000000E+00
> 
> So for PDC curve how can i take the high symmetry
> directions
> -- 
> Bipul Rakshit
> PhD Student,
> Barkatullah University,
> Bhopal 462026,
> MP, India
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From zhaohscas at yahoo.com.cn  Sat Dec 27 17:30:33 2008
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Sun, 28 Dec 2008 00:30:33 +0800
Subject: [Pw_forum] Consider the relativistic effect for heavy element
	within pwscf.
Message-ID: <1315559370.20081228003033@yahoo.com.cn>

Dear users,

Currently I'm doing some research on the element Hf, a pretty heavy element.  If I want to take the relativistic effect into
account in my calculation.  Is this possible within pwscf?  If so, what parameters should I use for the input files?  Any hints will be highly appreciated.  Thanks in advance.

Regards,
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn> 
Xinjiang Technical Institute of Physics and Chemistry
Chinese Academy of Sciences 
GnuPG DSA: 0xD108493
2008-12-27


From akohlmey at cmm.chem.upenn.edu  Sat Dec 27 22:24:33 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 27 Dec 2008 16:24:33 -0500 (EST)
Subject: [Pw_forum] Consider the relativistic effect for heavy element
 within pwscf.
In-Reply-To: <1315559370.20081228003033@yahoo.com.cn>
References: <1315559370.20081228003033@yahoo.com.cn>
Message-ID: <Pine.LNX.4.64.0812271159480.2391@localhost.localdomain>

On Sun, 28 Dec 2008, Hongsheng Zhao wrote:

HZ> Dear users,

dear zhao,
 
HZ> Currently I'm doing some research on the element Hf, a pretty heavy 
HZ> element.  If I want to take the relativistic effect into account in 
HZ> my calculation.  Is this possible within pwscf?  If so, what 
HZ> parameters should I use for the input files?  Any hints will be 
HZ> highly appreciated.  Thanks in advance.

pseudopotentials created from a scalar relativistic already include
relativistic effects in some sort of mean-field approach. practially
all pseudopotential generation codes that i know do that by default.

the atomic code bundled with Q-E also allows to generate fully
relativistic pseudopotentials, but do you expect any relativistic 
effects that require explicit spin-orbit? and particularly any 
effects that will be significant beyond the errors that you 
make by using DFT to begin with? i'm not an expert in this field,
but if a fully relativistic treatment of Hf would be important,
there should be a significant body of literature on the subject...

cheers,
   axel.

 
HZ> Regards,
HZ> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From 041019019 at fudan.edu.cn  Sun Dec 28 16:50:05 2008
From: 041019019 at fudan.edu.cn (Wang Qinjing)
Date: Sun, 28 Dec 2008 23:50:05 +0800
Subject: [Pw_forum] Different TRC will be obtained for the same system?
Message-ID: <000e01c96903$f4075770$3f7c620a@fduphy778548b0>

Dear all:

I am a new PWSCF user and I was confused by two things.

One thing is different TRC (Transimission coefficient) at the same energy point will be obtained for the same system. After get the wave functions by the scf calculation, I tried to get the TRC. First I just calculate the TRC at the fermi energy, i.e., the inputfile cond.in for the pwcond.x fiis as follows:

=========
    energy0=0.0d0,
    denergy=0.0d0,
/
    1
    0.0  0.0  1.0
1
  0.0
=========
in this way the TRC at fermi energy is about 0.106

But if I calculate the TRCs for different energies, i.e., the input file for the pwcond.x is as:

========
    energy0=2.0d0,
    denergy=-0.02d0,
/
 1
    0.0  0.0  1.0
201
========
in this way a series of TRC is obtained and the TRC at fermi energy is 5*10^-3. There must be something wrong. Is it a bug? or related to the complie problem?

Thank you in advance.

Yours Wang


------------------------------------
??????????????
Wang Qinjing, Physics Department, 
Fudan University
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From jameslipd at gmail.com  Mon Dec 29 02:59:26 2008
From: jameslipd at gmail.com (Jiaye, Li)
Date: Mon, 29 Dec 2008 09:59:26 +0800
Subject: [Pw_forum]  Problem on pp.x
Message-ID: <b5d787260812281759y7823f30cj1e059ae59aac0ca@mail.gmail.com>

Hi

I think my input file should be correct, since I made it according to the
example. But when I submit a job, it always report:
     Program POST-PROC v.4.0.3  starts ...
     Today is 29Dec2008 at 17:36:39
     Parallel version (MPI)
     Number of processors in use:       2
     R & G space division:  proc/pool =    2
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from postproc : error #       225
     reading inputpp namelist
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
As a previous post pointed out that it may be due to the input file error,
however, I think the input file should be a standard input file for surface
calculation, could you help me with pick out where the error is from my
input file? Thanks.

 &inputPP
   outdir='/home/blade/jamesli/test/tmp',                       # temp files
   plot_num=11                          # the V_bare + V_H potential
   filplot = 'IO-O.pp'                  # the quantity selected by plot_num
/
 &plot
   iflag= 3,                                    # 3D plot
   output_format=3                              # format suitable for
XCRYSDEN  (1D, 2D, 3D)
/


-- 
Sincerely

Jiaye Li



==============================================
Li, Jiaye

M.S. in designing and developing novel materials

Research experience:
*ALD precursor. ie. Metal complexes
*Surface modification. ie. Indium tin oxide, SiO2
*Gas storage and adsorption. ie. Ionic Liquids

Skills:
*ab-initial method, DFT simulation and Force Field simulation

Please contact me at:
1. jameslipd at gmail.com  or
2. jameslibd at gmail.com

==============================================
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From jjr19 at uakron.edu  Mon Dec 29 03:18:09 2008
From: jjr19 at uakron.edu (J. J. Ramsey)
Date: Sun, 28 Dec 2008 18:18:09 -0800 (PST)
Subject: [Pw_forum] Problem on pp.x
References: <b5d787260812281759y7823f30cj1e059ae59aac0ca@mail.gmail.com>
Message-ID: <87483.81936.qm@web50902.mail.re2.yahoo.com>

________________________________
From: "Jiaye, Li" <jameslipd at gmail.com>
To: pw_forum at pwscf.org
Sent: Sunday, December 28, 2008 8:59:26 PM
Subject: [Pw_forum]  Problem on pp.x


Hi
 
I think my input file should be correct, since I made it according to the example.
________________________________

I'm not sure if the example file has comments, but I suggest either removing the comments from your own input file or at the very least using "!" in place of "#" as the comment character. There is some documentation on the use of comments in namelists here:

http://publib.boulder.ibm.com/infocenter/comphelp/v8v101/index.jsp?topic=/com.ibm.xlf101a.doc/xlflr/namelistio.htm

It's stated that in Fortran 95 that comments are allowed in namelists, but the comments start with a "!", not a "#".



      

From njuxuyuehua at gmail.com  Mon Dec 29 03:39:37 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Mon, 29 Dec 2008 10:39:37 +0800
Subject: [Pw_forum] can pwscf compute the phonon of properties of excited
	state?
Message-ID: <aca2feb20812281839p1013ef71m1055a0a96dbac517@mail.gmail.com>

hi all
i face a problem when calculate the phonon at G  of  excited state?
 iter #  78 total cpu time : 20566.8 secs   av.it.: 141.6
      thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.430+113
      iter #  79 total cpu time : 21036.5 secs   av.it.: 144.1
      thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.236+115
      iter #  80 total cpu time : 21484.8 secs   av.it.: 146.4
      thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.198+119
      iter #  81 total cpu time : 21946.2 secs   av.it.: 151.2
      thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.311+122
     kpoint   1 ibnd  17 solve_e: root not converged  0.113E-01
     kpoint   1 ibnd  17 solve_e: root not converged  0.142E-01
      iter #  82 total cpu time : 22423.0 secs   av.it.: 155.6
      thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.207+127
     kpoint   1 ibnd  17 solve_e: root not converged  0.140E-01
     kpoint   1 ibnd  17 solve_e: root not converged  0.520E-01
     kpoint   1 ibnd  17 solve_e: root not converged  0.558E-01
     kpoint   2 ibnd  17 solve_e: root not converged  0.127E-01
     kpoint   2 ibnd  17 solve_e: root not converged  0.544E-02
     kpoint   2 ibnd  17 solve_e: root not converged  0.522E-02
so i want to ask can pwscf compute the phonon of properties of excited
state?

