From nedward at MIT.EDU  Fri Apr  1 00:42:09 2011
From: nedward at MIT.EDU (Nicholas Edward Miller)
Date: Thu, 31 Mar 2011 18:42:09 -0400
Subject: [Pw_forum] Work function for Al100 in example files
In-Reply-To: <398502.47742.qm@web43412.mail.sp1.yahoo.com>
References: <398502.47742.qm@web43412.mail.sp1.yahoo.com>
Message-ID: <20110331184209.umci63wlus8k8gg8@webmail.mit.edu>

Hi Izaak,

Practically speaking the input values for a lot of the examples are either not
converged or do not lead to a well converged results. ?This is definitely the
case for this example, where you would need a finer k-mesh for both
calculations, and more slab layers for the slab.

You are correct that having proportional k-point meshes for the corresponding
calculation should also help, and I would suggest that if you are going to use
a "bulk reference" for the Fermi energy, that you use the slab unit as your
bulk building block (you can match the k-point in plane exactly, and you can
have exactly matching FFT grids). ?Although in my experience the use of the
bulk fermi energy in not strictly necessary, with enough slab layers you can
take the fermi energy and vacuum potential all from the slab calculation.

Hope that helps,

Nick

Quoting Izaak Williamson <izaakw89 at yahoo.com>:

> Dear all,
>
>
>
> I was looking at the example of the work function calculation for Al100 and
> noticed that the following celldm(1) and kpoints are used:
>
>
> For slab ---> celldm(1)= 5.4235090117,   kpoints=3x3x1
> For bulk ---> celldm(1)= 7.67000000,       kpoints=3x3x3
> With these values, one gets work functions of Wf1=4.15219 eV and 
> Wf2=4.54641 eV.
>
>
> Since, celldm(1) for slab calculation is smaller than celldm(1) for bulk,
> shouldn't we use a higher k-mesh for the slab calculation? Is this correct?
>
> When I use a kmesh of 4x4x1, I get very different values of work functions:
> Wf1=4.0412 eV
> Wf2=3.82069 eV
>
> Does this make sense?
>
> Thank you.
>
> --
> Izaak Williamson
> Research Assistant
> Physics Department
> Boise State University



From tanycimr at gmail.com  Fri Apr  1 05:21:57 2011
From: tanycimr at gmail.com (=?Big5?B?zuu0xqbB?=)
Date: Fri, 1 Apr 2011 11:21:57 +0800
Subject: [Pw_forum] phonon lifetime about quantum espresso
Message-ID: <AANLkTin2V+FpjKDH2sJGGqt3nVP7zn8yj0mQC2jRN5Wu@mail.gmail.com>

Dear all :

i just began to learn how to use the quantum espresso . there is a question
when i calculated the phonon lifetime by QE . how could i read out the the
outcome of phonon lifetime  in d3.out file ? I means i just found the
information about "Atomic displacements" .

thanks in advance


student  tanyci
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From liweig at mtu.edu  Fri Apr  1 05:32:08 2011
From: liweig at mtu.edu (Liwei Geng)
Date: Thu, 31 Mar 2011 23:32:08 -0400 (EDT)
Subject: [Pw_forum] Valence state identification
In-Reply-To: <1810275387.8468801301628408321.JavaMail.root@zcs-mbs03.it.mtu.edu>
Message-ID: <553676677.8469631301628728911.JavaMail.root@zcs-mbs03.it.mtu.edu>




Dear all, 



I've done the scf calculation using atom pseudopotential files, but I can't know their valence state. Could?you tell me how to identify the valence state of each ion in?BaTiO3 using QE? Say, how can I know that the Ba is Ba2+ or O is O2-? 



Thanks, 

Liwei 
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From zero.whoami at gmail.com  Fri Apr  1 06:38:00 2011
From: zero.whoami at gmail.com (whoami ZERO)
Date: Fri, 1 Apr 2011 10:08:00 +0530
Subject: [Pw_forum] Regarding how to get isosurafces of frontier orbitals
Message-ID: <AANLkTimbdvky1kGmCL0QNSQRxew9M4Z3PR=wxKEGtDVu@mail.gmail.com>

Dear PWScf users,

I am trying to get Isosurfaces of the HOMO, LUMO and LUMO+n (n=integer)
states for a system having an organic dye which is adsorbed on TiO2 (101)
surface.

Please some one let me know, is it possible to get the above mentioned
Isosurfaces by employing PWScf code, if possible, please provide relavant
information, to get it.


Thank You in advance.

-- 
regards

(Mithu)
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From nkxirainbow at gmail.com  Fri Apr  1 07:07:14 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Fri, 1 Apr 2011 13:07:14 +0800
Subject: [Pw_forum] Valence state identification
In-Reply-To: <553676677.8469631301628728911.JavaMail.root@zcs-mbs03.it.mtu.edu>
References: <1810275387.8468801301628408321.JavaMail.root@zcs-mbs03.it.mtu.edu>
	<553676677.8469631301628728911.JavaMail.root@zcs-mbs03.it.mtu.edu>
Message-ID: <AANLkTin_GbMnzXdzxgbLPHPf+3N6_eLxU1HCAuLhwVU9@mail.gmail.com>

Dear Geng:
First of all,  Professor Nicola Marzari answered your question the day
before yesterday.
>The oxidation state is a phenomenological concept, and not well defined.
>The closest physical thing is the Born effective charge.
>The number of valence electrons for any pseudopotential is given
>by Z valence, in the header of that pseudopotential file.
>                       nicola

Do not continue to ask the same question. It is a wast of your time and
others!

Secondly,I do not think you can get Ba2+ or O O2-.
The valence state your mentioned is static charge.
However, static charge is not a well-defined quality, as all valence
electrons belong to the crystal, not atoms.
Maybe Mulliken charge is what you want, but I do not think QE can give it.
But QE can give Bader and Lowdin analysis, referring to
http://www.democritos.it/pipermail/pw_forum/2010-June/017204.html
http://www.democritos.it/pipermail/pw_forum/2010-May/016847.html

Alternatively, you can get dynamical charge with QE.For dynamical charge, Ba
maybe is smaller than 2 and O bigger than 2.


On Fri, Apr 1, 2011 at 11:32 AM, Liwei Geng <liweig at mtu.edu> wrote:

>  Dear all,
>
>
>
> I've done the scf calculation using atom pseudopotential files, but I can't
> know their valence state. Could you tell me how to identify the valence
> state of each ion in BaTiO3 using QE? Say, how can I know that the Ba is
> Ba2+ or O is O2-?
>
>
>
> Thanks,
>
> Liwei
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From nkxirainbow at gmail.com  Fri Apr  1 07:09:33 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Fri, 1 Apr 2011 13:09:33 +0800
Subject: [Pw_forum] Calculational equation of PDOS
In-Reply-To: <2303D1A5-9350-4A9E-AB39-75C7D7D19A4D@sissa.it>
References: <AANLkTinh4fpCv-xG0FsPmhGPXkT1d92YvYiHX6q3qRSZ@mail.gmail.com>
	<2303D1A5-9350-4A9E-AB39-75C7D7D19A4D@sissa.it>
Message-ID: <AANLkTi=wLS_uuaCKdXPQhNnUHyB+3nO80kkB_uSLfGNb@mail.gmail.com>

Dear Professor Gabriele Sclauzero:
Thank you for your prompt help.
I read your thesis and benefit a lot from it:)
Thanks again:P


On Thu, Mar 31, 2011 at 7:58 PM, Gabriele Sclauzero <sclauzer at sissa.it>wrote:

> Dear Wang,
>
>     I remember that I put down a formula for that in my PhD thesis (
> http://www.sissa.it/cm/thesis/2010/SclauzeroG_PhDthesis.pdf), if this may
> help you (see eq. 2.74 at page 58). I'm sure you could find it in many other
> places, though.
>
>    I believe there's no such thing as the Rcut you write in your formula
> below. As you say, the atomic wavefunctions are built from the radial part
> R_nl(r), which is taken from the pseudopotential file, and the spherical
> harmonics. However you should not forget that there is also structure factor
> which comes from the translation of the nucleus from the origin.
> The integral is done in reciprocal space for each k-point, hence a
> k-dependence is added to the atomic wavefunction when transforming it to the
> G-basis (have a look in PW/atomic_wfc.f90).
>
> The following paper might also be useful to you:
>
> Solid State Communications, Vol. 95, No. 10, pp. 685-690, 1995
>
>
>
>
> HTH
>
> GS
>
> Il giorno 31/mar/2011, alle ore 12.27, xirainbow ha scritto:
>
> Dear all:
>           I want to know the calculational equation of partial density of
> state(PDOS) in QE.
>           I could not find the equation on any paper. I think it may be:
> \int_0^{Rcut}  \Psi(\vec r)*R_n(r)*Y_{lm}(\theta,\phi)*r^2 dr d\theta
> d\phi.
> where the Psi(\vec r) is the KS wave function of solid. Y_{lm}(\theta,\phi)
> is the spherical harmonics. R_n(r) is the the radial wave function of a
> isolated atom.
>     If I was right, what is the formation of R_n(r)?
>
> Thanks in advance:)
>
> --
> ____________________________________
> Hui Wang
> School of physics, Fudan University, Shanghai, China
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *   PH H2 462, Station 3, CH-1015 Lausanne*
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From luoxuhui at uic.edu  Fri Apr  1 07:23:27 2011
From: luoxuhui at uic.edu (xuhui luo)
Date: Fri, 1 Apr 2011 01:23:27 -0400
Subject: [Pw_forum] How to read two wave-functions in one program?
Message-ID: <AANLkTinWcQwpq-BOTBi+PyQ_EnDsJ0A=juceCkd=e7yQ@mail.gmail.com>

Dear Prefessor Giannozzi,

Thanks for your suggestions. Now we am thinking how to save
wavefunctions in real space. The two possible way as I know are the
tight-binding method and wannier functional method. We already tried
the tight-binding method. But the projection onto atomic orbitals
sometimes behaves badly. Again I come here to ask for help from
PWscf-experts. Can you (or anyone) tell me the best way to save
wavefunction psi(ik, iband, ispin) on a grid of real space. Thanks in
advance!

Best,

Xuhui

University of Illinois at Chicago

> On Mar 16, 2011, at 1:11 , xuhui luo wrote:
>>
>> But what I would like to do is to taking inner product of (n,k)
>> from one structure and (n',k') from another perturbed structure.
>> Thus I need to read two set of wavefunction at the same time.
>> Do you have suggestions to deal with this situation?
>
>>
>
> save wavefunctions in real space. It will be much easier:
> no problems with ordering of k+G vectors
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222

From sclauzer at sissa.it  Fri Apr  1 10:04:49 2011
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Fri, 1 Apr 2011 10:04:49 +0200
Subject: [Pw_forum] Calculational equation of PDOS
In-Reply-To: <AANLkTi=wLS_uuaCKdXPQhNnUHyB+3nO80kkB_uSLfGNb@mail.gmail.com>
References: <AANLkTinh4fpCv-xG0FsPmhGPXkT1d92YvYiHX6q3qRSZ@mail.gmail.com>
	<2303D1A5-9350-4A9E-AB39-75C7D7D19A4D@sissa.it>
	<AANLkTi=wLS_uuaCKdXPQhNnUHyB+3nO80kkB_uSLfGNb@mail.gmail.com>
Message-ID: <A5840D9A-E6F7-4BC2-9CE2-2EE53D667372@sissa.it>


Il giorno 01/apr/2011, alle ore 07.09, xirainbow ha scritto:

> Dear Professor 

Thanks for upgrading my position :D

> Gabriele Sclauzero:
> Thank you for your prompt help.
> I read your thesis and benefit a lot from it:)

I'm glad of that, at least all the efforts I put in writing it could be useful to someone (thanks also to those who corrected the manuscript...)


Cheers,


GS

> Thanks again:P
> 
> 
> On Thu, Mar 31, 2011 at 7:58 PM, Gabriele Sclauzero <sclauzer at sissa.it> wrote:
> Dear Wang,
> 
>     I remember that I put down a formula for that in my PhD thesis (http://www.sissa.it/cm/thesis/2010/SclauzeroG_PhDthesis.pdf), if this may help you (see eq. 2.74 at page 58). I'm sure you could find it in many other places, though.
> 
>    I believe there's no such thing as the Rcut you write in your formula below. As you say, the atomic wavefunctions are built from the radial part R_nl(r), which is taken from the pseudopotential file, and the spherical harmonics. However you should not forget that there is also structure factor which comes from the translation of the nucleus from the origin.
> The integral is done in reciprocal space for each k-point, hence a k-dependence is added to the atomic wavefunction when transforming it to the G-basis (have a look in PW/atomic_wfc.f90).
> 
> The following paper might also be useful to you:
> 
> Solid State Communications, Vol. 95, No. 10, pp. 685-690, 1995
> 
> 
> 
> 
> HTH
> 
> GS
> 
> Il giorno 31/mar/2011, alle ore 12.27, xirainbow ha scritto:
> 
>> Dear all:
>>           I want to know the calculational equation of partial density of state(PDOS) in QE.
>>           I could not find the equation on any paper. I think it may be:
>> \int_0^{Rcut}  \Psi(\vec r)*R_n(r)*Y_{lm}(\theta,\phi)*r^2 dr d\theta d\phi.
>> where the Psi(\vec r) is the KS wave function of solid. Y_{lm}(\theta,\phi) is the spherical harmonics. R_n(r) is the the radial wave function of a isolated atom.
>>    If I was right, what is the formation of R_n(r)?
>> 
>> Thanks in advance:)
>> 
>> -- 
>> ____________________________________
>> Hui Wang
>> School of physics, Fudan University, Shanghai, China
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>    PH H2 462, Station 3, CH-1015 Lausanne
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> 
> 
> -- 
> ____________________________________
> Hui Wang
> School of physics, Fudan University, Shanghai, China
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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

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From amit99266 at rediffmail.com  Fri Apr  1 12:15:56 2011
From: amit99266 at rediffmail.com (Yamit )
Date: 1 Apr 2011 10:15:56 -0000
Subject: [Pw_forum] =?utf-8?q?phonon_lifetime_about_quantum_espresso?=
In-Reply-To: <AANLkTin2V+FpjKDH2sJGGqt3nVP7zn8yj0mQC2jRN5Wu@mail.gmail.com>
Message-ID: <1301628103.S.5970.7964.F.H.Wc7rtMamwQBbUHdfZm9ydW1dIHBob25vbiBsaWZldGltZSBhYm91dCBxdWFudHVtIGVzcHJlc3Nv.f4-234-207.old.1301652956.59302@webmail.rediffmail.com>


Dear Tancyi

For phonon lifetime you can refer the following post:

http://www.democritos.it/pipermail/pw_forum/2010-June/017392.html

The pointers there can resolve your doubts.

(Please mention your affiliations.)

Regards
Amit N Harode
CR Labs INDIA

On Fri, 01 Apr 2011 08:51:43 +0530  wrote
>Dear all :

i just began to learn how to use the quantum espresso . there is a question when i calculated the phonon lifetime by QE . how could i read out the the outcome of phonon lifetime? in d3.out file ? I means i just found the information about "Atomic displacements" . 


thanks in advance
?
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? student? tanyci

_______________________________________________

Pw_forum mailing list

Pw_forum at pwscf.org

http://www.democritos.it/mailman/listinfo/pw_forum

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From rndgiro at ig.com.br  Fri Apr  1 14:08:58 2011
From: rndgiro at ig.com.br (Ronaldo Giro)
Date: Fri, 1 Apr 2011 09:08:58 -0300
Subject: [Pw_forum] Problem to run GIPAW
Message-ID: <AANLkTinuibpKkNSsroeG8Oj5ejydjexB2aH2NmrbL5iw@mail.gmail.com>

Dear all

I tried to run GIPAW module to calculate the nmr chemical shift and epr
parameter but I had some problems:

If a tried to calculate 'efg' - electrical field gradient, everything goes
fine.
But if I tried other options like 'nmr', 'g_tensor', 'f_sum' I got the
following error:


     This program is part of the open-source Quantum ESPRESSO suite
     for quantum simulation of materials; please acknowledge
         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          URL http://www.quantum-espresso.org",
     in publications or presentations arising from this work. More details
at
     http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO

     Parallel version (MPI), running on     4 processors
     R & G space division:  proc/pool =    4

     Planes per process (thick) : nr3 =  30 npp =    8 ncplane =   900

     Proc/  planes cols     G    planes cols    G      columns  G
     Pool       (dense grid)       (smooth grid)      (wavefct grid)
        1     8    160     3014    8    160     3014     48      526
        2     8    159     3013    8    159     3013     48      526
        3     7    161     3013    7    161     3013     49      527
        4     7    161     3013    7    161     3013     48      524
     tot     30    641    12053   30    641    12053    193     2103


     init_gipaw_1: projectors nearly linearly dependent:
     ntyp =  1, l/n1/n2 =  0 2 1 -0.99707079
     init_gipaw_1: projectors nearly linearly dependent:
     ntyp =  2, l/n1/n2 =  1 2 1 -0.99430547
     init_gipaw_1: projectors nearly linearly dependent:
     ntyp =  3, l/n1/n2 =  1 2 1 -0.99382826


NMR: species H, no information on the core
NMR: species C, contribution to shift due to core =  200.333
NMR: species O, contribution to shift due to core =  270.669

     GIPAW        :     0.30s CPU time,        0.35s WALL time

 WARNING: rho_diff zero!
     Computing the magnetic susceptibilityrank 3 in job 30  admin_51775
caused collective abort of all ranks
  exit status of rank 3: killed by signal 11
rank 1 in job 30  admin_51775   caused collective abort of all ranks
  exit status of rank 1: killed by signal 11


It looks like threre is a problem in the routine to compute the magnetic
susceptibility, which
is a common routine to both calculations. How can I solve this problem?

Another question: Is possible to calculate  the hyperfine tensor with the
option 'hyperfine'?
I look at the main routine of GIPAW and i found that, authought this option
is implemented,
I did not find the subroutine hyperfine.

Best regards,

Ronaldo Giro
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From giannozz at democritos.it  Fri Apr  1 14:30:51 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 01 Apr 2011 14:30:51 +0200
Subject: [Pw_forum] Problem to run GIPAW
In-Reply-To: <AANLkTinuibpKkNSsroeG8Oj5ejydjexB2aH2NmrbL5iw@mail.gmail.com>
References: <AANLkTinuibpKkNSsroeG8Oj5ejydjexB2aH2NmrbL5iw@mail.gmail.com>
Message-ID: <1301661051.18827.63.camel@fe12lx.fisica.uniud.it>

On Fri, 2011-04-01 at 09:08 -0300, Ronaldo Giro wrote:

>      Computing the magnetic susceptibilityrank 3 in job 30
> admin_51775   caused collective abort of all ranks
>   exit status of rank 3: killed by signal 11 
> rank 1 in job 30  admin_51775   caused collective abort of all ranks
>   exit status of rank 1: killed by signal 11

no later than a few days ago, I updated this page:
  http://www.quantum-espresso.org/wiki/index.php/Bugs
with the final sentence:
  "Segmentation violation" or obscure MPI error messages are 
  NEVER a sufficient piece of information.

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



From kucukben at sissa.it  Fri Apr  1 14:39:37 2011
From: kucukben at sissa.it (Emine Kucukbenli)
Date: Fri, 01 Apr 2011 14:39:37 +0200
Subject: [Pw_forum] Problem to run GIPAW
In-Reply-To: <AANLkTinuibpKkNSsroeG8Oj5ejydjexB2aH2NmrbL5iw@mail.gmail.com>
References: <AANLkTinuibpKkNSsroeG8Oj5ejydjexB2aH2NmrbL5iw@mail.gmail.com>
Message-ID: <20110401143937.z6wu7u6tcg8wws00@webmail.sissa.it>

Dear Ronaldo,
If I am not mistaken,as the difference between up spin - down spin  
density is zero, the code gets confused how to choose the  
majority/minority spin and doesnt assign anything to these arrays but  
they will still be called during the program.That is why you end up  
with a segmentation fault I believe.

I think a fixed assignment would do for now if you know what you are doing :
in g_tensor_crystal.f90 , line 106
   else
      write ( stdout, * ) "WARNING: rho_diff zero!"
      s_maj=1
      s_min=npsin
   end if

mind that I dont know if this would mess something else somewhere else  
in the code, apparently it has never been used for abs(tot spin  
density difference) < 1.0d-3 case
I dont see how this is a problem when you are running with option  
'nmr' though..

emine kucukbenli, phd student, sissa, italy


Quoting Ronaldo Giro <rndgiro at ig.com.br>:

> Dear all
>
> I tried to run GIPAW module to calculate the nmr chemical shift and epr
> parameter but I had some problems:
>
> If a tried to calculate 'efg' - electrical field gradient, everything goes
> fine.
> But if I tried other options like 'nmr', 'g_tensor', 'f_sum' I got the
> following error:
>
>
>      This program is part of the open-source Quantum ESPRESSO suite
>      for quantum simulation of materials; please acknowledge
>          "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>           URL http://www.quantum-espresso.org",
>      in publications or presentations arising from this work. More details
> at
>      http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
>
>      Parallel version (MPI), running on     4 processors
>      R & G space division:  proc/pool =    4
>
>      Planes per process (thick) : nr3 =  30 npp =    8 ncplane =   900
>
>      Proc/  planes cols     G    planes cols    G      columns  G
>      Pool       (dense grid)       (smooth grid)      (wavefct grid)
>         1     8    160     3014    8    160     3014     48      526
>         2     8    159     3013    8    159     3013     48      526
>         3     7    161     3013    7    161     3013     49      527
>         4     7    161     3013    7    161     3013     48      524
>      tot     30    641    12053   30    641    12053    193     2103
>
>
>      init_gipaw_1: projectors nearly linearly dependent:
>      ntyp =  1, l/n1/n2 =  0 2 1 -0.99707079
>      init_gipaw_1: projectors nearly linearly dependent:
>      ntyp =  2, l/n1/n2 =  1 2 1 -0.99430547
>      init_gipaw_1: projectors nearly linearly dependent:
>      ntyp =  3, l/n1/n2 =  1 2 1 -0.99382826
>
>
> NMR: species H, no information on the core
> NMR: species C, contribution to shift due to core =  200.333
> NMR: species O, contribution to shift due to core =  270.669
>
>      GIPAW        :     0.30s CPU time,        0.35s WALL time
>
>  WARNING: rho_diff zero!
>      Computing the magnetic susceptibilityrank 3 in job 30  admin_51775
> caused collective abort of all ranks
>   exit status of rank 3: killed by signal 11
> rank 1 in job 30  admin_51775   caused collective abort of all ranks
>   exit status of rank 1: killed by signal 11
>
>
> It looks like threre is a problem in the routine to compute the magnetic
> susceptibility, which
> is a common routine to both calculations. How can I solve this problem?
>
> Another question: Is possible to calculate  the hyperfine tensor with the
> option 'hyperfine'?
> I look at the main routine of GIPAW and i found that, authought this option
> is implemented,
> I did not find the subroutine hyperfine.
>
> Best regards,
>
> Ronaldo Giro
>



----------------------------------------------------------------
   SISSA Webmail https://webmail.sissa.it/
   Powered by Horde http://www.horde.org/



From kucukben at sissa.it  Fri Apr  1 14:46:19 2011
From: kucukben at sissa.it (Emine Kucukbenli)
Date: Fri, 01 Apr 2011 14:46:19 +0200
Subject: [Pw_forum] Problem to run GIPAW
In-Reply-To: <AANLkTinuibpKkNSsroeG8Oj5ejydjexB2aH2NmrbL5iw@mail.gmail.com>
References: <AANLkTinuibpKkNSsroeG8Oj5ejydjexB2aH2NmrbL5iw@mail.gmail.com>
Message-ID: <20110401144619.pzadxfkeo8o8soso@webmail.sissa.it>

The hyperfine subroutine is in efg.f90
cheers,
emine kucukbenli, phd student, sissa, italy

Quoting Ronaldo Giro <rndgiro at ig.com.br>:
> Another question: Is possible to calculate  the hyperfine tensor with the
> option 'hyperfine'?
> I look at the main routine of GIPAW and i found that, authought this option
> is implemented,
> I did not find the subroutine hyperfine.






----------------------------------------------------------------
   SISSA Webmail https://webmail.sissa.it/
   Powered by Horde http://www.horde.org/



From davide.ceresoli at materials.ox.ac.uk  Fri Apr  1 14:59:38 2011
From: davide.ceresoli at materials.ox.ac.uk (Davide Ceresoli)
Date: Fri, 01 Apr 2011 13:59:38 +0100
Subject: [Pw_forum] Problem to run GIPAW
In-Reply-To: <AANLkTinuibpKkNSsroeG8Oj5ejydjexB2aH2NmrbL5iw@mail.gmail.com>
References: <AANLkTinuibpKkNSsroeG8Oj5ejydjexB2aH2NmrbL5iw@mail.gmail.com>
Message-ID: <4D95CC3A.2050409@materials.ox.ac.uk>

On 04/01/2011 01:08 PM, Ronaldo Giro wrote:
> Dear all
>
> If a tried to calculate 'efg' - electrical field gradient, everything goes fine.
> But if I tried other options like 'nmr', 'g_tensor', 'f_sum' I got the
Dear Ronaldo,
    are you sure you get the error message also with job='nmr'?
There is no such check in suscept_crystal.f90 (which calculates
the NMR shielding), unless you modified the code.

Also, is your system spin polarized? if not it doesn't make sense
to calculate the g-tensor.

Finally, the message is a warning but the code should continue
although results will make no sense. Definitely, it should not
crash with an MPI error. It looks like that there might a
problem with your compiler/libraries.

Cheers,
     Davide


From tanycimr at gmail.com  Fri Apr  1 15:09:05 2011
From: tanycimr at gmail.com (=?Big5?B?zuu0xqbB?=)
Date: Fri, 1 Apr 2011 21:09:05 +0800
Subject: [Pw_forum] phonon lifetime about quantum espresso
In-Reply-To: <1301628103.S.5970.7964.F.H.Wc7rtMamwQBbUHdfZm9ydW1dIHBob25vbiBsaWZldGltZSBhYm91dCBxdWFudHVtIGVzcHJlc3Nv.f4-234-207.old.1301652956.59302@webmail.rediffmail.com>
References: <AANLkTin2V+FpjKDH2sJGGqt3nVP7zn8yj0mQC2jRN5Wu@mail.gmail.com>
	<1301628103.S.5970.7964.F.H.Wc7rtMamwQBbUHdfZm9ydW1dIHBob25vbiBsaWZldGltZSBhYm91dCBxdWFudHVtIGVzcHJlc3Nv.f4-234-207.old.1301652956.59302@webmail.rediffmail.com>
Message-ID: <AANLkTi=UuWOG80CRDxB95hdg7-AR-QijG7Xw-nfa0HOz@mail.gmail.com>

Dear Yamit

thanks for your advice . it gives me a lot of help .

p.s. my affiliations ? it was my carelessness . thank you for reminding me .


tanyci
nankai university,tianjin
China



2011/4/1 Yamit <amit99266 at rediffmail.com>

>
> Dear Tancyi
>
> For phonon lifetime you can refer the following post:
>
> http://www.democritos.it/pipermail/pw_forum/2010-June/017392.html
>
> The pointers there can resolve your doubts.
>
> (Please mention your affiliations.)
>
> Regards
> Amit N Harode
> CR Labs INDIA
>
> On Fri, 01 Apr 2011 08:51:43 +0530 wrote
>
> >Dear all :
>
> i just began to learn how to use the quantum espresso . there is a question
> when i calculated the phonon lifetime by QE . how could i read out the the
> outcome of phonon lifetime  in d3.out file ? I means i just found the
> information about "Atomic displacements" .
>
>
> thanks in advance
>
>
> student  tanyci
>
> _______________________________________________
>
> Pw_forum mailing list
>
> Pw_forum at pwscf.org
>
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm at Middle?>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From degironc at sissa.it  Fri Apr  1 15:12:07 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 01 Apr 2011 15:12:07 +0200
Subject: [Pw_forum] Problem with pseudopotential
In-Reply-To: <562843.64501.qm@web43413.mail.sp1.yahoo.com>
References: <562843.64501.qm@web43413.mail.sp1.yahoo.com>
Message-ID: <4D95CF27.9050908@sissa.it>

They look reasonable to me ...
but you can check that lattice parameter, interlayer surface relaxation, 
or bond length in Cu2 dimer are ok to have some feeling that the 
pseudopotentials are working properly.

stefano

On 03/31/2011 11:26 PM, Izaak Williamson wrote:
> Dear Stefano,
>
> I plotted the average charge and it seems reasonable to me for both the
> pseudopotentials. I am attaching both plots, it would be nice to get your input.
>
> Thank you.
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From nkxirainbow at gmail.com  Fri Apr  1 16:11:48 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Fri, 1 Apr 2011 22:11:48 +0800
Subject: [Pw_forum] Calculational equation of PDOS
In-Reply-To: <A5840D9A-E6F7-4BC2-9CE2-2EE53D667372@sissa.it>
References: <AANLkTinh4fpCv-xG0FsPmhGPXkT1d92YvYiHX6q3qRSZ@mail.gmail.com>
	<2303D1A5-9350-4A9E-AB39-75C7D7D19A4D@sissa.it>
	<AANLkTi=wLS_uuaCKdXPQhNnUHyB+3nO80kkB_uSLfGNb@mail.gmail.com>
	<A5840D9A-E6F7-4BC2-9CE2-2EE53D667372@sissa.it>
Message-ID: <AANLkTi=Gf+93dQr0OtBvq3Z-61frm+P2xGrToUspo1o6@mail.gmail.com>

Dear Professor Gabriele Sclauzero:
After reading your thesis, I examine the Si.pbe-rrkj.UPF and find that there
is not d orbital for Si.

This the date in Si.pbe-rrkj.UPF:
______________________________________________________
    2    3             Number of Wavefunctions, Number of Projectors
 Wavefunctions         nl  l   occ
                       3S  0  2.00
                       3P  1  2.00
<PP_BETA>
    1    0             Beta    L
    2    0             Beta    L
    3    1             Beta    L
?????????????????????????????

However, in the table II of Phys. Rev. B 26, 4199 (1982,Pseudopotentials
that work From H to Pu), the configurations used to derive pseudopotential
always have d orbital for all kinds of atoms, including H.

Does this sugguest that there is no pseudopotential for d orbital in
Si.pbe-rrkj.UPF?
Does this sugguest that the pdos of d orbital is always zero based on
Si.pbe-rrkj.UPF?
I am a little confused:(

On Fri, Apr 1, 2011 at 4:04 PM, Gabriele Sclauzero <sclauzer at sissa.it>wrote:

>
> Il giorno 01/apr/2011, alle ore 07.09, xirainbow ha scritto:
>
> Dear Professor
>
>
> Thanks for upgrading my position :D
>
> Gabriele Sclauzero:
> Thank you for your prompt help.
> I read your thesis and benefit a lot from it:)
>
>
> I'm glad of that, at least all the efforts I put in writing it could be
> useful to someone (thanks also to those who corrected the manuscript...)
>
>
> Cheers,
>
>
> GS
>
> Thanks again:P
>
>
> On Thu, Mar 31, 2011 at 7:58 PM, Gabriele Sclauzero <sclauzer at sissa.it>wrote:
>
>> Dear Wang,
>>
>>     I remember that I put down a formula for that in my PhD thesis (
>> http://www.sissa.it/cm/thesis/2010/SclauzeroG_PhDthesis.pdf), if this may
>> help you (see eq. 2.74 at page 58). I'm sure you could find it in many other
>> places, though.
>>
>>    I believe there's no such thing as the Rcut you write in your formula
>> below. As you say, the atomic wavefunctions are built from the radial part
>> R_nl(r), which is taken from the pseudopotential file, and the spherical
>> harmonics. However you should not forget that there is also structure factor
>> which comes from the translation of the nucleus from the origin.
>> The integral is done in reciprocal space for each k-point, hence a
>> k-dependence is added to the atomic wavefunction when transforming it to the
>> G-basis (have a look in PW/atomic_wfc.f90).
>>
>> The following paper might also be useful to you:
>>
>> Solid State Communications, Vol. 95, No. 10, pp. 685-690, 1995
>>
>>
>>
>>
>> HTH
>>
>> GS
>>
>> Il giorno 31/mar/2011, alle ore 12.27, xirainbow ha scritto:
>>
>> Dear all:
>>           I want to know the calculational equation of partial density of
>> state(PDOS) in QE.
>>           I could not find the equation on any paper. I think it may be:
>> \int_0^{Rcut}  \Psi(\vec r)*R_n(r)*Y_{lm}(\theta,\phi)*r^2 dr d\theta
>> d\phi.
>> where the Psi(\vec r) is the KS wave function of solid.
>> Y_{lm}(\theta,\phi) is the spherical harmonics. R_n(r) is the the radial
>> wave function of a isolated atom.
>>     If I was right, what is the formation of R_n(r)?
>>
>> Thanks in advance:)
>>
>> --
>> ____________________________________
>> Hui Wang
>> School of physics, Fudan University, Shanghai, China
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>>
>> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>> *   PH H2 462, Station 3, CH-1015 Lausanne*
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> ____________________________________
> Hui Wang
> School of physics, Fudan University, Shanghai, China
>  _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *   PH H2 462, Station 3, CH-1015 Lausanne*
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From giannozz at democritos.it  Fri Apr  1 18:11:49 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 01 Apr 2011 18:11:49 +0200
Subject: [Pw_forum] Quantum ESPRESSO v.4.3
Message-ID: <1301674309.648.11.camel@fe12lx.fisica.uniud.it>

Version 4.3 of the Quantum ESPRESSO distribution is available for
download from the website http://www.quantum-espresso.org . This
release contains the following improvements over previous versions:

* vdW-DF - Dispersion interactions (van der Waals) with nonlocal
functional
  in PWscf (Brian Kolb, Timo Thonhauser, Riccardo Sabatini, SdG)
* New package TDDFPT for calculations of spectra using Time-Dependent
  Density-Functional Perturbation Theory (SB, Ralph Gebauer, Baris
Malcioglu,
  Dario Rocca, Brent Walker)
* Additions to projwfc: k-resolved DOS, LDOS integrated in selected
  real-space regions
* Constant-volume variable-cell optimization
* Non-colinear and spin-orbit PAW
* CP only, experimental: parallelization over Kohn-Sham states
* CP only, experimental: penalty functional technique in DFT+U
calculations

Note the following major change:

* code pw.x no longer performs NEB calculations. NEB is now computed
  by a separate code, NEB/neb.x . NEB-specific variables are no longer
  read by pw.x; they are read by neb.x after all pw.x variables
* NEB for cp.x no longer available

For other minor improvements, changes, bug fixes, see file
Doc/release-notes

Everybody who is using the Quantum-ESPRESSO distribution is encouraged
to upgrade and to report problems to the mailing list.

The Quantum ESPRESSO group


From parishok at gmail.com  Fri Apr  1 21:36:51 2011
From: parishok at gmail.com (pari shok)
Date: Fri, 1 Apr 2011 15:36:51 -0400
Subject: [Pw_forum] shift of energy
Message-ID: <BANLkTi=aa3UsxZQh+pGbqPeJP3u-Q95mYg@mail.gmail.com>

Dear All,
Hello and Happy Spring.
I am working on SiC structures:

   1. The DOS of 72-atom SiC (supercell) shows a shift of energy. I was
   wondering what this "shift of energy" shows.
   2. How possibly I choose the k-point that I would be able to compare
   8-atom SiC with 72-atom structure?

I really appreciate your help.
Yours
P Shok
UMD
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From giannozz at democritos.it  Fri Apr  1 22:00:11 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 1 Apr 2011 22:00:11 +0200
Subject: [Pw_forum] shift of energy
In-Reply-To: <BANLkTi=aa3UsxZQh+pGbqPeJP3u-Q95mYg@mail.gmail.com>
References: <BANLkTi=aa3UsxZQh+pGbqPeJP3u-Q95mYg@mail.gmail.com>
Message-ID: <411269DB-B95B-42D3-BB9F-D4B89478959E@democritos.it>


On Apr 1, 2011, at 21:36 , pari shok wrote:

> The DOS of 72-atom SiC (supercell) shows a shift of energy.

a shift with respect to what?
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From degironc at sissa.it  Fri Apr  1 23:01:25 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 01 Apr 2011 23:01:25 +0200
Subject: [Pw_forum] Calculational equation of PDOS
In-Reply-To: <AANLkTi=Gf+93dQr0OtBvq3Z-61frm+P2xGrToUspo1o6@mail.gmail.com>
References: <AANLkTinh4fpCv-xG0FsPmhGPXkT1d92YvYiHX6q3qRSZ@mail.gmail.com>	<2303D1A5-9350-4A9E-AB39-75C7D7D19A4D@sissa.it>	<AANLkTi=wLS_uuaCKdXPQhNnUHyB+3nO80kkB_uSLfGNb@mail.gmail.com>	<A5840D9A-E6F7-4BC2-9CE2-2EE53D667372@sissa.it>
	<AANLkTi=Gf+93dQr0OtBvq3Z-61frm+P2xGrToUspo1o6@mail.gmail.com>
Message-ID: <4D963D25.4000308@sissa.it>

In all pseudopotentials there are a number of angular momenta for which 
the non local part mimic the orthogonality condition with respect to the 
removed core electrons.. and there is a local part that is applied to 
all angular momenta and can be determined inverting the pseudo KS eqs 
for some angular momentum or just obtained smoothing the AE potential...

Silicon has s and p core states.. does not have d core states; so s and 
p non locality only should be necessary.
In the BHS paper the local part of the potential is computed from the 
nodeless 3d orbital.
In Si.pbe-rrkj.UPF the local part is probably obtained smoothing the AE 
local potential or anyway there is no projector associated with it...

The pdos is another story. Which angular momenta are available in pdos 
depends on which atomic wavefunctions are defined... In the case of Si, 
3s and 3p only... so no d pdos.

pdos have (limited) meaning only when the wavefunctions on which one is 
projecting are rather localized .. otherwise results are rather random.. 
I think that adding a rather delocalized 3d orbital to the 
pseudopotential would not produce very meaningful pdos.

hope this helps

stefano

  On 04/01/2011 04:11 PM, xirainbow wrote:
> Dear Professor Gabriele Sclauzero:
> After reading your thesis, I examine the Si.pbe-rrkj.UPF and find that there
> is not d orbital for Si.
>
> This the date in Si.pbe-rrkj.UPF:
> ______________________________________________________
>      2    3             Number of Wavefunctions, Number of Projectors
>   Wavefunctions         nl  l   occ
>                         3S  0  2.00
>                         3P  1  2.00
> <PP_BETA>
>      1    0             Beta    L
>      2    0             Beta    L
>      3    1             Beta    L
> ?????????????????????????????
>
> However, in the table II of Phys. Rev. B 26, 4199 (1982,Pseudopotentials
> that work From H to Pu), the configurations used to derive pseudopotential
> always have d orbital for all kinds of atoms, including H.
>
> Does this sugguest that there is no pseudopotential for d orbital in
> Si.pbe-rrkj.UPF?
> Does this sugguest that the pdos of d orbital is always zero based on
> Si.pbe-rrkj.UPF?
> I am a little confused:(
>
> On Fri, Apr 1, 2011 at 4:04 PM, Gabriele Sclauzero<sclauzer at sissa.it>wrote:
>
>> Il giorno 01/apr/2011, alle ore 07.09, xirainbow ha scritto:
>>
>> Dear Professor
>>
>>
>> Thanks for upgrading my position :D
>>
>> Gabriele Sclauzero:
>> Thank you for your prompt help.
>> I read your thesis and benefit a lot from it:)
>>
>>
>> I'm glad of that, at least all the efforts I put in writing it could be
>> useful to someone (thanks also to those who corrected the manuscript...)
>>
>>
>> Cheers,
>>
>>
>> GS
>>
>> Thanks again:P
>>
>>
>> On Thu, Mar 31, 2011 at 7:58 PM, Gabriele Sclauzero<sclauzer at sissa.it>wrote:
>>
>>> Dear Wang,
>>>
>>>      I remember that I put down a formula for that in my PhD thesis (
>>> http://www.sissa.it/cm/thesis/2010/SclauzeroG_PhDthesis.pdf), if this may
>>> help you (see eq. 2.74 at page 58). I'm sure you could find it in many other
>>> places, though.
>>>
>>>     I believe there's no such thing as the Rcut you write in your formula
>>> below. As you say, the atomic wavefunctions are built from the radial part
>>> R_nl(r), which is taken from the pseudopotential file, and the spherical
>>> harmonics. However you should not forget that there is also structure factor
>>> which comes from the translation of the nucleus from the origin.
>>> The integral is done in reciprocal space for each k-point, hence a
>>> k-dependence is added to the atomic wavefunction when transforming it to the
>>> G-basis (have a look in PW/atomic_wfc.f90).
>>>
>>> The following paper might also be useful to you:
>>>
>>> Solid State Communications, Vol. 95, No. 10, pp. 685-690, 1995
>>>
>>>
>>>
>>>
>>> HTH
>>>
>>> GS
>>>
>>> Il giorno 31/mar/2011, alle ore 12.27, xirainbow ha scritto:
>>>
>>> Dear all:
>>>            I want to know the calculational equation of partial density of
>>> state(PDOS) in QE.
>>>            I could not find the equation on any paper. I think it may be:
>>> \int_0^{Rcut}  \Psi(\vec r)*R_n(r)*Y_{lm}(\theta,\phi)*r^2 dr d\theta
>>> d\phi.
>>> where the Psi(\vec r) is the KS wave function of solid.
>>> Y_{lm}(\theta,\phi) is the spherical harmonics. R_n(r) is the the radial
>>> wave function of a isolated atom.
>>>      If I was right, what is the formation of R_n(r)?
>>>
>>> Thanks in advance:)
>>>
>>> --
>>> ____________________________________
>>> Hui Wang
>>> School of physics, Fudan University, Shanghai, China
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>>>
>>> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>>> *   PH H2 462, Station 3, CH-1015 Lausanne*
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>>
>> --
>> ____________________________________
>> Hui Wang
>> School of physics, Fudan University, Shanghai, China
>>   _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>>
>> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>> *   PH H2 462, Station 3, CH-1015 Lausanne*
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From jorge.gallardo at cab.cnea.gov.ar  Fri Apr  1 23:01:45 2011
From: jorge.gallardo at cab.cnea.gov.ar (jorge.gallardo at cab.cnea.gov.ar)
Date: Fri, 1 Apr 2011 18:01:45 -0300 (ART)
Subject: [Pw_forum] charge density output format from pp.x
In-Reply-To: <1290592007.12941.6.camel@ulisse.cm.sissa.it>
References: <4CEBFF39.40505@fu-berlin.de>
	<1290592007.12941.6.camel@ulisse.cm.sissa.it>
Message-ID: <54782.200.0.233.52.1301691705.squirrel@mail.cab.cnea.gov.ar>

Hello!,

I need to calculate the charge density of an aluminum nano-structure.

There is a way to get the electron density as a function of spatial
coordinates(say, rho(x,y,z) ) using Quantum Espresso?

In adition, The "pp.x" program generates a file "al.pp.dat", which can
then be drawn, for example with "plotrho.x", if I want to plot it with
GNUplot I did output_format = 0 in the "al.pp.in" file, the I ran pp.x.
The output file "al.rho.dat" has a single column: how can I draw this file
using gnuplot?

Thanks in advance

____

Lic. Jorge Gallardo
Materiales Metalicos y Nanoestructurados
TeMaDi
Bariloche Atomic Center
CNEA



From jbrkeith at gmail.com  Sat Apr  2 02:38:56 2011
From: jbrkeith at gmail.com (j brandon keith)
Date: Fri, 1 Apr 2011 17:38:56 -0700
Subject: [Pw_forum] problem with fftw3
Message-ID: <AANLkTi=nZOK9Kf9iChf9ZDifRynp0CMhDiU0kSW0MdwY@mail.gmail.com>

Hi, I used to run quantum espresso all the time, but now when I try to
compile (old or new version), I get an error in fftw3 library...an
example is example01:

This example shows how to use pw.x to calculate the total energy and
the band structure of four simple systems: Si, Al, Cu, Ni.

  executables directory: /home/jbk/espresso-4.3/bin
  pseudo directory:      /home/jbk/espresso-4.3/pseudo
  temporary directory:   /home/jbk/tmp
  checking that needed directories and files exist... done

  running pw.x as: mpirun -np 1 /home/jbk/espresso-4.3/bin/pw.x
  running bands.x as: mpirun -np 1 /home/jbk/espresso-4.3/bin/bands.x

  cleaning /home/jbk/tmp... done
  running the scf calculation for Si...[zen:03240] *** Process
received signal ***
[zen:03240] Signal: Segmentation fault (11)
[zen:03240] Signal code:  (128)
[zen:03240] Failing at address: (nil)
[zen:03240] [ 0] [0xb772040c]
[zen:03240] [ 1] /usr/lib/libfftw3.so.3(+0x1965a) [0xb6a6e65a]
[zen:03240] [ 2] /usr/lib/libfftw3.so.3(+0x1c217) [0xb6a71217]
[zen:03240] [ 3] /usr/lib/libfftw3.so.3(+0x1c733) [0xb6a71733]
[zen:03240] [ 4] /usr/lib/libfftw3.so.3(dfftw_execute_dft_+0x74) [0xb6b06f64]
[zen:03240] [ 5]
/home/jbk/espresso-4.3/bin/pw.x(__fft_scalar_MOD_cft_2xy+0xf38)
[0x81f5448]
[zen:03240] [ 6]
/home/jbk/espresso-4.3/bin/pw.x(__fft_parallel_MOD_tg_cft3s+0x122f)
[0x81f29bf]
[zen:03240] [ 7] /home/jbk/espresso-4.3/bin/pw.x(fwfft_x_+0x130) [0x81f0b90]
[zen:03240] [ 8] /home/jbk/espresso-4.3/bin/pw.x(addusstres_+0x398) [0x81c5b88]
[zen:03240] [ 9] /home/jbk/espresso-4.3/bin/pw.x(stres_knl_+0x788) [0x81b94b8]
[zen:03240] [10] /home/jbk/espresso-4.3/bin/pw.x(stress_+0x2a4) [0x80e0344]
[zen:03240] [11] /home/jbk/espresso-4.3/bin/pw.x(MAIN__+0x44d) [0x806dccd]
[zen:03240] [12] /home/jbk/espresso-4.3/bin/pw.x(main+0x2b) [0x833e42b]
[zen:03240] [13] /lib/libc.so.6(__libc_start_main+0xe7) [0xb6633ce7]
[zen:03240] [14] /home/jbk/espresso-4.3/bin/pw.x() [0x806d7e1]
[zen:03240] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 3240 on node zen exited on
signal 11 (Segmentation fault).
--------------------------------------------------------------------------
Error condition encountered during test: exit status = 139
Aborting


Any ideas what is going on?...should i try to tell configure to use
fftw2?...dunno...

brandon

From degironc at sissa.it  Sat Apr  2 10:14:03 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Sat, 02 Apr 2011 10:14:03 +0200
Subject: [Pw_forum] charge density output format from pp.x
In-Reply-To: <54782.200.0.233.52.1301691705.squirrel@mail.cab.cnea.gov.ar>
References: <4CEBFF39.40505@fu-berlin.de>	<1290592007.12941.6.camel@ulisse.cm.sissa.it>
	<54782.200.0.233.52.1301691705.squirrel@mail.cab.cnea.gov.ar>
Message-ID: <4D96DACB.5050507@sissa.it>

I think the easiest way is to save the file in xcrysden format using the 
pp.x code and then visualize it using xcrysden. for 2D plots one can 
also use the plotrho.x code.
have a look to example05 and example16

stefano

On 04/01/2011 11:01 PM, jorge.gallardo at cab.cnea.gov.ar wrote:
> Hello!,
>
> I need to calculate the charge density of an aluminum nano-structure.
>
> There is a way to get the electron density as a function of spatial
> coordinates(say, rho(x,y,z) ) using Quantum Espresso?
>
> In adition, The "pp.x" program generates a file "al.pp.dat", which can
> then be drawn, for example with "plotrho.x", if I want to plot it with
> GNUplot I did output_format = 0 in the "al.pp.in" file, the I ran pp.x.
> The output file "al.rho.dat" has a single column: how can I draw this file
> using gnuplot?
>
> Thanks in advance
>
> ____
>
> Lic. Jorge Gallardo
> Materiales Metalicos y Nanoestructurados
> TeMaDi
> Bariloche Atomic Center
> CNEA
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From degironc at sissa.it  Sat Apr  2 10:19:35 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Sat, 02 Apr 2011 10:19:35 +0200
Subject: [Pw_forum] problem with fftw3
In-Reply-To: <AANLkTi=nZOK9Kf9iChf9ZDifRynp0CMhDiU0kSW0MdwY@mail.gmail.com>
References: <AANLkTi=nZOK9Kf9iChf9ZDifRynp0CMhDiU0kSW0MdwY@mail.gmail.com>
Message-ID: <4D96DC17.9060408@sissa.it>

does it work in serial ? with internal fftw ?
it's funny because it crashes in the calculation of stress and by the 
time it reaches there it has done zillions ffts  ... Is the output 
correct up to that point ?
stefano

On 04/02/2011 02:38 AM, j brandon keith wrote:
> Hi, I used to run quantum espresso all the time, but now when I try to
> compile (old or new version), I get an error in fftw3 library...an
> example is example01:
>
> This example shows how to use pw.x to calculate the total energy and
> the band structure of four simple systems: Si, Al, Cu, Ni.
>
>    executables directory: /home/jbk/espresso-4.3/bin
>    pseudo directory:      /home/jbk/espresso-4.3/pseudo
>    temporary directory:   /home/jbk/tmp
>    checking that needed directories and files exist... done
>
>    running pw.x as: mpirun -np 1 /home/jbk/espresso-4.3/bin/pw.x
>    running bands.x as: mpirun -np 1 /home/jbk/espresso-4.3/bin/bands.x
>
>    cleaning /home/jbk/tmp... done
>    running the scf calculation for Si...[zen:03240] *** Process
> received signal ***
> [zen:03240] Signal: Segmentation fault (11)
> [zen:03240] Signal code:  (128)
> [zen:03240] Failing at address: (nil)
> [zen:03240] [ 0] [0xb772040c]
> [zen:03240] [ 1] /usr/lib/libfftw3.so.3(+0x1965a) [0xb6a6e65a]
> [zen:03240] [ 2] /usr/lib/libfftw3.so.3(+0x1c217) [0xb6a71217]
> [zen:03240] [ 3] /usr/lib/libfftw3.so.3(+0x1c733) [0xb6a71733]
> [zen:03240] [ 4] /usr/lib/libfftw3.so.3(dfftw_execute_dft_+0x74) [0xb6b06f64]
> [zen:03240] [ 5]
> /home/jbk/espresso-4.3/bin/pw.x(__fft_scalar_MOD_cft_2xy+0xf38)
> [0x81f5448]
> [zen:03240] [ 6]
> /home/jbk/espresso-4.3/bin/pw.x(__fft_parallel_MOD_tg_cft3s+0x122f)
> [0x81f29bf]
> [zen:03240] [ 7] /home/jbk/espresso-4.3/bin/pw.x(fwfft_x_+0x130) [0x81f0b90]
> [zen:03240] [ 8] /home/jbk/espresso-4.3/bin/pw.x(addusstres_+0x398) [0x81c5b88]
> [zen:03240] [ 9] /home/jbk/espresso-4.3/bin/pw.x(stres_knl_+0x788) [0x81b94b8]
> [zen:03240] [10] /home/jbk/espresso-4.3/bin/pw.x(stress_+0x2a4) [0x80e0344]
> [zen:03240] [11] /home/jbk/espresso-4.3/bin/pw.x(MAIN__+0x44d) [0x806dccd]
> [zen:03240] [12] /home/jbk/espresso-4.3/bin/pw.x(main+0x2b) [0x833e42b]
> [zen:03240] [13] /lib/libc.so.6(__libc_start_main+0xe7) [0xb6633ce7]
> [zen:03240] [14] /home/jbk/espresso-4.3/bin/pw.x() [0x806d7e1]
> [zen:03240] *** End of error message ***
> --------------------------------------------------------------------------
> mpirun noticed that process rank 0 with PID 3240 on node zen exited on
> signal 11 (Segmentation fault).
> --------------------------------------------------------------------------
> Error condition encountered during test: exit status = 139
> Aborting
>
>
> Any ideas what is going on?...should i try to tell configure to use
> fftw2?...dunno...
>
> brandon
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From parishok at gmail.com  Sun Apr  3 01:34:51 2011
From: parishok at gmail.com (pari shok)
Date: Sat, 2 Apr 2011 19:34:51 -0400
Subject: [Pw_forum] shift of energy
Message-ID: <BANLkTimvccm1rGhPpZ2aq8YS+Qk6mhpp+g@mail.gmail.com>

Dear Paolo,
DOS of 72-atom SiC shows a shift of energy with respect to 8-atom
SiC.The bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is
around 5-7 eV.
Would you please help me to understand this shift.
Thanks again.
P Shok
UMD
On Apr 1, 2011, at 21:36 , pari shok wrote:

>* The DOS of 72-atom SiC (supercell) shows a shift of energy.
*
a shift with respect to what?
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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From faccin.giovani at gmail.com  Sun Apr  3 02:19:53 2011
From: faccin.giovani at gmail.com (Giovani Faccin)
Date: Sat, 2 Apr 2011 20:19:53 -0400
Subject: [Pw_forum] Fixing starting starting_ns_eigenvalue
In-Reply-To: <4D925077.7060201@sissa.it>
References: <AANLkTimjp8F_gvmEFYNJY7QQDuz9VLCqzQFtPMyHFWKo@mail.gmail.com>
	<A0F500C2-D04A-428A-A0C2-E126E9DEA5E3@sissa.it>
	<AANLkTin7=oHuaUkdkEgCN5wHopnGqfFxFP9WidEBduWR@mail.gmail.com>
	<4D925077.7060201@sissa.it>
Message-ID: <BANLkTindZ16oFM_Y_ucJMZTt6_Ch1ZqVPg@mail.gmail.com>

Hi Stefano,

Thanks for the reply!

I tried your patch and it did not fix the eigenvalues. So I changed it a
little bit:

Original:
       *IF ( first .AND. istep == 0 .AND. &
                starting_pot == 'atomic' ) CALL ns_adj() ;  rhoin%ns =
rho%ns*

New one:
       *IF ( first .AND. istep == 0 .AND. &
       starting_pot == 'atomic' ) CALL ns_adj();

       IF ( first .AND. istep == 0 .AND. &
       starting_pot == 'atomic' ) rhoin%ns = rho%ns;*

I tested both cases on the same setup (using the intel compiler), and the
second one works out. Maybe it should be updated on cvs?

Regards,

Giovani Faccin
IFGW/Unicamp - Brazil



2011/3/29 Stefano de Gironcoli <degironc at sissa.it>

>  I think this is a bug ...
>
> The initial value of ns should be overwritten by the input request...
> A simple way to obtain this should be to replace, in electrons.f90, the
> line
>
>             IF ( first .AND. istep == 0 .AND. &
>                 starting_pot == 'atomic' ) CALL ns_adj()
> by
>
>           IF ( first .AND. istep == 0 .AND. &
>                 starting_pot == 'atomic' ) CALL ns_adj() ;  rhoin%ns =
> rho%ns
>
> I updated the cvs version.
>
> stefano
>
>
>
> On 03/29/2011 06:55 PM, Giovani Faccin wrote:
>
> Dear Gabriele,
>
> Yes, I tried mixing_fixed_ns. The problem is that this command fixes the
> initial occupation during all the run, not the occupation imposed on step 2
> with starting_ns eigenvalues. I'm attaching an example input and output file
> that shows this happening.
>
> As you can see on the output.txt file, after iteraction 1 the program
> inserts the eigenvalues I wanted on atom 1 spin2 and atom 2 spin2. However,
> just after this it prints:
>
>
> RESET ns to initial values (iter <= mixing_fixed_ns)
>
> on every new iteration. Looking at the end of the calculation, you can see
> that the final states are exactly the default states from step 0. In other
> words, it overwrites the eigenvalues defined by starting_ns eigenvalues,
> placing the default initial occupations instead. Perhaps an "if" clause
> could be added to the code to manage situations when both mixing_fixed_ns
> and starting_ns eigenvalues are defined by the user? Or maybe I'm doing this
> all wrong?
>
> Regards,
>
> Giovani Faccin
>
> IFGW/Unicamp-Brazil
>
>
>
>
>
> 2011/3/29 Gabriele Sclauzero <sclauzer at sissa.it> <sclauzer at sissa.it>
>
>  Dear Giovani,
>
>     have you tried with mixing_fixed_ns?
>
>     Could you please provide your affiliation?
>
>
> Regards,
>
>
> GS
>
> mixing_fixed_ns
> Il giorno 29/mar/2011, alle ore 18.16, Giovani Faccin ha scritto:
>
> Hi all!
>
> Is it possible, in a LDA+U calculation, to fix the starting_ns eigenvalues
> for the entire calculation run, instead of just the second interaction?
>
> Specifically, I'd like to be able to track how a certain electronic
> configuration's associated energy varies when other parameters (ex: atomic
> distances) change. But in order to do that, I need to be able to impose
> specific electronic configurations for the system, even if those
> configurations are not the global energy mininum.
>
> Can that be done in QE?
>
> Thanks!
>
> --
> Giovani
>
>
> _______________________________________________
> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *   PH H2 462, Station 3, CH-1015 Lausanne*
>
>
> _______________________________________________
> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum
>
>
> _______________________________________________
> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Giovani
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From kucukben at sissa.it  Sun Apr  3 02:49:37 2011
From: kucukben at sissa.it (Emine Kucukbenli)
Date: Sun, 03 Apr 2011 02:49:37 +0200
Subject: [Pw_forum] shift of energy
In-Reply-To: <BANLkTimvccm1rGhPpZ2aq8YS+Qk6mhpp+g@mail.gmail.com>
References: <BANLkTimvccm1rGhPpZ2aq8YS+Qk6mhpp+g@mail.gmail.com>
Message-ID: <20110403024937.ot1t4n8e844oss84@webmail.sissa.it>

Dear P,
Is everything else the same in your input file (did you just change  
the unit cell size and number of atoms) ? in that case, you wont have  
a one to one comparison. or is your kpoint sampling equivalent ?  
expansion of wavefunctions/density (ecut parameters) etc ?
especially with not-tightly-converged values for these parameters you  
are bound to get some differences between these two calculations.
cheers,
emine kucukbenli, phd student, sissa, italy

Quoting pari shok <parishok at gmail.com>:

> Dear Paolo,
> DOS of 72-atom SiC shows a shift of energy with respect to 8-atom
> SiC.The bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is
> around 5-7 eV.
> Would you please help me to understand this shift.
> Thanks again.
> P Shok
> UMD
> On Apr 1, 2011, at 21:36 , pari shok wrote:
>
>> * The DOS of 72-atom SiC (supercell) shows a shift of energy.
> *
> a shift with respect to what?
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>



----------------------------------------------------------------
   SISSA Webmail https://webmail.sissa.it/
   Powered by Horde http://www.horde.org/



From eyvaz_isaev at yahoo.com  Sun Apr  3 10:59:17 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sun, 3 Apr 2011 01:59:17 -0700 (PDT)
Subject: [Pw_forum] shift of energy
In-Reply-To: <BANLkTimvccm1rGhPpZ2aq8YS+Qk6mhpp+g@mail.gmail.com>
References: <BANLkTimvccm1rGhPpZ2aq8YS+Qk6mhpp+g@mail.gmail.com>
Message-ID: <369458.61028.qm@web65713.mail.ac4.yahoo.com>

Hi, 

 
>The bandgap of 8-atoms is around 10-12 eV, 
>but that of 72-atom is around 5-7 eV.

This is unbelievable, as SiC is an indirect band gap semiconductor and 
the bandgap is around (2.5 - 3)eV depending on crystal modification 
(3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.). 
See http://www.matprop.ru/SiC_bandstr

So, check carefully your input/output files.

Bests,
Eyvaz.

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

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

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




________________________________
From: pari shok <parishok at gmail.com>
To: pw_forum at pwscf.org
Sent: Sun, April 3, 2011 1:34:51 AM
Subject: [Pw_forum] shift of energy


Dear Paolo,
DOS of 72-atom SiC shows a shift of energy with respect to 8-atom SiC.The 
bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around 5-7 eV.
Would you please help me to understand this shift.
 Thanks again.
P Shok
UMD
On Apr 1, 2011, at 21:36 , pari shok wrote:

> The DOS of 72-atom SiC (supercell) shows a shift of energy.

a shift with respect to what?
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222



      
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From vitruss at gmail.com  Sun Apr  3 13:41:28 2011
From: vitruss at gmail.com (Vit)
Date: Sun, 3 Apr 2011 18:41:28 +0700
Subject: [Pw_forum] 4.3 compile error.
Message-ID: <201104031841.28578.vitruss@gmail.com>

Dear QE users!
I'm having troubles compiling new release. I'm trying to use ACML where 
apllicable, but I'm getting the same error even with distro (debian 6.0.1) 
blas and lapack and internal fftw.
Could you please help me resolving this issue?

mpif90 -g -o turbo_lanczos.x \                                                                                   
                lr_variables.o lr_charg_resp.o bcast_lr_input.o lr_readin.o 
lr_alloc_init.o lr_calc_dens.o lr_dot.o lr_dealloc.o lr_ortho.o lr_read_wf.o 
lr_normalise.o lr_lanczos.o lr_apply_liouvillian.o lr_main.o lr_dv_setup.o 
lr_setup_dgc.o lr_solve_e.o lr_dvpsi_e.o lr_ch_psi_all.o lr_cgsolve_all.o 
lr_h_psiq.o lr_sm1_psi.o stop_lr.o lr_read_d0psi.o lr_restart.o 
lr_write_restart.o print_clock_lr.o sd0psi.o lr_set_boxes_density.o 
lr_init_nfo.o  ../../PH/libph.a ../../PW/libpw.a ../../Modules/libqemod.a 
../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a 
../../iotk/src/libiotk.a   -L/opt/acml4.4.0/gfortran64/lib -lacml -
L/opt/acml4.4.0/gfortran64/lib -lacml -L/opt/acml4.4.0/gfortran64/lib -lacml                                                                                    
lr_main.o: In function `lr_main':                                                                                
/opt/qe/4.3/TDDFPT/src/lr_main.f90:252: undefined reference to `lr_wri_'                                         
collect2: ld returned 1 exit status                                                                              
make[2]: *** [turbo_lanczos.x] Error 1                                                                           
make[2]: Leaving directory `/opt/qe/4.3/TDDFPT/src'                                                              
make[2]: Entering directory `/opt/qe/4.3/TDDFPT/tools'                                                           
test -n "" && ( cd ../.. ; make -w  || exit 1) || :                                                              
mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__ACML -D__MPI -
D__PARA -I../../include -I../../iotk/src -I../../Modules -I. -c 
tddfpt_calculate_spectrum.f90                                                           
mpif90 -g -o turbo_spectrum.x \                                                                                  
        tddfpt_calculate_spectrum.o ../../Modules/libqemod.a ../../PW/libpw.a 
../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a 
../../iotk/src/libiotk.a   -L/opt/acml4.4.0/gfortran64/lib -lacml -
L/opt/acml4.4.0/gfortran64/lib -lacml -L/opt/acml4.4.0/gfortran64/lib -lacml                                                              
( cd ../../bin ; ln -fs ../TDDFPT/tools/turbo_spectrum.x . )                                                     
if [ -d ../bin ] ; then  ( cd ../bin ; ln -fs ../tools/turbo_spectrum.x . ); 
fi                                  
make[2]: Leaving directory `/opt/qe/4.3/TDDFPT/tools'                                                            
make[1]: Leaving directory `/opt/qe/4.3/TDDFPT'       

With best regards,
Koroteev Victor.

From giannozz at democritos.it  Sun Apr  3 17:34:01 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 3 Apr 2011 17:34:01 +0200
Subject: [Pw_forum] 4.3 compile error.
In-Reply-To: <201104031841.28578.vitruss@gmail.com>
References: <201104031841.28578.vitruss@gmail.com>
Message-ID: <894C08A1-0F9A-498C-9AB2-F45E60337CF3@democritos.it>


On Apr 3, 2011, at 13:41 , Vit wrote:

> /opt/qe/4.3/TDDFPT/src/lr_main.f90:252: undefined reference to  
> `lr_wri_'

break line 252, it excees 132 characters (some compilers don't like it)

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





From giannozz at democritos.it  Sun Apr  3 17:37:10 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 3 Apr 2011 17:37:10 +0200
Subject: [Pw_forum] Fixing starting starting_ns_eigenvalue
In-Reply-To: <BANLkTindZ16oFM_Y_ucJMZTt6_Ch1ZqVPg@mail.gmail.com>
References: <AANLkTimjp8F_gvmEFYNJY7QQDuz9VLCqzQFtPMyHFWKo@mail.gmail.com>
	<A0F500C2-D04A-428A-A0C2-E126E9DEA5E3@sissa.it>
	<AANLkTin7=oHuaUkdkEgCN5wHopnGqfFxFP9WidEBduWR@mail.gmail.com>
	<4D925077.7060201@sissa.it>
	<BANLkTindZ16oFM_Y_ucJMZTt6_Ch1ZqVPg@mail.gmail.com>
Message-ID: <72F0DA5A-167A-453D-A69E-7E4259D4B911@democritos.it>


On Apr 3, 2011, at 2:19 , Giovani Faccin wrote:

> I tested both cases on the same setup (using the intel compiler),
> and the second one works out. Maybe it should be updated on cvs?

it should already be updated in v.4.3:
http://qe-forge.org/cgi-bin/cvstrac/q-e/chngview?cn=8601

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





From giannozz at democritos.it  Sun Apr  3 17:40:15 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 3 Apr 2011 17:40:15 +0200
Subject: [Pw_forum] problem with fftw3
In-Reply-To: <AANLkTi=nZOK9Kf9iChf9ZDifRynp0CMhDiU0kSW0MdwY@mail.gmail.com>
References: <AANLkTi=nZOK9Kf9iChf9ZDifRynp0CMhDiU0kSW0MdwY@mail.gmail.com>
Message-ID: <CFB11BC9-0632-41E4-9AB5-60E8D78DBB21@democritos.it>


On Apr 2, 2011, at 2:38 , j brandon keith wrote:

> Any ideas what is going on?...should i try to tell configure to use
> fftw2?...dunno...

maybe you should try to compile your own fftw3. If you have
a recent version of MKL, you can link the fftw3 interface
contained in it

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





From giannozz at democritos.it  Sun Apr  3 17:45:33 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 3 Apr 2011 17:45:33 +0200
Subject: [Pw_forum] charge density output format from pp.x
In-Reply-To: <54782.200.0.233.52.1301691705.squirrel@mail.cab.cnea.gov.ar>
References: <4CEBFF39.40505@fu-berlin.de>
	<1290592007.12941.6.camel@ulisse.cm.sissa.it>
	<54782.200.0.233.52.1301691705.squirrel@mail.cab.cnea.gov.ar>
Message-ID: <A9314ABA-E41D-482F-B549-D5852F6C8405@democritos.it>


On Apr 1, 2011, at 23:01 , jorge.gallardo at cab.cnea.gov.ar wrote:

> Is there a way to get the electron density as a function of spatial
> coordinates(say, rho(x,y,z) ) using Quantum Espresso?

you can extract the charge density (with pp.x) in a number of different
formats. For the relation between indices and positions in real space:
http://www.quantum-espresso.org/user_guide/node23.html

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





From giannozz at democritos.it  Sun Apr  3 18:33:58 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 3 Apr 2011 18:33:58 +0200
Subject: [Pw_forum] How to read two wave-functions in one program?
In-Reply-To: <AANLkTinWcQwpq-BOTBi+PyQ_EnDsJ0A=juceCkd=e7yQ@mail.gmail.com>
References: <AANLkTinWcQwpq-BOTBi+PyQ_EnDsJ0A=juceCkd=e7yQ@mail.gmail.com>
Message-ID: <B77CBE70-CE4C-442D-ADA7-F5604CD0619D@democritos.it>


On Apr 1, 2011, at 7:23 , xuhui luo wrote:
>
> Can you (or anyone) tell me the best way to save wavefunction
> psi(ik, iband, ispin) on a grid of real space


just use the real-space FFT grid: wavefunctions are Fourier
transformed all the time from real to reciprocal space.
Remember than wavefunctions in FFT format should be
multiplied by the Bloch factor exp(-i k*r).

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





From baroni at sissa.it  Mon Apr  4 08:43:50 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 4 Apr 2011 08:43:50 +0200
Subject: [Pw_forum] How to read two wave-functions in one program?
In-Reply-To: <B77CBE70-CE4C-442D-ADA7-F5604CD0619D@democritos.it>
References: <AANLkTinWcQwpq-BOTBi+PyQ_EnDsJ0A=juceCkd=e7yQ@mail.gmail.com>
	<B77CBE70-CE4C-442D-ADA7-F5604CD0619D@democritos.it>
Message-ID: <F15F272A-5011-467B-8C37-622F09C7BF66@sissa.it>


On Apr 3, 2011, at 6:33 PM, Paolo Giannozzi wrote:

> 
> On Apr 1, 2011, at 7:23 , xuhui luo wrote:
>> 
>> Can you (or anyone) tell me the best way to save wavefunction
>> psi(ik, iband, ispin) on a grid of real space
> 
> 
> just use the real-space FFT grid: wavefunctions are Fourier
> transformed all the time from real to reciprocal space.
> Remember than wavefunctions in FFT format should be
> multiplied by the Bloch factor exp(-i k*r).

shouldn't it rather be exp(+i k*r)? (for the few who would care ...)

SB


---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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



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From giannozz at democritos.it  Mon Apr  4 08:46:49 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 4 Apr 2011 08:46:49 +0200
Subject: [Pw_forum] How to read two wave-functions in one program?
In-Reply-To: <F15F272A-5011-467B-8C37-622F09C7BF66@sissa.it>
References: <AANLkTinWcQwpq-BOTBi+PyQ_EnDsJ0A=juceCkd=e7yQ@mail.gmail.com>
	<B77CBE70-CE4C-442D-ADA7-F5604CD0619D@democritos.it>
	<F15F272A-5011-467B-8C37-622F09C7BF66@sissa.it>
Message-ID: <8241C13E-D8DD-48A2-B7FB-861D6BC4F39C@democritos.it>


On Apr 4, 2011, at 8:43 , Stefano Baroni wrote:

> shouldn't it rather be exp(+i k*r)? (for the few who would care ...)


yes, sure

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





From sclauzer at sissa.it  Mon Apr  4 09:39:18 2011
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Mon, 4 Apr 2011 09:39:18 +0200
Subject: [Pw_forum] shift of energy
In-Reply-To: <369458.61028.qm@web65713.mail.ac4.yahoo.com>
References: <BANLkTimvccm1rGhPpZ2aq8YS+Qk6mhpp+g@mail.gmail.com>
	<369458.61028.qm@web65713.mail.ac4.yahoo.com>
Message-ID: <CB9B72E8-8C7E-4BBF-AEA8-084F76D058B0@sissa.it>

Yes, 

   I perfectly agree with Eyvaz! Moreover the experimental bandgap is underestimated within LDA or GGA, and for 4H-SiC you would get about 2.2-2.3 eV with LDA. 

   How do you measure the bandgap? Beware that in the fundamental cell the bandgap is not a direct one, but it might become such when you use a supercell (because of the refolding of the Brillouin zones).


HTH

GS

Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto:

> Hi, 
>  
> >The bandgap of 8-atoms is around 10-12 eV, 
> >but that of 72-atom is around 5-7 eV.
>  
> This is unbelievable, as SiC is an indirect band gap semiconductor and 
> the bandgap is around (2.5 - 3)eV depending on crystal modification 
> (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.). 
> See http://www.matprop.ru/SiC_bandstr
> 
> So, check carefully your input/output files.
> 
> Bests,
> Eyvaz.
> 
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev, 
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
> 
> 
> From: pari shok <parishok at gmail.com>
> To: pw_forum at pwscf.org
> Sent: Sun, April 3, 2011 1:34:51 AM
> Subject: [Pw_forum] shift of energy
> 
> Dear Paolo,
> DOS of 72-atom SiC shows a shift of energy with respect to 8-atom SiC.The bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around 5-7 eV.
> Would you please help me to understand this shift.
> 
> Thanks again.
> P Shok
> UMD
> On Apr 1, 2011, at 21:36 , pari shok wrote:
> 
> > The DOS of 72-atom SiC (supercell) shows a shift of energy.
> 
> a shift with respect to what?
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> 
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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

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From giuseppe.mattioli at mlib.ism.cnr.it  Mon Apr  4 11:46:48 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Mon, 4 Apr 2011 10:46:48 +0100
Subject: [Pw_forum] shift of energy
In-Reply-To: <CB9B72E8-8C7E-4BBF-AEA8-084F76D058B0@sissa.it>
References: <BANLkTimvccm1rGhPpZ2aq8YS+Qk6mhpp+g@mail.gmail.com>
	<369458.61028.qm@web65713.mail.ac4.yahoo.com>
	<CB9B72E8-8C7E-4BBF-AEA8-084F76D058B0@sissa.it>
Message-ID: <201104041146.48566.giuseppe.mattioli@mlib.ism.cnr.it>


Dear all
I suspect that a a little misunderstanding has been going on here...
I try to reformulate the question: in the case of a 8-atoms cell the valence 
band maximum (VBM) has been found around 10 eV and the conduction band 
minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift in the 
position of VBM and CBM when calculated in a 72-atoms supercell, but the band 
gap value is the same. Then, the answer to P Shok could be: plane wave 
pseudopotential calculations do not ensure an universal alignment of 
eigenvalues. You should use some "internal" reference, like the 1s eigenvalue 
of an He atom, in your cell; or trust that the two VBM values are aligned "de 
facto".
HTH

Giuseppe

On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote:
> Yes,
>
>    I perfectly agree with Eyvaz! Moreover the experimental bandgap is
> underestimated within LDA or GGA, and for 4H-SiC you would get about
> 2.2-2.3 eV with LDA.
>
>    How do you measure the bandgap? Beware that in the fundamental cell the
> bandgap is not a direct one, but it might become such when you use a
> supercell (because of the refolding of the Brillouin zones).
>
>
> HTH
>
> GS
>
> Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto:
> > Hi,
> >
> > >The bandgap of 8-atoms is around 10-12 eV,
> > >but that of 72-atom is around 5-7 eV.
> >
> > This is unbelievable, as SiC is an indirect band gap semiconductor and
> > the bandgap is around (2.5 - 3)eV depending on crystal modification
> > (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.).
> > See http://www.matprop.ru/SiC_bandstr
> >
> > So, check carefully your input/output files.
> >
> > Bests,
> > Eyvaz.
> >
> > -------------------------------------------------------------------
> > Prof. Eyvaz Isaev,
> > Department of Physics, Chemistry, and Biology (IFM), Linkoping
> > University, Sweden Theoretical Physics Department, Moscow State Institute
> > of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
> >
> >
> > From: pari shok <parishok at gmail.com>
> > To: pw_forum at pwscf.org
> > Sent: Sun, April 3, 2011 1:34:51 AM
> > Subject: [Pw_forum] shift of energy
> >
> > Dear Paolo,
> > DOS of 72-atom SiC shows a shift of energy with respect to 8-atom SiC.The
> > bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around 5-7
> > eV. Would you please help me to understand this shift.
> >
> > Thanks again.
> > P Shok
> > UMD
> >
> > On Apr 1, 2011, at 21:36 , pari shok wrote:
> > > The DOS of 72-atom SiC (supercell) shows a shift of energy.
> >
> > a shift with respect to what?
> > ---
> > Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> >
> > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> > Phone +39-0432-558216, fax +39-0432-558222
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>    PH H2 462, Station 3, CH-1015 Lausanne



-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? 
? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ?
? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ?
? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ?
? ?E-mail: <giuseppe.mattioli at ism.cnr.it>

From degironc at sissa.it  Mon Apr  4 12:24:12 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Mon, 04 Apr 2011 12:24:12 +0200
Subject: [Pw_forum] shift of energy
In-Reply-To: <201104041146.48566.giuseppe.mattioli@mlib.ism.cnr.it>
References: <BANLkTimvccm1rGhPpZ2aq8YS+Qk6mhpp+g@mail.gmail.com>	<369458.61028.qm@web65713.mail.ac4.yahoo.com>	<CB9B72E8-8C7E-4BBF-AEA8-084F76D058B0@sissa.it>
	<201104041146.48566.giuseppe.mattioli@mlib.ism.cnr.it>
Message-ID: <4D999C4C.1070500@sissa.it>

Dear  All,
     let me clarify a little point.
     The potential (hence the eigenvalues) of  any calculation in 
periodic boundary conditions, not just a plane-wave one , is defined up 
to  an additive constant... In a finite system a reeference can be fixed 
by requiring that the potential goes to zero at infinite distance but in 
a periodic system this cannot be defined as there is nothing like a 
point at infinite distance ...
    In most codes (and in pw.x) this arbitrary constant is fixed by 
setting the average electrostatic potential to zero. If the supercell is 
properly constructed, with the properly scaled dimensions, the same 
cutoff, equivalent k-points etc.. the two calculations should be 
equivalent and the eigenvalues should be exactly mapped, the average 
potential should be the same, the total energy should be an exact 
multiple of the one of the original cell.

If this does not happen one is NOT doing the supercell calculation properly.

So if when doing a supercell you do not get the scaled result check your 
system definition.

stefano


On 04/04/2011 11:46 AM, Giuseppe Mattioli wrote:
> Dear all
> I suspect that a a little misunderstanding has been going on here...
> I try to reformulate the question: in the case of a 8-atoms cell the valence
> band maximum (VBM) has been found around 10 eV and the conduction band
> minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift in the
> position of VBM and CBM when calculated in a 72-atoms supercell, but the band
> gap value is the same. Then, the answer to P Shok could be: plane wave
> pseudopotential calculations do not ensure an universal alignment of
> eigenvalues. You should use some "internal" reference, like the 1s eigenvalue
> of an He atom, in your cell; or trust that the two VBM values are aligned "de
> facto".
> HTH
>
> Giuseppe
>
> On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote:
>> Yes,
>>
>>     I perfectly agree with Eyvaz! Moreover the experimental bandgap is
>> underestimated within LDA or GGA, and for 4H-SiC you would get about
>> 2.2-2.3 eV with LDA.
>>
>>     How do you measure the bandgap? Beware that in the fundamental cell the
>> bandgap is not a direct one, but it might become such when you use a
>> supercell (because of the refolding of the Brillouin zones).
>>
>>
>> HTH
>>
>> GS
>>
>> Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto:
>>> Hi,
>>>
>>>> The bandgap of 8-atoms is around 10-12 eV,
>>>> but that of 72-atom is around 5-7 eV.
>>> This is unbelievable, as SiC is an indirect band gap semiconductor and
>>> the bandgap is around (2.5 - 3)eV depending on crystal modification
>>> (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.).
>>> See http://www.matprop.ru/SiC_bandstr
>>>
>>> So, check carefully your input/output files.
>>>
>>> Bests,
>>> Eyvaz.
>>>
>>> -------------------------------------------------------------------
>>> Prof. Eyvaz Isaev,
>>> Department of Physics, Chemistry, and Biology (IFM), Linkoping
>>> University, Sweden Theoretical Physics Department, Moscow State Institute
>>> of Steel&  Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>>>
>>>
>>> From: pari shok<parishok at gmail.com>
>>> To: pw_forum at pwscf.org
>>> Sent: Sun, April 3, 2011 1:34:51 AM
>>> Subject: [Pw_forum] shift of energy
>>>
>>> Dear Paolo,
>>> DOS of 72-atom SiC shows a shift of energy with respect to 8-atom SiC.The
>>> bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around 5-7
>>> eV. Would you please help me to understand this shift.
>>>
>>> Thanks again.
>>> P Shok
>>> UMD
>>>
>>> On Apr 1, 2011, at 21:36 , pari shok wrote:
>>>> The DOS of 72-atom SiC (supercell) shows a shift of energy.
>>> a shift with respect to what?
>>> ---
>>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>>>
>>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>>> Phone +39-0432-558216, fax +39-0432-558222
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>>     PH H2 462, Station 3, CH-1015 Lausanne
>
>


From m_pazoki at physics.sharif.edu  Mon Apr  4 14:36:56 2011
From: m_pazoki at physics.sharif.edu (meysam pazoki)
Date: Mon, 4 Apr 2011 17:06:56 +0430
Subject: [Pw_forum] Average.x
Message-ID: <BANLkTimp8uyRBz9KZB_VPy0HKHoLbSrBVQ@mail.gmail.com>

Dear pwscf users
Could any one help me about average.x input parameters?
I cant find anything about it in the help files of espresso.
Thanks in advance
Meysam PAzoki
SUT
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From sclauzer at sissa.it  Mon Apr  4 14:42:34 2011
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Mon, 4 Apr 2011 14:42:34 +0200
Subject: [Pw_forum] Average.x
In-Reply-To: <BANLkTimp8uyRBz9KZB_VPy0HKHoLbSrBVQ@mail.gmail.com>
References: <BANLkTimp8uyRBz9KZB_VPy0HKHoLbSrBVQ@mail.gmail.com>
Message-ID: <D19567E9-15E4-40AC-965A-327B8CCA26B5@sissa.it>


You should read the first few lines of the source file PP/average.f90, the input is explained there.

HTH


GS

Il giorno 04/apr/2011, alle ore 14.36, meysam pazoki ha scritto:

> Dear pwscf users
> Could any one help me about average.x input parameters?
> I cant find anything about it in the help files of espresso.
> Thanks in advance
> Meysam PAzoki
> SUT
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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

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From giannozz at democritos.it  Mon Apr  4 14:49:25 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 04 Apr 2011 14:49:25 +0200
Subject: [Pw_forum] Average.x
In-Reply-To: <BANLkTimp8uyRBz9KZB_VPy0HKHoLbSrBVQ@mail.gmail.com>
References: <BANLkTimp8uyRBz9KZB_VPy0HKHoLbSrBVQ@mail.gmail.com>
Message-ID: <1301921365.4421.3.camel@fe12lx.fisica.uniud.it>

On Mon, 2011-04-04 at 17:06 +0430, meysam pazoki wrote:

> Could any one help me about average.x input parameters?
> I cant find anything about it in the help files of espresso.
from the user's guide, PostProcessing section:
"All codes for which input documentation is not explicitly 
 mentioned have documentation in the header of the fortran
 sources"

P.
-- 
 Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222 


From Adriano.Mosca.Conte at roma2.infn.it  Mon Apr  4 15:27:08 2011
From: Adriano.Mosca.Conte at roma2.infn.it (Adriano Mosca Conte)
Date: Mon, 4 Apr 2011 15:27:08 +0200 (CEST)
Subject: [Pw_forum] Van der Waals
Message-ID: <59184.141.108.248.78.1301923628.squirrel@141.108.248.78>

I have two questions about the calculations with VdW forces
(input_dft       = 'vdW-DF'):
1- Is it possible to perform VdW calculations with any kind of functional?
Or is it mandatory to use revPBE?
2- I generated a VdW table on two different machines (sp6 of CINECA,
matrix of  CASPUR). I got different numbers in the files vdW_kernel_table
(sign
and order of magnitude are different in many cases). Could it depend on the
modules I loaded on matrix? Which are the libraries used to generate
the table?
Adriano


-- 
Universit? degli Studi Tor Vergata
via della Ricerca Scientifica 1
00133 Roma, Italia
Tel. +39 06 7259 4741
Fax  +39 06 2023507

From parishok at gmail.com  Mon Apr  4 16:32:53 2011
From: parishok at gmail.com (pari shok)
Date: Mon, 4 Apr 2011 10:32:53 -0400
Subject: [Pw_forum] Shift of Energy
Message-ID: <BANLkTi=EzJF-KgYL0Cf2Yxe45cWJte4y9g@mail.gmail.com>

Dear All,
Thank you very much for your help.
Please let me ask my final question w.r.t DOS shift of energy of SiC
supercell.
The total energy of the 8-atom cell of SiC is: -76.276 Ry, while that of
72-atom SiC is -694 Ry. Neglecting almost -7 Ry, the total energy is scaling
accordingly.
However, I still see the shift of energy in DOS diagram of two slabs (the
max and min of bandgap shifts, although the gap is almost 2.1 eV for both
4H-SiC slabs). I was wondering whether this shift of energy is inevitable or
it is as the result of my input file.
I kept k points (w.r.t. crystal), and cut off energy the same for both
structures. Should I scale the cut off energy as well. If positive, is there
any relation between scaling the cell and cut off energy.
As you know, I need to find a reference for my further calculations.
I really really appreciate your help.
Yours
P Shok

Dear  All,
     let me clarify a little point.
     The potential (hence the eigenvalues) of  any calculation in
periodic boundary conditions, not just a plane-wave one , is defined up
to  an additive constant... In a finite system a reeference can be fixed
by requiring that the potential goes to zero at infinite distance but in
a periodic system this cannot be defined as there is nothing like a
point at infinite distance ...
    In most codes (and in pw.x) this arbitrary constant is fixed by
setting the average electrostatic potential to zero. If the supercell is
properly constructed, with the properly scaled dimensions, the same
cutoff, equivalent k-points etc.. the two calculations should be
equivalent and the eigenvalues should be exactly mapped, the average
potential should be the same, the total energy should be an exact
multiple of the one of the original cell.

If this does not happen one is NOT doing the supercell calculation properly.

So if when doing a supercell you do not get the scaled result check your
system definition.

stefano


On 04/04/2011 11:46 AM, Giuseppe Mattioli wrote:
>* Dear all
*>* I suspect that a a little misunderstanding has been going on here...
*>* I try to reformulate the question: in the case of a 8-atoms cell the valence
*>* band maximum (VBM) has been found around 10 eV and the conduction band
*>* minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift in the
*>* position of VBM and CBM when calculated in a 72-atoms supercell,
but the band
*>* gap value is the same. Then, the answer to P Shok could be: plane wave
*>* pseudopotential calculations do not ensure an universal alignment of
*>* eigenvalues. You should use some "internal" reference, like the 1s
eigenvalue
*>* of an He atom, in your cell; or trust that the two VBM values are
aligned "de
*>* facto".
*>* HTH
*>*
*>* Giuseppe
*>*
*>* On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote:
*>>* Yes,
*>>*
*>>*     I perfectly agree with Eyvaz! Moreover the experimental bandgap is
*>>* underestimated within LDA or GGA, and for 4H-SiC you would get about
*>>* 2.2-2.3 eV with LDA.
*>>*
*>>*     How do you measure the bandgap? Beware that in the fundamental cell the
*>>* bandgap is not a direct one, but it might become such when you use a
*>>* supercell (because of the refolding of the Brillouin zones).
*>>*
*>>*
*>>* HTH
*>>*
*>>* GS
*>>*
*>>* Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto:
*>>>* Hi,
*>>>*
*>>>>* The bandgap of 8-atoms is around 10-12 eV,
*>>>>* but that of 72-atom is around 5-7 eV.
*>>>* This is unbelievable, as SiC is an indirect band gap semiconductor and
*>>>* the bandgap is around (2.5 - 3)eV depending on crystal modification
*>>>* (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.).
*>>>* See http://www.matprop.ru/SiC_bandstr
*>>>*
*>>>* So, check carefully your input/output files.
*>>>*
*>>>* Bests,
*>>>* Eyvaz.
*>>>*
*>>>* -------------------------------------------------------------------
*>>>* Prof. Eyvaz Isaev,
*>>>* Department of Physics, Chemistry, and Biology (IFM), Linkoping
*>>>* University, Sweden Theoretical Physics Department, Moscow State Institute
*>>>* of Steel&  Alloys, Russia, isaev at ifm.liu.se
<http://www.democritos.it/mailman/listinfo/pw_forum>, eyvaz_isaev at
yahoo.com <http://www.democritos.it/mailman/listinfo/pw_forum>
*>>>*
*>>>*
*>>>* From: pari shok<parishok at gmail.com
<http://www.democritos.it/mailman/listinfo/pw_forum>>
*>>>* To: pw_forum at pwscf.org
<http://www.democritos.it/mailman/listinfo/pw_forum>
*>>>* Sent: Sun, April 3, 2011 1:34:51 AM
*>>>* Subject: [Pw_forum] shift of energy
*>>>*
*>>>* Dear Paolo,
*>>>* DOS of 72-atom SiC shows a shift of energy with respect to 8-atom SiC.The
*>>>* bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around 5-7
*>>>* eV. Would you please help me to understand this shift.
*>>>*
*>>>* Thanks again.
*>>>* P Shok
*>>>* UMD
*>>>*
*>>>* On Apr 1, 2011, at 21:36 , pari shok wrote:
*>>>>* The DOS of 72-atom SiC (supercell) shows a shift of energy.
*>>>* a shift with respect to what?
*>>>* ---
*>>>* Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
*>>>*
*>>>* Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
*>>>* Phone +39-0432-558216, fax +39-0432-558222
*>>>*
*>>>* _______________________________________________
*>>>* Pw_forum mailing list
*>>>* Pw_forum at pwscf.org <http://www.democritos.it/mailman/listinfo/pw_forum>
*>>>* http://www.democritos.it/mailman/listinfo/pw_forum
*>>* ? Gabriele Sclauzero, EPFL SB ITP CSEA
*>>*     PH H2 462, Station 3, CH-1015 Lausanne
*>*
*>*
*
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From ttduyle at gmail.com  Mon Apr  4 17:04:51 2011
From: ttduyle at gmail.com (Duy Le)
Date: Mon, 4 Apr 2011 11:04:51 -0400
Subject: [Pw_forum] Shift of Energy
In-Reply-To: <BANLkTi=EzJF-KgYL0Cf2Yxe45cWJte4y9g@mail.gmail.com>
References: <BANLkTi=EzJF-KgYL0Cf2Yxe45cWJte4y9g@mail.gmail.com>
Message-ID: <BANLkTi=keZQ5tpRzvHs7t_d4x7V7Jrw7Qw@mail.gmail.com>

On Mon, Apr 4, 2011 at 10:32 AM, pari shok <parishok at gmail.com> wrote:
> Dear All,
> Thank you very much for your help.
> Please let me ask my final question w.r.t DOS shift of energy of SiC
> supercell.
> The total energy of the 8-atom cell of SiC is: -76.276 Ry, while that of
> 72-atom SiC is -694 Ry. Neglecting almost -7 Ry, the total energy is scaling
> accordingly.
If you are doing correctly, the results must be identical. So make
sure to check the structures, and the convergence of total energy vs.
cutoff energy and k-point sampling.
> However, I still see the shift of energy in DOS diagram of two slabs (the
> max and min of bandgap shifts, although the gap is almost 2.1 eV for both
> 4H-SiC slabs). I was wondering whether this shift of energy is inevitable or
> it is as the result of my input file.
Slab? I though you are performing bulk calculation. Anyway, the shift
of energies' levels is normal. You should set the reference as center
of the gap (set it to be zero) then compare the DOS or band
structures.
By the way, if your bigger slab experiences the reconstruction, the
two slabs (8 atoms and 72 atoms) won't be identical => you should not
get the same results in this case. But 7Ry seems to be huge.
> I kept k points (w.r.t. crystal), and cut off energy the same for both
> structures. Should I scale the cut off energy as well. If positive, is there
Okie, but you should scale the k-point sampling accordingly because
the BZ of 72 atoms cell is smaller. But this won't harm the results if
total energy is already converged vs. k-point sampling.
> any relation between scaling the cell and cut off energy.
No. Cut off energy depends on only pseudo potential.
> As you know, I need to find a reference for my further calculations.
> I really really appreciate your help.
> Yours
> P Shok
>

--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"
> Dear  All,
>      let me clarify a little point.
>      The potential (hence the eigenvalues) of  any calculation in
> periodic boundary conditions, not just a plane-wave one , is defined up
>
> to  an additive constant... In a finite system a reeference can be fixed
> by requiring that the potential goes to zero at infinite distance but in
> a periodic system this cannot be defined as there is nothing like a
>
> point at infinite distance ...
>     In most codes (and in pw.x) this arbitrary constant is fixed by
> setting the average electrostatic potential to zero. If the supercell is
> properly constructed, with the properly scaled dimensions, the same
>
> cutoff, equivalent k-points etc.. the two calculations should be
> equivalent and the eigenvalues should be exactly mapped, the average
> potential should be the same, the total energy should be an exact
> multiple of the one of the original cell.
>
>
> If this does not happen one is NOT doing the supercell calculation properly.
>
> So if when doing a supercell you do not get the scaled result check your
> system definition.
>
> stefano
>
>
> On 04/04/2011 11:46 AM, Giuseppe Mattioli wrote:
>
>> Dear all
>> I suspect that a a little misunderstanding has been going on here...
>> I try to reformulate the question: in the case of a 8-atoms cell the
>> valence
>> band maximum (VBM) has been found around 10 eV and the conduction band
>
>> minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift in
>> the
>> position of VBM and CBM when calculated in a 72-atoms supercell, but the
>> band
>> gap value is the same. Then, the answer to P Shok could be: plane wave
>
>> pseudopotential calculations do not ensure an universal alignment of
>> eigenvalues. You should use some "internal" reference, like the 1s
>> eigenvalue
>> of an He atom, in your cell; or trust that the two VBM values are aligned
>> "de
>
>> facto".
>> HTH
>>
>> Giuseppe
>>
>> On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote:
>>> Yes,
>>>
>>>     I perfectly agree with Eyvaz! Moreover the experimental bandgap is
>
>>> underestimated within LDA or GGA, and for 4H-SiC you would get about
>>> 2.2-2.3 eV with LDA.
>>>
>>>     How do you measure the bandgap? Beware that in the fundamental cell
>>> the
>
>>> bandgap is not a direct one, but it might become such when you use a
>>> supercell (because of the refolding of the Brillouin zones).
>>>
>>>
>>> HTH
>
>>>
>>> GS
>>>
>>> Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto:
>>>> Hi,
>>>>
>>>>> The bandgap of 8-atoms is around 10-12 eV,
>
>>>>> but that of 72-atom is around 5-7 eV.
>>>> This is unbelievable, as SiC is an indirect band gap semiconductor and
>>>> the bandgap is around (2.5 - 3)eV depending on crystal modification
>
>>>> (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.).
>>>> See http://www.matprop.ru/SiC_bandstr
>>>>
>>>> So, check carefully your input/output files.
>
>>>>
>>>> Bests,
>>>> Eyvaz.
>>>>
>>>> -------------------------------------------------------------------
>>>> Prof. Eyvaz Isaev,
>
>>>> Department of Physics, Chemistry, and Biology (IFM), Linkoping
>>>> University, Sweden Theoretical Physics Department, Moscow State
>>>> Institute
>>>> of Steel&  Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>>>>
>>>>
>>>> From: pari shok<parishok at gmail.com>
>>>> To: pw_forum at pwscf.org
>
>>>> Sent: Sun, April 3, 2011 1:34:51 AM
>>>> Subject: [Pw_forum] shift of energy
>>>>
>>>> Dear Paolo,
>>>> DOS of 72-atom SiC shows a shift of energy with respect to 8-atom
>>>> SiC.The
>
>>>> bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around 5-7
>>>> eV. Would you please help me to understand this shift.
>>>>
>>>> Thanks again.
>
>>>> P Shok
>>>> UMD
>>>>
>>>> On Apr 1, 2011, at 21:36 , pari shok wrote:
>>>>> The DOS of 72-atom SiC (supercell) shows a shift of energy.
>
>>>> a shift with respect to what?
>>>> ---
>>>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>>>>
>>>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>
>>>> Phone +39-0432-558216, fax +39-0432-558222
>>>>
>>>> _______________________________________________
>>>> Pw_forum mailing list
>>>> Pw_forum at pwscf.org
>
>>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>>>     PH H2 462, Station 3, CH-1015 Lausanne
>
>>
>>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

From flux_ray12 at 163.com  Mon Apr  4 18:14:21 2011
From: flux_ray12 at 163.com (=?GBK?B?0KFT?=)
Date: Tue, 5 Apr 2011 00:14:21 +0800 (CST)
Subject: [Pw_forum] 4.3 compile error.
In-Reply-To: <201104031841.28578.vitruss@gmail.com>
References: <201104031841.28578.vitruss@gmail.com>
Message-ID: <174f5d1.7e22.12f214b1d61.Coremail.flux_ray12@163.com>

Hi, Vit.
I got the same problem like you.

You can open the file TDDFPT/src/lr_main.f90 and find the line 252. It should be written as:
IF ( lr_io_level > 0 .and. (mod(LR_iteration,restart_step)==0 .OR. LR_iteration==itermax .OR. LR_iteration==1) ) CALL lr_write_restart()
Then, you can add a '&' after '==1) )' and put 'CALL lr_write_restart()' to the next line.
Do not forget add enough space before 'CALL lr_write_restart()', otherwise it would become annotate instead of code.
The modified one could like:
IF ( lr_io_level > 0 .and. (mod(LR_iteration,restart_step)==0 .OR. LR_iteration==itermax .OR. LR_iteration==1) )  &
           CALL lr_write_restart()


At 2011-04-03 19:41:28?Vit <vitruss at gmail.com> wrote:

>Dear QE users!
>I'm having troubles compiling new release. I'm trying to use ACML where 
>apllicable, but I'm getting the same error even with distro (debian 6.0.1) 
>blas and lapack and internal fftw.
>Could you please help me resolving this issue?
>
>mpif90 -g -o turbo_lanczos.x \                                                                                   
>                lr_variables.o lr_charg_resp.o bcast_lr_input.o lr_readin.o 
>lr_alloc_init.o lr_calc_dens.o lr_dot.o lr_dealloc.o lr_ortho.o lr_read_wf.o 
>lr_normalise.o lr_lanczos.o lr_apply_liouvillian.o lr_main.o lr_dv_setup.o 
>lr_setup_dgc.o lr_solve_e.o lr_dvpsi_e.o lr_ch_psi_all.o lr_cgsolve_all.o 
>lr_h_psiq.o lr_sm1_psi.o stop_lr.o lr_read_d0psi.o lr_restart.o 
>lr_write_restart.o print_clock_lr.o sd0psi.o lr_set_boxes_density.o 
>lr_init_nfo.o  ../../PH/libph.a ../../PW/libpw.a ../../Modules/libqemod.a 
>../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a 
>../../iotk/src/libiotk.a   -L/opt/acml4.4.0/gfortran64/lib -lacml -
>L/opt/acml4.4.0/gfortran64/lib -lacml -L/opt/acml4.4.0/gfortran64/lib -lacml                                                                                    
>lr_main.o: In function `lr_main':                                                                                
>/opt/qe/4.3/TDDFPT/src/lr_main.f90:252: undefined reference to `lr_wri_'                                         
>collect2: ld returned 1 exit status                                                                              
>make[2]: *** [turbo_lanczos.x] Error 1                                                                           
>make[2]: Leaving directory `/opt/qe/4.3/TDDFPT/src'                                                              
>make[2]: Entering directory `/opt/qe/4.3/TDDFPT/tools'                                                           
>test -n "" && ( cd ../.. ; make -w  || exit 1) || :                                                              
>mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__ACML -D__MPI -
>D__PARA -I../../include -I../../iotk/src -I../../Modules -I. -c 
>tddfpt_calculate_spectrum.f90                                                           
>mpif90 -g -o turbo_spectrum.x \                                                                                  
>        tddfpt_calculate_spectrum.o ../../Modules/libqemod.a ../../PW/libpw.a 
>../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a 
>../../iotk/src/libiotk.a   -L/opt/acml4.4.0/gfortran64/lib -lacml -
>L/opt/acml4.4.0/gfortran64/lib -lacml -L/opt/acml4.4.0/gfortran64/lib -lacml                                                              
>( cd ../../bin ; ln -fs ../TDDFPT/tools/turbo_spectrum.x . )                                                     
>if [ -d ../bin ] ; then  ( cd ../bin ; ln -fs ../tools/turbo_spectrum.x . ); 
>fi                                  
>make[2]: Leaving directory `/opt/qe/4.3/TDDFPT/tools'                                                            
>make[1]: Leaving directory `/opt/qe/4.3/TDDFPT'       
>
>With best regards,
>Koroteev Victor.
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
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From degironc at sissa.it  Mon Apr  4 18:37:07 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Mon, 04 Apr 2011 18:37:07 +0200
Subject: [Pw_forum] Shift of Energy
In-Reply-To: <BANLkTi=EzJF-KgYL0Cf2Yxe45cWJte4y9g@mail.gmail.com>
References: <BANLkTi=EzJF-KgYL0Cf2Yxe45cWJte4y9g@mail.gmail.com>
Message-ID: <4D99F3B3.5090701@sissa.it>

Dear Pari Shok,

  a 7 Ry difference is A LOT ! you are not doing things properly.
  Then any further analysis is irrelevant

   cheers,

    stefano

On 04/04/2011 04:32 PM, pari shok wrote:
> Dear All,
> Thank you very much for your help.
> Please let me ask my final question w.r.t DOS shift of energy of SiC
> supercell.
> The total energy of the 8-atom cell of SiC is: -76.276 Ry, while that of
> 72-atom SiC is -694 Ry. Neglecting almost -7 Ry, the total energy is scaling
> accordingly.
> However, I still see the shift of energy in DOS diagram of two slabs (the
> max and min of bandgap shifts, although the gap is almost 2.1 eV for both
> 4H-SiC slabs). I was wondering whether this shift of energy is inevitable or
> it is as the result of my input file.
> I kept k points (w.r.t. crystal), and cut off energy the same for both
> structures. Should I scale the cut off energy as well. If positive, is there
> any relation between scaling the cell and cut off energy.
> As you know, I need to find a reference for my further calculations.
> I really really appreciate your help.
> Yours
> P Shok
>
> Dear  All,
>       let me clarify a little point.
>       The potential (hence the eigenvalues) of  any calculation in
> periodic boundary conditions, not just a plane-wave one , is defined up
> to  an additive constant... In a finite system a reeference can be fixed
> by requiring that the potential goes to zero at infinite distance but in
> a periodic system this cannot be defined as there is nothing like a
> point at infinite distance ...
>      In most codes (and in pw.x) this arbitrary constant is fixed by
> setting the average electrostatic potential to zero. If the supercell is
> properly constructed, with the properly scaled dimensions, the same
> cutoff, equivalent k-points etc.. the two calculations should be
> equivalent and the eigenvalues should be exactly mapped, the average
> potential should be the same, the total energy should be an exact
> multiple of the one of the original cell.
>
> If this does not happen one is NOT doing the supercell calculation properly.
>
> So if when doing a supercell you do not get the scaled result check your
> system definition.
>
> stefano
>
>
> On 04/04/2011 11:46 AM, Giuseppe Mattioli wrote:
>> * Dear all
> *>* I suspect that a a little misunderstanding has been going on here...
> *>* I try to reformulate the question: in the case of a 8-atoms cell the valence
> *>* band maximum (VBM) has been found around 10 eV and the conduction band
> *>* minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift in the
> *>* position of VBM and CBM when calculated in a 72-atoms supercell,
> but the band
> *>* gap value is the same. Then, the answer to P Shok could be: plane wave
> *>* pseudopotential calculations do not ensure an universal alignment of
> *>* eigenvalues. You should use some "internal" reference, like the 1s
> eigenvalue
> *>* of an He atom, in your cell; or trust that the two VBM values are
> aligned "de
> *>* facto".
> *>* HTH
> *>*
> *>* Giuseppe
> *>*
> *>* On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote:
> *>>* Yes,
> *>>*
> *>>*     I perfectly agree with Eyvaz! Moreover the experimental bandgap is
> *>>* underestimated within LDA or GGA, and for 4H-SiC you would get about
> *>>* 2.2-2.3 eV with LDA.
> *>>*
> *>>*     How do you measure the bandgap? Beware that in the fundamental cell the
> *>>* bandgap is not a direct one, but it might become such when you use a
> *>>* supercell (because of the refolding of the Brillouin zones).
> *>>*
> *>>*
> *>>* HTH
> *>>*
> *>>* GS
> *>>*
> *>>* Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto:
> *>>>* Hi,
> *>>>*
> *>>>>* The bandgap of 8-atoms is around 10-12 eV,
> *>>>>* but that of 72-atom is around 5-7 eV.
> *>>>* This is unbelievable, as SiC is an indirect band gap semiconductor and
> *>>>* the bandgap is around (2.5 - 3)eV depending on crystal modification
> *>>>* (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.).
> *>>>* See http://www.matprop.ru/SiC_bandstr
> *>>>*
> *>>>* So, check carefully your input/output files.
> *>>>*
> *>>>* Bests,
> *>>>* Eyvaz.
> *>>>*
> *>>>* -------------------------------------------------------------------
> *>>>* Prof. Eyvaz Isaev,
> *>>>* Department of Physics, Chemistry, and Biology (IFM), Linkoping
> *>>>* University, Sweden Theoretical Physics Department, Moscow State Institute
> *>>>* of Steel&   Alloys, Russia, isaev at ifm.liu.se
> <http://www.democritos.it/mailman/listinfo/pw_forum>, eyvaz_isaev at
> yahoo.com<http://www.democritos.it/mailman/listinfo/pw_forum>
> *>>>*
> *>>>*
> *>>>* From: pari shok<parishok at gmail.com
> <http://www.democritos.it/mailman/listinfo/pw_forum>>
> *>>>* To: pw_forum at pwscf.org
> <http://www.democritos.it/mailman/listinfo/pw_forum>
> *>>>* Sent: Sun, April 3, 2011 1:34:51 AM
> *>>>* Subject: [Pw_forum] shift of energy
> *>>>*
> *>>>* Dear Paolo,
> *>>>* DOS of 72-atom SiC shows a shift of energy with respect to 8-atom SiC.The
> *>>>* bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around 5-7
> *>>>* eV. Would you please help me to understand this shift.
> *>>>*
> *>>>* Thanks again.
> *>>>* P Shok
> *>>>* UMD
> *>>>*
> *>>>* On Apr 1, 2011, at 21:36 , pari shok wrote:
> *>>>>* The DOS of 72-atom SiC (supercell) shows a shift of energy.
> *>>>* a shift with respect to what?
> *>>>* ---
> *>>>* Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> *>>>*
> *>>>* Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> *>>>* Phone +39-0432-558216, fax +39-0432-558222
> *>>>*
> *>>>* _______________________________________________
> *>>>* Pw_forum mailing list
> *>>>* Pw_forum at pwscf.org<http://www.democritos.it/mailman/listinfo/pw_forum>
> *>>>* http://www.democritos.it/mailman/listinfo/pw_forum
> *>>* ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *>>*     PH H2 462, Station 3, CH-1015 Lausanne
> *>*
> *>*
> *
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From eariel99 at gmail.com  Mon Apr  4 18:56:50 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Mon, 4 Apr 2011 13:56:50 -0300
Subject: [Pw_forum] Pw_forum] Shift of Energy
Message-ID: <BANLkTinZXt=L7LYsUuJndteDxC4-MtQQAA@mail.gmail.com>

Hi Pari,

I think you should read this book.

Density functional theory: a practical introduction  David S. Sholl,Janice
A. Steckel

http://books.google.com/books?id=Q8iNmtswLWYC&printsec=frontcover&dq=Janice+Steckel++Sholl&source=bl&ots=BBHL-SfWoi&sig=HLO4FmyafC7bKh22C0Qf1353Lug&hl=es&ei=KfaZTaajFImatwfQ95iVDA&sa=X&oi=book_result&ct=result&resnum=1&ved=0CBcQ6AEwAA#v=onepage&q&f=false

72/8
9.00000000000000000000
694/9
77.11111111111111111111
694/9-76.276
.83511111111111111111
So, where does the 7 Ry difference arise?

Best regards

Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez


>
>
> ---------- Mensaje reenviado ----------
> From: pari shok <parishok at gmail.com>
> To: pw_forum at pwscf.org
> Date: Mon, 4 Apr 2011 10:32:53 -0400
> Subject: [Pw_forum] Shift of Energy
> Dear All,
> Thank you very much for your help.
> Please let me ask my final question w.r.t DOS shift of energy of SiC
> supercell.
> The total energy of the 8-atom cell of SiC is: -76.276 Ry, while that of
> 72-atom SiC is -694 Ry. Neglecting almost -7 Ry, the total energy is scaling
> accordingly.
> However, I still see the shift of energy in DOS diagram of two slabs (the
> max and min of bandgap shifts, although the gap is almost 2.1 eV for both
> 4H-SiC slabs). I was wondering whether this shift of energy is inevitable or
> it is as the result of my input file.
> I kept k points (w.r.t. crystal), and cut off energy the same for both
> structures. Should I scale the cut off energy as well. If positive, is there
> any relation between scaling the cell and cut off energy.
> As you know, I need to find a reference for my further calculations.
> I really really appreciate your help.
> Yours
> P Shok
>
>
> --
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From giannozz at democritos.it  Mon Apr  4 19:08:54 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 04 Apr 2011 19:08:54 +0200
Subject: [Pw_forum] Pw_forum] Shift of Energy
In-Reply-To: <BANLkTinZXt=L7LYsUuJndteDxC4-MtQQAA@mail.gmail.com>
References: <BANLkTinZXt=L7LYsUuJndteDxC4-MtQQAA@mail.gmail.com>
Message-ID: <1301936934.2938.13.camel@fe12lx.fisica.uniud.it>

On Mon, 2011-04-04 at 13:56 -0300, Eduardo Ariel Menendez Proupin wrote:

> Density functional theory: a practical introduction
>   David S. Sholl,Janice A. Steckel

interesting reference!

> 72/8
> 9.00000000000000000000
> 694/9
> 77.11111111111111111111
> 694/9-76.276
> .83511111111111111111
> So, where does the 7 Ry difference arise?

694-76.276*9=7.516 :-)

P.

-- 
 Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222 


From bahaartv at gmail.com  Mon Apr  4 20:13:34 2011
From: bahaartv at gmail.com (bahaareh tavakoli nejad)
Date: Mon, 4 Apr 2011 11:13:34 -0700
Subject: [Pw_forum] Teter ''extended norm-conserving'' pseudopotential
Message-ID: <BANLkTikMm-=Y+DetV80dQmaj4-nhqxSzgg@mail.gmail.com>

On Mon, Apr 4, 2011 at 9:29 AM, <pw_forum-request at pwscf.org> wrote:

> Send Pw_forum mailing list submissions to
>        pw_forum at pwscf.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://www.democritos.it/mailman/listinfo/pw_forum
> or, via email, send a message with subject or body 'help' to
>        pw_forum-request at pwscf.org
>
> You can reach the person managing the list at
>        pw_forum-owner at pwscf.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
>   1. Van der Waals (Adriano Mosca Conte)
>   2. Shift of Energy (pari shok)
>   3. Re: Shift of Energy (Duy Le)
>   4. Re: 4.3 compile error. (?S)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 4 Apr 2011 15:27:08 +0200 (CEST)
> From: "Adriano Mosca Conte" <Adriano.Mosca.Conte at roma2.infn.it>
> Subject: [Pw_forum] Van der Waals
> To: Pw_forum at pwscf.org
> Message-ID: <59184.141.108.248.78.1301923628.squirrel at 141.108.248.78>
> Content-Type: text/plain;charset=iso-8859-1
>
> I have two questions about the calculations with VdW forces
> (input_dft       = 'vdW-DF'):
> 1- Is it possible to perform VdW calculations with any kind of functional?
> Or is it mandatory to use revPBE?
> 2- I generated a VdW table on two different machines (sp6 of CINECA,
> matrix of  CASPUR). I got different numbers in the files vdW_kernel_table
> (sign
> and order of magnitude are different in many cases). Could it depend on the
> modules I loaded on matrix? Which are the libraries used to generate
> the table?
> Adriano
>
>
> --
> Universit? degli Studi Tor Vergata
> via della Ricerca Scientifica 1
> 00133 Roma, Italia
> Tel. +39 06 7259 4741
> Fax  +39 06 2023507
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 4 Apr 2011 10:32:53 -0400
> From: pari shok <parishok at gmail.com>
> Subject: [Pw_forum] Shift of Energy
> To: pw_forum at pwscf.org
> Message-ID: <BANLkTi=EzJF-KgYL0Cf2Yxe45cWJte4y9g at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear All,
> Thank you very much for your help.
> Please let me ask my final question w.r.t DOS shift of energy of SiC
> supercell.
> The total energy of the 8-atom cell of SiC is: -76.276 Ry, while that of
> 72-atom SiC is -694 Ry. Neglecting almost -7 Ry, the total energy is
> scaling
> accordingly.
> However, I still see the shift of energy in DOS diagram of two slabs (the
> max and min of bandgap shifts, although the gap is almost 2.1 eV for both
> 4H-SiC slabs). I was wondering whether this shift of energy is inevitable
> or
> it is as the result of my input file.
> I kept k points (w.r.t. crystal), and cut off energy the same for both
> structures. Should I scale the cut off energy as well. If positive, is
> there
> any relation between scaling the cell and cut off energy.
> As you know, I need to find a reference for my further calculations.
> I really really appreciate your help.
> Yours
> P Shok
>
> Dear  All,
>     let me clarify a little point.
>     The potential (hence the eigenvalues) of  any calculation in
> periodic boundary conditions, not just a plane-wave one , is defined up
> to  an additive constant... In a finite system a reeference can be fixed
> by requiring that the potential goes to zero at infinite distance but in
> a periodic system this cannot be defined as there is nothing like a
> point at infinite distance ...
>    In most codes (and in pw.x) this arbitrary constant is fixed by
> setting the average electrostatic potential to zero. If the supercell is
> properly constructed, with the properly scaled dimensions, the same
> cutoff, equivalent k-points etc.. the two calculations should be
> equivalent and the eigenvalues should be exactly mapped, the average
> potential should be the same, the total energy should be an exact
> multiple of the one of the original cell.
>
> If this does not happen one is NOT doing the supercell calculation
> properly.
>
> So if when doing a supercell you do not get the scaled result check your
> system definition.
>
> stefano
>
>
> On 04/04/2011 11:46 AM, Giuseppe Mattioli wrote:
> >* Dear all
> *>* I suspect that a a little misunderstanding has been going on here...
> *>* I try to reformulate the question: in the case of a 8-atoms cell the
> valence
> *>* band maximum (VBM) has been found around 10 eV and the conduction band
> *>* minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift in
> the
> *>* position of VBM and CBM when calculated in a 72-atoms supercell,
> but the band
> *>* gap value is the same. Then, the answer to P Shok could be: plane wave
> *>* pseudopotential calculations do not ensure an universal alignment of
> *>* eigenvalues. You should use some "internal" reference, like the 1s
> eigenvalue
> *>* of an He atom, in your cell; or trust that the two VBM values are
> aligned "de
> *>* facto".
> *>* HTH
> *>*
> *>* Giuseppe
> *>*
> *>* On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote:
> *>>* Yes,
> *>>*
> *>>*     I perfectly agree with Eyvaz! Moreover the experimental bandgap is
> *>>* underestimated within LDA or GGA, and for 4H-SiC you would get about
> *>>* 2.2-2.3 eV with LDA.
> *>>*
> *>>*     How do you measure the bandgap? Beware that in the fundamental
> cell the
> *>>* bandgap is not a direct one, but it might become such when you use a
> *>>* supercell (because of the refolding of the Brillouin zones).
> *>>*
> *>>*
> *>>* HTH
> *>>*
> *>>* GS
> *>>*
> *>>* Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto:
> *>>>* Hi,
> *>>>*
> *>>>>* The bandgap of 8-atoms is around 10-12 eV,
> *>>>>* but that of 72-atom is around 5-7 eV.
> *>>>* This is unbelievable, as SiC is an indirect band gap semiconductor
> and
> *>>>* the bandgap is around (2.5 - 3)eV depending on crystal modification
> *>>>* (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.).
> *>>>* See http://www.matprop.ru/SiC_bandstr
> *>>>*
> *>>>* So, check carefully your input/output files.
> *>>>*
> *>>>* Bests,
> *>>>* Eyvaz.
> *>>>*
> *>>>* -------------------------------------------------------------------
> *>>>* Prof. Eyvaz Isaev,
> *>>>* Department of Physics, Chemistry, and Biology (IFM), Linkoping
> *>>>* University, Sweden Theoretical Physics Department, Moscow State
> Institute
> *>>>* of Steel&  Alloys, Russia, isaev at ifm.liu.se
> <http://www.democritos.it/mailman/listinfo/pw_forum>, eyvaz_isaev at
> yahoo.com <http://www.democritos.it/mailman/listinfo/pw_forum>
> *>>>*
> *>>>*
> *>>>* From: pari shok<parishok at gmail.com
> <http://www.democritos.it/mailman/listinfo/pw_forum>>
> *>>>* To: pw_forum at pwscf.org
> <http://www.democritos.it/mailman/listinfo/pw_forum>
> *>>>* Sent: Sun, April 3, 2011 1:34:51 AM
> *>>>* Subject: [Pw_forum] shift of energy
> *>>>*
> *>>>* Dear Paolo,
> *>>>* DOS of 72-atom SiC shows a shift of energy with respect to 8-atom
> SiC.The
> *>>>* bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around
> 5-7
> *>>>* eV. Would you please help me to understand this shift.
> *>>>*
> *>>>* Thanks again.
> *>>>* P Shok
> *>>>* UMD
> *>>>*
> *>>>* On Apr 1, 2011, at 21:36 , pari shok wrote:
> *>>>>* The DOS of 72-atom SiC (supercell) shows a shift of energy.
> *>>>* a shift with respect to what?
> *>>>* ---
> *>>>* Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> *>>>*
> *>>>* Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> *>>>* Phone +39-0432-558216, fax +39-0432-558222
> *>>>*
> *>>>* _______________________________________________
> *>>>* Pw_forum mailing list
> *>>>* Pw_forum at pwscf.org <
> http://www.democritos.it/mailman/listinfo/pw_forum>
> *>>>* http://www.democritos.it/mailman/listinfo/pw_forum
> *>>* ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *>>*     PH H2 462, Station 3, CH-1015 Lausanne
> *>*
> *>*
> *
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>
> ------------------------------
>
> Message: 3
> Date: Mon, 4 Apr 2011 11:04:51 -0400
> From: Duy Le <ttduyle at gmail.com>
> Subject: Re: [Pw_forum] Shift of Energy
> To: PWSCF Forum <pw_forum at pwscf.org>
> Cc: pari shok <parishok at gmail.com>
> Message-ID: <BANLkTi=keZQ5tpRzvHs7t_d4x7V7Jrw7Qw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Mon, Apr 4, 2011 at 10:32 AM, pari shok <parishok at gmail.com> wrote:
> > Dear All,
> > Thank you very much for your help.
> > Please let me ask my final question w.r.t DOS shift of energy of SiC
> > supercell.
> > The total energy of the 8-atom cell of SiC is: -76.276 Ry, while that of
> > 72-atom SiC is -694 Ry. Neglecting almost -7 Ry, the total energy is
> scaling
> > accordingly.
> If you are doing correctly, the results must be identical. So make
> sure to check the structures, and the convergence of total energy vs.
> cutoff energy and k-point sampling.
> > However, I still see the shift of energy in DOS diagram of two slabs (the
> > max and min of bandgap shifts, although the gap is almost 2.1 eV for both
> > 4H-SiC slabs). I was wondering whether this shift of energy is inevitable
> or
> > it is as the result of my input file.
> Slab? I though you are performing bulk calculation. Anyway, the shift
> of energies' levels is normal. You should set the reference as center
> of the gap (set it to be zero) then compare the DOS or band
> structures.
> By the way, if your bigger slab experiences the reconstruction, the
> two slabs (8 atoms and 72 atoms) won't be identical => you should not
> get the same results in this case. But 7Ry seems to be huge.
> > I kept k points (w.r.t. crystal), and cut off energy the same for both
> > structures. Should I scale the cut off energy as well. If positive, is
> there
> Okie, but you should scale the k-point sampling accordingly because
> the BZ of 72 atoms cell is smaller. But this won't harm the results if
> total energy is already converged vs. k-point sampling.
> > any relation between scaling the cell and cut off energy.
> No. Cut off energy depends on only pseudo potential.
> > As you know, I need to find a reference for my further calculations.
> > I really really appreciate your help.
> > Yours
> > P Shok
> >
>
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
> > Dear  All,
> >      let me clarify a little point.
> >      The potential (hence the eigenvalues) of  any calculation in
> > periodic boundary conditions, not just a plane-wave one , is defined up
> >
> > to  an additive constant... In a finite system a reeference can be fixed
> > by requiring that the potential goes to zero at infinite distance but in
> > a periodic system this cannot be defined as there is nothing like a
> >
> > point at infinite distance ...
> >     In most codes (and in pw.x) this arbitrary constant is fixed by
> > setting the average electrostatic potential to zero. If the supercell is
> > properly constructed, with the properly scaled dimensions, the same
> >
> > cutoff, equivalent k-points etc.. the two calculations should be
> > equivalent and the eigenvalues should be exactly mapped, the average
> > potential should be the same, the total energy should be an exact
> > multiple of the one of the original cell.
> >
> >
> > If this does not happen one is NOT doing the supercell calculation
> properly.
> >
> > So if when doing a supercell you do not get the scaled result check your
> > system definition.
> >
> > stefano
> >
> >
> > On 04/04/2011 11:46 AM, Giuseppe Mattioli wrote:
> >
> >> Dear all
> >> I suspect that a a little misunderstanding has been going on here...
> >> I try to reformulate the question: in the case of a 8-atoms cell the
> >> valence
> >> band maximum (VBM) has been found around 10 eV and the conduction band
> >
> >> minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift in
> >> the
> >> position of VBM and CBM when calculated in a 72-atoms supercell, but the
> >> band
> >> gap value is the same. Then, the answer to P Shok could be: plane wave
> >
> >> pseudopotential calculations do not ensure an universal alignment of
> >> eigenvalues. You should use some "internal" reference, like the 1s
> >> eigenvalue
> >> of an He atom, in your cell; or trust that the two VBM values are
> aligned
> >> "de
> >
> >> facto".
> >> HTH
> >>
> >> Giuseppe
> >>
> >> On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote:
> >>> Yes,
> >>>
> >>>     I perfectly agree with Eyvaz! Moreover the experimental bandgap is
> >
> >>> underestimated within LDA or GGA, and for 4H-SiC you would get about
> >>> 2.2-2.3 eV with LDA.
> >>>
> >>>     How do you measure the bandgap? Beware that in the fundamental cell
> >>> the
> >
> >>> bandgap is not a direct one, but it might become such when you use a
> >>> supercell (because of the refolding of the Brillouin zones).
> >>>
> >>>
> >>> HTH
> >
> >>>
> >>> GS
> >>>
> >>> Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto:
> >>>> Hi,
> >>>>
> >>>>> The bandgap of 8-atoms is around 10-12 eV,
> >
> >>>>> but that of 72-atom is around 5-7 eV.
> >>>> This is unbelievable, as SiC is an indirect band gap semiconductor and
> >>>> the bandgap is around (2.5 - 3)eV depending on crystal modification
> >
> >>>> (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.).
> >>>> See http://www.matprop.ru/SiC_bandstr
> >>>>
> >>>> So, check carefully your input/output files.
> >
> >>>>
> >>>> Bests,
> >>>> Eyvaz.
> >>>>
> >>>> -------------------------------------------------------------------
> >>>> Prof. Eyvaz Isaev,
> >
> >>>> Department of Physics, Chemistry, and Biology (IFM), Linkoping
> >>>> University, Sweden Theoretical Physics Department, Moscow State
> >>>> Institute
> >>>> of Steel&  Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at
> yahoo.com
> >
> >>>>
> >>>>
> >>>> From: pari shok<parishok at gmail.com>
> >>>> To: pw_forum at pwscf.org
> >
> >>>> Sent: Sun, April 3, 2011 1:34:51 AM
> >>>> Subject: [Pw_forum] shift of energy
> >>>>
> >>>> Dear Paolo,
> >>>> DOS of 72-atom SiC shows a shift of energy with respect to 8-atom
> >>>> SiC.The
> >
> >>>> bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around
> 5-7
> >>>> eV. Would you please help me to understand this shift.
> >>>>
> >>>> Thanks again.
> >
> >>>> P Shok
> >>>> UMD
> >>>>
> >>>> On Apr 1, 2011, at 21:36 , pari shok wrote:
> >>>>> The DOS of 72-atom SiC (supercell) shows a shift of energy.
> >
> >>>> a shift with respect to what?
> >>>> ---
> >>>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> >>>>
> >>>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> >
> >>>> Phone +39-0432-558216, fax +39-0432-558222
> >>>>
> >>>> _______________________________________________
> >>>> Pw_forum mailing list
> >>>> Pw_forum at pwscf.org
> >
> >>>> http://www.democritos.it/mailman/listinfo/pw_forum
> >>> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> >>>     PH H2 462, Station 3, CH-1015 Lausanne
> >
> >>
> >>
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 5 Apr 2011 00:14:21 +0800 (CST)
> From: ?S <flux_ray12 at 163.com>
> Subject: Re: [Pw_forum] 4.3 compile error.
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Message-ID: <174f5d1.7e22.12f214b1d61.Coremail.flux_ray12 at 163.com>
> Content-Type: text/plain; charset="gbk"
>
> Hi, Vit.
> I got the same problem like you.
>
> You can open the file TDDFPT/src/lr_main.f90 and find the line 252. It
> should be written as:
> IF ( lr_io_level > 0 .and. (mod(LR_iteration,restart_step)==0 .OR.
> LR_iteration==itermax .OR. LR_iteration==1) ) CALL lr_write_restart()
> Then, you can add a '&' after '==1) )' and put 'CALL lr_write_restart()' to
> the next line.
> Do not forget add enough space before 'CALL lr_write_restart()', otherwise
> it would become annotate instead of code.
> The modified one could like:
> IF ( lr_io_level > 0 .and. (mod(LR_iteration,restart_step)==0 .OR.
> LR_iteration==itermax .OR. LR_iteration==1) )  &
>           CALL lr_write_restart()
>
>
> At 2011-04-03 19:41:28?Vit <vitruss at gmail.com> wrote:
>
> >Dear QE users!
> >I'm having troubles compiling new release. I'm trying to use ACML where
> >apllicable, but I'm getting the same error even with distro (debian 6.0.1)
> >blas and lapack and internal fftw.
> >Could you please help me resolving this issue?
> >
> >mpif90 -g -o turbo_lanczos.x \
> >                lr_variables.o lr_charg_resp.o bcast_lr_input.o
> lr_readin.o
> >lr_alloc_init.o lr_calc_dens.o lr_dot.o lr_dealloc.o lr_ortho.o
> lr_read_wf.o
> >lr_normalise.o lr_lanczos.o lr_apply_liouvillian.o lr_main.o lr_dv_setup.o
> >lr_setup_dgc.o lr_solve_e.o lr_dvpsi_e.o lr_ch_psi_all.o lr_cgsolve_all.o
> >lr_h_psiq.o lr_sm1_psi.o stop_lr.o lr_read_d0psi.o lr_restart.o
> >lr_write_restart.o print_clock_lr.o sd0psi.o lr_set_boxes_density.o
> >lr_init_nfo.o  ../../PH/libph.a ../../PW/libpw.a ../../Modules/libqemod.a
> >../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a
> >../../iotk/src/libiotk.a   -L/opt/acml4.4.0/gfortran64/lib -lacml -
> >L/opt/acml4.4.0/gfortran64/lib -lacml -L/opt/acml4.4.0/gfortran64/lib
> -lacml
> >lr_main.o: In function `lr_main':
> >/opt/qe/4.3/TDDFPT/src/lr_main.f90:252: undefined reference to `lr_wri_'
> >collect2: ld returned 1 exit status
> >make[2]: *** [turbo_lanczos.x] Error 1
> >make[2]: Leaving directory `/opt/qe/4.3/TDDFPT/src'
> >make[2]: Entering directory `/opt/qe/4.3/TDDFPT/tools'
> >test -n "" && ( cd ../.. ; make -w  || exit 1) || :
> >mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__ACML -D__MPI -
> >D__PARA -I../../include -I../../iotk/src -I../../Modules -I. -c
> >tddfpt_calculate_spectrum.f90
> >mpif90 -g -o turbo_spectrum.x \
> >        tddfpt_calculate_spectrum.o ../../Modules/libqemod.a
> ../../PW/libpw.a
> >../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a
> >../../iotk/src/libiotk.a   -L/opt/acml4.4.0/gfortran64/lib -lacml -
> >L/opt/acml4.4.0/gfortran64/lib -lacml -L/opt/acml4.4.0/gfortran64/lib
> -lacml
> >( cd ../../bin ; ln -fs ../TDDFPT/tools/turbo_spectrum.x . )
> >if [ -d ../bin ] ; then  ( cd ../bin ; ln -fs ../tools/turbo_spectrum.x .
> );
> >fi
> >make[2]: Leaving directory `/opt/qe/4.3/TDDFPT/tools'
> >make[1]: Leaving directory `/opt/qe/4.3/TDDFPT'
> >
> >With best regards,
> >Koroteev Victor.
> >_______________________________________________
> >Pw_forum mailing list
> >Pw_forum at pwscf.org
> >http://www.democritos.it/mailman/listinfo/pw_forum
> -------------- nex t part --------------
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>
> ------------------------------
>
> ___xx____________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 46, Issue 10
> ****************************************
>
   Hi dear users
is there anyone who knows about Teter pseudopotential?Sr has 38 electrons
and valence electrons Should be 4s2 4p6 5s2 4d0 in ground state but in this
pseudopotetial Zion=10 and the valence electrons are 4s2 4p6 5s0 4d0!
what's the meaning of it? can i use it for ground state?
Ok! this pseudopotential is used in abinit but i coulden't ask my question
of them yet.
thank's alot.
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From bahaartv at gmail.com  Mon Apr  4 20:48:02 2011
From: bahaartv at gmail.com (bahaareh tavakoli nejad)
Date: Mon, 4 Apr 2011 11:48:02 -0700
Subject: [Pw_forum] Teter''extended norm conserving'' pseudotential
Message-ID: <BANLkTin5qZEB4=8XTgFTFGipTp9ZW9LUOg@mail.gmail.com>

On Mon, Apr 4, 2011 at 9:29 AM, <pw_forum-request at pwscf.org> wrote:

> Send Pw_forum mailing list submissions to
>        pw_forum at pwscf.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://www.democritos.it/mailman/listinfo/pw_forum
> or, via email, send a message with subject or body 'help' to
>        pw_forum-request at pwscf.org
>
> You can reach the person managing the list at
>        pw_forum-owner at pwscf.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
>   1. Van der Waals (Adriano Mosca Conte)
>   2. Shift of Energy (pari shok)
>   3. Re: Shift of Energy (Duy Le)
>   4. Re: 4.3 compile error. (?S)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 4 Apr 2011 15:27:08 +0200 (CEST)
> From: "Adriano Mosca Conte" <Adriano.Mosca.Conte at roma2.infn.it>
> Subject: [Pw_forum] Van der Waals
> To: Pw_forum at pwscf.org
> Message-ID: <59184.141.108.248.78.1301923628.squirrel at 141.108.248.78>
> Content-Type: text/plain;charset=iso-8859-1
>
> I have two questions about the calculations with VdW forces
> (input_dft       = 'vdW-DF'):
> 1- Is it possible to perform VdW calculations with any kind of functional?
> Or is it mandatory to use revPBE?
> 2- I generated a VdW table on two different machines (sp6 of CINECA,
> matrix of  CASPUR). I got different numbers in the files vdW_kernel_table
> (sign
> and order of magnitude are different in many cases). Could it depend on the
> modules I loaded on matrix? Which are the libraries used to generate
> the table?
> Adriano
>
>
> --
> Universit? degli Studi Tor Vergata
> via della Ricerca Scientifica 1
> 00133 Roma, Italia
> Tel. +39 06 7259 4741
> Fax  +39 06 2023507
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 4 Apr 2011 10:32:53 -0400
> From: pari shok <parishok at gmail.com>
> Subject: [Pw_forum] Shift of Energy
> To: pw_forum at pwscf.org
> Message-ID: <BANLkTi=EzJF-KgYL0Cf2Yxe45cWJte4y9g at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear All,
> Thank you very much for your help.
> Please let me ask my final question w.r.t DOS shift of energy of SiC
> supercell.
> The total energy of the 8-atom cell of SiC is: -76.276 Ry, while that of
> 72-atom SiC is -694 Ry. Neglecting almost -7 Ry, the total energy is
> scaling
> accordingly.
> However, I still see the shift of energy in DOS diagram of two slabs (the
> max and min of bandgap shifts, although the gap is almost 2.1 eV for both
> 4H-SiC slabs). I was wondering whether this shift of energy is inevitable
> or
> it is as the result of my input file.
> I kept k points (w.r.t. crystal), and cut off energy the same for both
> structures. Should I scale the cut off energy as well. If positive, is
> there
> any relation between scaling the cell and cut off energy.
> As you know, I need to find a reference for my further calculations.
> I really really appreciate your help.
> Yours
> P Shok
>
> Dear  All,
>     let me clarify a little point.
>     The potential (hence the eigenvalues) of  any calculation in
> periodic boundary conditions, not just a plane-wave one , is defined up
> to  an additive constant... In a finite system a reeference can be fixed
> by requiring that the potential goes to zero at infinite distance but in
> a periodic system this cannot be defined as there is nothing like a
> point at infinite distance ...
>    In most codes (and in pw.x) this arbitrary constant is fixed by
> setting the average electrostatic potential to zero. If the supercell is
> properly constructed, with the properly scaled dimensions, the same
> cutoff, equivalent k-points etc.. the two calculations should be
> equivalent and the eigenvalues should be exactly mapped, the average
> potential should be the same, the total energy should be an exact
> multiple of the one of the original cell.
>
> If this does not happen one is NOT doing the supercell calculation
> properly.
>
> So if when doing a supercell you do not get the scaled result check your
> system definition.
>
> stefano
>
>
> On 04/04/2011 11:46 AM, Giuseppe Mattioli wrote:
> >* Dear all
> *>* I suspect that a a little misunderstanding has been going on here...
> *>* I try to reformulate the question: in the case of a 8-atoms cell the
> valence
> *>* band maximum (VBM) has been found around 10 eV and the conduction band
> *>* minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift in
> the
> *>* position of VBM and CBM when calculated in a 72-atoms supercell,
> but the band
> *>* gap value is the same. Then, the answer to P Shok could be: plane wave
> *>* pseudopotential calculations do not ensure an universal alignment of
> *>* eigenvalues. You should use some "internal" reference, like the 1s
> eigenvalue
> *>* of an He atom, in your cell; or trust that the two VBM values are
> aligned "de
> *>* facto".
> *>* HTH
> *>*
> *>* Giuseppe
> *>*
> *>* On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote:
> *>>* Yes,
> *>>*
> *>>*     I perfectly agree with Eyvaz! Moreover the experimental bandgap is
> *>>* underestimated within LDA or GGA, and for 4H-SiC you would get about
> *>>* 2.2-2.3 eV with LDA.
> *>>*
> *>>*     How do you measure the bandgap? Beware that in the fundamental
> cell the
> *>>* bandgap is not a direct one, but it might become such when you use a
> *>>* supercell (because of the refolding of the Brillouin zones).
> *>>*
> *>>*
> *>>* HTH
> *>>*
> *>>* GS
> *>>*
> *>>* Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto:
> *>>>* Hi,
> *>>>*
> *>>>>* The bandgap of 8-atoms is around 10-12 eV,
> *>>>>* but that of 72-atom is around 5-7 eV.
> *>>>* This is unbelievable, as SiC is an indirect band gap semiconductor
> and
> *>>>* the bandgap is around (2.5 - 3)eV depending on crystal modification
> *>>>* (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.).
> *>>>* See http://www.matprop.ru/SiC_bandstr
> *>>>*
> *>>>* So, check carefully your input/output files.
> *>>>*
> *>>>* Bests,
> *>>>* Eyvaz.
> *>>>*
> *>>>* -------------------------------------------------------------------
> *>>>* Prof. Eyvaz Isaev,
> *>>>* Department of Physics, Chemistry, and Biology (IFM), Linkoping
> *>>>* University, Sweden Theoretical Physics Department, Moscow State
> Institute
> *>>>* of Steel&  Alloys, Russia, isaev at ifm.liu.se
> <http://www.democritos.it/mailman/listinfo/pw_forum>, eyvaz_isaev at
> yahoo.com <http://www.democritos.it/mailman/listinfo/pw_forum>
> *>>>*
> *>>>*
> *>>>* From: pari shok<parishok at gmail.com
> <http://www.democritos.it/mailman/listinfo/pw_forum>>
> *>>>* To: pw_forum at pwscf.org
> <http://www.democritos.it/mailman/listinfo/pw_forum>
> *>>>* Sent: Sun, April 3, 2011 1:34:51 AM
> *>>>* Subject: [Pw_forum] shift of energy
> *>>>*
> *>>>* Dear Paolo,
> *>>>* DOS of 72-atom SiC shows a shift of energy with respect to 8-atom
> SiC.The
> *>>>* bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around
> 5-7
> *>>>* eV. Would you please help me to understand this shift.
> *>>>*
> *>>>* Thanks again.
> *>>>* P Shok
> *>>>* UMD
> *>>>*
> *>>>* On Apr 1, 2011, at 21:36 , pari shok wrote:
> *>>>>* The DOS of 72-atom SiC (supercell) shows a shift of energy.
> *>>>* a shift with respect to what?
> *>>>* ---
> *>>>* Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> *>>>*
> *>>>* Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> *>>>* Phone +39-0432-558216, fax +39-0432-558222
> *>>>*
> *>>>* _______________________________________________
> *>>>* Pw_forum mailing list
> *>>>* Pw_forum at pwscf.org <
> http://www.democritos.it/mailman/listinfo/pw_forum>
> *>>>* http://www.democritos.it/mailman/listinfo/pw_forum
> *>>* ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *>>*     PH H2 462, Station 3, CH-1015 Lausanne
> *>*
> *>*
> *
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 3
> Date: Mon, 4 Apr 2011 11:04:51 -0400
> From: Duy Le <ttduyle at gmail.com>
> Subject: Re: [Pw_forum] Shift of Energy
> To: PWSCF Forum <pw_forum at pwscf.org>
> Cc: pari shok <parishok at gmail.com>
> Message-ID: <BANLkTi=keZQ5tpRzvHs7t_d4x7V7Jrw7Qw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Mon, Apr 4, 2011 at 10:32 AM, pari shok <parishok at gmail.com> wrote:
> > Dear All,
> > Thank you very much for your help.
> > Please let me ask my final question w.r.t DOS shift of energy of SiC
> > supercell.
> > The total energy of the 8-atom cell of SiC is: -76.276 Ry, while that of
> > 72-atom SiC is -694 Ry. Neglecting almost -7 Ry, the total energy is
> scaling
> > accordingly.
> If you are doing correctly, the results must be identical. So make
> sure to check the structures, and the convergence of total energy vs.
> cutoff energy and k-point sampling.
> > However, I still see the shift of energy in DOS diagram of two slabs (the
> > max and min of bandgap shifts, although the gap is almost 2.1 eV for both
> > 4H-SiC slabs). I was wondering whether this shift of energy is inevitable
> or
> > it is as the result of my input file.
> Slab? I though you are performing bulk calculation. Anyway, the shift
> of energies' levels is normal. You should set the reference as center
> of the gap (set it to be zero) then compare the DOS or band
> structures.
> By the way, if your bigger slab experiences the reconstruction, the
> two slabs (8 atoms and 72 atoms) won't be identical => you should not
> get the same results in this case. But 7Ry seems to be huge.
> > I kept k points (w.r.t. crystal), and cut off energy the same for both
> > structures. Should I scale the cut off energy as well. If positive, is
> there
> Okie, but you should scale the k-point sampling accordingly because
> the BZ of 72 atoms cell is smaller. But this won't harm the results if
> total energy is already converged vs. k-point sampling.
> > any relation between scaling the cell and cut off energy.
> No. Cut off energy depends on only pseudo potential.
> > As you know, I need to find a reference for my further calculations.
> > I really really appreciate your help.
> > Yours
> > P Shok
> >
>
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
> > Dear  All,
> >      let me clarify a little point.
> >      The potential (hence the eigenvalues) of  any calculation in
> > periodic boundary conditions, not just a plane-wave one , is defined up
> >
> > to  an additive constant... In a finite system a reeference can be fixed
> > by requiring that the potential goes to zero at infinite distance but in
> > a periodic system this cannot be defined as there is nothing like a
> >
> > point at infinite distance ...
> >     In most codes (and in pw.x) this arbitrary constant is fixed by
> > setting the average electrostatic potential to zero. If the supercell is
> > properly constructed, with the properly scaled dimensions, the same
> >
> > cutoff, equivalent k-points etc.. the two calculations should be
> > equivalent and the eigenvalues should be exactly mapped, the average
> > potential should be the same, the total energy should be an exact
> > multiple of the one of the original cell.
> >
> >
> > If this does not happen one is NOT doing the supercell calculation
> properly.
> >
> > So if when doing a supercell you do not get the scaled result check your
> > system definition.
> >
> > stefano
> >
> >
> > On 04/04/2011 11:46 AM, Giuseppe Mattioli wrote:
> >
> >> Dear all
> >> I suspect that a a little misunderstanding has been going on here...
> >> I try to reformulate the question: in the case of a 8-atoms cell the
> >> valence
> >> band maximum (VBM) has been found around 10 eV and the conduction band
> >
> >> minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift in
> >> the
> >> position of VBM and CBM when calculated in a 72-atoms supercell, but the
> >> band
> >> gap value is the same. Then, the answer to P Shok could be: plane wave
> >
> >> pseudopotential calculations do not ensure an universal alignment of
> >> eigenvalues. You should use some "internal" reference, like the 1s
> >> eigenvalue
> >> of an He atom, in your cell; or trust that the two VBM values are
> aligned
> >> "de
> >
> >> facto".
> >> HTH
> >>
> >> Giuseppe
> >>
> >> On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote:
> >>> Yes,
> >>>
> >>>     I perfectly agree with Eyvaz! Moreover the experimental bandgap is
> >
> >>> underestimated within LDA or GGA, and for 4H-SiC you would get about
> >>> 2.2-2.3 eV with LDA.
> >>>
> >>>     How do you measure the bandgap? Beware that in the fundamental cell
> >>> the
> >
> >>> bandgap is not a direct one, but it might become such when you use a
> >>> supercell (because of the refolding of the Brillouin zones).
> >>>
> >>>
> >>> HTH
> >
> >>>
> >>> GS
> >>>
> >>> Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto:
> >>>> Hi,
> >>>>
> >>>>> The bandgap of 8-atoms is around 10-12 eV,
> >
> >>>>> but that of 72-atom is around 5-7 eV.
> >>>> This is unbelievable, as SiC is an indirect band gap semiconductor and
> >>>> the bandgap is around (2.5 - 3)eV depending on crystal modification
> >
> >>>> (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.).
> >>>> See http://www.matprop.ru/SiC_bandstr
> >>>>
> >>>> So, check carefully your input/output files.
> >
> >>>>
> >>>> Bests,
> >>>> Eyvaz.
> >>>>
> >>>> -------------------------------------------------------------------
> >>>> Prof. Eyvaz Isaev,
> >
> >>>> Department of Physics, Chemistry, and Biology (IFM), Linkoping
> >>>> University, Sweden Theoretical Physics Department, Moscow State
> >>>> Institute
> >>>> of Steel&  Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at
> yahoo.com
> >
> >>>>
> >>>>
> >>>> From: pari shok<parishok at gmail.com>
> >>>> To: pw_forum at pwscf.org
> >
> >>>> Sent: Sun, April 3, 2011 1:34:51 AM
> >>>> Subject: [Pw_forum] shift of energy
> >>>>
> >>>> Dear Paolo,
> >>>> DOS of 72-atom SiC shows a shift of energy with respect to 8-atom
> >>>> SiC.The
> >
> >>>> bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around
> 5-7
> >>>> eV. Would you please help me to understand this shift.
> >>>>
> >>>> Thanks again.
> >
> >>>> P Shok
> >>>> UMD
> >>>>
> >>>> On Apr 1, 2011, at 21:36 , pari shok wrote:
> >>>>> The DOS of 72-atom SiC (supercell) shows a shift of energy.
> >
> >>>> a shift with respect to what?
> >>>> ---
> >>>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> >>>>
> >>>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> >
> >>>> Phone +39-0432-558216, fax +39-0432-558222
> >>>>
> >>>> _______________________________________________
> >>>> Pw_forum mailing list
> >>>> Pw_forum at pwscf.org
> >
> >>>> http://www.democritos.it/mailman/listinfo/pw_forum
> >>> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> >>>     PH H2 462, Station 3, CH-1015 Lausanne
> >
> >>
> >>
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 5 Apr 2011 00:14:21 +0800 (CST)
> From: ?S <flux_ray12 at 163.com>
> Subject: Re: [Pw_forum] 4.3 compile error.
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Message-ID: <174f5d1.7e22.12f214b1d61.Coremail.flux_ray12 at 163.com>
> Content-Type: text/plain; charset="gbk"
>
> Hi, Vit.
> I got the same problem like you.
>
> You can open the file TDDFPT/src/lr_main.f90 and find the line 252. It
> should be written as:
> IF ( lr_io_level > 0 .and. (mod(LR_iteration,restart_step)==0 .OR.
> LR_iteration==itermax .OR. LR_iteration==1) ) CALL lr_write_restart()
> Then, you can add a '&' after '==1) )' and put 'CALL lr_write_restart()' to
> the next line.
> Do not forget add enough space before 'CALL lr_write_restart()', otherwise
> it would become annotate instead of code.
> The modified one could like:
> IF ( lr_io_level > 0 .and. (mod(LR_iteration,restart_step)==0 .OR.
> LR_iteration==itermax .OR. LR_iteration==1) )  &
>           CALL lr_write_restart()
>
>
> At 2011-04-03 19:41:28?Vit <vitruss at gmail.com> wrote:
>
> >Dear QE users!
> >I'm having troubles compiling new release. I'm trying to use ACML where
> >apllicable, but I'm getting the same error even with distro (debian 6.0.1)
> >blas and lapack and internal fftw.
> >Could you please help me resolving this issue?
> >
> >mpif90 -g -o turbo_lanczos.x \
> >                lr_variables.o lr_charg_resp.o bcast_lr_input.o
> lr_readin.o
> >lr_alloc_init.o lr_calc_dens.o lr_dot.o lr_dealloc.o lr_ortho.o
> lr_read_wf.o
> >lr_normalise.o lr_lanczos.o lr_apply_liouvillian.o lr_main.o lr_dv_setup.o
> >lr_setup_dgc.o lr_solve_e.o lr_dvpsi_e.o lr_ch_psi_all.o lr_cgsolve_all.o
> >lr_h_psiq.o lr_sm1_psi.o stop_lr.o lr_read_d0psi.o lr_restart.o
> >lr_write_restart.o print_clock_lr.o sd0psi.o lr_set_boxes_density.o
> >lr_init_nfo.o  ../../PH/libph.a ../../PW/libpw.a ../../Modules/libqemod.a
> >../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a
> >../../iotk/src/libiotk.a   -L/opt/acml4.4.0/gfortran64/lib -lacml -
> >L/opt/acml4.4.0/gfortran64/lib -lacml -L/opt/acml4.4.0/gfortran64/lib
> -lacml
> >lr_main.o: In function `lr_main':
> >/opt/qe/4.3/TDDFPT/src/lr_main.f90:252: undefined reference to `lr_wri_'
> >collect2: ld returned 1 exit status
> >make[2]: *** [turbo_lanczos.x] Error 1
> >make[2]: Leaving directory `/opt/qe/4.3/TDDFPT/src'
> >make[2]: Entering directory `/opt/qe/4.3/TDDFPT/tools'
> >test -n "" && ( cd ../.. ; make -w  || exit 1) || :
> >mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__ACML -D__MPI -
> >D__PARA -I../../include -I../../iotk/src -I../../Modules -I. -c
> >tddfpt_calculate_spectrum.f90
> >mpif90 -g -o turbo_spectrum.x \
> >        tddfpt_calculate_spectrum.o ../../Modules/libqemod.a
> ../../PW/libpw.a
> >../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a
> >../../iotk/src/libiotk.a   -L/opt/acml4.4.0/gfortran64/lib -lacml -
> >L/opt/acml4.4.0/gfortran64/lib -lacml -L/opt/acml4.4.0/gfortran64/lib
> -lacml
> >( cd ../../bin ; ln -fs ../TDDFPT/tools/turbo_spectrum.x . )
> >if [ -d ../bin ] ; then  ( cd ../bin ; ln -fs ../tools/turbo_spectrum.x .
> );
> >fi
> >make[2]: Leaving directory `/opt/qe/4.3/TDDFPT/tools'
> >make[1]: Leaving directory `/opt/qe/4.3/TDDFPT'
> >
> >With best regards,
> >Koroteev Victor.
> >_______________________________________________
> >Pw_forum mailing list
> >Pw_forum at pwscf.org
> >http://www.democritos.it/mailman/listinfo/pw_forum
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>
>   Hi dear users.
  is there anybody who's know about Teter pseudopotential.I used it for
Sr.Sr has 38 electrons and valence electrons should be 4s2 4p6 5s2 4d0 in
ground state but in this pseudopotential zion=10 and the valence electrons
are 4s2 4p6 5s0 4d0!whate's the maning of it?can i use it for ground state
alculation?
Ok! this pseudopotential is used in abinit but i can't ask my question of
them.
thank's alot.

> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 46, Issue 10
> ****************************************
>
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From jorge.gallardo at cab.cnea.gov.ar  Mon Apr  4 21:25:22 2011
From: jorge.gallardo at cab.cnea.gov.ar (jorge.gallardo at cab.cnea.gov.ar)
Date: Mon, 4 Apr 2011 16:25:22 -0300 (ART)
Subject: [Pw_forum] charge density output format from pp.x
In-Reply-To: <A9314ABA-E41D-482F-B549-D5852F6C8405@democritos.it>
References: <4CEBFF39.40505@fu-berlin.de>
	<1290592007.12941.6.camel@ulisse.cm.sissa.it>
	<54782.200.0.233.52.1301691705.squirrel@mail.cab.cnea.gov.ar>
	<A9314ABA-E41D-482F-B549-D5852F6C8405@democritos.it>
Message-ID: <42158.200.0.233.52.1301945122.squirrel@mail.cab.cnea.gov.ar>


> you can extract the charge density (with pp.x) in a number of different
> formats. For the relation between indices and positions in real space:
> http://www.quantum-espresso.org/user_guide/node23.html
>

thank you for you response.

I tried to do something like that, but I cannot understand the content of
the file "al.rho.dat". I suppose that the density is in the big block of 6
numerical columns "DATAGRID_3D_UNKNOWN", but, How is ordered that block? ,
In what order should I read it?.

I need the electronic density rho(x,y,z) for a further calculation.

thank you again.

jorge


From giannozz at democritos.it  Mon Apr  4 22:06:37 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 4 Apr 2011 22:06:37 +0200
Subject: [Pw_forum] charge density output format from pp.x
In-Reply-To: <42158.200.0.233.52.1301945122.squirrel@mail.cab.cnea.gov.ar>
References: <4CEBFF39.40505@fu-berlin.de>
	<1290592007.12941.6.camel@ulisse.cm.sissa.it>
	<54782.200.0.233.52.1301691705.squirrel@mail.cab.cnea.gov.ar>
	<A9314ABA-E41D-482F-B549-D5852F6C8405@democritos.it>
	<42158.200.0.233.52.1301945122.squirrel@mail.cab.cnea.gov.ar>
Message-ID: <E5C2A7D8-4B9D-4FD8-89C5-D5D8B1250E8E@democritos.it>


On Apr 4, 2011, at 21:25 , jorge.gallardo at cab.cnea.gov.ar wrote:

> I need the electronic density rho(x,y,z) for a further calculation.

modify one of the many postprocessing codes that manipulate
the charge density

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





From rose1988.mary at gmail.com  Tue Apr  5 00:27:10 2011
From: rose1988.mary at gmail.com (Rose Mary)
Date: Mon, 4 Apr 2011 23:27:10 +0100
Subject: [Pw_forum] Number of plane waves in output files
Message-ID: <BANLkTikN2uX8oEpsdMpSefz4M-mcqpi+OQ@mail.gmail.com>

Hi Quantum espresso users,

I would like to know how do we find the total number of plane waves from the
output file of quantum espresso?Is it the term '* npwx = 1887' *for the
following output file which has been given as one of the examples of
 Quantum espresso.
*The output*
Program PWSCF v.2.0 starts ...
Today is 16Feb2004 at 16: 6:28
Ultrasoft (Vanderbilt) Pseudopotentials
Current dimensions of program pwscf are:
ntypx =10 npk =40000 lmax = 3
nchix = 6 ndim = 2000 nbrx = 8 nqfm = 8
bravais-lattice index = 4
lattice parameter (a_0) = 4.2470 a.u.
unit-cell volume = 1061.4448 (a.u.)^3
number of atoms/cell = 12
number of atomic types = 1
kinetic-energy cutoff = 22.0000 Ry
charge density cutoff = 88.0000 Ry
convergence threshold = 1.0E-06
beta = 0.7000
number of iterations used = 8 plain mixing
Exchange-correlation = PZ (1100)
iswitch = 0celldm(1)= 4.247000 celldm(2)= 0.000000 celldm(3)= 16.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
crystal axes: (cart. coord. in units of a_0)
a(1) = ( 1.000000 0.000000 0.000000 )
a(2) = ( -0.500000 0.866025 0.000000 )
a(3) = ( 0.000000 0.000000 16.000000 )
reciprocal axes: (cart. coord. in units 2 pi/a_0)
b(1) = ( 1.000000 0.577350 0.000000 )
b(2) = ( 0.000000 1.154701 0.000000 )
b(3) = ( 0.000000 0.000000 0.062500 )
PSEUDO 1 is Be (vbc) zval = 2.0 lmax= 1 lloc= 1
i= 1 2 3
core
alpha = 0.99964 0.0000
a(i) = 1.0000 0.0000
l = 0
alpha = 1.7068 0.0000 0.0000
a(i) = 5.4710 0.0000 0.0000
a(i+3)= -1.6312 0.0000 0.0000
l = 1
alpha = 0.78031 0.0000 0.0000
a(i) = -1.6972 0.0000 0.0000
a(i+3)= 0.48457 0.0000 0.0000
nonlinear core correction: rho(r) = ( a + b r^2) exp(-alpha r^2)
a = 0.95153E-01
b = 0.24127
alpha= 2.7594atomic species valence mass pseudopotential
Be 2.00 1.00000 Be( 1.00)
12 Sym.Ops. (with inversion)
Cartesian axes
site n. atom positions (a_0 units)
1 Be tau( 1) = ( 0.0000000 -0.2886751 4.3596671 )
2 Be tau( 2) = ( 0.0000000 0.2886751 3.5484854 )
3 Be tau( 3) = ( 0.0000000 -0.2886751 2.7546560 )
4 Be tau( 4) = ( 0.0000000 0.2886751 1.9655547 )
5 Be tau( 5) = ( 0.0000000 -0.2886751 1.1789015 )
6 Be tau( 6) = ( 0.0000000 0.2886751 0.3929197 )
7 Be tau( 7) = ( 0.0000000 -0.2886751 -0.3929197 )
8 Be tau( 8) = ( 0.0000000 0.2886751 -1.1789015 )
9 Be tau( 9) = ( 0.0000000 -0.2886751 -1.9655547 )
10 Be tau( 10) = ( 0.0000000 0.2886751 -2.7546560 )
11 Be tau( 11) = ( 0.0000000 -0.2886751 -3.5484854 )
12 Be tau( 12) = ( 0.0000000 0.2886751 -4.3596671 )number of k points= 30
gaussian broad. (ryd)= 0.0500 ngauss = 1
cart. coord. in units 2pi/a_0
k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0078125
k( 2) = ( 0.0625000 0.0360844 0.0000000), wk = 0.0468750
k( 3) = ( 0.1250000 0.0721688 0.0000000), wk = 0.0468750
k( 4) = ( 0.1875000 0.1082532 0.0000000), wk = 0.0468750
...........................................................
......... . .. ........... ......... ......... . . .. ..
k( 27) = ( 0.2500000 0.4330127 0.0000000), wk = 0.0468750
k( 28) = ( 0.3125000 0.4690971 0.0000000), wk = 0.0937500
k( 29) = ( 0.3750000 0.5051815 0.0000000), wk = 0.0468750
k( 30) = ( 0.3125000 0.5412659 0.0000000), wk = 0.0468750
G cutoff = 40.2057 ( 14795 G-vectors) FFT grid: ( 16, 16,216)
nbndx = 80 nbnd = 20 natomwfc = 12* npwx = 1887--------------Is this the
number of plane wave in the calculation?*
nelec = 24.00 nkb = 12 ngl = 94
.
Best regards
Rose Mary
Masters student
semiconductor Physics
Belgium
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From lorenzo.paulatto at impmc.upmc.fr  Tue Apr  5 08:26:26 2011
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Tue, 05 Apr 2011 08:26:26 +0200
Subject: [Pw_forum] Number of plane waves in output files
In-Reply-To: <BANLkTikN2uX8oEpsdMpSefz4M-mcqpi+OQ@mail.gmail.com>
References: <BANLkTikN2uX8oEpsdMpSefz4M-mcqpi+OQ@mail.gmail.com>
Message-ID: <op.vtgb6cr45jfbqb@paulax>

In data 05 aprile 2011 alle ore 00:27:10, Rose Mary  
<rose1988.mary at gmail.com> ha scritto:
> I would like to know how do we find the total number of plane waves from  
> the output file of quantum espresso?Is it the term '* npwx = 1887' *for  
> the
> following output file which has been given as one of the examples of

Dear Rose Mary,
the number of plane waves depends (very weakly) on the k-point, while npwx  
is the maximum among all k-points. If you wish to know the number of pw at  
each point you can edit PW/hinit0.f90 to add a print statement after line  
57, i.e.:
   IF ( nks > 1 ) WRITE( iunigk ) igk !line 57
   write(*,*) "kpt,npw:", ik, npw


best regards


-- 
Lorenzo Paulatto
post-doc @ IMPMC/UPMC - Universit? Paris 6
phone: +33 (0)1 44 27 74 89
www:   http://www-int.impmc.upmc.fr/~paulatto/

previously (take note of the change!):
phd student @ SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
www:   http://people.sissa.it/~paulatto/

From giannozz at democritos.it  Tue Apr  5 08:49:36 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 05 Apr 2011 08:49:36 +0200
Subject: [Pw_forum] Number of plane waves in output files
In-Reply-To: <op.vtgb6cr45jfbqb@paulax>
References: <BANLkTikN2uX8oEpsdMpSefz4M-mcqpi+OQ@mail.gmail.com>
	<op.vtgb6cr45jfbqb@paulax>
Message-ID: <1301986176.4140.3.camel@fe12lx.fisica.uniud.it>

On Tue, 2011-04-05 at 08:26 +0200, Lorenzo Paulatto wrote:

> If you wish to know the number of pw at each point you can edit  
> PW/hinit0.f90 to add a print statement after line 57

or wait until the end of the scf cycle and look for lines like
          k = 0.2500 0.2500 0.2500 (   180 PWs)   bands (ev):
(PWs=number of plane waves for wave vector k; k in 2pi/a units)

P.
-- 
 Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222 


From sclauzer at sissa.it  Tue Apr  5 08:50:53 2011
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 5 Apr 2011 08:50:53 +0200
Subject: [Pw_forum] Teter''extended norm conserving'' pseudotential
In-Reply-To: <BANLkTin5qZEB4=8XTgFTFGipTp9ZW9LUOg@mail.gmail.com>
References: <BANLkTin5qZEB4=8XTgFTFGipTp9ZW9LUOg@mail.gmail.com>
Message-ID: <B09BB535-49C2-455D-A7E0-F7FB5C33A791@sissa.it>

Dear user, 

   where is your request? 

  I guess no one wants to chase the few relevant lines among thousands of lines that have nothing to do with your question. Does it look rational to you to write such a kind of message?? 