-- 
Xu Yuehua
physics Department of Nanjing university
China
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From paulatto at sissa.it  Mon Dec 29 09:26:50 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Mon, 29 Dec 2008 09:26:50 +0100
Subject: [Pw_forum] Problem on pp.x
In-Reply-To: <b5d787260812281759y7823f30cj1e059ae59aac0ca@mail.gmail.com>
References: <b5d787260812281759y7823f30cj1e059ae59aac0ca@mail.gmail.com>
Message-ID: <op.umw0e0mba8x26q@linux-hvn6>

On Mon, 29 Dec 2008 02:59:26 +0100, Jiaye, Li <jameslipd at gmail.com> wrote:
> I think my input file should be correct, since I made it according to the
> example. But when I submit a job, it always report:

Dear Li Jiaye,
you cannot use "#" as a comment marker in an input file; it works in the example because it is inserted in a bash script. Replace the "#" with "!" and it will work.

regards



-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

     *** save italian brains ***
 http://saveitalianbrains.wordpress.com/

From lzh-ming at 163.com  Mon Dec 29 12:46:46 2008
From: lzh-ming at 163.com (lzh-ming)
Date: Mon, 29 Dec 2008 19:46:46 +0800 (CST)
Subject: [Pw_forum] problem about calculation with ph.x
Message-ID: <32140301.425081230551206372.JavaMail.coremail@bj163app120.163.com>

Hello everyone,
  I have tried to calculate the phonon disperation of CdCNi3.
I wrote in the file CdCNi3.ph.in as follow:
  
  ldisp=.true.,
  nq1=4, nq2=4, nq3=4,
  iq1=2, iq2=1, iq3=1,
 
but in the file CdCNi3.dyn0 , I got 
  4 4 4
  1
  0.0 0.0 0.0 
 
I changed the value of iq1,iq2,iq3 to 2,2,1, I still got 0.0 0.0 0.0.
I set the value as 3 3 2, I got 0.25 0.25 0.25.
When the value is 3 3 3, I got -0.5 -0.5 -0.5.(This is right.)
 
I tried all the 10 unequivalent points of 4*4*4 grid(simple cube),
I only got 3 different outputs.
 
What's the problem? Can you help me?
 
Thanks a lot!
 
li-ming-fan
 


 
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From penghua8503 at 163.com  Mon Dec 29 13:20:24 2008
From: penghua8503 at 163.com (penghua)
Date: Mon, 29 Dec 2008 20:20:24 +0800 (CST)
Subject: [Pw_forum] electron-phonon interaction
Message-ID: <33376796.361751230553224598.JavaMail.coremail@bj163app136.163.com>

Dear pwscf users, 

In example 07, how to calculate electron-phonon interaction is shown. But, why twice scf calculations are done in this calculation? What is the intention of each calculation?

Besides can I calculation the electron-phonon interaction of semiconductor?

Thank you in advance.

 

Penghua

Penghua8503 at 163.com

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From eyvaz_isaev at yahoo.com  Mon Dec 29 14:13:38 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 29 Dec 2008 05:13:38 -0800 (PST)
Subject: [Pw_forum] problem about calculation with ph.x
In-Reply-To: <32140301.425081230551206372.JavaMail.coremail@bj163app120.163.com>
Message-ID: <887862.14159.qm@web65713.mail.ac4.yahoo.com>

Dear li-ming-fan,

In order to calculate phonon dispersion curves you need to calculate real space Interatomic Force Constants matrix F(R). This can be obtained via the FFT using the dynamical matricies F(q). 

In order to get F(q) set, you should use only nq1,nq2,nq3, but not iq1,iq2,iq3 which are used to calculate F(q) for a given q-point(s).

After F(q)=> F(R) transformation you have to supply a list of q-points along high symmetry directions and calculate phonon modes for these points.

Bests,
Eyvaz.


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


--- On Mon, 12/29/08, lzh-ming <lzh-ming at 163.com> wrote:

> From: lzh-ming <lzh-ming at 163.com>
> Subject: [Pw_forum] problem about calculation with ph.x
> To: "Pw_forum" <pw_forum at pwscf.org>
> Date: Monday, December 29, 2008, 2:46 PM
> Hello everyone,
>   I have tried to calculate the phonon disperation of
> CdCNi3.
> I wrote in the file CdCNi3.ph.in as follow:
>   
>   ldisp=.true.,
>   nq1=4, nq2=4, nq3=4,
>   iq1=2, iq2=1, iq3=1,
>  
> but in the file CdCNi3.dyn0 , I got 
>   4 4 4
>   1
>   0.0 0.0 0.0 
>  
> I changed the value of iq1,iq2,iq3 to 2,2,1, I still got
> 0.0 0.0 0.0.
> I set the value as 3 3 2, I got 0.25 0.25 0.25.
> When the value is 3 3 3, I got -0.5 -0.5 -0.5.(This is
> right.)
>  
> I tried all the 10 unequivalent points of 4*4*4 grid(simple
> cube),
> I only got 3 different outputs.
>  
> What's the problem? Can you help me?
>  
> Thanks a lot!
>  
> li-ming-fan
>  
> 
> 
>  _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From paulatto at sissa.it  Mon Dec 29 14:45:27 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Mon, 29 Dec 2008 14:45:27 +0100
Subject: [Pw_forum] electron-phonon interaction
In-Reply-To: <33376796.361751230553224598.JavaMail.coremail@bj163app136.163.com>
References: <33376796.361751230553224598.JavaMail.coremail@bj163app136.163.com>
Message-ID: <op.umxe51zra8x26q@linux-hvn6>

On Mon, 29 Dec 2008 13:20:24 +0100, penghua <penghua8503 at 163.com> wrote:
> But, why twice scf calculations are done in this calculation? What is  
> the intention of each calculation?

It is explained quite clearly in the README file in the example07 directory: the first one is for DOS calculation, the second for phonons. Please read the README file accurately, as it provides vital hints and answers your question in detail.


> Besides can I calculation the electron-phonon interaction of  
> semiconductor?

I don't see any problem with it, but I don't really know the matter in depth thus some technical problems may arise.

cheers

P.S. please provide your affiliation when writing to pw forum!


-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

     *** save italian brains ***
 http://saveitalianbrains.wordpress.com/

From akohlmey at cmm.chem.upenn.edu  Mon Dec 29 16:27:59 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 29 Dec 2008 10:27:59 -0500 (EST)
Subject: [Pw_forum] can pwscf compute the phonon of properties of
 excited state?
In-Reply-To: <aca2feb20812281839p1013ef71m1055a0a96dbac517@mail.gmail.com>
References: <aca2feb20812281839p1013ef71m1055a0a96dbac517@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0812291018010.2391@localhost.localdomain>

On Mon, 29 Dec 2008, xu yuehua wrote:

YX> hi all
YX> i face a problem when calculate the phonon at G  of  excited state?

what _kind_ of excited state? 
what are the inputs that you were using? 

as has been mentioned here _many_ times, the more details 
you provide, the better chances you have of getting a useful 
answer, or any answer at all.

axel.

YX>  iter #  78 total cpu time : 20566.8 secs   av.it.: 141.6

[...]


-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From 041019019 at fudan.edu.cn  Mon Dec 29 18:05:01 2008
From: 041019019 at fudan.edu.cn (Wang Qinjing)
Date: Tue, 30 Dec 2008 01:05:01 +0800
Subject: [Pw_forum] Too many data communications between nodes when run pw.x
	in parallel?
Message-ID: <001401c969d7$966cd610$3f7c620a@fduphy778548b0>

Dear all:

I noted that if I made calculation by pw.x in paralllel, there were too many data communications between nodes. That was attributed to the data communication of wave functions. There is a severe delay to get information from these nodes.