Cheers,


GS

Il giorno 04/apr/2011, alle ore 20.48, bahaareh tavakoli nejad ha scritto:

> 
> 
> On Mon, Apr 4, 2011 at 9:29 AM, <pw_forum-request at pwscf.org> wrote:
> Send Pw_forum mailing list submissions to
>        pw_forum at pwscf.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://www.democritos.it/mailman/listinfo/pw_forum
> or, via email, send a message with subject or body 'help' to
>        pw_forum-request at pwscf.org
> 
> You can reach the person managing the list at
>        pw_forum-owner at pwscf.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
> 
> 
> Today's Topics:
> 
>   1. Van der Waals (Adriano Mosca Conte)
>   2. Shift of Energy (pari shok)
>   3. Re: Shift of Energy (Duy Le)
>   4. Re: 4.3 compile error. (?S)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 4 Apr 2011 15:27:08 +0200 (CEST)
> From: "Adriano Mosca Conte" <Adriano.Mosca.Conte at roma2.infn.it>
> Subject: [Pw_forum] Van der Waals
> To: Pw_forum at pwscf.org
> Message-ID: <59184.141.108.248.78.1301923628.squirrel at 141.108.248.78>
> Content-Type: text/plain;charset=iso-8859-1
> 
> I have two questions about the calculations with VdW forces
> (input_dft       = 'vdW-DF'):
> 1- Is it possible to perform VdW calculations with any kind of functional?
> Or is it mandatory to use revPBE?
> 2- I generated a VdW table on two different machines (sp6 of CINECA,
> matrix of  CASPUR). I got different numbers in the files vdW_kernel_table
> (sign
> and order of magnitude are different in many cases). Could it depend on the
> modules I loaded on matrix? Which are the libraries used to generate
> the table?
> Adriano
> 
> 
> --
> Universit? degli Studi Tor Vergata
> via della Ricerca Scientifica 1
> 00133 Roma, Italia
> Tel. +39 06 7259 4741
> Fax  +39 06 2023507
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 4 Apr 2011 10:32:53 -0400
> From: pari shok <parishok at gmail.com>
> Subject: [Pw_forum] Shift of Energy
> To: pw_forum at pwscf.org
> Message-ID: <BANLkTi=EzJF-KgYL0Cf2Yxe45cWJte4y9g at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear All,
> Thank you very much for your help.
> Please let me ask my final question w.r.t DOS shift of energy of SiC
> supercell.
> The total energy of the 8-atom cell of SiC is: -76.276 Ry, while that of
> 72-atom SiC is -694 Ry. Neglecting almost -7 Ry, the total energy is scaling
> accordingly.
> However, I still see the shift of energy in DOS diagram of two slabs (the
> max and min of bandgap shifts, although the gap is almost 2.1 eV for both
> 4H-SiC slabs). I was wondering whether this shift of energy is inevitable or
> it is as the result of my input file.
> I kept k points (w.r.t. crystal), and cut off energy the same for both
> structures. Should I scale the cut off energy as well. If positive, is there
> any relation between scaling the cell and cut off energy.
> As you know, I need to find a reference for my further calculations.
> I really really appreciate your help.
> Yours
> P Shok
> 
> Dear  All,
>     let me clarify a little point.
>     The potential (hence the eigenvalues) of  any calculation in
> periodic boundary conditions, not just a plane-wave one , is defined up
> to  an additive constant... In a finite system a reeference can be fixed
> by requiring that the potential goes to zero at infinite distance but in
> a periodic system this cannot be defined as there is nothing like a
> point at infinite distance ...
>    In most codes (and in pw.x) this arbitrary constant is fixed by
> setting the average electrostatic potential to zero. If the supercell is
> properly constructed, with the properly scaled dimensions, the same
> cutoff, equivalent k-points etc.. the two calculations should be
> equivalent and the eigenvalues should be exactly mapped, the average
> potential should be the same, the total energy should be an exact
> multiple of the one of the original cell.
> 
> If this does not happen one is NOT doing the supercell calculation properly.
> 
> So if when doing a supercell you do not get the scaled result check your
> system definition.
> 
> stefano
> 
> 
> On 04/04/2011 11:46 AM, Giuseppe Mattioli wrote:
> >* Dear all
> *>* I suspect that a a little misunderstanding has been going on here...
> *>* I try to reformulate the question: in the case of a 8-atoms cell the valence
> *>* band maximum (VBM) has been found around 10 eV and the conduction band
> *>* minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift in the
> *>* position of VBM and CBM when calculated in a 72-atoms supercell,
> but the band
> *>* gap value is the same. Then, the answer to P Shok could be: plane wave
> *>* pseudopotential calculations do not ensure an universal alignment of
> *>* eigenvalues. You should use some "internal" reference, like the 1s
> eigenvalue
> *>* of an He atom, in your cell; or trust that the two VBM values are
> aligned "de
> *>* facto".
> *>* HTH
> *>*
> *>* Giuseppe
> *>*
> *>* On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote:
> *>>* Yes,
> *>>*
> *>>*     I perfectly agree with Eyvaz! Moreover the experimental bandgap is
> *>>* underestimated within LDA or GGA, and for 4H-SiC you would get about
> *>>* 2.2-2.3 eV with LDA.
> *>>*
> *>>*     How do you measure the bandgap? Beware that in the fundamental cell the
> *>>* bandgap is not a direct one, but it might become such when you use a
> *>>* supercell (because of the refolding of the Brillouin zones).
> *>>*
> *>>*
> *>>* HTH
> *>>*
> *>>* GS
> *>>*
> *>>* Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto:
> *>>>* Hi,
> *>>>*
> *>>>>* The bandgap of 8-atoms is around 10-12 eV,
> *>>>>* but that of 72-atom is around 5-7 eV.
> *>>>* This is unbelievable, as SiC is an indirect band gap semiconductor and
> *>>>* the bandgap is around (2.5 - 3)eV depending on crystal modification
> *>>>* (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.).
> *>>>* See http://www.matprop.ru/SiC_bandstr
> *>>>*
> *>>>* So, check carefully your input/output files.
> *>>>*
> *>>>* Bests,
> *>>>* Eyvaz.
> *>>>*
> *>>>* -------------------------------------------------------------------
> *>>>* Prof. Eyvaz Isaev,
> *>>>* Department of Physics, Chemistry, and Biology (IFM), Linkoping
> *>>>* University, Sweden Theoretical Physics Department, Moscow State Institute
> *>>>* of Steel&  Alloys, Russia, isaev at ifm.liu.se
> <http://www.democritos.it/mailman/listinfo/pw_forum>, eyvaz_isaev at
> yahoo.com <http://www.democritos.it/mailman/listinfo/pw_forum>
> *>>>*
> *>>>*
> *>>>* From: pari shok<parishok at gmail.com
> <http://www.democritos.it/mailman/listinfo/pw_forum>>
> *>>>* To: pw_forum at pwscf.org
> <http://www.democritos.it/mailman/listinfo/pw_forum>
> *>>>* Sent: Sun, April 3, 2011 1:34:51 AM
> *>>>* Subject: [Pw_forum] shift of energy
> *>>>*
> *>>>* Dear Paolo,
> *>>>* DOS of 72-atom SiC shows a shift of energy with respect to 8-atom SiC.The
> *>>>* bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around 5-7
> *>>>* eV. Would you please help me to understand this shift.
> *>>>*
> *>>>* Thanks again.
> *>>>* P Shok
> *>>>* UMD
> *>>>*
> *>>>* On Apr 1, 2011, at 21:36 , pari shok wrote:
> *>>>>* The DOS of 72-atom SiC (supercell) shows a shift of energy.
> *>>>* a shift with respect to what?
> *>>>* ---
> *>>>* Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> *>>>*
> *>>>* Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> *>>>* Phone +39-0432-558216, fax +39-0432-558222
> *>>>*
> *>>>* _______________________________________________
> *>>>* Pw_forum mailing list
> *>>>* Pw_forum at pwscf.org <http://www.democritos.it/mailman/listinfo/pw_forum>
> *>>>* http://www.democritos.it/mailman/listinfo/pw_forum
> *>>* ? Gabriele Sclauzero, EPFL SB ITP CSEA
> *>>*     PH H2 462, Station 3, CH-1015 Lausanne
> *>*
> *>*
> *
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> 
> ------------------------------
> 
> Message: 3
> Date: Mon, 4 Apr 2011 11:04:51 -0400
> From: Duy Le <ttduyle at gmail.com>
> Subject: Re: [Pw_forum] Shift of Energy
> To: PWSCF Forum <pw_forum at pwscf.org>
> Cc: pari shok <parishok at gmail.com>
> Message-ID: <BANLkTi=keZQ5tpRzvHs7t_d4x7V7Jrw7Qw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> On Mon, Apr 4, 2011 at 10:32 AM, pari shok <parishok at gmail.com> wrote:
> > Dear All,
> > Thank you very much for your help.
> > Please let me ask my final question w.r.t DOS shift of energy of SiC
> > supercell.
> > The total energy of the 8-atom cell of SiC is: -76.276 Ry, while that of
> > 72-atom SiC is -694 Ry. Neglecting almost -7 Ry, the total energy is scaling
> > accordingly.
> If you are doing correctly, the results must be identical. So make
> sure to check the structures, and the convergence of total energy vs.
> cutoff energy and k-point sampling.
> > However, I still see the shift of energy in DOS diagram of two slabs (the
> > max and min of bandgap shifts, although the gap is almost 2.1 eV for both
> > 4H-SiC slabs). I was wondering whether this shift of energy is inevitable or
> > it is as the result of my input file.
> Slab? I though you are performing bulk calculation. Anyway, the shift
> of energies' levels is normal. You should set the reference as center
> of the gap (set it to be zero) then compare the DOS or band
> structures.
> By the way, if your bigger slab experiences the reconstruction, the
> two slabs (8 atoms and 72 atoms) won't be identical => you should not
> get the same results in this case. But 7Ry seems to be huge.
> > I kept k points (w.r.t. crystal), and cut off energy the same for both
> > structures. Should I scale the cut off energy as well. If positive, is there
> Okie, but you should scale the k-point sampling accordingly because
> the BZ of 72 atoms cell is smaller. But this won't harm the results if
> total energy is already converged vs. k-point sampling.
> > any relation between scaling the cell and cut off energy.
> No. Cut off energy depends on only pseudo potential.
> > As you know, I need to find a reference for my further calculations.
> > I really really appreciate your help.
> > Yours
> > P Shok
> >
> 
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
> 
> "Men don't need hand to do things"
> > Dear  All,
> >      let me clarify a little point.
> >      The potential (hence the eigenvalues) of  any calculation in
> > periodic boundary conditions, not just a plane-wave one , is defined up
> >
> > to  an additive constant... In a finite system a reeference can be fixed
> > by requiring that the potential goes to zero at infinite distance but in
> > a periodic system this cannot be defined as there is nothing like a
> >
> > point at infinite distance ...
> >     In most codes (and in pw.x) this arbitrary constant is fixed by
> > setting the average electrostatic potential to zero. If the supercell is
> > properly constructed, with the properly scaled dimensions, the same
> >
> > cutoff, equivalent k-points etc.. the two calculations should be
> > equivalent and the eigenvalues should be exactly mapped, the average
> > potential should be the same, the total energy should be an exact
> > multiple of the one of the original cell.
> >
> >
> > If this does not happen one is NOT doing the supercell calculation properly.
> >
> > So if when doing a supercell you do not get the scaled result check your
> > system definition.
> >
> > stefano
> >
> >
> > On 04/04/2011 11:46 AM, Giuseppe Mattioli wrote:
> >
> >> Dear all
> >> I suspect that a a little misunderstanding has been going on here...
> >> I try to reformulate the question: in the case of a 8-atoms cell the
> >> valence
> >> band maximum (VBM) has been found around 10 eV and the conduction band
> >
> >> minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift in
> >> the
> >> position of VBM and CBM when calculated in a 72-atoms supercell, but the
> >> band
> >> gap value is the same. Then, the answer to P Shok could be: plane wave
> >
> >> pseudopotential calculations do not ensure an universal alignment of
> >> eigenvalues. You should use some "internal" reference, like the 1s
> >> eigenvalue
> >> of an He atom, in your cell; or trust that the two VBM values are aligned
> >> "de
> >
> >> facto".
> >> HTH
> >>
> >> Giuseppe
> >>
> >> On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote:
> >>> Yes,
> >>>
> >>>     I perfectly agree with Eyvaz! Moreover the experimental bandgap is
> >
> >>> underestimated within LDA or GGA, and for 4H-SiC you would get about
> >>> 2.2-2.3 eV with LDA.
> >>>
> >>>     How do you measure the bandgap? Beware that in the fundamental cell
> >>> the
> >
> >>> bandgap is not a direct one, but it might become such when you use a
> >>> supercell (because of the refolding of the Brillouin zones).
> >>>
> >>>
> >>> HTH
> >
> >>>
> >>> GS
> >>>
> >>> Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto:
> >>>> Hi,
> >>>>
> >>>>> The bandgap of 8-atoms is around 10-12 eV,
> >
> >>>>> but that of 72-atom is around 5-7 eV.
> >>>> This is unbelievable, as SiC is an indirect band gap semiconductor and
> >>>> the bandgap is around (2.5 - 3)eV depending on crystal modification
> >
> >>>> (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.).
> >>>> See http://www.matprop.ru/SiC_bandstr
> >>>>
> >>>> So, check carefully your input/output files.
> >
> >>>>
> >>>> Bests,
> >>>> Eyvaz.
> >>>>
> >>>> -------------------------------------------------------------------
> >>>> Prof. Eyvaz Isaev,
> >
> >>>> Department of Physics, Chemistry, and Biology (IFM), Linkoping
> >>>> University, Sweden Theoretical Physics Department, Moscow State
> >>>> Institute
> >>>> of Steel&  Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
> >
> >>>>
> >>>>
> >>>> From: pari shok<parishok at gmail.com>
> >>>> To: pw_forum at pwscf.org
> >
> >>>> Sent: Sun, April 3, 2011 1:34:51 AM
> >>>> Subject: [Pw_forum] shift of energy
> >>>>
> >>>> Dear Paolo,
> >>>> DOS of 72-atom SiC shows a shift of energy with respect to 8-atom
> >>>> SiC.The
> >
> >>>> bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around 5-7
> >>>> eV. Would you please help me to understand this shift.
> >>>>
> >>>> Thanks again.
> >
> >>>> P Shok
> >>>> UMD
> >>>>
> >>>> On Apr 1, 2011, at 21:36 , pari shok wrote:
> >>>>> The DOS of 72-atom SiC (supercell) shows a shift of energy.
> >
> >>>> a shift with respect to what?
> >>>> ---
> >>>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> >>>>
> >>>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> >
> >>>> Phone +39-0432-558216, fax +39-0432-558222
> >>>>
> >>>> _______________________________________________
> >>>> Pw_forum mailing list
> >>>> Pw_forum at pwscf.org
> >
> >>>> http://www.democritos.it/mailman/listinfo/pw_forum
> >>> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> >>>     PH H2 462, Station 3, CH-1015 Lausanne
> >
> >>
> >>
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Tue, 5 Apr 2011 00:14:21 +0800 (CST)
> From: ?S <flux_ray12 at 163.com>
> Subject: Re: [Pw_forum] 4.3 compile error.
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Message-ID: <174f5d1.7e22.12f214b1d61.Coremail.flux_ray12 at 163.com>
> Content-Type: text/plain; charset="gbk"
> 
> Hi, Vit.
> I got the same problem like you.
> 
> You can open the file TDDFPT/src/lr_main.f90 and find the line 252. It should be written as:
> IF ( lr_io_level > 0 .and. (mod(LR_iteration,restart_step)==0 .OR. LR_iteration==itermax .OR. LR_iteration==1) ) CALL lr_write_restart()
> Then, you can add a '&' after '==1) )' and put 'CALL lr_write_restart()' to the next line.
> Do not forget add enough space before 'CALL lr_write_restart()', otherwise it would become annotate instead of code.
> The modified one could like:
> IF ( lr_io_level > 0 .and. (mod(LR_iteration,restart_step)==0 .OR. LR_iteration==itermax .OR. LR_iteration==1) )  &
>           CALL lr_write_restart()
> 
> 
> At 2011-04-03 19:41:28?Vit <vitruss at gmail.com> wrote:
> 
> >Dear QE users!
> >I'm having troubles compiling new release. I'm trying to use ACML where
> >apllicable, but I'm getting the same error even with distro (debian 6.0.1)
> >blas and lapack and internal fftw.
> >Could you please help me resolving this issue?
> >
> >mpif90 -g -o turbo_lanczos.x \
> >                lr_variables.o lr_charg_resp.o bcast_lr_input.o lr_readin.o
> >lr_alloc_init.o lr_calc_dens.o lr_dot.o lr_dealloc.o lr_ortho.o lr_read_wf.o
> >lr_normalise.o lr_lanczos.o lr_apply_liouvillian.o lr_main.o lr_dv_setup.o
> >lr_setup_dgc.o lr_solve_e.o lr_dvpsi_e.o lr_ch_psi_all.o lr_cgsolve_all.o
> >lr_h_psiq.o lr_sm1_psi.o stop_lr.o lr_read_d0psi.o lr_restart.o
> >lr_write_restart.o print_clock_lr.o sd0psi.o lr_set_boxes_density.o
> >lr_init_nfo.o  ../../PH/libph.a ../../PW/libpw.a ../../Modules/libqemod.a
> >../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a
> >../../iotk/src/libiotk.a   -L/opt/acml4.4.0/gfortran64/lib -lacml -
> >L/opt/acml4.4.0/gfortran64/lib -lacml -L/opt/acml4.4.0/gfortran64/lib -lacml
> >lr_main.o: In function `lr_main':
> >/opt/qe/4.3/TDDFPT/src/lr_main.f90:252: undefined reference to `lr_wri_'
> >collect2: ld returned 1 exit status
> >make[2]: *** [turbo_lanczos.x] Error 1
> >make[2]: Leaving directory `/opt/qe/4.3/TDDFPT/src'
> >make[2]: Entering directory `/opt/qe/4.3/TDDFPT/tools'
> >test -n "" && ( cd ../.. ; make -w  || exit 1) || :
> >mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__ACML -D__MPI -
> >D__PARA -I../../include -I../../iotk/src -I../../Modules -I. -c
> >tddfpt_calculate_spectrum.f90
> >mpif90 -g -o turbo_spectrum.x \
> >        tddfpt_calculate_spectrum.o ../../Modules/libqemod.a ../../PW/libpw.a
> >../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a
> >../../iotk/src/libiotk.a   -L/opt/acml4.4.0/gfortran64/lib -lacml -
> >L/opt/acml4.4.0/gfortran64/lib -lacml -L/opt/acml4.4.0/gfortran64/lib -lacml
> >( cd ../../bin ; ln -fs ../TDDFPT/tools/turbo_spectrum.x . )
> >if [ -d ../bin ] ; then  ( cd ../bin ; ln -fs ../tools/turbo_spectrum.x . );
> >fi
> >make[2]: Leaving directory `/opt/qe/4.3/TDDFPT/tools'
> >make[1]: Leaving directory `/opt/qe/4.3/TDDFPT'
> >
> >With best regards,
> >Koroteev Victor.
> >_______________________________________________
> >Pw_forum mailing list
> >Pw_forum at pwscf.org
> >http://www.democritos.it/mailman/listinfo/pw_forum
> -------------- next part --------------
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> URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110405/a5f0eb48/attachment.htm
> 
>   Hi dear users.
>   is there anybody who's know about Teter pseudopotential.I used it for Sr.Sr has 38 electrons and valence electrons should be 4s2 4p6 5s2 4d0 in ground state but in this pseudopotential zion=10 and the valence electrons are 4s2 4p6 5s0 4d0!whate's the maning of it?can i use it for ground state alculation?
> Ok! this pseudopotential is used in abinit but i can't ask my question of them.
> thank's alot.
> ------------------------------
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> End of Pw_forum Digest, Vol 46, Issue 10
> ****************************************
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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

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From iiysidi at gmail.com  Tue Apr  5 14:33:22 2011
From: iiysidi at gmail.com (ilyes hamdi)
Date: Tue, 5 Apr 2011 14:33:22 +0200
Subject: [Pw_forum] Problems with electrostatic corrections (Makov-Payne or
 density counter charge) for aperiodic systems in 4.2 version
Message-ID: <BANLkTim-pdx5Mcbs1HbQeKhTTEoDWtco2Q@mail.gmail.com>

Dear espresso users,

1) I'm a bit confused with the implementation of the Makov-Payne
electrostatic corrections in PW/makov-payne.f90 in Version 4.2:
- In their original paper, Makov and Payne define the first order correction
E11 =  - \alpha * q^2/(2\epsilon* L). This quantity should be negative for
cubic systems, however
the writing statement in PW/makov-payne.f90 subroutine defines the
correction to be -E11 (leading to a positive value).
- The second order correction E12 is propertional to q Q/L^3 and is also
defined as -E12 in the PW/makov-payne.f90 subroutine.
- The total energy should be Etot = E0 + E11 + E12 = E0 - \alpha *
q^2/(2\epsilon* L) + 2 \pi * q * Q / ( 3 \epsilon L^3), however it is
implemented as E0-E11-E12.

2) Why the DCC correction is disabled in version 4.2? Indeed when setting
asume_isolated = 'dcc' and &EE input parameters to their default  values, I
obtain an error message "DCC correction is disabled". Looking in the
PW/input.f90 subroutine, one found that the dcc correction is disabled by an
immediate call to errore subroutine.

Please can any one verify if I'm correct or did I miss something.

Best regards


-- 
Dr. Ilyes Hamdi, Assistant professor
Department of Electronic and Automatics,
Institute of Applied Sciences and Technology
Gafsa, Tunisia
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From iiysidi at gmail.com  Tue Apr  5 14:37:02 2011
From: iiysidi at gmail.com (ilyes hamdi)
Date: Tue, 5 Apr 2011 14:37:02 +0200
Subject: [Pw_forum] Problems with electrostatic corrections (Makov-Payne or
 density counter charge) for aperiodic systems in 4.2 version
Message-ID: <BANLkTikK7o_2mn3-2-5eE3Le8-1LFCh5wg@mail.gmail.com>

Dear espresso users,

1) I'm a bit confused with the implementation of the Makov-Payne
electrostatic corrections in PW/makov-payne.f90 in Version 4.2:
- In their original paper, Makov and Payne define the first order correction
E11 =  - \alpha * q^2/(2\epsilon* L). This quantity should be negative for
cubic systems, however
the writing statement in PW/makov-payne.f90 subroutine defines the
correction to be -E11 (leading to a positive value).
- The second order correction E12 is propertional to q Q/L^3 and is also
defined as -E12 in the PW/makov-payne.f90 subroutine.
- The total energy should be Etot = E0 + E11 + E12 = E0 - \alpha *
q^2/(2\epsilon* L) + 2 \pi * q * Q / ( 3 \epsilon L^3), however it is
implemented as E0-E11-E12.

2) Why the DCC correction is disabled in version 4.2? Indeed when setting
asume_isolated = 'dcc' and &EE input parameters to their default  values, I
obtain an error message "DCC correction is disabled". Looking in the
PW/input.f90 subroutine, one found that the dcc correction is disabled by an
immediate call to errore subroutine.

Please can any one verify if I'm correct or did I miss something.

Best regards


-- 
Dr. Ilyes Hamdi, Assistant professor
Department of Electronic and Automatics,
Institute of Applied Sciences and Technology
Gafsa, Tunisia
-------------- next part --------------
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From bahaartv at gmail.com  Tue Apr  5 14:38:56 2011
From: bahaartv at gmail.com (bahaareh tavakoli nejad)
Date: Tue, 5 Apr 2011 05:38:56 -0700
Subject: [Pw_forum] Pw_forum Digest, Vol 46, Issue 12
In-Reply-To: <mailman.11031.1301942887.1814.pw_forum@pwscf.org>
References: <mailman.11031.1301942887.1814.pw_forum@pwscf.org>
Message-ID: <BANLkTimugLgbqG91uNgWKCi_wYQFeKbjxA@mail.gmail.com>

On Mon, Apr 4, 2011 at 11:48 AM, <pw_forum-request at pwscf.org> wrote:

> Send Pw_forum mailing list submissions to
>        pw_forum at pwscf.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://www.democritos.it/mailman/listinfo/pw_forum
> or, via email, send a message with subject or body 'help' to
>        pw_forum-request at pwscf.org
>
> You can reach the person managing the list at
>        pw_forum-owner at pwscf.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
>   1. Teter''extended norm conserving'' pseudotential
>      (bahaareh tavakoli nejad)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 4 Apr 2011 11:48:02 -0700
> From: bahaareh tavakoli nejad <bahaartv at gmail.com>
> Subject: [Pw_forum] Teter''extended norm conserving'' pseudotential
> To: pw_forum at pwscf.org
> Message-ID: <BANLkTin5qZEB4=8XTgFTFGipTp9ZW9LUOg at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On Mon, Apr 4, 2011 at 9:29 AM, <pw_forum-request at pwscf.org> wrote:
>
> > Send Pw_forum mailing list submissions to
> >        pw_forum at pwscf.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >        http://www.democritos.it/mailman/listinfo/pw_forum
> > or, via email, send a message with subject or body 'help' to
> >        pw_forum-request at pwscf.org
> >
> > You can reach the person managing the list at
> >        pw_forum-owner at pwscf.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Pw_forum digest..."
> >
> >
> > Today's Topics:
> >
> >   1. Van der Waals (Adriano Mosca Conte)
> >   2. Shift of Energy (pari shok)
> >   3. Re: Shift of Energy (Duy Le)
> >   4. Re: 4.3 compile error. (?S)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 4 Apr 2011 15:27:08 +0200 (CEST)
> > From: "Adriano Mosca Conte" <Adriano.Mosca.Conte at roma2.infn.it>
> > Subject: [Pw_forum] Van der Waals
> > To: Pw_forum at pwscf.org
> > Message-ID: <59184.141.108.248.78.1301923628.squirrel at 141.108.248.78>
> > Content-Type: text/plain;charset=iso-8859-1
> >
> > I have two questions about the calculations with VdW forces
> > (input_dft       = 'vdW-DF'):
> > 1- Is it possible to perform VdW calculations with any kind of
> functional?
> > Or is it mandatory to use revPBE?
> > 2- I generated a VdW table on two different machines (sp6 of CINECA,
> > matrix of  CASPUR). I got different numbers in the files vdW_kernel_table
> > (sign
> > and order of magnitude are different in many cases). Could it depend on
> the
> > modules I loaded on matrix? Which are the libraries used to generate
> > the table?
> > Adriano
> >
> >
> > --
> > Universit? degli Studi Tor Vergata
> > via della Ricerca Scientifica 1
> > 00133 Roma, Italia
> > Tel. +39 06 7259 4741
> > Fax  +39 06 2023507
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 4 Apr 2011 10:32:53 -0400
> > From: pari shok <parishok at gmail.com>
> > Subject: [Pw_forum] Shift of Energy
> > To: pw_forum at pwscf.org
> > Message-ID: <BANLkTi=EzJF-KgYL0Cf2Yxe45cWJte4y9g at mail.gmail.com>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Dear All,
> > Thank you very much for your help.
> > Please let me ask my final question w.r.t DOS shift of energy of SiC
> > supercell.
> > The total energy of the 8-atom cell of SiC is: -76.276 Ry, while that of
> > 72-atom SiC is -694 Ry. Neglecting almost -7 Ry, the total energy is
> > scaling
> > accordingly.
> > However, I still see the shift of energy in DOS diagram of two slabs (the
> > max and min of bandgap shifts, although the gap is almost 2.1 eV for both
> > 4H-SiC slabs). I was wondering whether this shift of energy is inevitable
> > or
> > it is as the result of my input file.
> > I kept k points (w.r.t. crystal), and cut off energy the same for both
> > structures. Should I scale the cut off energy as well. If positive, is
> > there
> > any relation between scaling the cell and cut off energy.
> > As you know, I need to find a reference for my further calculations.
> > I really really appreciate your help.
> > Yours
> > P Shok
> >
> > Dear  All,
> >     let me clarify a little point.
> >     The potential (hence the eigenvalues) of  any calculation in
> > periodic boundary conditions, not just a plane-wave one , is defined up
> > to  an additive constant... In a finite system a reeference can be fixed
> > by requiring that the potential goes to zero at infinite distance but in
> > a periodic system this cannot be defined as there is nothing like a
> > point at infinite distance ...
> >    In most codes (and in pw.x) this arbitrary constant is fixed by
> > setting the average electrostatic potential to zero. If the supercell is
> > properly constructed, with the properly scaled dimensions, the same
> > cutoff, equivalent k-points etc.. the two calculations should be
> > equivalent and the eigenvalues should be exactly mapped, the average
> > potential should be the same, the total energy should be an exact
> > multiple of the one of the original cell.
> >
> > If this does not happen one is NOT doing the supercell calculation
> > properly.
> >
> > So if when doing a supercell you do not get the scaled result check your
> > system definition.
> >
> > stefano
> >
> >
> > On 04/04/2011 11:46 AM, Giuseppe Mattioli wrote:
> > >* Dear all
> > *>* I suspect that a a little misunderstanding has been going on here...
> > *>* I try to reformulate the question: in the case of a 8-atoms cell the
> > valence
> > *>* band maximum (VBM) has been found around 10 eV and the conduction
> band
> > *>* minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift
> in
> > the
> > *>* position of VBM and CBM when calculated in a 72-atoms supercell,
> > but the band
> > *>* gap value is the same. Then, the answer to P Shok could be: plane
> wave
> > *>* pseudopotential calculations do not ensure an universal alignment of
> > *>* eigenvalues. You should use some "internal" reference, like the 1s
> > eigenvalue
> > *>* of an He atom, in your cell; or trust that the two VBM values are
> > aligned "de
> > *>* facto".
> > *>* HTH
> > *>*
> > *>* Giuseppe
> > *>*
> > *>* On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote:
> > *>>* Yes,
> > *>>*
> > *>>*     I perfectly agree with Eyvaz! Moreover the experimental bandgap
> is
> > *>>* underestimated within LDA or GGA, and for 4H-SiC you would get about
> > *>>* 2.2-2.3 eV with LDA.
> > *>>*
> > *>>*     How do you measure the bandgap? Beware that in the fundamental
> > cell the
> > *>>* bandgap is not a direct one, but it might become such when you use a
> > *>>* supercell (because of the refolding of the Brillouin zones).
> > *>>*
> > *>>*
> > *>>* HTH
> > *>>*
> > *>>* GS
> > *>>*
> > *>>* Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto:
> > *>>>* Hi,
> > *>>>*
> > *>>>>* The bandgap of 8-atoms is around 10-12 eV,
> > *>>>>* but that of 72-atom is around 5-7 eV.
> > *>>>* This is unbelievable, as SiC is an indirect band gap semiconductor
> > and
> > *>>>* the bandgap is around (2.5 - 3)eV depending on crystal modification
> > *>>>* (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.).
> > *>>>* See http://www.matprop.ru/SiC_bandstr
> > *>>>*
> > *>>>* So, check carefully your input/output files.
> > *>>>*
> > *>>>* Bests,
> > *>>>* Eyvaz.
> > *>>>*
> > *>>>* -------------------------------------------------------------------
> > *>>>* Prof. Eyvaz Isaev,
> > *>>>* Department of Physics, Chemistry, and Biology (IFM), Linkoping
> > *>>>* University, Sweden Theoretical Physics Department, Moscow State
> > Institute
> > *>>>* of Steel&  Alloys, Russia, isaev at ifm.liu.se
> > <http://www.democritos.it/mailman/listinfo/pw_forum>, eyvaz_isaev at
> > yahoo.com <http://www.democritos.it/mailman/listinfo/pw_forum>
> > *>>>*
> > *>>>*
> > *>>>* From: pari shok<parishok at gmail.com
> > <http://www.democritos.it/mailman/listinfo/pw_forum>>
> > *>>>* To: pw_forum at pwscf.org
> > <http://www.democritos.it/mailman/listinfo/pw_forum>
> > *>>>* Sent: Sun, April 3, 2011 1:34:51 AM
> > *>>>* Subject: [Pw_forum] shift of energy
> > *>>>*
> > *>>>* Dear Paolo,
> > *>>>* DOS of 72-atom SiC shows a shift of energy with respect to 8-atom
> > SiC.The
> > *>>>* bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is
> around
> > 5-7
> > *>>>* eV. Would you please help me to understand this shift.
> > *>>>*
> > *>>>* Thanks again.
> > *>>>* P Shok
> > *>>>* UMD
> > *>>>*
> > *>>>* On Apr 1, 2011, at 21:36 , pari shok wrote:
> > *>>>>* The DOS of 72-atom SiC (supercell) shows a shift of energy.
> > *>>>* a shift with respect to what?
> > *>>>* ---
> > *>>>* Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> > *>>>*
> > *>>>* Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> > *>>>* Phone +39-0432-558216, fax +39-0432-558222
> > *>>>*
> > *>>>* _______________________________________________
> > *>>>* Pw_forum mailing list
> > *>>>* Pw_forum at pwscf.org <
> > http://www.democritos.it/mailman/listinfo/pw_forum>
> > *>>>* http://www.democritos.it/mailman/listinfo/pw_forum
> > *>>* ? Gabriele Sclauzero, EPFL SB ITP CSEA
> > *>>*     PH H2 462, Station 3, CH-1015 Lausanne
> > *>*
> > *>*
> > *
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://www.democritos.it/pipermail/pw_forum/attachments/20110404/6c0c645c/attachment-0001.htm
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Mon, 4 Apr 2011 11:04:51 -0400
> > From: Duy Le <ttduyle at gmail.com>
> > Subject: Re: [Pw_forum] Shift of Energy
> > To: PWSCF Forum <pw_forum at pwscf.org>
> > Cc: pari shok <parishok at gmail.com>
> > Message-ID: <BANLkTi=keZQ5tpRzvHs7t_d4x7V7Jrw7Qw at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > On Mon, Apr 4, 2011 at 10:32 AM, pari shok <parishok at gmail.com> wrote:
> > > Dear All,
> > > Thank you very much for your help.
> > > Please let me ask my final question w.r.t DOS shift of energy of SiC
> > > supercell.
> > > The total energy of the 8-atom cell of SiC is: -76.276 Ry, while that
> of
> > > 72-atom SiC is -694 Ry. Neglecting almost -7 Ry, the total energy is
> > scaling
> > > accordingly.
> > If you are doing correctly, the results must be identical. So make
> > sure to check the structures, and the convergence of total energy vs.
> > cutoff energy and k-point sampling.
> > > However, I still see the shift of energy in DOS diagram of two slabs
> (the
> > > max and min of bandgap shifts, although the gap is almost 2.1 eV for
> both
> > > 4H-SiC slabs). I was wondering whether this shift of energy is
> inevitable
> > or
> > > it is as the result of my input file.
> > Slab? I though you are performing bulk calculation. Anyway, the shift
> > of energies' levels is normal. You should set the reference as center
> > of the gap (set it to be zero) then compare the DOS or band
> > structures.
> > By the way, if your bigger slab experiences the reconstruction, the
> > two slabs (8 atoms and 72 atoms) won't be identical => you should not
> > get the same results in this case. But 7Ry seems to be huge.
> > > I kept k points (w.r.t. crystal), and cut off energy the same for both
> > > structures. Should I scale the cut off energy as well. If positive, is
> > there
> > Okie, but you should scale the k-point sampling accordingly because
> > the BZ of 72 atoms cell is smaller. But this won't harm the results if
> > total energy is already converged vs. k-point sampling.
> > > any relation between scaling the cell and cut off energy.
> > No. Cut off energy depends on only pseudo potential.
> > > As you know, I need to find a reference for my further calculations.
> > > I really really appreciate your help.
> > > Yours
> > > P Shok
> > >
> >
> > --------------------------------------------------
> > Duy Le
> > PhD Student
> > Department of Physics
> > University of Central Florida.
> >
> > "Men don't need hand to do things"
> > > Dear  All,
> > >      let me clarify a little point.
> > >      The potential (hence the eigenvalues) of  any calculation in
> > > periodic boundary conditions, not just a plane-wave one , is defined up
> > >
> > > to  an additive constant... In a finite system a reeference can be
> fixed
> > > by requiring that the potential goes to zero at infinite distance but
> in
> > > a periodic system this cannot be defined as there is nothing like a
> > >
> > > point at infinite distance ...
> > >     In most codes (and in pw.x) this arbitrary constant is fixed by
> > > setting the average electrostatic potential to zero. If the supercell
> is
> > > properly constructed, with the properly scaled dimensions, the same
> > >
> > > cutoff, equivalent k-points etc.. the two calculations should be
> > > equivalent and the eigenvalues should be exactly mapped, the average
> > > potential should be the same, the total energy should be an exact
> > > multiple of the one of the original cell.
> > >
> > >
> > > If this does not happen one is NOT doing the supercell calculation
> > properly.
> > >
> > > So if when doing a supercell you do not get the scaled result check
> your
> > > system definition.
> > >
> > > stefano
> > >
> > >
> > > On 04/04/2011 11:46 AM, Giuseppe Mattioli wrote:
> > >
> > >> Dear all
> > >> I suspect that a a little misunderstanding has been going on here...
> > >> I try to reformulate the question: in the case of a 8-atoms cell the
> > >> valence
> > >> band maximum (VBM) has been found around 10 eV and the conduction band
> > >
> > >> minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift
> in
> > >> the
> > >> position of VBM and CBM when calculated in a 72-atoms supercell, but
> the
> > >> band
> > >> gap value is the same. Then, the answer to P Shok could be: plane wave
> > >
> > >> pseudopotential calculations do not ensure an universal alignment of
> > >> eigenvalues. You should use some "internal" reference, like the 1s
> > >> eigenvalue
> > >> of an He atom, in your cell; or trust that the two VBM values are
> > aligned
> > >> "de
> > >
> > >> facto".
> > >> HTH
> > >>
> > >> Giuseppe
> > >>
> > >> On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote:
> > >>> Yes,
> > >>>
> > >>>     I perfectly agree with Eyvaz! Moreover the experimental bandgap
> is
> > >
> > >>> underestimated within LDA or GGA, and for 4H-SiC you would get about
> > >>> 2.2-2.3 eV with LDA.
> > >>>
> > >>>     How do you measure the bandgap? Beware that in the fundamental
> cell
> > >>> the
> > >
> > >>> bandgap is not a direct one, but it might become such when you use a
> > >>> supercell (because of the refolding of the Brillouin zones).
> > >>>
> > >>>
> > >>> HTH
> > >
> > >>>
> > >>> GS
> > >>>
> > >>> Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto:
> > >>>> Hi,
> > >>>>
> > >>>>> The bandgap of 8-atoms is around 10-12 eV,
> > >
> > >>>>> but that of 72-atom is around 5-7 eV.
> > >>>> This is unbelievable, as SiC is an indirect band gap semiconductor
> and
> > >>>> the bandgap is around (2.5 - 3)eV depending on crystal modification
> > >
> > >>>> (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.).
> > >>>> See http://www.matprop.ru/SiC_bandstr
> > >>>>
> > >>>> So, check carefully your input/output files.
> > >
> > >>>>
> > >>>> Bests,
> > >>>> Eyvaz.
> > >>>>
> > >>>> -------------------------------------------------------------------
> > >>>> Prof. Eyvaz Isaev,
> > >
> > >>>> Department of Physics, Chemistry, and Biology (IFM), Linkoping
> > >>>> University, Sweden Theoretical Physics Department, Moscow State
> > >>>> Institute
> > >>>> of Steel&  Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at
> > yahoo.com
> > >
> > >>>>
> > >>>>
> > >>>> From: pari shok<parishok at gmail.com>
> > >>>> To: pw_forum at pwscf.org
> > >
> > >>>> Sent: Sun, April 3, 2011 1:34:51 AM
> > >>>> Subject: [Pw_forum] shift of energy
> > >>>>
> > >>>> Dear Paolo,
> > >>>> DOS of 72-atom SiC shows a shift of energy with respect to 8-atom
> > >>>> SiC.The
> > >
> > >>>> bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around
> > 5-7
> > >>>> eV. Would you please help me to understand this shift.
> > >>>>
> > >>>> Thanks again.
> > >
> > >>>> P Shok
> > >>>> UMD
> > >>>>
> > >>>> On Apr 1, 2011, at 21:36 , pari shok wrote:
> > >>>>> The DOS of 72-atom SiC (supercell) shows a shift of energy.
> > >
> > >>>> a shift with respect to what?
> > >>>> ---
> > >>>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> > >>>>
> > >>>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> > >
> > >>>> Phone +39-0432-558216, fax +39-0432-558222
> > >>>>
> > >>>> _______________________________________________
> > >>>> Pw_forum mailing list
> > >>>> Pw_forum at pwscf.org
> > >
> > >>>> http://www.democritos.it/mailman/listinfo/pw_forum
> > >>> ? Gabriele Sclauzero, EPFL SB ITP CSEA
> > >>>     PH H2 462, Station 3, CH-1015 Lausanne
> > >
> > >>
> > >>
> > >
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> > >
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Tue, 5 Apr 2011 00:14:21 +0800 (CST)
> > From: ?S <flux_ray12 at 163.com>
> > Subject: Re: [Pw_forum] 4.3 compile error.
> > To: "PWSCF Forum" <pw_forum at pwscf.org>
> > Message-ID: <174f5d1.7e22.12f214b1d61.Coremail.flux_ray12 at 163.com>
> > Content-Type: text/plain; charset="gbk"
> >
> > Hi, Vit.
> > I got the same problem like you.
> >
> > You can open the file TDDFPT/src/lr_main.f90 and find the line 252. It
> > should be written as:
> > IF ( lr_io_level > 0 .and. (mod(LR_iteration,restart_step)==0 .OR.
> > LR_iteration==itermax .OR. LR_iteration==1) ) CALL lr_write_restart()
> > Then, you can add a '&' after '==1) )' and put 'CALL lr_write_restart()'
> to
> > the next line.
> > Do not forget add enough space before 'CALL lr_write_restart()',
> otherwise
> > it would become annotate instead of code.
> > The modified one could like:
> > IF ( lr_io_level > 0 .and. (mod(LR_iteration,restart_step)==0 .OR.
> > LR_iteration==itermax .OR. LR_iteration==1) )  &
> >           CALL lr_write_restart()
> >
> >
> > At 2011-04-03 19:41:28?Vit <vitruss at gmail.com> wrote:
> >
> > >Dear QE users!
> > >I'm having troubles compiling new release. I'm trying to use ACML where
> > >apllicable, but I'm getting the same error even with distro (debian
> 6.0.1)
> > >blas and lapack and internal fftw.
> > >Could you please help me resolving this issue?
> > >
> > >mpif90 -g -o turbo_lanczos.x \
> > >                lr_variables.o lr_charg_resp.o bcast_lr_input.o
> > lr_readin.o
> > >lr_alloc_init.o lr_calc_dens.o lr_dot.o lr_dealloc.o lr_ortho.o
> > lr_read_wf.o
> > >lr_normalise.o lr_lanczos.o lr_apply_liouvillian.o lr_main.o
> lr_dv_setup.o
> > >lr_setup_dgc.o lr_solve_e.o lr_dvpsi_e.o lr_ch_psi_all.o
> lr_cgsolve_all.o
> > >lr_h_psiq.o lr_sm1_psi.o stop_lr.o lr_read_d0psi.o lr_restart.o
> > >lr_write_restart.o print_clock_lr.o sd0psi.o lr_set_boxes_density.o
> > >lr_init_nfo.o  ../../PH/libph.a ../../PW/libpw.a
> ../../Modules/libqemod.a
> > >../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a
> > >../../iotk/src/libiotk.a   -L/opt/acml4.4.0/gfortran64/lib -lacml -
> > >L/opt/acml4.4.0/gfortran64/lib -lacml -L/opt/acml4.4.0/gfortran64/lib
> > -lacml
> > >lr_main.o: In function `lr_main':
> > >/opt/qe/4.3/TDDFPT/src/lr_main.f90:252: undefined reference to `lr_wri_'
> > >collect2: ld returned 1 exit status
> > >make[2]: *** [turbo_lanczos.x] Error 1
> > >make[2]: Leaving directory `/opt/qe/4.3/TDDFPT/src'
> > >make[2]: Entering directory `/opt/qe/4.3/TDDFPT/tools'
> > >test -n "" && ( cd ../.. ; make -w  || exit 1) || :
> > >mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__ACML -D__MPI
> -
> > >D__PARA -I../../include -I../../iotk/src -I../../Modules -I. -c
> > >tddfpt_calculate_spectrum.f90
> > >mpif90 -g -o turbo_spectrum.x \
> > >        tddfpt_calculate_spectrum.o ../../Modules/libqemod.a
> > ../../PW/libpw.a
> > >../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a
> > >../../iotk/src/libiotk.a   -L/opt/acml4.4.0/gfortran64/lib -lacml -
> > >L/opt/acml4.4.0/gfortran64/lib -lacml -L/opt/acml4.4.0/gfortran64/lib
> > -lacml
> > >( cd ../../bin ; ln -fs ../TDDFPT/tools/turbo_spectrum.x . )
> > >if [ -d ../bin ] ; then  ( cd ../bin ; ln -fs ../tools/turbo_spectrum.x
> .
> > );
> > >fi
> > >make[2]: Leaving directory `/opt/qe/4.3/TDDFPT/tools'
> > >make[1]: Leaving directory `/opt/qe/4.3/TDDFPT'
> > >
> > >With best regards,
> > >Koroteev Victor.
> > >_______________________________________________
> > >Pw_forum mailing list
> > >Pw_forum at pwscf.org
> > >http://www.democritos.it/mailman/listinfo/pw_forum
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
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> >
> http://www.democritos.it/pipermail/pw_forum/attachments/20110405/a5f0eb48/attachment.htm
> >
> >   Hi dear users.
>  is there anybody who's know about Teter pseudopotential.I used it for
> Sr.Sr has 38 electrons and valence electrons should be 4s2 4p6 5s2 4d0 in
> ground state but in this pseudopotential zion=10 and the valence electrons
> are 4s2 4p6 5s0 4d0!whate's the maning of it?can i use it for ground state
> alculation?
> Ok! this pseudopotential is used in abinit but i can't ask my question of
> them.
> thank's alot.
>
> > ------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> > End of Pw_forum Digest, Vol 46, Issue 10
> > ****************************************
> >
> -------------- next part --------------
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>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 46, Issue 12
> ****************************************
>

dear Gabriele
Ok!in this stage my question is about pseudopotentials in general no
software.
I guessed maybe one has information about various parameters in
pseudopotentials and know what are applications different kinds of them or
recommend me refrence.my question was'nt only Teter pseudopotential and are
general.it is irrational?
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From eariel99 at gmail.com  Tue Apr  5 15:44:10 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Tue, 5 Apr 2011 10:44:10 -0300
Subject: [Pw_forum] Problems with electrostatic corrections (Makov-Payne or
 density counter charge) for aperiodic systems in 4.2 version
Message-ID: <BANLkTinTEAmVsonPUjmefjCuQ3xfi0hZ3w@mail.gmail.com>

2) Why the DCC correction is disabled in version 4.2? Indeed when setting
asume_isolated = 'dcc' and &EE input parameters to their default  values, I
obtain an error message "DCC correction is disabled". Looking in the
PW/input.f90 subroutine, one found that the dcc correction is disabled by an
immediate call to errore subroutine.

I guess some bug was discovered ans is not fixed yet.
I take the occasion to ask if the DCC correction has been or will be
available for slab calculations.
-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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From degironc at sissa.it  Tue Apr  5 15:46:12 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Tue, 05 Apr 2011 15:46:12 +0200
Subject: [Pw_forum] Pw_forum Digest, Vol 46, Issue 12
In-Reply-To: <BANLkTimugLgbqG91uNgWKCi_wYQFeKbjxA@mail.gmail.com>
References: <mailman.11031.1301942887.1814.pw_forum@pwscf.org>
	<BANLkTimugLgbqG91uNgWKCi_wYQFeKbjxA@mail.gmail.com>
Message-ID: <20110405154612.xtjk8ix28ksw4cww@webmail.sissa.it>

Dear  bahaareh tavakoli nejad,

   please make an effort to
    1) provide a meaningful subject line
    2) not reply including a full Digest email full of junk
    3) provide your affiliation

   In order to maximize your chance of getting an answer you should  
make it understandable and possibly sopecific.

   HTH

    stefano

Quoting bahaareh tavakoli nejad <bahaartv at gmail.com>:
.... AFTER TONS OF JUNK
>
> dear Gabriele
> Ok!in this stage my question is about pseudopotentials in general no
> software.
> I guessed maybe one has information about various parameters in
> pseudopotentials and know what are applications different kinds of them or
> recommend me refrence.my question was'nt only Teter pseudopotential and are
> general.it is irrational?
>



----------------------------------------------------------------
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From giannozz at democritos.it  Tue Apr  5 16:35:15 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 05 Apr 2011 16:35:15 +0200
Subject: [Pw_forum] Problems with electrostatic corrections	(Makov-Payne
	or density counter charge) for aperiodic systems in 4.2 version
In-Reply-To: <BANLkTinTEAmVsonPUjmefjCuQ3xfi0hZ3w@mail.gmail.com>
References: <BANLkTinTEAmVsonPUjmefjCuQ3xfi0hZ3w@mail.gmail.com>
Message-ID: <1302014115.6852.3.camel@fe12lx.fisica.uniud.it>

On Tue, 2011-04-05 at 10:44 -0300, Eduardo Ariel Menendez Proupin wrote:

> I guess some bug was discovered ans is not fixed yet. 

"bit-rotting" : if you leave a piece of code unattended, it will cease
to work for no apparent reason. 

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



From oliviero at MIT.EDU  Tue Apr  5 16:37:59 2011
From: oliviero at MIT.EDU (Oliviero Andreussi)
Date: Tue, 05 Apr 2011 15:37:59 +0100
Subject: [Pw_forum] Problems with electrostatic corrections (Makov-Payne
 or density counter charge) for aperiodic systems in 4.2 version
Message-ID: <4D9B2947.6020609@mit.edu>



1) Roughly speaking, eq. 15 of the original Makov-Payne paper express
the energy of periodic system (E) in terms of the energy of the isolated
system (E0) plus the energy of interaction between the periodic replicas
(E11 and E12). Neglecting the fact that the E12 term has the wrong sing
in the original equation (as it is stressed in a comment in the code),
to obtain the energy of the isolated system you want to subtract E11 and
E12 from your periodic total energy, as it is done in the code, i.e.
E0=E-E11-E12.

2) The DCC correction was not bugged or bit-rotting, and, as far as I know,
it was also working for 2D cases. It was removed from the code in order to clean it
and make pw's compilation easier: this is because DCC required an external
multigrid solver an a somehow cumbersome implementation. One of the
developers of the original DCC code (Ismaila Dabo) is now working on a
different version of the DCC that do not require multigrid solvers.

Best,

Oliviero Andreussi

Postdoctoral Associate MIT-DMSE,
77 Massachusetts Ave, Office 13-4084,
Cambridge, MA, 02139 USA

Visiting Researcher, Oxford University,
Departments of Materials, Rex Richards Building,
Park Road, Oxford, Oxon, OX1 3PH, UK

-------- Original Message --------
>  Subject: 	[Pw_forum] Problems with electrostatic corrections
>  (Makov-Payne or density counter charge) for aperiodic systems in 4.2 version
>  Date: 	Tue, 5 Apr 2011 13:33:22 +0100
>  From: 	ilyes hamdi<iiysidi at gmail.com>
>  Reply-To: 	PWSCF Forum<pw_forum at pwscf.org>
>  To: 	pw_forum at pwscf.org<pw_forum at pwscf.org>
>
>
>
>  Dear espresso users,
>
>  1) I'm a bit confused with the implementation of the Makov-Payne
>  electrostatic corrections in PW/makov-payne.f90 in Version 4.2:
>  - In their original paper, Makov and Payne define the first order
>  correction E11 =  - \alpha * q^2/(2\epsilon* L). This quantity should be
>  negative for cubic systems, however
>  the writing statement in PW/makov-payne.f90 subroutine defines the
>  correction to be -E11 (leading to a positive value).
>  - The second order correction E12 is propertional to q Q/L^3 and is also
>  defined as -E12 in the PW/makov-payne.f90 subroutine.
>  - The total energy should be Etot = E0 + E11 + E12 = E0 - \alpha *
>  q^2/(2\epsilon* L) + 2 \pi * q * Q / ( 3 \epsilon L^3), however it is
>  implemented as E0-E11-E12.
>
>  2) Why the DCC correction is disabled in version 4.2? Indeed when
>  setting asume_isolated = 'dcc' and&EE input parameters to their
>  default  values, I obtain an error message "DCC correction is disabled".
>  Looking in the PW/input.f90 subroutine, one found that the dcc
>  correction is disabled by an immediate call to errore subroutine.
>
>  Please can any one verify if I'm correct or did I miss something.
>
>  Best regards
>
>
>


From meinert at physik.uni-bielefeld.de  Tue Apr  5 18:06:22 2011
From: meinert at physik.uni-bielefeld.de (Markus Meinert)
Date: Tue, 05 Apr 2011 18:06:22 +0200
Subject: [Pw_forum] Nonlinear scaling with pool parallelization
Message-ID: <13591_1302019580_ZZh0n7G2X1ZlY.00_4D9B3DFE.9060400@physik.uni-bielefeld.de>

Dear QE users and developers,

for some larger calculations I just obtained a small Beowulf type 
cluster, consisting of three machines with hexacore i7 CPUs, connected 
with gigabit ethernet. It runs Ubuntu 64bit, QE 4.2.1 is compiled with 
GCC 4.4, and I have compiled OpenMPI 1.4.3. The code is linked against 
the pre-compiled libatlas-corei7sse3 from Ubuntu.

I want to perform calculations of quite large supercells for interface 
and surface studies of magnetic materials. Now, I'm testing the 
parallelization schemes. My understanding is that pool parallelization 
should scale approximately linearly with nodes. Indeed, the calculation 
of a bulk material scales nearly linearly with the number of nodes when 
I assign each node an individual pool. In contrast, if I do not assign 
pools, the calculations slow down extremely because of the communication 
overhead.

Now we come to the strange part: the slab calculation. I did some quick 
timing tests which I would like to share with you. The times given in 
seconds are just the numbers the code provides when it runs (checked 
them however with htop).

WITH pools:
np	npool	setup	first iteration
6	1	108s	250s
12	2	78s	180s
18	3	69s	152s

WITHOUT pools:
np	setup	first iteration
6	108s	250s
12	75s	186s
18	59s	152s

Without pools I have heavy load on the ethernet, but the calculations 
are about as fast as the ones with pools. With pools, there's almost no 
communication, apart from a few bursts. More importantly, the scaling of 
the calculation with pools is far from linear. With three machines, I 
get less than a factor of two in speed. The gain when going from two to 
three machines is just of the order of 25%.

My program call is:
mpirun -np 18 -hostfile ~/.mpi_hostfile 
~/espresso/espresso-4.2.1/bin/pw.x -npool 3 -in pw.in | tee pw.out

The pw.x program understands the call:

      Parallel version (MPI), running on    18 processors
      K-points division:     npool     =    3
      R & G space division:  proc/pool =    6

Can you explain this behavior? Is there anything I can tune to get a 
better scaling? Is there a known bottleneck for a setup like this? Can 
this be associated with the choice of k-point meshes? For bulk I have a 
shifted 8x8x8 mesh, for the slab I have a 8 8 1 1 1 0 setting.

If you would like to have the input files to reproduce the problem, 
please tell me.

With kind regards,
Markus Meinert


-- 
Dipl.-Phys. Markus Meinert

Thin Films and Physics of Nanostructures
Department of Physics
Bielefeld University
Universit?tsstra?e 25
33615 Bielefeld

Room D2-118
e-mail: meinert at physik.uni-bielefeld.de
Phone: +49 521 106 2661

From giannozz at democritos.it  Tue Apr  5 18:54:34 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 05 Apr 2011 18:54:34 +0200
Subject: [Pw_forum] Nonlinear scaling with pool parallelization
In-Reply-To: <13591_1302019580_ZZh0n7G2X1ZlY.00_4D9B3DFE.9060400@physik.uni-bielefeld.de>
References: <13591_1302019580_ZZh0n7G2X1ZlY.00_4D9B3DFE.9060400@physik.uni-bielefeld.de>
Message-ID: <1302022474.6852.36.camel@fe12lx.fisica.uniud.it>

On Tue, 2011-04-05 at 18:06 +0200, Markus Meinert wrote:

> For bulk I have a shifted 8x8x8 mesh, for the slab I have a 8 8 1 1 1 0 setting.

how many k-points? P.
-- 
 Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222 


From meinert at physik.uni-bielefeld.de  Tue Apr  5 19:54:35 2011
From: meinert at physik.uni-bielefeld.de (Markus Meinert)
Date: Tue, 05 Apr 2011 19:54:35 +0200
Subject: [Pw_forum] Nonlinear scaling with pool parallelization
Message-ID: <17556_1302026072_ZZh0n0H4l0ks_.00_4D9B575B.4060208@physik.uni-bielefeld.de>

Sorry, I should go into a little bit more detail here. I used an 
_unshifted_ k-mesh. When I use a 8x8x8 mesh, yielding 58 points, I get a 
speedup of about 2 on three machines. With a 12x12x12 mesh with 144 
points the speedup becomes better (factor 2.6 for cpu time and 2.3 for 
WALL). I used to think that's because of communication. In the former 
case, an iteration takes less than a second. With more k points, the 
speedup converges slowly towards 3.

The slab has 20 k points. But, since a single iteration takes about 100 
seconds, I do not see where the time is being spent, when the k points 
are independent.

Regards,
Markus

-- 
Dipl.-Phys. Markus Meinert

Thin Films and Physics of Nanostructures
Department of Physics
Bielefeld University
Universit?tsstra?e 25
33615 Bielefeld

Room D2-118
e-mail: meinert at physik.uni-bielefeld.de
Phone: +49 521 106 2661

From giannozz at democritos.it  Tue Apr  5 21:54:02 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 5 Apr 2011 21:54:02 +0200
Subject: [Pw_forum] Nonlinear scaling with pool parallelization
In-Reply-To: <17556_1302026072_ZZh0n0H4l0ks_.00_4D9B575B.4060208@physik.uni-bielefeld.de>
References: <17556_1302026072_ZZh0n0H4l0ks_.00_4D9B575B.4060208@physik.uni-bielefeld.de>
Message-ID: <65F016CA-33E7-47CA-A04B-3FCBCFCB143B@democritos.it>

On Apr 5, 2011, at 19:54 , Markus Meinert wrote:

> I used an _unshifted_ k-mesh

it doesn't matter if it is shifted or unshifted: only the number of k- 
points
matters for k-point parallelization.

> The slab has 20 k points.

20 k-points on 3 processors = 7+7+6: load balancing is not ideal.
This is likely to be a minor factor, though.

> But, since a single iteration takes about 100 seconds, I do not
> see where the time is being spent, when the k points are independent.

you do not see because you do not know where to look. Not that it
is explained somewhere...have a look into the final report:
* the time spent in "c_bands" and called routines is proportional to the
   number of k-points, so it will scale linearly with the number of  
"k-point pools"
* the time spent in "sum_band" is only in part proportional to the  
number
   of k-points and will partially scale
* the time spent in "v_of_rho", "newd", "mix_rho", is independent  
upon the
   number of of k-points and will not scale at all
* k-point parallelization does not reduce memory
* The rest is usually irrelevant
Also note that
* FFT parallelization distributes most memory
* FFT parallelization speeds up (with varying efficiency) almost all  
routines,
   with the exception of "cdiaghg" or "rdiaghg"
* linear-algebra parallelization (that you are not using) will (not  
always) speed
   up   "cdiaghg" or "rdiaghg" and distribute more memory
Alles klar?

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





From trambui at u.boisestate.edu  Tue Apr  5 23:42:56 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Tue, 5 Apr 2011 15:42:56 -0600
Subject: [Pw_forum] Generating ultra soft pseudopotential
Message-ID: <BANLkTi=pmuBY4W3_84vsE_m1okCtMSg0rQ@mail.gmail.com>

Dear Folks,
     I'm trying to build an input file for generating the Cs
pseudopotential. when I run the ld1.x on my input file. I got an error
message saying that i'm using the wrong core. would you help me with extra
information of where I can find the help for how to choose the right core
for some atoms such as in my case it is Cs.

Thank you very much,

Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From ttduyle at gmail.com  Wed Apr  6 02:35:08 2011
From: ttduyle at gmail.com (Duy Le)
Date: Tue, 5 Apr 2011 20:35:08 -0400
Subject: [Pw_forum] Generating ultra soft pseudopotential
In-Reply-To: <BANLkTi=pmuBY4W3_84vsE_m1okCtMSg0rQ@mail.gmail.com>
References: <BANLkTi=pmuBY4W3_84vsE_m1okCtMSg0rQ@mail.gmail.com>
Message-ID: <BANLkTinwZhgYzbc+H_wsrxCPOO_SsJ=1tg@mail.gmail.com>

Some available PP of Cs can be found at
http://charter.cnf.cornell.edu/psplist.php?element=Cs
If you can not find what you need there, you can follow the
instruction (videos and slides) July 25
http://media.quantum-espresso.org/santa_barbara_2009_07/index.php
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Tue, Apr 5, 2011 at 5:42 PM, Tram Bui <trambui at u.boisestate.edu> wrote:
> Dear Folks,
> ???? I'm trying to build an input file for generating the Cs
> pseudopotential. when I run the ld1.x on my input file. I got an error
> message saying that i'm using the wrong core. would you help me with extra
> information of where I can find the help for how to choose the right core
> for some atoms such as in my case it is Cs.
>
> Thank you very much,
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

From alex968873 at yahoo.com.cn  Wed Apr  6 07:06:01 2011
From: alex968873 at yahoo.com.cn (=?gb2312?B?wO6x8w==?=)
Date: Wed, 6 Apr 2011 13:06:01 +0800 (CST)
Subject: [Pw_forum] noncollinear stress + GGA not implemented
Message-ID: <238973.63990.qm@web15108.mail.cnb.yahoo.com>

Dear all,

I wanna do 'vc-relax' calculation with noncollinear magnetisim, but the output file says
 'noncollinear stress + GGA not implemented' and the relaxation result didn't change the
 lattice parameters. So how to deal with that? employ  LDA in the calculation?

Thank you! 
B. Li


From germaneau at gucas.ac.cn  Wed Apr  6 19:20:36 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Wed, 06 Apr 2011 13:20:36 -0400
Subject: [Pw_forum] graphite cell optimization failed
In-Reply-To: <500945398.02595@test1.gucas.ac.cn>
References: <500855720.31742@test1.gucas.ac.cn>
	<500945398.02595@test1.gucas.ac.cn>
Message-ID: <4D9CA0E4.3010602@gucas.ac.cn>

Dear all,

For people who are interested here is the result of my graphite 
calculations including vdW-DF method from the release 4.3.


GGA                                            GGA - london GGA - 
vdW-DF                           LDA                                  EXP

a = 2.46854 angs                  a =  2.46283 angs a = 2.47107  angs 
                    a = 2.44424                  a = 2.46067
c = 8.02141 angs  (1.3514)    c =  6.39949 angs (0.2705) c = 7.27887 
angs (0.60887)    c = 6.49579 (0.1742)    c = 6.705 (6.67 at 0K)

The number in parenthesize is abs(exp-calc).
 From my calculations the best option after LDA approach to include vdW 
interactionsis still GGA + London.
I thank you again for your help.

                  Eric.


On 03/24/2011 01:45 PM, Eric Germaneau wrote:
> Dear QE users,
>
> First of all I thank you all so much for your very useful replies and 
> advices.
> I did again the calculation this time using 16x16x8 k-points with cold 
> smearing  as suggested in PRB 71, 205214 (2005).
> I've also increased the precision of the atomic coordinates.
> Finally, I preformed the calculation using GGA only, GGA+london, and LDA.
> I got the following results:
>
> GGA                             GGA - 
> london                                
> LDA                                                             EXP
>
> a = 2.46854 angs       a =  2.46283 angs                          a = 
> 2.44424                                         a = 2.46067
> c = 8.02141 angs       c =  6.39949 angs                          c = 
> 6.49579                                         c = 6.705 (6.67 at 0K)
> energy = -155.032      energy =  -155.146 ev/atom           energy = 
> -155.481 ev/atom
>
> The DFT-D approach improve significatively the length of the c axis.
> I'm currently trying to do the same thing with the vdW-DF method 
> implemented in QE 4.3a but the program crash with the error:
>
> /     from ggen : error #     45126
>      too many g-vectors/
>
> Best,
>
>              Eric.
>
> On 03/23/2011 12:33 PM, Eric Germaneau wrote:
>> Dear all,
>>
>> I'm trying to optimize unit cell parameter of graphite.
>> The problem is the c axis gets too long.
>> Starting from published data my initial parameters are a=4.59203 Bohr 
>> and c=12.513 Bohr.
>> The final values are 4.664 and 15.829 respectively.
>> I need someone to explain to me what I did wrong, I've attached my 
>> input file.
>> That's a basic calculation so it's very frustrating to not make it done.
>> I thank you in advance,
>>
>>                                     Eric.
>>
>> -- 
>> /Be the change you wish to see in the world
>> / --- Mahatma Gandhi ---
>>
>> Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>
>>
>> College of Physical Sciences
>> Graduate University of Chinese Academy of Sciences
>> Yuquan Road 19A
>> Beijing 100049
>> China
>>
>> /Please consider the environment before printing this email.
>> Consid?rez svp l'environnement avant d'imprimer cet email. /
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
> -- 
> /Be the change you wish to see in the world
> / --- Mahatma Gandhi ---
>
> Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>
>
> College of Physical Sciences
> Graduate University of Chinese Academy of Sciences
> Yuquan Road 19A
> Beijing 100049
> China
>
> /Please consider the environment before printing this email.
> Consid?rez svp l'environnement avant d'imprimer cet email. /
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/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 tone.kokalj at ijs.si  Wed Apr  6 16:36:13 2011
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Wed, 06 Apr 2011 16:36:13 +0200
Subject: [Pw_forum] charge density output format from pp.x
In-Reply-To: <42158.200.0.233.52.1301945122.squirrel@mail.cab.cnea.gov.ar>
References: <4CEBFF39.40505@fu-berlin.de>
	<1290592007.12941.6.camel@ulisse.cm.sissa.it>
	<54782.200.0.233.52.1301691705.squirrel@mail.cab.cnea.gov.ar>
	<A9314ABA-E41D-482F-B549-D5852F6C8405@democritos.it>
	<42158.200.0.233.52.1301945122.squirrel@mail.cab.cnea.gov.ar>
Message-ID: <1302100573.3296.17.camel@catalyst.ijs.si>

On Mon, 2011-04-04 at 16:25 -0300, jorge.gallardo at cab.cnea.gov.ar wrote:
> > you can extract the charge density (with pp.x) in a number of different
> > formats. For the relation between indices and positions in real space:
> > http://www.quantum-espresso.org/user_guide/node23.html
> >
> 
> thank you for you response.
> 
> I tried to do something like that, but I cannot understand the content of
> the file "al.rho.dat". I suppose that the density is in the big block of 6
> numerical columns "DATAGRID_3D_UNKNOWN", but, How is ordered that block? ,
> In what order should I read it?.

I would suggest you follow the hint of Paolo, nevertheless, here is the
order of how the datagrid is written:

write(*,*) (((value(ix,iy,iz),ix=1,nx),iy=1,ny),iz=1,nz)

for more specs, see: 
http://www.xcrysden.org/doc/XSF.html

Regards, Tone

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html


From meinert at physik.uni-bielefeld.de  Wed Apr  6 17:52:22 2011
From: meinert at physik.uni-bielefeld.de (Markus Meinert)
Date: Wed, 06 Apr 2011 17:52:22 +0200
Subject: [Pw_forum] Nonlinear scaling with pool parallelization
In-Reply-To: <65F016CA-33E7-47CA-A04B-3FCBCFCB143B@democritos.it>
References: <17556_1302026072_ZZh0n0H4l0ks_.00_4D9B575B.4060208@physik.uni-bielefeld.de>
	<65F016CA-33E7-47CA-A04B-3FCBCFCB143B@democritos.it>
Message-ID: <16009_1302105139_ZZh0n3M_acaSe.00_4D9C8C36.8080803@physik.uni-bielefeld.de>

Dear Paolo,

thank you very much for the detailed explanation. That's exactly what I 
needed.

Regards,
Markus

-- 
Dipl.-Phys. Markus Meinert

Thin Films and Physics of Nanostructures
Department of Physics
Bielefeld University
Universit?tsstra?e 25
33615 Bielefeld

Room D2-118
e-mail: meinert at physik.uni-bielefeld.de
Phone: +49 521 106 2661

From bahaartv at gmail.com  Wed Apr  6 21:20:00 2011
From: bahaartv at gmail.com (bahaareh tavakoli nejad)
Date: Wed, 6 Apr 2011 12:20:00 -0700
Subject: [Pw_forum] Problem with concept of parameters in pseudopotentials
Message-ID: <BANLkTimfmd5Kb8V7nCZ_wR7L-iR-9U9oUw@mail.gmail.com>

On Tue, Apr 5, 2011 at 5:35 PM, <pw_forum-request at pwscf.org> wrote:

> Send Pw_forum mailing list submissions to
>        pw_forum at pwscf.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://www.democritos.it/mailman/listinfo/pw_forum
> or, via email, send a message with subject or body 'help' to
>        pw_forum-request at pwscf.org
>
> You can reach the person managing the list at
>        pw_forum-owner at pwscf.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
>   1. Problems with electrostatic corrections (Makov-Payne or
>      density counter charge) for aperiodic systems in 4.2 version
>      (Eduardo Ariel Menendez Proupin)
>   2. Re: Pw_forum Digest, Vol 46, Issue 12 (Stefano de Gironcoli)
>   3. Re: Problems with electrostatic corrections       (Makov-Payne    or
>      density counter charge) for aperiodic systems in 4.2 version
>      (Paolo Giannozzi)
>   4. Re: Problems with electrostatic corrections (Makov-Payne or
>      density counter charge) for aperiodic systems in 4.2 version
>      (Oliviero Andreussi)
>   5. Nonlinear scaling with pool parallelization (Markus Meinert)
>   6. Re: Nonlinear scaling with pool parallelization (Paolo Giannozzi)
>   7. Nonlinear scaling with pool parallelization (Markus Meinert)
>   8. Re: Nonlinear scaling with pool parallelization (Paolo Giannozzi)
>   9. Generating ultra soft pseudopotential (Tram Bui)
>  10. Re: Generating ultra soft pseudopotential (Duy Le)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 5 Apr 2011 10:44:10 -0300
> From: Eduardo Ariel Menendez Proupin <eariel99 at gmail.com>
> Subject: [Pw_forum] Problems with electrostatic corrections
>        (Makov-Payne or density counter charge) for aperiodic systems in 4.2
>        version
> To: pw_forum at pwscf.org
> Message-ID: <BANLkTinTEAmVsonPUjmefjCuQ3xfi0hZ3w at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 2) Why the DCC correction is disabled in version 4.2? Indeed when setting
> asume_isolated = 'dcc' and &EE input parameters to their default  values, I
> obtain an error message "DCC correction is disabled". Looking in the
> PW/input.f90 subroutine, one found that the dcc correction is disabled by
> an
> immediate call to errore subroutine.
>
> I guess some bug was discovered ans is not fixed yet.
> I take the occasion to ask if the DCC correction has been or will be
> available for slab calculations.
> --
>
>
> Eduardo Menendez
> Departamento de Fisica
> Facultad de Ciencias
> Universidad de Chile
> Phone: (56)(2)9787439
> URL: http://fisica.ciencias.uchile.cl/~emenendez
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>
> ------------------------------
>
> Message: 2
> Date: Tue, 05 Apr 2011 15:46:12 +0200
> From: Stefano de Gironcoli <degironc at sissa.it>
> Subject: Re: [Pw_forum] Pw_forum Digest, Vol 46, Issue 12
> To: pw_forum at pwscf.org
> Message-ID: <20110405154612.xtjk8ix28ksw4cww at webmail.sissa.it>
> Content-Type: text/plain;       charset=ISO-8859-1;     DelSp="Yes";
>        format="flowed"
>
> Dear  bahaareh tavakoli nejad,
>
>   please make an effort to
>    1) provide a meaningful subject line
>    2) not reply including a full Digest email full of junk
>    3) provide your affiliation
>
>   In order to maximize your chance of getting an answer you should
> make it understandable and possibly sopecific.
>
>   HTH
>
>    stefano
>
> Quoting bahaareh tavakoli nejad <bahaartv at gmail.com>:
> .... AFTER TONS OF JUNK
> >
> > dear Gabriele
> > Ok!in this stage my question is about pseudopotentials in general no
> > software.
> > I guessed maybe one has information about various parameters in
> > pseudopotentials and know what are applications different kinds of them
> or
> > recommend me refrence.my question was'nt only Teter pseudopotential and
> are
> > general.it is irrational?
> >
>
>
>
> ----------------------------------------------------------------
>   SISSA Webmail https://webmail.sissa.it/
>   Powered by Horde http://www.horde.org/
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 05 Apr 2011 16:35:15 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] Problems with electrostatic corrections
>        (Makov-Payne    or density counter charge) for aperiodic systems in
> 4.2
>        version
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <1302014115.6852.3.camel at fe12lx.fisica.uniud.it>
> Content-Type: text/plain
>
> On Tue, 2011-04-05 at 10:44 -0300, Eduardo Ariel Menendez Proupin wrote:
>
> > I guess some bug was discovered ans is not fixed yet.
>
> "bit-rotting" : if you leave a piece of code unattended, it will cease
> to work for no apparent reason.
>
> P.
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 05 Apr 2011 15:37:59 +0100
> From: Oliviero Andreussi <oliviero at MIT.EDU>
> Subject: Re: [Pw_forum] Problems with electrostatic corrections
>        (Makov-Payne or density counter charge) for aperiodic systems in 4.2
>        version
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4D9B2947.6020609 at mit.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> 1) Roughly speaking, eq. 15 of the original Makov-Payne paper express
> the energy of periodic system (E) in terms of the energy of the isolated
> system (E0) plus the energy of interaction between the periodic replicas
> (E11 and E12). Neglecting the fact that the E12 term has the wrong sing
> in the original equation (as it is stressed in a comment in the code),
> to obtain the energy of the isolated system you want to subtract E11 and
> E12 from your periodic total energy, as it is done in the code, i.e.
> E0=E-E11-E12.
>
> 2) The DCC correction was not bugged or bit-rotting, and, as far as I know,
> it was also working for 2D cases. It was removed from the code in order to
> clean it
> and make pw's compilation easier: this is because DCC required an external
> multigrid solver an a somehow cumbersome implementation. One of the
> developers of the original DCC code (Ismaila Dabo) is now working on a
> different version of the DCC that do not require multigrid solvers.
>
> Best,
>
> Oliviero Andreussi
>
> Postdoctoral Associate MIT-DMSE,
> 77 Massachusetts Ave, Office 13-4084,
> Cambridge, MA, 02139 USA
>
> Visiting Researcher, Oxford University,
> Departments of Materials, Rex Richards Building,
> Park Road, Oxford, Oxon, OX1 3PH, UK
>
> -------- Original Message --------
> >  Subject:     [Pw_forum] Problems with electrostatic corrections
> >  (Makov-Payne or density counter charge) for aperiodic systems in 4.2
> version
> >  Date:        Tue, 5 Apr 2011 13:33:22 +0100
> >  From:        ilyes hamdi<iiysidi at gmail.com>
> >  Reply-To:    PWSCF Forum<pw_forum at pwscf.org>
> >  To:  pw_forum at pwscf.org<pw_forum at pwscf.org>
> >
> >
> >
> >  Dear espresso users,
> >
> >  1) I'm a bit confused with the implementation of the Makov-Payne
> >  electrostatic corrections in PW/makov-payne.f90 in Version 4.2:
> >  - In their original paper, Makov and Payne define the first order
> >  correction E11 =  - \alpha * q^2/(2\epsilon* L). This quantity should be
> >  negative for cubic systems, however
> >  the writing statement in PW/makov-payne.f90 subroutine defines the
> >  correction to be -E11 (leading to a positive value).
> >  - The second order correction E12 is propertional to q Q/L^3 and is also
> >  defined as -E12 in the PW/makov-payne.f90 subroutine.
> >  - The total energy should be Etot = E0 + E11 + E12 = E0 - \alpha *
> >  q^2/(2\epsilon* L) + 2 \pi * q * Q / ( 3 \epsilon L^3), however it is
> >  implemented as E0-E11-E12.
> >
> >  2) Why the DCC correction is disabled in version 4.2? Indeed when
> >  setting asume_isolated = 'dcc' and&EE input parameters to their
> >  default  values, I obtain an error message "DCC correction is disabled".
> >  Looking in the PW/input.f90 subroutine, one found that the dcc
> >  correction is disabled by an immediate call to errore subroutine.
> >
> >  Please can any one verify if I'm correct or did I miss something.
> >
> >  Best regards
> >
> >
> >
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 05 Apr 2011 18:06:22 +0200
> From: Markus Meinert <meinert at physik.uni-bielefeld.de>
> Subject: [Pw_forum] Nonlinear scaling with pool parallelization
> To: pw_forum at pwscf.org
> Message-ID:
>        <
> 13591_1302019580_ZZh0n7G2X1ZlY.00_4D9B3DFE.9060400 at physik.uni-bielefeld.de
> >
>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
> Dear QE users and developers,
>
> for some larger calculations I just obtained a small Beowulf type
> cluster, consisting of three machines with hexacore i7 CPUs, connected
> with gigabit ethernet. It runs Ubuntu 64bit, QE 4.2.1 is compiled with
> GCC 4.4, and I have compiled OpenMPI 1.4.3. The code is linked against
> the pre-compiled libatlas-corei7sse3 from Ubuntu.
>
> I want to perform calculations of quite large supercells for interface
> and surface studies of magnetic materials. Now, I'm testing the
> parallelization schemes. My understanding is that pool parallelization
> should scale approximately linearly with nodes. Indeed, the calculation
> of a bulk material scales nearly linearly with the number of nodes when
> I assign each node an individual pool. In contrast, if I do not assign
> pools, the calculations slow down extremely because of the communication
> overhead.
>
> Now we come to the strange part: the slab calculation. I did some quick
> timing tests which I would like to share with you. The times given in
> seconds are just the numbers the code provides when it runs (checked
> them however with htop).
>
> WITH pools:
> np      npool   setup   first iteration
> 6       1       108s    250s
> 12      2       78s     180s
> 18      3       69s     152s
>
> WITHOUT pools:
> np      setup   first iteration
> 6       108s    250s
> 12      75s     186s
> 18      59s     152s
>
> Without pools I have heavy load on the ethernet, but the calculations
> are about as fast as the ones with pools. With pools, there's almost no
> communication, apart from a few bursts. More importantly, the scaling of
> the calculation with pools is far from linear. With three machines, I
> get less than a factor of two in speed. The gain when going from two to
> three machines is just of the order of 25%.
>
> My program call is:
> mpirun -np 18 -hostfile ~/.mpi_hostfile
> ~/espresso/espresso-4.2.1/bin/pw.x -npool 3 -in pw.in | tee pw.out
>
> The pw.x program understands the call:
>
>      Parallel version (MPI), running on    18 processors
>      K-points division:     npool     =    3
>      R & G space division:  proc/pool =    6
>
> Can you explain this behavior? Is there anything I can tune to get a
> better scaling? Is there a known bottleneck for a setup like this? Can
> this be associated with the choice of k-point meshes? For bulk I have a
> shifted 8x8x8 mesh, for the slab I have a 8 8 1 1 1 0 setting.
>
> If you would like to have the input files to reproduce the problem,
> please tell me.
>
> With kind regards,
> Markus Meinert
>
>
> --
> Dipl.-Phys. Markus Meinert
>
> Thin Films and Physics of Nanostructures
> Department of Physics
> Bielefeld University
> Universit?tsstra?e 25
> 33615 Bielefeld
>
> Room D2-118
> e-mail: meinert at physik.uni-bielefeld.de
> Phone: +49 521 106 2661
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 05 Apr 2011 18:54:34 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] Nonlinear scaling with pool parallelization
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <1302022474.6852.36.camel at fe12lx.fisica.uniud.it>
> Content-Type: text/plain
>
> On Tue, 2011-04-05 at 18:06 +0200, Markus Meinert wrote:
>
> > For bulk I have a shifted 8x8x8 mesh, for the slab I have a 8 8 1 1 1 0
> setting.
>
> how many k-points? P.
> --
>  Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
>  Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>  Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 05 Apr 2011 19:54:35 +0200
> From: Markus Meinert <meinert at physik.uni-bielefeld.de>
> Subject: [Pw_forum] Nonlinear scaling with pool parallelization
> To: pw_forum at pwscf.org
> Message-ID:
>        <
> 17556_1302026072_ZZh0n0H4l0ks_.00_4D9B575B.4060208 at physik.uni-bielefeld.de
> >
>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
> Sorry, I should go into a little bit more detail here. I used an
> _unshifted_ k-mesh. When I use a 8x8x8 mesh, yielding 58 points, I get a
> speedup of about 2 on three machines. With a 12x12x12 mesh with 144
> points the speedup becomes better (factor 2.6 for cpu time and 2.3 for
> WALL). I used to think that's because of communication. In the former
> case, an iteration takes less than a second. With more k points, the
> speedup converges slowly towards 3.
>
> The slab has 20 k points. But, since a single iteration takes about 100
> seconds, I do not see where the time is being spent, when the k points
> are independent.
>
> Regards,
> Markus
>
> --
> Dipl.-Phys. Markus Meinert
>
> Thin Films and Physics of Nanostructures
> Department of Physics
> Bielefeld University
> Universit?tsstra?e 25
> 33615 Bielefeld
>
> Room D2-118
> e-mail: meinert at physik.uni-bielefeld.de
> Phone: +49 521 106 2661
>
>
> ------------------------------
>
> Message: 8
> Date: Tue, 5 Apr 2011 21:54:02 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] Nonlinear scaling with pool parallelization
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <65F016CA-33E7-47CA-A04B-3FCBCFCB143B at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> On Apr 5, 2011, at 19:54 , Markus Meinert wrote:
>
> > I used an _unshifted_ k-mesh
>
> it doesn't matter if it is shifted or unshifted: only the number of k-
> points
> matters for k-point parallelization.
>
> > The slab has 20 k points.
>
> 20 k-points on 3 processors = 7+7+6: load balancing is not ideal.
> This is likely to be a minor factor, though.
>
> > But, since a single iteration takes about 100 seconds, I do not
> > see where the time is being spent, when the k points are independent.
>
> you do not see because you do not know where to look. Not that it
> is explained somewhere...have a look into the final report:
> * the time spent in "c_bands" and called routines is proportional to the
>   number of k-points, so it will scale linearly with the number of
> "k-point pools"
> * the time spent in "sum_band" is only in part proportional to the
> number
>   of k-points and will partially scale
> * the time spent in "v_of_rho", "newd", "mix_rho", is independent
> upon the
>   number of of k-points and will not scale at all
> * k-point parallelization does not reduce memory
> * The rest is usually irrelevant
> Also note that
> * FFT parallelization distributes most memory
> * FFT parallelization speeds up (with varying efficiency) almost all
> routines,
>   with the exception of "cdiaghg" or "rdiaghg"
> * linear-algebra parallelization (that you are not using) will (not
> always) speed
>   up   "cdiaghg" or "rdiaghg" and distribute more memory
> Alles klar?
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Tue, 5 Apr 2011 15:42:56 -0600
> From: Tram Bui <trambui at u.boisestate.edu>
> Subject: [Pw_forum] Generating ultra soft pseudopotential
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <BANLkTi=pmuBY4W3_84vsE_m1okCtMSg0rQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Folks,
>     I'm trying to build an input file for generating the Cs
> pseudopotential. when I run the ld1.x on my input file. I got an error
> message saying that i'm using the wrong core. would you help me with extra
> information of where I can find the help for how to choose the right core
> for some atoms such as in my case it is Cs.
>
> Thank you very much,
>
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
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>
> ------------------------------
>
> Message: 10
> Date: Tue, 5 Apr 2011 20:35:08 -0400
> From: Duy Le <ttduyle at gmail.com>
> Subject: Re: [Pw_forum] Generating ultra soft pseudopotential
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <BANLkTinwZhgYzbc+H_wsrxCPOO_SsJ=1tg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Some available PP of Cs can be found at
> http://charter.cnf.cornell.edu/psplist.php?element=Cs
> If you can not find what you need there, you can follow the
> instruction (videos and slides) July 25
> http://media.quantum-espresso.org/santa_barbara_2009_07/index.php
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
>
> On Tue, Apr 5, 2011 at 5:42 PM, Tram Bui <trambui at u.boisestate.edu> wrote:
> > Dear Folks,
> > ???? I'm trying to build an input file for generating the Cs
> > pseudopotential. when I run the ld1.x on my input file. I got an error
> > message saying that i'm using the wrong core. would you help me with
> extra
> > information of where I can find the help for how to choose the right core
> > for some atoms such as in my case it is Cs.
> >
> > Thank you very much,
> > Tram Bui
> >
> > M.S. Materials Science & Engineering
> > trambui at u.boisestate.edu
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
>
>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 46, Issue 15
> ****************************************
>
I'm trying calculate density of state and other quantities for SrS but i
have problems about concept of different parameters in pseudopotentials, for
example on top of Teter pseudopotential we have :


(Ar+3d10) + 4s2 4p6 5s0 4d0; rcs=rcp=rcd=1.7, no chem-hard, exnc(11);ecut
25/34
  38.00000  10.00000  950923      z,zion,pspdat
  4         3         2   2      2001    0
pspcod,pspxc,lmax,lloc,mmax,r2well
  0  0  0   2    1.69654886360351576          l,e99.0,e99.9,nproj,rcpsp
  .000 .000 .000 .000                         rms,ekb1,ekb2,epsatm
  1  0  0   2    1.69654886360351576          l,e99.0,e99.9,nproj,rcpsp
  .000 .000 .000 .000                         rms,ekb1,ekb2,epsatm
  2  0  0   0    1.69654886360351576          l,e99.0,e99.9,nproj,rcpsp
  .000 .000 .000 .000                         rms,ekb1,ekb2,epsatm
  .000   .000   .000                          rchrg,fchrg,qchrg
  0 = l
is the first line of this pseudopotenial means that only 8 valence electron
are used in calculations (for example calculation of density of states,
bandstructure....)and 4d and 5s orbitals are empty and don't participate in
calculation?

Thanks
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From chenhanghuipwscf at gmail.com  Wed Apr  6 22:01:41 2011
From: chenhanghuipwscf at gmail.com (hanghui chen)
Date: Wed, 6 Apr 2011 16:01:41 -0400
Subject: [Pw_forum] constrained dynamics
Message-ID: <BANLkTimtZ=s+YYuxcbzJFJppR+tZE8XFwA@mail.gmail.com>

To whom it may concern,
     I want to run constrained dynamics to relax the atoms. However, it
seems that if I use 'ion_dynamics = bfgs', the SHAKE algorithm does not
work. Is this true that the SHAKE algorithm is not implemented I use 'bfgs'
method to relax the atoms? Or I did something wrong? The input file is
attached below.
     Thank you very much.

Hanghui Chen
Department of Physics, Yale University

&CONTROL
 calculation='relax'
 wf_collect=.false.
 pseudo_dir = '~/psp'
 outdir='/home/sohrab/hc336/scratch'
 wfcdir='/home/sohrab/hc336/scratch'
 prefix='STO-constrained'
 tprnfor = .true.
 tstress = .true.
 disk_io='none'
 verbosity='default'
 dt=80.D0
/
&SYSTEM
 ibrav=  6
 celldm(1) = 7.27
 celldm(3) = 4.0
 nat=  10
 ntyp= 3
 ecutwfc = 30.0
 ecutrho = 180.0
 occupations= 'smearing'
 smearing= 'gauss'
 degauss=0.005
/
&ELECTRONS
 diagonalization='david'
 mixing_beta = 0.7D0
 diago_david_ndim = 4
 startingwfc='random'
 startingpot='atomic'
 conv_thr = 1.0d-9
/
&IONS
 ion_dynamics = 'bfgs'
 phase_space = 'full'
/
&CELL
 cell_dynamics = 'bfgs'
/
ATOMIC_SPECIES
 Sr  87.62   038-Sr-ca-sp-vgrp.uspp.format.UPF
 Ti  47.90   022-Ti-ca-sp-vgrp.uspp.format.UPF
 O   16.00   008-O-ca--vgrp.uspp.format.UPF
ATOMIC_POSITIONS alat
 Sr 0.00 0.00 0.00
 Ti 0.50 0.50 0.50
 O  0.50 0.50 0.01
 O  0.00 0.50 0.52
 O  0.50 0.00 0.52
 Sr 0.00 0.00 1.01
 Ti 0.50 0.50 1.50
 O  0.50 0.50 1.02
 O  0.00 0.50 1.51
 O  0.50 0.00 1.51
K_POINTS automatic
6 6 2 1 1 1
CONSTRAINTS
 1
 'distance'  1 2
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From mashiatalaaii at gmail.com  Wed Apr  6 22:14:26 2011
From: mashiatalaaii at gmail.com (mashiat alaaii)
Date: Wed, 6 Apr 2011 16:14:26 -0400
Subject: [Pw_forum] the effect of smearing on density of states
Message-ID: <BANLkTi=jkwfX9Oca5KFMVDfONoNTe0b5nw@mail.gmail.com>

Dear All,
Hi and thank you for accepting me in the forum.
I made a Si/SiO2 supercell.
Since scf gave me this error: "charge is wrong, smearing in needed", and I
could not fix it by adding the number of the bands or number of electrons, I
used cold smearing with degauss=0.018.
I was wondering what the effect of this cold smearing is on the density of
states. I mean, if by any chance, I could get the DOS without smearing, how
would that be different from this one?
By the way, is there a way to get the DOS without smearing?
Thank you very much for the software.
I appreciate your help.
Mashiat
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From giannozz at democritos.it  Wed Apr  6 22:43:20 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 6 Apr 2011 22:43:20 +0200
Subject: [Pw_forum] constrained dynamics
In-Reply-To: <BANLkTimtZ=s+YYuxcbzJFJppR+tZE8XFwA@mail.gmail.com>
References: <BANLkTimtZ=s+YYuxcbzJFJppR+tZE8XFwA@mail.gmail.com>
Message-ID: <0CF768DD-0612-472D-BF43-C13DC58A963D@democritos.it>


On Apr 6, 2011, at 22:01 , hanghui chen wrote:

> I want to run constrained dynamics to relax the atoms.
> However, it seems that if I use 'ion_dynamics = bfgs',
> the SHAKE algorithm does not work. Is this true that the
> SHAKE algorithm is not implemented I use 'bfgs' method
> to relax the atoms?

it is. bfgs is not a "dynamics", anyway: it is an optimization
scheme. You can use SHAKE only in conjunction with
'verlet' dynamics, I think (no warranty)

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





From germaneau at gucas.ac.cn  Thu Apr  7 12:40:38 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Thu, 07 Apr 2011 06:40:38 -0400
Subject: [Pw_forum] charge density output format from pp.x
In-Reply-To: <502100239.09638@test1.gucas.ac.cn>
References: <4CEBFF39.40505@fu-berlin.de>	<1290592007.12941.6.camel@ulisse.cm.sissa.it>	<54782.200.0.233.52.1301691705.squirrel@mail.cab.cnea.gov.ar>	<A9314ABA-E41D-482F-B549-D5852F6C8405@democritos.it>	<42158.200.0.233.52.1301945122.squirrel@mail.cab.cnea.gov.ar>
	<502100239.09638@test1.gucas.ac.cn>
Message-ID: <4D9D94A6.2050003@gucas.ac.cn>

I think this format is very similar to the electron density map file 
xplor format 
<http://www.pasteur.fr/recherche/unites/Binfs/xplor/manual/node312.html#SECTION001530000000000000000> 
or that one 
<http://cdnetworks-kr-1.dl.sourceforge.net/project/discus/Manuals/kupl_man.pdf> 
page 22.
I may have routines to read those files somewhere.
Give me some time to get them and I will send them to you by tomorrow if 
I find them.
Yours,


                Eric.




On 04/06/2011 10:36 AM, Tone Kokalj wrote:
> On Mon, 2011-04-04 at 16:25 -0300, jorge.gallardo at cab.cnea.gov.ar wrote:
>>> you can extract the charge density (with pp.x) in a number of different
>>> formats. For the relation between indices and positions in real space:
>>> http://www.quantum-espresso.org/user_guide/node23.html
>>>
>> thank you for you response.
>>
>> I tried to do something like that, but I cannot understand the content of
>> the file "al.rho.dat". I suppose that the density is in the big block of 6
>> numerical columns "DATAGRID_3D_UNKNOWN", but, How is ordered that block? ,
>> In what order should I read it?.
> I would suggest you follow the hint of Paolo, nevertheless, here is the
> order of how the datagrid is written:
>
> write(*,*) (((value(ix,iy,iz),ix=1,nx),iy=1,ny),iz=1,nz)
>
> for more specs, see:
> http://www.xcrysden.org/doc/XSF.html
>
> Regards, Tone
>

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/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 germaneau at gucas.ac.cn  Thu Apr  7 13:55:49 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Thu, 07 Apr 2011 07:55:49 -0400
Subject: [Pw_forum] plotrho output in color
Message-ID: <4D9DA645.3040606@gucas.ac.cn>

Dear all,

My question is simple, I wonder whether the plotrho program can generate 
a colored output.
Yours,

            Eric.

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/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 bahaartv at gmail.com  Thu Apr  7 08:26:11 2011
From: bahaartv at gmail.com (bahaareh tavakoli nejad)
Date: Wed, 6 Apr 2011 23:26:11 -0700
Subject: [Pw_forum] Problem with concept of parameters in
	pseudopotentials
Message-ID: <BANLkTi==WL2qUuy7Pzt17F0k1boo6+Zp3w@mail.gmail.com>

I'm trying calculate density of state and other quantities for SrS but i
have problems about concept of different parameters in pseudopotentials, for
example on top of Teter pseudopotential we have :

(Ar+3d10) + 4s2 4p6 5s0 4d0; rcs=rcp=rcd=1.7, no chem-hard, exnc(11);ecut
25/34
 38.00000  10.00000  950923      z,zion,pspdat
 4         3         2   2      2001    0
pspcod,pspxc,lmax,lloc,mmax,r2well
 0  0  0   2    1.69654886360351576          l,e99.0,e99.9,nproj,rcpsp:
 .000 .000 .000 .000                         rms,ekb1,ekb2,epsatm
 1  0  0   2    1.69654886360351576          l,e99.0,e99.9,nproj,rcpsp
 .000 .000 .000 .000                         rms,ekb1,ekb2,epsatm
 2  0  0   0    1.69654886360351576          l,e99.0,e99.9,nproj,rcpsp
 .000 .000 .000 .000                         rms,ekb1,ekb2,epsatm
 .000   .000   .000                          rchrg,fchrg,qchrg
 0 = l

is the first line of this pseudopotenial means that only 8 valence electrons
are used in calculations (for example calculation of density of states,
bandstructure....)and 4d and 5s orbitals are empty and don't participate in
calculation?

Thanks
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From degironc at sissa.it  Thu Apr  7 09:03:12 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 07 Apr 2011 09:03:12 +0200
Subject: [Pw_forum] plotrho output in color
In-Reply-To: <4D9DA645.3040606@gucas.ac.cn>
References: <4D9DA645.3040606@gucas.ac.cn>
Message-ID: <4D9D61B0.8040108@sissa.it>

not really, but you can edit the produced postscript file and replace 
the bunch of lines at the beginning defining the grayscale

/s0 {1.00 setgray newpath moveto lineto lineto lineto fill} def
/t0 {1.00 setgray newpath moveto lineto lineto fill} def
/s1 {0.88 setgray newpath moveto lineto lineto lineto fill} def
/t1 {0.88 setgray newpath moveto lineto lineto fill} def
...

with something like

/s0 {1.00 1.0 1.0 sethsbcolor  newpath moveto lineto lineto lineto fill} def
/t0 {1.00 1.0 1.0 sethsbcolor  newpath moveto lineto lineto fill} def
/s1 {0.88 1.0 1.0 sethsbcolor  newpath moveto lineto lineto lineto fill} def
/t1 {0.88 1.0 1.0 sethsbcolor  newpath moveto lineto lineto fill} def
...

that define the colors in terms of hue,saturation and brightness.


HTH

  stefano

On 04/07/2011 01:55 PM, Eric Germaneau wrote:
> Dear all,
>
> My question is simple, I wonder whether the plotrho program can 
> generate a colored output.
> Yours,
>
>            Eric.
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From m.abbasnejad at gmail.com  Thu Apr  7 09:28:20 2011
From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad)
Date: Thu, 7 Apr 2011 11:58:20 +0430
Subject: [Pw_forum] Born effective charge
Message-ID: <BANLkTinmWP4NNYojbPpTh5zjRRC5HmsAFA@mail.gmail.com>

Dear all,

Trying to calculate the born effective charges of my case, the obtained
diagonalized principal values of effective charge tensor have imaginary
part.

The system has been relaxed carefully using Perdew-Zunger ultrasoft
psuedopotentilas by ecutoff=50 (55) Ry, and performing the BZ integration in
a 6?6?6 grid with 27 reduced
number of k points in the irreducible edge of the 1st BZ.

What may cause the problem?


Thanks for any comment.

Yours,
M. Abbasnejad
University of Tehran
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From degironc at sissa.it  Thu Apr  7 09:34:44 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 07 Apr 2011 09:34:44 +0200
Subject: [Pw_forum] Born effective charge
In-Reply-To: <BANLkTinmWP4NNYojbPpTh5zjRRC5HmsAFA@mail.gmail.com>
References: <BANLkTinmWP4NNYojbPpTh5zjRRC5HmsAFA@mail.gmail.com>
Message-ID: <4D9D6914.4010406@sissa.it>

what is your system ?
born effective charges are not necessarily hermitian although very often 
they are.
stefano

On 04/07/2011 09:28 AM, mohaddeseh abbasnejad wrote:
> Dear all,
>
> Trying to calculate the born effective charges of my case, the obtained
> diagonalized principal values of effective charge tensor have imaginary
> part.
>
> The system has been relaxed carefully using Perdew-Zunger ultrasoft
> psuedopotentilas by ecutoff=50 (55) Ry, and performing the BZ integration in
> a 6?6?6 grid with 27 reduced
> number of k points in the irreducible edge of the 1st BZ.
>
> What may cause the problem?
>
>
> Thanks for any comment.
>
> Yours,
> M. Abbasnejad
> University of Tehran
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From nkxirainbow at gmail.com  Thu Apr  7 09:40:47 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Thu, 7 Apr 2011 15:40:47 +0800
Subject: [Pw_forum] Born effective charge
In-Reply-To: <BANLkTinmWP4NNYojbPpTh5zjRRC5HmsAFA@mail.gmail.com>
References: <BANLkTinmWP4NNYojbPpTh5zjRRC5HmsAFA@mail.gmail.com>
Message-ID: <BANLkTikMcxZYUp=kho6MA-3RwaPxNnKwjA@mail.gmail.com>

Dear M. Abbasnejad:



Trying to calculate the born effective charges of my case, the obtained
> diagonalized principal values of effective charge tensor have imaginary
> part.

Is the  ?diagonalized principal values? is calculated by yourself , or it is
written in the output file?
If it is the first occasion, I think it is your fault.
Based on the definition of Born effective charge, it is a  "*real symmetric
matrix*?.
The eigen value of real symmetric matrix should not have imaginary part.



-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From m.abbasnejad at gmail.com  Thu Apr  7 09:54:23 2011
From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad)
Date: Thu, 7 Apr 2011 12:24:23 +0430
Subject: [Pw_forum] Born effective charge
In-Reply-To: <4D9D6914.4010406@sissa.it>
References: <BANLkTinmWP4NNYojbPpTh5zjRRC5HmsAFA@mail.gmail.com>
	<4D9D6914.4010406@sissa.it>
Message-ID: <BANLkTinWn9K1Zoqyb2aWuDXWdcEJxgw-hA@mail.gmail.com>

Thanks for your reply.
I am working on one of the orthorhombic structures of TiO2.
and it is the first time I have faced this problem.

Yours,
M. Abbasnejad
University of Tehran


On Thu, Apr 7, 2011 at 12:04 PM, Stefano de Gironcoli <degironc at sissa.it>wrote:

>  what is your system ?
> born effective charges are not necessarily hermitian although very often
> they are.
> stefano
>
>
> On 04/07/2011 09:28 AM, mohaddeseh abbasnejad wrote:
>
> Dear all,
>
> Trying to calculate the born effective charges of my case, the obtained
> diagonalized principal values of effective charge tensor have imaginary
> part.
>
> The system has been relaxed carefully using Perdew-Zunger ultrasoft
> psuedopotentilas by ecutoff=50 (55) Ry, and performing the BZ integration in
> a 6?6?6 grid with 27 reduced
> number of k points in the irreducible edge of the 1st BZ.
>
> What may cause the problem?
>
>
> Thanks for any comment.
>
> Yours,
> M. Abbasnejad
> University of Tehran
>
>
>
> _______________________________________________
> Pw_forum mailing listPw_forum at pwscf.orghttp://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 degironc at sissa.it  Thu Apr  7 10:14:34 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 07 Apr 2011 10:14:34 +0200
Subject: [Pw_forum] Born effective charge
In-Reply-To: <BANLkTinWn9K1Zoqyb2aWuDXWdcEJxgw-hA@mail.gmail.com>
References: <BANLkTinmWP4NNYojbPpTh5zjRRC5HmsAFA@mail.gmail.com>	<4D9D6914.4010406@sissa.it>
	<BANLkTinWn9K1Zoqyb2aWuDXWdcEJxgw-hA@mail.gmail.com>
Message-ID: <4D9D726A.8010708@sissa.it>

by searching google "non symmetric born effective charge" I found the 
following reference to a pw_forum previous entry
http://www.democritos.it/pipermail/pw_forum/2006-January/003511.html
that may be of interest.

There is also a reference to a paper Cockayne-Burton PRB 62, 3735 (2000) 
on CaTiO3 that maybe is relevant to your case.

stefano

On 04/07/2011 09:54 AM, mohaddeseh abbasnejad wrote:
> Thanks for your reply.
> I am working on one of the orthorhombic structures of TiO2.
> and it is the first time I have faced this problem.
>
> Yours,
> M. Abbasnejad
> University of Tehran
>
>
> On Thu, Apr 7, 2011 at 12:04 PM, Stefano de Gironcoli<degironc at sissa.it>wrote:
>
>>   what is your system ?
>> born effective charges are not necessarily hermitian although very often
>> they are.
>> stefano
>>
>>
>> On 04/07/2011 09:28 AM, mohaddeseh abbasnejad wrote:
>>
>> Dear all,
>>
>> Trying to calculate the born effective charges of my case, the obtained
>> diagonalized principal values of effective charge tensor have imaginary
>> part.
>>
>> The system has been relaxed carefully using Perdew-Zunger ultrasoft
>> psuedopotentilas by ecutoff=50 (55) Ry, and performing the BZ integration in
>> a 6?6?6 grid with 27 reduced
>> number of k points in the irreducible edge of the 1st BZ.
>>
>> What may cause the problem?
>>
>>
>> Thanks for any comment.
>>
>> Yours,
>> M. Abbasnejad
>> University of Tehran
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing listPw_forum at pwscf.orghttp://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

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From giannozz at democritos.it  Thu Apr  7 10:35:12 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 7 Apr 2011 10:35:12 +0200
Subject: [Pw_forum] Born effective charge
In-Reply-To: <BANLkTikMcxZYUp=kho6MA-3RwaPxNnKwjA@mail.gmail.com>
References: <BANLkTinmWP4NNYojbPpTh5zjRRC5HmsAFA@mail.gmail.com>
	<BANLkTikMcxZYUp=kho6MA-3RwaPxNnKwjA@mail.gmail.com>
Message-ID: <B18BF285-7C7B-42C9-822D-9700A41D4C17@democritos.it>


On Apr 7, 2011, at 9:40 , xirainbow wrote:

> Based on the definition of Born effective charge, it is a  "real  
> symmetric matrix?.

real, but not symmetric, in general

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





From giannozz at democritos.it  Thu Apr  7 10:38:52 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 7 Apr 2011 10:38:52 +0200
Subject: [Pw_forum] the effect of smearing on density of states
In-Reply-To: <BANLkTi=jkwfX9Oca5KFMVDfONoNTe0b5nw@mail.gmail.com>
References: <BANLkTi=jkwfX9Oca5KFMVDfONoNTe0b5nw@mail.gmail.com>
Message-ID: <3DFF309F-74E3-4C72-88E0-FF8396F0C06D@democritos.it>


On Apr 6, 2011, at 22:14 , mashiat alaaii wrote:

> Since scf gave me this error: "charge is wrong, smearing in needed",
> and I could not fix it by adding the number of the bands or number
> of electrons, I used cold smearing with degauss=0.018.

if the code says "smearing is needed", smearing is needed.
Are you sure you used it? what the code uses should be
reprinted on output

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





From psavita at crlindia.com  Thu Apr  7 12:24:02 2011
From: psavita at crlindia.com (psavita at crlindia.com)
Date: Thu, 7 Apr 2011 15:54:02 +0530
Subject: [Pw_forum] Interpretation of NEB output
In-Reply-To: <mailman.11124.1302159806.1814.pw_forum@pwscf.org>
References: <mailman.11124.1302159806.1814.pw_forum@pwscf.org>
Message-ID: <OFA47C6A88.6A90712F-ON6525786B.003921F8-6525786B.003921FA@crlindia.com>

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From nkxirainbow at gmail.com  Thu Apr  7 12:48:53 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Thu, 7 Apr 2011 18:48:53 +0800
Subject: [Pw_forum] Born effective charge
In-Reply-To: <B18BF285-7C7B-42C9-822D-9700A41D4C17@democritos.it>
References: <BANLkTinmWP4NNYojbPpTh5zjRRC5HmsAFA@mail.gmail.com>
	<BANLkTikMcxZYUp=kho6MA-3RwaPxNnKwjA@mail.gmail.com>
	<B18BF285-7C7B-42C9-822D-9700A41D4C17@democritos.it>
Message-ID: <BANLkTim3iaOMJ0Z2v+7jtPYd0EyGLvnYqQ@mail.gmail.com>

Dear Paolo Giannozzi:
Thank you  very much for your correction:)
I couldn't imagine the physical meaning of imaginary part. I hope I can
understand it after reading the paper (PRB62,3735).

On Thu, Apr 7, 2011 at 4:35 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Apr 7, 2011, at 9:40 , xirainbow wrote:
>
> > Based on the definition of Born effective charge, it is a  "real
> > symmetric matrix?.
>
> real, but not symmetric, in general
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From prasenjit.jnc at gmail.com  Thu Apr  7 13:39:04 2011
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Thu, 7 Apr 2011 17:09:04 +0530
Subject: [Pw_forum] Interpretation of NEB output
In-Reply-To: <OFA47C6A88.6A90712F-ON6525786B.003921F8-6525786B.003921FA@crlindia.com>
References: <mailman.11124.1302159806.1814.pw_forum@pwscf.org>
	<OFA47C6A88.6A90712F-ON6525786B.003921F8-6525786B.003921FA@crlindia.com>
Message-ID: <BANLkTin3os2741O=mZdhBTxj+22JG-v6LQ@mail.gmail.com>

Dear Savita,


>          1       -393.7939748            1.417692            T
>          2       -394.0215500            0.040078            F
>          3       -391.2951677            0.080152            F
>          4       -391.4855499            0.081938            F
>          5       -391.5735955            2.666114            T
>
>
>
These are the perpendicular (to the path) component of the forces acting on
the image.

With regards,

Prasenjit

-- 
PRASENJIT GHOSH,
Assistant Professor,
IISER Pune,
First floor, Central Tower, Sai Trinity Building
Garware Circle, Sutarwadi, Pashan
Pune, Maharashtra 411021, India

Phone: +91 (20) 2590 8203
Fax: +91 (20) 2589 9790
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From jorge.gallardo at cab.cnea.gov.ar  Thu Apr  7 16:21:49 2011
From: jorge.gallardo at cab.cnea.gov.ar (jorge.gallardo at cab.cnea.gov.ar)
Date: Thu, 7 Apr 2011 11:21:49 -0300 (ART)
Subject: [Pw_forum] charge density output format from pp.x
In-Reply-To: <4D9D94A6.2050003@gucas.ac.cn>
References: <4CEBFF39.40505@fu-berlin.de>	<1290592007.12941.6.camel@ulisse.cm.sissa.it>	<54782.200.0.233.52.1301691705.squirrel@mail.cab.cnea.gov.ar>	<A9314ABA-E41D-482F-B549-D5852F6C8405@democritos.it>	<42158.200.0.233.52.1301945122.squirrel@mail.cab.cnea.gov.ar>
	<502100239.09638@test1.gucas.ac.cn> <4D9D94A6.2050003@gucas.ac.cn>
Message-ID: <14548.190.230.143.47.1302186109.squirrel@mail.cab.cnea.gov.ar>

> I may have routines to read those files somewhere.
> Give me some time to get them and I will send them to you by tomorrow if
> I find them.
> Yours,
>
>                 Eric.
>

That would be very useful for me, thanks




From mashiatalaaii at gmail.com  Thu Apr  7 17:37:25 2011
From: mashiatalaaii at gmail.com (mashiat alaaii)
Date: Thu, 7 Apr 2011 11:37:25 -0400
Subject: [Pw_forum] The effect of cold smearing on DOS
Message-ID: <BANLkTik0sQpX+2DKRbBn8Sz3dSs-vh9MnQ@mail.gmail.com>

Dear Paolo,
I did use cold smearing and the output shows the smearing contribution
(which is almost -0.01 RY (I don't know what negative sign means)).
However, my concern is the effect of cold smearing on DOS. Does using
"cold smearing" change DOS. If positive, I was wondering whether it
adds some specific parts to it or it changes DOS radically.
I really really appreciate your help.
Yours
Mashiat
On Apr 6, 2011, at 22:14 , mashiat alaaii wrote:

>* Since scf gave me this error: "charge is wrong, smearing in needed",
*>* and I could not fix it by adding the number of the bands or number
*>* of electrons, I used cold smearing with degauss=0.018.
*
if the code says "smearing is needed", smearing is needed.
Are you sure you used it? what the code uses should be
reprinted on output

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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From reza.sarhaddi at yahoo.com  Thu Apr  7 17:42:25 2011
From: reza.sarhaddi at yahoo.com (reza sarhaddi)
Date: Thu, 7 Apr 2011 08:42:25 -0700 (PDT)
Subject: [Pw_forum] =?utf-8?q?The_spin=E2=80=93orbit_coupling?=
Message-ID: <483449.11331.qm@web120607.mail.ne1.yahoo.com>

Dear all,

How can the spin?orbit coupling take into account in calculations?
do exist any parameter in input file? 

Regards,
Reza

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From faccin.giovani at gmail.com  Thu Apr  7 17:53:14 2011
From: faccin.giovani at gmail.com (Giovani Faccin)
Date: Thu, 7 Apr 2011 11:53:14 -0400
Subject: [Pw_forum] =?windows-1252?q?The_spin=96orbit_coupling?=
In-Reply-To: <483449.11331.qm@web120607.mail.ne1.yahoo.com>
References: <483449.11331.qm@web120607.mail.ne1.yahoo.com>
Message-ID: <BANLkTik-Z2kvCXaJQeX35tgbcBWXF09jYw@mail.gmail.com>

Hi Reza,

Take a look at example 22 that comes with quantum espresso. I believe it
might help.

Giovani Faccin
UFMS/UNICAMP - Brazil

2011/4/7 reza sarhaddi <reza.sarhaddi at yahoo.com>

> Dear all,
>
> How can the spin?orbit coupling take into account in calculations?
> do exist any parameter in input file?
>
> Regards,
> Reza
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Giovani
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From yuz10 at uci.edu  Thu Apr  7 18:56:16 2011
From: yuz10 at uci.edu (Yu Zhang)
Date: Thu, 07 Apr 2011 09:56:16 -0700
Subject: [Pw_forum] XSpectra can not run
Message-ID: <4D9DECB0.4060005@uci.edu>

hi, all,
      I'm a newcomer to the QE world. I want to do some XAS calculations 
with XSpectra. So I followed the steps in the file run_example_diamond, 
got the pseudopotential, finished the scf calculation, generated the 
core state (C.wfc put in the working directory). Well, when I tried to 
run xspectra.x with the example input file, e. g., 
diamond.xspectra_fermi.in, I found xspectra.x does not exist (why hasn't 
it been compiled with all the other QE modules?). So I came to the 
XSpetra directory and ran make, it came up with some error message that 
some .o files under ../GIPAW were required. I hd to go to ../GIPAW and 
ran make. This time it seemed working. Then I went back to XSpectra/ and 
ran make. It came up with some warning like

################
xspectra.f90(431): remark #8290: Recommended relationship between field 
width 'W' and the number of fractional digits 'D' in this edit 
descriptor is 'W>=D+3'.
      WRITE (stdout,'(a,1x,3(f10.8, 1x))') 'xepsilon(:)=', 
(xepsilon(i),i=1,3)
-----------------------------^
###############

but still generated the xspectra.x executable. The problem came when I 
ran xspectra.x<diamond.xspectra_fermi.in>diamond.xspectra_fermi.out, 
with the following error:

###############
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
xspectra.x         0000000000674016  fft_types_mp_fft_         568  
fft_types.f90
xspectra.x         0000000000646F8E  stick_set_mp_psti         224  
stick_set.f90
xspectra.x         000000000046B8AA  data_structure_            62  
data_structure.f90
xspectra.x         00000000004569D7  allocate_fft_              38  
allocate_fft.f90
xspectra.x         0000000000431A55  read_file_xspectr         231  
read_file_xspectra.f90
xspectra.x         0000000000405C13  MAIN__                    371  
xspectra.f90
xspectra.x         00000000004050FC  Unknown               Unknown  Unknown
libc.so.6          00007F71CF6F4D8E  Unknown               Unknown  Unknown
xspectra.x         0000000000404FF9  Unknown               Unknown  Unknown
##############

     My input file is:
&input_xspectra
     calculation='fermi_level',
     prefix='diamond',
     outdir='./',
     xread_wf=.true.,
  /
&plot
  /
&pseudos
     filecore='./C.wfc',
  /
&cut_occ
  /
4 4 4 0 0 0


     What's wrong with my compilation? I'm using ifort V.12 with MKL and 
under a Linux64 system. The compilation of pw.x and many other 
executables are ok.  Sorry for this long post. Any help will be greatly 
appreciated!
best regards
Yu Zhang

From m.abbasnejad at gmail.com  Thu Apr  7 19:18:55 2011
From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad)
Date: Thu, 7 Apr 2011 21:48:55 +0430
Subject: [Pw_forum] LDA+U & phonon
Message-ID: <BANLkTimkRuOUr_eVCV6xA1S+uksVcKntfg@mail.gmail.com>

Dear all,

I was wondering if the LDA+U has been implemented in the phonon code in CVS
version of the code or not?

Yours,
M. Abbasnejad,
University of Tehran
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From giannozz at democritos.it  Thu Apr  7 19:53:48 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 7 Apr 2011 19:53:48 +0200
Subject: [Pw_forum] XSpectra can not run
In-Reply-To: <4D9DECB0.4060005@uci.edu>
References: <4D9DECB0.4060005@uci.edu>
Message-ID: <2D4EA7C3-30CC-47A4-B6AC-599C97BD901E@democritos.it>


On Apr 7, 2011, at 18:56 , Yu Zhang wrote:

> (why hasn't it been compiled with all the other QE modules?)

$ make
to install, type at the shell prompt:
   ./configure
   make target
where target is one of the following:
   pw           basic code for scf, structure optimization, MD
   cp           CP code: CP MD with ultrasoft pseudopotentials
   ph           phonon code
   neb          code for Nudged Elastic Band method
   tddfpt       time dependent dft code
   pp           postprocessing programs
   gamma        Gamma-only version of phonon code
   pwcond       ballistic conductance
   d3           third-order derivatives
   vdw          vdW calculation
   gipaw        magnetic response (NMR, EPR, ...)
   w90          Maximally localised Wannier Functions
   want         Quantum Transport with Wannier functions
   plumed       Patch for calculating free-energy paths with pw or cp
   gww          GW with Wannier Functions
   yambo        electronic excitations with plane waves
   tools        misc tools for data analysis
   ld1          utilities for pseudopotential generation
   upf          utilities for pseudopotential conversion
   xspectra     X-ray core-hole spectroscopy calculations
   pwall        same as "make pw ph pp gamma pwcond d3 tools"
   all          same as "make pwall cp ld1 upf tddfpt"
  ....

As you can see, some specialized code are not compiled
by "make all"

> So I came to the  XSpetra directory and ran make

"make xspectra" should be run from the root QE directory

> xspectra.f90(431): remark #8290: Recommended relationship between  
> field
> width 'W' and the number of fractional digits 'D' in this edit  
> descriptor is 'W>=D+3'.

this is completely irrelevant

> forrtl: severe (174): SIGSEGV, segmentation fault occurred

does it work for the provided example?

> I'm using ifort V.12 with MKL and under a Linux64 system.

v.12.0.2 should work; v.12.0.0 doesn't

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





From giannozz at democritos.it  Thu Apr  7 19:56:15 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 7 Apr 2011 19:56:15 +0200
Subject: [Pw_forum] The effect of cold smearing on DOS
In-Reply-To: <BANLkTik0sQpX+2DKRbBn8Sz3dSs-vh9MnQ@mail.gmail.com>
References: <BANLkTik0sQpX+2DKRbBn8Sz3dSs-vh9MnQ@mail.gmail.com>
Message-ID: <92BC7BF6-8949-4B05-A1EB-C93559386F82@democritos.it>


On Apr 7, 2011, at 17:37 , mashiat alaaii wrote:

> However, my concern is the effect of cold smearing on DOS.
> Does using "cold smearing" change DOS.

of course it does, but if properly used, smearing yields very good
results. Please have a look at the various tutorials available on
the quantum-espresso.org web site on metals and smearing

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





From giannozz at democritos.it  Thu Apr  7 20:00:22 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 7 Apr 2011 20:00:22 +0200
Subject: [Pw_forum] Problem with concept of parameters in
	pseudopotentials
In-Reply-To: <BANLkTi==WL2qUuy7Pzt17F0k1boo6+Zp3w@mail.gmail.com>
References: <BANLkTi==WL2qUuy7Pzt17F0k1boo6+Zp3w@mail.gmail.com>
Message-ID: <BCAD3D0D-6F1C-4E27-9155-50927968B467@democritos.it>


On Apr 7, 2011, at 8:26 , bahaareh tavakoli nejad wrote:

> is the first line of this pseudopotential means that only 8 valence  
> electrons are used in calculations
>
yes: with pseudopotentials, only valence electrons are considered

> and 4d and 5s orbitals are empty and don't participate in calculation?

no: this is the reference electronic configuration used to generate  
the pseudopotentials.
Please learn some basic facts about pseudopotentials before starting  
calculations.

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





From yuz10 at uci.edu  Thu Apr  7 20:26:09 2011
From: yuz10 at uci.edu (Yu Zhang)
Date: Thu, 07 Apr 2011 11:26:09 -0700
Subject: [Pw_forum] XSpectra can not run
In-Reply-To: <2D4EA7C3-30CC-47A4-B6AC-599C97BD901E@democritos.it>
References: <4D9DECB0.4060005@uci.edu>
	<2D4EA7C3-30CC-47A4-B6AC-599C97BD901E@democritos.it>
Message-ID: <4D9E01C1.4090708@uci.edu>

hi, Paolo,
Thank you very much for your help. I deleted *.o and *.x under /GIPAW 
and /Xspectra and then ran make gipaw and make xspectra in the QE root 
directory, as you suggested. No error found in compilation. Well, when I 
ran
xspectra.x<diamond.xspectra_fermi.in>diamond.xspectra_fermi.out again,
I saw the same error as before. diamond.xspectra_fermi.in is from the 
example file. What should I do next? My intel fortran is V 12.0.3. Many 
thanks again!
best regards
Yu Zhang

On 2011?04?07? 10:53, Paolo Giannozzi wrote:
> On Apr 7, 2011, at 18:56 , Yu Zhang wrote:
>
>> (why hasn't it been compiled with all the other QE modules?)
> $ make
> to install, type at the shell prompt:
>     ./configure
>     make target
> where target is one of the following:
>     pw           basic code for scf, structure optimization, MD
>     cp           CP code: CP MD with ultrasoft pseudopotentials
>     ph           phonon code
>     neb          code for Nudged Elastic Band method
>     tddfpt       time dependent dft code
>     pp           postprocessing programs
>     gamma        Gamma-only version of phonon code
>     pwcond       ballistic conductance
>     d3           third-order derivatives
>     vdw          vdW calculation
>     gipaw        magnetic response (NMR, EPR, ...)
>     w90          Maximally localised Wannier Functions
>     want         Quantum Transport with Wannier functions
>     plumed       Patch for calculating free-energy paths with pw or cp
>     gww          GW with Wannier Functions
>     yambo        electronic excitations with plane waves
>     tools        misc tools for data analysis
>     ld1          utilities for pseudopotential generation
>     upf          utilities for pseudopotential conversion
>     xspectra     X-ray core-hole spectroscopy calculations
>     pwall        same as "make pw ph pp gamma pwcond d3 tools"
>     all          same as "make pwall cp ld1 upf tddfpt"
>    ....
>
> As you can see, some specialized code are not compiled
> by "make all"
>
>> So I came to the  XSpetra directory and ran make
> "make xspectra" should be run from the root QE directory
>
>> xspectra.f90(431): remark #8290: Recommended relationship between
>> field
>> width 'W' and the number of fractional digits 'D' in this edit
>> descriptor is 'W>=D+3'.
> this is completely irrelevant
>
>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> does it work for the provided example?
>
>> I'm using ifort V.12 with MKL and under a Linux64 system.
> v.12.0.2 should work; v.12.0.0 doesn't
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


From arvifis at gmail.com  Thu Apr  7 20:32:57 2011
From: arvifis at gmail.com (Arles V. Gil Rebaza)
Date: Thu, 7 Apr 2011 15:32:57 -0300
Subject: [Pw_forum] charge density output format from pp.x
In-Reply-To: <14548.190.230.143.47.1302186109.squirrel@mail.cab.cnea.gov.ar>
References: <4CEBFF39.40505@fu-berlin.de>
	<1290592007.12941.6.camel@ulisse.cm.sissa.it>
	<54782.200.0.233.52.1301691705.squirrel@mail.cab.cnea.gov.ar>
	<A9314ABA-E41D-482F-B549-D5852F6C8405@democritos.it>
	<42158.200.0.233.52.1301945122.squirrel@mail.cab.cnea.gov.ar>
	<502100239.09638@test1.gucas.ac.cn> <4D9D94A6.2050003@gucas.ac.cn>
	<14548.190.230.143.47.1302186109.squirrel@mail.cab.cnea.gov.ar>
Message-ID: <BANLkTinPHZ=NZ9FR8LOmkUkqvLPn=rtmUQ@mail.gmail.com>

Jorge I've a little script in matlab for read the output file name.dat and
show the charge density in contours.

Email me if you want my script. (arlesv at fisica.unlp.edu.ar)

Arles V. Gil Rebaza
IFLP - Argentina

2011/4/7 <jorge.gallardo at cab.cnea.gov.ar>

> > I may have routines to read those files somewhere.
> > Give me some time to get them and I will send them to you by tomorrow if
> > I find them.
> > Yours,
> >
> >                 Eric.
> >
>
> That would be very useful for me, thanks
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
###--------->   Arles V.   <---------###
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From giannozz at democritos.it  Thu Apr  7 21:55:24 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 7 Apr 2011 21:55:24 +0200
Subject: [Pw_forum] XSpectra can not run
In-Reply-To: <4D9E01C1.4090708@uci.edu>
References: <4D9DECB0.4060005@uci.edu>
	<2D4EA7C3-30CC-47A4-B6AC-599C97BD901E@democritos.it>
	<4D9E01C1.4090708@uci.edu>
Message-ID: <7E09EDF3-B9E3-4828-AA87-DE21C7D8F69B@democritos.it>


On Apr 7, 2011, at 20:26 , Yu Zhang wrote:

> What should I do next?

answer the following question:

>> does it work for the provided example?

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





From yuz10 at uci.edu  Thu Apr  7 23:25:47 2011
From: yuz10 at uci.edu (Yu Zhang)
Date: Thu, 07 Apr 2011 14:25:47 -0700
Subject: [Pw_forum] XSpectra can not run
In-Reply-To: <7E09EDF3-B9E3-4828-AA87-DE21C7D8F69B@democritos.it>
References: <4D9DECB0.4060005@uci.edu>	<2D4EA7C3-30CC-47A4-B6AC-599C97BD901E@democritos.it>	<4D9E01C1.4090708@uci.edu>
	<7E09EDF3-B9E3-4828-AA87-DE21C7D8F69B@democritos.it>
Message-ID: <4D9E2BDB.9090409@uci.edu>

hi, Paolo,
I run run_example_diamond from the XSpectra example directory and the 
program stops at the XAS fermi level calculation step and produces the 
same error. Sorry for not mention this before. Thanks.
Yu Zhang

On 2011?04?07? 12:55, Paolo Giannozzi wrote:
> On Apr 7, 2011, at 20:26 , Yu Zhang wrote:
>
>> What should I do next?
> answer the following question:
>
>>> does it work for the provided example?
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


From degironc at sissa.it  Fri Apr  8 00:05:48 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 08 Apr 2011 00:05:48 +0200
Subject: [Pw_forum] LDA+U & phonon
In-Reply-To: <BANLkTimkRuOUr_eVCV6xA1S+uksVcKntfg@mail.gmail.com>
References: <BANLkTimkRuOUr_eVCV6xA1S+uksVcKntfg@mail.gmail.com>
Message-ID: <4D9E353C.2000506@sissa.it>

LDA+U has been implemented in the phonon code by Andrea Floris, Matteo 
Cococcioni (with some contribution by myself). Porting to the CVS 
version is underway.
Stefano de Gironcoli - SISSA and DEMOCRITOS

On 04/07/2011 07:18 PM, mohaddeseh abbasnejad wrote:
> Dear all,
>
> I was wondering if the LDA+U has been implemented in the phonon code in CVS
> version of the code or not?
>
> Yours,
> M. Abbasnejad,
> University of Tehran
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From eyvaz_isaev at yahoo.com  Fri Apr  8 00:30:27 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 7 Apr 2011 15:30:27 -0700 (PDT)
Subject: [Pw_forum] =?utf-8?q?The_spin=E2=80=93orbit_coupling?=
In-Reply-To: <483449.11331.qm@web120607.mail.ne1.yahoo.com>
References: <483449.11331.qm@web120607.mail.ne1.yahoo.com>
Message-ID: <45445.42161.qm@web65702.mail.ac4.yahoo.com>

Hi,

You can do that if generate  a fully-relativistic pseudopotential using ld1.x 
code (or have it).

Please provide your affiliation.

Bests,
Eyvaz.

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

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

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




________________________________
From: reza sarhaddi <reza.sarhaddi at yahoo.com>
To: pw_forum at pwscf.org
Sent: Thu, April 7, 2011 5:42:25 PM
Subject: [Pw_forum] The spin?orbit coupling


Dear all,

How can the spin?orbit coupling take into account in calculations?
do exist any parameter in input file? 

Regards,
Reza


      
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From psavita at crlindia.com  Fri Apr  8 06:54:40 2011
From: psavita at crlindia.com (psavita at crlindia.com)
Date: Fri, 8 Apr 2011 10:24:40 +0530
Subject: [Pw_forum] Interpretation of NEB output (Prasenjit Ghosh)
In-Reply-To: <mailman.11154.1302198849.1814.pw_forum@pwscf.org>
References: <mailman.11154.1302198849.1814.pw_forum@pwscf.org>
Message-ID: <OFCD6F9F4C.094AB12D-ON6525786C.001AFA71-6525786C.001AFA79@crlindia.com>

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From prasenjit.jnc at gmail.com  Fri Apr  8 07:38:45 2011
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Fri, 8 Apr 2011 11:08:45 +0530
Subject: [Pw_forum] Interpretation of NEB output (Prasenjit Ghosh)
In-Reply-To: <OFCD6F9F4C.094AB12D-ON6525786C.001AFA71-6525786C.001AFA79@crlindia.com>
References: <mailman.11154.1302198849.1814.pw_forum@pwscf.org>
	<OFCD6F9F4C.094AB12D-ON6525786C.001AFA71-6525786C.001AFA79@crlindia.com>
Message-ID: <BANLkTimm87M4KX+CJ90YEWBCbQUfOJ8qBg@mail.gmail.com>

On 8 April 2011 10:24, <psavita at crlindia.com> wrote:

> Dear Prasenjit,
>
> Thank for your clarification.
> Then I have more questions:
> Are those the perpendicular components of the string force or the true
> force?
>

It is the total force....PE + spring


> Do the values signify convergence?
>
>
Yes, the default value is 0.05 eV/A. When the force on each image is less
than the default value, the calculation is said to be converged.

Prasenjit

-- 
PRASENJIT GHOSH,
Assistant Professor,
IISER Pune,
First floor, Central Tower, Sai Trinity Building
Garware Circle, Sutarwadi, Pashan
Pune, Maharashtra 411021, India

Phone: +91 (20) 2590 8203
Fax: +91 (20) 2589 9790
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From 1009ukumar at gmail.com  Fri Apr  8 10:11:05 2011
From: 1009ukumar at gmail.com (sonu kumar)
Date: Fri, 8 Apr 2011 13:41:05 +0530
Subject: [Pw_forum] further: born charges in rhombohedral unit cell.
Message-ID: <BANLkTi=U59zLnWBvgYGgpJju5+uROWYm9g@mail.gmail.com>

Dear Prof. Stefano de Gironcoli  and QE users,

So one would expect to have anisotropic born charges with off-diagonal
elements for unit cell with R-3m space group.
However, in PHYSICAL REVIEW B 73, 155114 ?2006? , NaHF2   have zero values
for off-diagonal
elements of born-charges.
xx


 and similary in CuAlO2 with same space group, i have found zero values of
off-diagonal elements of born tensor.



-- 
Sonu Kumar

IITD
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From 1009ukumar at gmail.com  Fri Apr  8 10:19:22 2011
From: 1009ukumar at gmail.com (sonu kumar)
Date: Fri, 8 Apr 2011 13:49:22 +0530
Subject: [Pw_forum] further: born charges in rhombohedral unit cell.
Message-ID: <BANLkTinOfHHrmJ2zXNtOY=-AvThgvS-ZDg@mail.gmail.com>

Sorry for my incomplete mail.

Dear Prof. Stefano de Gironcoli  and QE users,

So one would expect to have anisotropic born charges with off-diagonal
elements for unit cell with R-3m space group.
However, in PHYSICAL REVIEW B 73, 155114 ?2006? , NaHF2   have zero values
for off-diagonal
elements of born-charges and diagonal elements are:

              H             F                   Na
xx/yy   .337        ~ -.7            1.057
zz         ~2     ~ -1.5         ~1

Similary in CuAlO2 with same space group, i have found zero values of
off-diagonal elements of born tensor.

How you explain this?

With kind regards,
Sonu Kumar
IITD
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From degironc at sissa.it  Fri Apr  8 11:30:13 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 08 Apr 2011 11:30:13 +0200
Subject: [Pw_forum] further: born charges in rhombohedral unit cell.
In-Reply-To: <BANLkTinOfHHrmJ2zXNtOY=-AvThgvS-ZDg@mail.gmail.com>
References: <BANLkTinOfHHrmJ2zXNtOY=-AvThgvS-ZDg@mail.gmail.com>
Message-ID: <4D9ED5A5.1080805@sissa.it>

I don't  know how to explain.. but when things are exactly zero it's 
because there is a symmetry reason.
like a mirror plane or something ...
If your symmetry allows the born effective charge to be non zero they 
will, much or little depending on the details of the system.

Are the symmetry operations determined in the two systems the same ?

stefano

On 04/08/2011 10:19 AM, sonu kumar wrote:
> Sorry for my incomplete mail.
>
> Dear Prof. Stefano de Gironcoli  and QE users,
>
> So one would expect to have anisotropic born charges with off-diagonal
> elements for unit cell with R-3m space group.
> However, in PHYSICAL REVIEW B 73, 155114 ?2006? , NaHF2   have zero values
> for off-diagonal
> elements of born-charges and diagonal elements are:
>
>                H             F                   Na
> xx/yy   .337        ~ -.7            1.057
> zz         ~2     ~ -1.5         ~1
>
> Similary in CuAlO2 with same space group, i have found zero values of
> off-diagonal elements of born tensor.
>
> How you explain this?
>
> With kind regards,
> Sonu Kumar
> IITD
>
>
>
> _______________________________________________
> 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  Fri Apr  8 11:36:47 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 08 Apr 2011 11:36:47 +0200
Subject: [Pw_forum] XSpectra can not run
In-Reply-To: <4D9E2BDB.9090409@uci.edu>
References: <4D9DECB0.4060005@uci.edu>
	<2D4EA7C3-30CC-47A4-B6AC-599C97BD901E@democritos.it>
	<4D9E01C1.4090708@uci.edu>
	<7E09EDF3-B9E3-4828-AA87-DE21C7D8F69B@democritos.it>
	<4D9E2BDB.9090409@uci.edu>
Message-ID: <1302255407.17618.5.camel@fe12lx.fisica.uniud.it>

On Thu, 2011-04-07 at 14:25 -0700, Yu Zhang wrote:

> I run run_example_diamond from the XSpectra example directory and the 
> program stops at the XAS fermi level calculation step and produces the 
> same error. Sorry for not mention this before.

replace read-file_xspectra.f90 with the attached version

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

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From psavita at crlindia.com  Fri Apr  8 12:05:05 2011
From: psavita at crlindia.com (psavita at crlindia.com)
Date: Fri, 8 Apr 2011 15:35:05 +0530
Subject: [Pw_forum] Interpretation of NEB output (Prasenjit Ghosh)
	(Prasenjit Ghosh)
In-Reply-To: <mailman.1.1302250081.9490.pw_forum@pwscf.org>
References: <mailman.1.1302250081.9490.pw_forum@pwscf.org>
Message-ID: <OF5AD70780.B2DFA3A9-ON6525786C.003765F8-6525786C.003765FA@crlindia.com>

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From 1009ukumar at gmail.com  Fri Apr  8 13:35:50 2011
From: 1009ukumar at gmail.com (sonu kumar)
Date: Fri, 8 Apr 2011 17:05:50 +0530
Subject: [Pw_forum] further: born charges in rhombohedral unit cell.
Message-ID: <BANLkTinqJ6bu6sLER7ndXe7ZeW9zJgG=oQ@mail.gmail.com>

 Respected Prof. Stefano de Gironcoli and QE users,

>Are the symmetry operations determined in the two systems the same ?

Yes.

>because there is a symmetry reason.
>like a mirror plane or something ...

 Na(H)  and F have  D3d , C3v  site sym resp.

>If your symmetry allows the born effective charge to be non zero they
>will, much or little depending on the details of the system.

NaHF2 is mainly ionic than CuAlO2, so one may  expect to have differences
in born-effective charges.

Thank you very much.

with regards,
Sonu
IITD
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From degironc at sissa.it  Fri Apr  8 13:43:57 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 08 Apr 2011 13:43:57 +0200
Subject: [Pw_forum] further: born charges in rhombohedral unit cell.
In-Reply-To: <BANLkTinqJ6bu6sLER7ndXe7ZeW9zJgG=oQ@mail.gmail.com>
References: <BANLkTinqJ6bu6sLER7ndXe7ZeW9zJgG=oQ@mail.gmail.com>
Message-ID: <4D9EF4FD.2000501@sissa.it>

On 04/08/2011 01:35 PM, sonu kumar wrote:
>   Respected Prof. Stefano de Gironcoli and QE users,
>
>> Are the symmetry operations determined in the two systems the same ?
> Yes.
>
>> because there is a symmetry reason.
>> like a mirror plane or something ...
>   Na(H)  and F have  D3d , C3v  site sym resp.
so, i guess, Na(H) should have diagonal Z* while F could have off 
diagonal one and could be non-symmetric ...

stefano

>> If your symmetry allows the born effective charge to be non zero they
>> will, much or little depending on the details of the system.
> NaHF2 is mainly ionic than CuAlO2, so one may  expect to have differences
> in born-effective charges.
>
> Thank you very much.
>
> with regards,
> Sonu
> IITD
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From tanycimr at gmail.com  Fri Apr  8 13:47:57 2011
From: tanycimr at gmail.com (=?Big5?B?zuu0xqbB?=)
Date: Fri, 8 Apr 2011 19:47:57 +0800
Subject: [Pw_forum] How to understand the outcome of d3.x
Message-ID: <BANLkTi=9mCEbZVkQ+Le-TqY=oD-RFrLunw@mail.gmail.com>

Dear all

I want to calculate the phonon lifetime by QE.  I have read some replays
about this question in this forum , and the thesis "Anharmonic Phonon
Lifetime in Semiconductors from Density-Functional Perturbation Theory" .
However I have not  understand how to use the outcome of d3.x . Actually  no
ideas about what the d3.x  calculate .  And  I can't find an answer about
this question in the forum .

Please forgive my ignorance . And I hope someone could tell me  it is not a
joke that QE can give us the outcome about phonon lifetime .

Thanks in advance . And best wishes .

Tanyci

Nankai university , tianjin

China
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From 1009ukumar at gmail.com  Fri Apr  8 16:11:35 2011
From: 1009ukumar at gmail.com (sonu kumar)
Date: Fri, 8 Apr 2011 19:41:35 +0530
Subject: [Pw_forum] further: born charges in rhombohedral unit cell.
In-Reply-To: <BANLkTinqJ6bu6sLER7ndXe7ZeW9zJgG=oQ@mail.gmail.com>
References: <BANLkTinqJ6bu6sLER7ndXe7ZeW9zJgG=oQ@mail.gmail.com>
Message-ID: <BANLkTik58ezyrgEfnhMTw+ttkZOByR+j7Q@mail.gmail.com>

Respected Prof. and QE users,

>so, i guess, Na(H) should have diagonal Z*

Yes.

>while F could have off
>diagonal one and could be non-symmetric ...

No, it also has only diagonal elements, which are* (along with H and Na)
(prb 73, 155114, ?2006,      section VII, part-C*)

 direction                      H           F          Na*

xx/yy*                         ~0.34     ~ -.7     ~1.06
zz                               ~2          ~ -1.5   ~ 1


Thank you.

with regards,
Sonu
IITD
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From degironc at sissa.it  Fri Apr  8 16:17:53 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 08 Apr 2011 16:17:53 +0200
Subject: [Pw_forum] further: born charges in rhombohedral unit cell.
In-Reply-To: <BANLkTik58ezyrgEfnhMTw+ttkZOByR+j7Q@mail.gmail.com>
References: <BANLkTinqJ6bu6sLER7ndXe7ZeW9zJgG=oQ@mail.gmail.com>
	<BANLkTik58ezyrgEfnhMTw+ttkZOByR+j7Q@mail.gmail.com>
Message-ID: <4D9F1911.2080309@sissa.it>

then I don't understand your previous posts where you say that the 
eigenvalues are complex.
stefano


On 04/08/2011 04:11 PM, sonu kumar wrote:
> Respected Prof. and QE users,
>
>> so, i guess, Na(H) should have diagonal Z*
> Yes.
>
>> while F could have off
>> diagonal one and could be non-symmetric ...
> No, it also has only diagonal elements, which are* (along with H and Na)
> (prb 73, 155114, ?2006,      section VII, part-C*)
>
>   direction                      H           F          Na*
>
> xx/yy*                         ~0.34     ~ -.7     ~1.06
> zz                               ~2          ~ -1.5   ~ 1
>
>
> Thank you.
>
> with regards,
> Sonu
> IITD
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From 1009ukumar at gmail.com  Fri Apr  8 17:58:37 2011
From: 1009ukumar at gmail.com (sonu kumar)
Date: Fri, 8 Apr 2011 21:28:37 +0530
Subject: [Pw_forum] Further: born charges in rhombohedral unit cell.
Message-ID: <BANLkTikaBtsniDLmSOjUeLLFSCrgn62qMw@mail.gmail.com>

>then I don't understand your previous posts where you say that the
>eigenvalues are complex.

i didn't say.


Regards,
Sonu
IITD
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From giannozz at democritos.it  Fri Apr  8 18:07:53 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 08 Apr 2011 18:07:53 +0200
Subject: [Pw_forum] further: born charges in rhombohedral unit cell.
In-Reply-To: <BANLkTik58ezyrgEfnhMTw+ttkZOByR+j7Q@mail.gmail.com>
References: <BANLkTinqJ6bu6sLER7ndXe7ZeW9zJgG=oQ@mail.gmail.com>
	<BANLkTik58ezyrgEfnhMTw+ttkZOByR+j7Q@mail.gmail.com>
Message-ID: <1302278873.21802.65.camel@fe12lx.fisica.uniud.it>

On Fri, 2011-04-08 at 19:41 +0530, sonu kumar wrote:

> No, it also has only diagonal elements, which are (along with 
> H and Na) (prb 73, 155114, ?2006,      section VII, part-C)

and so, what is the problem? does the phonon code yield a different
result?

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



From dstrubbe at berkeley.edu  Fri Apr  8 20:39:07 2011
From: dstrubbe at berkeley.edu (David Strubbe)
Date: Fri, 8 Apr 2011 11:39:07 -0700
Subject: [Pw_forum] implementation of variation of occupations and Fermi
	level with perturbations
Message-ID: <BANLkTi=sidNdheP906hgk2LznewjBqYkFA@mail.gmail.com>

Dear developers,

I am trying to understand how the variation of occupations and Fermi level
is implemented in density-functional perturbation theory for metals. In the
Baroni, de Gironcoli, and Dal Corso Rev Mod Phys paper on DFPT, this issue
appears in equations 68 and 75-79. I see that routine ef_shift can implement
the result of a shift in the Fermi level as in either eq. 68 or eq. 75
depending on the value of "flag". But for the calculation of the shift
itself, I do not see the correspondence between what is done in the code and
the equations in the paper. Eq. 79 refers to a quantity \Delta n_{ext} and
an integral of the LDOS with \Delta V_{SCF} to calculate the shift in Fermi
level. However in ef_shift it appears that the density response drhoscf is
used instead of these quantities in the numerator, which doesn't seem like
the same thing. Can you explain what the relation is between the calculation
in the code and the equations in the RMP paper?

Thank you,
David Strubbe
UC Berkeley
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From yuz10 at uci.edu  Fri Apr  8 20:49:33 2011
From: yuz10 at uci.edu (Yu Zhang)
Date: Fri, 08 Apr 2011 11:49:33 -0700
Subject: [Pw_forum] XSpectra can not run
In-Reply-To: <1302255407.17618.5.camel@fe12lx.fisica.uniud.it>
References: <4D9DECB0.4060005@uci.edu>	<2D4EA7C3-30CC-47A4-B6AC-599C97BD901E@democritos.it>	<4D9E01C1.4090708@uci.edu>	<7E09EDF3-B9E3-4828-AA87-DE21C7D8F69B@democritos.it>	<4D9E2BDB.9090409@uci.edu>
	<1302255407.17618.5.camel@fe12lx.fisica.uniud.it>
Message-ID: <4D9F58BD.6040602@uci.edu>

hi, Paolo,
     This really solves my problem! Thank you very much. Could you 
please explain briefly what the cause  of the problem is?
best regards
Yu Zhang

On 2011?04?08? 02:36, Paolo Giannozzi wrote:
> On Thu, 2011-04-07 at 14:25 -0700, Yu Zhang wrote:
>
>> I run run_example_diamond from the XSpectra example directory and the
>> program stops at the XAS fermi level calculation step and produces the
>> same error. Sorry for not mention this before.
> replace read-file_xspectra.f90 with the attached version
>
> P.
>
>
> _______________________________________________
> 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  Fri Apr  8 21:18:00 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 8 Apr 2011 21:18:00 +0200
Subject: [Pw_forum] XSpectra can not run
In-Reply-To: <4D9F58BD.6040602@uci.edu>
References: <4D9DECB0.4060005@uci.edu>	<2D4EA7C3-30CC-47A4-B6AC-599C97BD901E@democritos.it>	<4D9E01C1.4090708@uci.edu>	<7E09EDF3-B9E3-4828-AA87-DE21C7D8F69B@democritos.it>	<4D9E2BDB.9090409@uci.edu>
	<1302255407.17618.5.camel@fe12lx.fisica.uniud.it>
	<4D9F58BD.6040602@uci.edu>
Message-ID: <8F0E039B-111F-4D60-A16C-F59EBE6E9870@democritos.it>


On Apr 8, 2011, at 20:49 , Yu Zhang wrote:

> This really solves my problem! Thank you very much.

you should thank Matteo Calandra, not me

> Could you please explain briefly what the cause  of the problem is?

the problem is that some recent changes to the initialization of FFT
grids, G-vectors, and other basic stuff, had not been propagated
to that particular routine. I had forgotten that XSpectra uses a
different routine to read the data file from all other QE codes.
Just an overlook.

Paolo
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From 1009ukumar at gmail.com  Sat Apr  9 15:00:39 2011
From: 1009ukumar at gmail.com (sonu kumar)
Date: Sat, 9 Apr 2011 18:30:39 +0530
Subject: [Pw_forum] further: born charges in rhombohedral unit cell.
Message-ID: <BANLkTikH8LrojSWC4Zxj4J-Lenyi7pu2ig@mail.gmail.com>

Respected Professors  Paolo Giannozzi,* Stefano de Gironcoli*, and QE users,

>and so, what is the problem? does the phonon code yield a different
>result?

No problem with phonon code, just trying to understand conceptually.

Any way,  thank you very much for your helpful replies.

with kind regards,
Sonu Kumar
Phd Student
Physics Department
Indian Institute of Technology
Delhi-110016, India
web:-http://www.iitd.ac.in/
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From romeda_8 at yahoo.com  Sat Apr  9 17:05:02 2011
From: romeda_8 at yahoo.com (r s)
Date: Sat, 9 Apr 2011 08:05:02 -0700 (PDT)
Subject: [Pw_forum] Calculation of DOS at the Fermi energy
Message-ID: <443717.93693.qm@web120408.mail.ne1.yahoo.com>

Dear all,
i want to calculate density of state at fermi energy,
therefore i use pp.x code with following input file:
?
&inputpp
??? prefix= 'ccb'
??? outdir= 'root/espresso-4.3/ccb/results',
??? plot_num= 3, 
??? filplot= 'dos'
/
?
but after running, get following text:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from local_dos : error #???? 1
guassian broadening needed
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
?
why the guassian broadening?!
i use smearing= 'mp' in my calculations and don't want to use gaussian broadening. 
please guide me, 
thanks,

Regards,
--
Romeda Azeen,
Bhavnagar University Bhavnagar 364002 Gujarat India


      
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From ttduyle at gmail.com  Sat Apr  9 17:17:49 2011
From: ttduyle at gmail.com (Duy Le)
Date: Sat, 9 Apr 2011 11:17:49 -0400
Subject: [Pw_forum] Calculation of DOS at the Fermi energy
In-Reply-To: <443717.93693.qm@web120408.mail.ne1.yahoo.com>
References: <443717.93693.qm@web120408.mail.ne1.yahoo.com>
Message-ID: <BANLkTimwriVh7VFUXpLzZhwDViePFcaK2Q@mail.gmail.com>

Did you call pp.x or dos.x?
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


On Sat, Apr 9, 2011 at 11:05 AM, r s <romeda_8 at yahoo.com> wrote:

> Dear all,
> i want to calculate density of state at fermi energy,
> therefore i use pp.x code with following input file:
>
> &inputpp
>     prefix= 'ccb'
>     outdir= 'root/espresso-4.3/ccb/results',
>     plot_num= 3,
>     filplot= 'dos'
> /
>
> but after running, get following text:
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> from local_dos : error #     1
> guassian broadening needed
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> why the guassian broadening?!
> i use smearing= 'mp' in my calculations and don't want to use gaussian
> broadening.
> please guide me,
> thanks,
>
> Regards,
> --
> Romeda Azeen,
> Bhavnagar University Bhavnagar 364002 Gujarat India
>
>
> _______________________________________________
> 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  Sat Apr  9 18:35:23 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 9 Apr 2011 18:35:23 +0200
Subject: [Pw_forum] Calculation of DOS at the Fermi energy
In-Reply-To: <443717.93693.qm@web120408.mail.ne1.yahoo.com>
References: <443717.93693.qm@web120408.mail.ne1.yahoo.com>
Message-ID: <D4387A1A-64E3-4030-AC65-99B6A4FA69F6@democritos.it>


On Apr 9, 2011, at 17:05 , r s wrote:

> from local_dos : error #     1
> gaussian broadening needed
> [...]
> why the gaussian broadening?!

"gaussian broadening" here indicates any kind of smearing

> I use smearing= 'mp' in my calculations

you think you used smearing='mp'. The code finds you didn't
use any smearing and stops.

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





From flux_ray12 at 163.com  Sun Apr 10 14:54:31 2011
From: flux_ray12 at 163.com (=?GBK?B?0KFT?=)
Date: Sun, 10 Apr 2011 20:54:31 +0800 (CST)
Subject: [Pw_forum] Calculation of DOS at the Fermi energy
In-Reply-To: <443717.93693.qm@web120408.mail.ne1.yahoo.com>
References: <443717.93693.qm@web120408.mail.ne1.yahoo.com>
Message-ID: <692cf4d9.dce5.12f3f7a501f.Coremail.flux_ray12@163.com>