If I set disk_io='low', things are much better. But the main node (or the first node) still has problem in net communication. I noticed a charge density file is still written after each scf step. Is that the problem?  Or is there anything I can do to improve this situation?

Thanks in advance.

Yours Wang

------------------------------------
??????????????
Wang Qinjing, Physics Department, 
Fudan University
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From akohlmey at cmm.chem.upenn.edu  Mon Dec 29 19:21:00 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 29 Dec 2008 13:21:00 -0500 (EST)
Subject: [Pw_forum] Too many data communications between nodes when run
 pw.x in parallel?
In-Reply-To: <001401c969d7$966cd610$3f7c620a@fduphy778548b0>
References: <001401c969d7$966cd610$3f7c620a@fduphy778548b0>
Message-ID: <Pine.LNX.4.64.0812291314350.2391@localhost.localdomain>

On Tue, 30 Dec 2008, Wang Qinjing wrote:

QW> Dear all:

QW> I noted that if I made calculation by pw.x in paralllel, there were 
QW> too many data communications between nodes. That was attributed to 
QW> the data communication of wave functions. There is a severe delay to 
QW> get information from these nodes.

please provide more detail about the kind of job you 
are running, how you were running it and the kind of 
hardware you are running it on.

there are several ways how you can improve parallel efficiency.
please see the documentation and the many previous discussions
on this topic and then make some scaling and performance tests
to see how to run most efficiently. the best settings can vary
a lot between different inputs and calculation types.
 
QW> If I set disk_io='low', things are much better. But the main node 

this is only one option and indicates that you are most likely
not running your job in a very efficient manner.

QW> (or the first node) still has problem in net communication. I 
QW> noticed a charge density file is still written after each scf step. 
QW> Is that the problem?  Or is there anything I can do to improve this 
QW> situation?

there is a lot that can be done, but since you don't provide any
information on what you are already doing, it is impossible to
give any recommendation beyond urging you to (re-)read the 
documentation and FAQs.

cheers,
   axel.

QW> Thanks in advance.
QW> 
QW> Yours Wang
QW> 
QW> ------------------------------------
QW> ????????????????????????????
QW> Wang Qinjing, Physics Department, 
QW> Fudan University

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From w2agz at pacbell.net  Mon Dec 29 19:40:25 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Mon, 29 Dec 2008 10:40:25 -0800
Subject: [Pw_forum] K_POINTS, tpiba or crystal
Message-ID: <000501c969e4$eb03bb00$c10b3100$@net>

When specifying a user generated mesh for an nscf run, should tpiba (the
default) or crystal coordinates be designated on the  K_POINTS card?
Frankly, I don't understand what "crystal" means wrt to reciprocal space
(ATOMIC_POSITIONS, yes), and it does seem to make a small difference
depending on the application (e.g. Fermi surface generation).

A Merry Winter Solstice Break to All.

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com <http://www.w2agz.com/> 
 
 


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From akohlmey at cmm.chem.upenn.edu  Mon Dec 29 20:20:07 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 29 Dec 2008 14:20:07 -0500 (EST)
Subject: [Pw_forum] K_POINTS, tpiba or crystal
In-Reply-To: <000501c969e4$eb03bb00$c10b3100$@net>
References: <000501c969e4$eb03bb00$c10b3100$@net>
Message-ID: <Pine.LNX.4.64.0812291413190.2391@localhost.localdomain>

On Mon, 29 Dec 2008, Paul M. Grant wrote:


hi paul,

PG> When specifying a user generated mesh for an nscf run, should tpiba (the
PG> default) or crystal coordinates be designated on the  K_POINTS card?

most likely tpiba.

PG> Frankly, I don't understand what "crystal" means wrt to reciprocal space
PG> (ATOMIC_POSITIONS, yes), and it does seem to make a small difference

in my understanding, crystal would be multiples of the 
reciprocal lattice vectors, i.e. the "b"-matrix printed
out at the beginning of a job.

cheers,
   axel.

PG> depending on the application (e.g. Fermi surface generation).


PG> 
PG> A Merry Winter Solstice Break to All.
PG> 
PG> Paul M. Grant, PhD
PG> Principal, W2AGZ Technologies
PG> Visiting Scholar, Applied Physics, Stanford (2005-2008)
PG> EPRI Science Fellow (Retired)
PG> IBM Research Staff Member Emeritus
PG> w2agz at pacbell.net
PG> http://www.w2agz.com <http://www.w2agz.com/> 
PG>  
PG>  
PG> 
PG> 
PG> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

From giannozz at democritos.it  Mon Dec 29 20:55:52 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 29 Dec 2008 20:55:52 +0100
Subject: [Pw_forum] Problems in compiling pw.x and ph.x using XLF and
	ESSL on IBM-PPC
In-Reply-To: <8cdd828c0812240454g2b2b7b4fla783ec9d921f16ab@mail.gmail.com>
References: <8cdd828c0812240454g2b2b7b4fla783ec9d921f16ab@mail.gmail.com>
Message-ID: <200812292055.52937.giannozz@democritos.it>

On Wednesday 24 December 2008 13:54, Zhong-Li Liu wrote:

> So could you find some missettings of the compilation parameters and
> something wrong? 

use -D__LINUX_ESSL instead of -D__ESSL . For parallel execution,
add -D__PARA. For the rest, complain with IBM or better with 
whoever bought that machine

-- 
Paolo Giannozzi, Democritos and Udine University


From giannozz at democritos.it  Mon Dec 29 21:22:38 2008
From: giannozz at democritos.it (giannozz at democritos.it)
Date: Mon, 29 Dec 2008 21:22:38 +0100
Subject: [Pw_forum] dynmat.x
In-Reply-To: <COL103-W4468958887B34377243A79E4EB0@phx.gbl>
References: <COL103-W21C71A35E17C019FDC2454E4EB0@phx.gbl>
	<COL103-W4468958887B34377243A79E4EB0@phx.gbl>
Message-ID: <20081229212238.r0qg7j0u80gs04g0@mail.democritos.it>

Quoting Adam Jacobsson <adams_mejl at hotmail.com>:

> My first thought was that the program wanted the direction from where 
> to approach the gamma point as a limit. Is that the case?

yes. If you specify a direction for q, dynmat.x will calculate the 
LO-TO splitting; if you specify q=0, it will not calculate it.

Paolo
--
Paolo Giannozzi, Democritos and Udine University


----------------------------------------------------------------
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From giannozz at democritos.it  Mon Dec 29 21:28:36 2008
From: giannozz at democritos.it (giannozz at democritos.it)
Date: Mon, 29 Dec 2008 21:28:36 +0100
Subject: [Pw_forum] K_POINTS, tpiba or crystal
In-Reply-To: <000501c969e4$eb03bb00$c10b3100$@net>
References: <000501c969e4$eb03bb00$c10b3100$@net>
Message-ID: <20081229212836.hut32tqv40csg404@mail.democritos.it>

Quoting "Paul M. Grant" <w2agz at pacbell.net>:

> Frankly, I don't understand what "crystal" means wrt to reciprocal space

it means "in units of the reciprocal lattice primitive vectors"

Paolo


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


From giannozz at democritos.it  Mon Dec 29 21:39:27 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 29 Dec 2008 21:39:27 +0100
Subject: [Pw_forum] Problem on pp.x
In-Reply-To: <b5d787260812251948q33f3495bg672250a81b7328fd@mail.gmail.com>
References: <b5d787260812251931r6192904eo27079f7dccb53333@mail.gmail.com>
	<b5d787260812251948q33f3495bg672250a81b7328fd@mail.gmail.com>
Message-ID: <200812292139.27983.giannozz@democritos.it>

On Friday 26 December 2008 04:48, Jiaye, Li wrote:
> I tried like this: mpirun -np 2 ~/bin/pp.x input.inp output.out

you should have tried like this:
  mpirun -np 2 ~/bin/pp.x < input.inp 
or
  mpirun -np 2 ~/bin/pp.x -in input.inp 
Paolo
-- 
Paolo Giannozzi, Democritos and Udine University

From jameslipd at gmail.com  Tue Dec 30 03:25:24 2008
From: jameslipd at gmail.com (Jiaye, Li)
Date: Tue, 30 Dec 2008 10:25:24 +0800
Subject: [Pw_forum]  Problem on pp.x
Message-ID: <b5d787260812291825j19069999tc4afdfd0d5a8c3ab@mail.gmail.com>

Dear Gentlemen

Thank you very much. It works when I changed the comment marker to "!".