In my opinion,  this means you should choose a guassian broadening parameter instead of by using guassian method.
The input code of smearing part should be:
occupations = 'smearing' ,
smearing = 'mv' ,
deguass = X.XX
~~~~~~~~~~~~~~~~~~  The last parameter is guassian broadening parameter.


At 2011-04-09 23:05:02?"r s" <romeda_8 at yahoo.com> wrote:

Dear all,
i want to calculate density of state at fermi energy,
therefore i use pp.x code with following input file:
 
&inputpp
    prefix= 'ccb'
    outdir= 'root/espresso-4.3/ccb/results',
    plot_num= 3,
    filplot= 'dos'
/
 
but after running, get following text:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from local_dos : error #     1
guassian broadening needed
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
why the guassian broadening?!
i use smearing= 'mp' in my calculations and don't want to use gaussian broadening.
please guide me,
thanks,

Regards,
--
Romeda Azeen,
Bhavnagar University Bhavnagar 364002 Gujarat India
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From agkvashnin at gmail.com  Sun Apr 10 17:32:57 2011
From: agkvashnin at gmail.com (Alexander G. Kvashnin)
Date: Sun, 10 Apr 2011 19:32:57 +0400
Subject: [Pw_forum] How to restart ph.x calculation?
Message-ID: <BANLkTime6F7TxD3tUvk+0MWWzuSgDh7scA@mail.gmail.com>

Dear QE users,

I have a little question about calculation of dynamical matrices using ph.x
code.
Calculations of dynamical matrices take much machine time, and not always I
have enough machine time to complete calculations, and my calculation
interrupted.
How can I restart my job with the interrupted step?


Thank you!

-- 
Sincerely yours
*Alexander G. Kvashnin*
--------------------------------------------------------------------------------------------------------------------------------
Student
Moscow Institute of Physics and Technology          http://mipt.ru/
141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia

Junior research scientist
Technological Institute for Superhard
and Novel Carbon Materials
http://www.ntcstm.troitsk.ru/
142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia
================================================================
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From eyvaz_isaev at yahoo.com  Sun Apr 10 18:01:54 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sun, 10 Apr 2011 09:01:54 -0700 (PDT)
Subject: [Pw_forum] How to restart ph.x calculation?
In-Reply-To: <BANLkTime6F7TxD3tUvk+0MWWzuSgDh7scA@mail.gmail.com>
References: <BANLkTime6F7TxD3tUvk+0MWWzuSgDh7scA@mail.gmail.com>
Message-ID: <138125.45706.qm@web65708.mail.ac4.yahoo.com>

Dear Alexandr,

Use start_q and last_q  keywords in ph.in file.  start_q is the point for which 
calculations were interrupted. last_q - a point to be calculated. 


There are also start_irr and last_irr  (irr - irreducible representation) 
keywords to continue calculations  for the interrupted  q-points. But I never 
used these keywords and not sure they 

will work if temporary files are lost.

Please see /Doc/INPUT_PH.txt file.

Bests,
Eyvaz.

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

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

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




________________________________
From: Alexander G. Kvashnin <agkvashnin at gmail.com>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Sun, April 10, 2011 5:32:57 PM
Subject: [Pw_forum] How to restart ph.x calculation?


Dear QE users,


I have a little question about calculation of dynamical matrices using ph.x 
code.
Calculations of dynamical matrices take much machine time, and not always I have 
enough machine time to complete calculations, and my calculation interrupted.
How can I restart my job with the interrupted step?


Thank you!

-- 

Sincerely yours
Alexander G. Kvashnin
--------------------------------------------------------------------------------------------------------------------------------

Student
Moscow Institute of Physics and Technology          http://mipt.ru/
141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia


Junior research scientist

Technological Institute for Superhard 
and Novel Carbon Materials                                   
http://www.ntcstm.troitsk.ru/
142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia
================================================================



      
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From physics.skgupta at gmail.com  Sun Apr 10 19:06:46 2011
From: physics.skgupta at gmail.com (Sanjeev Gupta)
Date: Sun, 10 Apr 2011 22:36:46 +0530
Subject: [Pw_forum] How to restart ph.x calculation?
In-Reply-To: <138125.45706.qm@web65708.mail.ac4.yahoo.com>
References: <BANLkTime6F7TxD3tUvk+0MWWzuSgDh7scA@mail.gmail.com>
	<138125.45706.qm@web65708.mail.ac4.yahoo.com>
Message-ID: <BANLkTimfVxgG+q8yvNDpY98r6M8gsfg1Lw@mail.gmail.com>

it works fine.
best regards
sanjeev

On Sun, Apr 10, 2011 at 9:31 PM, Eyvaz Isaev <eyvaz_isaev at yahoo.com> wrote:

> Dear Alexandr,
>
> Use start_q and last_q  keywords in ph.in file.  start_q is the point for
> which calculations were interrupted. last_q - a point to be calculated.
>
> There are also start_irr and last_irr  (irr - irreducible representation)
> keywords to continue calculations  for the interrupted  q-points. But I
> never used these keywords and not sure they
> will work if temporary files are lost.
>
> Please see /Doc/INPUT_PH.txt file.
>
> Bests,
> Eyvaz.
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
> Sweden
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
> Russia,
> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
> ------------------------------
> *From:* Alexander G. Kvashnin <agkvashnin at gmail.com>
> *To:* PWSCF Forum <pw_forum at pwscf.org>
> *Sent:* Sun, April 10, 2011 5:32:57 PM
> *Subject:* [Pw_forum] How to restart ph.x calculation?
>
> Dear QE users,
>
> I have a little question about calculation of dynamical matrices using ph.x
> code.
> Calculations of dynamical matrices take much machine time, and not always I
> have enough machine time to complete calculations, and my calculation
> interrupted.
> How can I restart my job with the interrupted step?
>
>
> Thank you!
>
> --
> Sincerely yours
> *Alexander G. Kvashnin*
>
> --------------------------------------------------------------------------------------------------------------------------------
> Student
> Moscow Institute of Physics and Technology          http://mipt.ru/
> 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia
>
> Junior research scientist
> Technological Institute for Superhard
> and Novel Carbon Materials
> http://www.ntcstm.troitsk.ru/
> 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia
> ================================================================
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
*Dr. Sanjeev Kumar Gupta*
*Post Doctoral Fellow,
(Ministry of New and Renewable Energy)
Department of Physics,
Bhavnagar University, Bhavnagar-364 022
Gujarat, India*
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From agkvashnin at gmail.com  Sun Apr 10 19:08:29 2011
From: agkvashnin at gmail.com (Alexander G. Kvashnin)
Date: Sun, 10 Apr 2011 21:08:29 +0400
Subject: [Pw_forum] How to restart ph.x calculation?
In-Reply-To: <BANLkTimfVxgG+q8yvNDpY98r6M8gsfg1Lw@mail.gmail.com>
References: <BANLkTime6F7TxD3tUvk+0MWWzuSgDh7scA@mail.gmail.com>
	<138125.45706.qm@web65708.mail.ac4.yahoo.com>
	<BANLkTimfVxgG+q8yvNDpY98r6M8gsfg1Lw@mail.gmail.com>
Message-ID: <BANLkTinCEw3Y8NgYReXfwcp7JT2RnNRUkw@mail.gmail.com>

I check it, it works.

Thank you!

On 10 April 2011 21:06, Sanjeev Gupta <physics.skgupta at gmail.com> wrote:

> it works fine.
> best regards
> sanjeev
>
> On Sun, Apr 10, 2011 at 9:31 PM, Eyvaz Isaev <eyvaz_isaev at yahoo.com>wrote:
>
>> Dear Alexandr,
>>
>> Use start_q and last_q  keywords in ph.in file.  start_q is the point for
>> which calculations were interrupted. last_q - a point to be calculated.
>>
>> There are also start_irr and last_irr  (irr - irreducible representation)
>> keywords to continue calculations  for the interrupted  q-points. But I
>> never used these keywords and not sure they
>> will work if temporary files are lost.
>>
>> Please see /Doc/INPUT_PH.txt file.
>>
>> Bests,
>> Eyvaz.
>>
>> -------------------------------------------------------------------
>> Prof. Eyvaz Isaev,
>> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
>> Sweden
>> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
>> Russia,
>> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>>
>>
>> ------------------------------
>> *From:* Alexander G. Kvashnin <agkvashnin at gmail.com>
>> *To:* PWSCF Forum <pw_forum at pwscf.org>
>> *Sent:* Sun, April 10, 2011 5:32:57 PM
>> *Subject:* [Pw_forum] How to restart ph.x calculation?
>>
>> Dear QE users,
>>
>> I have a little question about calculation of dynamical matrices using
>> ph.x code.
>> Calculations of dynamical matrices take much machine time, and not always
>> I have enough machine time to complete calculations, and my calculation
>> interrupted.
>> How can I restart my job with the interrupted step?
>>
>>
>> Thank you!
>>
>> --
>> Sincerely yours
>> *Alexander G. Kvashnin*
>>
>> --------------------------------------------------------------------------------------------------------------------------------
>> Student
>> Moscow Institute of Physics and Technology          http://mipt.ru/
>> 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia
>>
>> Junior research scientist
>> Technological Institute for Superhard
>> and Novel Carbon Materials
>> http://www.ntcstm.troitsk.ru/
>> 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia
>> ================================================================
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> *Dr. Sanjeev Kumar Gupta*
> *Post Doctoral Fellow,
> (Ministry of New and Renewable Energy)
> Department of Physics,
> Bhavnagar University, Bhavnagar-364 022
> Gujarat, India*
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Sincerely yours
*Alexander G. Kvashnin*
--------------------------------------------------------------------------------------------------------------------------------
Student
Moscow Institute of Physics and Technology          http://mipt.ru/
141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia

Junior research scientist
Technological Institute for Superhard
and Novel Carbon Materials
http://www.ntcstm.troitsk.ru/
142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia
================================================================
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From yuz10 at uci.edu  Sun Apr 10 19:44:42 2011
From: yuz10 at uci.edu (Yu Zhang)
Date: Sun, 10 Apr 2011 10:44:42 -0700
Subject: [Pw_forum] XSpectra run problem
Message-ID: <4DA1EC8A.3030802@uci.edu>

hi, all,
      Sorry for a long post again. Now I want to calculate the C1s XANES 
spectra of a NMA molecule. So I built a large supercell, ran relax and 
scf calculations, and then tried to run xspectra calculation. My input 
is as the following:

##############
&input_xspectra
     calculation='xanes_dipole'
     prefix='NMA',
     outdir='./',
     xonly_plot=.false.,
     xniter=2000,
     xcheck_conv=50,
     xepsilon(1)=1.0,
     xepsilon(2)=1.0,
     xepsilon(3)=0.0,
     xiabs=1,
     x_save_file='NMA.xspectra_x.sav',
     xread_wf=.false.,
     ef_r=-0.2359705,
     xerror=0.001,
     wf_collect=.true.,
  /
&plot
     xnepoint=1000,
     xgamma=0.8,
     xemin=-10.0,
     xemax=100.0,
     terminator=.true.,
     cut_occ_states=.true.,
&end
&pseudos
     filecore='C.wfc',
&end
&cut_occ
     cut_desmooth=0.1,
&end
K_POINTS gamma
################

     I just copy&modify the input file from some example, so the 
parameters may not be appropriate. Well, I got some similar fortran 
error (some reading error?) to that in my last question:

################
forrtl: severe (59): list-directed I/O syntax error, unit -5, file 
Internal List-Directed Read
Image              PC                Routine            Line        Source
xspectra.x         000000000084FEFA  Unknown               Unknown  Unknown
xspectra.x         000000000084EA75  Unknown               Unknown  Unknown
xspectra.x         00000000007F3556  Unknown               Unknown  Unknown
xspectra.x         000000000078E205  Unknown               Unknown  Unknown
xspectra.x         000000000078D9C1  Unknown               Unknown  Unknown
xspectra.x         00000000007B140E  Unknown               Unknown  Unknown
xspectra.x         00000000007AF00F  Unknown               Unknown  Unknown
xspectra.x         0000000000432494  read_file_xspectr         219  
read_file_xspectra.f90
xspectra.x         0000000000405C13  MAIN__                    371  
xspectra.f90
xspectra.x         00000000004050FC  Unknown               Unknown  Unknown
libc.so.6          00007F3988231D8E  Unknown               Unknown  Unknown
xspectra.x         0000000000404FF9  Unknown               Unknown  Unknown
################

    I use C_PBE_TM_2pj.UPF for C, H.pbe-tm-gipaw.UPF for H, 
O.pbe-van_gipaw.UPF for O and N.pbe-rrkjus.UPF for N. In the output file 
of my xspectra.x run, there are messages like the following (I don't 
know whether they are relevant):

################
      file N.pbe-rrkjus.UPF: wavefunction(s)  2S renormalized
      WARNING: atomic wfc #  2 for atom type 5 has zero norm
      WARNING: atomic wfc #  4 for atom type 5 has zero norm
      WARNING: atomic wfc #  5 for atom type 5 has zero norm
################

  I'm quite new to the computational solid state world, so please 
forgive me if I did something stupid. Any help will be greatly appreciated!
best regards
Yu Zhang


From L-marks at northwestern.edu  Sun Apr 10 23:13:52 2011
From: L-marks at northwestern.edu (Laurence Marks)
Date: Sun, 10 Apr 2011 16:13:52 -0500
Subject: [Pw_forum] One minor bug, one not minor and two questions
Message-ID: <BANLkTimpo976SxfyDctMvwAg8U8bSAo+9A@mail.gmail.com>

A very minor bug that you probably known: some of the routines in
S3DE/iotk/src have lines such as "# 1 "iotk_write_interf.spp" ". Most
sensible preprocessors will ignore these and just give warnings.

A more serious bug. Your bfgs code does not have curvature failure
conditions trapped. Not to get too technical here (contact me offline
if needed), unless one is close to the minimum bfgs fails unless this
is done. The failure is well documented, less well known, as is the
change needed (at least the standard form). I am attaching a modified
version with the standard fix. It gives a slightly lower energy with
smaller forces in about the same number of iterations -- due to
numerical limitations I cannot compare exactly with your reference
directory. I am a newbie with this code so there could be other
repercussions of this change if it is used for something except
optimizing the atomic positions, so perhaps a few tests are
appropriate for harder problems.

A quick question. In the ion optimization it looks like you are
starting from some iterpolation of the new density (i.e. "NEW-OLD
atomic charge density approx. for the potential"), what is it?

Another quick one: line 1766 of install/configure.ac nulls out
scalapack_libs and the lines below look like they are special tests,
which seems to be inconsistent with line 150 and standard protocols of
letting the user define input variables. (OK, while scalapack is
probably only useful for large problems I might want to do some.)

-- 
Professor Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Research is to see what everybody else has seen, and to think what
nobody else has thought
Albert Szent-Gyorgi
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From L-marks at northwestern.edu  Mon Apr 11 01:11:06 2011
From: L-marks at northwestern.edu (Laurence Marks)
Date: Sun, 10 Apr 2011 18:11:06 -0500
Subject: [Pw_forum] One minor bug, one not minor and two questions
In-Reply-To: <BANLkTimpo976SxfyDctMvwAg8U8bSAo+9A@mail.gmail.com>
References: <BANLkTimpo976SxfyDctMvwAg8U8bSAo+9A@mail.gmail.com>
Message-ID: <BANLkTimPv-96Y==_or9f_k0iL_Xqsrs8-A@mail.gmail.com>

For completeness, added proper comments.

On Sun, Apr 10, 2011 at 4:13 PM, Laurence Marks
<L-marks at northwestern.edu> wrote:
> A very minor bug that you probably known: some of the routines in
> S3DE/iotk/src have lines such as "# 1 "iotk_write_interf.spp" ". Most
> sensible preprocessors will ignore these and just give warnings.
>
> A more serious bug. Your bfgs code does not have curvature failure
> conditions trapped. Not to get too technical here (contact me offline
> if needed), unless one is close to the minimum bfgs fails unless this
> is done. The failure is well documented, less well known, as is the
> change needed (at least the standard form). I am attaching a modified
> version with the standard fix. It gives a slightly lower energy with
> smaller forces in about the same number of iterations -- due to
> numerical limitations I cannot compare exactly with your reference
> directory. I am a newbie with this code so there could be other
> repercussions of this change if it is used for something except
> optimizing the atomic positions, so perhaps a few tests are
> appropriate for harder problems.
>
> A quick question. In the ion optimization it looks like you are
> starting from some iterpolation of the new density (i.e. "NEW-OLD
> atomic charge density approx. for the potential"), what is it?
>
> Another quick one: line 1766 of install/configure.ac nulls out
> scalapack_libs and the lines below look like they are special tests,
> which seems to be inconsistent with line 150 and standard protocols of
> letting the user define input variables. (OK, while scalapack is
> probably only useful for large problems I might want to do some.)
>
> --
> Professor Laurence Marks
> Department of Materials Science and Engineering
> MSE Rm 2036 Cook Hall
> 2220 N Campus Drive
> Northwestern University
> Evanston, IL 60208, USA
> Tel: (847) 491-3996 Fax: (847) 491-7820
> email: L-marks at northwestern dot edu
> Web: www.numis.northwestern.edu
> Chair, Commission on Electron Crystallography of IUCR
> www.numis.northwestern.edu/
> Research is to see what everybody else has seen, and to think what
> nobody else has thought
> Albert Szent-Gyorgi
>



-- 
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Research is to see what everybody else has seen, and to think what
nobody else has thought
Albert Szent-Gyorgi
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From tanycimr at gmail.com  Mon Apr 11 07:02:24 2011
From: tanycimr at gmail.com (=?Big5?B?zuu0xqbB?=)
Date: Mon, 11 Apr 2011 13:02:24 +0800
Subject: [Pw_forum] how to get the Eigendisplacements by ph.x
Message-ID: <BANLkTi=TJ3=EW+n1mZteZksD9ZRt=VLeqA@mail.gmail.com>

Dear all

i want to know how to get the Eigendisplacements  by ph.x . what i found in
the dyn_G file is just "Diagonalizing the dynamical matrix"

please forgive my ignorance . i hope someone could give me some help .

thanks in advance



tanyci

nankai university , tianjin

china
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From prayerz.omo at gmail.com  Mon Apr 11 08:52:58 2011
From: prayerz.omo at gmail.com (Omololu Akin-Ojo)
Date: Mon, 11 Apr 2011 02:52:58 -0400
Subject: [Pw_forum] serial run when parallel intended
Message-ID: <BANLkTim1o1kks4NAwzNnqnBT1nbRAPExiA@mail.gmail.com>

Hi,

I was aiming to run QE in parallel but I see the following message in
my output file; what am i doing wrong?

     Subspace diagonalization in iterative solution of the eigenvalue problem:
     a serial algorithm will be used

Why is QE using a serial algorithm? I am using openmpi and QE
recognizes the number of processors correctly:
     Parallel version (MPI), running on     8 processors
     R & G space division:  proc/pool =    8

I could give more info if needed.

Thanks in advance for any help.

o.

Postdoctoral fellow,
CMSP section,
ICTP, Italy.



-- 
***************** Seek GOD! *************

From degironc at sissa.it  Mon Apr 11 10:17:37 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Mon, 11 Apr 2011 10:17:37 +0200
Subject: [Pw_forum] serial run when parallel intended
In-Reply-To: <BANLkTim1o1kks4NAwzNnqnBT1nbRAPExiA@mail.gmail.com>
References: <BANLkTim1o1kks4NAwzNnqnBT1nbRAPExiA@mail.gmail.com>
Message-ID: <4DA2B921.704@sissa.it>

because the code estimate that the communication overhead would exceed 
the gain due to the distribution of the operation across the processors.
This apply to the subspace diagonalization, the rest of the run is parallel

stefano

On 04/11/2011 08:52 AM, Omololu Akin-Ojo wrote:
> Hi,
>
> I was aiming to run QE in parallel but I see the following message in
> my output file; what am i doing wrong?
>
>       Subspace diagonalization in iterative solution of the eigenvalue problem:
>       a serial algorithm will be used
>
> Why is QE using a serial algorithm? I am using openmpi and QE
> recognizes the number of processors correctly:
>       Parallel version (MPI), running on     8 processors
>       R&  G space division:  proc/pool =    8
>
> I could give more info if needed.
>
> Thanks in advance for any help.
>
> o.
>
> Postdoctoral fellow,
> CMSP section,
> ICTP, Italy.
>
>
>


From degironc at sissa.it  Mon Apr 11 11:57:42 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Mon, 11 Apr 2011 11:57:42 +0200
Subject: [Pw_forum] One minor bug, one not minor and two questions
In-Reply-To: <BANLkTimPv-96Y==_or9f_k0iL_Xqsrs8-A@mail.gmail.com>
References: <BANLkTimpo976SxfyDctMvwAg8U8bSAo+9A@mail.gmail.com>
	<BANLkTimPv-96Y==_or9f_k0iL_Xqsrs8-A@mail.gmail.com>
Message-ID: <4DA2D096.4040802@sissa.it>

dear Laurence Marks

      thank you for contributing this patch for bfgs !
> A quick question. In the ion optimization it looks like you are
> starting from some iterpolation of the new density (i.e. "NEW-OLD
> atomic charge density approx. for the potential"), what is it?
if i remember correctly the charge density of the new positions is written
as the superposition of atomic charges plus a reminder which is computed
as the scf rho minus the superposition of atomic charges at the old 
positions.

rho_trial_new = rho_atomic_newR + (rho_scf_oldR - rho_atomic_oldR)

this is done for the first ionic iteration and assumes that the main 
change in the density is due to rigid displacement of atomic-like 
contributions.

At subsequent iterations the reminder (rho_scf_oldR-rho_atomic_oldR) can 
be extrapolated on the basis of its change in the previous couple of 
iterations

  Stefano de Gironcoli

On 04/11/2011 01:11 AM, Laurence Marks wrote:
> For completeness, added proper comments.
>
> On Sun, Apr 10, 2011 at 4:13 PM, Laurence Marks
> <L-marks at northwestern.edu>  wrote:
>> A very minor bug that you probably known: some of the routines in
>> S3DE/iotk/src have lines such as "# 1 "iotk_write_interf.spp" ". Most
>> sensible preprocessors will ignore these and just give warnings.
>>
>> A more serious bug. Your bfgs code does not have curvature failure
>> conditions trapped. Not to get too technical here (contact me offline
>> if needed), unless one is close to the minimum bfgs fails unless this
>> is done. The failure is well documented, less well known, as is the
>> change needed (at least the standard form). I am attaching a modified
>> version with the standard fix. It gives a slightly lower energy with
>> smaller forces in about the same number of iterations -- due to
>> numerical limitations I cannot compare exactly with your reference
>> directory. I am a newbie with this code so there could be other
>> repercussions of this change if it is used for something except
>> optimizing the atomic positions, so perhaps a few tests are
>> appropriate for harder problems.
>>
>> A quick question. In the ion optimization it looks like you are
>> starting from some iterpolation of the new density (i.e. "NEW-OLD
>> atomic charge density approx. for the potential"), what is it?
>>
>> Another quick one: line 1766 of install/configure.ac nulls out
>> scalapack_libs and the lines below look like they are special tests,
>> which seems to be inconsistent with line 150 and standard protocols of
>> letting the user define input variables. (OK, while scalapack is
>> probably only useful for large problems I might want to do some.)
>>
>> --
>> Professor Laurence Marks
>> Department of Materials Science and Engineering
>> MSE Rm 2036 Cook Hall
>> 2220 N Campus Drive
>> Northwestern University
>> Evanston, IL 60208, USA
>> Tel: (847) 491-3996 Fax: (847) 491-7820
>> email: L-marks at northwestern dot edu
>> Web: www.numis.northwestern.edu
>> Chair, Commission on Electron Crystallography of IUCR
>> www.numis.northwestern.edu/
>> Research is to see what everybody else has seen, and to think what
>> nobody else has thought
>> Albert Szent-Gyorgi
>>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From degironc at sissa.it  Mon Apr 11 12:12:52 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Mon, 11 Apr 2011 12:12:52 +0200
Subject: [Pw_forum] One minor bug, one not minor and two questions
In-Reply-To: <4DA2D096.4040802@sissa.it>
References: <BANLkTimpo976SxfyDctMvwAg8U8bSAo+9A@mail.gmail.com>
	<BANLkTimPv-96Y==_or9f_k0iL_Xqsrs8-A@mail.gmail.com>
	<4DA2D096.4040802@sissa.it>
Message-ID: <4DA2D424.1030100@sissa.it>

in my previous  post

reminder -> remainder

stefano

On 04/11/2011 11:57 AM, Stefano de Gironcoli wrote:
> dear Laurence Marks
>
>      thank you for contributing this patch for bfgs !
>> A quick question. In the ion optimization it looks like you are
>> starting from some iterpolation of the new density (i.e. "NEW-OLD
>> atomic charge density approx. for the potential"), what is it?
> if i remember correctly the charge density of the new positions is 
> written
> as the superposition of atomic charges plus a reminder which is computed
> as the scf rho minus the superposition of atomic charges at the old 
> positions.
>
> rho_trial_new = rho_atomic_newR + (rho_scf_oldR - rho_atomic_oldR)
>
> this is done for the first ionic iteration and assumes that the main 
> change in the density is due to rigid displacement of atomic-like 
> contributions.
>
> At subsequent iterations the reminder (rho_scf_oldR-rho_atomic_oldR) 
> can be extrapolated on the basis of its change in the previous couple 
> of iterations
>
>  Stefano de Gironcoli
>
> On 04/11/2011 01:11 AM, Laurence Marks wrote:
>> For completeness, added proper comments.
>>
>> On Sun, Apr 10, 2011 at 4:13 PM, Laurence Marks
>> <L-marks at northwestern.edu>  wrote:
>>> A very minor bug that you probably known: some of the routines in
>>> S3DE/iotk/src have lines such as "# 1 "iotk_write_interf.spp" ". Most
>>> sensible preprocessors will ignore these and just give warnings.
>>>
>>> A more serious bug. Your bfgs code does not have curvature failure
>>> conditions trapped. Not to get too technical here (contact me offline
>>> if needed), unless one is close to the minimum bfgs fails unless this
>>> is done. The failure is well documented, less well known, as is the
>>> change needed (at least the standard form). I am attaching a modified
>>> version with the standard fix. It gives a slightly lower energy with
>>> smaller forces in about the same number of iterations -- due to
>>> numerical limitations I cannot compare exactly with your reference
>>> directory. I am a newbie with this code so there could be other
>>> repercussions of this change if it is used for something except
>>> optimizing the atomic positions, so perhaps a few tests are
>>> appropriate for harder problems.
>>>
>>> A quick question. In the ion optimization it looks like you are
>>> starting from some iterpolation of the new density (i.e. "NEW-OLD
>>> atomic charge density approx. for the potential"), what is it?
>>>
>>> Another quick one: line 1766 of install/configure.ac nulls out
>>> scalapack_libs and the lines below look like they are special tests,
>>> which seems to be inconsistent with line 150 and standard protocols of
>>> letting the user define input variables. (OK, while scalapack is
>>> probably only useful for large problems I might want to do some.)
>>>
>>> -- 
>>> Professor Laurence Marks
>>> Department of Materials Science and Engineering
>>> MSE Rm 2036 Cook Hall
>>> 2220 N Campus Drive
>>> Northwestern University
>>> Evanston, IL 60208, USA
>>> Tel: (847) 491-3996 Fax: (847) 491-7820
>>> email: L-marks at northwestern dot edu
>>> Web: www.numis.northwestern.edu
>>> Chair, Commission on Electron Crystallography of IUCR
>>> www.numis.northwestern.edu/
>>> Research is to see what everybody else has seen, and to think what
>>> nobody else has thought
>>> Albert Szent-Gyorgi
>>>
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


From autieri at sa.infn.it  Mon Apr 11 13:53:57 2011
From: autieri at sa.infn.it (Carmine Autieri)
Date: Mon, 11 Apr 2011 13:53:57 +0200 (CEST)
Subject: [Pw_forum] plot the wave function for different spin
In-Reply-To: <d56ee317-c2a3-4c69-96fd-c711dcb7e565@mail.sa.infn.it>
Message-ID: <3710caa6-f53b-47d4-8403-491fd3135f13@mail.sa.infn.it>

Dear all, 

I am a phd student an I am new on this forum. I want to know how can I plot the wavefunction in the real space in LSDA.
I found in the forum that I can use 

plot_num = 7
kpoint = 1 (Gamma point if I understood well)
lsign = .true.
kband = band near fermi level

but how can I distingue between up and down spin in LSDA calculation??
On the web site I found 

Options for |psi|^2 (plot_num=7): 
LSDA:  k-point and spin polarization to be plotted
(spin-up and spin-down correspond to different k-points!)

but wich are these different k-points?
 

Thanks
Carmine

From eariel99 at gmail.com  Mon Apr 11 14:15:30 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Mon, 11 Apr 2011 09:15:30 -0300
Subject: [Pw_forum]  how to get the Eigendisplacements by ph.x
Message-ID: <BANLkTimeAsj_F91L9XCwvM_Rz2-FCETRKg@mail.gmail.com>

> want to know how to get the Eigendisplacements  by ph.x . what i found in
the dyn_G file is just "Diagonalizing the dynamical matrix"

Use dynmat.x after ph.x.

In the source file you will find the keywords explained
PH/dynmat.f90

Good luck,
-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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From giannozz at democritos.it  Mon Apr 11 14:23:07 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 11 Apr 2011 14:23:07 +0200
Subject: [Pw_forum] plot the wave function for different spin
In-Reply-To: <3710caa6-f53b-47d4-8403-491fd3135f13@mail.sa.infn.it>
References: <3710caa6-f53b-47d4-8403-491fd3135f13@mail.sa.infn.it>
Message-ID: <1302524587.25613.30.camel@fe12lx.fisica.uniud.it>

On Mon, 2011-04-11 at 13:53 +0200, Carmine Autieri wrote:

> LSDA:  k-point and spin polarization to be plotted
> (spin-up and spin-down correspond to different k-points!)
> 
> but which are these different k-points?

the first half are spin up, the second half spin down.
e.g. for Gamma:  kpoint=1 => spin up, kpoint=2 => spin down

P.
-- 
 Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222 


From jibanez008 at ikasle.ehu.es  Mon Apr 11 15:00:13 2011
From: jibanez008 at ikasle.ehu.es (Julen Ibanez Azpiroz)
Date: Mon, 11 Apr 2011 15:00:13 +0200
Subject: [Pw_forum] noncollinear stress + GGA not implemented
In-Reply-To: <238973.63990.qm@web15108.mail.cnb.yahoo.com>
References: <238973.63990.qm@web15108.mail.cnb.yahoo.com>
Message-ID: <BANLkTi=SdgMnrp97xTVsiNjkny+FVPJMyg@mail.gmail.com>

Dear B. Li,

I did a calculation in a noncollinear system ('noncolin=true') not with
'vc-relax'but with 'relax' option for relaxation, using pseudopotentials
built with GGA parametrization. The PW output also told me


     entering subroutine stress ...

     Message from routine stres:
     noncollinear stress + GGA not implemented

so it did not compute the stress. Aniway, it did compute the forces, and
relax succesfully the system taking into account these forces, using the
options
/
&IONS
  bfgs_ndim = 3,
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
/
So, in principle, you can relax a noncollinear system using GGA parametrized
pseudopotentials, if that is what you want. Hope this helps.



-- 

?========================================
 Julen Iba?ez Azpiroz
 Materia Kondentsatuaren Fisika Saila
 Zientzia eta Teknologia Fakultatea
 Euskal Herriko Unibertsitatea
 644 Posta Kutxatila, 48080 Bilbo, Spain

 Telefonoa: +34 946015326
 Mail: jibanez008 at ikasle.ehu.es
========================================
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From prayerz.omo at gmail.com  Mon Apr 11 15:02:33 2011
From: prayerz.omo at gmail.com (Omololu Akin-Ojo)
Date: Mon, 11 Apr 2011 15:02:33 +0200
Subject: [Pw_forum] serial run when parallel intended
In-Reply-To: <4DA2B921.704@sissa.it>
References: <BANLkTim1o1kks4NAwzNnqnBT1nbRAPExiA@mail.gmail.com>
	<4DA2B921.704@sissa.it>
Message-ID: <BANLkTin8ue=qLpgSTm2hcCeL0yL2CFHW4g@mail.gmail.com>

Thank you for your response, Stefano. I appreciate it.

o.

On Mon, Apr 11, 2011 at 10:17 AM, Stefano de Gironcoli
<degironc at sissa.it> wrote:
> because the code estimate that the communication overhead would exceed
> the gain due to the distribution of the operation across the processors.
> This apply to the subspace diagonalization, the rest of the run is parallel
>
> stefano
>
> On 04/11/2011 08:52 AM, Omololu Akin-Ojo wrote:
>> Hi,
>>
>> I was aiming to run QE in parallel but I see the following message in
>> my output file; what am i doing wrong?
>>
>> ? ? ? Subspace diagonalization in iterative solution of the eigenvalue problem:
>> ? ? ? a serial algorithm will be used
>>
>> Why is QE using a serial algorithm? I am using openmpi and QE
>> recognizes the number of processors correctly:
>> ? ? ? Parallel version (MPI), running on ? ? 8 processors
>> ? ? ? R& ?G space division: ?proc/pool = ? ?8
>>
>> I could give more info if needed.
>>
>> Thanks in advance for any help.
>>
>> o.
>>
>> Postdoctoral fellow,
>> CMSP section,
>> ICTP, Italy.
>>
>>
>>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
***************** Seek GOD! *************

From autieri at sa.infn.it  Mon Apr 11 15:15:49 2011
From: autieri at sa.infn.it (Carmine Autieri)
Date: Mon, 11 Apr 2011 15:15:49 +0200 (CEST)
Subject: [Pw_forum] plot the wave function for different spin
In-Reply-To: <3710caa6-f53b-47d4-8403-491fd3135f13@mail.sa.infn.it>
Message-ID: <79264e96-0b7f-408a-9459-505114074e36@mail.sa.infn.it>

Thank you very much

Carmine

From eyvaz_isaev at yahoo.com  Mon Apr 11 15:58:58 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 11 Apr 2011 06:58:58 -0700 (PDT)
Subject: [Pw_forum] how to get the Eigendisplacements by ph.x
In-Reply-To: <BANLkTimeAsj_F91L9XCwvM_Rz2-FCETRKg@mail.gmail.com>
References: <BANLkTimeAsj_F91L9XCwvM_Rz2-FCETRKg@mail.gmail.com>
Message-ID: <949916.75234.qm@web65710.mail.ac4.yahoo.com>

Hi,

>Use dynmat.x after ph.x.
>In the source file you will find the keywords explained PH/dynmat.f90

Yes, it is true, if  one interested in the Gamma-point only.
Otherwise, one has to use matdyn.x for an arbitrary q-point. Sure, Interatomic 
Force Constants 

Matrix is required.

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

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

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




________________________________
From: Eduardo Ariel Menendez Proupin <eariel99 at gmail.com>
To: pw_forum at pwscf.org
Sent: Mon, April 11, 2011 2:15:30 PM
Subject: [Pw_forum]  how to get the Eigendisplacements by ph.x


> want to know how to get the Eigendisplacements  by ph.x . what i found in the 
>dyn_G file is just "Diagonalizing the dynamical matrix"


Use dynmat.x after ph.x.

In the source file you will find the keywords explainedPH/dynmat.f90


Good luck,
-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez



      
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From eyvaz_isaev at yahoo.com  Mon Apr 11 16:40:04 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 11 Apr 2011 07:40:04 -0700 (PDT)
Subject: [Pw_forum] how to get the Eigendisplacements by ph.x
In-Reply-To: <949916.75234.qm@web65710.mail.ac4.yahoo.com>
References: <BANLkTimeAsj_F91L9XCwvM_Rz2-FCETRKg@mail.gmail.com>
	<949916.75234.qm@web65710.mail.ac4.yahoo.com>
Message-ID: <994120.70341.qm@web65702.mail.ac4.yahoo.com>

Well, I was somewhat wrong. If you need eigendisplacements for q-points (from 
nq1*nq2*nq3 mesh in ph.in file) then just have look at  *.dynN files. They 
contain both frequencies and eigendisplacements for these q-ponts.

  
Eyvaz.


________________________________
From: Eyvaz Isaev <eyvaz_isaev at yahoo.com>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Mon, April 11, 2011 3:58:58 PM
Subject: Re: [Pw_forum] how to get the Eigendisplacements by ph.x


Hi,

>Use dynmat.x after ph.x.
>In the source file you will find the keywords explained PH/dynmat.f90

Yes, it is true, if  one interested in the Gamma-point only.
Otherwise, one has to use matdyn.x for an arbitrary q-point. Sure, Interatomic 
Force Constants 

Matrix is required.

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

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

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




________________________________
From: Eduardo Ariel Menendez Proupin <eariel99 at gmail.com>
To: pw_forum at pwscf.org
Sent: Mon, April 11, 2011 2:15:30 PM
Subject: [Pw_forum]  how to get the Eigendisplacements by ph.x


> want to know how to get the Eigendisplacements  by ph.x . what i found in the 
>dyn_G file is just "Diagonalizing the dynamical matrix"


Use dynmat.x after ph.x.

In the source file you will find the keywords explainedPH/dynmat.f90


Good luck,
-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/%7Eemenendez


      
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From L-marks at northwestern.edu  Mon Apr 11 17:25:23 2011
From: L-marks at northwestern.edu (Laurence Marks)
Date: Mon, 11 Apr 2011 10:25:23 -0500
Subject: [Pw_forum] One minor bug, one not minor and two questions
In-Reply-To: <4DA2D424.1030100@sissa.it>
References: <BANLkTimpo976SxfyDctMvwAg8U8bSAo+9A@mail.gmail.com>
	<BANLkTimPv-96Y==_or9f_k0iL_Xqsrs8-A@mail.gmail.com>
	<4DA2D096.4040802@sissa.it> <4DA2D424.1030100@sissa.it>
Message-ID: <BANLkTim5k7pcSAiQ92=or_-P7rk8UCC-OA@mail.gmail.com>

Thanks.

Another question if I may. From the looks of PW/mix_rho.f90 you do not
use the weights in the Johnson paper, just a straight inverse of
betamix (what would be called Y^T Y in the optimization literature) at
lines 289-295? Have you considered a regularization, e.g. adding after
line 278 something like

        betamix(i,i)=betamix(i,i) + 1.D-7/iter_used

which is about right for your Al (001) example. The regularization
term (e.g. PRB 78, 075114 (2008)) is a bit empirical, although I might
be able to change this.

This is safe, so long as mix_rho.f90 is only used for mixing densities
during the scf iterations -- is it used elsewhere?

On Mon, Apr 11, 2011 at 5:12 AM, Stefano de Gironcoli <degironc at sissa.it> wrote:
> in my previous ?post
>
> reminder -> remainder
>
> stefano
>
> On 04/11/2011 11:57 AM, Stefano de Gironcoli wrote:
>> dear Laurence Marks
>>
>> ? ? ?thank you for contributing this patch for bfgs !
>>> A quick question. In the ion optimization it looks like you are
>>> starting from some iterpolation of the new density (i.e. "NEW-OLD
>>> atomic charge density approx. for the potential"), what is it?
>> if i remember correctly the charge density of the new positions is
>> written
>> as the superposition of atomic charges plus a reminder which is computed
>> as the scf rho minus the superposition of atomic charges at the old
>> positions.
>>
>> rho_trial_new = rho_atomic_newR + (rho_scf_oldR - rho_atomic_oldR)
>>
>> this is done for the first ionic iteration and assumes that the main
>> change in the density is due to rigid displacement of atomic-like
>> contributions.
>>
>> At subsequent iterations the reminder (rho_scf_oldR-rho_atomic_oldR)
>> can be extrapolated on the basis of its change in the previous couple
>> of iterations
>>
>> ?Stefano de Gironcoli
>>
>> On 04/11/2011 01:11 AM, Laurence Marks wrote:
>>> For completeness, added proper comments.
>>>
>>> On Sun, Apr 10, 2011 at 4:13 PM, Laurence Marks
>>> <L-marks at northwestern.edu> ?wrote:
>>>> A very minor bug that you probably known: some of the routines in
>>>> S3DE/iotk/src have lines such as "# 1 "iotk_write_interf.spp" ". Most
>>>> sensible preprocessors will ignore these and just give warnings.
>>>>
>>>> A more serious bug. Your bfgs code does not have curvature failure
>>>> conditions trapped. Not to get too technical here (contact me offline
>>>> if needed), unless one is close to the minimum bfgs fails unless this
>>>> is done. The failure is well documented, less well known, as is the
>>>> change needed (at least the standard form). I am attaching a modified
>>>> version with the standard fix. It gives a slightly lower energy with
>>>> smaller forces in about the same number of iterations -- due to
>>>> numerical limitations I cannot compare exactly with your reference
>>>> directory. I am a newbie with this code so there could be other
>>>> repercussions of this change if it is used for something except
>>>> optimizing the atomic positions, so perhaps a few tests are
>>>> appropriate for harder problems.
>>>>
>>>> A quick question. In the ion optimization it looks like you are
>>>> starting from some iterpolation of the new density (i.e. "NEW-OLD
>>>> atomic charge density approx. for the potential"), what is it?
>>>>
>>>> Another quick one: line 1766 of install/configure.ac nulls out
>>>> scalapack_libs and the lines below look like they are special tests,
>>>> which seems to be inconsistent with line 150 and standard protocols of
>>>> letting the user define input variables. (OK, while scalapack is
>>>> probably only useful for large problems I might want to do some.)
>>>>
>>>> --
>>>> Professor Laurence Marks
>>>> Department of Materials Science and Engineering
>>>> MSE Rm 2036 Cook Hall
>>>> 2220 N Campus Drive
>>>> Northwestern University
>>>> Evanston, IL 60208, USA
>>>> Tel: (847) 491-3996 Fax: (847) 491-7820
>>>> email: L-marks at northwestern dot edu
>>>> Web: www.numis.northwestern.edu
>>>> Chair, Commission on Electron Crystallography of IUCR
>>>> www.numis.northwestern.edu/
>>>> Research is to see what everybody else has seen, and to think what
>>>> nobody else has thought
>>>> Albert Szent-Gyorgi
>>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>



-- 
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Research is to see what everybody else has seen, and to think what
nobody else has thought
Albert Szent-Gyorgi

From naromero at gmail.com  Mon Apr 11 20:02:30 2011
From: naromero at gmail.com (Nichols A. Romero)
Date: Mon, 11 Apr 2011 13:02:30 -0500
Subject: [Pw_forum] I/O performance on BG/P systems
In-Reply-To: <A452B8A9-37B9-4CEB-8B6C-77D25D9D6095@democritos.it>
References: <4D8C916B.8010800@sissa.it>
	<0F327142-3AB3-47B8-A6DA-723C9AFF135B@democritos.it>
	<4090C379-5D47-4916-945B-428D1B32F501@sissa.it>
	<F3DC331D-4C15-4619-8132-7416B3DB02FE@democritos.it>
	<BDF827EC-3042-483A-8D52-DA17A7B8BD62@sissa.it>
	<A452B8A9-37B9-4CEB-8B6C-77D25D9D6095@democritos.it>
Message-ID: <BANLkTinW14uKL7FpyqSLKWd3fMkj0Qan+Q@mail.gmail.com>

Sorry for not replying earlier, but I missed this e-mail due to the
APS March Meeting.

The GPFS file system on BG/P does a poor job at handling writes to more than
one file per node. My guess is that Gabriele was running QE in either dual
or VN mode (2 and 4 MPI tasks per node, respectively). So on BG/P,
you basically
want to write one file per node (which GPFS is designed to handle) or
one big file
using MPI-I/O.

At ANL, we are thinking about re-writing some of the I/O
using parallel I/O (e.g. HDF5, Parallel NetCDF). The simplest
approach, though highly
unportable, is to use the MPI I/O directly.

Has anyone on this list worked on parallel I/O with QE? Or have any
strong opinions
on this issue?


On Wed, Mar 30, 2011 at 11:57 AM, Paolo Giannozzi
<giannozz at democritos.it> wrote:
>
> On Mar 30, 2011, at 11:20 , Gabriele Sclauzero wrote:
>
>> Do you think that having an additional optional level of I/O
>> (let's say that it might be called "medium")
>
> I propose 'rare', 'medium', 'well done'
>
>> would be too confusing for users?
>
> some users get confused no matter what
>
>> I could try to implement and test it.
>
> ok: just follow the "io_level" variable. Try first to understand
> what the actual behavior is (the documentation is not so
> clear on this point) and then think what it should be, if you
> have some clear ideas
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Nichols A. Romero, Ph.D.
Argonne Leadership Computing Facility
Argonne, IL 60490
(630) 447-9793

From sclauzer at sissa.it  Mon Apr 11 22:50:48 2011
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Mon, 11 Apr 2011 22:50:48 +0200
Subject: [Pw_forum] I/O performance on BG/P systems
In-Reply-To: <BANLkTinW14uKL7FpyqSLKWd3fMkj0Qan+Q@mail.gmail.com>
References: <4D8C916B.8010800@sissa.it>
	<0F327142-3AB3-47B8-A6DA-723C9AFF135B@democritos.it>
	<4090C379-5D47-4916-945B-428D1B32F501@sissa.it>
	<F3DC331D-4C15-4619-8132-7416B3DB02FE@democritos.it>
	<BDF827EC-3042-483A-8D52-DA17A7B8BD62@sissa.it>
	<A452B8A9-37B9-4CEB-8B6C-77D25D9D6095@democritos.it>
	<BANLkTinW14uKL7FpyqSLKWd3fMkj0Qan+Q@mail.gmail.com>
Message-ID: <C71A92C1-8515-413D-B84E-BAC478403CDB@sissa.it>

Dear Paolo and Nichols,

    as a follow up, I had a brief meeting with the sysadmin of our local BGP. It looks like the timings I was reporting actually correspond to the maximum I/O throughput of that specific rack, which depends on the number of I/O nodes present on the rack itself (in that case, 4 I/O nodes per midplane, each of them capable of 350 MB/s, corresponding to 1.7 GB/s for that midplane).
In the example I was reporting:
     davcio       :   1083.30s CPU   1083.30s WALL (      38 calls)

I've been running on just 128 nodes (512 cores in VN mode), therefore I had only one I/O node (1 midplane = 4 x 128 nodes, for the non-BG/P-ers). Now, the total size of the .wfc files was around 9200 MB, which cannot be written in less than 9200/350 = 26.3 sec, according to the figures that the sysadmins gave me. 
In my case the timings give: 1083.30s/38=28.5s, which is close to the theoretical maximum. 
I will perform more testing and I will take into consideration the suggestion of Nichols about the number of files per node. In our machine we have one rack with 16 I/O nodes per midplane, I will try to see if the I/O performance scales accordingly.

As a side effect, I met a problem in the timing procedure. I found very different davcio timings (i.e. 3 orders of magnitude!) for two jobs where the size of the wavefunctions differed by a factor 2 only (the jobs have been executed on the same rack and with the same number of processors and same parallelization scheme). 
The sysadmins replied that I/O bandwidth measured in the fastest case is not attainable on BG/P, and should be imputed to an inaccurate measurement of cputime/walltime. 
I'm going to investigate this anyway.

I'm not aware of anyone working on MPI I/O porting.

Thanks so far for your suggestions,



Gabriele



Il giorno 11/apr/2011, alle ore 20.02, Nichols A. Romero ha scritto:

> Sorry for not replying earlier, but I missed this e-mail due to the
> APS March Meeting.
> 
> The GPFS file system on BG/P does a poor job at handling writes to more than
> one file per node. My guess is that Gabriele was running QE in either dual
> or VN mode (2 and 4 MPI tasks per node, respectively). So on BG/P,
> you basically
> want to write one file per node (which GPFS is designed to handle) or
> one big file
> using MPI-I/O.
> 
> At ANL, we are thinking about re-writing some of the I/O
> using parallel I/O (e.g. HDF5, Parallel NetCDF). The simplest
> approach, though highly
> unportable, is to use the MPI I/O directly.
> 
> Has anyone on this list worked on parallel I/O with QE? Or have any
> strong opinions
> on this issue?
> 
> 
> On Wed, Mar 30, 2011 at 11:57 AM, Paolo Giannozzi
> <giannozz at democritos.it> wrote:
>> 
>> On Mar 30, 2011, at 11:20 , Gabriele Sclauzero wrote:
>> 
>>> Do you think that having an additional optional level of I/O
>>> (let's say that it might be called "medium")
>> 
>> I propose 'rare', 'medium', 'well done'
>> 
>>> would be too confusing for users?
>> 
>> some users get confused no matter what
>> 
>>> I could try to implement and test it.
>> 
>> ok: just follow the "io_level" variable. Try first to understand
>> what the actual behavior is (the documentation is not so
>> clear on this point) and then think what it should be, if you
>> have some clear ideas
>> 
>> P.
>> ---
>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>> 
> 
> 
> 
> -- 
> Nichols A. Romero, Ph.D.
> Argonne Leadership Computing Facility
> Argonne, IL 60490
> (630) 447-9793
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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

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From yuz10 at uci.edu  Mon Apr 11 23:02:09 2011
From: yuz10 at uci.edu (Yu Zhang)
Date: Mon, 11 Apr 2011 14:02:09 -0700
Subject: [Pw_forum] XSpectra can not run
In-Reply-To: <8F0E039B-111F-4D60-A16C-F59EBE6E9870@democritos.it>
References: <4D9DECB0.4060005@uci.edu>	<2D4EA7C3-30CC-47A4-B6AC-599C97BD901E@democritos.it>	<4D9E01C1.4090708@uci.edu>	<7E09EDF3-B9E3-4828-AA87-DE21C7D8F69B@democritos.it>	<4D9E2BDB.9090409@uci.edu>	<1302255407.17618.5.camel@fe12lx.fisica.uniud.it>	<4D9F58BD.6040602@uci.edu>
	<8F0E039B-111F-4D60-A16C-F59EBE6E9870@democritos.it>
Message-ID: <4DA36C51.1080200@uci.edu>

hi, Paolo,
      Thank Matteo and you very much! Well, I got some similar reading 
error when I tried to do XSpectra calculation with my own input file. 
Could you please see the post
http://www.democritos.it/pipermail/pw_forum/2011-April/020020.html
  for me (I apologize if you've already seen it)? Thank you very much!
best wishes
Yu Zhang

On 04/08/2011 12:18, Paolo Giannozzi wrote:
> On Apr 8, 2011, at 20:49 , Yu Zhang wrote:
>
>> This really solves my problem! Thank you very much.
> you should thank Matteo Calandra, not me
>
>> Could you please explain briefly what the cause  of the problem is?
> the problem is that some recent changes to the initialization of FFT
> grids, G-vectors, and other basic stuff, had not been propagated
> to that particular routine. I had forgotten that XSpectra uses a
> different routine to read the data file from all other QE codes.
> Just an overlook.
>
> Paolo
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


From naromero at gmail.com  Tue Apr 12 00:15:33 2011
From: naromero at gmail.com (Nichols A. Romero)
Date: Mon, 11 Apr 2011 17:15:33 -0500
Subject: [Pw_forum] I/O performance on BG/P systems
In-Reply-To: <C71A92C1-8515-413D-B84E-BAC478403CDB@sissa.it>
References: <4D8C916B.8010800@sissa.it>
	<0F327142-3AB3-47B8-A6DA-723C9AFF135B@democritos.it>
	<4090C379-5D47-4916-945B-428D1B32F501@sissa.it>
	<F3DC331D-4C15-4619-8132-7416B3DB02FE@democritos.it>
	<BDF827EC-3042-483A-8D52-DA17A7B8BD62@sissa.it>
	<A452B8A9-37B9-4CEB-8B6C-77D25D9D6095@democritos.it>
	<BANLkTinW14uKL7FpyqSLKWd3fMkj0Qan+Q@mail.gmail.com>
	<C71A92C1-8515-413D-B84E-BAC478403CDB@sissa.it>
Message-ID: <BANLkTi=69xUZNwVpeOhmN29gCC=kK7Pkxg@mail.gmail.com>

Gabriele,

A couple of other technical details that I am remembering:
1. The BG/P at ANL has 1 I/O node per 64 nodes, 8 I/O nodes per mid-plane
2. The bottleneck of writing multiple files per MPI tasks does not
become serious
    until about 8+ racks.

On Mon, Apr 11, 2011 at 3:50 PM, Gabriele Sclauzero <sclauzer at sissa.it> wrote:
> Dear Paolo and Nichols,
> ?? ?as a follow up, I had a brief meeting with the sysadmin of our local
> BGP. It looks like the timings I was reporting actually correspond to the
> maximum I/O throughput of that specific rack, which depends on the number of
> I/O nodes present on the rack itself (in that case, 4 I/O nodes per
> midplane, each of them capable of 350 MB/s, corresponding to 1.7 GB/s for
> that midplane).
> In the example I was reporting:
> ?? ? davcio ??????: ??1083.30s?CPU ??1083.30s WALL ( ?????38 calls)
> I've been running on just 128 nodes (512 cores in VN mode), therefore I had
> only one I/O node (1 midplane = 4 x 128 nodes, for the non-BG/P-ers). Now,
> the total size of the .wfc files was around 9200 MB, which cannot be written
> in less than 9200/350 = 26.3 sec, according to the figures that the
> sysadmins gave me.
> In my case the timings give:?1083.30s/38=28.5s, which is close to the
> theoretical maximum.
> I will perform more testing and I will take into consideration the
> suggestion of Nichols about the number of files per node. In our machine we
> have one rack with 16 I/O nodes per midplane, I will try to see if the I/O
> performance scales accordingly.
> As a side effect, I met a problem in the timing procedure. I found very
> different davcio timings (i.e. 3 orders of magnitude!) for two jobs where
> the size of the wavefunctions differed by a factor 2 only (the jobs?have
> been executed on the same rack and with the same number of processors and
> same parallelization scheme).
> The sysadmins replied that I/O bandwidth measured in the?fastest case is not
> attainable on BG/P, and should be imputed to an inaccurate measurement of
> cputime/walltime.
> I'm going to investigate this anyway.
> I'm not aware of anyone working on MPI I/O porting.
> Thanks so far for your suggestions,
>
>
> Gabriele
>
>
> Il giorno 11/apr/2011, alle ore 20.02, Nichols A. Romero ha scritto:
>
> Sorry for not replying earlier, but I missed this e-mail due to the
> APS March Meeting.
>
> The GPFS file system on BG/P does a poor job at handling writes to more than
> one file per node. My guess is that Gabriele was running QE in either dual
> or VN mode (2 and 4 MPI tasks per node, respectively). So on BG/P,
> you basically
> want to write one file per node (which GPFS is designed to handle) or
> one big file
> using MPI-I/O.
>
> At ANL, we are thinking about re-writing some of the I/O
> using parallel I/O (e.g. HDF5, Parallel NetCDF). The simplest
> approach, though highly
> unportable, is to use the MPI I/O directly.
>
> Has anyone on this list worked on parallel I/O with QE? Or have any
> strong opinions
> on this issue?
>
>
> On Wed, Mar 30, 2011 at 11:57 AM, Paolo Giannozzi
> <giannozz at democritos.it> wrote:
>
> On Mar 30, 2011, at 11:20 , Gabriele Sclauzero wrote:
>
> Do you think that having an additional optional level of I/O
>
> (let's say that it might be called "medium")
>
> I propose 'rare', 'medium', 'well done'
>
> would be too confusing for users?
>
> some users get confused no matter what
>
> I could try to implement and test it.
>
> ok: just follow the "io_level" variable. Try first to understand
>
> what the actual behavior is (the documentation is not so
>
> clear on this point) and then think what it should be, if you
>
> have some clear ideas
>
> P.
>
> ---
>
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
>
> Pw_forum mailing list
>
> Pw_forum at pwscf.org
>
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> --
> Nichols A. Romero, Ph.D.
> Argonne Leadership Computing Facility
> Argonne, IL 60490
> (630) 447-9793
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> ? Gabriele Sclauzero,?EPFL SB ITP CSEA
> ?? PH H2 462, Station 3,?CH-1015 Lausanne
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>



-- 
Nichols A. Romero, Ph.D.
Argonne Leadership Computing Facility
Argonne, IL 60490
(630) 447-9793

From L-marks at northwestern.edu  Tue Apr 12 01:36:44 2011
From: L-marks at northwestern.edu (Laurence Marks)
Date: Mon, 11 Apr 2011 18:36:44 -0500
Subject: [Pw_forum] One minor bug, one not minor and two questions
In-Reply-To: <BANLkTim5k7pcSAiQ92=or_-P7rk8UCC-OA@mail.gmail.com>
References: <BANLkTimpo976SxfyDctMvwAg8U8bSAo+9A@mail.gmail.com>
	<BANLkTimPv-96Y==_or9f_k0iL_Xqsrs8-A@mail.gmail.com>
	<4DA2D096.4040802@sissa.it> <4DA2D424.1030100@sissa.it>
	<BANLkTim5k7pcSAiQ92=or_-P7rk8UCC-OA@mail.gmail.com>
Message-ID: <BANLkTinUPT6hiucfZ+9RFvqiRXSgrw68tA@mail.gmail.com>

Correction, I did not notice that you are not renormalizing. With
#define __NORMALIZE_BETAMIX it should be more like

          if(iter_used .gt. 1)betamix(i,i)=betamix(i,i) + 2.0D-5

which, interestingly, is almost exactly the same regularization as
used elsewhere.

On Mon, Apr 11, 2011 at 10:25 AM, Laurence Marks
<L-marks at northwestern.edu> wrote:
> Thanks.
>
> Another question if I may. From the looks of PW/mix_rho.f90 you do not
> use the weights in the Johnson paper, just a straight inverse of
> betamix (what would be called Y^T Y in the optimization literature) at
> lines 289-295? Have you considered a regularization, e.g. adding after
> line 278 something like
>
> ? ? ? ?betamix(i,i)=betamix(i,i) + 1.D-7/iter_used
>
> which is about right for your Al (001) example. The regularization
> term (e.g. PRB 78, 075114 (2008)) is a bit empirical, although I might
> be able to change this.
>
> This is safe, so long as mix_rho.f90 is only used for mixing densities
> during the scf iterations -- is it used elsewhere?
>
> On Mon, Apr 11, 2011 at 5:12 AM, Stefano de Gironcoli <degironc at sissa.it> wrote:
>> in my previous ?post
>>
>> reminder -> remainder
>>
>> stefano
>>
>> On 04/11/2011 11:57 AM, Stefano de Gironcoli wrote:
>>> dear Laurence Marks
>>>
>>> ? ? ?thank you for contributing this patch for bfgs !
>>>> A quick question. In the ion optimization it looks like you are
>>>> starting from some iterpolation of the new density (i.e. "NEW-OLD
>>>> atomic charge density approx. for the potential"), what is it?
>>> if i remember correctly the charge density of the new positions is
>>> written
>>> as the superposition of atomic charges plus a reminder which is computed
>>> as the scf rho minus the superposition of atomic charges at the old
>>> positions.
>>>
>>> rho_trial_new = rho_atomic_newR + (rho_scf_oldR - rho_atomic_oldR)
>>>
>>> this is done for the first ionic iteration and assumes that the main
>>> change in the density is due to rigid displacement of atomic-like
>>> contributions.
>>>
>>> At subsequent iterations the reminder (rho_scf_oldR-rho_atomic_oldR)
>>> can be extrapolated on the basis of its change in the previous couple
>>> of iterations
>>>
>>> ?Stefano de Gironcoli
>>>
>>> On 04/11/2011 01:11 AM, Laurence Marks wrote:
>>>> For completeness, added proper comments.
>>>>
>>>> On Sun, Apr 10, 2011 at 4:13 PM, Laurence Marks
>>>> <L-marks at northwestern.edu> ?wrote:
>>>>> A very minor bug that you probably known: some of the routines in
>>>>> S3DE/iotk/src have lines such as "# 1 "iotk_write_interf.spp" ". Most
>>>>> sensible preprocessors will ignore these and just give warnings.
>>>>>
>>>>> A more serious bug. Your bfgs code does not have curvature failure
>>>>> conditions trapped. Not to get too technical here (contact me offline
>>>>> if needed), unless one is close to the minimum bfgs fails unless this
>>>>> is done. The failure is well documented, less well known, as is the
>>>>> change needed (at least the standard form). I am attaching a modified
>>>>> version with the standard fix. It gives a slightly lower energy with
>>>>> smaller forces in about the same number of iterations -- due to
>>>>> numerical limitations I cannot compare exactly with your reference
>>>>> directory. I am a newbie with this code so there could be other
>>>>> repercussions of this change if it is used for something except
>>>>> optimizing the atomic positions, so perhaps a few tests are
>>>>> appropriate for harder problems.
>>>>>
>>>>> A quick question. In the ion optimization it looks like you are
>>>>> starting from some iterpolation of the new density (i.e. "NEW-OLD
>>>>> atomic charge density approx. for the potential"), what is it?
>>>>>
>>>>> Another quick one: line 1766 of install/configure.ac nulls out
>>>>> scalapack_libs and the lines below look like they are special tests,
>>>>> which seems to be inconsistent with line 150 and standard protocols of
>>>>> letting the user define input variables. (OK, while scalapack is
>>>>> probably only useful for large problems I might want to do some.)
>>>>>
>>>>> --
>>>>> Professor Laurence Marks
>>>>> Department of Materials Science and Engineering
>>>>> MSE Rm 2036 Cook Hall
>>>>> 2220 N Campus Drive
>>>>> Northwestern University
>>>>> Evanston, IL 60208, USA
>>>>> Tel: (847) 491-3996 Fax: (847) 491-7820
>>>>> email: L-marks at northwestern dot edu
>>>>> Web: www.numis.northwestern.edu
>>>>> Chair, Commission on Electron Crystallography of IUCR
>>>>> www.numis.northwestern.edu/
>>>>> Research is to see what everybody else has seen, and to think what
>>>>> nobody else has thought
>>>>> Albert Szent-Gyorgi
>>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>
>
>
>
> --
> Laurence Marks
> Department of Materials Science and Engineering
> MSE Rm 2036 Cook Hall
> 2220 N Campus Drive
> Northwestern University
> Evanston, IL 60208, USA
> Tel: (847) 491-3996 Fax: (847) 491-7820
> email: L-marks at northwestern dot edu
> Web: www.numis.northwestern.edu
> Chair, Commission on Electron Crystallography of IUCR
> www.numis.northwestern.edu/
> Research is to see what everybody else has seen, and to think what
> nobody else has thought
> Albert Szent-Gyorgi
>



-- 
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Research is to see what everybody else has seen, and to think what
nobody else has thought
Albert Szent-Gyorgi

From tanycimr at gmail.com  Tue Apr 12 02:37:25 2011
From: tanycimr at gmail.com (tanycimr at gmail.com)
Date: Tue, 12 Apr 2011 08:37:25 +0800
Subject: [Pw_forum] how to get the Eigendisplacements by ph.x
References: <BANLkTimeAsj_F91L9XCwvM_Rz2-FCETRKg@mail.gmail.com>
	<949916.75234.qm@web65710.mail.ac4.yahoo.com>
	<994120.70341.qm@web65702.mail.ac4.yahoo.com>
Message-ID: <4DA39EC5.000001.03892@LBDZ-12271421>

Thanks  . The advice give me a lot of help

Tanyci
Nankai university , tianjin 
China 
 
 
 
 
-------Original Message-------
 
From: Eyvaz Isaev
Date: 2011-4-11 22:40:44
To: PWSCF Forum
Subject: Re: [Pw_forum] how to get the Eigendisplacements by ph.x
 
Well, I was somewhat wrong. If you need eigendisplacements for q-points
(from nq1*nq2*nq3 mesh in ph.in file) then just have look at  *.dynN files.
They contain both frequencies and eigendisplacements for these q-ponts.

  
Eyvaz.



From: Eyvaz Isaev <eyvaz_isaev at yahoo.com>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Mon, April 11, 2011 3:58:58 PM
Subject: Re: [Pw_forum] how to get the Eigendisplacements by ph.x


Hi,

>Use dynmat.x after ph.x.
>In the source file you will find the keywords explained PH/dynmat.f90

Yes, it is true, if  one interested in the Gamma-point only.
Otherwise, one has to use matdyn.x for an arbitrary q-point. Sure,
Interatomic Force Constants 
Matrix is required.

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






From: Eduardo Ariel Menendez Proupin <eariel99 at gmail.com>
To: pw_forum at pwscf.org
Sent: Mon, April 11, 2011 2:15:30 PM
Subject: [Pw_forum] how to get the Eigendisplacements by ph.x


> want to know how to get the Eigendisplacements  by ph.x . what i found in
the dyn_G file is just "Diagonalizing the dynamical matrix"



Use dynmat.x after ph.x.


In the source file you will find the keywords explained
PH/dynmat.f90


Good luck,
-- 





Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/%7Eemenendez





 
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From flux_ray12 at 163.com  Tue Apr 12 07:54:39 2011
From: flux_ray12 at 163.com (souledge)
Date: Tue, 12 Apr 2011 13:54:39 +0800 (CST)
Subject: [Pw_forum] pw.x stopped during vc-relax running
Message-ID: <169ddebb.175fa.12f4846a3cd.Coremail.flux_ray12@163.com>

Dear QE developers and user:
I am using QE 4.3, now, and met a problem about vc-relax calculation.
I tried to do vc-relax on Gamma-Fe (FCC structure), however, after finishing "BFGS Geometry Optimization" and running  "A final scf calculation at the relaxed structure" to "number of k points=    84  Methfessel-Paxton smearing.......", pw.x program suddenly stopped with the error:
 "rank 1 in job 5 ZrGe-RHEL6Server_48502   caused collective abort of all ranks
  exit status of rank 1: killed by signal 9 " in output file and:
"application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1" in terminate when it displayed the 56th k-point "k(   56) = (  -0.2294673   0.5354236  -0.0764891), wk =   0.0436959" in output file.
---------------------Software Environment----------------------------
My system is Red Hat Enterprise Linux 6 Server, the software environment lists here:
MPI: MPICH2,
FFT: FFTW 3.2.2
FC: gfortran
C: gcc
MPI-FC: mpif90
----------------------Hardware Environment---------------------------
CPU: Athlon2 x2 245 2.9GHz Dual-core
RAM: DDR2 800MHz 2*2GB
HDD: Hitachi, with an empty space of 8.8GB
----------------------input file for vc-relax----------------------------
 &CONTROL
                 calculation = 'vc-relax' ,
                restart_mode = 'from_scratch' ,
                  wf_collect = .false. ,
                      outdir = '$TempDIR/' ,
                  pseudo_dir = '$PPDIR/' ,
                      prefix = 'Fe' ,
                     disk_io = 'default' ,
                   verbosity = 'default' ,
                       nstep = 150 ,
                     tstress = .true. ,
                     tprnfor = .true. ,
                     tefield = .false. ,
                    dipfield = .false. ,
                    lelfield = .false. ,
                      lberry = .false. ,
 /
 &SYSTEM
                       ibrav = 2,
                   celldm(1) = 6.481760142 ,
                         nat = 1,
                        ntyp = 1,
                     ecutwfc = 42.26170535 ,
                     ecutrho = 422.6170535 ,
                 occupations = 'smearing' ,
                    smearing = 'mp' ,
                     degauss = 0.015 ,
 /
 &ELECTRONS
                    conv_thr = 1.0D-8 ,
            electron_maxstep = 150,
                 startingpot = 'atomic' ,
                 startingwfc = 'atomic+random' ,
                 mixing_mode = 'plain' ,
             diagonalization = 'david' ,
              diago_full_acc = .false. ,
                         tqr = .false. ,
 /
 &IONS
                       ion_dynamics = 'bfgs' ,
                      ion_positions = 'from_input' ,
                        phase_space = 'full' ,
                  pot_extrapolation = 'second_order' ,
                  wfc_extrapolation = 'second_order' ,
 /
 &CELL
                      cell_dynamics = 'bfgs' ,
 /
ATOMIC_SPECIES
    Fe   55.84   Fe.pbe-sp-van_ak.UPF
ATOMIC_POSITIONS crystal
    Fe   0.000000   0.000000   0.000000      
K_POINTS automatic
  13 13 13   0 0 0
----------------------------------------------------------------------
P.S.: I have not found this problem in both of QE 4.2 and 4.2.1, which was in the same computer and software environment. What should I do to overcome this problem?
Looking forward to your reply and help, thanks very much.



--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea
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From flux_ray12 at 163.com  Tue Apr 12 08:34:32 2011
From: flux_ray12 at 163.com (=?UTF-8?Q?GAO=C2=A0Zhe?=)
Date: Tue, 12 Apr 2011 14:34:32 +0800 (CST)
Subject: [Pw_forum] Advanced error report about vc-relax of pw.x
Message-ID: <64e20f84.180e5.12f486b254c.Coremail.flux_ray12@163.com>

Dear QE developer and users:
I tried running vc-relax on one CPU core and set parameter as verbosity = 'high', then, I obtained more detailed error report:
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from sym_rho_init_shell : error #         2
     lone vector
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
Unfortunately, I cannot understand the meaning of error info...... Would you like to  kindly helping me out? I really do not have any idea about this error~~~
Best Regards.



--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea
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From degironc at sissa.it  Tue Apr 12 08:41:39 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Tue, 12 Apr 2011 08:41:39 +0200
Subject: [Pw_forum] One minor bug, one not minor and two questions
In-Reply-To: <BANLkTim5k7pcSAiQ92=or_-P7rk8UCC-OA@mail.gmail.com>
References: <BANLkTimpo976SxfyDctMvwAg8U8bSAo+9A@mail.gmail.com>	<BANLkTimPv-96Y==_or9f_k0iL_Xqsrs8-A@mail.gmail.com>	<4DA2D096.4040802@sissa.it>
	<4DA2D424.1030100@sissa.it>
	<BANLkTim5k7pcSAiQ92=or_-P7rk8UCC-OA@mail.gmail.com>
Message-ID: <4DA3F423.4060808@sissa.it>

It has been there for some time, didn't seem to have any relevant effect.
do you have evidence of the contrary?
stefano

On 04/11/2011 05:25 PM, Laurence Marks wrote:
> Thanks.
>
> Another question if I may. From the looks of PW/mix_rho.f90 you do not
> use the weights in the Johnson paper, just a straight inverse of
> betamix (what would be called Y^T Y in the optimization literature) at
> lines 289-295? Have you considered a regularization, e.g. adding after
> line 278 something like
>
>          betamix(i,i)=betamix(i,i) + 1.D-7/iter_used
>
> which is about right for your Al (001) example. The regularization
> term (e.g. PRB 78, 075114 (2008)) is a bit empirical, although I might
> be able to change this.
>
> This is safe, so long as mix_rho.f90 is only used for mixing densities
> during the scf iterations -- is it used elsewhere?
>
> On Mon, Apr 11, 2011 at 5:12 AM, Stefano de Gironcoli<degironc at sissa.it>  wrote:
>> in my previous  post
>>
>> reminder ->  remainder
>>
>> stefano
>>
>> On 04/11/2011 11:57 AM, Stefano de Gironcoli wrote:
>>> dear Laurence Marks
>>>
>>>       thank you for contributing this patch for bfgs !
>>>> A quick question. In the ion optimization it looks like you are
>>>> starting from some iterpolation of the new density (i.e. "NEW-OLD
>>>> atomic charge density approx. for the potential"), what is it?
>>> if i remember correctly the charge density of the new positions is
>>> written
>>> as the superposition of atomic charges plus a reminder which is computed
>>> as the scf rho minus the superposition of atomic charges at the old
>>> positions.
>>>
>>> rho_trial_new = rho_atomic_newR + (rho_scf_oldR - rho_atomic_oldR)
>>>
>>> this is done for the first ionic iteration and assumes that the main
>>> change in the density is due to rigid displacement of atomic-like
>>> contributions.
>>>
>>> At subsequent iterations the reminder (rho_scf_oldR-rho_atomic_oldR)
>>> can be extrapolated on the basis of its change in the previous couple
>>> of iterations
>>>
>>>   Stefano de Gironcoli
>>>
>>> On 04/11/2011 01:11 AM, Laurence Marks wrote:
>>>> For completeness, added proper comments.
>>>>
>>>> On Sun, Apr 10, 2011 at 4:13 PM, Laurence Marks
>>>> <L-marks at northwestern.edu>    wrote:
>>>>> A very minor bug that you probably known: some of the routines in
>>>>> S3DE/iotk/src have lines such as "# 1 "iotk_write_interf.spp" ". Most
>>>>> sensible preprocessors will ignore these and just give warnings.
>>>>>
>>>>> A more serious bug. Your bfgs code does not have curvature failure
>>>>> conditions trapped. Not to get too technical here (contact me offline
>>>>> if needed), unless one is close to the minimum bfgs fails unless this
>>>>> is done. The failure is well documented, less well known, as is the
>>>>> change needed (at least the standard form). I am attaching a modified
>>>>> version with the standard fix. It gives a slightly lower energy with
>>>>> smaller forces in about the same number of iterations -- due to
>>>>> numerical limitations I cannot compare exactly with your reference
>>>>> directory. I am a newbie with this code so there could be other
>>>>> repercussions of this change if it is used for something except
>>>>> optimizing the atomic positions, so perhaps a few tests are
>>>>> appropriate for harder problems.
>>>>>
>>>>> A quick question. In the ion optimization it looks like you are
>>>>> starting from some iterpolation of the new density (i.e. "NEW-OLD
>>>>> atomic charge density approx. for the potential"), what is it?
>>>>>
>>>>> Another quick one: line 1766 of install/configure.ac nulls out
>>>>> scalapack_libs and the lines below look like they are special tests,
>>>>> which seems to be inconsistent with line 150 and standard protocols of
>>>>> letting the user define input variables. (OK, while scalapack is
>>>>> probably only useful for large problems I might want to do some.)
>>>>>
>>>>> --
>>>>> Professor Laurence Marks
>>>>> Department of Materials Science and Engineering
>>>>> MSE Rm 2036 Cook Hall
>>>>> 2220 N Campus Drive
>>>>> Northwestern University
>>>>> Evanston, IL 60208, USA
>>>>> Tel: (847) 491-3996 Fax: (847) 491-7820
>>>>> email: L-marks at northwestern dot edu
>>>>> Web: www.numis.northwestern.edu
>>>>> Chair, Commission on Electron Crystallography of IUCR
>>>>> www.numis.northwestern.edu/
>>>>> Research is to see what everybody else has seen, and to think what
>>>>> nobody else has thought
>>>>> Albert Szent-Gyorgi
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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 physik.shyam at gmail.com  Tue Apr 12 08:43:12 2011
From: physik.shyam at gmail.com (Shyam Khambholja)
Date: Tue, 12 Apr 2011 12:13:12 +0530
Subject: [Pw_forum] Regarding accuracy in total energy
Message-ID: <BANLkTikoiY=RrAQqLBN+t48BPr5e4Oz6ig@mail.gmail.com>

Dear all,

I want to calculate total energy of compounds with accuarcy upto tenth digit
after decimal point. what should I need to edit ?

with thanks,
-- 
Mr. Shyam G Khambholja,
Research student,
Depratment of Physics,
Sardar Patel University, Gujarat
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From L-marks at northwestern.edu  Tue Apr 12 08:51:45 2011
From: L-marks at northwestern.edu (Laurence Marks)
Date: Tue, 12 Apr 2011 01:51:45 -0500
Subject: [Pw_forum] One minor bug, one not minor and two questions
In-Reply-To: <4DA3F423.4060808@sissa.it>
References: <BANLkTimpo976SxfyDctMvwAg8U8bSAo+9A@mail.gmail.com>
	<BANLkTimPv-96Y==_or9f_k0iL_Xqsrs8-A@mail.gmail.com>
	<4DA2D096.4040802@sissa.it> <4DA2D424.1030100@sissa.it>
	<BANLkTim5k7pcSAiQ92=or_-P7rk8UCC-OA@mail.gmail.com>
	<4DA3F423.4060808@sissa.it>
Message-ID: <BANLkTimvNyQv7fWdpsBypGrZ0bhm0XtEtA@mail.gmail.com>

The renormalization will only matter if the inverse of betamix is
regularized. I am not that familiar with how the Johnson algorithm behaves
for bad problems to know if regularization helps in practice, or does matter
for a multisecant method.
On Apr 12, 2011 1:41 AM, "Stefano de Gironcoli" <degironc at sissa.it> wrote:
> It has been there for some time, didn't seem to have any relevant effect.
> do you have evidence of the contrary?
> stefano
>
> On 04/11/2011 05:25 PM, Laurence Marks wrote:
>> Thanks.
>>
>> Another question if I may. From the looks of PW/mix_rho.f90 you do not
>> use the weights in the Johnson paper, just a straight inverse of
>> betamix (what would be called Y^T Y in the optimization literature) at
>> lines 289-295? Have you considered a regularization, e.g. adding after
>> line 278 something like
>>
>> betamix(i,i)=betamix(i,i) + 1.D-7/iter_used
>>
>> which is about right for your Al (001) example. The regularization
>> term (e.g. PRB 78, 075114 (2008)) is a bit empirical, although I might
>> be able to change this.
>>
>> This is safe, so long as mix_rho.f90 is only used for mixing densities
>> during the scf iterations -- is it used elsewhere?
>>
>> On Mon, Apr 11, 2011 at 5:12 AM, Stefano de Gironcoli<degironc at sissa.it>
wrote:
>>> in my previous post
>>>
>>> reminder -> remainder
>>>
>>> stefano
>>>
>>> On 04/11/2011 11:57 AM, Stefano de Gironcoli wrote:
>>>> dear Laurence Marks
>>>>
>>>> thank you for contributing this patch for bfgs !
>>>>> A quick question. In the ion optimization it looks like you are
>>>>> starting from some iterpolation of the new density (i.e. "NEW-OLD
>>>>> atomic charge density approx. for the potential"), what is it?
>>>> if i remember correctly the charge density of the new positions is
>>>> written
>>>> as the superposition of atomic charges plus a reminder which is
computed
>>>> as the scf rho minus the superposition of atomic charges at the old
>>>> positions.
>>>>
>>>> rho_trial_new = rho_atomic_newR + (rho_scf_oldR - rho_atomic_oldR)
>>>>
>>>> this is done for the first ionic iteration and assumes that the main
>>>> change in the density is due to rigid displacement of atomic-like
>>>> contributions.
>>>>
>>>> At subsequent iterations the reminder (rho_scf_oldR-rho_atomic_oldR)
>>>> can be extrapolated on the basis of its change in the previous couple
>>>> of iterations
>>>>
>>>> Stefano de Gironcoli
>>>>
>>>> On 04/11/2011 01:11 AM, Laurence Marks wrote:
>>>>> For completeness, added proper comments.
>>>>>
>>>>> On Sun, Apr 10, 2011 at 4:13 PM, Laurence Marks
>>>>> <L-marks at northwestern.edu> wrote:
>>>>>> A very minor bug that you probably known: some of the routines in
>>>>>> S3DE/iotk/src have lines such as "# 1 "iotk_write_interf.spp" ". Most
>>>>>> sensible preprocessors will ignore these and just give warnings.
>>>>>>
>>>>>> A more serious bug. Your bfgs code does not have curvature failure
>>>>>> conditions trapped. Not to get too technical here (contact me offline
>>>>>> if needed), unless one is close to the minimum bfgs fails unless this
>>>>>> is done. The failure is well documented, less well known, as is the
>>>>>> change needed (at least the standard form). I am attaching a modified
>>>>>> version with the standard fix. It gives a slightly lower energy with
>>>>>> smaller forces in about the same number of iterations -- due to
>>>>>> numerical limitations I cannot compare exactly with your reference
>>>>>> directory. I am a newbie with this code so there could be other
>>>>>> repercussions of this change if it is used for something except
>>>>>> optimizing the atomic positions, so perhaps a few tests are
>>>>>> appropriate for harder problems.
>>>>>>
>>>>>> A quick question. In the ion optimization it looks like you are
>>>>>> starting from some iterpolation of the new density (i.e. "NEW-OLD
>>>>>> atomic charge density approx. for the potential"), what is it?
>>>>>>
>>>>>> Another quick one: line 1766 of install/configure.ac nulls out
>>>>>> scalapack_libs and the lines below look like they are special tests,
>>>>>> which seems to be inconsistent with line 150 and standard protocols
of
>>>>>> letting the user define input variables. (OK, while scalapack is
>>>>>> probably only useful for large problems I might want to do some.)
>>>>>>
>>>>>> --
>>>>>> Professor Laurence Marks
>>>>>> Department of Materials Science and Engineering
>>>>>> MSE Rm 2036 Cook Hall
>>>>>> 2220 N Campus Drive
>>>>>> Northwestern University
>>>>>> Evanston, IL 60208, USA
>>>>>> Tel: (847) 491-3996 Fax: (847) 491-7820
>>>>>> email: L-marks at northwestern dot edu
>>>>>> Web: www.numis.northwestern.edu
>>>>>> Chair, Commission on Electron Crystallography of IUCR
>>>>>> www.numis.northwestern.edu/
>>>>>> Research is to see what everybody else has seen, and to think what
>>>>>> nobody else has thought
>>>>>> Albert Szent-Gyorgi
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
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From degironc at sissa.it  Tue Apr 12 08:52:57 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Tue, 12 Apr 2011 08:52:57 +0200
Subject: [Pw_forum] Regarding accuracy in total energy
In-Reply-To: <BANLkTikoiY=RrAQqLBN+t48BPr5e4Oz6ig@mail.gmail.com>
References: <BANLkTikoiY=RrAQqLBN+t48BPr5e4Oz6ig@mail.gmail.com>
Message-ID: <4DA3F6C9.5060605@sissa.it>

change the format statements in electrons (label  9060 and the like) and 
converge energy accordingly.
however ... why do you need more than 10 digits ?

stefano


On 04/12/2011 08:43 AM, Shyam Khambholja wrote:
> Dear all,
>
> I want to calculate total energy of compounds with accuarcy upto tenth digit
> after decimal point. what should I need to edit ?
>
> with thanks,
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From matteo.calandra at impmc.jussieu.fr  Tue Apr 12 09:21:06 2011
From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra)
Date: Tue, 12 Apr 2011 09:21:06 +0200
Subject: [Pw_forum] XSpectra can not run
In-Reply-To: <mailman.11296.1302568668.1814.pw_forum@pwscf.org>
References: <mailman.11296.1302568668.1814.pw_forum@pwscf.org>
Message-ID: <4DA3FD62.9020608@impmc.jussieu.fr>

> hi, Paolo,
>       Thank Matteo and you very much! Well, I got some similar reading 
> error when I tried to do XSpectra calculation with my own input file. 
> Could you please see the post
> http://www.democritos.it/pipermail/pw_forum/2011-April/020020.html
>   for me (I apologize if you've already seen it)? Thank you very much!
> best wishes
> Yu Zhang
>

Dear Yu Zhang,

  I think the problem is that some of your pseudopotentials do not
have gipaw reconstruction inside.

In principle this is needed only for the absorbing atom, but for
the moment the code requires that all the pseudo do have gipaw
reconstruction.

I have to modify this as soon as I have some time.

Th second problem is that xspectra does not work with the
Gamma only version of the code. So you should run both the
scf and xspectra not with

K_POINTS gamma

but with

K_POINTS automatic
1 1 1 0 0 0

It should then work.

M.


> On 04/08/2011 12:18, Paolo Giannozzi wrote:
>> On Apr 8, 2011, at 20:49 , Yu Zhang wrote:
>>
>>> This really solves my problem! Thank you very much.
>> you should thank Matteo Calandra, not me
>>
>>> Could you please explain briefly what the cause  of the problem is?
>> the problem is that some recent changes to the initialization of FFT
>> grids, G-vectors, and other basic stuff, had not been propagated
>> to that particular routine. I had forgotten that XSpectra uses a
>> different routine to read the data file from all other QE codes.
>> Just an overlook.
>>
>> Paolo
>> ---
>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 11 Apr 2011 17:15:33 -0500
> From: "Nichols A. Romero" <naromero at gmail.com>
> Subject: Re: [Pw_forum] I/O performance on BG/P systems
> To: PWSCF Forum <pw_forum at pwscf.org>
> Cc: Gabriele Sclauzero <sclauzer at sissa.it>
> Message-ID: <BANLkTi=69xUZNwVpeOhmN29gCC=kK7Pkxg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Gabriele,
> 
> A couple of other technical details that I am remembering:
> 1. The BG/P at ANL has 1 I/O node per 64 nodes, 8 I/O nodes per mid-plane
> 2. The bottleneck of writing multiple files per MPI tasks does not
> become serious
>     until about 8+ racks.
> 
> On Mon, Apr 11, 2011 at 3:50 PM, Gabriele Sclauzero <sclauzer at sissa.it> wrote:
>> Dear Paolo and Nichols,
>> ?? ?as a follow up, I had a brief meeting with the sysadmin of our local
>> BGP. It looks like the timings I was reporting actually correspond to the
>> maximum I/O throughput of that specific rack, which depends on the number of
>> I/O nodes present on the rack itself (in that case, 4 I/O nodes per
>> midplane, each of them capable of 350 MB/s, corresponding to 1.7 GB/s for
>> that midplane).
>> In the example I was reporting:
>> ?? ? davcio ??????: ??1083.30s?CPU ??1083.30s WALL ( ?????38 calls)
>> I've been running on just 128 nodes (512 cores in VN mode), therefore I had
>> only one I/O node (1 midplane = 4 x 128 nodes, for the non-BG/P-ers). Now,
>> the total size of the .wfc files was around 9200 MB, which cannot be written
>> in less than 9200/350 = 26.3 sec, according to the figures that the
>> sysadmins gave me.
>> In my case the timings give:?1083.30s/38=28.5s, which is close to the
>> theoretical maximum.
>> I will perform more testing and I will take into consideration the
>> suggestion of Nichols about the number of files per node. In our machine we
>> have one rack with 16 I/O nodes per midplane, I will try to see if the I/O
>> performance scales accordingly.
>> As a side effect, I met a problem in the timing procedure. I found very
>> different davcio timings (i.e. 3 orders of magnitude!) for two jobs where
>> the size of the wavefunctions differed by a factor 2 only (the jobs?have
>> been executed on the same rack and with the same number of processors and
>> same parallelization scheme).
>> The sysadmins replied that I/O bandwidth measured in the?fastest case is not
>> attainable on BG/P, and should be imputed to an inaccurate measurement of
>> cputime/walltime.
>> I'm going to investigate this anyway.
>> I'm not aware of anyone working on MPI I/O porting.
>> Thanks so far for your suggestions,
>>
>>
>> Gabriele
>>
>>
>> Il giorno 11/apr/2011, alle ore 20.02, Nichols A. Romero ha scritto:
>>
>> Sorry for not replying earlier, but I missed this e-mail due to the
>> APS March Meeting.
>>
>> The GPFS file system on BG/P does a poor job at handling writes to more than
>> one file per node. My guess is that Gabriele was running QE in either dual
>> or VN mode (2 and 4 MPI tasks per node, respectively). So on BG/P,
>> you basically
>> want to write one file per node (which GPFS is designed to handle) or
>> one big file
>> using MPI-I/O.
>>
>> At ANL, we are thinking about re-writing some of the I/O
>> using parallel I/O (e.g. HDF5, Parallel NetCDF). The simplest
>> approach, though highly
>> unportable, is to use the MPI I/O directly.
>>
>> Has anyone on this list worked on parallel I/O with QE? Or have any
>> strong opinions
>> on this issue?
>>
>>
>> On Wed, Mar 30, 2011 at 11:57 AM, Paolo Giannozzi
>> <giannozz at democritos.it> wrote:
>>
>> On Mar 30, 2011, at 11:20 , Gabriele Sclauzero wrote:
>>
>> Do you think that having an additional optional level of I/O
>>
>> (let's say that it might be called "medium")
>>
>> I propose 'rare', 'medium', 'well done'
>>
>> would be too confusing for users?
>>
>> some users get confused no matter what
>>
>> I could try to implement and test it.
>>
>> ok: just follow the "io_level" variable. Try first to understand
>>
>> what the actual behavior is (the documentation is not so
>>
>> clear on this point) and then think what it should be, if you
>>
>> have some clear ideas
>>
>> P.
>>
>> ---
>>
>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>>
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>>
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>>
>>
>> _______________________________________________
>>
>> Pw_forum mailing list
>>
>> Pw_forum at pwscf.org
>>
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>>
>>
>> --
>> Nichols A. Romero, Ph.D.
>> Argonne Leadership Computing Facility
>> Argonne, IL 60490
>> (630) 447-9793
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>> ? Gabriele Sclauzero,?EPFL SB ITP CSEA
>> ?? PH H2 462, Station 3,?CH-1015 Lausanne
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
> 
> 
> 


-- 
* * * *
Matteo Calandra, Charge de Recherche (CR1)
Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris
Universit? Pierre et Marie Curie, tour 23, 3eme etage, case 115
4 Place Jussieu, 75252 Paris Cedex 05 France
Tel: +33-1-44 27 52 16       Fax: +33-1-44 27 37 85
http://www.impmc.jussieu.fr/~calandra

From farzad_c81 at yahoo.com  Tue Apr 12 10:34:10 2011
From: farzad_c81 at yahoo.com (Farzad Molani)
Date: Tue, 12 Apr 2011 01:34:10 -0700 (PDT)
Subject: [Pw_forum] fermi energy from scf vs nscf calculations
Message-ID: <585873.1659.qm@web55703.mail.re3.yahoo.com>

Hello pwscf users,
I want to study my system by DOS calculations, I have a question about my result. Fermi energy ?In SCF calculation is defferent from nscf calculation. which of them is correct?
with the best regards.?

Farzad Molani,
Ph.D Student,
Department of Theoretical Physical Chemistry,
K. N. Toosi University of Technology,
Tehran, Iran.
Tel.: 009891 4442 3308
Tel.: 009821 2306 4280 
Fax: 009821 2285 3650 
Web: http://www.chem.kntu.ac.ir/~sjalili:/
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From nkxirainbow at gmail.com  Tue Apr 12 12:40:48 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Tue, 12 Apr 2011 18:40:48 +0800
Subject: [Pw_forum] fermi energy from scf vs nscf calculations
In-Reply-To: <585873.1659.qm@web55703.mail.re3.yahoo.com>
References: <585873.1659.qm@web55703.mail.re3.yahoo.com>
Message-ID: <BANLkTi=iQkvQVscGYQEw=i3MD+n+YgnXzw@mail.gmail.com>

Dear Farzad Molani:
    Is the difference big?
    Maybe you do not do the convergence test about k-mesh or encut. If all
parameters are converged, nscf will give the same fermi energy with scf.

On Tue, Apr 12, 2011 at 4:34 PM, Farzad Molani <farzad_c81 at yahoo.com> wrote:

> Hello pwscf users,
> I want to study my system by DOS calculations, I have a question about my
> result. Fermi energy  In SCF calculation is defferent from nscf calculation.
> which of them is correct?
> with the best regards.
>
> Farzad Molani,
> Ph.D Student,
> Department of Theoretical Physical Chemistry,
> K. N. Toosi University of Technology,
> Tehran, Iran.
> Tel.: 009891 4442 3308
> Tel.: 009821 2306 4280
> Fax: 009821 2285 3650
> Web: http://www.chem.kntu.ac.ir/~sjalili:/
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From giannozz at democritos.it  Tue Apr 12 15:17:11 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 12 Apr 2011 15:17:11 +0200
Subject: [Pw_forum] Advanced error report about vc-relax of pw.x
In-Reply-To: <64e20f84.180e5.12f486b254c.Coremail.flux_ray12@163.com>
References: <64e20f84.180e5.12f486b254c.Coremail.flux_ray12@163.com>
Message-ID: <1302614231.28191.66.camel@fe12lx.fisica.uniud.it>

On Tue, 2011-04-12 at 14:34 +0800, GAO Zhe wrote:

>      from sym_rho_init_shell : error #         2
>      lone vector

this is a consequence of non-local interactions between recent
changes to the way G-vectors are computed and the final scf step,
performed in variable-cell optimization only, with G-vectors set 
for the final cell (and not for the initial cell as it is done during
the optimization). Apparently in this last step some G-vectors are
"lost" and the algorithm that collects G-vector shells complains.
 
For the time being, waiting for a better solution, increase the
FFT grid to nr1=32, nr2=32, nr3=32. Also note that you can get the 
final coordinates and lattice parameters from output and perform
the final scf calculation (as it used to be done some time ago)
if you want. The last step is done only to make it clear what
the result will look like with the final cell.

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



From giannozz at democritos.it  Tue Apr 12 15:55:53 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 12 Apr 2011 15:55:53 +0200
Subject: [Pw_forum] One minor bug, one not minor and two questions
In-Reply-To: <BANLkTimpo976SxfyDctMvwAg8U8bSAo+9A@mail.gmail.com>
References: <BANLkTimpo976SxfyDctMvwAg8U8bSAo+9A@mail.gmail.com>
Message-ID: <1302616553.28191.87.camel@fe12lx.fisica.uniud.it>

On Sun, 2011-04-10 at 16:13 -0500, Laurence Marks wrote:

> Another quick one: line 1766 of install/configure.ac nulls out
> scalapack_libs and the lines below look like they are special tests,
> which seems to be inconsistent with line 150 and standard protocols of
> letting the user define input variables.

very likely so. The problem is that scalapack is typically available 
on large parallel machines. It is not obvious to have access to more
than a few of them, and each machine seems to have a different idea 
on where scalapack should be. The present status of configure.ac is
the results of trial and error attempts on a few machines. With so much
variety and so few people daring to look inside configure.ac, it is not
obvious how to set up a better and more general scalapack test. 
Suggestions are most welcome (and not only on scalapack)

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



From ttduyle at gmail.com  Tue Apr 12 16:00:38 2011
From: ttduyle at gmail.com (Duy Le)
Date: Tue, 12 Apr 2011 10:00:38 -0400
Subject: [Pw_forum] Regarding accuracy in total energy
In-Reply-To: <4DA3F6C9.5060605@sissa.it>
References: <BANLkTikoiY=RrAQqLBN+t48BPr5e4Oz6ig@mail.gmail.com>
	<4DA3F6C9.5060605@sissa.it>
Message-ID: <BANLkTikzdg6-2cvj3tO=fUg-_W7V_3jBng@mail.gmail.com>

On Tue, Apr 12, 2011 at 2:52 AM, Stefano de Gironcoli <degironc at sissa.it> wrote:
> change the format statements in electrons (label? 9060 and the like) and
> converge energy accordingly.
Is this true? This solution will give you number of digits but how
about the accuracy as Shyam asked? Due to the numerical error, I don't
think we can get that accuracy.
BTW, you need also to set all convergence categories to 1.0D-10 at least.
> however ... why do you need more than 10 digits ?
Perhaps to calculate Lamb Shift :)
>

--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"
>
> On 04/12/2011 08:43 AM, Shyam Khambholja wrote:
>
> Dear all,
>
> I want to calculate total energy of compounds with accuarcy upto tenth digit
> after decimal point. what should I need to edit ?
>
> with thanks,
>
> _______________________________________________
> 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 flux_ray12 at 163.com  Wed Apr 13 05:48:51 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Wed, 13 Apr 2011 11:48:51 +0800 (CST)
Subject: [Pw_forum] Advanced error report about vc-relax of pw.x
In-Reply-To: <1302614231.28191.66.camel@fe12lx.fisica.uniud.it>
References: <1302614231.28191.66.camel@fe12lx.fisica.uniud.it>
	<64e20f84.180e5.12f486b254c.Coremail.flux_ray12@163.com>
Message-ID: <51074368.5fd7.12f4cf9d220.Coremail.flux_ray12@163.com>

Thank you very much, Prof. Giannozzi.
I added nr1 = 32, nr2 = 32, nr3 = 32 in the namecard of SYSTEM, then the vc-relax works well.


At 2011-04-12 21:17:11?"Paolo Giannozzi" <giannozz at democritos.it> wrote:

>On Tue, 2011-04-12 at 14:34 +0800, GAO Zhe wrote:
>
>>      from sym_rho_init_shell : error #         2
>>      lone vector
>
>this is a consequence of non-local interactions between recent
>changes to the way G-vectors are computed and the final scf step,
>performed in variable-cell optimization only, with G-vectors set 
>for the final cell (and not for the initial cell as it is done during
>the optimization). Apparently in this last step some G-vectors are
>"lost" and the algorithm that collects G-vector shells complains.
> 
>For the time being, waiting for a better solution, increase the
>FFT grid to nr1=32, nr2=32, nr3=32. Also note that you can get the 
>final coordinates and lattice parameters from output and perform
>the final scf calculation (as it used to be done some time ago)
>if you want. The last step is done only to make it clear what
>the result will look like with the final cell.
>
>P.
>-- 
>Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum




--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea
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From physik.shyam at gmail.com  Wed Apr 13 06:30:13 2011
From: physik.shyam at gmail.com (Shyam Khambholja)
Date: Wed, 13 Apr 2011 10:00:13 +0530
Subject: [Pw_forum] total energy
Message-ID: <BANLkTikw29uODBRDwUv9_tarNpSiDhcwrQ@mail.gmail.com>

Thank you Dr. Stefano.

I need it for calculation of themodynamic properties.

-- 
Mr. Shyam G Khambholja,
Research student,
Depratment of Physics,
Sardar Patel University, Gujarat
Cell No. : +91 999 888 3867
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From germaneau at gucas.ac.cn  Wed Apr 13 19:09:32 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Wed, 13 Apr 2011 13:09:32 -0400
Subject: [Pw_forum] inconsistent number of sticks ?
Message-ID: <4DA5D8CC.90603@gucas.ac.cn>

Dear QE users,

I got the following error at the end of a vc-relax run :

End final coordinates



      A final scf calculation at the relaxed structure.

      The G-vectors are recalculated.

    Stick Mesh
    ----------
    nst =  2525,  nstw =   297, nsts =  1185
   *            1  *          562  /=          592
   *            2  *          562  /=          592
   *            3  *          561  /=          592
   *            4  *          565  /=          593

  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      from  fft_dlay_set  : error #         8
       inconsistent number of sticks
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

      stopping ...

Can you please tell me what does it mean.
I use the 4.3 release with mpi on a intel quad core CPU.
Thanks,

                          Eric.

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/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  Wed Apr 13 09:03:35 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 13 Apr 2011 09:03:35 +0200
Subject: [Pw_forum] inconsistent number of sticks ?
In-Reply-To: <4DA5D8CC.90603@gucas.ac.cn>
References: <4DA5D8CC.90603@gucas.ac.cn>
Message-ID: <2B0A3D23-F1E7-4D77-9E34-5E2767512A50@democritos.it>


On Apr 13, 2011, at 19:09 , Eric Germaneau wrote:

>      from  fft_dlay_set  : error #         8
>       inconsistent number of sticks

> Can you please tell me what does it mean.

it means the same thing as in this message:
http://www.democritos.it/pipermail/pw_forum/2011-April/020052.html

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





From degironc at sissa.it  Wed Apr 13 09:47:09 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 13 Apr 2011 09:47:09 +0200
Subject: [Pw_forum] total energy
In-Reply-To: <BANLkTikw29uODBRDwUv9_tarNpSiDhcwrQ@mail.gmail.com>
References: <BANLkTikw29uODBRDwUv9_tarNpSiDhcwrQ@mail.gmail.com>
Message-ID: <4DA554FD.8030407@sissa.it>

I don't think you'll need so many digits...
anyhow if you add a few digits in the output and you tighten the 
conv_thr to less than 1.d-10
the numbers you'll get should be self-consistent at that level...
however, it would be extremely difficult to converge k-point sampling 
and/or cutoff at that accuracy.
not to mention the uncertain error due to the choice of xc.

stefano


On 04/13/2011 06:30 AM, Shyam Khambholja wrote:
> Thank you Dr. Stefano.
>
> I need it for calculation of themodynamic properties.
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From daijiayu at nudt.edu.cn  Wed Apr 13 09:48:28 2011
From: daijiayu at nudt.edu.cn (jiayudai)
Date: Wed, 13 Apr 2011 15:48:28 +0800
Subject: [Pw_forum] Spectra from GW and TDDFPT
Message-ID: <110413154828b75378a4bc391222a455b64bbfed1d4a@nudt.edu.cn>


Dear users,

It is well known that GW method can give much more accurate band gap since it considers many body interaction, and thus it can give more accurate optical properties. What i am thinking is that what's the difference between the optical properties from TDDFPT and GW. I mean, TDDFPT has the same accuracy as the GW method? or what's the advantage of TDDFPT over the GW except the computationl cost?

Thanks a lot.

Jiayu


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

 
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From L-marks at northwestern.edu  Wed Apr 13 10:06:10 2011
From: L-marks at northwestern.edu (Laurence Marks)
Date: Wed, 13 Apr 2011 03:06:10 -0500
Subject: [Pw_forum] total energy
In-Reply-To: <4DA554FD.8030407@sissa.it>
References: <BANLkTikw29uODBRDwUv9_tarNpSiDhcwrQ@mail.gmail.com>
	<4DA554FD.8030407@sissa.it>
Message-ID: <BANLkTimOt3UpoUQzMK78rOYBeV3x3g70nA@mail.gmail.com>

Hmmmm, error from Exc & Vxc, more than 0.01 eV per atom.....
On Apr 13, 2011 2:47 AM, "Stefano de Gironcoli" <degironc at sissa.it> wrote:
> I don't think you'll need so many digits...
> anyhow if you add a few digits in the output and you tighten the
> conv_thr to less than 1.d-10
> the numbers you'll get should be self-consistent at that level...
> however, it would be extremely difficult to converge k-point sampling
> and/or cutoff at that accuracy.
> not to mention the uncertain error due to the choice of xc.
>
> stefano
>
>
> On 04/13/2011 06:30 AM, Shyam Khambholja wrote:
>> Thank you Dr. Stefano.
>>
>> I need it for calculation of themodynamic properties.
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From romeda_8 at yahoo.com  Wed Apr 13 10:37:18 2011
From: romeda_8 at yahoo.com (r s)
Date: Wed, 13 Apr 2011 01:37:18 -0700 (PDT)
Subject: [Pw_forum] How to calculate DOS at the Fermi Energy?
Message-ID: <366310.99840.qm@web120406.mail.ne1.yahoo.com>

Dear prof. Paolo Giannozzi and QE developers:
I am using QE 4.3 and want to calculate density of state at fermi energy per a certain direction for example down,
for this purpose, in the first step, running of the pw.x code with following document as input file:
?&control
??? calculation='scf',
??? prefix= 'ccb'
??? outdir= 'root/espresso-4.3/ccb/results',
??? .
??? . 
?/
?&system 
??? .
??? .
??? occupations='smearing', smearing= 'mp', degauss= 0.02 ,
/
.
.
.
and then, running of the pw.x code with tetrahedra occupation:
?&control
??? calculation='nscf',
??? prefix= 'ccb'
??? outdir= 'root/espresso-4.3/ccb/results',
??? . 
??? .
?/
?&system 
??? .
??? .
??? occupations='tetrahedra',
/
and in the long run, for calculation of total Dos, running of the dos.x code with below text:
&INPUTPP
prefix = 'ccb'
outdir='root/espresso-4.3/ccb/results' ,
fildos = 'ccb.dos.dat' ,
ngauss = 1 ,
degauss = 0.02
Emin= 1.0 ,Emax= 25.0 ,DeltaE= 0.1 ,
?/
now for calculation of density of state at fermi energy, i call pp.x code with following input file:
&inputpp
??? prefix= 'ccb'
??? outdir= 'root/espresso-4.3/ccb/results',
??? plot_num= 3, 
??? filplot= 'dos'
/

but after running, the code says:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
task #??? 0
from local_dos : error #???? 1
guassian broadening needed
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
why guassian broadening needed?!
While degauss= 0.02,
What should I do to overcome this problem?
To ensure more,running of all these steps with "gaussian" smearing namely smearing= 'gaussian' and even with change of degauss parameter, but 
the same error is displayed!
why the code says i didn't use any smearing, degauss and stops.
?
Looking forward to your reply and help, thanks very much.
Regards,

--
Romeda Azeen,
Bhavnagar University Bhavnagar 364002 Gujarat India
?
?


      
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From modaresi.mohsen at gmail.com  Wed Apr 13 13:59:50 2011
From: modaresi.mohsen at gmail.com (mohsen modaresi)
Date: Wed, 13 Apr 2011 04:59:50 -0700
Subject: [Pw_forum] Spectra from GW and TDDFPT
In-Reply-To: <110413154828b75378a4bc391222a455b64bbfed1d4a@nudt.edu.cn>
References: <110413154828b75378a4bc391222a455b64bbfed1d4a@nudt.edu.cn>
Message-ID: <BANLkTin08MNURB3qHumpiLcFqBowcTGV=A@mail.gmail.com>

Dear Jiayu Dai,
Prof. R. Godby is one of the most famous scientist who worked on many-body
theory. i think this lecture should be help full for you.
{Many-Body Theory and DFT / TDDFT
Rex Godby"
http://docs.google.com/viewer?a=v&q=cache:gBMHk9QaO3cJ:www.tddft.org/TDDFT2006/2006tddft/docs/school/Godby.pdf+TDDFT+and+GW&hl=en&pid=bl&srcid=ADGEESiq9Au0dGZsFvyPUtLL9nEaPg44xzN8NzkJiiguvyAdyTFUpucP8XOKWMyrKammwPLMDfQZncmtgoh8NA-PFsRKaUxsRnrdbFId7a7dW2mkkOHqrr4TFgpalZC775KF1njtbF4p&sig=AHIEtbTLv5XgSx5m0wfXO3sMV7vzJlgOtg&pli=1

Hope it helps,


2011/4/13 jiayudai <daijiayu at nudt.edu.cn>

>  Dear users,
>
> It is well known that GW method can give much more accurate band gap since
> it considers many body interaction, and thus it can give more accurate
> optical properties. What i am thinking is that what's the difference between
> the optical properties from TDDFPT and GW. I mean, TDDFPT has the same
> accuracy as the GW method? or what's the advantage of TDDFPT over the GW
> except the computationl cost?
>
> Thanks a lot.
>
> Jiayu
>
>
> -------------------------------------------
> Jiayu Dai
> Department of PhysicsNational University of Defense Technology,
> Changsha, 410073, P R China
> -----------------------------------------
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Mohsen Modarresi,
PhD student of Solid State Physics, Ferdowsi University of Mashhad, Iran.
Phone +98-9133452131
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From eariel99 at gmail.com  Wed Apr 13 14:10:51 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Wed, 13 Apr 2011 09:10:51 -0300
Subject: [Pw_forum] npool in nscf calculation
Message-ID: <BANLkTi=SDHdGp5tnEWQU070RFGr2S98kfw@mail.gmail.com>

Hi,
Does it makes sense to use npool in a non self consistent calculation (for
DOS) with pw.x ?


-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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From giuseppe.mattioli at mlib.ism.cnr.it  Wed Apr 13 14:32:01 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Wed, 13 Apr 2011 14:32:01 +0200
Subject: [Pw_forum] Spectra from GW and TDDFPT
In-Reply-To: <BANLkTin08MNURB3qHumpiLcFqBowcTGV=A@mail.gmail.com>
References: <110413154828b75378a4bc391222a455b64bbfed1d4a@nudt.edu.cn>
	<BANLkTin08MNURB3qHumpiLcFqBowcTGV=A@mail.gmail.com>
Message-ID: <201104131432.02080.giuseppe.mattioli@mlib.ism.cnr.it>


And, practically speaking, you can obtain corrected (i.e., quasiparticle) 
eigenvalues by using GWW, and absorption spectra by using turbo_lanczos, that 
is, the GW and TDDFPT current implementations that you find embedded into the 
QE (4.3) distribution. Within the above limitations, the computational cost 
of both methods can be considered rather low.
HTH

Giuseppe


On Wednesday 13 April 2011 13:59:50 mohsen modaresi wrote:
> Dear Jiayu Dai,
> Prof. R. Godby is one of the most famous scientist who worked on many-body
> theory. i think this lecture should be help full for you.
> {Many-Body Theory and DFT / TDDFT
> Rex Godby"
> http://docs.google.com/viewer?a=v&q=cache:gBMHk9QaO3cJ:www.tddft.org/TDDFT2
>006/2006tddft/docs/school/Godby.pdf+TDDFT+and+GW&hl=en&pid=bl&srcid=ADGEESiq
>9Au0dGZsFvyPUtLL9nEaPg44xzN8NzkJiiguvyAdyTFUpucP8XOKWMyrKammwPLMDfQZncmtgoh8
>NA-PFsRKaUxsRnrdbFId7a7dW2mkkOHqrr4TFgpalZC775KF1njtbF4p&sig=AHIEtbTLv5XgSx5
>m0wfXO3sMV7vzJlgOtg&pli=1
>
> Hope it helps,
>
>
> 2011/4/13 jiayudai <daijiayu at nudt.edu.cn>
>
> >  Dear users,
> >
> > It is well known that GW method can give much more accurate band gap
> > since it considers many body interaction, and thus it can give more
> > accurate optical properties. What i am thinking is that what's the
> > difference between the optical properties from TDDFPT and GW. I mean,
> > TDDFPT has the same accuracy as the GW method? or what's the advantage of
> > TDDFPT over the GW except the computationl cost?
> >
> > Thanks a lot.
> >
> > Jiayu
> >
> >
> > -------------------------------------------
> > Jiayu Dai
> > Department of PhysicsNational University of Defense Technology,
> > Changsha, 410073, P R China
> > -----------------------------------------
> >
> >
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum



-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? 
? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ?
? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ?
? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ?
? ?E-mail: <giuseppe.mattioli at ism.cnr.it>

From daijiayu at nudt.edu.cn  Wed Apr 13 15:20:59 2011
From: daijiayu at nudt.edu.cn (jiayudai)
Date: Wed, 13 Apr 2011 21:20:59 +0800
Subject: [Pw_forum] Spectra from GW and TDDFPT
In-Reply-To: <502697821.13522@nudt.edu.cn>
References: <502697821.13522@nudt.edu.cn>
Message-ID: <11041321205928ed089fb06ec17482477fe231a8a5bb@nudt.edu.cn>

Thanks for your recommendation and reply, mohsen and Giuseppe. So, Giuseppe,  i understand what 's your meaning is
 that the GWW and  TDDFPT in QE distribution (4.3)  can be used for different purposes, but they are both accurate in their fields. In addition, they both have the advantage of efficient computation speed becuase they used different method from the tranditional methods. Is it?

Thanks again.

Jiayu

> Pw_forum at pwscf.org
From: Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>
Subject: Re: [Pw_forum] Spectra from GW and TDDFPT
To: pw_forum at pwscf.org
Message-ID: <201104131432.02080.giuseppe.mattioli at mlib.ism.cnr.it>
Content-Type: text/plain; charset="utf-8"


And, practically speaking, you can obtain corrected (i.e., quasiparticle)
eigenvalues by using GWW, and absorption spectra by using turbo_lanczos, that
is, the GW and TDDFPT current implementations that you find embedded into the
QE (4.3) distribution. Within the above limitations, the computational cost
of both methods can be considered rather low.
HTH

Giuseppe


On Wednesday 13 April 2011 13:59:50 mohsen modaresi wrote:
> Dear Jiayu Dai,
> Prof. R. Godby is one of the most famous scientist who worked on many-body
> theory. i think this lecture should be help full for you.
> {Many-Body Theory and DFT / TDDFT
> Rex Godby"
> http://docs.google.com/viewer?a=v&q=cache:gBMHk9QaO3cJ:www.tddft.org/TDDFT2
>006/2006tddft/docs/school/Godby.pdf+TDDFT+and+GW&hl=en&pid=bl&srcid=ADGEESiq
>9Au0dGZsFvyPUtLL9nEaPg44xzN8NzkJiiguvyAdyTFUpucP8XOKWMyrKammwPLMDfQZncmtgoh8
>NA-PFsRKaUxsRnrdbFId7a7dW2mkkOHqrr4TFgpalZC775KF1njtbF4p&sig=AHIEtbTLv5XgSx5
>m0wfXO3sMV7vzJlgOtg&pli=1
>
> Hope it helps,
>
>
> 2011/4/13 jiayudai <daijiayu at nudt.edu.cn>
>
> > Dear users,
> >
> > It is well known that GW method can give much more accurate band gap
> > since it considers many body interaction, and thus it can give more
> > accurate optical properties. What i am thinking is that what's the
> > difference between the optical properties from TDDFPT and GW. I mean,
> > TDDFPT has the same accuracy as the GW method? or what's the advantage of
> > TDDFPT over the GW except the computationl cost?
> >
> > Thanks a lot.
> >
> > Jiayu
> >
> >
> > -------------------------------------------
> > Jiayu Dai
> > Department of PhysicsNational University of Defense Technology,
> > Changsha, 410073, P R China
> > -----------------------------------------
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From L-marks at northwestern.edu  Wed Apr 13 15:32:29 2011
From: L-marks at northwestern.edu (Laurence Marks)
Date: Wed, 13 Apr 2011 08:32:29 -0500
Subject: [Pw_forum] One minor bug, one not minor and two questions
In-Reply-To: <1302616553.28191.87.camel@fe12lx.fisica.uniud.it>
References: <BANLkTimpo976SxfyDctMvwAg8U8bSAo+9A@mail.gmail.com>
	<1302616553.28191.87.camel@fe12lx.fisica.uniud.it>
Message-ID: <BANLkTi=bPMpyOh0NRZPyoObjeQw65SQEiA@mail.gmail.com>

Agreed. One could (maybe) write a macro for this but it would be way
too specialized. Just removing the over-ride should enable the user to
specify it; most cluster sysadmins should have this posted or one can
use the ifort linking guide.

N.B., I would test myself, but at least on the cluster where I have
PWSCF installed it complains that at configure.ac:30 the language is
set as C not Fortran. This might be a bug in the autoconf I have there
or real -- getting the language set right is a pain and I've had
problems with this in the past for other code.

On Tue, Apr 12, 2011 at 8:55 AM, Paolo Giannozzi <giannozz at democritos.it> wrote:
> On Sun, 2011-04-10 at 16:13 -0500, Laurence Marks wrote:
>
>> Another quick one: line 1766 of install/configure.ac nulls out
>> scalapack_libs and the lines below look like they are special tests,
>> which seems to be inconsistent with line 150 and standard protocols of
>> letting the user define input variables.
>
> very likely so. The problem is that scalapack is typically available
> on large parallel machines. It is not obvious to have access to more
> than a few of them, and each machine seems to have a different idea
> on where scalapack should be. The present status of configure.ac is
> the results of trial and error attempts on a few machines. With so much
> variety and so few people daring to look inside configure.ac, it is not
> obvious how to set up a better and more general scalapack test.
> Suggestions are most welcome (and not only on scalapack)
>
> P.
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Research is to see what everybody else has seen, and to think what
nobody else has thought
Albert Szent-Gyorgi

From L-marks at northwestern.edu  Wed Apr 13 15:32:56 2011
From: L-marks at northwestern.edu (Laurence Marks)
Date: Wed, 13 Apr 2011 08:32:56 -0500
Subject: [Pw_forum] One minor bug, one not minor and two questions
In-Reply-To: <BANLkTi=bPMpyOh0NRZPyoObjeQw65SQEiA@mail.gmail.com>
References: <BANLkTimpo976SxfyDctMvwAg8U8bSAo+9A@mail.gmail.com>
	<1302616553.28191.87.camel@fe12lx.fisica.uniud.it>
	<BANLkTi=bPMpyOh0NRZPyoObjeQw65SQEiA@mail.gmail.com>
Message-ID: <BANLkTikh6g=g7EovHaY1U3vEuosSYfDK-Q@mail.gmail.com>

Type: configure.ac:306 (not 30).

On Wed, Apr 13, 2011 at 8:32 AM, Laurence Marks
<L-marks at northwestern.edu> wrote:
> Agreed. One could (maybe) write a macro for this but it would be way
> too specialized. Just removing the over-ride should enable the user to
> specify it; most cluster sysadmins should have this posted or one can
> use the ifort linking guide.
>
> N.B., I would test myself, but at least on the cluster where I have
> PWSCF installed it complains that at configure.ac:30 the language is
> set as C not Fortran. This might be a bug in the autoconf I have there
> or real -- getting the language set right is a pain and I've had
> problems with this in the past for other code.
>
> On Tue, Apr 12, 2011 at 8:55 AM, Paolo Giannozzi <giannozz at democritos.it> wrote:
>> On Sun, 2011-04-10 at 16:13 -0500, Laurence Marks wrote:
>>
>>> Another quick one: line 1766 of install/configure.ac nulls out
>>> scalapack_libs and the lines below look like they are special tests,
>>> which seems to be inconsistent with line 150 and standard protocols of
>>> letting the user define input variables.
>>
>> very likely so. The problem is that scalapack is typically available
>> on large parallel machines. It is not obvious to have access to more
>> than a few of them, and each machine seems to have a different idea
>> on where scalapack should be. The present status of configure.ac is
>> the results of trial and error attempts on a few machines. With so much
>> variety and so few people daring to look inside configure.ac, it is not
>> obvious how to set up a better and more general scalapack test.
>> Suggestions are most welcome (and not only on scalapack)
>>
>> P.
>> --
>> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
> --
> Laurence Marks
> Department of Materials Science and Engineering
> MSE Rm 2036 Cook Hall
> 2220 N Campus Drive
> Northwestern University
> Evanston, IL 60208, USA
> Tel: (847) 491-3996 Fax: (847) 491-7820
> email: L-marks at northwestern dot edu
> Web: www.numis.northwestern.edu
> Chair, Commission on Electron Crystallography of IUCR
> www.numis.northwestern.edu/
> Research is to see what everybody else has seen, and to think what
> nobody else has thought
> Albert Szent-Gyorgi
>



-- 
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Research is to see what everybody else has seen, and to think what
nobody else has thought
Albert Szent-Gyorgi

From L-marks at northwestern.edu  Wed Apr 13 15:35:01 2011
From: L-marks at northwestern.edu (Laurence Marks)
Date: Wed, 13 Apr 2011 08:35:01 -0500
Subject: [Pw_forum] Dielectric Band Structure
Message-ID: <BANLkTikE=2gxD88RDj704J2XPokMwu3Fug@mail.gmail.com>

Is this currently in the distribution?

-- 
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Research is to see what everybody else has seen, and to think what
nobody else has thought
Albert Szent-Gyorgi

From giuseppe.mattioli at mlib.ism.cnr.it  Wed Apr 13 16:49:52 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Wed, 13 Apr 2011 16:49:52 +0200
Subject: [Pw_forum] Spectra from GW and TDDFPT
In-Reply-To: <11041321205928ed089fb06ec17482477fe231a8a5bb@nudt.edu.cn>
References: <502697821.13522@nudt.edu.cn>
	<11041321205928ed089fb06ec17482477fe231a8a5bb@nudt.edu.cn>
Message-ID: <201104131649.52909.giuseppe.mattioli@mlib.ism.cnr.it>

Dear Jiayu
Yes, it is. With only one additional warning: the TDDFPT code works only at 
Gamma (and fixed occupations). It is not designed to deal with periodic 
systems where you need k-points, but (in my experience) it works well with 
molecules.

On Wednesday 13 April 2011 15:20:59 jiayudai wrote:
> Thanks for your recommendation and reply, mohsen and Giuseppe. So,
> Giuseppe,  i understand what 's your meaning is that the GWW and  TDDFPT in
> QE distribution (4.3)  can be used for different purposes, but they are
> both accurate in their fields. In addition, they both have the advantage of
> efficient computation speed becuase they used different method from the
> tranditional methods. Is it?
>
> Thanks again.
>
> Jiayu
>
> > Pw_forum at pwscf.org
>
> From: Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>
> Subject: Re: [Pw_forum] Spectra from GW and TDDFPT
> To: pw_forum at pwscf.org
> Message-ID: <201104131432.02080.giuseppe.mattioli at mlib.ism.cnr.it>
> Content-Type: text/plain; charset="utf-8"
>
>
> And, practically speaking, you can obtain corrected (i.e., quasiparticle)
> eigenvalues by using GWW, and absorption spectra by using turbo_lanczos,
> that is, the GW and TDDFPT current implementations that you find embedded
> into the QE (4.3) distribution. Within the above limitations, the
> computational cost of both methods can be considered rather low.
> HTH
>
> Giuseppe
>
> On Wednesday 13 April 2011 13:59:50 mohsen modaresi wrote:
> > Dear Jiayu Dai,
> > Prof. R. Godby is one of the most famous scientist who worked on
> > many-body theory. i think this lecture should be help full for you.
> > {Many-Body Theory and DFT / TDDFT
> > Rex Godby"
> > http://docs.google.com/viewer?a=v&q=cache:gBMHk9QaO3cJ:www.tddft.org/TDDF
> >T2
> > 006/2006tddft/docs/school/Godby.pdf+TDDFT+and+GW&hl=en&pid=bl&srcid=ADGEE
> >Siq
> > 9Au0dGZsFvyPUtLL9nEaPg44xzN8NzkJiiguvyAdyTFUpucP8XOKWMyrKammwPLMDfQZncmtg
> >oh8
> > NA-PFsRKaUxsRnrdbFId7a7dW2mkkOHqrr4TFgpalZC775KF1njtbF4p&sig=AHIEtbTLv5Xg
> >Sx5 m0wfXO3sMV7vzJlgOtg&pli=1
> >
> > Hope it helps,
> >
> >
> > 2011/4/13 jiayudai <daijiayu at nudt.edu.cn>
> >
> > > Dear users,
> > >
> > > It is well known that GW method can give much more accurate band gap
> > > since it considers many body interaction, and thus it can give more
> > > accurate optical properties. What i am thinking is that what's the
> > > difference between the optical properties from TDDFPT and GW. I mean,
> > > TDDFPT has the same accuracy as the GW method? or what's the advantage
> > > of TDDFPT over the GW except the computationl cost?
> > >
> > > Thanks a lot.
> > >
> > > Jiayu
> > >
> > >
> > > -------------------------------------------
> > > Jiayu Dai
> > > Department of PhysicsNational University of Defense Technology,
> > > Changsha, 410073, P R China
> > > -----------------------------------------



-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? 
? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ?
? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ?
? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ?
? ?E-mail: <giuseppe.mattioli at ism.cnr.it>

From giannozz at democritos.it  Wed Apr 13 19:40:29 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 13 Apr 2011 19:40:29 +0200
Subject: [Pw_forum] npool in nscf calculation
In-Reply-To: <BANLkTi=SDHdGp5tnEWQU070RFGr2S98kfw@mail.gmail.com>
References: <BANLkTi=SDHdGp5tnEWQU070RFGr2S98kfw@mail.gmail.com>
Message-ID: <CDF6223D-0440-46AA-AFC4-3923AAD19B6A@democritos.it>


On Apr 13, 2011, at 14:10 , Eduardo Ariel Menendez Proupin wrote:

> Does it makes sense to use npool in a non self consistent calculation
> (for DOS) with pw.x ?

it should - P.

---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From giannozz at democritos.it  Wed Apr 13 22:43:07 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 13 Apr 2011 22:43:07 +0200
Subject: [Pw_forum] How to calculate DOS at the Fermi Energy?
In-Reply-To: <366310.99840.qm@web120406.mail.ne1.yahoo.com>
References: <366310.99840.qm@web120406.mail.ne1.yahoo.com>
Message-ID: <6FDCAD04-C7E8-4F68-9377-C275F4460555@democritos.it>


On Apr 13, 2011, at 10:37 , r s wrote:

> running of the pw.x code with following document as input file:
> [...]
>     occupations='smearing', smearing= 'mp', degauss= 0.02 ,
> [...]
> and then, running of the pw.x code with tetrahedra occupation:
> [...]
> for calculation of total Dos, running of the dos.x code with below  
> text:
> [...]
> now for calculation of density of state at fermi energy, i call  
> pp.x code with following input file:
> [...]
> but after running, the code says:
> [...]
> from local_dos : error #     1
> guassian broadening needed

first of all: it says "gaussian broadening needed". Error message may  
not be optimally
clear, but they are not misspelled, usually.

pp.x reads the data file produced by the second pw.x run, which  
overwrites the contents
of the data file written in the first pw.x run. So pp.x sees  
tetrahedra and tetrahedra are
not implemented for the calculation of local dos. The value of the  
gaussian broadening
taken in input by dos.x is used by dos.x and cannot propagate to  
other codes (dos.x
does not change the data file produced by pw.x). By the way: it  
doesn't make sense to
perform calculations with tetrahedra (useful for DOS) and throw the  
results away by
using gaussian broadening for DOS

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





From sxu2 at ncsu.edu  Thu Apr 14 02:05:41 2011
From: sxu2 at ncsu.edu (shu xu)
Date: Wed, 13 Apr 2011 20:05:41 -0400
Subject: [Pw_forum] npool in nscf calculation
In-Reply-To: <CDF6223D-0440-46AA-AFC4-3923AAD19B6A@democritos.it>
References: <BANLkTi=SDHdGp5tnEWQU070RFGr2S98kfw@mail.gmail.com>
	<CDF6223D-0440-46AA-AFC4-3923AAD19B6A@democritos.it>
Message-ID: <BANLkTiktmMK5323E=oRE3WoaOts=S2BrKg@mail.gmail.com>

Hi,

How should I set up npool for nscf?
Shall I use an integer which is divided exactly by the number of K_POINTS in
scf or an integer
which is divided exactly by the number of k points along the k-path I choose
for the band structure?

Shu

NCSU
PHD
Physics
On Wed, Apr 13, 2011 at 1:40 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Apr 13, 2011, at 14:10 , Eduardo Ariel Menendez Proupin wrote:
>
> > Does it makes sense to use npool in a non self consistent calculation
> > (for DOS) with pw.x ?
>
> it should - P.
>
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From degironc at sissa.it  Thu Apr 14 08:59:51 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 14 Apr 2011 08:59:51 +0200
Subject: [Pw_forum] npool in nscf calculation
In-Reply-To: <BANLkTiktmMK5323E=oRE3WoaOts=S2BrKg@mail.gmail.com>
References: <BANLkTi=SDHdGp5tnEWQU070RFGr2S98kfw@mail.gmail.com>	<CDF6223D-0440-46AA-AFC4-3923AAD19B6A@democritos.it>
	<BANLkTiktmMK5323E=oRE3WoaOts=S2BrKg@mail.gmail.com>
Message-ID: <4DA69B67.4020908@sissa.it>

there is no need for the number of pools to be a whole divisor of the 
number of k-point. This would produce the optimal balance but is not 
necessary. The k-points are distributed across pools as evenly as 
possible so that there is at most one kpoint difference (example: 10 
kpoints in 4 pools are distributed as 3,3,2,2).

The number of points that matters is the number that the code needs to 
compute: that is the number of inequivalent point AFTER the symmetry 
checks have been performed in a scf run, and the number of points given 
in input in the case of a nscf calculation.

stefano
SISSA and DEMOCRITOS

On 04/14/2011 02:05 AM, shu xu wrote:
> Hi,
>
> How should I set up npool for nscf?
> Shall I use an integer which is divided exactly by the number of K_POINTS in
> scf or an integer
> which is divided exactly by the number of k points along the k-path I choose
> for the band structure?
>
> Shu
>
> NCSU
> PHD
> Physics
> On Wed, Apr 13, 2011 at 1:40 PM, Paolo Giannozzi<giannozz at democritos.it>wrote:
>
>> On Apr 13, 2011, at 14:10 , Eduardo Ariel Menendez Proupin wrote:
>>
>>> Does it makes sense to use npool in a non self consistent calculation
>>> (for DOS) with pw.x ?
>> it should - P.
>>
>> ---
>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://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 daijiayu at nudt.edu.cn  Thu Apr 14 11:58:34 2011
From: daijiayu at nudt.edu.cn (jiayudai)
Date: Thu, 14 Apr 2011 17:58:34 +0800
Subject: [Pw_forum] Spectra from GW and TDDFPT
In-Reply-To: <502727273.28514@nudt.edu.cn>
References: <502727273.28514@nudt.edu.cn>
Message-ID: <11041417583468ef59a553486e5ae3c17da982d0c203@nudt.edu.cn>

Dear Giuseppe,

I think the current TDDFPT can only work without spin polarization, is it? Besides, i do not know is there any limitation in theory to deal with more k_points and metallic case? In my test, it can not deal with the molecule such as NO2, since it needs the smearing method in the scf calculations.

Thanks.

Jiayu


From: Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>
Subject: Re: [Pw_forum] Spectra from GW and TDDFPT
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <201104131649.52909.giuseppe.mattioli at mlib.ism.cnr.it>
Content-Type: text/plain; charset="utf-8"

Dear Jiayu
Yes, it is. With only one additional warning: the TDDFPT code works only at
Gamma (and fixed occupations). It is not designed to deal with periodic
systems where you need k-points, but (in my experience) it works well with
molecules.

On Wednesday 13 April 2011 15:20:59 jiayudai wrote:
> Thanks for your recommendation and reply, mohsen and Giuseppe. So,
> Giuseppe, i understand what 's your meaning is that the GWW and TDDFPT in
> QE distribution (4.3) can be used for different purposes, but they are
> both accurate in their fields. In addition, they both have the advantage of
> efficient computation speed becuase they used different method from the
> tranditional methods. Is it?
>
> Thanks again.
>
> Jiayu
>
> > Pw_forum at pwscf.org
>
> From: Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>
> Subject: Re: [Pw_forum] Spectra from GW and TDDFPT
> To: pw_forum at pwscf.org
> Message-ID: <201104131432.02080.giuseppe.mattioli at mlib.ism.cnr.it>
> Content-Type: text/plain; charset="utf-8"
>
>
> And, practically speaking, you can obtain corrected (i.e., quasiparticle)
> eigenvalues by using GWW, and absorption spectra by using turbo_lanczos,
> that is, the GW and TDDFPT current implementations that you find embedded
> into the QE (4.3) distribution. Within the above limitations, the
> computational cost of both methods can be considered rather low.
> HTH
>
> Giuseppe
>
> On Wednesday 13 April 2011 13:59:50 mohsen modaresi wrote:
> > Dear Jiayu Dai,
> > Prof. R. Godby is one of the most famous scientist who worked on
> > many-body theory. i think this lecture should be help full for you.
> > {Many-Body Theory and DFT / TDDFT
> > Rex Godby"
> > http://docs.google.com/viewer?a=v&q=cache:gBMHk9QaO3cJ:www.tddft.org/TDDF
> >T2
> > 006/2006tddft/docs/school/Godby.pdf+TDDFT+and+GW&hl=en&pid=bl&srcid=ADGEE
> >Siq
> > 9Au0dGZsFvyPUtLL9nEaPg44xzN8NzkJiiguvyAdyTFUpucP8XOKWMyrKammwPLMDfQZncmtg
> >oh8
> > NA-PFsRKaUxsRnrdbFId7a7dW2mkkOHqrr4TFgpalZC775KF1njtbF4p&sig=AHIEtbTLv5Xg
> >Sx5 m0wfXO3sMV7vzJlgOtg&pli=1
> >
> > Hope it helps,
> >
> >
> > 2011/4/13 jiayudai <daijiayu at nudt.edu.cn>
> >
> > > Dear users,
> > >
> > > It is well known that GW method can give much more accurate band gap
> > > since it considers many body interaction, and thus it can give more
> > > accurate optical properties. What i am thinking is that what's the
> > > difference between the optical properties from TDDFPT and GW. I mean,
> > > TDDFPT has the same accuracy as the GW method? or what's the advantage
> > > of TDDFPT over the GW except the computationl cost?
> > >
> > > Thanks a lot.
> > >
> > > Jiayu
> > >
> > >
> > > -------------------------------------------
> > > Jiayu Dai
> > > Department of PhysicsNational University of Defense Technology,
> > > Changsha, 410073, P R China
> > > -----------------------------------------
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From giuseppe.mattioli at mlib.ism.cnr.it  Thu Apr 14 12:39:45 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Thu, 14 Apr 2011 12:39:45 +0200
Subject: [Pw_forum] Spectra from GW and TDDFPT
In-Reply-To: <11041417583468ef59a553486e5ae3c17da982d0c203@nudt.edu.cn>
References: <502727273.28514@nudt.edu.cn>
	<11041417583468ef59a553486e5ae3c17da982d0c203@nudt.edu.cn>
Message-ID: <201104141239.45865.giuseppe.mattioli@mlib.ism.cnr.it>


Dear Jiayu
Yes, it is. You can perform TDDFPT calculations by using the gamma point, 
nspin=1 and fixed occupations (no smearing). There are no theoretical 
limitations regarding k-points, but they are currently not implemented.
Yours
G.

On Thursday 14 April 2011 11:58:34 jiayudai wrote:
> Dear Giuseppe,
>
> I think the current TDDFPT can only work without spin polarization, is it?
> Besides, i do not know is there any limitation in theory to deal with more
> k_points and metallic case? In my test, it can not deal with the molecule
> such as NO2, since it needs the smearing method in the scf calculations.
>
> Thanks.
>
> Jiayu
>
>
> From: Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>
> Subject: Re: [Pw_forum] Spectra from GW and TDDFPT
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <201104131649.52909.giuseppe.mattioli at mlib.ism.cnr.it>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Jiayu
> Yes, it is. With only one additional warning: the TDDFPT code works only at
> Gamma (and fixed occupations). It is not designed to deal with periodic
> systems where you need k-points, but (in my experience) it works well with
> molecules.
>
> On Wednesday 13 April 2011 15:20:59 jiayudai wrote:
> > Thanks for your recommendation and reply, mohsen and Giuseppe. So,
> > Giuseppe, i understand what 's your meaning is that the GWW and TDDFPT in
> > QE distribution (4.3) can be used for different purposes, but they are
> > both accurate in their fields. In addition, they both have the advantage
> > of efficient computation speed becuase they used different method from
> > the tranditional methods. Is it?
> >
> > Thanks again.
> >
> > Jiayu
> >
> > > Pw_forum at pwscf.org
> >
> > From: Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>
> > Subject: Re: [Pw_forum] Spectra from GW and TDDFPT
> > To: pw_forum at pwscf.org
> > Message-ID: <201104131432.02080.giuseppe.mattioli at mlib.ism.cnr.it>
> > Content-Type: text/plain; charset="utf-8"
> >
> >
> > And, practically speaking, you can obtain corrected (i.e., quasiparticle)
> > eigenvalues by using GWW, and absorption spectra by using turbo_lanczos,
> > that is, the GW and TDDFPT current implementations that you find embedded
> > into the QE (4.3) distribution. Within the above limitations, the
> > computational cost of both methods can be considered rather low.
> > HTH
> >
> > Giuseppe
> >
> > On Wednesday 13 April 2011 13:59:50 mohsen modaresi wrote:
> > > Dear Jiayu Dai,
> > > Prof. R. Godby is one of the most famous scientist who worked on
> > > many-body theory. i think this lecture should be help full for you.
> > > {Many-Body Theory and DFT / TDDFT
> > > Rex Godby"
> > > http://docs.google.com/viewer?a=v&q=cache:gBMHk9QaO3cJ:www.tddft.org/TD
> > >DF T2
> > > 006/2006tddft/docs/school/Godby.pdf+TDDFT+and+GW&hl=en&pid=bl&srcid=ADG
> > >EE Siq
> > > 9Au0dGZsFvyPUtLL9nEaPg44xzN8NzkJiiguvyAdyTFUpucP8XOKWMyrKammwPLMDfQZncm
> > >tg oh8
> > > NA-PFsRKaUxsRnrdbFId7a7dW2mkkOHqrr4TFgpalZC775KF1njtbF4p&sig=AHIEtbTLv5
> > >Xg Sx5 m0wfXO3sMV7vzJlgOtg&pli=1
> > >
> > > Hope it helps,
> > >
> > >
> > > 2011/4/13 jiayudai <daijiayu at nudt.edu.cn>
> > >
> > > > Dear users,
> > > >
> > > > It is well known that GW method can give much more accurate band gap
> > > > since it considers many body interaction, and thus it can give more
> > > > accurate optical properties. What i am thinking is that what's the
> > > > difference between the optical properties from TDDFPT and GW. I mean,
> > > > TDDFPT has the same accuracy as the GW method? or what's the
> > > > advantage of TDDFPT over the GW except the computationl cost?
> > > >
> > > > Thanks a lot.
> > > >
> > > > Jiayu
> > > >
> > > >
> > > > -------------------------------------------
> > > > Jiayu Dai
> > > > Department of PhysicsNational University of Defense Technology,
> > > > Changsha, 410073, P R China
> > > > -----------------------------------------



-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? 
? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ?
? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ?
? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ?
? ?E-mail: <giuseppe.mattioli at ism.cnr.it>

From autieri at sa.infn.it  Thu Apr 14 14:12:28 2011
From: autieri at sa.infn.it (Carmine Autieri)
Date: Thu, 14 Apr 2011 14:12:28 +0200 (CEST)
Subject: [Pw_forum] NSCF calculation
In-Reply-To: <mailman.1.1302767380.31798.pw_forum@pwscf.org>
Message-ID: <2ad62884-7202-47ef-9022-a5b1d5f8674e@mail.sa.infn.it>

Dear all,
I have a theoretical question, wich I was not able to find the answer.
In a non self constintent calculation, 
the charge density is costant but what is the variable that changes during the iteration in a plane wave code? 

thanks
Carmine

From Lorenzo.Paulatto at impmc.upmc.fr  Thu Apr 14 14:36:26 2011
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Thu, 14 Apr 2011 14:36:26 +0200
Subject: [Pw_forum] NSCF calculation
In-Reply-To: <2ad62884-7202-47ef-9022-a5b1d5f8674e@mail.sa.infn.it>
References: <2ad62884-7202-47ef-9022-a5b1d5f8674e@mail.sa.infn.it>
Message-ID: <op.vtxha0zvxuur8c@vanoxite.impmc.jussieu.fr>

On Thu, 14 Apr 2011 14:12:28 +0200, Carmine Autieri <autieri at sa.infn.it>  
wrote:
> I have a theoretical question, wich I was not able to find the answer.
> In a non self constintent calculation,
> the charge density is costant but what is the variable that changes  
> during the iteration in a plane wave code?

If I understand you question correctly, it is the iterative process of  
diagonalization which is used to find the eigenstates (wavefunctions),  
depending on your input it can be the Davidson algorithm (default) or  
conjugate-gradient minimization.

best regards


-- 
Lorenzo Paulatto (IdR)
IMPMC - CNRS UMR 7590 & Universit? P&M Curie
T23-C23/24-4e16 - 4 place Jussieu - 75252 Paris Cedex5
phone: +33 (0)144 27 5211
www:   http://www-int.impmc.upmc.fr/~paulatto/

From degironc at sissa.it  Thu Apr 14 16:05:22 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 14 Apr 2011 16:05:22 +0200
Subject: [Pw_forum] NSCF calculation
In-Reply-To: <2ad62884-7202-47ef-9022-a5b1d5f8674e@mail.sa.infn.it>
References: <2ad62884-7202-47ef-9022-a5b1d5f8674e@mail.sa.infn.it>
Message-ID: <4DA6FF22.6080703@sissa.it>

there are no iterations... the potential is fixed.
the hamiltonian is diagonalized iteratively (variing the wavefunction 
Fourier components).
stefano

On 04/14/2011 02:12 PM, Carmine Autieri wrote:
> Dear all,
> I have a theoretical question, wich I was not able to find the answer.
> In a non self constintent calculation,
> the charge density is costant but what is the variable that changes during the iteration in a plane wave code?
>
> thanks
> Carmine
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From physik.shyam at gmail.com  Fri Apr 15 08:31:03 2011
From: physik.shyam at gmail.com (Shyam Khambholja)
Date: Fri, 15 Apr 2011 12:01:03 +0530
Subject: [Pw_forum] total energy
Message-ID: <BANLkTikrbiHrufbOP6iv4BCOgKZDqSAEnA@mail.gmail.com>

Thank you Prof. Stefano and others,

I need accuracy up to that level to calculate thermal properties at low
temperatures.

also, i need it to calculate thermal properties numerically.

also, I have done a try, in which I interpolated calculated total energies,
upto 10 digits, bur it gave me errors.

again thanks,
-- 

Mr. Shyam G Khambholja,
Research student,
Depratment of Physics,
Sardar Patel University, Gujarat
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From degironc at sissa.it  Fri Apr 15 08:38:34 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 15 Apr 2011 08:38:34 +0200
Subject: [Pw_forum] total energy
In-Reply-To: <BANLkTikrbiHrufbOP6iv4BCOgKZDqSAEnA@mail.gmail.com>
References: <BANLkTikrbiHrufbOP6iv4BCOgKZDqSAEnA@mail.gmail.com>
Message-ID: <4DA7E7EA.4000407@sissa.it>

thermal properties at low temperature via quasi harmonic approximation ?
MD is wrong at low temperature .... it never equilibrates and is classical.
stefano

On 04/15/2011 08:31 AM, Shyam Khambholja wrote:
> Thank you Prof. Stefano and others,
>
> I need accuracy up to that level to calculate thermal properties at low
> temperatures.
> also, i need it to calculate thermal properties numerically.
>
> also, I have done a try, in which I interpolated calculated total energies,
> upto 10 digits, bur it gave me errors.
>
> again thanks,
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From autieri at sa.infn.it  Fri Apr 15 11:23:22 2011
From: autieri at sa.infn.it (Carmine Autieri)
Date: Fri, 15 Apr 2011 11:23:22 +0200 (CEST)
Subject: [Pw_forum] NSCF calculation
In-Reply-To: <2ad62884-7202-47ef-9022-a5b1d5f8674e@mail.sa.infn.it>
Message-ID: <48577f76-3fe4-4cf3-b3e7-8908ab73ff24@mail.sa.infn.it>

thank you
Best

Carmine

From physik.shyam at gmail.com  Fri Apr 15 11:46:44 2011
From: physik.shyam at gmail.com (Shyam Khambholja)
Date: Fri, 15 Apr 2011 15:16:44 +0530
Subject: [Pw_forum] total energy
Message-ID: <BANLkTi=QGbBDmwgO3839wUsR0RpuYB1zbQ@mail.gmail.com>

no, neither using qha nor md,
but using mean field potential approach or quasi harmonic debye model.



-- 
Mr. Shyam G Khambholja,
Research student,
Depratment of Physics,
Sardar Patel University, Gujarat
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From mdt26 at cam.ac.uk  Fri Apr 15 12:59:08 2011
From: mdt26 at cam.ac.uk (Mike Towler)
Date: Fri, 15 Apr 2011 11:59:08 +0100 (BST)
Subject: [Pw_forum] PWSCF QMC interface
Message-ID: <Pine.LNX.4.63.1104151149200.9844@pc53.tcm.phy.cam.ac.uk>



Dear all,

I've been asked to provide a brief overview of the new interface to the 
CASINO quantum Monte Carlo program available in the new release of PWSCF.

For those of you who don't know, QMC is a highly-accurate technique with 
similar or better accuracy than the best high-order quantum chemistry 
methods (such as CCSD(T) etc.). Its advantage lies in the fact that the 
required CPU time scales only quadratically with system size (rather than 
as N^7 or whatever) meaning that it is potentially applicable to large 
systems - periodic or otherwise - of up to several thousand electrons. 
It's the same technique that Ceperley and Alder used to do their 
essentially exact calculations of the homogeneous electron gas thirty 
years ago that led to the development of the LDA exchange-correlation 
functionals etc., but we use it to study real systems with atoms.

It's significantly more expensive than DFT, of course, but unlike PW-DFT 
or standard quantum chemistry techniques the QMC algorithm can be made to 
have essentially perfect parallel efficiency and our CASINO code can 
easily exploit as many cores as you like on the biggest machines 
available. For example, it was recently tested on 120000 nodes of the ORNL 
Jaguar machine showing perfect parallel scaling.  For more details, 
together with a recent accessible review of the technique, see last 
February's Psi-k highlight written by me, Dario Alfe and Mike Gillan - 
available here:

http://www.tcm.phy.cam.ac.uk/~mdt26/papers/petascale_psik.pdf

Why the interface with PWSCF? Because QMC requires a 'starting guess' for 
the many-body wave function - which can be, for example, a determinant of 
Kohn-Sham orbitals multiplied by a so-called 'Jastrow factor' (the latter 
introduces an explicit dependence on the distances between pairs of 
particles). The KS orbitals need to be obtained from a DFT calculation, 
for example, with PWSCF (though we also support CASTEP, ABINIT, GP etc.. 
as well as various programs using other basis sets such as Gaussians).

Full instructions are provided in the 'Direct interface with CASINO' 
section of the latest Espresso user guide, and in the documentation 
provided with the 2.9 version of CASINO. But basically it involves little 
more than adding a '-pw2casino' flag when invoking pw.x, thus:

pw.x -pw2casino < input_file > output_file

will produce a wave function file readable by CASINO.

For more information, the CASINO web site is here:

http://www.tcm.phy.cam.ac.uk/~mdt26/casino2.html

If anybody wants to try some QMC calculations, the code is given away for 
free to academics (to see how to get it, click the 'Introduction' link in 
the left-hand sidebar).

Finally, PWSCF users wishing to learn how to use CASINO may like to attend 
one of our annual CASINO summer schools in my "Apuan Alps Centre for 
Physics" institute - a 15th century monastery in a beautiful mountain 
village in Tuscany, Italy. The sixth event in this series will be held 
this year from 30th July to 6th August - there are still some place 
available so if you wish to attend then let me know.. The official ad for 
this is below, and more details are available on the website:

http://www.vallico.net/tti/tti.html (Click 'Public Events').

I hope that the Espresso community will find the new QMC interface useful 
(and thanks to Norbert Nemec, Layla Martin-Samos, and Simon Binnie for 
help with creating it). Have fun!

Best wishes,
Mike

+------------------------------------------------------------------------+
|Dr. Mike Towler (mdt26 at cam.ac.uk) Theory of Condensed Matter (Rm 529)|
|  Cavendish Laboratory, University of Cambridge, Cambridge  CB3 0HE, UK |
|Tel. +44-(0)1223-337378 OR -334256 (College)     Fax. +44-(0)1223-337356|
+----------------------: www.tcm.phy.cam.ac.uk/~mdt26 :------------------+



                    SUMMER SCHOOL ANNOUNCEMENT

          "Quantum Monte Carlo and the CASINO program VI"
          ===============================================

               Sat 30th July - Sat 6th August 2011
  Apuan Alps Centre for Physics @ TTI, Vallico Sotto, Tuscany, Italy

              http://www.vallico.net/tti/tti.html

            A4 POSTER FOR THE SCHOOL AVAILABLE HERE :
         http://www.tcm.phy.cam.ac.uk/~mdt26/poster.png


The sixth international summer school in the series "Quantum Monte Carlo 
and the CASINO program" will take place during August 2011 at the TTI 
monastery in the Tuscan Apuan Alps in Italy, organized and hosted by 
members of Cambridge University physics department's Theory of Condensed 
Matter Group. The aim of the school is to give students a thorough 
introduction to quantum Monte Carlo as a method for performing 
high-quality calculations of the electronic structure of atoms, molecules, 
and materials. The course is designed for young quantum chemists or 
theoretical physicists who have no previous experience with this 
technique, though anyone interested is welcome to take part, including old 
people.

The monastery is a unique venue where the community spirit and magnificent 
location have inspired memorable workshops in the past. It is a delightful 
16th century building incorporating an ancient church, and is situated in 
the isolated but spectacular setting of the Tuscan mountain village of 
Vallico Sotto. The church is fully equipped with relevant presentation and 
computer technology, and all accommodation is on-site.  As with all events 
at the Institute, formal lectures are restricted to the mornings, and 
participants are given the freedom and space to think and to contemplate 
and discuss the issues at hand. In addition to hands-on exercises, a 
programme of healthy recreational activities will be organized in the 
afternoons, and it is hoped that by following this strict regime, together 
with breathing clean mountain air and by preparing and sampling fine 
Tuscan cuisine, the participant will be able to return home mentally and 
physically refreshed as well as better informed.

Describing the complex behaviour of materials at the atomic level requires 
a sophisticated description of the correlated motion of the electrons. 
Quantum Monte Carlo (QMC) is an increasingly popular and explicitly 
many-body method with the unusual capability of yielding highly accurate 
results whilst also exhibiting a very favourable scaling of computational 
cost with system size. Over the last eighteen years, the Cambridge group 
have been researching QMC methods and we have created a powerful, general 
computer program - CASINO - to carry out the calculations. The school will 
focus both on the basic theory of QMC and on more advanced practical 
techniques, and will include a thorough introduction to the CASINO 
program. A background in density functional theory or similar - though not 
essential - is normally thought to be useful.

Instructors at the school will include the main authors of the CASINO program
(Dr. Mike Towler, Dr. Neil Drummond and Dr. Pablo Lopez Rios) and possibly
others.

Participants would normally need to book a flight to Pisa airport from
where onward transportation will be arranged (though other destinations
are possible). Details of previous schools - including photographs - are
available under the PUBLIC EVENTS link on the TTI web site.

Interested students should email Mike Towler (mdt26 at cam.ac.uk) for
registration and further details.


From ttduyle at gmail.com  Fri Apr 15 15:30:41 2011
From: ttduyle at gmail.com (Duy Le)
Date: Fri, 15 Apr 2011 09:30:41 -0400
Subject: [Pw_forum] total energy
In-Reply-To: <BANLkTi=QGbBDmwgO3839wUsR0RpuYB1zbQ@mail.gmail.com>
References: <BANLkTi=QGbBDmwgO3839wUsR0RpuYB1zbQ@mail.gmail.com>
Message-ID: <BANLkTinn8aKy72-2e0mmroM6GjZ8DLmo2A@mail.gmail.com>

Maybe I am too picky. You should NOT start a new email when replying any
message in the forum. Followers can not understand what you are trying to
say. Just hit reply and do NOT delete relevant body message. Thank you.
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


On Fri, Apr 15, 2011 at 5:46 AM, Shyam Khambholja <physik.shyam at gmail.com>wrote:

> no, neither using qha nor md,
> but using mean field potential approach or quasi harmonic debye model.
>
>
>
> --
> Mr. Shyam G Khambholja,
> Research student,
> Depratment of Physics,
> Sardar Patel University, Gujarat
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From jorge.gallardo at cab.cnea.gov.ar  Fri Apr 15 22:33:22 2011
From: jorge.gallardo at cab.cnea.gov.ar (jorge.gallardo at cab.cnea.gov.ar)
Date: Fri, 15 Apr 2011 17:33:22 -0300 (ART)
Subject: [Pw_forum] Parallel configure does not work
In-Reply-To: <BANLkTinn8aKy72-2e0mmroM6GjZ8DLmo2A@mail.gmail.com>
References: <BANLkTi=QGbBDmwgO3839wUsR0RpuYB1zbQ@mail.gmail.com>
	<BANLkTinn8aKy72-2e0mmroM6GjZ8DLmo2A@mail.gmail.com>
Message-ID: <59653.200.0.233.52.1302899602.squirrel@mail.cab.cnea.gov.ar>

Hello All!

I'm trying to compile Quantum Espresso with the new "Intel? Fortran
Composer XE for Linux" (formerly Intel? Fortran Compiler) with the OpenMPI
libraries previously installed, on an Intel i7 multicore processor
machine. But when I try

 ./configure LIBDIRS= "/opt/intel/mkl/lib/intel64
/usr/lib/openmpi/lib/openmpi"

where

/opt/intel/mkl/lib/intel64

and

/usr/lib/openmpi/lib/openmpi

are respectively the folders where mkl and open-mpi libraries are, I get

"
...

MKL not found
in /usr/lib/openmpi/lib/openmpi: checking for library containing dgemm... no
MKL not found
in /opt/intel/mkl/lib/intel64: checking for library containing dgemm...
-lmkl_intel_lp64
checking for library containing dspev... none required
setting BLAS_LIBS... -L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64
-lmkl_sequential -lmkl_core
setting LAPACK_LIBS...
checking for library containing dfftw_execute_dft... no
in /usr/lib/openmpi/lib/openmpi: checking for library containing
dfftw_execute_dft... no
in /opt/intel/mkl/lib/intel64: checking for library containing
dfftw_execute_dft... no
in /usr/local/lib: checking for library containing dfftw_execute_dft... no

...

checking for library containing mpi_init... no
setting MPI_LIBS...
checking for library containing mpi_init... (cached) no

...

The following libraries have been found:
  BLAS_LIBS=-L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64 
-lmkl_sequential -lmkl_core
  LAPACK_LIBS=
  FFT_LIBS=
Please check if this is what you expect.

...

Parallel environment not detected \(is this a parallel machine?\).\
Configured for compilation of serial executables.

...
"

meaning, I think, that only a few mkl-library-files where found and none
of open-mpi, so the parallel compilation is not posible with this
configuration.

Have you any idea how can I tell properly to the configuration script,
where the open-mpi, and intel-mkl-library-files are, in order to compile
for a parallel machine?


Tank you in advance!


____

Lic. Jorge A. Garc?a Gallardo
Materiales Metalicos y Nanoestructurados
TeMaDi
Bariloche Atomic Center
CNEA


From trambui at u.boisestate.edu  Fri Apr 15 22:59:59 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Fri, 15 Apr 2011 14:59:59 -0600
Subject: [Pw_forum] Generating ultra soft pseudopotential
In-Reply-To: <BANLkTinwZhgYzbc+H_wsrxCPOO_SsJ=1tg@mail.gmail.com>
References: <BANLkTi=pmuBY4W3_84vsE_m1okCtMSg0rQ@mail.gmail.com>
	<BANLkTinwZhgYzbc+H_wsrxCPOO_SsJ=1tg@mail.gmail.com>
Message-ID: <BANLkTikFY3Ozqbt5TpgbZiiLXAHqZLKPsw@mail.gmail.com>

Hi Duy,
Thank you very much for your help!
Tram
On Tue, Apr 5, 2011 at 6:35 PM, Duy Le <ttduyle at gmail.com> wrote:

> Some available PP of Cs can be found at
> http://charter.cnf.cornell.edu/psplist.php?element=Cs
> If you can not find what you need there, you can follow the
> instruction (videos and slides) July 25
> http://media.quantum-espresso.org/santa_barbara_2009_07/index.php
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
>
> On Tue, Apr 5, 2011 at 5:42 PM, Tram Bui <trambui at u.boisestate.edu> wrote:
> > Dear Folks,
> >      I'm trying to build an input file for generating the Cs
> > pseudopotential. when I run the ld1.x on my input file. I got an error
> > message saying that i'm using the wrong core. would you help me with
> extra
> > information of where I can find the help for how to choose the right core
> > for some atoms such as in my case it is Cs.
> >
> > Thank you very much,
> > Tram Bui
> >
> > M.S. Materials Science & Engineering
> > trambui at u.boisestate.edu
> >
> >
> > _______________________________________________
> > 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
>



-- 
Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From trambui at u.boisestate.edu  Fri Apr 15 23:10:28 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Fri, 15 Apr 2011 15:10:28 -0600
Subject: [Pw_forum] Generating ultra soft pseudopotential
In-Reply-To: <BANLkTi=pmuBY4W3_84vsE_m1okCtMSg0rQ@mail.gmail.com>
References: <BANLkTi=pmuBY4W3_84vsE_m1okCtMSg0rQ@mail.gmail.com>
Message-ID: <BANLkTi==wM_-JiKNapvgyf4sc6KagUB7Yg@mail.gmail.com>

Dear Everyone,
      From the lecture on July 25 2009
http://media.quantum-espresso.org/santa_barbara_2009_07/index.php, there is
an example file where the Si was used to demonstrate the step by step for
generating the pseudopotential. And I have some follow up questions based on
that file as follow :
  - In the FOURTH directory, the Si configuration is defined as :' [ Ne] 3s2
3p2 3d-1' , what does it mean by having "-1" for 3d orbital in this case?
  - Also in the same directory, what are/is the reason(s) for matching the
"pseudo logarithmic derivative" with the "all-electron logarithmic
derivative" plot.

Best regard,
Tram Bui

On Tue, Apr 5, 2011 at 3:42 PM, Tram Bui <trambui at u.boisestate.edu> wrote:

> Dear Folks,
>      I'm trying to build an input file for generating the Cs
> pseudopotential. when I run the ld1.x on my input file. I got an error
> message saying that i'm using the wrong core. would you help me with extra
> information of where I can find the help for how to choose the right core
> for some atoms such as in my case it is Cs.
>
> Thank you very much,
>
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
>
>


-- 
Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From elie.moujaes at hotmail.co.uk  Sat Apr 16 01:15:28 2011
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Sat, 16 Apr 2011 00:15:28 +0100
Subject: [Pw_forum] Fortan compiler cannot create executables
Message-ID: <SNT114-W3130B58A8E87FDCB8FEAE9D3AC0@phx.gbl>


Hello everyone,


 
 I am trying to re-install quantum espresso-4.3 on the University's LINUX interface (because of a recent crash and I lost most of my files).

 when I "sudo ./configure ",  It is giving an error stating that : 

checking building system type... x86_64-unknown-linux-gnu

checking architecture... x86_64

checking for ifort.. no

checking for pgf90... no

checking for pathf95.. no

checking for sunf95.. no

checking for openf95... no

checking for gfortran... no

checking for g95... no

checking for f90... no

checking for Fortran compiler default output... configure: error: Fortran compiler cannot create executables

See `config.log' for more details.



I have already installed g95.  I really don't know why 
this error is coming. 
 Please can anyone help.

Thanks

Elie Moujaes
University of Nottingham
Nottingham
NG7 2RD
 		 	   		  
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From flux_ray12 at 163.com  Sat Apr 16 05:05:55 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Sat, 16 Apr 2011 11:05:55 +0800 (CST)
Subject: [Pw_forum] Parallel configure does not work
In-Reply-To: <59653.200.0.233.52.1302899602.squirrel@mail.cab.cnea.gov.ar>
References: <59653.200.0.233.52.1302899602.squirrel@mail.cab.cnea.gov.ar>
	<BANLkTi=QGbBDmwgO3839wUsR0RpuYB1zbQ@mail.gmail.com>
	<BANLkTinn8aKy72-2e0mmroM6GjZ8DLmo2A@mail.gmail.com>
Message-ID: <135133.bc98.12f5c45965f.Coremail.flux_ray12@163.com>

Put your MPI binary directory into environment variable.
For example, if your OpenMPI installed at ~/OpenMPI, then you can add PATH=$PATH:~/OpenMPI/bin into the end of file ~/.bashrc and re-config QE again.
BTW: it may be better that OpenMPI was also compiled by ifort.




At 2011-04-16 04:33:22?jorge.gallardo at cab.cnea.gov.ar wrote:

>Hello All!
>
>I'm trying to compile Quantum Espresso with the new "Intel? Fortran
>Composer XE for Linux" (formerly Intel? Fortran Compiler) with the OpenMPI
>libraries previously installed, on an Intel i7 multicore processor
>machine. But when I try
>
> ./configure LIBDIRS= "/opt/intel/mkl/lib/intel64
>/usr/lib/openmpi/lib/openmpi"
>
>where
>
>/opt/intel/mkl/lib/intel64
>
>and
>
>/usr/lib/openmpi/lib/openmpi
>
>are respectively the folders where mkl and open-mpi libraries are, I get
>
>"
>...
>
>MKL not found
>in /usr/lib/openmpi/lib/openmpi: checking for library containing dgemm... no
>MKL not found
>in /opt/intel/mkl/lib/intel64: checking for library containing dgemm...
>-lmkl_intel_lp64
>checking for library containing dspev... none required
>setting BLAS_LIBS... -L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64
>-lmkl_sequential -lmkl_core
>setting LAPACK_LIBS...
>checking for library containing dfftw_execute_dft... no
>in /usr/lib/openmpi/lib/openmpi: checking for library containing
>dfftw_execute_dft... no
>in /opt/intel/mkl/lib/intel64: checking for library containing
>dfftw_execute_dft... no
>in /usr/local/lib: checking for library containing dfftw_execute_dft... no
>
>...
>
>checking for library containing mpi_init... no
>setting MPI_LIBS...
>checking for library containing mpi_init... (cached) no
>
>...
>
>The following libraries have been found:
>  BLAS_LIBS=-L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64 
>-lmkl_sequential -lmkl_core
>  LAPACK_LIBS=
>  FFT_LIBS=
>Please check if this is what you expect.
>
>...
>
>Parallel environment not detected \(is this a parallel machine?\).\
>Configured for compilation of serial executables.
>
>...
>"
>
>meaning, I think, that only a few mkl-library-files where found and none
>of open-mpi, so the parallel compilation is not posible with this
>configuration.
>
>Have you any idea how can I tell properly to the configuration script,
>where the open-mpi, and intel-mkl-library-files are, in order to compile
>for a parallel machine?
>
>
>Tank you in advance!
>
>
>____
>
>Lic. Jorge A. Garc?a Gallardo
>Materiales Metalicos y Nanoestructurados
>TeMaDi
>Bariloche Atomic Center
>CNEA
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
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From lorenzo.paulatto at impmc.upmc.fr  Sat Apr 16 10:06:37 2011
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Sat, 16 Apr 2011 10:06:37 +0200
Subject: [Pw_forum] Fortan compiler cannot create executables
In-Reply-To: <SNT114-W3130B58A8E87FDCB8FEAE9D3AC0@phx.gbl>
References: <SNT114-W3130B58A8E87FDCB8FEAE9D3AC0@phx.gbl>
Message-ID: <op.vt0t5adr5jfbqb@paulax>

In data 16 aprile 2011 alle ore 01:15:28, Elie Moujaes  
<elie.moujaes at hotmail.co.uk> ha scritto:
> checking for g95... no

Dear Elie,
it means that the g95 compiler is not in your PATH  
<http://en.wikipedia.org/wiki/PATH_(variable)>, thus it is not found by  
configure. Other sources for the same error are possible but unlikely.

Have a look at the corresponding entry in the FAQ:  
<http://www.quantum-espresso.org/user_guide/node59.html#SECTION000132020000000000000>

Please note that this problem has nothing to do with Quantum-ESPRESSO,  
being rather a misconfiguration of your Linux environment. It would be  
much easier for you to look for help from your system administrators or  
some experienced colleague, as this kind of issues are extremely difficult  
to solve without having physical access to the machine.

best regards


-- 
Lorenzo Paulatto
post-doc @ IMPMC/UPMC - Universit? Paris 6
phone: +33 (0)1 44 27 74 89
www:   http://www-int.impmc.upmc.fr/~paulatto/

previously (take note of the change!):
phd student @ SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
www:   http://people.sissa.it/~paulatto/

From masoudnahali at gmail.com  Sat Apr 16 11:41:00 2011
From: masoudnahali at gmail.com (Masoud Nahali)
Date: Sat, 16 Apr 2011 14:11:00 +0430
Subject: [Pw_forum] Fortan compiler cannot create executables
Message-ID: <BANLkTinq+YNw8o-OJnujO4NQgsGK0N8Afg@mail.gmail.com>

Dear Elie

Try "export PATH=$PATH:/path/to/your/directory/where/g95/installed" then
update your database (updatedb command) and restart your computer. Also, you
can copy g95 binary files from where you have installed the g95 to /bin.You
should examine "g95" or "gfortran" commands in your linux console before
trying to compile the QE. I hope it helps.


Best Wishes

 Masoud

--------------
Masoud Nahali, Ph. D Student
Sharif University of Technology



On Sat, Apr 16, 2011 at 11:57 AM, Elie Moujaes wrote :

>
> Hello everyone,
>
>
>
>  I am trying to re-install quantum espresso-4.3 on the University's LINUX
> interface (because of a recent crash and I lost most of my files).
>
>  when I "sudo ./configure ",  It is giving an error stating that :
>
> checking building system type... x86_64-unknown-linux-gnu
>
> checking architecture... x86_64
>
> checking for ifort.. no
>
> checking for pgf90... no
>
> checking for pathf95.. no
>
> checking for sunf95.. no
>
> checking for openf95... no
>
> checking for gfortran... no
>
> checking for g95... no
>
> checking for f90... no
>
> checking for Fortran compiler default output... configure: error: Fortran
> compiler cannot create executables
>
> See `config.log' for more details.
>
>
>
> I have already installed g95.  I really don't know why
> this error is coming.
>  Please can anyone help.
>
> Thanks
>
> Elie Moujaes
> University of Nottingham
> Nottingham
> NG7 2RD
>
>
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From kucukben at sissa.it  Sat Apr 16 12:00:04 2011
From: kucukben at sissa.it (Emine Kucukbenli)
Date: Sat, 16 Apr 2011 12:00:04 +0200
Subject: [Pw_forum] Generating ultra soft pseudopotential
In-Reply-To: <BANLkTi==wM_-JiKNapvgyf4sc6KagUB7Yg@mail.gmail.com>
References: <BANLkTi=pmuBY4W3_84vsE_m1okCtMSg0rQ@mail.gmail.com>
	<BANLkTi==wM_-JiKNapvgyf4sc6KagUB7Yg@mail.gmail.com>
Message-ID: <20110416120004.nezqlez5csgw0o8k@webmail.sissa.it>



Quoting Tram Bui <trambui at u.boisestate.edu>:

> Dear Everyone,
>       From the lecture on July 25 2009
> http://media.quantum-espresso.org/santa_barbara_2009_07/index.php, there is
> an example file where the Si was used to demonstrate the step by step for
> generating the pseudopotential. And I have some follow up questions based on
> that file as follow :
>   - In the FOURTH directory, the Si configuration is defined as :' [ Ne] 3s2
> 3p2 3d-1' , what does it mean by having "-1" for 3d orbital in this case?

that it is an unbound state

>   - Also in the same directory, what are/is the reason(s) for matching the