-- 
Sincerely

Jiaye Li



==============================================
Li, Jiaye

M.S. in designing and developing novel materials

Research experience:
*ALD precursor. ie. Metal complexes
*Surface modification. ie. Indium tin oxide, SiO2
*Gas storage and adsorption. ie. Ionic Liquids

Skills:
*ab-initial method, DFT simulation and Force Field simulation

Please contact me at:
1. jameslipd at gmail.com  or
2. jameslibd at gmail.com

==============================================
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From lzh-ming at 163.com  Tue Dec 30 04:29:04 2008
From: lzh-ming at 163.com (lzh-ming)
Date: Tue, 30 Dec 2008 11:29:04 +0800 (CST)
Subject: [Pw_forum] problem about calculation with ph.x
In-Reply-To: <887862.14159.qm@web65713.mail.ac4.yahoo.com>
References: <887862.14159.qm@web65713.mail.ac4.yahoo.com>
Message-ID: <4578150.654991230607744581.JavaMail.coremail@bj163app19.163.com>

Dear Prof. Eyvaz Isaev, 
  Thanks for your answering and instruction.
 
  I haved downloaded examples_disp.tgz through the site www.quantum-espresso.org and learn how to calculate phonon dispersion curves with that routine. But since I cann't run the programs in a parallel style,it will be time-consuming calculating with that way.(But I can submit many jobs. I cann't compile the source in a parallel style.)
 
  So I wonder if I can calculate the  F(q) for each required q-points then get the files dyn1:10 together, and run q2r.x, matdyn.x to get the phonon dispersions.
  Actually I have runned in this way with the ph.in files setted such as
    ldisp=.false.
   /
    0.0 0.0 0.0 (other points)
 
and I got the dyn files, the CdCNi3-444.fc file and the CdCNi3-444.freq file in the right format. But there are negative frequencies in them. 
 
So I wonder if there are some underlying settings different between ldisp=.true. and ldisp=.false. , so I tried ph.in files in the former one. And I get the reported problem.
 
Right yesterday I learned from the site www.quantum-espresso.org(F.A.Q.) that negative frequencies may be resulted from a non-converged groundstate (Ecut, #k, ...). Maybe I set the ecut and k-grid too small. But the reported problem still be. So is my settings wrong or there is a flaw in the ph.x ?
 
Best regards,
 
li-ming-fan 
 
 
 


?2008-12-29?"Eyvaz Isaev" <eyvaz_isaev at yahoo.com> ???
>Dear li-ming-fan,
>
>In order to calculate phonon dispersion curves you need to calculate real space Interatomic Force Constants matrix F(R). This can be obtained via the FFT using the dynamical matricies F(q). 
>
>In order to get F(q) set, you should use only nq1,nq2,nq3, but not iq1,iq2,iq3 which are used to calculate F(q) for a given q-point(s).
>
>After F(q)=> F(R) transformation you have to supply a list of q-points along high symmetry directions and calculate phonon modes for these points.
>
>Bests,
>Eyvaz.
>
>
>-------------------------------------------------------------------
>Prof. Eyvaz Isaev, 
>Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
>Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
>Condensed Matter Theory Group, Uppsala University, Sweden 
>Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
>--- On Mon, 12/29/08, lzh-ming <lzh-ming at 163.com> wrote:
>
>> From: lzh-ming <lzh-ming at 163.com>
>> Subject: [Pw_forum] problem about calculation with ph.x
>> To: "Pw_forum" <pw_forum at pwscf.org>
>> Date: Monday, December 29, 2008, 2:46 PM
>> Hello everyone,
>>   I have tried to calculate the phonon disperation of
>> CdCNi3.
>> I wrote in the file CdCNi3.ph.in as follow:
>>   
>>   ldisp=.true.,
>>   nq1=4, nq2=4, nq3=4,
>>   iq1=2, iq2=1, iq3=1,
>>  
>> but in the file CdCNi3.dyn0 , I got 
>>   4 4 4
>>   1
>>   0.0 0.0 0.0 
>>  
>> I changed the value of iq1,iq2,iq3 to 2,2,1, I still got
>> 0.0 0.0 0.0.
>> I set the value as 3 3 2, I got 0.25 0.25 0.25.
>> When the value is 3 3 3, I got -0.5 -0.5 -0.5.(This is
>> right.)
>>  
>> I tried all the 10 unequivalent points of 4*4*4 grid(simple
>> cube),
>> I only got 3 different outputs.
>>  
>> What's the problem? Can you help me?
>>  
>> Thanks a lot!
>>  
>> li-ming-fan
>>  
>> 
>> 
>>  _______________________________________________
>> 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 w2agz at pacbell.net  Tue Dec 30 05:56:59 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Mon, 29 Dec 2008 20:56:59 -0800
Subject: [Pw_forum] K_POINTS, tpiba or crystal
In-Reply-To: <20081229212836.hut32tqv40csg404@mail.democritos.it>
References: <000501c969e4$eb03bb00$c10b3100$@net>
	<20081229212836.hut32tqv40csg404@mail.democritos.it>
Message-ID: <005901c96a3b$0c9de960$25d9bc20$@net>

OK, let's get specific...suppose I want to generate a uniformly distributed
set of k-points for the reciprocal lattice of the primitive cell of an fcc
lattice.  The output of an scf run (and common sense matrix algebra) tells
me the reciprocal lattice is defined as

reciprocal axes: (cart. coord. in units 2 pi/a_0)
               b(1) = (  1.000000  0.000000  0.000000 )  
               b(2) = (  0.000000  1.000000  0.000000 )  
               b(3) = (  0.000000  0.000000  1.000000 )  

OK (again)...I now generate a(n) uniformly distributed grid over the "b"
vectors, and plot the points via xcrysden with PRIMVEC as above and see that
grid fills the entire basic reciprocal cell (that is, with translation
vector = O).  No specification of celldm(1).

Now, I want to input this grid to an nscf run via K_POINTS...is my grid
"tpiba" or "crystal?"

BTW, we (this community) owe a huge debt to Paolo and Axel.

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com
?
?

-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of giannozz at democritos.it
Sent: Monday, December 29, 2008 12:29 PM
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] K_POINTS, tpiba or crystal

Quoting "Paul M. Grant" <w2agz at pacbell.net>:

> Frankly, I don't understand what "crystal" means wrt to reciprocal space

it means "in units of the reciprocal lattice primitive vectors"

Paolo


----------------------------------------------------------------
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 dmitry at korotin.name  Tue Dec 30 07:12:46 2008
From: dmitry at korotin.name (Dmitry Korotin)
Date: Tue, 30 Dec 2008 11:12:46 +0500
Subject: [Pw_forum] Coordinate system
Message-ID: <166cd7c60812292212l7cd07e09o11f5a295b247de10@mail.gmail.com>

Dear Quantum-ESPRESSO users and developers. Does QE use left-hand
triple of coordinate vectors or right-hand one?
Thank you in advance.