> "pseudo logarithmic derivative" with the "all-electron logarithmic
> derivative" plot.
you know that the pseudowavefunctions match all electron ones beyond  
core radii for the generation energy. log. der. is a way to check  
whether this matching behavior is valid not just for the generation  
energy but for a range..
if log. der. match, you can probably use that pseudo in other energy  
ranges,systems as well (it is transferable).. also it is one of the  
things to look at while hunting ghost states..spikes in pseudo log.  
der. that dont conrrespond to all electron ones means you have a ghost  
state..

emine kucukbenli , phd student, sissa, italy

>
> Best regard,
> Tram Bui
>
> On Tue, Apr 5, 2011 at 3:42 PM, Tram Bui <trambui at u.boisestate.edu> wrote:
>
>> Dear Folks,
>>      I'm trying to build an input file for generating the Cs
>> pseudopotential. when I run the ld1.x on my input file. I got an error
>> message saying that i'm using the wrong core. would you help me with extra
>> information of where I can find the help for how to choose the right core
>> for some atoms such as in my case it is Cs.
>>
>> Thank you very much,
>>
>> Tram Bui
>>
>> M.S. Materials Science & Engineering
>> trambui at u.boisestate.edu
>>
>>
>
>
> --
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
>



----------------------------------------------------------------
   SISSA Webmail https://webmail.sissa.it/
   Powered by Horde http://www.horde.org/



From giuseppe.mattioli at mlib.ism.cnr.it  Sat Apr 16 14:54:15 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Sat, 16 Apr 2011 14:54:15 +0200
Subject: [Pw_forum] problems with input_dft='vdW-DF' in neb.x calculations
In-Reply-To: <59184.141.108.248.78.1301923628.squirrel@141.108.248.78>
References: <59184.141.108.248.78.1301923628.squirrel@141.108.248.78>
Message-ID: <201104161454.15991.giuseppe.mattioli@mlib.ism.cnr.it>

Dear all
I'm facing a strange problem when performing neb.x calculations with the 
input_dft='vdW-DF' flag.
I've tried the very same calculation (same machine, same QE 4.3 version...) 
but for the vdW, e.g., in the case of cyclohexane isomerization (input files 
below). Everything is fine in the non-corrected case. On the contrary, this 
is the only standard output in the vdW case:

      Program NEB v.4.3          starts on 16Apr2011 at 14:14: 6

     This program is part of the open-source Quantum ESPRESSO suite
     for quantum simulation of materials; please cite
         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          URL http://www.quantum-espresso.org",
     in publications or presentations arising from this work. More details at
     http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO

     Parallel version (MPI), running on     8 processors
     R & G space division:  proc/pool =    8
Warning: card   &IONS ignored
Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
Warning: card      ION_DYNAMICS='BFGS' ignored
Warning: card   / ignored

     XC functional enforced from input :
     Exchange-correlation      = VDW-DF (1449)
     EXX-fraction              =        0.00
     !!! Any further DFT definition will be discarded
     !!! Please, verify this is what you really want !

Warning: card   &IONS ignored
Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
Warning: card      ION_DYNAMICS='BFGS' ignored
Warning: card   / ignored

     XC functional enforced from input :
     Exchange-correlation      = VDW-DF (1449)
     EXX-fraction              =        0.00
     !!! Any further DFT definition will be discarded
     !!! Please, verify this is what you really want !

and this is the reported system error:

"kernel_table.f90", line 172: 1525-108 Error encountered while attempting to 
allocate a data object.  The program will stop.

vdW calculations run of course without problems in standard pw.x jobs.
A look at the above file has not provided any enlightenment (at least to 
me...)

A minor question: why are the following printed in the standard output file?
Warning: card   &IONS ignored
Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
Warning: card      ION_DYNAMICS='BFGS' ignored
Warning: card   / ignored
I followed the run_example template in the QE/examples/example17 directory 
which contains the cards
&IONS
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
/

A further minor question: where can I found any documentation to set up a smd 
calculation using cards like:
BEGIN_PATH_INPUT
&PATH
  string_method     = 'smd',
  opt_scheme        = "langevin",
  temp_req          = 200.0
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT

Any comment or suggestion?
Thank you in advance
Giuseppe

This is the one which works fine:

export FILE="test"
export INPFILE=$FILE-1.inp
export OUTFILE=$FILE-1.out
echo " $FILE"
echo " $INPFILE"
echo " $OUTFILE"

cat > $INPFILE << EOF
BEGIN
BEGIN_PATH_INPUT
&PATH
  restart_mode      = 'from_scratch',
  string_method     = 'neb',
  nstep_path        = 200,
  ds                = 2.D0,
  opt_scheme        = "broyden",
  num_of_images     = 9,
  CI_scheme         = "no-CI",
  path_thr          = 0.1D0,
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT
 &CONTROL
    prefix='$FILE',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/',
 /
 &SYSTEM
    ibrav=1, celldm(1)=20.0000
    nat=18, ntyp=2,
    ecutwfc = 25.0,
    ecutrho = 200.0,
    occupations='smearing', degauss=0.01,
    nspin=1,
 /
 &ELECTRONS
    mixing_mode='plain'
    mixing_beta=0.2
    conv_thr=1.0d-8
    electron_maxstep=200
 /
 &IONS
    pot_extrapolation = "second_order",
    wfc_extrapolation = "second_order",
    ion_dynamics='bfgs'
 /
ATOMIC_SPECIES
C    12.011     C_pbe.van.UPF
H     1.008     H_pbe.van.UPF
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS {angstrom}
C        6.098316160   3.760656270   4.654408584
C        5.535560000   5.029242896   4.000000000
C        5.535560000   2.491939382   4.000000000
C        4.000840929   5.027202726   4.000000000
C        4.000950457   2.493714962   4.000000000
C        3.441730882   3.760373055   3.339304890
H        5.825930677   3.760664232   5.733651283
H        7.207790908   3.760649901   4.611224167
H        5.898266497   5.087596300   2.948897106
H        5.921942861   5.933612152   4.514551016
H        5.898578752   2.433310631   2.949074312
H        5.922060506   1.587859796   4.515020902
H        3.637454955   2.444160918   5.051149794
H        3.611787526   1.587642834   3.490637392
H        3.637077165   5.076985202   5.050984568
H        3.611543166   5.933006456   3.490221051
H        2.332375720   3.760276416   3.383439061
H        3.714361008   3.760355870   2.259592492
LAST_IMAGE
ATOMIC_POSITIONS {angstrom}
C        6.121592696   3.760535885   4.641499347
C        5.535560000   5.025712602   4.000000000
C        5.535560000   2.495388270   4.000000000
C        3.977918610   5.023959085   4.000000000
C        3.977930112   2.497154140   4.000000000
C        3.393609861   3.760551962   4.644872629
H        5.913189538   3.760513868   5.732562614
H        7.227121303   3.760507977   4.543954834
H        5.908541836   5.092099491   2.955785191
H        5.923102018   5.926437334   4.518072829
H        5.908479393   2.429064594   2.955753950
H        5.923126757   1.594603868   4.517936370
H        3.590403695   1.596442101   4.516411429
H        3.603091688   2.435078428   2.956089377
H        3.590454294   5.924681359   4.516455545
H        3.603071258   5.086031218   2.956078488
H        3.602033618   3.760529459   5.735973241
H        2.288228742   3.760541827   4.546696293
END_POSITIONS
K_POINTS {gamma}
END_ENGINE_INPUT
END
EOF
$PARA_PREFIX $ESPRESSO/neb.x -inp $INPFILE >> $OUTFILE

if I only add input_dft='vdW-DF' in the &SYSTEM list it does not work anymore.

-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? 
? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ?
? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ?
? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ?
? ?E-mail: <giuseppe.mattioli at ism.cnr.it>

From giannozz at democritos.it  Sat Apr 16 19:46:39 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 16 Apr 2011 19:46:39 +0200
Subject: [Pw_forum] problems with input_dft='vdW-DF' in neb.x
	calculations
In-Reply-To: <201104161454.15991.giuseppe.mattioli@mlib.ism.cnr.it>
References: <59184.141.108.248.78.1301923628.squirrel@141.108.248.78>
	<201104161454.15991.giuseppe.mattioli@mlib.ism.cnr.it>
Message-ID: <C5C0EAEA-6D08-4EC6-8E07-943EB16C5C97@democritos.it>


On Apr 16, 2011, at 14:54 , Giuseppe Mattioli wrote:

> A minor question: why are the following printed in the standard  
> output file?
> Warning: card   &IONS ignored
> Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
> Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
> Warning: card      ION_DYNAMICS='BFGS' ignored
> Warning: card   / ignored
> I followed the run_example template in the QE/examples/example17  
> directory

the example is not consistent with the documentation. First- and  
second-order
interpolation are expected to work only for molecular dynamics run,  
as specified
in the documentation: in all other cases, they give no advantage.

> A further minor question: where can I found any documentation to  
> set up a smd
> calculation using cards like:

>   string_method     = 'smd',
>   opt_scheme        = "langevin",
>   temp_req          = 200.0

nowhere. Some exotic cases have never had any documentation,
and will never have any, until somebody who know if and how
they work writes down it.

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





From elie.moujaes at hotmail.co.uk  Sun Apr 17 01:31:35 2011
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Sun, 17 Apr 2011 00:31:35 +0100
Subject: [Pw_forum] Fortan compiler cannot create executables
In-Reply-To: <BANLkTinq+YNw8o-OJnujO4NQgsGK0N8Afg@mail.gmail.com>
References: <BANLkTinq+YNw8o-OJnujO4NQgsGK0N8Afg@mail.gmail.com>
Message-ID: <SNT114-W2330C6149DDEB4B0054327D3AF0@phx.gbl>


Dear Masoud,

thanks very much for your help. I knew that I need to change the path but i did not know how so thanks for thr info. Unfortunately, my CSH shell does not support the EXPORT command so whenever I use it it outputs : Export: command not found. I do not have a /bin because this is running on my network account..I even tried before to use ln -s to copy stuff but permission was denied. is there any other command you are aware of for a csh/sh shell (other than export I mean)?

Thank you

ELie

Date: Sat, 16 Apr 2011 14:11:00 +0430
From: masoudnahali at gmail.com
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] Fortan compiler cannot create executables

Dear Elie

Try "export PATH=$PATH:/path/to/your/directory/where/g95/installed" then update your database (updatedb command) and restart your computer. Also, you can copy g95 binary files from where you have installed the g95 to /bin.You should examine "g95" or "gfortran" commands in your linux console before trying to compile the QE. I hope it helps.     


Best Wishes


 Masoud

--------------
Masoud Nahali, Ph. D Student
Sharif University of Technology




On Sat, Apr 16, 2011 at 11:57 AM, Elie Moujaes wrote :





Hello everyone,







 I am trying to re-install quantum espresso-4.3 on the University's LINUX interface (because of a recent crash and I lost most of my files).



 when I "sudo ./configure ",  It is giving an error stating that :



checking building system type... x86_64-unknown-linux-gnu



checking architecture... x86_64



checking for ifort.. no



checking for pgf90... no



checking for pathf95.. no



checking for sunf95.. no



checking for openf95... no



checking for gfortran... no



checking for g95... no



checking for f90... no



checking for Fortran compiler default output... configure: error: Fortran compiler cannot create executables



See `config.log' for more details.







I have already installed g95.  I really don't know why

this error is coming.

 Please can anyone help.



Thanks



Elie Moujaes

University of Nottingham

Nottingham

NG7 2RD





_______________________________________________
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From masoudnahali at gmail.com  Sun Apr 17 06:56:17 2011
From: masoudnahali at gmail.com (Masoud Nahali)
Date: Sun, 17 Apr 2011 09:26:17 +0430
Subject: [Pw_forum] Fortan compiler cannot create executables
Message-ID: <BANLkTinb9QkrtV7FHDcREx+K2qboaUVRUQ@mail.gmail.com>

   Dear Elie

  Using csh/tcsh you should try "setenv" instead of "export".



Elie on Sun, 17 Apr 2011 00:31:35 wrote:
>
> Unfortunately, my CSH shell does not support the EXPORT command.
>
>

Best Wishes


 Masoud
--------------
Masoud Nahali, Ph. D Student
Sharif University of Technology
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From giannozz at democritos.it  Sun Apr 17 13:53:29 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 17 Apr 2011 13:53:29 +0200
Subject: [Pw_forum] Parallel configure does not work
In-Reply-To: <59653.200.0.233.52.1302899602.squirrel@mail.cab.cnea.gov.ar>
References: <BANLkTi=QGbBDmwgO3839wUsR0RpuYB1zbQ@mail.gmail.com>
	<BANLkTinn8aKy72-2e0mmroM6GjZ8DLmo2A@mail.gmail.com>
	<59653.200.0.233.52.1302899602.squirrel@mail.cab.cnea.gov.ar>
Message-ID: <D9F264A7-CFE3-416F-8F54-98475598B50D@democritos.it>


On Apr 15, 2011, at 22:33 , jorge.gallardo at cab.cnea.gov.ar wrote:

> Parallel environment not detected

your "mpif90" script must be in your execution path, it must
invoke the intel compiler, it must be properly installed. If it is,
there is no need to specify the location of mpi libraries. More
details in the user guide

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





From elie.moujaes at hotmail.co.uk  Mon Apr 18 02:52:03 2011
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Mon, 18 Apr 2011 01:52:03 +0100
Subject: [Pw_forum] Fortan compiler cannot create executables
In-Reply-To: <BANLkTinb9QkrtV7FHDcREx+K2qboaUVRUQ@mail.gmail.com>
References: <BANLkTinb9QkrtV7FHDcREx+K2qboaUVRUQ@mail.gmail.com>
Message-ID: <SNT114-W4F2F9275B14503DC1A974D3910@phx.gbl>


Dear Masoud,

I have tried setenv but it did not really work. Initially, my PATH was: /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/ysr/games now I used setenv and the new path is:

/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install

but when I ./configure again, I still get checking for g95..no....so I am not sure what is still going wrong

ELie

Date: Sun, 17 Apr 2011 09:26:17 +0430
From: masoudnahali at gmail.com
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] Fortan compiler cannot create executables

   Dear Elie

  Using csh/tcsh you should try "setenv" instead of "export".




Elie on Sun, 17 Apr 2011 00:31:35 wrote:

Unfortunately, my CSH shell does not support the EXPORT command.
 Best Wishes



 Masoud
--------------
Masoud Nahali, Ph. D Student
Sharif University of Technology



_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum 		 	   		  
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From ttduyle at gmail.com  Mon Apr 18 02:55:58 2011
From: ttduyle at gmail.com (Duy Le)
Date: Sun, 17 Apr 2011 20:55:58 -0400
Subject: [Pw_forum] Fortan compiler cannot create executables
In-Reply-To: <SNT114-W4F2F9275B14503DC1A974D3910@phx.gbl>
References: <BANLkTinb9QkrtV7FHDcREx+K2qboaUVRUQ@mail.gmail.com>
	<SNT114-W4F2F9275B14503DC1A974D3910@phx.gbl>
Message-ID: <BANLkTikk7YcOvuGX59erHNua_YrYNj9owA@mail.gmail.com>

You just need to identify CORRECTLY the PATH of g95 excutable, not the
source code PATH

On Sunday, April 17, 2011, Elie Moujaes <elie.moujaes at hotmail.co.uk> wrote:
>
>
>
>
>
> Dear Masoud,
>
> I have tried setenv but it did not really work. Initially, my PATH was: /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/ysr/games now I used setenv and the new path is:
>
> /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install
>
> but when I ./configure again, I still get checking for g95..no....so I am not sure what is still going wrong
>
> ELie
>
> Date: Sun, 17 Apr 2011 09:26:17 +0430
> From: masoudnahali at gmail.com
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Fortan compiler cannot create executables
>
> ?? Dear Elie
>
> ? Using csh/tcsh you should try "setenv" instead of "export".
>
>
>
>
> Elie on Sun, 17 Apr 2011 00:31:35 wrote:
>
> Unfortunately, my CSH shell does not support the EXPORT command.
>  Best Wishes
>
>
> ?Masoud
> --------------
> Masoud Nahali, Ph. D Student
> Sharif University of Technology
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum 		 	   		
>

-- 
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"

From elie.moujaes at hotmail.co.uk  Mon Apr 18 03:16:22 2011
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Mon, 18 Apr 2011 02:16:22 +0100
Subject: [Pw_forum] Fortan compiler cannot create executables
In-Reply-To: <BANLkTikk7YcOvuGX59erHNua_YrYNj9owA@mail.gmail.com>
References: <BANLkTinb9QkrtV7FHDcREx+K2qboaUVRUQ@mail.gmail.com>,
	<SNT114-W4F2F9275B14503DC1A974D3910@phx.gbl>,
	<BANLkTikk7YcOvuGX59erHNua_YrYNj9owA@mail.gmail.com>
Message-ID: <SNT114-W27684FA147C9C51BBB89A7D3910@phx.gbl>


Dear Duy Le,

Thanks for your reply. The executable is "i686-pc-linux-gnu-g95" and is in the bin folder in g95-install. Adding this to the path i.e : /exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install/bin produces the same error  : checking for g95...no

Elie

> Date: Sun, 17 Apr 2011 20:55:58 -0400
> From: ttduyle at gmail.com
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Fortan compiler cannot create executables
> 
> You just need to identify CORRECTLY the PATH of g95 excutable, not the
> source code PATH
> 
> On Sunday, April 17, 2011, Elie Moujaes <elie.moujaes at hotmail.co.uk> wrote:
> >
> >
> >
> >
> >
> > Dear Masoud,
> >
> > I have tried setenv but it did not really work. Initially, my PATH was: /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/ysr/games now I used setenv and the new path is:
> >
> > /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install
> >
> > but when I ./configure again, I still get checking for g95..no....so I am not sure what is still going wrong
> >
> > ELie
> >
> > Date: Sun, 17 Apr 2011 09:26:17 +0430
> > From: masoudnahali at gmail.com
> > To: pw_forum at pwscf.org
> > Subject: Re: [Pw_forum] Fortan compiler cannot create executables
> >
> >    Dear Elie
> >
> >   Using csh/tcsh you should try "setenv" instead of "export".
> >
> >
> >
> >
> > Elie on Sun, 17 Apr 2011 00:31:35 wrote:
> >
> > Unfortunately, my CSH shell does not support the EXPORT command.
> >  Best Wishes
> >
> >
> >  Masoud
> > --------------
> > Masoud Nahali, Ph. D Student
> > Sharif University of Technology
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum 		 	   		
> >
> 
> -- 
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
> 
> "Men don't need hand to do things"
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
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From germaneau at gucas.ac.cn  Mon Apr 18 15:22:16 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Mon, 18 Apr 2011 09:22:16 -0400
Subject: [Pw_forum] Fortan compiler cannot create executables
In-Reply-To: <503088904.11633@test1.gucas.ac.cn>
References: <BANLkTinb9QkrtV7FHDcREx+K2qboaUVRUQ@mail.gmail.com>,
	<SNT114-W4F2F9275B14503DC1A974D3910@phx.gbl>,
	<BANLkTikk7YcOvuGX59erHNua_YrYNj9owA@mail.gmail.com>
	<503088904.11633@test1.gucas.ac.cn>
Message-ID: <4DAC3B08.1070407@gucas.ac.cn>

Hey Elie,

Did you build this executable your self?
Did you successfully compile a small program with it?
Why don't you just use gfortran which is available on pretty much  all 
machines?


On 04/17/2011 09:16 PM, Elie Moujaes wrote:
> Dear Duy Le,
>
> Thanks for your reply. The executable is "i686-pc-linux-gnu-g95" and 
> is in the bin folder in g95-install. Adding this to the path i.e : 
> /exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install/bin 
> produces the same error  : checking for g95...no
>
> Elie
>
> > Date: Sun, 17 Apr 2011 20:55:58 -0400
> > From: ttduyle at gmail.com
> > To: pw_forum at pwscf.org
> > Subject: Re: [Pw_forum] Fortan compiler cannot create executables
> >
> > You just need to identify CORRECTLY the PATH of g95 excutable, not the
> > source code PATH
> >
> > On Sunday, April 17, 2011, Elie Moujaes <elie.moujaes at hotmail.co.uk> 
> wrote:
> > >
> > >
> > >
> > >
> > >
> > > Dear Masoud,
> > >
> > > I have tried setenv but it did not really work. Initially, my PATH 
> was: /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/ysr/games now I used 
> setenv and the new path is:
> > >
> > > 
> /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install
> > >
> > > but when I ./configure again, I still get checking for 
> g95..no....so I am not sure what is still going wrong
> > >
> > > ELie
> > >
> > > Date: Sun, 17 Apr 2011 09:26:17 +0430
> > > From: masoudnahali at gmail.com
> > > To: pw_forum at pwscf.org
> > > Subject: Re: [Pw_forum] Fortan compiler cannot create executables
> > >
> > >    Dear Elie
> > >
> > >   Using csh/tcsh you should try "setenv" instead of "export".
> > >
> > >
> > >
> > >
> > > Elie on Sun, 17 Apr 2011 00:31:35 wrote:
> > >
> > > Unfortunately, my CSH shell does not support the EXPORT command.
> > > Best Wishes
> > >
> > >
> > >  Masoud
> > > --------------
> > > Masoud Nahali, Ph. D Student
> > > Sharif University of Technology
> > >
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> >
> > --
> > --------------------------------------------------
> > Duy Le
> > PhD Student
> > Department of Physics
> > University of Central Florida.
> >
> > "Men don't need hand to do things"
> > _______________________________________________
> > 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

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/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 ttduyle at gmail.com  Mon Apr 18 03:23:36 2011
From: ttduyle at gmail.com (Duy Le)
Date: Sun, 17 Apr 2011 21:23:36 -0400
Subject: [Pw_forum] Fortan compiler cannot create executables
In-Reply-To: <SNT114-W27684FA147C9C51BBB89A7D3910@phx.gbl>
References: <BANLkTinb9QkrtV7FHDcREx+K2qboaUVRUQ@mail.gmail.com>
	<SNT114-W4F2F9275B14503DC1A974D3910@phx.gbl>
	<BANLkTikk7YcOvuGX59erHNua_YrYNj9owA@mail.gmail.com>
	<SNT114-W27684FA147C9C51BBB89A7D3910@phx.gbl>
Message-ID: <BANLkTikEabhX6eOvu-89xuwPhfsgN=BzMA@mail.gmail.com>

Rename or make an sanple link i686-pc-linux-gnu-g95  to g95 and try. QE
looks for g95 file, you don't have it.
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


On Sun, Apr 17, 2011 at 9:16 PM, Elie Moujaes <elie.moujaes at hotmail.co.uk>wrote:

>  Dear Duy Le,
>
> Thanks for your reply. The executable is "i686-pc-linux-gnu-g95" and is in
> the bin folder in g95-install. Adding this to the path i.e :
> /exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install/bin produces the
> same error  : checking for g95...no
>
> Elie
>
> > Date: Sun, 17 Apr 2011 20:55:58 -0400
> > From: ttduyle at gmail.com
>
> > To: pw_forum at pwscf.org
> > Subject: Re: [Pw_forum] Fortan compiler cannot create executables
> >
> > You just need to identify CORRECTLY the PATH of g95 excutable, not the
> > source code PATH
> >
> > On Sunday, April 17, 2011, Elie Moujaes <elie.moujaes at hotmail.co.uk>
> wrote:
> > >
> > >
> > >
> > >
> > >
> > > Dear Masoud,
> > >
> > > I have tried setenv but it did not really work. Initially, my PATH was:
> /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/ysr/games now I used setenv and
> the new path is:
> > >
> > >
> /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install
> > >
> > > but when I ./configure again, I still get checking for g95..no....so I
> am not sure what is still going wrong
> > >
> > > ELie
> > >
> > > Date: Sun, 17 Apr 2011 09:26:17 +0430
> > > From: masoudnahali at gmail.com
> > > To: pw_forum at pwscf.org
> > > Subject: Re: [Pw_forum] Fortan compiler cannot create executables
> > >
> > >    Dear Elie
> > >
> > >   Using csh/tcsh you should try "setenv" instead of "export".
> > >
> > >
> > >
> > >
> > > Elie on Sun, 17 Apr 2011 00:31:35 wrote:
> > >
> > > Unfortunately, my CSH shell does not support the EXPORT command.
> > > Best Wishes
> > >
> > >
> > >  Masoud
> > > --------------
> > > Masoud Nahali, Ph. D Student
> > > Sharif University of Technology
> > >
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> >
> > --
> > --------------------------------------------------
> > Duy Le
> > PhD Student
> > Department of Physics
> > University of Central Florida.
> >
> > "Men don't need hand to do things"
> > _______________________________________________
> > 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 elie.moujaes at hotmail.co.uk  Mon Apr 18 04:13:36 2011
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Mon, 18 Apr 2011 03:13:36 +0100
Subject: [Pw_forum] Fortan compiler cannot create executables
In-Reply-To: <BANLkTikEabhX6eOvu-89xuwPhfsgN=BzMA@mail.gmail.com>
References: <BANLkTinb9QkrtV7FHDcREx+K2qboaUVRUQ@mail.gmail.com>,
	<SNT114-W4F2F9275B14503DC1A974D3910@phx.gbl>,
	<BANLkTikk7YcOvuGX59erHNua_YrYNj9owA@mail.gmail.com>,
	<SNT114-W27684FA147C9C51BBB89A7D3910@phx.gbl>,
	<BANLkTikEabhX6eOvu-89xuwPhfsgN=BzMA@mail.gmail.com>
Message-ID: <SNT114-W303E88F45CE480BE576738D3910@phx.gbl>


I am really thankful for your help. I renamed it and now it displayed : checking for g95.....g95 but it stopped with another error:

Configure: WARNING: In the future, Auticonfig will not detect cross-tools whose name does not start with the host triplet. If you think this configuration is useful to you, please write to autoconf at gnu.org. Checking for Fortran compiler default output filename...Configure: error: Fortran compiler cannot create executables


Elie

From: ttduyle at gmail.com
Date: Sun, 17 Apr 2011 21:23:36 -0400
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] Fortan compiler cannot create executables

Rename or make an sanple link i686-pc-linux-gnu-g95  to g95 and try. QE looks for g95 file, you don't have it.--------------------------------------------------
Duy Le
PhD Student
Department of Physics


University of Central Florida.

"Men don't need hand to do things"



On Sun, Apr 17, 2011 at 9:16 PM, Elie Moujaes <elie.moujaes at hotmail.co.uk> wrote:







Dear Duy Le,

Thanks for your reply. The executable is "i686-pc-linux-gnu-g95" and is in the bin folder in g95-install. Adding this to the path i.e : /exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install/bin produces the same error  : checking for g95...no



Elie

> Date: Sun, 17 Apr 2011 20:55:58 -0400
> From: ttduyle at gmail.com
> To: pw_forum at pwscf.org


> Subject: Re: [Pw_forum] Fortan compiler cannot create executables
> 
> You just need to identify CORRECTLY the PATH of g95 excutable, not the
> source code PATH
> 
> On Sunday, April 17, 2011, Elie Moujaes <elie.moujaes at hotmail.co.uk> wrote:


> >
> >
> >
> >
> >
> > Dear Masoud,
> >
> > I have tried setenv but it did not really work. Initially, my PATH was: /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/ysr/games now I used setenv and the new path is:


> >
> > /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install
> >
> > but when I ./configure again, I still get checking for g95..no....so I am not sure what is still going wrong


> >
> > ELie
> >
> > Date: Sun, 17 Apr 2011 09:26:17 +0430
> > From: masoudnahali at gmail.com
> > To: pw_forum at pwscf.org


> > Subject: Re: [Pw_forum] Fortan compiler cannot create executables
> >
> >    Dear Elie
> >
> >   Using csh/tcsh you should try "setenv" instead of "export".


> >
> >
> >
> >
> > Elie on Sun, 17 Apr 2011 00:31:35 wrote:
> >
> > Unfortunately, my CSH shell does not support the EXPORT command.
> >  Best Wishes


> >
> >
> >  Masoud
> > --------------
> > Masoud Nahali, Ph. D Student
> > Sharif University of Technology
> >
> >
> > _______________________________________________


> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum 		 	   		


> >
> 
> -- 
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
> 
> "Men don't need hand to do things"


> _______________________________________________
> 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 		 	   		  
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From ttduyle at gmail.com  Mon Apr 18 04:26:43 2011
From: ttduyle at gmail.com (Duy Le)
Date: Sun, 17 Apr 2011 22:26:43 -0400
Subject: [Pw_forum] Fortan compiler cannot create executables
In-Reply-To: <SNT114-W303E88F45CE480BE576738D3910@phx.gbl>
References: <BANLkTinb9QkrtV7FHDcREx+K2qboaUVRUQ@mail.gmail.com>
	<SNT114-W4F2F9275B14503DC1A974D3910@phx.gbl>
	<BANLkTikk7YcOvuGX59erHNua_YrYNj9owA@mail.gmail.com>
	<SNT114-W27684FA147C9C51BBB89A7D3910@phx.gbl>
	<BANLkTikEabhX6eOvu-89xuwPhfsgN=BzMA@mail.gmail.com>
	<SNT114-W303E88F45CE480BE576738D3910@phx.gbl>
Message-ID: <BANLkTi=ggo=NjNGfwBz3dpOR1GH6pmcwRQ@mail.gmail.com>

So you simply don't have a fortran compiler installed properly. Need to get
one first before compiling QE
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


On Sun, Apr 17, 2011 at 10:13 PM, Elie Moujaes
<elie.moujaes at hotmail.co.uk>wrote:

>  I am really thankful for your help. I renamed it and now it displayed :
> checking for g95.....g95 but it stopped with another error:
>
> Configure: WARNING: In the future, Auticonfig will not detect cross-tools
> whose name does not start with the host triplet. If you think this
> configuration is useful to you, please write to autoconf at gnu.org. Checking
> for Fortran compiler default output filename...Configure: error: Fortran
> compiler cannot create executables
>
>
> Elie
>
> ------------------------------
> From: ttduyle at gmail.com
> Date: Sun, 17 Apr 2011 21:23:36 -0400
>
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Fortan compiler cannot create executables
>
> Rename or make an sanple link i686-pc-linux-gnu-g95  to g95 and try. QE
> looks for g95 file, you don't have it.
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
> On Sun, Apr 17, 2011 at 9:16 PM, Elie Moujaes <elie.moujaes at hotmail.co.uk>wrote:
>
>  Dear Duy Le,
>
> Thanks for your reply. The executable is "i686-pc-linux-gnu-g95" and is in
> the bin folder in g95-install. Adding this to the path i.e :
> /exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install/bin produces the
> same error  : checking for g95...no
>
> Elie
>
> > Date: Sun, 17 Apr 2011 20:55:58 -0400
> > From: ttduyle at gmail.com
>
> > To: pw_forum at pwscf.org
> > Subject: Re: [Pw_forum] Fortan compiler cannot create executables
> >
> > You just need to identify CORRECTLY the PATH of g95 excutable, not the
> > source code PATH
> >
> > On Sunday, April 17, 2011, Elie Moujaes <elie.moujaes at hotmail.co.uk>
> wrote:
> > >
> > >
> > >
> > >
> > >
> > > Dear Masoud,
> > >
> > > I have tried setenv but it did not really work. Initially, my PATH was:
> /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/ysr/games now I used setenv and
> the new path is:
> > >
> > >
> /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install
> > >
> > > but when I ./configure again, I still get checking for g95..no....so I
> am not sure what is still going wrong
> > >
> > > ELie
> > >
> > > Date: Sun, 17 Apr 2011 09:26:17 +0430
> > > From: masoudnahali at gmail.com
> > > To: pw_forum at pwscf.org
> > > Subject: Re: [Pw_forum] Fortan compiler cannot create executables
> > >
> > >    Dear Elie
> > >
> > >   Using csh/tcsh you should try "setenv" instead of "export".
> > >
> > >
> > >
> > >
> > > Elie on Sun, 17 Apr 2011 00:31:35 wrote:
> > >
> > > Unfortunately, my CSH shell does not support the EXPORT command.
> > > Best Wishes
> > >
> > >
> > >  Masoud
> > > --------------
> > > Masoud Nahali, Ph. D Student
> > > Sharif University of Technology
> > >
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> >
> > --
> > --------------------------------------------------
> > Duy Le
> > PhD Student
> > Department of Physics
> > University of Central Florida.
> >
> > "Men don't need hand to do things"
> > _______________________________________________
> > 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
>
>
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From tanycimr at gmail.com  Mon Apr 18 04:32:08 2011
From: tanycimr at gmail.com (=?Big5?B?zuu0xqbB?=)
Date: Mon, 18 Apr 2011 10:32:08 +0800
Subject: [Pw_forum] The atomic displacements By QE and Abinit
Message-ID: <BANLkTinGofccYQGSnOEqhD+DVQixeUQ4uQ@mail.gmail.com>

Dear all

i have run the program ph.x and got the outfile  *.dyn_G. from what I
understand, the diagonalized dynamical matrix should give displacements of
each atom. and each column gives the real and imaginary components of the
displacements .so in the output

omega( 1) =      -0.294635 [THz] =      -9.828034 [cm-1]
 (  0.000006  0.000000 -0.000003  0.000000  0.288697  0.000000 )
 (  0.000000  0.000000  0.000007  0.000000  0.288697  0.000000 )
 ( -0.000006  0.000000 -0.000003  0.000000  0.288697  0.000000 )
 (  0.000010  0.000000 -0.000006  0.000000  0.288654  0.000000 )
 (  0.000000  0.000000  0.000011  0.000000  0.288654  0.000000 )
 ( -0.000010  0.000000 -0.000006  0.000000  0.288654  0.000000 )
 (  0.000006  0.000000 -0.000003  0.000000  0.288697  0.000000 )
 (  0.000000  0.000000  0.000007  0.000000  0.288697  0.000000 )
 ( -0.000006  0.000000 -0.000003  0.000000  0.288697  0.000000 )
 (  0.000010  0.000000 -0.000006  0.000000  0.288654  0.000000 )
 (  0.000000  0.000000  0.000011  0.000000  0.288654  0.000000 )
 ( -0.000010  0.000000 -0.000006  0.000000  0.288654  0.000000 )

however it is different from the the outcome of Abinit

Eigendisplacements
 (will be given, for each mode : in cartesian coordinates
   for each atom the real part of the displacement vector,
   then the imaginary part of the displacement vector)
  Mode number    1   Energy    0.000000E+00
 Attention : low frequency mode.
   (Could be unstable or acoustic mode)
;  1  0.00000000E+00  0.00000000E+00 -2.05634696E-03
;     0.00000000E+00  0.00000000E+00  0.00000000E+00
;  2  0.00000000E+00  0.00000000E+00 -2.05634695E-03
;     0.00000000E+00  0.00000000E+00  0.00000000E+00
;  3  0.00000000E+00  0.00000000E+00 -2.05634695E-03
;     0.00000000E+00  0.00000000E+00  0.00000000E+00
;  4  0.00000000E+00  0.00000000E+00 -2.05634696E-03
;     0.00000000E+00  0.00000000E+00  0.00000000E+00
;  5  0.00000000E+00  0.00000000E+00 -2.05634696E-03
;     0.00000000E+00  0.00000000E+00  0.00000000E+00
;  6  0.00000000E+00  0.00000000E+00 -2.05634696E-03
;     0.00000000E+00  0.00000000E+00  0.00000000E+00
;  7  0.00000000E+00  0.00000000E+00 -2.05634696E-03
;     0.00000000E+00  0.00000000E+00  0.00000000E+00
;  8  0.00000000E+00  0.00000000E+00 -2.05634695E-03
;     0.00000000E+00  0.00000000E+00  0.00000000E+00
;  9  0.00000000E+00  0.00000000E+00 -2.05634695E-03
;     0.00000000E+00  0.00000000E+00  0.00000000E+00
; 10  0.00000000E+00  0.00000000E+00 -2.05634696E-03
;     0.00000000E+00  0.00000000E+00  0.00000000E+00
; 11  0.00000000E+00  0.00000000E+00 -2.05634696E-03
;     0.00000000E+00  0.00000000E+00  0.00000000E+00
; 12  0.00000000E+00  0.00000000E+00 -2.05634696E-03
;     0.00000000E+00  0.00000000E+00  0.00000000E+00

how could i understand it .why the QE and Abinit give the different outcome
. i hope some help . and thanks in advance

tanyci
nankai university , tianjin
china
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From lmartinsamos at gmail.com  Mon Apr 18 08:27:19 2011
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Mon, 18 Apr 2011 08:27:19 +0200
Subject: [Pw_forum] problems with input_dft='vdW-DF' in neb.x
	calculations
In-Reply-To: <201104161454.15991.giuseppe.mattioli@mlib.ism.cnr.it>
References: <59184.141.108.248.78.1301923628.squirrel@141.108.248.78>
	<201104161454.15991.giuseppe.mattioli@mlib.ism.cnr.it>
Message-ID: <BANLkTinwgxAaETaxLMhtVF74TcjaV4C1CA@mail.gmail.com>

Dear Giuseppe, the problem allocating the object is probably related to some
"unexistent" deallocation. I'll take a look I give you a more precise
answer.

bests

Layla

2011/4/16 Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>

> Dear all
> I'm facing a strange problem when performing neb.x calculations with the
> input_dft='vdW-DF' flag.
> I've tried the very same calculation (same machine, same QE 4.3 version...)
> but for the vdW, e.g., in the case of cyclohexane isomerization (input
> files
> below). Everything is fine in the non-corrected case. On the contrary, this
> is the only standard output in the vdW case:
>
>      Program NEB v.4.3          starts on 16Apr2011 at 14:14: 6
>
>     This program is part of the open-source Quantum ESPRESSO suite
>     for quantum simulation of materials; please cite
>         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>          URL http://www.quantum-espresso.org",
>     in publications or presentations arising from this work. More details
> at
>     http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
>
>     Parallel version (MPI), running on     8 processors
>     R & G space division:  proc/pool =    8
> Warning: card   &IONS ignored
> Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
> Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
> Warning: card      ION_DYNAMICS='BFGS' ignored
> Warning: card   / ignored
>
>     XC functional enforced from input :
>     Exchange-correlation      = VDW-DF (1449)
>     EXX-fraction              =        0.00
>     !!! Any further DFT definition will be discarded
>     !!! Please, verify this is what you really want !
>
> Warning: card   &IONS ignored
> Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
> Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
> Warning: card      ION_DYNAMICS='BFGS' ignored
> Warning: card   / ignored
>
>     XC functional enforced from input :
>     Exchange-correlation      = VDW-DF (1449)
>     EXX-fraction              =        0.00
>     !!! Any further DFT definition will be discarded
>     !!! Please, verify this is what you really want !
>
> and this is the reported system error:
>
> "kernel_table.f90", line 172: 1525-108 Error encountered while attempting
> to
> allocate a data object.  The program will stop.
>
> vdW calculations run of course without problems in standard pw.x jobs.
> A look at the above file has not provided any enlightenment (at least to
> me...)
>
> A minor question: why are the following printed in the standard output
> file?
> Warning: card   &IONS ignored
> Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
> Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
> Warning: card      ION_DYNAMICS='BFGS' ignored
> Warning: card   / ignored
> I followed the run_example template in the QE/examples/example17 directory
> which contains the cards
> &IONS
>  pot_extrapolation = "second_order",
>  wfc_extrapolation = "second_order",
> /
>
> A further minor question: where can I found any documentation to set up a
> smd
> calculation using cards like:
> BEGIN_PATH_INPUT
> &PATH
>  string_method     = 'smd',
>  opt_scheme        = "langevin",
>  temp_req          = 200.0
> /
> END_PATH_INPUT
> BEGIN_ENGINE_INPUT
>
> Any comment or suggestion?
> Thank you in advance
> Giuseppe
>
> This is the one which works fine:
>
> export FILE="test"
> export INPFILE=$FILE-1.inp
> export OUTFILE=$FILE-1.out
> echo " $FILE"
> echo " $INPFILE"
> echo " $OUTFILE"
>
> cat > $INPFILE << EOF
> BEGIN
> BEGIN_PATH_INPUT
> &PATH
>  restart_mode      = 'from_scratch',
>  string_method     = 'neb',
>  nstep_path        = 200,
>  ds                = 2.D0,
>  opt_scheme        = "broyden",
>  num_of_images     = 9,
>  CI_scheme         = "no-CI",
>  path_thr          = 0.1D0,
> /
> END_PATH_INPUT
> BEGIN_ENGINE_INPUT
>  &CONTROL
>    prefix='$FILE',
>    pseudo_dir = '$PSEUDO_DIR/',
>    outdir='$TMP_DIR/',
>  /
>  &SYSTEM
>    ibrav=1, celldm(1)=20.0000
>    nat=18, ntyp=2,
>    ecutwfc = 25.0,
>    ecutrho = 200.0,
>    occupations='smearing', degauss=0.01,
>    nspin=1,
>  /
>  &ELECTRONS
>    mixing_mode='plain'
>    mixing_beta=0.2
>    conv_thr=1.0d-8
>    electron_maxstep=200
>  /
>  &IONS
>    pot_extrapolation = "second_order",
>    wfc_extrapolation = "second_order",
>    ion_dynamics='bfgs'
>  /
> ATOMIC_SPECIES
> C    12.011     C_pbe.van.UPF
> H     1.008     H_pbe.van.UPF
> BEGIN_POSITIONS
> FIRST_IMAGE
> ATOMIC_POSITIONS {angstrom}
> C        6.098316160   3.760656270   4.654408584
> C        5.535560000   5.029242896   4.000000000
> C        5.535560000   2.491939382   4.000000000
> C        4.000840929   5.027202726   4.000000000
> C        4.000950457   2.493714962   4.000000000
> C        3.441730882   3.760373055   3.339304890
> H        5.825930677   3.760664232   5.733651283
> H        7.207790908   3.760649901   4.611224167
> H        5.898266497   5.087596300   2.948897106
> H        5.921942861   5.933612152   4.514551016
> H        5.898578752   2.433310631   2.949074312
> H        5.922060506   1.587859796   4.515020902
> H        3.637454955   2.444160918   5.051149794
> H        3.611787526   1.587642834   3.490637392
> H        3.637077165   5.076985202   5.050984568
> H        3.611543166   5.933006456   3.490221051
> H        2.332375720   3.760276416   3.383439061
> H        3.714361008   3.760355870   2.259592492
> LAST_IMAGE
> ATOMIC_POSITIONS {angstrom}
> C        6.121592696   3.760535885   4.641499347
> C        5.535560000   5.025712602   4.000000000
> C        5.535560000   2.495388270   4.000000000
> C        3.977918610   5.023959085   4.000000000
> C        3.977930112   2.497154140   4.000000000
> C        3.393609861   3.760551962   4.644872629
> H        5.913189538   3.760513868   5.732562614
> H        7.227121303   3.760507977   4.543954834
> H        5.908541836   5.092099491   2.955785191
> H        5.923102018   5.926437334   4.518072829
> H        5.908479393   2.429064594   2.955753950
> H        5.923126757   1.594603868   4.517936370
> H        3.590403695   1.596442101   4.516411429
> H        3.603091688   2.435078428   2.956089377
> H        3.590454294   5.924681359   4.516455545
> H        3.603071258   5.086031218   2.956078488
> H        3.602033618   3.760529459   5.735973241
> H        2.288228742   3.760541827   4.546696293
> END_POSITIONS
> K_POINTS {gamma}
> END_ENGINE_INPUT
> END
> EOF
> $PARA_PREFIX $ESPRESSO/neb.x -inp $INPFILE >> $OUTFILE
>
> if I only add input_dft='vdW-DF' in the &SYSTEM list it does not work
> anymore.
>
> --
> ********************************************************
> - Article premier - Les hommes naissent et demeurent
> libres et ?gaux en droits. Les distinctions sociales
> ne peuvent ?tre fond?es que sur l'utilit? commune
> - Article 2 - Le but de toute association politique
> est la conservation des droits naturels et
> imprescriptibles de l'homme. Ces droits sont la libert?,
> la propri?t?, la s?ret? et la r?sistance ? l'oppression.
> ********************************************************
>
>    Giuseppe Mattioli
>    CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
>    v. Salaria Km 29,300 - C.P. 10
>    I 00015 - Monterotondo Stazione (RM)
>    Tel + 39 06 90672836 - Fax +39 06 90672316
>    E-mail: <giuseppe.mattioli at ism.cnr.it>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From dstrubbe at berkeley.edu  Mon Apr 18 08:33:27 2011
From: dstrubbe at berkeley.edu (David Strubbe)
Date: Sun, 17 Apr 2011 23:33:27 -0700
Subject: [Pw_forum] implementation of variation of occupations and Fermi
	level with perturbations
In-Reply-To: <BANLkTi=sidNdheP906hgk2LznewjBqYkFA@mail.gmail.com>
References: <BANLkTi=sidNdheP906hgk2LznewjBqYkFA@mail.gmail.com>
Message-ID: <BANLkTi=8b+528Yk+VOxLPaqFmPVZ5=mZCg@mail.gmail.com>

Hello,

I am still wondering about this question and haven't gotten any response.
Can anyone help clarify the relation between the equations in the Rev Mod
Phys paper and the code?

Thanks,
David Strubbe
UC Berkeley

On Fri, Apr 8, 2011 at 11:39 AM, David Strubbe <dstrubbe at berkeley.edu>wrote:

> Dear developers,
>
> I am trying to understand how the variation of occupations and Fermi level
> is implemented in density-functional perturbation theory for metals. In the
> Baroni, de Gironcoli, and Dal Corso Rev Mod Phys paper on DFPT, this issue
> appears in equations 68 and 75-79. I see that routine ef_shift can implement
> the result of a shift in the Fermi level as in either eq. 68 or eq. 75
> depending on the value of "flag". But for the calculation of the shift
> itself, I do not see the correspondence between what is done in the code and
> the equations in the paper. Eq. 79 refers to a quantity \Delta n_{ext} and
> an integral of the LDOS with \Delta V_{SCF} to calculate the shift in Fermi
> level. However in ef_shift it appears that the density response drhoscf is
> used instead of these quantities in the numerator, which doesn't seem like
> the same thing. Can you explain what the relation is between the calculation
> in the code and the equations in the RMP paper?
>
> Thank you,
> David Strubbe
> UC Berkeley
>
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From lmartinsamos at gmail.com  Mon Apr 18 08:58:31 2011
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Mon, 18 Apr 2011 08:58:31 +0200
Subject: [Pw_forum] bfgs patch
In-Reply-To: <BANLkTimVupKX6ANgaiP2xmPVoGjNST9s6w@mail.gmail.com>
References: <BANLkTimVupKX6ANgaiP2xmPVoGjNST9s6w@mail.gmail.com>
Message-ID: <BANLkTi=B5=YhTGOumMu2zs0dHYCqC9QNqA@mail.gmail.com>

Dear Prof Marks, your patch has been commited few days ago.

thank you very much for contributing to the QUANTUM ESPRESSO project.

bests regards

Layla
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From lmartinsamos at gmail.com  Mon Apr 18 09:04:59 2011
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Mon, 18 Apr 2011 09:04:59 +0200
Subject: [Pw_forum] problems with input_dft='vdW-DF' in neb.x
	calculations
In-Reply-To: <BANLkTinwgxAaETaxLMhtVF74TcjaV4C1CA@mail.gmail.com>
References: <59184.141.108.248.78.1301923628.squirrel@141.108.248.78>
	<201104161454.15991.giuseppe.mattioli@mlib.ism.cnr.it>
	<BANLkTinwgxAaETaxLMhtVF74TcjaV4C1CA@mail.gmail.com>
Message-ID: <BANLkTin6=Cf6ORgtwG8iBtdseEx7s7_uGQ@mail.gmail.com>

In kernel table I change at line 172
allocate(...) with if(.not. allocated) allocate

    if(.not.allocated(q_mesh)) allocate( q_mesh(Nqs) )
    if(.not.allocated(kernel)) allocate( kernel(0:Nr_points,Nqs,Nqs))
    if(.not.allocated(d2phi_dk2)) allocate(d2phi_dk2(0:Nr_points,Nqs,Nqs) )

you can download the svn version of the routines or change it by hand.

(neb calls n_input_image times the read input routines of pwscf, so it was
trying to allocate an object that was already allocated).


bests

Layla


2011/4/18 Layla Martin-Samos <lmartinsamos at gmail.com>

> Dear Giuseppe, the problem allocating the object is probably related to
> some "unexistent" deallocation. I'll take a look I give you a more precise
> answer.
>
> bests
>
> Layla
>
>
> 2011/4/16 Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>
>
>> Dear all
>> I'm facing a strange problem when performing neb.x calculations with the
>> input_dft='vdW-DF' flag.
>> I've tried the very same calculation (same machine, same QE 4.3
>> version...)
>> but for the vdW, e.g., in the case of cyclohexane isomerization (input
>> files
>> below). Everything is fine in the non-corrected case. On the contrary,
>> this
>> is the only standard output in the vdW case:
>>
>>      Program NEB v.4.3          starts on 16Apr2011 at 14:14: 6
>>
>>     This program is part of the open-source Quantum ESPRESSO suite
>>     for quantum simulation of materials; please cite
>>         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>>          URL http://www.quantum-espresso.org",
>>     in publications or presentations arising from this work. More details
>> at
>>
>> http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
>>
>>     Parallel version (MPI), running on     8 processors
>>     R & G space division:  proc/pool =    8
>> Warning: card   &IONS ignored
>> Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
>> Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
>> Warning: card      ION_DYNAMICS='BFGS' ignored
>> Warning: card   / ignored
>>
>>     XC functional enforced from input :
>>     Exchange-correlation      = VDW-DF (1449)
>>     EXX-fraction              =        0.00
>>     !!! Any further DFT definition will be discarded
>>     !!! Please, verify this is what you really want !
>>
>> Warning: card   &IONS ignored
>> Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
>> Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
>> Warning: card      ION_DYNAMICS='BFGS' ignored
>> Warning: card   / ignored
>>
>>     XC functional enforced from input :
>>     Exchange-correlation      = VDW-DF (1449)
>>     EXX-fraction              =        0.00
>>     !!! Any further DFT definition will be discarded
>>     !!! Please, verify this is what you really want !
>>
>> and this is the reported system error:
>>
>> "kernel_table.f90", line 172: 1525-108 Error encountered while attempting
>> to
>> allocate a data object.  The program will stop.
>>
>> vdW calculations run of course without problems in standard pw.x jobs.
>> A look at the above file has not provided any enlightenment (at least to
>> me...)
>>
>> A minor question: why are the following printed in the standard output
>> file?
>> Warning: card   &IONS ignored
>> Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
>> Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
>> Warning: card      ION_DYNAMICS='BFGS' ignored
>> Warning: card   / ignored
>> I followed the run_example template in the QE/examples/example17 directory
>> which contains the cards
>> &IONS
>>  pot_extrapolation = "second_order",
>>  wfc_extrapolation = "second_order",
>> /
>>
>> A further minor question: where can I found any documentation to set up a
>> smd
>> calculation using cards like:
>> BEGIN_PATH_INPUT
>> &PATH
>>  string_method     = 'smd',
>>  opt_scheme        = "langevin",
>>  temp_req          = 200.0
>> /
>> END_PATH_INPUT
>> BEGIN_ENGINE_INPUT
>>
>> Any comment or suggestion?
>> Thank you in advance
>> Giuseppe
>>
>> This is the one which works fine:
>>
>> export FILE="test"
>> export INPFILE=$FILE-1.inp
>> export OUTFILE=$FILE-1.out
>> echo " $FILE"
>> echo " $INPFILE"
>> echo " $OUTFILE"
>>
>> cat > $INPFILE << EOF
>> BEGIN
>> BEGIN_PATH_INPUT
>> &PATH
>>  restart_mode      = 'from_scratch',
>>  string_method     = 'neb',
>>  nstep_path        = 200,
>>  ds                = 2.D0,
>>  opt_scheme        = "broyden",
>>  num_of_images     = 9,
>>  CI_scheme         = "no-CI",
>>  path_thr          = 0.1D0,
>> /
>> END_PATH_INPUT
>> BEGIN_ENGINE_INPUT
>>  &CONTROL
>>    prefix='$FILE',
>>    pseudo_dir = '$PSEUDO_DIR/',
>>    outdir='$TMP_DIR/',
>>  /
>>  &SYSTEM
>>    ibrav=1, celldm(1)=20.0000
>>    nat=18, ntyp=2,
>>    ecutwfc = 25.0,
>>    ecutrho = 200.0,
>>    occupations='smearing', degauss=0.01,
>>    nspin=1,
>>  /
>>  &ELECTRONS
>>    mixing_mode='plain'
>>    mixing_beta=0.2
>>    conv_thr=1.0d-8
>>    electron_maxstep=200
>>  /
>>  &IONS
>>    pot_extrapolation = "second_order",
>>    wfc_extrapolation = "second_order",
>>    ion_dynamics='bfgs'
>>  /
>> ATOMIC_SPECIES
>> C    12.011     C_pbe.van.UPF
>> H     1.008     H_pbe.van.UPF
>> BEGIN_POSITIONS
>> FIRST_IMAGE
>> ATOMIC_POSITIONS {angstrom}
>> C        6.098316160   3.760656270   4.654408584
>> C        5.535560000   5.029242896   4.000000000
>> C        5.535560000   2.491939382   4.000000000
>> C        4.000840929   5.027202726   4.000000000
>> C        4.000950457   2.493714962   4.000000000
>> C        3.441730882   3.760373055   3.339304890
>> H        5.825930677   3.760664232   5.733651283
>> H        7.207790908   3.760649901   4.611224167
>> H        5.898266497   5.087596300   2.948897106
>> H        5.921942861   5.933612152   4.514551016
>> H        5.898578752   2.433310631   2.949074312
>> H        5.922060506   1.587859796   4.515020902
>> H        3.637454955   2.444160918   5.051149794
>> H        3.611787526   1.587642834   3.490637392
>> H        3.637077165   5.076985202   5.050984568
>> H        3.611543166   5.933006456   3.490221051
>> H        2.332375720   3.760276416   3.383439061
>> H        3.714361008   3.760355870   2.259592492
>> LAST_IMAGE
>> ATOMIC_POSITIONS {angstrom}
>> C        6.121592696   3.760535885   4.641499347
>> C        5.535560000   5.025712602   4.000000000
>> C        5.535560000   2.495388270   4.000000000
>> C        3.977918610   5.023959085   4.000000000
>> C        3.977930112   2.497154140   4.000000000
>> C        3.393609861   3.760551962   4.644872629
>> H        5.913189538   3.760513868   5.732562614
>> H        7.227121303   3.760507977   4.543954834
>> H        5.908541836   5.092099491   2.955785191
>> H        5.923102018   5.926437334   4.518072829
>> H        5.908479393   2.429064594   2.955753950
>> H        5.923126757   1.594603868   4.517936370
>> H        3.590403695   1.596442101   4.516411429
>> H        3.603091688   2.435078428   2.956089377
>> H        3.590454294   5.924681359   4.516455545
>> H        3.603071258   5.086031218   2.956078488
>> H        3.602033618   3.760529459   5.735973241
>> H        2.288228742   3.760541827   4.546696293
>> END_POSITIONS
>> K_POINTS {gamma}
>> END_ENGINE_INPUT
>> END
>> EOF
>> $PARA_PREFIX $ESPRESSO/neb.x -inp $INPFILE >> $OUTFILE
>>
>> if I only add input_dft='vdW-DF' in the &SYSTEM list it does not work
>> anymore.
>>
>> --
>> ********************************************************
>> - Article premier - Les hommes naissent et demeurent
>> libres et ?gaux en droits. Les distinctions sociales
>> ne peuvent ?tre fond?es que sur l'utilit? commune
>> - Article 2 - Le but de toute association politique
>> est la conservation des droits naturels et
>> imprescriptibles de l'homme. Ces droits sont la libert?,
>> la propri?t?, la s?ret? et la r?sistance ? l'oppression.
>> ********************************************************
>>
>>    Giuseppe Mattioli
>>    CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
>>    v. Salaria Km 29,300 - C.P. 10
>>    I 00015 - Monterotondo Stazione (RM)
>>    Tel + 39 06 90672836 - Fax +39 06 90672316
>>    E-mail: <giuseppe.mattioli at ism.cnr.it>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
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From yuminqian at gmail.com  Mon Apr 18 10:21:18 2011
From: yuminqian at gmail.com (yumin qian)
Date: Mon, 18 Apr 2011 16:21:18 +0800
Subject: [Pw_forum] Prolems with tetrahedra method
Message-ID: <BANLkTikNO8eiukqDLTpaNwH8mgP522FnhQ@mail.gmail.com>

Dear PWscf user
        I met several prolems for the calculation of Projected density of
state and Ferim surface, for the first step of scf calcualtion I use the
tetrahedra method,
  then

1>I can not calculated projected density of state (PDOS) with projwfc.x .
      It always the same error :

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from projwfc : error #       239
     reading inputpp namelist
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...


  2>     When I use the kvecs_FS.x to generate the k-points for the nscf
calculation, the output return :

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from tetrahedra : error #         1
     cannot remap grid on k-point list
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...

    I find that not all of the generated k-points are within the first
Brillouin zone,  is there any one tell me what is the problem?

3>  I contiune my nscf calcualtion with  tetrahedra method to plot the band
structure along high symmetry lines but there is not prolem, I check all the
k-point are within
    first Brillouin zone.


another quesiton, I think that tetrahedra method can not be used in every
case in PWSCF, except for the force calculation that tetrahedra method may
cause prolems, who can tell me, where we can not use tetrahedra method

 Thank you


-- 
Best Regards
Sincerely Y. M. Qian (???)
Laboratory of Condensed Matter Theory and Materials Computation
Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
Tel:        + 8610 8264 9827
E-Mail:    yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From giuseppe.mattioli at mlib.ism.cnr.it  Mon Apr 18 10:52:59 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Mon, 18 Apr 2011 10:52:59 +0200
Subject: [Pw_forum] problems with input_dft='vdW-DF' in neb.x
	calculations
In-Reply-To: <BANLkTin6=Cf6ORgtwG8iBtdseEx7s7_uGQ@mail.gmail.com>
References: <59184.141.108.248.78.1301923628.squirrel@141.108.248.78>
	<BANLkTinwgxAaETaxLMhtVF74TcjaV4C1CA@mail.gmail.com>
	<BANLkTin6=Cf6ORgtwG8iBtdseEx7s7_uGQ@mail.gmail.com>
Message-ID: <201104181052.59838.giuseppe.mattioli@mlib.ism.cnr.it>


Dear Layla
Thank you!
It works fine.
Giuseppe

On Monday 18 April 2011 09:04:59 Layla Martin-Samos wrote:
> In kernel table I change at line 172
> allocate(...) with if(.not. allocated) allocate
>
>     if(.not.allocated(q_mesh)) allocate( q_mesh(Nqs) )
>     if(.not.allocated(kernel)) allocate( kernel(0:Nr_points,Nqs,Nqs))
>     if(.not.allocated(d2phi_dk2)) allocate(d2phi_dk2(0:Nr_points,Nqs,Nqs) )
>
> you can download the svn version of the routines or change it by hand.
>
> (neb calls n_input_image times the read input routines of pwscf, so it was
> trying to allocate an object that was already allocated).
>
>
> bests
>
> Layla
>
>
> 2011/4/18 Layla Martin-Samos <lmartinsamos at gmail.com>
>
> > Dear Giuseppe, the problem allocating the object is probably related to
> > some "unexistent" deallocation. I'll take a look I give you a more
> > precise answer.
> >
> > bests
> >
> > Layla
> >
> >
> > 2011/4/16 Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>
> >
> >> Dear all
> >> I'm facing a strange problem when performing neb.x calculations with the
> >> input_dft='vdW-DF' flag.
> >> I've tried the very same calculation (same machine, same QE 4.3
> >> version...)
> >> but for the vdW, e.g., in the case of cyclohexane isomerization (input
> >> files
> >> below). Everything is fine in the non-corrected case. On the contrary,
> >> this
> >> is the only standard output in the vdW case:
> >>
> >>      Program NEB v.4.3          starts on 16Apr2011 at 14:14: 6
> >>
> >>     This program is part of the open-source Quantum ESPRESSO suite
> >>     for quantum simulation of materials; please cite
> >>         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
> >>          URL http://www.quantum-espresso.org",
> >>     in publications or presentations arising from this work. More
> >> details at
> >>
> >> http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
> >>
> >>     Parallel version (MPI), running on     8 processors
> >>     R & G space division:  proc/pool =    8
> >> Warning: card   &IONS ignored
> >> Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
> >> Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
> >> Warning: card      ION_DYNAMICS='BFGS' ignored
> >> Warning: card   / ignored
> >>
> >>     XC functional enforced from input :
> >>     Exchange-correlation      = VDW-DF (1449)
> >>     EXX-fraction              =        0.00
> >>     !!! Any further DFT definition will be discarded
> >>     !!! Please, verify this is what you really want !
> >>
> >> Warning: card   &IONS ignored
> >> Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
> >> Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
> >> Warning: card      ION_DYNAMICS='BFGS' ignored
> >> Warning: card   / ignored
> >>
> >>     XC functional enforced from input :
> >>     Exchange-correlation      = VDW-DF (1449)
> >>     EXX-fraction              =        0.00
> >>     !!! Any further DFT definition will be discarded
> >>     !!! Please, verify this is what you really want !
> >>
> >> and this is the reported system error:
> >>
> >> "kernel_table.f90", line 172: 1525-108 Error encountered while
> >> attempting to
> >> allocate a data object.  The program will stop.
> >>
> >> vdW calculations run of course without problems in standard pw.x jobs.
> >> A look at the above file has not provided any enlightenment (at least to
> >> me...)
> >>
> >> A minor question: why are the following printed in the standard output
> >> file?
> >> Warning: card   &IONS ignored
> >> Warning: card      POT_EXTRAPOLATION = "SECOND_ORDER", ignored
> >> Warning: card      WFC_EXTRAPOLATION = "SECOND_ORDER", ignored
> >> Warning: card      ION_DYNAMICS='BFGS' ignored
> >> Warning: card   / ignored
> >> I followed the run_example template in the QE/examples/example17
> >> directory which contains the cards
> >> &IONS
> >>  pot_extrapolation = "second_order",
> >>  wfc_extrapolation = "second_order",
> >> /
> >>
> >> A further minor question: where can I found any documentation to set up
> >> a smd
> >> calculation using cards like:
> >> BEGIN_PATH_INPUT
> >> &PATH
> >>  string_method     = 'smd',
> >>  opt_scheme        = "langevin",
> >>  temp_req          = 200.0
> >> /
> >> END_PATH_INPUT
> >> BEGIN_ENGINE_INPUT
> >>
> >> Any comment or suggestion?
> >> Thank you in advance
> >> Giuseppe
> >>
> >> This is the one which works fine:
> >>
> >> export FILE="test"
> >> export INPFILE=$FILE-1.inp
> >> export OUTFILE=$FILE-1.out
> >> echo " $FILE"
> >> echo " $INPFILE"
> >> echo " $OUTFILE"
> >>
> >> cat > $INPFILE << EOF
> >> BEGIN
> >> BEGIN_PATH_INPUT
> >> &PATH
> >>  restart_mode      = 'from_scratch',
> >>  string_method     = 'neb',
> >>  nstep_path        = 200,
> >>  ds                = 2.D0,
> >>  opt_scheme        = "broyden",
> >>  num_of_images     = 9,
> >>  CI_scheme         = "no-CI",
> >>  path_thr          = 0.1D0,
> >> /
> >> END_PATH_INPUT
> >> BEGIN_ENGINE_INPUT
> >>  &CONTROL
> >>    prefix='$FILE',
> >>    pseudo_dir = '$PSEUDO_DIR/',
> >>    outdir='$TMP_DIR/',
> >>  /
> >>  &SYSTEM
> >>    ibrav=1, celldm(1)=20.0000
> >>    nat=18, ntyp=2,
> >>    ecutwfc = 25.0,
> >>    ecutrho = 200.0,
> >>    occupations='smearing', degauss=0.01,
> >>    nspin=1,
> >>  /
> >>  &ELECTRONS
> >>    mixing_mode='plain'
> >>    mixing_beta=0.2
> >>    conv_thr=1.0d-8
> >>    electron_maxstep=200
> >>  /
> >>  &IONS
> >>    pot_extrapolation = "second_order",
> >>    wfc_extrapolation = "second_order",
> >>    ion_dynamics='bfgs'
> >>  /
> >> ATOMIC_SPECIES
> >> C    12.011     C_pbe.van.UPF
> >> H     1.008     H_pbe.van.UPF
> >> BEGIN_POSITIONS
> >> FIRST_IMAGE
> >> ATOMIC_POSITIONS {angstrom}
> >> C        6.098316160   3.760656270   4.654408584
> >> C        5.535560000   5.029242896   4.000000000
> >> C        5.535560000   2.491939382   4.000000000
> >> C        4.000840929   5.027202726   4.000000000
> >> C        4.000950457   2.493714962   4.000000000
> >> C        3.441730882   3.760373055   3.339304890
> >> H        5.825930677   3.760664232   5.733651283
> >> H        7.207790908   3.760649901   4.611224167
> >> H        5.898266497   5.087596300   2.948897106
> >> H        5.921942861   5.933612152   4.514551016
> >> H        5.898578752   2.433310631   2.949074312
> >> H        5.922060506   1.587859796   4.515020902
> >> H        3.637454955   2.444160918   5.051149794
> >> H        3.611787526   1.587642834   3.490637392
> >> H        3.637077165   5.076985202   5.050984568
> >> H        3.611543166   5.933006456   3.490221051
> >> H        2.332375720   3.760276416   3.383439061
> >> H        3.714361008   3.760355870   2.259592492
> >> LAST_IMAGE
> >> ATOMIC_POSITIONS {angstrom}
> >> C        6.121592696   3.760535885   4.641499347
> >> C        5.535560000   5.025712602   4.000000000
> >> C        5.535560000   2.495388270   4.000000000
> >> C        3.977918610   5.023959085   4.000000000
> >> C        3.977930112   2.497154140   4.000000000
> >> C        3.393609861   3.760551962   4.644872629
> >> H        5.913189538   3.760513868   5.732562614
> >> H        7.227121303   3.760507977   4.543954834
> >> H        5.908541836   5.092099491   2.955785191
> >> H        5.923102018   5.926437334   4.518072829
> >> H        5.908479393   2.429064594   2.955753950
> >> H        5.923126757   1.594603868   4.517936370
> >> H        3.590403695   1.596442101   4.516411429
> >> H        3.603091688   2.435078428   2.956089377
> >> H        3.590454294   5.924681359   4.516455545
> >> H        3.603071258   5.086031218   2.956078488
> >> H        3.602033618   3.760529459   5.735973241
> >> H        2.288228742   3.760541827   4.546696293
> >> END_POSITIONS
> >> K_POINTS {gamma}
> >> END_ENGINE_INPUT
> >> END
> >> EOF
> >> $PARA_PREFIX $ESPRESSO/neb.x -inp $INPFILE >> $OUTFILE
> >>
> >> if I only add input_dft='vdW-DF' in the &SYSTEM list it does not work
> >> anymore.
> >>
> >> --
> >> ********************************************************
> >> - Article premier - Les hommes naissent et demeurent
> >> libres et ?gaux en droits. Les distinctions sociales
> >> ne peuvent ?tre fond?es que sur l'utilit? commune
> >> - Article 2 - Le but de toute association politique
> >> est la conservation des droits naturels et
> >> imprescriptibles de l'homme. Ces droits sont la libert?,
> >> la propri?t?, la s?ret? et la r?sistance ? l'oppression.
> >> ********************************************************
> >>
> >>    Giuseppe Mattioli
> >>    CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> >>    v. Salaria Km 29,300 - C.P. 10
> >>    I 00015 - Monterotondo Stazione (RM)
> >>    Tel + 39 06 90672836 - Fax +39 06 90672316
> >>    E-mail: <giuseppe.mattioli at ism.cnr.it>
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum



-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? 
? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ?
? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ?
? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ?
? ?E-mail: <giuseppe.mattioli at ism.cnr.it>

From psavita at crlindia.com  Mon Apr 18 11:09:40 2011
From: psavita at crlindia.com (psavita at crlindia.com)
Date: Mon, 18 Apr 2011 14:39:40 +0530
Subject: [Pw_forum] NEB calculation
Message-ID: <OF5B77E36D.27D1B059-ON65257876.003252EA-65257876.003252EC@crlindia.com>

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From lmartinsamos at gmail.com  Mon Apr 18 11:39:38 2011
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Mon, 18 Apr 2011 11:39:38 +0200
Subject: [Pw_forum] NEB calculation
In-Reply-To: <OF5B77E36D.27D1B059-ON65257876.003252EA-65257876.003252EC@crlindia.com>
References: <OF5B77E36D.27D1B059-ON65257876.003252EA-65257876.003252EC@crlindia.com>
Message-ID: <BANLkTikr2d50+mifqeoquMt68CyPKT=h-w@mail.gmail.com>

Dear Savita, when there is no idea about the atomic configuration of
intermediate minima, it is usually more convenient to divide your problem in
two steps or more, because NEB converge better if the MEP contains only one
main single barrier, for instance:

1) formation of CO2 (maybe this should be divided in more steps)
2) CO2 desorption

bests regards

Layla

2011/4/18 <psavita at crlindia.com>

> Hello,
>
> I am performing NEB calculation wherein first image has CO and O adsorbed
> at the atop and fcc sites respectively
> on 3 layer Pt(111). The last image is a linear CO2 about 10 bohr away from
> the slab, a vacuum layer of 40 bohr is used
> above the slab. This is turning into quite a compute intensive task, there
> is no sign of convergence even after 20
> NEB iterations, the residual forces are still quite large. I have a total
> of 5 images and there is no CI.
>
> Is this no. of images proper?
> Which other factors do I need to control better to get meaningful results?
>
> Thank you in advance,
>
> Sincerely,
>
> Savita Pundlik
> Computational Materials Applied Research Group
> Computational Research Laboratories Ltd.,
> Taco House, Damle Path, Off Law College Road
> Pune - 411004, India.
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From prasenjit.jnc at gmail.com  Mon Apr 18 11:52:00 2011
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Mon, 18 Apr 2011 15:22:00 +0530
Subject: [Pw_forum] NEB calculation
In-Reply-To: <BANLkTikr2d50+mifqeoquMt68CyPKT=h-w@mail.gmail.com>
References: <OF5B77E36D.27D1B059-ON65257876.003252EA-65257876.003252EC@crlindia.com>
	<BANLkTikr2d50+mifqeoquMt68CyPKT=h-w@mail.gmail.com>
Message-ID: <BANLkTimYCwsjmCtoe3GTb-sMd1w2pzPcng@mail.gmail.com>

Dear Savita,

In addition to what Layla has said, I think 40 bohrs vacuum is too
large.....until & unless you have evidence that you really need 40 bohrs, I
would suggest you to reduce the vacuum to about 25 bohr.

Also try to post your input file......without that it is difficult to
provide any suggestions.

Prasenjit.

On 18 April 2011 15:09, Layla Martin-Samos <lmartinsamos at gmail.com> wrote:

> Dear Savita, when there is no idea about the atomic configuration of
> intermediate minima, it is usually more convenient to divide your problem in
> two steps or more, because NEB converge better if the MEP contains only one
> main single barrier, for instance:
>
> 1) formation of CO2 (maybe this should be divided in more steps)
> 2) CO2 desorption
>
> bests regards
>
> Layla
>
> 2011/4/18 <psavita at crlindia.com>
>
>> Hello,
>>
>> I am performing NEB calculation wherein first image has CO and O adsorbed
>> at the atop and fcc sites respectively
>> on 3 layer Pt(111). The last image is a linear CO2 about 10 bohr away from
>> the slab, a vacuum layer of 40 bohr is used
>> above the slab. This is turning into quite a compute intensive task, there
>> is no sign of convergence even after 20
>> NEB iterations, the residual forces are still quite large. I have a total
>> of 5 images and there is no CI.
>>
>> Is this no. of images proper?
>> Which other factors do I need to control better to get meaningful results?
>>
>> Thank you in advance,
>>
>> Sincerely,
>>
>> Savita Pundlik
>> Computational Materials Applied Research Group
>> Computational Research Laboratories Ltd.,
>> Taco House, Damle Path, Off Law College Road
>> Pune - 411004, India.
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
PRASENJIT GHOSH,
Assistant Professor,
IISER Pune,
First floor, Central Tower, Sai Trinity Building
Garware Circle, Sutarwadi, Pashan
Pune, Maharashtra 411021, India

Phone: +91 (20) 2590 8203
Fax: +91 (20) 2589 9790
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From eyvaz_isaev at yahoo.com  Mon Apr 18 11:58:58 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 18 Apr 2011 02:58:58 -0700 (PDT)
Subject: [Pw_forum] Prolems with tetrahedra method
In-Reply-To: <BANLkTikNO8eiukqDLTpaNwH8mgP522FnhQ@mail.gmail.com>
References: <BANLkTikNO8eiukqDLTpaNwH8mgP522FnhQ@mail.gmail.com>
Message-ID: <939618.53698.qm@web65711.mail.ac4.yahoo.com>

Hi,

 


________________________________
From: yumin qian <yuminqian at gmail.com>
 
1>I can not calculated projected density of state (PDOS) with projwfc.x .

>     from projwfc : error #       239
>    reading inputpp namelist

Something is wrong in your inputpp file. Please check it carefully. In PDOS 
calculations tetrahedra is not implemented/allowed.


2>    When I use the kvecs_FS.x to generate the k-points for the nscf 
calculation, the output return :
         
>     from tetrahedra : error #         1
>     cannot remap grid on k-point list 

I can not understand this, because kvecs_FS is not related  with any program, in 
particular,  to tetrahedra, who complains.


>I find that not all of the generated k-points are within the first Brillouin 
>zone,  is there any one tell >me what is the problem?
  
These k-vectors are distributed over the full BZ, not  only in the first BZ.


>another quesiton, I think that tetrahedra method can not be used in every case 
>in PWSCF, except >for the force calculation that tetrahedra method may cause 
>prolems, who can tell me, where we >can not use tetrahedra method
 
For example, to calculate electron-phonon coupling coefficient, for isolated 
systems, etc., etc., 


Bests,
Eyvaz.

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

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

isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
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From virginie.trinite at thalesgroup.com  Mon Apr 18 12:17:48 2011
From: virginie.trinite at thalesgroup.com (TRINITE Virginie)
Date: Mon, 18 Apr 2011 12:17:48 +0200
Subject: [Pw_forum] questions about PWCOND
Message-ID: <29121_1303121870_4DAC0FCE_29121_220_1_908CBC9017354841B2F32BBEC70A05A101C154717C33@THSONEA01CMS01P.one.grp>

Dear all,
I try to use PWCOND, and I have two questions:
>In which units are the boundary in the input file (bdl, bds, bdr)?

>I have run the two examples 12 and 22 without problem and found results in agreement with the publications but when
I try a more heavy system, I obtain zero conductance.
The example that I have used, is the Magnetic Tunnel Junction given in Alexandre Smogounov's home page.
The program finished normally without error or complain but all the transmission are nearly zero.
I didn't check any convergence, because I want only to test the program. Did I miss something?


Dr Virginie Trinite
---------------------------------------
Modeling Infra-Red Lasers and Detectors
III-V Lab THALES Research&  Technology, France

Campus Polytechnique
1, avenue Augustin Fresnel 91767 Palaiseau cedex France
Phone : +33 (0)1.69.41.58.20


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From yuminqian at gmail.com  Mon Apr 18 12:32:01 2011
From: yuminqian at gmail.com (yumin qian)
Date: Mon, 18 Apr 2011 18:32:01 +0800
Subject: [Pw_forum] Prolems with tetrahedra method
In-Reply-To: <939618.53698.qm@web65711.mail.ac4.yahoo.com>
References: <BANLkTikNO8eiukqDLTpaNwH8mgP522FnhQ@mail.gmail.com>
	<939618.53698.qm@web65711.mail.ac4.yahoo.com>
Message-ID: <BANLkTikwDoY4CvzKjOHG6=i_4xpcEm=Rfw@mail.gmail.com>

Dear   Eyvaz Isaev
         Thank you for your reply, it is very kind of you,
 2>    When I use the kvecs_FS.x to generate the k-points for the nscf
calculation, the output return :

>     from tetrahedra : error #         1
>     cannot remap grid on k-point list

I can not understand this, because kvecs_FS is not related  with any
program, in particular,  to tetrahedra, who complains.


what I mean is when I use the kvec_FS.x to generate the k-points and add the
k-points to the the input file for the nscf calculation
 I run the pw.x  the output give

>     from tetrahedra : error #         1
>     cannot remap grid on k-point list

For example, to calculate electron-phonon coupling coefficient, for isolated
systems, etc., etc.,

There are so many case that you can't use tetrahedra method, or can you tell
me for which case that the tetrehedra method can be used safely?.

Thank you.


2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>

>  Hi,
>
>  ------------------------------
> *From:* yumin qian <yuminqian at gmail.com>
> * *
> 1>I can not calculated projected density of state (PDOS) with projwfc.x .
>
>  >     from projwfc : error #       239
> >    reading inputpp namelist
>
> Something is wrong in your inputpp file. Please check it carefully. In PDOS
> calculations tetrahedra is not implemented/allowed.
>
>  2>    When I use the kvecs_FS.x to generate the k-points for the nscf
> calculation, the output return :
>
> >     from tetrahedra : error #         1
> >     cannot remap grid on k-point list
>
> I can not understand this, because kvecs_FS is not related  with any
> program, in particular,  to tetrahedra, who complains.
>
>  >I find that not all of the generated k-points are within the first
> Brillouin zone,  is there any one tell >me what is the problem?
>
> These k-vectors are distributed over the full BZ, not  only in the first
> BZ.
>
>  >another quesiton, I think that tetrahedra method can not be used in
> every case in PWSCF, except >for the force calculation that tetrahedra
> method may cause prolems, who can tell me, where we >can not use tetrahedra
> method
>
> For example, to calculate electron-phonon coupling coefficient, for
> isolated systems, etc., etc.,
>
> Bests,
> Eyvaz.
>  -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
> Sweden
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
> Russia,
> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Best Regards
Sincerely Y. M. Qian (???)
Laboratory of Condensed Matter Theory and Materials Computation
Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
Tel:        + 8610 8264 9827
E-Mail:    yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From psavita at crlindia.com  Mon Apr 18 12:50:06 2011
From: psavita at crlindia.com (psavita at crlindia.com)
Date: Mon, 18 Apr 2011 16:20:06 +0530
Subject: [Pw_forum] NEB calculation
In-Reply-To: <mailman.11495.1303120324.1814.pw_forum@pwscf.org>
References: <mailman.11495.1303120324.1814.pw_forum@pwscf.org>
Message-ID: <OFE0AA335B.449E1A9C-ON65257876.003B84E8-65257876.003B84EA@crlindia.com>

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From lmartinsamos at gmail.com  Mon Apr 18 13:13:46 2011
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Mon, 18 Apr 2011 13:13:46 +0200
Subject: [Pw_forum] NEB calculation
In-Reply-To: <OFE0AA335B.449E1A9C-ON65257876.003B84E8-65257876.003B84EA@crlindia.com>
References: <mailman.11495.1303120324.1814.pw_forum@pwscf.org>
	<OFE0AA335B.449E1A9C-ON65257876.003B84E8-65257876.003B84EA@crlindia.com>
Message-ID: <BANLkTikYA-WyTFv2+SoBX4Sw5SmCwzB=4w@mail.gmail.com>

Dear Savita, atention the NEB input has changed in version 4.3. There is an
independent executable that parses a file, see example17. For identifying
the last image configuration, maybe you should make a simple relaxation of
CO at a fcc site and O very close to CO. Then you can start a NEB
calculation with  first image as CO and O at two near fcc sites and the last
image as the relaxed configuration obtained from the previous relaxation.

cheers

Layla

2011/4/18 <psavita at crlindia.com>

> Dear Layla and Prasenjeet,
>
> I think I should take Layla's suggestion and first consider CO2 formation.
> But then can I assume that O moves towards CO and CO2 forms at atop?
> Also as per Prasenjeet's advice, I should reduce vacuum layer to 25 bohr.
> I am giving here my input file for you to comment more.
> Thank you so much.
>
>
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> &CONTROL
>   calculation = 'neb',
>   restart_mode = 'from_scratch'
>   prefix='pt_co',
>   pseudo_dir  =
> "/home/nano/sivaram/simulation_zone/dft_simulation/year_2011_work/NEB",
>   outdir      =
> "/home/nano/sivaram/simulation_zone/dft_simulation/year_2011_work/NEB/relax",
> !  nstep       = 50,
> /
> &SYSTEM
>   ibrav       = 0,
>   nat         = 15,
>   ntyp        = 3,
>   ecutwfc     = 60.00,
>   ecutrho     = 360.00,
>   occupations = "smearing",
>   smearing    = "mp",
>   degauss     = 0.014699,
>   nspin       = 2,
>   starting_magnetization = 0.5
> /
> &ELECTRONS
>   electron_maxstep = 100,
>   conv_thr    = 1.D-7,
>   mixing_beta = 0.2,
>   diagonalization = 'cg'
> /
> &IONS
>   ds                = 2.0d0,
>   opt_scheme        = "broyden",
>   num_of_images     = 5,
>   k_max             = 0.4,
>   k_min             = 0.3,
>   CI_scheme         = "no-CI"
>   pot_extrapolation = "second_order",
>   wfc_extrapolation = "second_order",
>   path_thr          = 0.1d0
> /
> CELL_PARAMETERS
> 10.476 0 0
> 0  9.0727 0
> 0 0 40.215
> ATOMIC_SPECIES
> Pt  195.08  Pt.pw91-n-van.UPF
> O   15.999  O.pw91-van_ak.UPF
> C   12.011  C.pw91-van_ak.UPF
> ATOMIC_POSITIONS {bohr}
> first_image
> Pt       0.000000000   0.000000000   0.000000000
> Pt       5.238100000   0.000000000   0.000000000
> Pt       2.619050000   4.536328000   0.000000000
> Pt       7.857150000   4.536328000   0.000000000
> Pt       2.619088571   1.512240622   4.513968243
> Pt       7.857077843   1.512255365   4.514105935
> Pt       5.238032011   6.048542598   4.513881620
> Pt      10.476075613   6.048536230   4.513989805
> Pt       0.000134895   3.029013846   9.028523678
> Pt       5.238095443   3.029034864   9.028457281
> Pt       2.619088295   7.565397431   9.028126889
> Pt       7.857080929   7.565358308   9.028145500
> C       7.857080929   7.565358308    11.5281455
> O       7.857080929   7.565358308    13.7013455
> O       2.619050000   4.536328000    11.5281455
> last_image
> Pt       0.000000000   0.000000000   0.000000000
> Pt       5.238100000   0.000000000   0.000000000
> Pt       2.619050000   4.536328000   0.000000000
> Pt       7.857150000   4.536328000   0.000000000