-- 
Best regards,
Dmitry Korotin

Ph. D. Student,
Institute of Metal Physics
S. Kovalevskaya, 18
620041 Ekaterinburg GSP-170
Russia

From wyanchao at gmail.com  Tue Dec 30 07:23:30 2008
From: wyanchao at gmail.com (wang yanchao)
Date: Tue, 30 Dec 2008 14:23:30 +0800
Subject: [Pw_forum] The question of "warning: symmetry operation # 2 not
	compatible with FFT grid"
Message-ID: <55639d30812292223w4eeef15ep33a50b5cb4205f5b@mail.gmail.com>

Dear all,

When I calculated the Raman of the structure which spacegroup is Fddd, I met
a question of  "warning: symmetry operation #  2 not compatible with FFT
grid" and "warning: symmetry operation #  5 not allowed.   fractional
translation:
      -0.2500000 -0.2500000 -0.2500000  in crystal coordinates".
 I have changed the value of ecutrho, and nr1,nr2,nr3,  but all isn't work.
Because  I  calculate  the Raman,   I  think  if  I can't get  the  correct
the  symmetry  operation , the result of raman will be not correct. So I
want to know if there are some helpful  suggestions. It  appreciate you if
you can help me. Thank you very much in advance.

Sincerely

-- 
Yanchao Wang
National lab of Superhard Materials,JiLin Univ.Changchun 130012,P.R.China
Email:wyanchao at gmail.com <Email%3Awyanchao at gmail.com>
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From lanhaiping at gmail.com  Tue Dec 30 08:00:36 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Tue, 30 Dec 2008 15:00:36 +0800
Subject: [Pw_forum] K_POINTS, tpiba or crystal
In-Reply-To: <005901c96a3b$0c9de960$25d9bc20$@net>
References: <000501c969e4$eb03bb00$c10b3100$@net>
	<20081229212836.hut32tqv40csg404@mail.democritos.it>
	<005901c96a3b$0c9de960$25d9bc20$@net>
Message-ID: <c92002fa0812292300j7ac0b7d5ye6da1ea3de03e823@mail.gmail.com>

Hi, Paul
I think this two choice wonot make difference for FCC crystal.
And I do agree with your last statement .
Thanks  Paolo and Axel, and Happy new year !

best wishes,
hai-ping

On Tue, Dec 30, 2008 at 12:56 PM, Paul M. Grant <w2agz at pacbell.net> wrote:

> OK, let's get specific...suppose I want to generate a uniformly distributed
> set of k-points for the reciprocal lattice of the primitive cell of an fcc
> lattice.  The output of an scf run (and common sense matrix algebra) tells
> me the reciprocal lattice is defined as
>
> reciprocal axes: (cart. coord. in units 2 pi/a_0)
>               b(1) = (  1.000000  0.000000  0.000000 )
>               b(2) = (  0.000000  1.000000  0.000000 )
>               b(3) = (  0.000000  0.000000  1.000000 )
>
> OK (again)...I now generate a(n) uniformly distributed grid over the "b"
> vectors, and plot the points via xcrysden with PRIMVEC as above and see
> that
> grid fills the entire basic reciprocal cell (that is, with translation
> vector = O).  No specification of celldm(1).
>
> Now, I want to input this grid to an nscf run via K_POINTS...is my grid
> "tpiba" or "crystal?"
>
> BTW, we (this community) owe a huge debt to Paolo and Axel.
>
> Paul M. Grant, PhD
> Principal, W2AGZ Technologies
> Visiting Scholar, Applied Physics, Stanford (2005-2008)
> EPRI Science Fellow (Retired)
> IBM Research Staff Member Emeritus
> w2agz at pacbell.net
> http://www.w2agz.com
>
>
>
> -----Original Message-----
> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
> Behalf Of giannozz at democritos.it
> Sent: Monday, December 29, 2008 12:29 PM
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] K_POINTS, tpiba or crystal
>
> Quoting "Paul M. Grant" <w2agz at pacbell.net>:
>
> > Frankly, I don't understand what "crystal" means wrt to reciprocal space
>
> it means "in units of the reciprocal lattice primitive vectors"
>
> Paolo
>
>
> ----------------------------------------------------------------
> 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
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From giannozz at democritos.it  Tue Dec 30 09:56:55 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 30 Dec 2008 09:56:55 +0100
Subject: [Pw_forum] The question of "warning: symmetry operation # 2 not
	compatible with FFT grid"
In-Reply-To: <55639d30812292223w4eeef15ep33a50b5cb4205f5b@mail.gmail.com>
References: <55639d30812292223w4eeef15ep33a50b5cb4205f5b@mail.gmail.com>
Message-ID: <200812300956.55470.giannozz@democritos.it>

On Tuesday 30 December 2008 07:23, wang yanchao wrote:

> Because  I  calculate  the Raman,   I  think  if  I can't get  the  correct
> the  symmetry  operation , the result of raman will be not correct. 

it may take more time, but the result will be correct, with or without
all symmetries

Paolo
-- 
Paolo Giannozzi, Democritos and Udine University

From giannozz at democritos.it  Tue Dec 30 09:58:40 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 30 Dec 2008 09:58:40 +0100
Subject: [Pw_forum] Coordinate system
In-Reply-To: <166cd7c60812292212l7cd07e09o11f5a295b247de10@mail.gmail.com>
References: <166cd7c60812292212l7cd07e09o11f5a295b247de10@mail.gmail.com>
Message-ID: <200812300958.41002.giannozz@democritos.it>

On Tuesday 30 December 2008 07:12, Dmitry Korotin wrote:

> Does QE use left-hand triple of coordinate vectors or right-hand one?

it uses the "traditional" one, i.e. right-hand side if I remember correctly.
Not that it makes any difference, except in some very specific cases.

Paolo
-- 
Paolo Giannozzi, Democritos and Udine University

From abdulrafiu.raji at uct.ac.za  Tue Dec 30 11:12:36 2008
From: abdulrafiu.raji at uct.ac.za (Abdulrafiu RAJI)
Date: Tue, 30 Dec 2008 12:12:36 +0200
Subject: [Pw_forum] QHA Code
Message-ID: <495A1034020000C50018ACC8@gwiasmtp.uct.ac.za>

Dear Prof Eyvaz Isaev,

Kindly send the QHA code to me as well. I made a request for this code to you, through an e-mail about two months back.Thanks for your anticipated cooperation.


Raji Abdulrafiu Tunde,
Condensed Matter and Material Physics Group,
Department of Physics,
University of Cape Town,
Rondebosch 7701,
Cape Town.
South Africa.





Raji Abdulrafiu Tunde,
Department of Physics,
University of Cape Town (RW James Bld.),Private Bag X3,
Rondebosch 7701,
Cape Town. South Africa.

Office number : Rm. 522
Cell:  +27722668228
Fax:   +27216503342

 
______________________________________________________________________________________________ 

UNIVERSITY OF CAPE TOWN 

This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 4500. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity.

_____________________________________________________________________________________________________
 

From giannozz at democritos.it  Tue Dec 30 14:20:46 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 30 Dec 2008 14:20:46 +0100
Subject: [Pw_forum] K_POINTS, tpiba or crystal
In-Reply-To: <005901c96a3b$0c9de960$25d9bc20$@net>
References: <000501c969e4$eb03bb00$c10b3100$@net>
	<20081229212836.hut32tqv40csg404@mail.democritos.it>
	<005901c96a3b$0c9de960$25d9bc20$@net>
Message-ID: <200812301420.47223.giannozz@democritos.it>

On Tuesday 30 December 2008 05:56, Paul M. Grant wrote:

>                b(1) = (  1.000000  0.000000  0.000000 )
>                b(2) = (  0.000000  1.000000  0.000000 )
>                b(3) = (  0.000000  0.000000  1.000000 )

these are the lattice vectors generating a simple cubic lattice

> Now, I want to input this grid to an nscf run via K_POINTS...is my grid
> "tpiba" or "crystal?"

in this particular case, it shouldn't matter, since the crystal and
cartesian axis are the same, and the length of crystal axis is 2pi/a .

Paolo
-- 
Paolo Giannozzi, Democritos and Udine University

From eyvaz_isaev at yahoo.com  Tue Dec 30 17:07:51 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 30 Dec 2008 08:07:51 -0800 (PST)
Subject: [Pw_forum] QHA Code
In-Reply-To: <495A1034020000C50018ACC8@gwiasmtp.uct.ac.za>
Message-ID: <564100.51106.qm@web65705.mail.ac4.yahoo.com>

Dear Abdulrafiu,

Sorry, but I have just sent you the code.

Bests,
Eyvaz.

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


--- On Tue, 12/30/08, Abdulrafiu RAJI <abdulrafiu.raji at uct.ac.za> wrote:

> From: Abdulrafiu RAJI <abdulrafiu.raji at uct.ac.za>
> Subject: [Pw_forum] QHA Code
> To: pw_forum at pwscf.org
> Date: Tuesday, December 30, 2008, 1:12 PM
> Dear Prof Eyvaz Isaev,
> 
> Kindly send the QHA code to me as well. I made a request
> for this code to you, through an e-mail about two months
> back.Thanks for your anticipated cooperation.
> 
> 
> Raji Abdulrafiu Tunde,
> Condensed Matter and Material Physics Group,
> Department of Physics,
> University of Cape Town,
> Rondebosch 7701,
> Cape Town.
> South Africa.
> 
> 
> 
> 
> 
> Raji Abdulrafiu Tunde,
> Department of Physics,
> University of Cape Town (RW James Bld.),Private Bag X3,
> Rondebosch 7701,
> Cape Town. South Africa.
> 
> Office number : Rm. 522
> Cell:  +27722668228
> Fax:   +27216503342
> 
>  
> ______________________________________________________________________________________________
> 
> 
> UNIVERSITY OF CAPE TOWN 
> 
> This e-mail is subject to the UCT ICT policies and e-mail
> disclaimer published on our website at
> http://www.uct.ac.za/about/policies/emaildisclaimer/ or
> obtainable from +27 21 650 4500. This e-mail is intended
> only for the person(s) to whom it is addressed. If the
> e-mail has reached you in error, please notify the author.
> If you are not the intended recipient of the e-mail you may
> not use, disclose, copy, redirect or print the content. If
> this e-mail is not related to the business of UCT it is sent
> by the sender in the sender's individual capacity.
> 
> _____________________________________________________________________________________________________
>  
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From w2agz at pacbell.net  Tue Dec 30 18:08:46 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Tue, 30 Dec 2008 09:08:46 -0800
Subject: [Pw_forum] K_POINTS, tpiba or crystal
In-Reply-To: <200812301420.47223.giannozz@democritos.it>
References: <000501c969e4$eb03bb00$c10b3100$@net>	<20081229212836.hut32tqv40csg404@mail.democritos.it>	<005901c96a3b$0c9de960$25d9bc20$@net>
	<200812301420.47223.giannozz@democritos.it>
Message-ID: <008801c96aa1$46ebb0a0$d4c311e0$@net>

That's what I thought too...but for some applications, it seems to.  I'll
recheck this and get back.

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com
?
?


-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of Paolo Giannozzi
Sent: Tuesday, December 30, 2008 5:21 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] K_POINTS, tpiba or crystal

On Tuesday 30 December 2008 05:56, Paul M. Grant wrote:

>                b(1) = (  1.000000  0.000000  0.000000 )
>                b(2) = (  0.000000  1.000000  0.000000 )
>                b(3) = (  0.000000  0.000000  1.000000 )

these are the lattice vectors generating a simple cubic lattice

> Now, I want to input this grid to an nscf run via K_POINTS...is my grid
> "tpiba" or "crystal?"

in this particular case, it shouldn't matter, since the crystal and
cartesian axis are the same, and the length of crystal axis is 2pi/a .

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


From luotengf at msu.edu  Tue Dec 30 19:47:05 2008
From: luotengf at msu.edu (Tengfei Luo)
Date: Tue, 30 Dec 2008 13:47:05 -0500
Subject: [Pw_forum] QHA Code
In-Reply-To: <564100.51106.qm@web65705.mail.ac4.yahoo.com>
References: <564100.51106.qm@web65705.mail.ac4.yahoo.com>
Message-ID: <F9474C50E0CC4D9C8FBA3F9378FD3669@WIN1DV2EQQQRS7>

Hi, Eyvaz:
Is the Debye.x removed from the package? I don't find it in the package.

Thank you!

Tengfei

----- Original Message ----- 
From: "Eyvaz Isaev" <eyvaz_isaev at yahoo.com>
To: "PWSCF Forum" <pw_forum at pwscf.org>
Sent: Tuesday, December 30, 2008 11:07 AM
Subject: Re: [Pw_forum] QHA Code


> Dear Abdulrafiu,
>
> Sorry, but I have just sent you the code.
>
> Bests,
> Eyvaz.
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, 
> Russia,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, 
> Sweden
> Condensed Matter Theory Group, Uppsala University, Sweden
> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
> --- On Tue, 12/30/08, Abdulrafiu RAJI <abdulrafiu.raji at uct.ac.za> wrote:
>
>> From: Abdulrafiu RAJI <abdulrafiu.raji at uct.ac.za>
>> Subject: [Pw_forum] QHA Code
>> To: pw_forum at pwscf.org
>> Date: Tuesday, December 30, 2008, 1:12 PM
>> Dear Prof Eyvaz Isaev,
>>
>> Kindly send the QHA code to me as well. I made a request
>> for this code to you, through an e-mail about two months
>> back.Thanks for your anticipated cooperation.
>>
>>
>> Raji Abdulrafiu Tunde,
>> Condensed Matter and Material Physics Group,
>> Department of Physics,
>> University of Cape Town,
>> Rondebosch 7701,
>> Cape Town.
>> South Africa.
>>
>>
>>
>>
>>
>> Raji Abdulrafiu Tunde,
>> Department of Physics,
>> University of Cape Town (RW James Bld.),Private Bag X3,
>> Rondebosch 7701,
>> Cape Town. South Africa.
>>
>> Office number : Rm. 522
>> Cell:  +27722668228
>> Fax:   +27216503342
>>
>>
>> ______________________________________________________________________________________________
>>
>>
>> UNIVERSITY OF CAPE TOWN
>>
>> This e-mail is subject to the UCT ICT policies and e-mail
>> disclaimer published on our website at
>> http://www.uct.ac.za/about/policies/emaildisclaimer/ or
>> obtainable from +27 21 650 4500. This e-mail is intended
>> only for the person(s) to whom it is addressed. If the
>> e-mail has reached you in error, please notify the author.
>> If you are not the intended recipient of the e-mail you may
>> not use, disclose, copy, redirect or print the content. If
>> this e-mail is not related to the business of UCT it is sent
>> by the sender in the sender's individual capacity.
>>
>> _____________________________________________________________________________________________________
>>
>> _______________________________________________
>> 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
> 


From eyvaz_isaev at yahoo.com  Tue Dec 30 23:51:27 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 30 Dec 2008 14:51:27 -0800 (PST)
Subject: [Pw_forum] QHA Code
In-Reply-To: <F9474C50E0CC4D9C8FBA3F9378FD3669@WIN1DV2EQQQRS7>
Message-ID: <443448.28340.qm@web65716.mail.ac4.yahoo.com>

Hi Tengfei,

Yes, it was removed intentionally. I was not sure for T_D at low temperatures.

The last version I am going to release now includes Debye and Mean Square Displacements calculations.

Bests,
Eyvaz.


--- On Tue, 12/30/08, Tengfei Luo <luotengf at msu.edu> wrote:

> From: Tengfei Luo <luotengf at msu.edu>
> Subject: Re: [Pw_forum] QHA Code
> To: eyvaz_isaev at yahoo.com, "PWSCF Forum" <pw_forum at pwscf.org>
> Date: Tuesday, December 30, 2008, 9:47 PM
> Hi, Eyvaz:
> Is the Debye.x removed from the package? I don't find
> it in the package.
> 
> Thank you!
> 
> Tengfei
> 
> ----- Original Message ----- 
> From: "Eyvaz Isaev" <eyvaz_isaev at yahoo.com>
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Sent: Tuesday, December 30, 2008 11:07 AM
> Subject: Re: [Pw_forum] QHA Code
> 
> 
> > Dear Abdulrafiu,
> >
> > Sorry, but I have just sent you the code.
> >
> > Bests,
> > Eyvaz.
> >
> >
> -------------------------------------------------------------------
> > Prof. Eyvaz Isaev,
> > Theoretical Physics Department, Moscow State Institute
> of Steel & Alloys, 
> > Russia,
> > Department of Physics, Chemistry, and Biology (IFM),
> Linkoping University, 
> > Sweden
> > Condensed Matter Theory Group, Uppsala University,
> Sweden
> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se,
> eyvaz_isaev at yahoo.com
> >
> >
> > --- On Tue, 12/30/08, Abdulrafiu RAJI
> <abdulrafiu.raji at uct.ac.za> wrote:
> >
> >> From: Abdulrafiu RAJI
> <abdulrafiu.raji at uct.ac.za>
> >> Subject: [Pw_forum] QHA Code
> >> To: pw_forum at pwscf.org
> >> Date: Tuesday, December 30, 2008, 1:12 PM
> >> Dear Prof Eyvaz Isaev,
> >>
> >> Kindly send the QHA code to me as well. I made a
> request
> >> for this code to you, through an e-mail about two
> months
> >> back.Thanks for your anticipated cooperation.
> >>
> >>
> >> Raji Abdulrafiu Tunde,
> >> Condensed Matter and Material Physics Group,
> >> Department of Physics,
> >> University of Cape Town,
> >> Rondebosch 7701,
> >> Cape Town.
> >> South Africa.
> >>
> >>
> >>
> >>
> >>
> >> Raji Abdulrafiu Tunde,
> >> Department of Physics,
> >> University of Cape Town (RW James Bld.),Private
> Bag X3,
> >> Rondebosch 7701,
> >> Cape Town. South Africa.
> >>
> >> Office number : Rm. 522
> >> Cell:  +27722668228
> >> Fax:   +27216503342
> >>
> >>
> >>
> ______________________________________________________________________________________________
> >>
> >>
> >> UNIVERSITY OF CAPE TOWN
> >>
> >> This e-mail is subject to the UCT ICT policies and
> e-mail
> >> disclaimer published on our website at
> >>
> http://www.uct.ac.za/about/policies/emaildisclaimer/ or
> >> obtainable from +27 21 650 4500. This e-mail is
> intended
> >> only for the person(s) to whom it is addressed. If
> the
> >> e-mail has reached you in error, please notify the
> author.
> >> If you are not the intended recipient of the
> e-mail you may
> >> not use, disclose, copy, redirect or print the
> content. If
> >> this e-mail is not related to the business of UCT
> it is sent
> >> by the sender in the sender's individual
> capacity.
> >>
> >>
> _____________________________________________________________________________________________________
> >>
> >> _______________________________________________
> >> 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
> > 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From luotengf at msu.edu  Wed Dec 31 00:39:21 2008
From: luotengf at msu.edu (Tengfei Luo)
Date: Tue, 30 Dec 2008 18:39:21 -0500
Subject: [Pw_forum] QHA Code
In-Reply-To: <443448.28340.qm@web65716.mail.ac4.yahoo.com>
References: <443448.28340.qm@web65716.mail.ac4.yahoo.com>
Message-ID: <1056B28A4F3C40EB81E74FBB39655D51@WIN1DV2EQQQRS7>

Eyvaz:
Great! I'm looking forward to it. Thank you very much!

Tengfei
----- Original Message ----- 
From: "Eyvaz Isaev" <eyvaz_isaev at yahoo.com>
To: "PWSCF Forum" <pw_forum at pwscf.org>
Sent: Tuesday, December 30, 2008 5:51 PM
Subject: Re: [Pw_forum] QHA Code


> Hi Tengfei,
>
> Yes, it was removed intentionally. I was not sure for T_D at low 
> temperatures.
>
> The last version I am going to release now includes Debye and Mean Square 
> Displacements calculations.
>
> Bests,
> Eyvaz.
>
>
> --- On Tue, 12/30/08, Tengfei Luo <luotengf at msu.edu> wrote:
>
>> From: Tengfei Luo <luotengf at msu.edu>
>> Subject: Re: [Pw_forum] QHA Code
>> To: eyvaz_isaev at yahoo.com, "PWSCF Forum" <pw_forum at pwscf.org>
>> Date: Tuesday, December 30, 2008, 9:47 PM
>> Hi, Eyvaz:
>> Is the Debye.x removed from the package? I don't find
>> it in the package.
>>
>> Thank you!
>>
>> Tengfei
>>
>> ----- Original Message ----- 
>> From: "Eyvaz Isaev" <eyvaz_isaev at yahoo.com>
>> To: "PWSCF Forum" <pw_forum at pwscf.org>
>> Sent: Tuesday, December 30, 2008 11:07 AM
>> Subject: Re: [Pw_forum] QHA Code
>>
>>
>> > Dear Abdulrafiu,
>> >
>> > Sorry, but I have just sent you the code.
>> >
>> > Bests,
>> > Eyvaz.
>> >
>> >
>> -------------------------------------------------------------------
>> > Prof. Eyvaz Isaev,
>> > Theoretical Physics Department, Moscow State Institute
>> of Steel & Alloys,
>> > Russia,
>> > Department of Physics, Chemistry, and Biology (IFM),
>> Linkoping University,
>> > Sweden
>> > Condensed Matter Theory Group, Uppsala University,
>> Sweden
>> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se,
>> eyvaz_isaev at yahoo.com
>> >
>> >
>> > --- On Tue, 12/30/08, Abdulrafiu RAJI
>> <abdulrafiu.raji at uct.ac.za> wrote:
>> >
>> >> From: Abdulrafiu RAJI
>> <abdulrafiu.raji at uct.ac.za>
>> >> Subject: [Pw_forum] QHA Code
>> >> To: pw_forum at pwscf.org
>> >> Date: Tuesday, December 30, 2008, 1:12 PM
>> >> Dear Prof Eyvaz Isaev,
>> >>
>> >> Kindly send the QHA code to me as well. I made a
>> request
>> >> for this code to you, through an e-mail about two
>> months
>> >> back.Thanks for your anticipated cooperation.
>> >>
>> >>
>> >> Raji Abdulrafiu Tunde,
>> >> Condensed Matter and Material Physics Group,
>> >> Department of Physics,
>> >> University of Cape Town,
>> >> Rondebosch 7701,
>> >> Cape Town.
>> >> South Africa.
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> Raji Abdulrafiu Tunde,
>> >> Department of Physics,
>> >> University of Cape Town (RW James Bld.),Private
>> Bag X3,
>> >> Rondebosch 7701,
>> >> Cape Town. South Africa.
>> >>
>> >> Office number : Rm. 522
>> >> Cell:  +27722668228
>> >> Fax:   +27216503342
>> >>
>> >>
>> >>
>> ______________________________________________________________________________________________
>> >>
>> >>
>> >> UNIVERSITY OF CAPE TOWN
>> >>
>> >> This e-mail is subject to the UCT ICT policies and
>> e-mail
>> >> disclaimer published on our website at
>> >>
>> http://www.uct.ac.za/about/policies/emaildisclaimer/ or
>> >> obtainable from +27 21 650 4500. This e-mail is
>> intended
>> >> only for the person(s) to whom it is addressed. If
>> the
>> >> e-mail has reached you in error, please notify the
>> author.
>> >> If you are not the intended recipient of the
>> e-mail you may
>> >> not use, disclose, copy, redirect or print the
>> content. If
>> >> this e-mail is not related to the business of UCT
>> it is sent
>> >> by the sender in the sender's individual
>> capacity.
>> >>
>> >>
>> _____________________________________________________________________________________________________
>> >>
>> >> _______________________________________________
>> >> 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
>> >
>>
>> _______________________________________________
>> 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
> 


From sezginaydin at gazi.edu.tr  Wed Dec 31 06:47:40 2008
From: sezginaydin at gazi.edu.tr (sezginaydin at gazi.edu.tr)
Date: Wed, 31 Dec 2008 05:47:40 -0000
Subject: [Pw_forum] Band structure
Message-ID: <twig.1230702460.22200@gazi.edu.tr>

Hi,
I am a new PWScf user.I did install espresso-4.0.1 to my computer successfully.
I did run the example01. How can I draw band structure or which program should
I use?

Res.Ass.Sezgin AYDIN
Department of Physics
Gazi Unv.,TURKEY




From sezginaydin at gazi.edu.tr  Wed Dec 31 06:44:38 2008
From: sezginaydin at gazi.edu.tr (sezginaydin at gazi.edu.tr)
Date: Wed, 31 Dec 2008 05:44:38 -0000
Subject: [Pw_forum] GIPAW
Message-ID: <twig.1230702278.4631@gazi.edu.tr>

Hi,
I am a new PWScf user.I did install espresso-4.0.1 to my computer successfully.
I want to work with GIPAW routine. When I run the GIPAW-example in
/examples/GIPAW_example, I get the following error message:
--------------------------
/home/sezgin/Desktop/espresso-4.0.1/examples/GIPAW_example : starting

This example shows how to use gipaw.x to calculate:
1) susceptibility and NMR chemical shift of Si and diamond
2) NMR chemical shift of two molecules: CH4 and C2H4
3) electric field gradients (EFG) in bulk quartz (this was example24)

  executables directory: /home/sezgin/Desktop/espresso-4.0.1/bin
  pseudo directory:     
/home/sezgin/Desktop/espresso-4.0.1/examples/GIPAW_example/pseudo
  temporary directory:   /home/sezgin/tmp
  checking that needed directories and files exist...
ERROR: /home/sezgin/Desktop/espresso-4.0.1/bin/gipaw.x not existent or not
executable
Aborting
--------------------------
How can I solve my problem.

Res.Ass.Sezgin AYDIN
Department of Physics
Gazi Unv.,TURKEY



From lfhuang at theory.issp.ac.cn  Wed Dec 31 08:49:41 2008
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Wed, 31 Dec 2008 15:49:41 +0800
Subject: [Pw_forum] =?utf-8?q?Band_structure?=
Message-ID: <20081231074941.23291.qmail@ms.hfcas.ac.cn>

Dear Sezginaydin:
    If you are new PWSCF user, why don't you read the userguide, inputfile documents, some useful tutorials 
in the QE website and the subscripts in the examples, before you make your poster? 
   The calculation mainly includes:
(1) scf calculation; pw.x
(2) nscf calculation with path given; pw.x
(3) collect band results for plotting; bands.x
(4) finally please execute plotband.x
Please refer to the sources I mentioned for details, and it won't hard.
Best Wishes!
                                           Yours Sincerely
                                             L.F.Huang


>    1. Band structure (sezginaydin at gazi.edu.tr)
> Date: Wed, 31 Dec 2008 05:47:40 -0000
> From: 
> Subject: [Pw_forum] Band structure
> To: 
> Message-ID: 
> 
> Hi,
> I am a new PWScf user.I did install espresso-4.0.1 to my computer successfully.
> I did run the example01. How can I draw band structure or which program should
> I use?
> 
> Res.Ass.Sezgin AYDIN
> Department of Physics
> Gazi Unv.,TURKEY
> 

------
======================================================================
L.F.Huang(???) lfhuang at theory.issp.ac.cn
======================================================================
Add: Research Laboratory for Computational Materials Sciences,
Instutue of Solid State Physics,the Chinese Academy of Sciences,
P.O.Box 1129, Hefei 230031, P.R.China
Tel: 86-551-5591464-328(office)
Fax: 86-551-5591434
Web: http://theory.issp.ac.cn (website of our theory group)
http://www.issp.ac.cn    (website of our institute)
======================================================================


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From eyvaz_isaev at yahoo.com  Wed Dec 31 10:24:30 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Wed, 31 Dec 2008 01:24:30 -0800 (PST)
Subject: [Pw_forum] GIPAW
In-Reply-To: <twig.1230702278.4631@gazi.edu.tr>
Message-ID: <479298.56614.qm@web65708.mail.ac4.yahoo.com>

Dear Sezgin,

Most likely you did not compile gipaw code. Just type "make gipaw" to do it.

Bests,
Eyvaz. 

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


--- On Wed, 12/31/08, sezginaydin at gazi.edu.tr <sezginaydin at gazi.edu.tr> wrote:

> From: sezginaydin at gazi.edu.tr <sezginaydin at gazi.edu.tr>
> Subject: [Pw_forum] GIPAW
> To: pw_forum at pwscf.org
> Date: Wednesday, December 31, 2008, 8:44 AM
> Hi,
> I am a new PWScf user.I did install espresso-4.0.1 to my
> computer successfully.
> I want to work with GIPAW routine. When I run the
> GIPAW-example in
> /examples/GIPAW_example, I get the following error message:
> --------------------------
> /home/sezgin/Desktop/espresso-4.0.1/examples/GIPAW_example
> : starting
> 
> This example shows how to use gipaw.x to calculate:
> 1) susceptibility and NMR chemical shift of Si and diamond
> 2) NMR chemical shift of two molecules: CH4 and C2H4
> 3) electric field gradients (EFG) in bulk quartz (this was
> example24)
> 
>   executables directory:
> /home/sezgin/Desktop/espresso-4.0.1/bin
>   pseudo directory:     
> /home/sezgin/Desktop/espresso-4.0.1/examples/GIPAW_example/pseudo
>   temporary directory:   /home/sezgin/tmp
>   checking that needed directories and files exist...
> ERROR: /home/sezgin/Desktop/espresso-4.0.1/bin/gipaw.x not
> existent or not
> executable
> Aborting
> --------------------------
> How can I solve my problem.
> 
> Res.Ass.Sezgin AYDIN
> Department of Physics
> Gazi Unv.,TURKEY
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


      

From giannozz at democritos.it  Wed Dec 31 14:42:33 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 31 Dec 2008 14:42:33 +0100
Subject: [Pw_forum] Band structure
In-Reply-To: <twig.1230702460.22200@gazi.edu.tr>
References: <twig.1230702460.22200@gazi.edu.tr>
Message-ID: <200812311442.33113.giannozz@democritos.it>

On Wednesday 31 December 2008 06:47, sezginaydin at gazi.edu.tr wrote:

> I am a new PWScf user.I did install espresso-4.0.1 to my computer

if you are new, you should install the new version as well 
(currently 4.0.4)

> How can I draw band structure or which program should I use?

there is an example in example05

Paolo
-- 
Paolo Giannozzi, Democritos and Udine University

From kazempoor2000 at yahoo.com  Wed Dec 31 21:51:58 2008
From: kazempoor2000 at yahoo.com (ali kazempoor)
Date: Wed, 31 Dec 2008 12:51:58 -0800 (PST)
Subject: [Pw_forum] epsilon
Message-ID: <83020.21942.qm@web33104.mail.mud.yahoo.com>

Dear all
When I run epsilon.x for silicon bulk after doing scf this error happen:
ban number of bands
why?
Ali Kazempour, IUT,IRAN



      
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From akohlmey at cmm.chem.upenn.edu  Wed Dec 31 22:38:54 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 31 Dec 2008 16:38:54 -0500 (EST)
Subject: [Pw_forum] epsilon
In-Reply-To: <83020.21942.qm@web33104.mail.mud.yahoo.com>
References: <83020.21942.qm@web33104.mail.mud.yahoo.com>
Message-ID: <Pine.LNX.4.64.0812311631590.9213@localhost.localdomain>

On Wed, 31 Dec 2008, ali kazempoor wrote:

AK> Dear all

dear ali,

AK> When I run epsilon.x for silicon bulk after doing scf this error happen:
AK> ban number of bands
AK> why?

most likely, because you made a mistake.

axel.

AK> Ali Kazempour, IUT,IRAN
AK> 
AK> 
AK> 
AK>       

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.