> Pt       2.619088571   1.512240622   4.513968243
> Pt       7.857077843   1.512255365   4.514105935
> Pt       5.238032011   6.048542598   4.513881620
> Pt      10.476075613   6.048536230   4.513989805
> Pt       0.000134895   3.029013846   9.028523678
> Pt       5.238095443   3.029034864   9.028457281
> Pt       2.619088295   7.565397431   9.028126889
> Pt       7.857080929   7.565358308   9.028145500
> C        3.9286        5.2972       20.000
> O        3.9286        3.1240       20.0
> O        3.9286        7.4704       20.0
> K_POINTS {automatic}
>  6 6 3 0 0 0
>
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>
> Savita Pundlik
> Computational Materials Applied Research Group
> Computational Research Laboratories Ltd.,
> Taco House, Damle Path, Off Law College Road
> Pune - 411004, India.
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From baroni at sissa.it  Mon Apr 18 13:24:39 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 18 Apr 2011 13:24:39 +0200
Subject: [Pw_forum] The atomic displacements By QE and Abinit
In-Reply-To: <BANLkTinGofccYQGSnOEqhD+DVQixeUQ4uQ@mail.gmail.com>
References: <BANLkTinGofccYQGSnOEqhD+DVQixeUQ4uQ@mail.gmail.com>
Message-ID: <E626711B-920E-46B0-999F-11C56E8C97EF@sissa.it>

eigenmodes for degenerate modes are only defined within a unitary transformation
normalization may also differ in different codes
codes other than those in the QE distribution may give wrong results ;-)

SB

On Apr 18, 2011, at 4:32 AM, ??? wrote:

> Dear all
> 
> i have run the program ph.x and got the outfile  *.dyn_G. from what I understand, the diagonalized dynamical matrix should give displacements of each atom. and each column gives the real and imaginary components of the displacements .so in the output
> 
> omega( 1) =      -0.294635 [THz] =      -9.828034 [cm-1]
>  (  0.000006  0.000000 -0.000003  0.000000  0.288697  0.000000 ) 
>  (  0.000000  0.000000  0.000007  0.000000  0.288697  0.000000 ) 
>  ( -0.000006  0.000000 -0.000003  0.000000  0.288697  0.000000 ) 
>  (  0.000010  0.000000 -0.000006  0.000000  0.288654  0.000000 ) 
>  (  0.000000  0.000000  0.000011  0.000000  0.288654  0.000000 ) 
>  ( -0.000010  0.000000 -0.000006  0.000000  0.288654  0.000000 ) 
>  (  0.000006  0.000000 -0.000003  0.000000  0.288697  0.000000 ) 
>  (  0.000000  0.000000  0.000007  0.000000  0.288697  0.000000 ) 
>  ( -0.000006  0.000000 -0.000003  0.000000  0.288697  0.000000 ) 
>  (  0.000010  0.000000 -0.000006  0.000000  0.288654  0.000000 ) 
>  (  0.000000  0.000000  0.000011  0.000000  0.288654  0.000000 ) 
>  ( -0.000010  0.000000 -0.000006  0.000000  0.288654  0.000000 ) 
> 
> however it is different from the the outcome of Abinit 
> 
> Eigendisplacements 
>  (will be given, for each mode : in cartesian coordinates
>    for each atom the real part of the displacement vector,
>    then the imaginary part of the displacement vector)
>   Mode number    1   Energy    0.000000E+00
>  Attention : low frequency mode.
>    (Could be unstable or acoustic mode)
> ;  1  0.00000000E+00  0.00000000E+00 -2.05634696E-03
> ;     0.00000000E+00  0.00000000E+00  0.00000000E+00
> ;  2  0.00000000E+00  0.00000000E+00 -2.05634695E-03
> ;     0.00000000E+00  0.00000000E+00  0.00000000E+00
> ;  3  0.00000000E+00  0.00000000E+00 -2.05634695E-03
> ;     0.00000000E+00  0.00000000E+00  0.00000000E+00
> ;  4  0.00000000E+00  0.00000000E+00 -2.05634696E-03
> ;     0.00000000E+00  0.00000000E+00  0.00000000E+00
> ;  5  0.00000000E+00  0.00000000E+00 -2.05634696E-03
> ;     0.00000000E+00  0.00000000E+00  0.00000000E+00
> ;  6  0.00000000E+00  0.00000000E+00 -2.05634696E-03
> ;     0.00000000E+00  0.00000000E+00  0.00000000E+00
> ;  7  0.00000000E+00  0.00000000E+00 -2.05634696E-03
> ;     0.00000000E+00  0.00000000E+00  0.00000000E+00
> ;  8  0.00000000E+00  0.00000000E+00 -2.05634695E-03
> ;     0.00000000E+00  0.00000000E+00  0.00000000E+00
> ;  9  0.00000000E+00  0.00000000E+00 -2.05634695E-03
> ;     0.00000000E+00  0.00000000E+00  0.00000000E+00
> ; 10  0.00000000E+00  0.00000000E+00 -2.05634696E-03
> ;     0.00000000E+00  0.00000000E+00  0.00000000E+00
> ; 11  0.00000000E+00  0.00000000E+00 -2.05634696E-03
> ;     0.00000000E+00  0.00000000E+00  0.00000000E+00
> ; 12  0.00000000E+00  0.00000000E+00 -2.05634696E-03
> ;     0.00000000E+00  0.00000000E+00  0.00000000E+00
> 
> how could i understand it .why the QE and Abinit give the different outcome . i hope some help . and thanks in advance 
> 
> tanyci
> nankai university , tianjin
> china
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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



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From baroni at sissa.it  Mon Apr 18 13:30:53 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 18 Apr 2011 13:30:53 +0200
Subject: [Pw_forum] Dielectric Band Structure
In-Reply-To: <BANLkTikE=2gxD88RDj704J2XPokMwu3Fug@mail.gmail.com>
References: <BANLkTikE=2gxD88RDj704J2XPokMwu3Fug@mail.gmail.com>
Message-ID: <3F0E77C6-34A8-46BA-8F15-E44D2834212E@sissa.it>

Sorry: I am afraid, it is not.
We are working on the implementation of the plasmon frequency dispersion, which is a related problem.
Stay tuned
Cheers - SB

On Apr 13, 2011, at 3:35 PM, Laurence Marks wrote:

> Is this currently in the distribution?
> 
> -- 
> Laurence Marks
> Department of Materials Science and Engineering
> MSE Rm 2036 Cook Hall
> 2220 N Campus Drive
> Northwestern University
> Evanston, IL 60208, USA
> Tel: (847) 491-3996 Fax: (847) 491-7820
> email: L-marks at northwestern dot edu
> Web: www.numis.northwestern.edu
> Chair, Commission on Electron Crystallography of IUCR
> www.numis.northwestern.edu/
> Research is to see what everybody else has seen, and to think what
> nobody else has thought
> Albert Szent-Gyorgi
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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



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From baroni at sissa.it  Mon Apr 18 13:32:25 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 18 Apr 2011 13:32:25 +0200
Subject: [Pw_forum] Spectra from GW and TDDFPT
In-Reply-To: <201104141239.45865.giuseppe.mattioli@mlib.ism.cnr.it>
References: <502727273.28514@nudt.edu.cn>
	<11041417583468ef59a553486e5ae3c17da982d0c203@nudt.edu.cn>
	<201104141239.45865.giuseppe.mattioli@mlib.ism.cnr.it>
Message-ID: <6B8230E7-1626-4800-9066-A95C318E7924@sissa.it>


On Apr 14, 2011, at 12:39 PM, Giuseppe Mattioli wrote:

> 
> Dear Jiayu
> Yes, it is. You can perform TDDFPT calculations by using the gamma point, 
> nspin=1 and fixed occupations (no smearing). There are no theoretical 
> limitations regarding k-points, but they are currently not implemented.

they will 
SB

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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



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From prasenjit.jnc at gmail.com  Mon Apr 18 13:57:52 2011
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Mon, 18 Apr 2011 17:27:52 +0530
Subject: [Pw_forum] NEB calculation
In-Reply-To: <BANLkTikYA-WyTFv2+SoBX4Sw5SmCwzB=4w@mail.gmail.com>
References: <mailman.11495.1303120324.1814.pw_forum@pwscf.org>
	<OFE0AA335B.449E1A9C-ON65257876.003B84E8-65257876.003B84EA@crlindia.com>
	<BANLkTikYA-WyTFv2+SoBX4Sw5SmCwzB=4w@mail.gmail.com>
Message-ID: <BANLkTi=3YNnryVb6q5QaUBEnsrsVxSs2qA@mail.gmail.com>

Dear Savita,

Clearly 5 images are not sufficient.....also right now you are asking the
code to interpolate the path for you by mentioning only the initial & final
state....unfortunately the interpolated path is not a good starting
guess......if you look at the path using xcrysden, in the second image, both
the CO & O are getting detached from the surface......So I would suggest
that you mention the starting path explicitly.....

You can refer to the following paper to get an idea of the reaction
pathway....Phys. Rev. Lett. 80, 3650?3653 (1998)

Hope this helps....

Prasenjit
-- 
PRASENJIT GHOSH,
Assistant Professor,
IISER Pune,
First floor, Central Tower, Sai Trinity Building
Garware Circle, Sutarwadi, Pashan
Pune, Maharashtra 411021, India

Phone: +91 (20) 2590 8203
Fax: +91 (20) 2589 9790
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From giannozz at democritos.it  Mon Apr 18 14:25:30 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 18 Apr 2011 14:25:30 +0200
Subject: [Pw_forum] Prolems with tetrahedra method
In-Reply-To: <BANLkTikwDoY4CvzKjOHG6=i_4xpcEm=Rfw@mail.gmail.com>
References: <BANLkTikNO8eiukqDLTpaNwH8mgP522FnhQ@mail.gmail.com>
	<939618.53698.qm@web65711.mail.ac4.yahoo.com>
	<BANLkTikwDoY4CvzKjOHG6=i_4xpcEm=Rfw@mail.gmail.com>
Message-ID: <B4241A09-6B3A-4EC3-B1B9-1AF4A65A92D1@democritos.it>


On Apr 18, 2011, at 12:32 , yumin qian wrote:
>
> what I mean is when I use the kvec_FS.x to generate
> the k-points and add the k-points to the the input file
> for the nscf calculation. I run the pw.x  the output give
>
> >     from tetrahedra : error #         1
> >     cannot remap grid on k-point list

you cannot do this. pw.x with tetrahedra works only if
the (unshifted) k-point grid is provided via keywords
K_POINTS automatic
N1 N2 N3 0 0 0

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





From eyvaz_isaev at yahoo.com  Mon Apr 18 14:29:18 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 18 Apr 2011 05:29:18 -0700 (PDT)
Subject: [Pw_forum] Prolems with tetrahedra method
In-Reply-To: <BANLkTikwDoY4CvzKjOHG6=i_4xpcEm=Rfw@mail.gmail.com>
References: <BANLkTikNO8eiukqDLTpaNwH8mgP522FnhQ@mail.gmail.com>
	<939618.53698.qm@web65711.mail.ac4.yahoo.com>
	<BANLkTikwDoY4CvzKjOHG6=i_4xpcEm=Rfw@mail.gmail.com>
Message-ID: <479874.56967.qm@web65701.mail.ac4.yahoo.com>


From: yumin qian <yuminqian at gmail.com>

 
>what I mean is when I use the kvec_FS.x to generate the k-points and add the 
>k-points to the the >input file for the nscf calculation 

 >I run the pw.x  the output give   
 
>     fro/m tetrahedra : error #         1
>     cannot remap grid on k-point list 

 
Please submit your input file.


>For example, to calculate electron-phonon coupling coefficient, for isolated 
>systems, etc., etc., 
>


>There are so many case that you can't use tetrahedra method, or can you tell me 
>for which case >that the tetrehedra method can be used safely?.
 
For total DOS calculations.

Bests,
Eyvaz.


 
2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>

Hi,
>
> 
>
>
________________________________
 From: yumin qian <yuminqian at gmail.com>
>  
>1>I can not calculated projected density of state (PDOS) with projwfc.x .
>
>>     from projwfc : error #       239
>>    reading inputpp namelist
>
>Something is wrong in your inputpp file. Please check it carefully. In PDOS 
>calculations tetrahedra is not implemented/allowed.
>
>
>2>    When I use the kvecs_FS.x to generate the k-points for the nscf 
>calculation, the output return :
>         
>>     from tetrahedra : error #         1
>>     cannot remap grid on k-point list 
>
>I can not understand this, because kvecs_FS is not related  with any program, in 
>particular,  to tetrahedra, who complains.
>
>
>>I find that not all of the generated k-points are within the first Brillouin 
>>zone,  is there any one tell >me what is the problem?
>  
>These k-vectors are distributed over the full BZ, not  only in the first BZ.
>
>
>>another quesiton, I think that tetrahedra method can not be used in every case 
>>in PWSCF, except >for the force calculation that tetrahedra method may cause 
>>prolems, who can tell me, where we >can not use tetrahedra method
> 
>For example, to calculate electron-phonon coupling coefficient, for isolated 
>systems, etc., etc., 
>
>
>Bests,
>Eyvaz.
>
>-------------------------------------------------------------------
>Prof. Eyvaz Isaev, 
>Department of Physics, Chemistry, and Biology (IFM), Linkoping University, 
>Sweden 
>
>Theoretical Physics Department, Moscow State Institute of Steel & Alloys, 
>Russia, 
>
>isaev at ifm.liu.se, eyvaz_isaev at yahoo.com 
>
> 
> 
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 

Best Regards 
Sincerely Y. M. Qian (???)
Laboratory of Condensed Matter Theory and Materials Computation 
Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
Tel:        + 8610 8264 9827
E-Mail:    yuminqian at gmail.com 
P.O.Box 603   Beijing 100190
China 
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From yuminqian at gmail.com  Mon Apr 18 15:12:26 2011
From: yuminqian at gmail.com (yumin qian)
Date: Mon, 18 Apr 2011 21:12:26 +0800
Subject: [Pw_forum] Prolems with tetrahedra method
In-Reply-To: <479874.56967.qm@web65701.mail.ac4.yahoo.com>
References: <BANLkTikNO8eiukqDLTpaNwH8mgP522FnhQ@mail.gmail.com>
	<939618.53698.qm@web65711.mail.ac4.yahoo.com>
	<BANLkTikwDoY4CvzKjOHG6=i_4xpcEm=Rfw@mail.gmail.com>
	<479874.56967.qm@web65701.mail.ac4.yahoo.com>
Message-ID: <BANLkTimsn2nee37D7VU669sBQgbTx37G6w@mail.gmail.com>

Dear Eyvaz Isaev

This is the input file.

 &control
    calculation='scf'
    restart_mode='from_scratch',
    pseudo_dir = '/home1/ymqian/soft/pwscf/psudo',
    outdir='./scfx'
    prefix='NaR',
    tstress = .true.
 /
 &system
    ibrav = 7, celldm(1) =7.767722331091487, celldm(3)=3.564658800632527,
    nat= 7, ntyp= 4, nbnd=60
    ecutwfc = 45.0, ecutrho = 400.0
    occupations='tetrahedra',
    nspin=1,
 /
 &electrons
    diagonalization='david'
    conv_thr = 1.0e-7
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
Na  22.98977  Na.pbe-sp-van_ak.UPF
Fe  55.845    Fe.pbe-sp-van.UPF
Se  78.96     Se.pbe-van.UPF
O   15.9994   O.pbe-van_ak.UPF
ATOMIC_POSITIONS {crystal}
Na  0.500   0.500   0.1636801516544324
Na  0.000   0.000   0.3363198483455676
Fe  0.500   0.000   0.0000000000000000
Fe  0.000   0.500   0.0000000000000000
Se  0.000   0.000   0.1090917831789682
Se  0.500   0.500   0.3909082168210318
O   0.500   0.500   0.0000000000000000
K_POINTS {crystal}
        729
    0.000000    0.000000    0.000000  1.00
    0.000000    0.000000    0.125000  1.00
    0.000000    0.000000    0.250000  1.00
    0.000000    0.000000    0.375000  1.00
    0.000000    0.000000    0.500000  1.00
    0.000000    0.000000    0.625000  1.00
    0.000000    0.000000    0.750000  1.00
    0.000000    0.000000    0.875000  1.00
    0.000000    0.000000    1.000000  1.00
   ..............................
2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>

>   *
> From:* yumin qian <yuminqian at gmail.com>
> * *
>  >what I mean is when I use the kvec_FS.x to generate the k-points and add
> the k-points to the the >input file for the nscf calculation
>
>  >I run the pw.x  the output give
>
> >     fro/m tetrahedra : error #         1
>
> >     cannot remap grid on k-point list
>
> Please submit your input file.
>
>  >For example, to calculate electron-phonon coupling coefficient, for
> isolated systems, etc., etc.,
>
> >There are so many case that you can't use tetrahedra method, or can you
> tell me for which case >that the tetrehedra method can be used safely?.
>
> For total DOS calculations.
>
> Bests,
> Eyvaz.
>
>
>   2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>
>
>>  Hi,
>>
>>  ------------------------------
>> *From:* yumin qian <yuminqian at gmail.com>
>> * *
>> 1>I can not calculated projected density of state (PDOS) with projwfc.x .
>>
>>  >     from projwfc : error #       239
>> >    reading inputpp namelist
>>
>> Something is wrong in your inputpp file. Please check it carefully. In
>> PDOS calculations tetrahedra is not implemented/allowed.
>>
>>  2>    When I use the kvecs_FS.x to generate the k-points for the nscf
>> calculation, the output return :
>>
>> >     from tetrahedra : error #         1
>> >     cannot remap grid on k-point list
>>
>> I can not understand this, because kvecs_FS is not related  with any
>> program, in particular,  to tetrahedra, who complains.
>>
>>  >I find that not all of the generated k-points are within the first
>> Brillouin zone,  is there any one tell >me what is the problem?
>>
>> These k-vectors are distributed over the full BZ, not  only in the first
>> BZ.
>>
>>  >another quesiton, I think that tetrahedra method can not be used in
>> every case in PWSCF, except >for the force calculation that tetrahedra
>> method may cause prolems, who can tell me, where we >can not use tetrahedra
>> method
>>
>> For example, to calculate electron-phonon coupling coefficient, for
>> isolated systems, etc., etc.,
>>
>> Bests,
>> Eyvaz.
>>  -------------------------------------------------------------------
>> Prof. Eyvaz Isaev,
>> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
>> Sweden
>> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
>> Russia,
>> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>>
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> Best Regards
> Sincerely Y. M. Qian (???)
> Laboratory of Condensed Matter Theory and Materials Computation
> Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
> Tel:        + 8610 8264 9827
> E-Mail:    yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
> P.O.Box 603   Beijing 100190
> China
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Best Regards
Sincerely Y. M. Qian (???)
Laboratory of Condensed Matter Theory and Materials Computation
Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
Tel:        + 8610 8264 9827
E-Mail:    yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From eyvaz_isaev at yahoo.com  Mon Apr 18 15:48:16 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 18 Apr 2011 06:48:16 -0700 (PDT)
Subject: [Pw_forum] Prolems with tetrahedra method
In-Reply-To: <BANLkTimsn2nee37D7VU669sBQgbTx37G6w@mail.gmail.com>
References: <BANLkTikNO8eiukqDLTpaNwH8mgP522FnhQ@mail.gmail.com>
	<939618.53698.qm@web65711.mail.ac4.yahoo.com>
	<BANLkTikwDoY4CvzKjOHG6=i_4xpcEm=Rfw@mail.gmail.com>
	<479874.56967.qm@web65701.mail.ac4.yahoo.com>
	<BANLkTimsn2nee37D7VU669sBQgbTx37G6w@mail.gmail.com>
Message-ID: <788811.37057.qm@web65705.mail.ac4.yahoo.com>

Well, you are wrong. k-points generated by kvecs_FS.x can not be used for scf 
calculation. They are designed for nscf calculations (to map the Fermi surface), 
given in units of 2\pi/a and are Cartesian. 


Bests,
Eyvaz.




________________________________
From: yumin qian <yuminqian at gmail.com>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Mon, April 18, 2011 3:12:26 PM
Subject: Re: [Pw_forum] Prolems with tetrahedra method


Dear Eyvaz Isaev
 
This is the input file.
 
 &control
    calculation='scf'
    restart_mode='from_scratch',
    pseudo_dir = '/home1/ymqian/soft/pwscf/psudo',
    outdir='./scfx'
    prefix='NaR',
    tstress = .true.
 /
 &system
    ibrav = 7, celldm(1) =7.767722331091487, celldm(3)=3.564658800632527,
    nat= 7, ntyp= 4, nbnd=60
    ecutwfc = 45.0, ecutrho = 400.0
    occupations='tetrahedra',
    nspin=1,
 /
 &electrons
    diagonalization='david'
    conv_thr = 1.0e-7
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
Na  22.98977  Na.pbe-sp-van_ak.UPF
Fe  55.845    Fe.pbe-sp-van.UPF
Se  78.96     Se.pbe-van.UPF
O   15.9994   O.pbe-van_ak.UPF
ATOMIC_POSITIONS {crystal}
Na  0.500   0.500   0.1636801516544324
Na  0.000   0.000   0.3363198483455676
Fe  0.500   0.000   0.0000000000000000
Fe  0.000   0.500   0.0000000000000000
Se  0.000   0.000   0.1090917831789682
Se  0.500   0.500   0.3909082168210318
O   0.500   0.500   0.0000000000000000
K_POINTS {crystal}
        729
    0.000000    0.000000    0.000000  1.00
    0.000000    0.000000    0.125000  1.00
    0.000000    0.000000    0.250000  1.00
    0.000000    0.000000    0.375000  1.00
    0.000000    0.000000    0.500000  1.00
    0.000000    0.000000    0.625000  1.00
    0.000000    0.000000    0.750000  1.00
    0.000000    0.000000    0.875000  1.00
    0.000000    0.000000    1.000000  1.00 
   ..............................

2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>


>From: yumin qian <yuminqian at gmail.com>
>
>  
>>what I mean is when I use the kvec_FS.x to generate the k-points and add the 
>>k-points to the the >input file for the nscf calculation 
>
> >I run the pw.x  the output give   
> 
>>     fro/m tetrahedra : error #         1 
>
>>     cannot remap grid on k-point list 
>
> 
>Please submit your input file.
>
>
>>For example, to calculate electron-phonon coupling coefficient, for isolated 
>>systems, etc., etc., 
>>
>
>
>>There are so many case that you can't use tetrahedra method, or can you tell me 
>>for which case >that the tetrehedra method can be used safely?.
> 
>For total DOS calculations.
>
>Bests,
>Eyvaz.
>
>
> 
>2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>
>
>Hi,
>>
>> 
>>
>>
________________________________
 From: yumin qian <yuminqian at gmail.com>
>>  
>>1>I can not calculated projected density of state (PDOS) with projwfc.x .
>>
>>>     from projwfc : error #       239
>>>    reading inputpp namelist
>>
>>Something is wrong in your inputpp file. Please check it carefully. In PDOS 
>>calculations tetrahedra is not implemented/allowed.
>>
>>
>>2>    When I use the kvecs_FS.x to generate the k-points for the nscf 
>>calculation, the output return :
>>         
>>>     from tetrahedra : error #         1
>>>     cannot remap grid on k-point list 
>>
>>I can not understand this, because kvecs_FS is not related  with any program, in 
>>particular,  to tetrahedra, who complains.
>>
>>
>>>I find that not all of the generated k-points are within the first Brillouin 
>>>zone,  is there any one tell >me what is the problem?
>>  
>>These k-vectors are distributed over the full BZ, not  only in the first BZ.
>>
>>
>>>another quesiton, I think that tetrahedra method can not be used in every case 
>>>in PWSCF, except >for the force calculation that tetrahedra method may cause 
>>>prolems, who can tell me, where we >can not use tetrahedra method
>> 
>>For example, to calculate electron-phonon coupling coefficient, for isolated 
>>systems, etc., etc., 
>>
>>
>>Bests,
>>Eyvaz.
>>
>>-------------------------------------------------------------------
>>Prof. Eyvaz Isaev, 
>>Department of Physics, Chemistry, and Biology (IFM), Linkoping University, 
>>Sweden 
>>
>>Theoretical Physics Department, Moscow State Institute of Steel & Alloys, 
>>Russia, 
>>
>>isaev at ifm.liu.se, eyvaz_isaev at yahoo.com 
>>
>> 
>> 
>>_______________________________________________
>>Pw_forum mailing list
>>Pw_forum at pwscf.org
>>http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
>-- 
>
>Best Regards 
>Sincerely Y. M. Qian (???)
>Laboratory of Condensed Matter Theory and Materials Computation 
>Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
>Tel:        + 8610 8264 9827
>E-Mail:    yuminqian at gmail.com 
>P.O.Box 603   Beijing 100190
>China 
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 

Best Regards 
Sincerely Y. M. Qian (???)
Laboratory of Condensed Matter Theory and Materials Computation 
Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
Tel:        + 8610 8264 9827
E-Mail:    yuminqian at gmail.com 
P.O.Box 603   Beijing 100190
China 
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From max.n.popov at gmail.com  Mon Apr 18 15:58:18 2011
From: max.n.popov at gmail.com (=?KOI8-R?B?7cHL08nNIPDP0M/X?=)
Date: Mon, 18 Apr 2011 15:58:18 +0200
Subject: [Pw_forum] new bfgs: strange behavior doing vc-relax
Message-ID: <BANLkTin4=1zogfWZwtYfS1dH0GqP2AzZaA@mail.gmail.com>

Dear QE developers,

comparing vc-relax calculations between BFGS(4.2.1) and the latest BFGS(from
CVS) I faced  with a following problem:
the newest QE calculates one extra point after achieving convergence
criteria (etot_conv_thr,force_conv_thr,press_conv_thr),
which leads to slightly higher total energy.

Here are the two latest energies from outputs:
       v.4.2.1                       CVS(18.04.2011)

-242.66342170 Ry       -242.66342267 Ry
-242.66342336 Ry       -242.66284562 Ry

One can see that there is a good agreement between the last energy by
v.4.2.1 and next to the last by CVS-version, whereas
the last energy by CVS is higher by ~ 0.5 mRy.

I tried relax (cell shape fixed) also - it works fine, no extra point
calculation.

-- 
Best regards, Max Popov
Ph.D. student
Materials center Leoben (MCL), Leoben, Austria.
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From yuminqian at gmail.com  Mon Apr 18 16:15:24 2011
From: yuminqian at gmail.com (yumin qian)
Date: Mon, 18 Apr 2011 22:15:24 +0800
Subject: [Pw_forum] Prolems with tetrahedra method
In-Reply-To: <788811.37057.qm@web65705.mail.ac4.yahoo.com>
References: <BANLkTikNO8eiukqDLTpaNwH8mgP522FnhQ@mail.gmail.com>
	<939618.53698.qm@web65711.mail.ac4.yahoo.com>
	<BANLkTikwDoY4CvzKjOHG6=i_4xpcEm=Rfw@mail.gmail.com>
	<479874.56967.qm@web65701.mail.ac4.yahoo.com>
	<BANLkTimsn2nee37D7VU669sBQgbTx37G6w@mail.gmail.com>
	<788811.37057.qm@web65705.mail.ac4.yahoo.com>
Message-ID: <BANLkTimFi3zhBmfH3a9MM9sx2AVqdNhMww@mail.gmail.com>

Thanks for your reply
I have  change the
calculation='scf'
but it still the same. why ?

2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>

>  Well, you are wrong. k-points generated by kvecs_FS.x can not be used for
> scf calculation. They are designed for nscf calculations (to map the Fermi
> surface), given in units of 2\pi/a and are Cartesian.
>
> Bests,
> Eyvaz.
>
>  ------------------------------
> *From:* yumin qian <yuminqian at gmail.com>
> *To:* PWSCF Forum <pw_forum at pwscf.org>
> *Sent:* Mon, April 18, 2011 3:12:26 PM
> *Subject:* Re: [Pw_forum] Prolems with tetrahedra method
>
> Dear Eyvaz Isaev
>
> This is the input file.
>
>  &control
>     calculation='scf'
>     restart_mode='from_scratch',
>     pseudo_dir = '/home1/ymqian/soft/pwscf/psudo',
>     outdir='./scfx'
>     prefix='NaR',
>     tstress = .true.
>  /
>  &system
>     ibrav = 7, celldm(1) =7.767722331091487, celldm(3)=3.564658800632527,
>     nat= 7, ntyp= 4, nbnd=60
>     ecutwfc = 45.0, ecutrho = 400.0
>     occupations='tetrahedra',
>     nspin=1,
>  /
>  &electrons
>     diagonalization='david'
>     conv_thr = 1.0e-7
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
> Na  22.98977  Na.pbe-sp-van_ak.UPF
> Fe  55.845    Fe.pbe-sp-van.UPF
> Se  78.96     Se.pbe-van.UPF
> O   15.9994   O.pbe-van_ak.UPF
> ATOMIC_POSITIONS {crystal}
> Na  0.500   0.500   0.1636801516544324
> Na  0.000   0.000   0.3363198483455676
> Fe  0.500   0.000   0.0000000000000000
> Fe  0.000   0.500   0.0000000000000000
> Se  0.000   0.000   0.1090917831789682
> Se  0.500   0.500   0.3909082168210318
> O   0.500   0.500   0.0000000000000000
> K_POINTS {crystal}
>         729
>     0.000000    0.000000    0.000000  1.00
>     0.000000    0.000000    0.125000  1.00
>     0.000000    0.000000    0.250000  1.00
>     0.000000    0.000000    0.375000  1.00
>     0.000000    0.000000    0.500000  1.00
>     0.000000    0.000000    0.625000  1.00
>     0.000000    0.000000    0.750000  1.00
>     0.000000    0.000000    0.875000  1.00
>     0.000000    0.000000    1.000000  1.00
>    ..............................
> 2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>
>
>>   *
>> From:* yumin qian <yuminqian at gmail.com>
>> * *
>>  >what I mean is when I use the kvec_FS.x to generate the
>> k-points and add the k-points to the the >input file for the nscf
>> calculation
>>
>>  >I run the pw.x  the output give
>>
>> >     fro/m tetrahedra : error #         1
>>
>> >     cannot remap grid on k-point list
>>
>> Please submit your input file.
>>
>>  >For example, to calculate electron-phonon coupling coefficient, for
>> isolated systems, etc., etc.,
>>
>> >There are so many case that you can't use tetrahedra method, or can you
>> tell me for which case >that the tetrehedra method can be used safely?.
>>
>> For total DOS calculations.
>>
>> Bests,
>> Eyvaz.
>>
>>
>>   2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>
>>
>>>  Hi,
>>>
>>>  ------------------------------
>>> *From:* yumin qian <yuminqian at gmail.com>
>>> * *
>>> 1>I can not calculated projected density of state (PDOS) with projwfc.x .
>>>
>>>  >     from projwfc : error #       239
>>> >    reading inputpp namelist
>>>
>>> Something is wrong in your inputpp file. Please check it carefully. In
>>> PDOS calculations tetrahedra is not implemented/allowed.
>>>
>>>  2>    When I use the kvecs_FS.x to generate the k-points for the nscf
>>> calculation, the output return :
>>>
>>> >     from tetrahedra : error #         1
>>> >     cannot remap grid on k-point list
>>>
>>> I can not understand this, because kvecs_FS is not related  with any
>>> program, in particular,  to tetrahedra, who complains.
>>>
>>>  >I find that not all of the generated k-points are within the first
>>> Brillouin zone,  is there any one tell >me what is the problem?
>>>
>>> These k-vectors are distributed over the full BZ, not  only in the first
>>> BZ.
>>>
>>>  >another quesiton, I think that tetrahedra method can not be used in
>>> every case in PWSCF, except >for the force calculation that tetrahedra
>>> method may cause prolems, who can tell me, where we >can not use tetrahedra
>>> method
>>>
>>> For example, to calculate electron-phonon coupling coefficient, for
>>> isolated systems, etc., etc.,
>>>
>>> Bests,
>>> Eyvaz.
>>>  -------------------------------------------------------------------
>>> Prof. Eyvaz Isaev,
>>> Department of Physics, Chemistry, and Biology (IFM), Linkoping
>>> University, Sweden
>>> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
>>> Russia,
>>> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>>
>>
>> --
>> Best Regards
>> Sincerely Y. M. Qian (???)
>> Laboratory of Condensed Matter Theory and Materials Computation
>> Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
>> Tel:        + 8610 8264 9827
>> E-Mail:    yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
>> P.O.Box 603   Beijing 100190
>> China
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> Best Regards
> Sincerely Y. M. Qian (???)
> Laboratory of Condensed Matter Theory and Materials Computation
> Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
> Tel:        + 8610 8264 9827
> E-Mail:    yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
> P.O.Box 603   Beijing 100190
> China
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Best Regards
Sincerely Y. M. Qian (???)
Laboratory of Condensed Matter Theory and Materials Computation
Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
Tel:        + 8610 8264 9827
E-Mail:    yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From eyvaz_isaev at yahoo.com  Mon Apr 18 16:44:37 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 18 Apr 2011 07:44:37 -0700 (PDT)
Subject: [Pw_forum] Prolems with tetrahedra method
In-Reply-To: <BANLkTimFi3zhBmfH3a9MM9sx2AVqdNhMww@mail.gmail.com>
References: <BANLkTikNO8eiukqDLTpaNwH8mgP522FnhQ@mail.gmail.com>
	<939618.53698.qm@web65711.mail.ac4.yahoo.com>
	<BANLkTikwDoY4CvzKjOHG6=i_4xpcEm=Rfw@mail.gmail.com>
	<479874.56967.qm@web65701.mail.ac4.yahoo.com>
	<BANLkTimsn2nee37D7VU669sBQgbTx37G6w@mail.gmail.com>
	<788811.37057.qm@web65705.mail.ac4.yahoo.com>
	<BANLkTimFi3zhBmfH3a9MM9sx2AVqdNhMww@mail.gmail.com>
Message-ID: <198339.38197.qm@web65713.mail.ac4.yahoo.com>

>    occupations='tetrahedra',
  Have you changed this to "smearing" and related keywords?

Eyvaz.




________________________________
From: yumin qian <yuminqian at gmail.com>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Mon, April 18, 2011 4:15:24 PM
Subject: Re: [Pw_forum] Prolems with tetrahedra method


Thanks for your reply
I have  change the 
calculation='scf' 
but it still the same. why ?


2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>

Well, you are wrong. k-points generated by kvecs_FS.x can not be used for scf 
calculation. They are designed for nscf calculations (to map the Fermi surface), 
given in units of 2\pi/a and are Cartesian. 

>
>Bests,
>Eyvaz.
>
>
>
>
________________________________
 
>From: yumin qian <yuminqian at gmail.com>
>To: PWSCF Forum <pw_forum at pwscf.org>
>Sent: Mon, April 18, 2011 3:12:26 PM
>Subject: Re: [Pw_forum] Prolems with tetrahedra method
> 
>
>
>Dear Eyvaz Isaev
> 
>This is the input file.
> 
> &control
>    calculation='scf'
>    restart_mode='from_scratch',
>    pseudo_dir = '/home1/ymqian/soft/pwscf/psudo',
>    outdir='./scfx'
>    prefix='NaR',
>    tstress = .true.
> /
> &system
>    ibrav = 7, celldm(1) =7.767722331091487, celldm(3)=3.564658800632527,
>    nat= 7, ntyp= 4, nbnd=60
>    ecutwfc = 45.0, ecutrho = 400.0
>    occupations='tetrahedra',
>    nspin=1,
> /
> &electrons
>    diagonalization='david'
>    conv_thr = 1.0e-7
>    mixing_beta = 0.7
> /
>ATOMIC_SPECIES
>Na  22.98977  Na.pbe-sp-van_ak.UPF
>Fe  55.845    Fe.pbe-sp-van.UPF
>Se  78.96     Se.pbe-van.UPF
>O   15.9994   O.pbe-van_ak.UPF
>ATOMIC_POSITIONS {crystal}
>Na  0.500   0.500   0.1636801516544324
>Na  0.000   0.000   0.3363198483455676
>Fe  0.500   0.000   0.0000000000000000
>Fe  0.000   0.500   0.0000000000000000
>Se  0.000   0.000   0.1090917831789682
>Se  0.500   0.500   0.3909082168210318
>O   0.500   0.500   0.0000000000000000
>K_POINTS {crystal}
>        729
>    0.000000    0.000000    0.000000  1.00
>    0.000000    0.000000    0.125000  1.00
>    0.000000    0.000000    0.250000  1.00
>    0.000000    0.000000    0.375000  1.00
>    0.000000    0.000000    0.500000  1.00
>    0.000000    0.000000    0.625000  1.00
>    0.000000    0.000000    0.750000  1.00
>    0.000000    0.000000    0.875000  1.00
>    0.000000    0.000000    1.000000  1.00 
>   ..............................
>
>2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>
>
>
>>From: yumin qian <yuminqian at gmail.com>
>>
>>  
>>>what I mean is when I use the kvec_FS.x to generate the k-points and add the 
>>>k-points to the the >input file for the nscf calculation 
>>
>> >I run the pw.x  the output give   
>> 
>>>     fro/m tetrahedra : error #         1 
>>
>>>     cannot remap grid on k-point list 
>>
>> 
>>Please submit your input file.
>>
>>
>>>For example, to calculate electron-phonon coupling coefficient, for isolated 
>>>systems, etc., etc., 
>>>
>>
>>
>>>There are so many case that you can't use tetrahedra method, or can you tell me 
>>>for which case >that the tetrehedra method can be used safely?.
>> 
>>For total DOS calculations.
>>
>>Bests,
>>Eyvaz.
>>
>>
>> 
>>2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>
>>
>>Hi,
>>>
>>> 
>>>
>>>
________________________________
 From: yumin qian <yuminqian at gmail.com>
>>>  
>>>1>I can not calculated projected density of state (PDOS) with projwfc.x .
>>>
>>>>     from projwfc : error #       239
>>>>    reading inputpp namelist
>>>
>>>Something is wrong in your inputpp file. Please check it carefully. In PDOS 
>>>calculations tetrahedra is not implemented/allowed.
>>>
>>>
>>>2>    When I use the kvecs_FS.x to generate the k-points for the nscf 
>>>calculation, the output return :
>>>         
>>>>     from tetrahedra : error #         1
>>>>     cannot remap grid on k-point list 
>>>
>>>I can not understand this, because kvecs_FS is not related  with any program, in 
>>>particular,  to tetrahedra, who complains.
>>>
>>>
>>>>I find that not all of the generated k-points are within the first Brillouin 
>>>>zone,  is there any one tell >me what is the problem?
>>>  
>>>These k-vectors are distributed over the full BZ, not  only in the first BZ.
>>>
>>>
>>>>another quesiton, I think that tetrahedra method can not be used in every case 
>>>>in PWSCF, except >for the force calculation that tetrahedra method may cause 
>>>>prolems, who can tell me, where we >can not use tetrahedra method
>>> 
>>>For example, to calculate electron-phonon coupling coefficient, for isolated 
>>>systems, etc., etc., 
>>>
>>>
>>>Bests,
>>>Eyvaz.
>>>
>>>-------------------------------------------------------------------
>>>Prof. Eyvaz Isaev, 
>>>Department of Physics, Chemistry, and Biology (IFM), Linkoping University, 
>>>Sweden 
>>>
>>>Theoretical Physics Department, Moscow State Institute of Steel & Alloys, 
>>>Russia, 
>>>
>>>isaev at ifm.liu.se, eyvaz_isaev at yahoo.com 
>>>
>>> 
>>> 
>>>_______________________________________________
>>>Pw_forum mailing list
>>>Pw_forum at pwscf.org
>>>http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>>
>>
>>-- 
>>
>>Best Regards 
>>Sincerely Y. M. Qian (???)
>>Laboratory of Condensed Matter Theory and Materials Computation 
>>Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
>>Tel:        + 8610 8264 9827
>>E-Mail:    yuminqian at gmail.com 
>>P.O.Box 603   Beijing 100190
>>China 
>>
>>_______________________________________________
>>Pw_forum mailing list
>>Pw_forum at pwscf.org
>>http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
>-- 
>
>Best Regards 
>Sincerely Y. M. Qian (???)
>Laboratory of Condensed Matter Theory and Materials Computation 
>Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
>Tel:        + 8610 8264 9827
>E-Mail:    yuminqian at gmail.com 
>P.O.Box 603   Beijing 100190
>China 
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 

Best Regards 
Sincerely Y. M. Qian (???)
Laboratory of Condensed Matter Theory and Materials Computation 
Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
Tel:        + 8610 8264 9827
E-Mail:    yuminqian at gmail.com 
P.O.Box 603   Beijing 100190
China 
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From yuminqian at gmail.com  Mon Apr 18 17:12:45 2011
From: yuminqian at gmail.com (yumin qian)
Date: Mon, 18 Apr 2011 23:12:45 +0800
Subject: [Pw_forum] Prolems with tetrahedra method
In-Reply-To: <198339.38197.qm@web65713.mail.ac4.yahoo.com>
References: <BANLkTikNO8eiukqDLTpaNwH8mgP522FnhQ@mail.gmail.com>
	<939618.53698.qm@web65711.mail.ac4.yahoo.com>
	<BANLkTikwDoY4CvzKjOHG6=i_4xpcEm=Rfw@mail.gmail.com>
	<479874.56967.qm@web65701.mail.ac4.yahoo.com>
	<BANLkTimsn2nee37D7VU669sBQgbTx37G6w@mail.gmail.com>
	<788811.37057.qm@web65705.mail.ac4.yahoo.com>
	<BANLkTimFi3zhBmfH3a9MM9sx2AVqdNhMww@mail.gmail.com>
	<198339.38197.qm@web65713.mail.ac4.yahoo.com>
Message-ID: <BANLkTikM0Zj2_fUN10jx==kbagCYP59ZHA@mail.gmail.com>

Yes, I tried this, it seems goos well.  This is very strange.

2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>

>  >    occupations='tetrahedra',
>
>  Have you changed this to "smearing" and related keywords?
>
> Eyvaz.
>
>  ------------------------------
> *From:* yumin qian <yuminqian at gmail.com>
> *To:* PWSCF Forum <pw_forum at pwscf.org>
> *Sent:* Mon, April 18, 2011 4:15:24 PM
>
> *Subject:* Re: [Pw_forum] Prolems with tetrahedra method
>
> Thanks for your reply
> I have  change the
> calculation='scf'
> but it still the same. why ?
>
> 2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>
>
>>  Well, you are wrong. k-points generated by kvecs_FS.x can not be used
>> for scf calculation. They are designed for nscf calculations (to map the
>> Fermi surface), given in units of 2\pi/a and are Cartesian.
>>
>> Bests,
>> Eyvaz.
>>
>>  ------------------------------
>> *From:* yumin qian <yuminqian at gmail.com>
>> *To:* PWSCF Forum <pw_forum at pwscf.org>
>> *Sent:* Mon, April 18, 2011 3:12:26 PM
>> *Subject:* Re: [Pw_forum] Prolems with tetrahedra method
>>
>> Dear Eyvaz Isaev
>>
>> This is the input file.
>>
>>  &control
>>     calculation='scf'
>>     restart_mode='from_scratch',
>>     pseudo_dir = '/home1/ymqian/soft/pwscf/psudo',
>>     outdir='./scfx'
>>     prefix='NaR',
>>     tstress = .true.
>>  /
>>  &system
>>     ibrav = 7, celldm(1) =7.767722331091487, celldm(3)=3.564658800632527,
>>     nat= 7, ntyp= 4, nbnd=60
>>     ecutwfc = 45.0, ecutrho = 400.0
>>     occupations='tetrahedra',
>>     nspin=1,
>>  /
>>  &electrons
>>     diagonalization='david'
>>     conv_thr = 1.0e-7
>>     mixing_beta = 0.7
>>  /
>> ATOMIC_SPECIES
>> Na  22.98977  Na.pbe-sp-van_ak.UPF
>> Fe  55.845    Fe.pbe-sp-van.UPF
>> Se  78.96     Se.pbe-van.UPF
>> O   15.9994   O.pbe-van_ak.UPF
>> ATOMIC_POSITIONS {crystal}
>> Na  0.500   0.500   0.1636801516544324
>> Na  0.000   0.000   0.3363198483455676
>> Fe  0.500   0.000   0.0000000000000000
>> Fe  0.000   0.500   0.0000000000000000
>> Se  0.000   0.000   0.1090917831789682
>> Se  0.500   0.500   0.3909082168210318
>> O   0.500   0.500   0.0000000000000000
>> K_POINTS {crystal}
>>         729
>>     0.000000    0.000000    0.000000  1.00
>>     0.000000    0.000000    0.125000  1.00
>>     0.000000    0.000000    0.250000  1.00
>>     0.000000    0.000000    0.375000  1.00
>>     0.000000    0.000000    0.500000  1.00
>>     0.000000    0.000000    0.625000  1.00
>>     0.000000    0.000000    0.750000  1.00
>>     0.000000    0.000000    0.875000  1.00
>>     0.000000    0.000000    1.000000  1.00
>>    ..............................
>> 2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>
>>
>>>   *
>>> From:* yumin qian <yuminqian at gmail.com>
>>> * *
>>>  >what I mean is when I use the kvec_FS.x to generate the
>>> k-points and add the k-points to the the >input file for the nscf
>>> calculation
>>>
>>>  >I run the pw.x  the output give
>>>
>>> >     fro/m tetrahedra : error #         1
>>>
>>> >     cannot remap grid on k-point list
>>>
>>> Please submit your input file.
>>>
>>>  >For example, to calculate electron-phonon coupling coefficient, for
>>> isolated systems, etc., etc.,
>>>
>>> >There are so many case that you can't use tetrahedra method, or can you
>>> tell me for which case >that the tetrehedra method can be used safely?.
>>>
>>> For total DOS calculations.
>>>
>>> Bests,
>>> Eyvaz.
>>>
>>>
>>>   2011/4/18 Eyvaz Isaev <eyvaz_isaev at yahoo.com>
>>>
>>>>  Hi,
>>>>
>>>>  ------------------------------
>>>> *From:* yumin qian <yuminqian at gmail.com>
>>>> * *
>>>> 1>I can not calculated projected density of state (PDOS) with projwfc.x
>>>> .
>>>>
>>>>  >     from projwfc : error #       239
>>>> >    reading inputpp namelist
>>>>
>>>> Something is wrong in your inputpp file. Please check it carefully. In
>>>> PDOS calculations tetrahedra is not implemented/allowed.
>>>>
>>>>  2>    When I use the kvecs_FS.x to generate the k-points for the nscf
>>>> calculation, the output return :
>>>>
>>>> >     from tetrahedra : error #         1
>>>> >     cannot remap grid on k-point list
>>>>
>>>> I can not understand this, because kvecs_FS is not related  with any
>>>> program, in particular,  to tetrahedra, who complains.
>>>>
>>>>  >I find that not all of the generated k-points are within the first
>>>> Brillouin zone,  is there any one tell >me what is the problem?
>>>>
>>>> These k-vectors are distributed over the full BZ, not  only in the first
>>>> BZ.
>>>>
>>>>  >another quesiton, I think that tetrahedra method can not be used in
>>>> every case in PWSCF, except >for the force calculation that tetrahedra
>>>> method may cause prolems, who can tell me, where we >can not use tetrahedra
>>>> method
>>>>
>>>> For example, to calculate electron-phonon coupling coefficient, for
>>>> isolated systems, etc., etc.,
>>>>
>>>> Bests,
>>>> Eyvaz.
>>>>  -------------------------------------------------------------------
>>>> Prof. Eyvaz Isaev,
>>>> Department of Physics, Chemistry, and Biology (IFM), Linkoping
>>>> University, Sweden
>>>> Theoretical Physics Department, Moscow State Institute of Steel &
>>>> Alloys, Russia,
>>>> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Pw_forum mailing list
>>>> Pw_forum at pwscf.org
>>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>>
>>>>
>>>
>>>
>>> --
>>> Best Regards
>>> Sincerely Y. M. Qian (???)
>>> Laboratory of Condensed Matter Theory and Materials Computation
>>> Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
>>> Tel:        + 8610 8264 9827
>>> E-Mail:    yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
>>> P.O.Box 603   Beijing 100190
>>> China
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>>
>>
>> --
>> Best Regards
>> Sincerely Y. M. Qian (???)
>> Laboratory of Condensed Matter Theory and Materials Computation
>> Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
>> Tel:        + 8610 8264 9827
>> E-Mail:    yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
>> P.O.Box 603   Beijing 100190
>> China
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> Best Regards
> Sincerely Y. M. Qian (???)
> Laboratory of Condensed Matter Theory and Materials Computation
> Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
> Tel:        + 8610 8264 9827
> E-Mail:    yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
> P.O.Box 603   Beijing 100190
> China
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Best Regards
Sincerely Y. M. Qian (???)
Laboratory of Condensed Matter Theory and Materials Computation
Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
Tel:        + 8610 8264 9827
E-Mail:    yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From doser at avmatsim.de  Mon Apr 18 17:27:42 2011
From: doser at avmatsim.de (Bernd Doser)
Date: Mon, 18 Apr 2011 17:27:42 +0200
Subject: [Pw_forum] Pseudo potentials for hybrid DFT
Message-ID: <4DAC586E.8040600@avmatsim.de>

Dear QuantumEspresso Community,

I am interested in calculating organic molecules using hybrid DFT
functionals like PBE0 or B3LYP. Therefore I searching pseudo potentials
mainly for the elements H, C, O, N, S, Cl, Br, and I. In the database of
QuantumEspresso I don't have found a consistent PP set for all these
elements. So, what is the best way to select pseudo potentials? Is it
important that pseudo potentials matches to the DFT functional?

Thank yo in advance,

Sincerely,

-- 
Dr Bernd Doser
Scientific Software Engineer

Avant-garde Materials Simulation
Merzhauser Strasse 177
79100 Freiburg im Breisgau, Germany

Phone: +49 761 479984-23
Homepage: http://www.avmatsim.de


From giuseppe.mattioli at mlib.ism.cnr.it  Mon Apr 18 17:56:05 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Mon, 18 Apr 2011 17:56:05 +0200
Subject: [Pw_forum] Pseudo potentials for hybrid DFT
In-Reply-To: <4DAC586E.8040600@avmatsim.de>
References: <4DAC586E.8040600@avmatsim.de>
Message-ID: <201104181756.05913.giuseppe.mattioli@mlib.ism.cnr.it>

Dear Bernd
The best choice is currently PBE-->PBE0 or BLYP-->B3LYP. But as you force the 
xc functional, you can use everything (reasonable). Remember that you can 
only use norm-conserving PP.
HTH
Giuseppe

On Monday 18 April 2011 17:27:42 Bernd Doser wrote:
> Dear QuantumEspresso Community,
>
> I am interested in calculating organic molecules using hybrid DFT
> functionals like PBE0 or B3LYP. Therefore I searching pseudo potentials
> mainly for the elements H, C, O, N, S, Cl, Br, and I. In the database of
> QuantumEspresso I don't have found a consistent PP set for all these
> elements. So, what is the best way to select pseudo potentials? Is it
> important that pseudo potentials matches to the DFT functional?
>
> Thank yo in advance,
>
> Sincerely,



-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? 
? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ?
? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ?
? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ?
? ?E-mail: <giuseppe.mattioli at ism.cnr.it>

From eyvaz_isaev at yahoo.com  Mon Apr 18 18:25:50 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 18 Apr 2011 09:25:50 -0700 (PDT)
Subject: [Pw_forum] Pseudo potentials for hybrid DFT
In-Reply-To: <4DAC586E.8040600@avmatsim.de>
References: <4DAC586E.8040600@avmatsim.de>
Message-ID: <227297.73975.qm@web65713.mail.ac4.yahoo.com>

Dear Brend,


From giannozz at democritos.it  Mon Apr 18 18:36:42 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 18 Apr 2011 18:36:42 +0200
Subject: [Pw_forum] Pseudo potentials for hybrid DFT
In-Reply-To: <227297.73975.qm@web65713.mail.ac4.yahoo.com>
References: <4DAC586E.8040600@avmatsim.de>
	<227297.73975.qm@web65713.mail.ac4.yahoo.com>
Message-ID: <8E0CF25E-5EE5-4DCF-8EC7-E04307BC8946@democritos.it>


On Apr 18, 2011, at 18:25 , Eyvaz Isaev wrote:

>  Variable:       input_dft
>  [...]
> But as far as I remember this works (at least, worked) for norm- 
> conserving pseudopotentials only.

just a remark: hybrid functionals work only for norm-conserving  
pseudopotentials,
but variable input_dft works in all cases

Paolo
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From Trinh.Vo at jpl.nasa.gov  Mon Apr 18 19:21:16 2011
From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Mon, 18 Apr 2011 10:21:16 -0700
Subject: [Pw_forum] Pseudo potentials for hybrid DFT
In-Reply-To: <8E0CF25E-5EE5-4DCF-8EC7-E04307BC8946@democritos.it>
Message-ID: <C9D1C11C.5C82%Trinh.Vo@jpl.nasa.gov>

Hi All,

I am sorry.  I sent the slides to a colaborator, but I made a mistake.
Please ignore my previous email.

Trinh


On 4/18/11 9:36 AM, "Paolo Giannozzi" <giannozz at democritos.it> wrote:

> 
> On Apr 18, 2011, at 18:25 , Eyvaz Isaev wrote:
> 
>>  Variable:       input_dft
>>  [...]
>> But as far as I remember this works (at least, worked) for norm-
>> conserving pseudopotentials only.
> 
> just a remark: hybrid functionals work only for norm-conserving
> pseudopotentials,
> but variable input_dft works in all cases
> 
> Paolo
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From eyvaz_isaev at yahoo.com  Mon Apr 18 20:19:37 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 18 Apr 2011 11:19:37 -0700 (PDT)
Subject: [Pw_forum] Pseudo potentials for hybrid DFT
In-Reply-To: <8E0CF25E-5EE5-4DCF-8EC7-E04307BC8946@democritos.it>
References: <4DAC586E.8040600@avmatsim.de>
	<227297.73975.qm@web65713.mail.ac4.yahoo.com>
	<8E0CF25E-5EE5-4DCF-8EC7-E04307BC8946@democritos.it>
Message-ID: <648574.10641.qm@web65715.mail.ac4.yahoo.com>



From: Paolo Giannozzi <giannozz at democritos.it>

To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Mon, April 18, 2011 6:36:42 PM
Subject: Re: [Pw_forum] Pseudo potentials for hybrid DFT


On Apr 18, 2011, at 18:25 , Eyvaz Isaev wrote:

>  Variable:       input_dft
>  [...]
> But as far as I remember this works (at least, worked) for norm- 
> conserving pseudopotentials only.

>just a remark: hybrid functionals work only for norm-conserving  
> pseudopotentials, but variable input_dft works in all cases

Paolo, thanks for the correction. Of course, I meant hybrid  functionals. 

Bests, 
Eyvaz.
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From L-marks at northwestern.edu  Mon Apr 18 21:35:00 2011
From: L-marks at northwestern.edu (Laurence Marks)
Date: Mon, 18 Apr 2011 14:35:00 -0500
Subject: [Pw_forum] new bfgs: strange behavior doing vc-relax
In-Reply-To: <BANLkTin4=1zogfWZwtYfS1dH0GqP2AzZaA@mail.gmail.com>
References: <BANLkTin4=1zogfWZwtYfS1dH0GqP2AzZaA@mail.gmail.com>
Message-ID: <BANLkTinEb1BM7Pm6h-ahT1RUsN-85qAjnw@mail.gmail.com>

The latest BFGS has a curvature trap which can change the behavior
particularly if you have too few k-points. Can you please do

grep -e "!    tot" -e bfgs WHATEVER.out

(where WHATEVER is relevant) and send it to me, perhaps at my private
email (or the full .out file). I am not an expert with QE, but might
be able to say something.

2011/4/18 ?????? ????? <max.n.popov at gmail.com>:
> Dear QE developers,
>
> comparing vc-relax calculations between BFGS(4.2.1) and the latest BFGS(from
> CVS) I faced? with a following problem:
> the newest QE calculates one extra point after achieving convergence
> criteria (etot_conv_thr,force_conv_thr,press_conv_thr),
> which leads to slightly higher total energy.
>
> Here are the two latest energies from outputs:
> ?????? v.4.2.1???????? ? ? ? ? ? ??? CVS(18.04.2011)
>
> -242.66342170 Ry?????? -242.66342267 Ry
> -242.66342336 Ry?????? -242.66284562 Ry
>
> One can see that there is a good agreement between the last energy by
> v.4.2.1 and next to the last by CVS-version, whereas
> the last energy by CVS is higher by ~ 0.5 mRy.
>
> I tried relax (cell shape fixed) also - it works fine, no extra point
> calculation.
>
> --
> Best regards, Max Popov
> Ph.D. student
> Materials center Leoben (MCL), Leoben, Austria.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>



-- 
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Research is to see what everybody else has seen, and to think what
nobody else has thought
Albert Szent-Gyorgi

From max.n.popov at gmail.com  Mon Apr 18 23:43:33 2011
From: max.n.popov at gmail.com (=?KOI8-R?B?7cHL08nNIPDP0M/X?=)
Date: Mon, 18 Apr 2011 23:43:33 +0200
Subject: [Pw_forum] new bfgs: strange behavior doing vc-relax
In-Reply-To: <BANLkTinEb1BM7Pm6h-ahT1RUsN-85qAjnw@mail.gmail.com>
References: <BANLkTin4=1zogfWZwtYfS1dH0GqP2AzZaA@mail.gmail.com>
	<BANLkTinEb1BM7Pm6h-ahT1RUsN-85qAjnw@mail.gmail.com>
Message-ID: <BANLkTikF_eUgE6tUcQ6XJyJT4W_Z-h8a_w@mail.gmail.com>

Dear Prof. Marks,

I've sent the whole output file to your private e-mail as you suggested.
Here I just put the result of grep command:

CVS version:
!    total energy              =    -242.65271405 Ry
     number of bfgs steps    =   0
!    total energy              =    -242.66331605 Ry
     number of bfgs steps    =   1
!    total energy              =    -242.66341971 Ry
     number of bfgs steps    =   2
!    total energy              =    -242.66342267 Ry
     bfgs converged in   4 scf cycles and   3 bfgs steps
!    total energy              =    -242.66284562 Ry

v.4.2.1
!    total energy              =    -242.65271405 Ry
     number of bfgs steps    =   0
!    total energy              =    -242.64460983 Ry
     number of bfgs steps    =   1
!    total energy              =    -242.66331847 Ry
     number of bfgs steps    =   1
!    total energy              =    -242.66341565 Ry
     number of bfgs steps    =   2
!    total energy              =    -242.66342170 Ry
     number of bfgs steps    =   3
!    total energy              =    -242.66342336 Ry
     bfgs converged in   6 scf cycles and   4 bfgs steps

Best regards,
Maxim.


2011/4/18 Laurence Marks <L-marks at northwestern.edu>

> The latest BFGS has a curvature trap which can change the behavior
> particularly if you have too few k-points. Can you please do
>
> grep -e "!    tot" -e bfgs WHATEVER.out
>
> (where WHATEVER is relevant) and send it to me, perhaps at my private
> email (or the full .out file). I am not an expert with QE, but might
> be able to say something.
>
> 2011/4/18 ?????? ????? <max.n.popov at gmail.com>:
> > Dear QE developers,
> >
> > comparing vc-relax calculations between BFGS(4.2.1) and the latest
> BFGS(from
> > CVS) I faced  with a following problem:
> > the newest QE calculates one extra point after achieving convergence
> > criteria (etot_conv_thr,force_conv_thr,press_conv_thr),
> > which leads to slightly higher total energy.
> >
> > Here are the two latest energies from outputs:
> >        v.4.2.1                       CVS(18.04.2011)
> >
> > -242.66342170 Ry       -242.66342267 Ry
> > -242.66342336 Ry       -242.66284562 Ry
> >
> > One can see that there is a good agreement between the last energy by
> > v.4.2.1 and next to the last by CVS-version, whereas
> > the last energy by CVS is higher by ~ 0.5 mRy.
> >
> > I tried relax (cell shape fixed) also - it works fine, no extra point
> > calculation.
> >
> > --
> > Best regards, Max Popov
> > Ph.D. student
> > Materials center Leoben (MCL), Leoben, Austria.
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
>
>
>
> --
> Laurence Marks
> Department of Materials Science and Engineering
> MSE Rm 2036 Cook Hall
> 2220 N Campus Drive
> Northwestern University
> Evanston, IL 60208, USA
> Tel: (847) 491-3996 Fax: (847) 491-7820
> email: L-marks at northwestern dot edu
> Web: www.numis.northwestern.edu
> Chair, Commission on Electron Crystallography of IUCR
> www.numis.northwestern.edu/
> Research is to see what everybody else has seen, and to think what
> nobody else has thought
> Albert Szent-Gyorgi
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From priya_johari at brown.edu  Tue Apr 19 00:27:08 2011
From: priya_johari at brown.edu (Johari, Priya Sudhir)
Date: Mon, 18 Apr 2011 18:27:08 -0400
Subject: [Pw_forum] TDDFT for periodic systems
Message-ID: <BANLkTindYpSYZfBrGKQoH4-CiDzTSkDy1A@mail.gmail.com>

Dear Developers,

I was wondering if recently implemented TD-DFPT tool in espresso-4.3 can be
used for calculating absorption spectrum of period systems (slab or so)?

Thanks in advance.

Regards,
Priya.
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From mahdi_fn109 at yahoo.com  Tue Apr 19 00:41:48 2011
From: mahdi_fn109 at yahoo.com (Mahdi Faqieh nasiri)
Date: Mon, 18 Apr 2011 15:41:48 -0700 (PDT)
Subject: [Pw_forum] Graphene band structure
Message-ID: <801183.33963.qm@web43142.mail.sp1.yahoo.com>

Dear all,
I'm trying to draw Graphene band structure.
 i write this input file, but it dosnt reach answer.
what is wrong in this input file?

?

?

&CONTROL

????????????????
calculation = 'scf' ,

???????????????
restart_mode = 'from_scratch' ,

???????????????
etot_conv_thr = 1.0E-6? , 

??????????????
forc_conv_thr = 1.0D-6 ,

??????
outdir='/home/mahdi/Desktop/Work/Graphene/Graphene2Atomi/3',

?????? pseudo_dir =
'/home/mahdi/Desktop/Work/Graphene/Pseudo',???????? 

???????????????
tprnfor?? = .true.

???????????????
tstress = .true.

?? /

??? &SYSTEM

??????????????????????
ibrav = 4,

???????????????????
celldm(1) = 4.647804023,

?????????????????? ?celldm(3) = 6 ,

????????????????????????
nat = 2,

???????????????????????
ntyp = 1,

????????????????????
ecutwfc = 50 ,

????????????????????
ecutrho = 500 ,??????????????????????


????????????????
occupations = 'smearing' ,

????????????????
degauss= 0.01 ,

????????????????
smearing= 'gaussian',

?/

?&ELECTRONS

?????????????????
conv_thr = 1.D-6 , 

?/

ATOMIC_SPECIES

C??? 12.0107??? C.pbe-van_bm.UPF

ATOMIC_POSITIONS (angstrom)

C??????? 0.0???????????? 0.0????????????? 0.0??????? 

C??????? 1.2306????????? 0.71048725?????? 0.0??????? 

?

K_POINTS {automatic}

20?? 20?? 1???????
0?? 0?? 0?? ?


Mahdi Faghih nasiri

MSC,

Guilan University,

Rasht, Iran.
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From L-marks at northwestern.edu  Tue Apr 19 00:57:09 2011
From: L-marks at northwestern.edu (Laurence Marks)
Date: Mon, 18 Apr 2011 17:57:09 -0500
Subject: [Pw_forum] new bfgs: strange behavior doing vc-relax
In-Reply-To: <BANLkTikF_eUgE6tUcQ6XJyJT4W_Z-h8a_w@mail.gmail.com>
References: <BANLkTin4=1zogfWZwtYfS1dH0GqP2AzZaA@mail.gmail.com>
	<BANLkTinEb1BM7Pm6h-ahT1RUsN-85qAjnw@mail.gmail.com>
	<BANLkTikF_eUgE6tUcQ6XJyJT4W_Z-h8a_w@mail.gmail.com>
Message-ID: <BANLkTimxFmEW0V54k_4ZgPOqwCGjMLhpOA@mail.gmail.com>


From germaneau at gucas.ac.cn  Tue Apr 19 13:35:05 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Tue, 19 Apr 2011 07:35:05 -0400
Subject: [Pw_forum] Graphene band structure
In-Reply-To: <503166017.11468@test1.gucas.ac.cn>
References: <503166017.11468@test1.gucas.ac.cn>
Message-ID: <4DAD7369.30406@gucas.ac.cn>

What do you mean by "it doesn't reach answer" ?
After the scf calculation you have to make a nscf calculation with 
"calculation='bands'" and a define a K-path.
Then execute bands.x. and plotband.x.
You;s better take a look to the examples for the procedure.

          Eric.

On 04/18/2011 06:41 PM, Mahdi Faqieh nasiri wrote:
> Dear all,
> I'm trying to draw Graphene band structure.
> i write this input file, but it dosnt reach answer.
> what is wrong in this input file?
>
> &CONTROL
>
> calculation = 'scf' ,
>
> restart_mode = 'from_scratch' ,
>
> etot_conv_thr = 1.0E-6,
>
> forc_conv_thr = 1.0D-6 ,
>
> outdir='/home/mahdi/Desktop/Work/Graphene/Graphene2Atomi/3',
>
> pseudo_dir = '/home/mahdi/Desktop/Work/Graphene/Pseudo',
>
> tprnfor= .true.
>
> tstress = .true.
>
> /
>
> &SYSTEM
>
> ibrav = 4,
>
> celldm(1) = 4.647804023,
>
> celldm(3) = 6 ,
>
> nat = 2,
>
> ntyp = 1,
>
> ecutwfc = 50 ,
>
> ecutrho = 500 ,
>
> occupations = 'smearing' ,
>
> degauss= 0.01 ,
>
> smearing= 'gaussian',
>
> /
>
> &ELECTRONS
>
> conv_thr = 1.D-6 ,
>
> /
>
> ATOMIC_SPECIES
>
> C12.0107C.pbe-van_bm.UPF
>
> ATOMIC_POSITIONS (angstrom)
>
> C0.00.00.0
>
> C1.23060.710487250.0
>
> K_POINTS {automatic}
>
> 20201000
>
>
>
>
> Mahdi Faghih nasiri
> MSC,
> Guilan University,
> Rasht, Iran.
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
/Be the change you wish to see in the world
/ ? Mahatma Gandhi ?

Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/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 arvifis at gmail.com  Tue Apr 19 02:30:40 2011
From: arvifis at gmail.com (Arles V. Gil Rebaza)
Date: Mon, 18 Apr 2011 21:30:40 -0300
Subject: [Pw_forum] about PP PAW to Ti
Message-ID: <BANLkTikOeDb0CNza3CZajOtEc6Rpmr4q+g@mail.gmail.com>

Hi QE user, i'm using QE 4.3 and i was trying to make a PP PAW to Ti, but a
have the next error message in the output file

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from new_paw_hamiltonian : error #         1
     negative rho
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...


This is my input file Ti.in . What's my mistake??

 &input
    title='Ti'
      zed=22,
    config='[Ar] 4s2 3d2 4p0'
    iswitch=3,
    dft='PBE'
    nld=3,
        eminld=-10,
        emaxld=10
        deld=0.01d0,
        rlderiv=2.3,
 /
 &inputp
   pseudotype=3,
   nlcc=.true.,
     new_core_ps = .true.
     rcore=1.2000
   lloc=-2,
     rcloc=2.2000
   file_pseudopw='Ti.pbe-paw_kj.UPF'
   zval=4
   lpaw=.true.
     lnc2paw=.false.
     which_augfun ='BESSEL'
     rmatch_augfun= 2.3000
   author='"Arles V." <arlesv at fisica.unlp.edu.ar>'
   tm = .true.
!nX n  l   occ   nrg   rmin   rcut
 /
6
3D  3 2 2.00    0.00    1.50    2.2000
3D  3 2 0.00   -0.40    1.50    2.2000
4S  1 0 2.00    0.00    1.50    2.2000
4S  1 0 0.00    0.30    1.50    2.2000
4P  2 1 0.00    0.00    1.50    2.2000
4P  2 1 0.00    0.70    1.50    2.2000


Thank for advance.

PhD stdn. Arles V. Gil Rebaza
Instituto de F?sica de La Plata
Argentina
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From ma at nano.ku.dk  Tue Apr 19 06:30:27 2011
From: ma at nano.ku.dk (Martin Andersson)
Date: Tue, 19 Apr 2011 06:30:27 +0200
Subject: [Pw_forum] about PP PAW to Ti
In-Reply-To: <BANLkTikOeDb0CNza3CZajOtEc6Rpmr4q+g@mail.gmail.com>
References: <BANLkTikOeDb0CNza3CZajOtEc6Rpmr4q+g@mail.gmail.com>
Message-ID: <4DAD0FE3.6030107@nano.ku.dk>

Hi,

You can download atompaw from 
http://www.wfu.edu/~natalie/papers/pwpaw/man.html

It can generate paw files for QE and has a dataset that works for Ti in 
its library.

Cheers,
Martin Andersson
University of Copenhagen

On 4/19/2011 2:30 AM, Arles V. Gil Rebaza wrote:
> Hi QE user, i'm using QE 4.3 and i was trying to make a PP PAW to Ti, 
> but a have the next error message in the output file
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from new_paw_hamiltonian : error #         1
>      negative rho
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>      stopping ...
>
>
> This is my input file Ti.in . What's my mistake??
>
> &input
>     title='Ti'
>       zed=22,
>     config='[Ar] 4s2 3d2 4p0'
>     iswitch=3,
>     dft='PBE'
>     nld=3,
>         eminld=-10,
>         emaxld=10
>         deld=0.01d0,
>         rlderiv=2.3,
>  /
> &inputp
>    pseudotype=3,
>    nlcc=.true.,
>      new_core_ps = .true.
>      rcore=1.2000
>    lloc=-2,
>      rcloc=2.2000
>    file_pseudopw='Ti.pbe-paw_kj.UPF'
>    zval=4
>    lpaw=.true.
>      lnc2paw=.false.
>      which_augfun ='BESSEL'
>      rmatch_augfun= 2.3000
>    author='"Arles V." <arlesv at fisica.unlp.edu.ar 
> <mailto:arlesv at fisica.unlp.edu.ar>>'
>    tm = .true.
> !nX n  l   occ   nrg   rmin   rcut
>  /
> 6
> 3D  3 2 2.00    0.00    1.50    2.2000
> 3D  3 2 0.00   -0.40    1.50    2.2000
> 4S  1 0 2.00    0.00    1.50    2.2000
> 4S  1 0 0.00    0.30    1.50    2.2000
> 4P  2 1 0.00    0.00    1.50    2.2000
> 4P  2 1 0.00    0.70    1.50    2.2000
>
>
> Thank for advance.
>
> PhD stdn. Arles V. Gil Rebaza
> Instituto de F?sica de La Plata
> Argentina
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From gianluca.giovannetti at gmail.com  Tue Apr 19 08:15:41 2011
From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti)
Date: Tue, 19 Apr 2011 08:15:41 +0200
Subject: [Pw_forum] radius of the sphere to calculate the projected density
	of states
Message-ID: <BANLkTi=vcKHsx-X8dNXYSDNBLRPhNSDf2w@mail.gmail.com>

Dear All,

i`m calculating the projected density of states of some material.

this should be done integrating within a sphere.

can i change the radius of such sphere in PW?

i thank you in advance.

cheers,

Gianluca Giovannetti
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From mahdi_fn109 at yahoo.com  Tue Apr 19 08:17:30 2011
From: mahdi_fn109 at yahoo.com (Mahdi Faqieh nasiri)
Date: Mon, 18 Apr 2011 23:17:30 -0700 (PDT)
Subject: [Pw_forum] Graphene band structure
Message-ID: <373139.1868.qm@web43138.mail.sp1.yahoo.com>

Dear all,
I'm trying to draw Graphene band structure.
i do "calculation= "scf" "bands'" and a define a K-path.
Then execute bands.x. and plotband.x.
but the graph in M-K is?Completely?different??with TB graph.
please take a look to this files.
Mahdi Faghih nasiri

MSC,

Guilan University,

Rasht, Iran.
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From mxchen.2011 at gmail.com  Tue Apr 19 08:34:50 2011
From: mxchen.2011 at gmail.com (Mingxing Chen)
Date: Tue, 19 Apr 2011 08:34:50 +0200
Subject: [Pw_forum] Shirley interpolation
Message-ID: <BANLkTinJifvUkmcJ8AOTjwe2v74Ujuo-qw@mail.gmail.com>

Dear all,

As stated in PRB 80, 235126 (2009) by David Prendergast, the Shirley's
interpolation scheme has been implemented as a post processing tool in QE.
However, I did not find it in the latest version of QE, i.e., Version 4.3.
Does anyone know that? Any suggestion would be appreciated. Thanks a lot.

Best regards,

Mingxing Chen

-- 

Mingxing Chen,
Institute for Physical Chemistry
University of Vienna
Email: mxchen.2011 at gmail.com <mingxing.chen at univie.ac.at>
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From dstrubbe at berkeley.edu  Tue Apr 19 08:44:40 2011
From: dstrubbe at berkeley.edu (David Strubbe)
Date: Mon, 18 Apr 2011 23:44:40 -0700
Subject: [Pw_forum] Shirley interpolation
In-Reply-To: <BANLkTinJifvUkmcJ8AOTjwe2v74Ujuo-qw@mail.gmail.com>
References: <BANLkTinJifvUkmcJ8AOTjwe2v74Ujuo-qw@mail.gmail.com>
Message-ID: <BANLkTi=9yfmPeQVZtCZt9QmCNf+0hs5Vkw@mail.gmail.com>

Mingxing,

Check out David's page about the code at http://shirley.lbl.gov/

David Strubbe
UC Berkeley

On Mon, Apr 18, 2011 at 11:34 PM, Mingxing Chen <mxchen.2011 at gmail.com>wrote:

> Dear all,
>
> As stated in PRB 80, 235126 (2009) by David Prendergast, the Shirley's
> interpolation scheme has been implemented as a post processing tool in QE.
> However, I did not find it in the latest version of QE, i.e., Version 4.3.
> Does anyone know that? Any suggestion would be appreciated. Thanks a lot.
>
> Best regards,
>
> Mingxing Chen
>
> --
>
> Mingxing Chen,
> Institute for Physical Chemistry
> University of Vienna
> Email: mxchen.2011 at gmail.com <mingxing.chen at univie.ac.at>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From mxchen.2011 at gmail.com  Tue Apr 19 08:58:10 2011
From: mxchen.2011 at gmail.com (Mingxing Chen)
Date: Tue, 19 Apr 2011 08:58:10 +0200
Subject: [Pw_forum] Shirley interpolation
In-Reply-To: <BANLkTi=9yfmPeQVZtCZt9QmCNf+0hs5Vkw@mail.gmail.com>
References: <BANLkTinJifvUkmcJ8AOTjwe2v74Ujuo-qw@mail.gmail.com>
	<BANLkTi=9yfmPeQVZtCZt9QmCNf+0hs5Vkw@mail.gmail.com>
Message-ID: <BANLkTikZgnps5CSdRLWfxseJku7eG_8WAg@mail.gmail.com>

Dear David Strubbe,

Thanks a lot for your reply. Yes, that is what I want. Thank you very much.

Best regards,

Mingxing Chen

On Tue, Apr 19, 2011 at 8:44 AM, David Strubbe <dstrubbe at berkeley.edu>wrote:

> Mingxing,
>
> Check out David's page about the code at http://shirley.lbl.gov/
>
> David Strubbe
> UC Berkeley
>
> On Mon, Apr 18, 2011 at 11:34 PM, Mingxing Chen <mxchen.2011 at gmail.com>wrote:
>
>> Dear all,
>>
>> As stated in PRB 80, 235126 (2009) by David Prendergast, the Shirley's
>> interpolation scheme has been implemented as a post processing tool in QE.
>> However, I did not find it in the latest version of QE, i.e., Version 4.3.
>> Does anyone know that? Any suggestion would be appreciated. Thanks a lot.
>>
>> Best regards,
>>
>> Mingxing Chen
>>
>> --
>>
>> Mingxing Chen,
>> Institute for Physical Chemistry
>> University of Vienna
>> Email: mxchen.2011 at gmail.com <mingxing.chen at univie.ac.at>
>>
>>
>>
>> _______________________________________________
>> 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
>
>


-- 

Mingxing Chen,
Institute for Physical Chemistry
University of Vienna
Email: mxchen.2011 at gmail.com <mingxing.chen at univie.ac.at>
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From giannozz at democritos.it  Tue Apr 19 09:42:27 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 19 Apr 2011 09:42:27 +0200
Subject: [Pw_forum] new bfgs: strange behavior doing vc-relax
In-Reply-To: <BANLkTin4=1zogfWZwtYfS1dH0GqP2AzZaA@mail.gmail.com>
References: <BANLkTin4=1zogfWZwtYfS1dH0GqP2AzZaA@mail.gmail.com>
Message-ID: <49016BE5-7859-4E92-8F4D-51EA85CE5B1F@democritos.it>


On Apr 18, 2011, at 15:58 , ?????? ????? wrote:

> comparing vc-relax calculations between BFGS(4.2.1)
> and the latest BFGS(from CVS) I faced  with a following problem

there is no problem, or at least, not in your output. There are
two differences wrt the previous version:
1)  the first optimization step in vc-relax algorithm was modified,
so vc-relax should now converge slightly better
2) since everybody was complaining all the time that "I made a
scf calculation and got different result from vc-relax", a final
scf step with G-vectors appropriate for the final cell was added.
Why one gets different results etc etc has been explained no
less than 1001 times in this mailing list.

There can be a problem in this last step, explained here:
http://www.democritos.it/pipermail/pw_forum/2011-April/020052.html
Solution, for the time being: ignore it.

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





From giannozz at democritos.it  Tue Apr 19 09:44:01 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 19 Apr 2011 09:44:01 +0200
Subject: [Pw_forum] radius of the sphere to calculate the projected
	density of states
In-Reply-To: <BANLkTi=vcKHsx-X8dNXYSDNBLRPhNSDf2w@mail.gmail.com>
References: <BANLkTi=vcKHsx-X8dNXYSDNBLRPhNSDf2w@mail.gmail.com>
Message-ID: <BAB8F75F-B155-4B83-A5CE-29848B6C19D9@democritos.it>


On Apr 19, 2011, at 8:15 , Gianluca Giovannetti wrote:

> i`m calculating the projected density of states of some material.
> this should be done integrating within a sphere.

it isn't done that way

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





From davide.sangalli at gmail.com  Tue Apr 19 10:26:42 2011
From: davide.sangalli at gmail.com (Davide Sangalli)
Date: Tue, 19 Apr 2011 10:26:42 +0200
Subject: [Pw_forum]  Born effective charges in spin polarized systems
In-Reply-To: <AANLkTinMyKLrTWOVKnnD=EG1mZaqHfuNv82zkTbvi4DK@mail.gmail.com>
References: <4D8B709B.3030404@gmail.com>	<4D8B732C.7080002@gmail.com>
	<AANLkTinMyKLrTWOVKnnD=EG1mZaqHfuNv82zkTbvi4DK@mail.gmail.com>
Message-ID: <4DAD4742.6090207@gmail.com>

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From max.n.popov at gmail.com  Tue Apr 19 10:49:37 2011
From: max.n.popov at gmail.com (=?KOI8-R?B?7cHL08nNIPDP0M/X?=)
Date: Tue, 19 Apr 2011 10:49:37 +0200
Subject: [Pw_forum] new bfgs: strange behavior doing vc-relax
In-Reply-To: <49016BE5-7859-4E92-8F4D-51EA85CE5B1F@democritos.it>
References: <BANLkTin4=1zogfWZwtYfS1dH0GqP2AzZaA@mail.gmail.com>
	<49016BE5-7859-4E92-8F4D-51EA85CE5B1F@democritos.it>
Message-ID: <BANLkTimLy-BuMwKLpBxz7DoUJM7PHRTbMQ@mail.gmail.com>

Dear Dr. Giannozzi,

thank you for the answer! I could find it myself looking in the output file
a bit more carefully...
One thing, which is somehow contrary to my expectations, is that the final
scf energy is higher
than the last one from vc-relax. Could you, please, elaborate a bit on the
matter?

Best  regards,
Maxim.

2011/4/19 Paolo Giannozzi <giannozz at democritos.it>

>
> On Apr 18, 2011, at 15:58 , ?????? ????? wrote:
>
> > comparing vc-relax calculations between BFGS(4.2.1)
> > and the latest BFGS(from CVS) I faced  with a following problem
>
> there is no problem, or at least, not in your output. There are
> two differences wrt the previous version:
> 1)  the first optimization step in vc-relax algorithm was modified,
> so vc-relax should now converge slightly better
> 2) since everybody was complaining all the time that "I made a
> scf calculation and got different result from vc-relax", a final
> scf step with G-vectors appropriate for the final cell was added.
> Why one gets different results etc etc has been explained no
> less than 1001 times in this mailing list.
>
> There can be a problem in this last step, explained here:
> http://www.democritos.it/pipermail/pw_forum/2011-April/020052.html
> Solution, for the time being: ignore it.
>
> P.
> --
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From degironc at sissa.it  Tue Apr 19 11:03:41 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Tue, 19 Apr 2011 11:03:41 +0200
Subject: [Pw_forum] new bfgs: strange behavior doing vc-relax
In-Reply-To: <BANLkTinEb1BM7Pm6h-ahT1RUsN-85qAjnw@mail.gmail.com>
References: <BANLkTin4=1zogfWZwtYfS1dH0GqP2AzZaA@mail.gmail.com>
	<BANLkTinEb1BM7Pm6h-ahT1RUsN-85qAjnw@mail.gmail.com>
Message-ID: <4DAD4FED.101@sissa.it>

dear  Max Popov
      have you bothered looking at the output ? has the bfgs procedure 
converged ?
      Notice that in recent versions of vcrelax one additional scf 
calculation is performed at the final configuration reinitializing 
reciprocal lattice vectors .
      this has nothing to do with the bfgs procedure. it's a check to 
verify what is the impact of the deformation of the cutoff "sphere" 
induced by the cell-shape change.
    if the cutoff is large enough the change should be very small. 0.5 
mRy looks small to me.

Stefano de Gironcoli
SISSA & DEMOCRITOS

On 04/18/2011 09:35 PM, Laurence Marks wrote:
> The latest BFGS has a curvature trap which can change the behavior
> particularly if you have too few k-points. Can you please do
>
> grep -e "!    tot" -e bfgs WHATEVER.out
>
> (where WHATEVER is relevant) and send it to me, perhaps at my private
> email (or the full .out file). I am not an expert with QE, but might
> be able to say something.
>
> 2011/4/18 ?????? ?????<max.n.popov at gmail.com>:
>> Dear QE developers,
>>
>> comparing vc-relax calculations between BFGS(4.2.1) and the latest BFGS(from
>> CVS) I faced  with a following problem:
>> the newest QE calculates one extra point after achieving convergence
>> criteria (etot_conv_thr,force_conv_thr,press_conv_thr),
>> which leads to slightly higher total energy.
>>
>> Here are the two latest energies from outputs:
>>         v.4.2.1                       CVS(18.04.2011)
>>
>> -242.66342170 Ry       -242.66342267 Ry
>> -242.66342336 Ry       -242.66284562 Ry
>>
>> One can see that there is a good agreement between the last energy by
>> v.4.2.1 and next to the last by CVS-version, whereas
>> the last energy by CVS is higher by ~ 0.5 mRy.
>>
>> I tried relax (cell shape fixed) also - it works fine, no extra point
>> calculation.
>>
>> --
>> Best regards, Max Popov
>> Ph.D. student
>> Materials center Leoben (MCL), Leoben, Austria.
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>


From asmogunov at gmail.com  Tue Apr 19 11:13:46 2011
From: asmogunov at gmail.com (Alex Smogunov)
Date: Tue, 19 Apr 2011 11:13:46 +0200
Subject: [Pw_forum] questions about PWCOND
In-Reply-To: <29121_1303121870_4DAC0FCE_29121_220_1_908CBC9017354841B2F32BBEC70A05A101C154717C33@THSONEA01CMS01P.one.grp>
References: <29121_1303121870_4DAC0FCE_29121_220_1_908CBC9017354841B2F32BBEC70A05A101C154717C33@THSONEA01CMS01P.one.grp>
Message-ID: <BANLkTik_D0V6NV38TKYBu+X4k5Tw11iuOQ@mail.gmail.com>

Dear Virginie.

2011/4/18 TRINITE Virginie <virginie.trinite at thalesgroup.com>

>  Dear all,
>
> I try to use PWCOND, and I have two questions:
>
> >In which units are the boundary in the input file (bdl, bds, bdr)?
>
>
>
>
  They are in alat units.


> >I have run the two examples 12 and 22 without problem and found results in
> agreement with the publications but when
>
> I try a more heavy system, I obtain zero conductance.
>
> The example that I have used, is the Magnetic Tunnel Junction given in
> Alexandre Smogounov?s home page.
>
> The program finished normally without error or complain but all the
> transmission are nearly zero.
>
> I didn?t check any convergence, because I want only to test the program.
> Did I miss something?
>
>
>

  I think it is normal since here you have a tunneling through an insulating
spacer and TMR effects.
 The conductances should get larger if you decrease the number of isolating
layers.

All the best,
Alexander

_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From gianluca.giovannetti at gmail.com  Tue Apr 19 11:18:24 2011
From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti)
Date: Tue, 19 Apr 2011 11:18:24 +0200
Subject: [Pw_forum] radius of the sphere to calculate the projected
 density of states
In-Reply-To: <BAB8F75F-B155-4B83-A5CE-29848B6C19D9@democritos.it>
References: <BANLkTi=vcKHsx-X8dNXYSDNBLRPhNSDf2w@mail.gmail.com>
	<BAB8F75F-B155-4B83-A5CE-29848B6C19D9@democritos.it>
Message-ID: <BANLkTik2oosq2y-D1Qjvx2r6pgTK1Of7kw@mail.gmail.com>

Dear Paolo,

where i can find some guide-lines how this is done in PW?

thank you.

ciao

G.

On Tue, Apr 19, 2011 at 9:44 AM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Apr 19, 2011, at 8:15 , Gianluca Giovannetti wrote:
>
> > i`m calculating the projected density of states of some material.
> > this should be done integrating within a sphere.
>
> it isn't done that way
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From giovanni.cantele at spin.cnr.it  Tue Apr 19 11:34:22 2011
From: giovanni.cantele at spin.cnr.it (Giovanni Cantele)
Date: Tue, 19 Apr 2011 11:34:22 +0200
Subject: [Pw_forum] Graphene band structure
In-Reply-To: <373139.1868.qm@web43138.mail.sp1.yahoo.com>
References: <373139.1868.qm@web43138.mail.sp1.yahoo.com>
Message-ID: <EB02328D-C925-4966-A626-752DA1DD6438@spin.cnr.it>


On Apr 19, 2011, at 8:17 AM, Mahdi Faqieh nasiri wrote:

> 
> Dear all,
> I'm trying to draw Graphene band structure.
> i do "calculation= "scf" "bands'" and a define a K-path.
> Then execute bands.x. and plotband.x.
> but the graph in M-K is Completely different  with TB graph.
> please take a look to this files.
> 
> Mahdi Faghih nasiri
> MSC,
> Guilan University,
> Rasht, Iran.
> <3.rar><bands 1.jpg>_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

As far as I understand, the path you follow is K-G-M-K.
Not sure about that, but maybe you chose the "wrong" M point. While any path within the BZ is acceptable,
the comparison with other calculations needs you follow exactly the same (or an equivalent) path.
Please refer to the attached pdf, but basically, the band structure you expect is (or should be!) obtained
if you replace your M=(0,0.58) with M'=(0.5,0.29).

Giovanni


PS just to point out that using free software should be everywhere encouraged,
the attached plot was produced in 5 minutes using the GeoGebra software.




--

**** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it

Giovanni Cantele, PhD
CNR-SPIN and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910 - Fax:   +39 081 676346
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it

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From max.n.popov at gmail.com  Tue Apr 19 11:59:51 2011
From: max.n.popov at gmail.com (=?KOI8-R?B?7cHL08nNIPDP0M/X?=)
Date: Tue, 19 Apr 2011 11:59:51 +0200
Subject: [Pw_forum] new bfgs: strange behavior doing vc-relax
In-Reply-To: <4DAD4FED.101@sissa.it>
References: <BANLkTin4=1zogfWZwtYfS1dH0GqP2AzZaA@mail.gmail.com>
	<BANLkTinEb1BM7Pm6h-ahT1RUsN-85qAjnw@mail.gmail.com>
	<4DAD4FED.101@sissa.it>
Message-ID: <BANLkTinJ=+OBUrWvbia0dt8YMZH-_Lv9EQ@mail.gmail.com>

Dear Stefano de Gironcoli,

2011/4/19 Stefano de Gironcoli <degironc at sissa.it>

>      have you bothered looking at the output ? has the bfgs procedure
> converged ?
>

Yes, I have looked. If you look carefully at one of the previous posts,
you'll see
that bfgs procedure converged.


>      Notice that in recent versions of vcrelax one additional scf
> calculation is performed at the final configuration reinitializing
> reciprocal lattice vectors .
>

This has been already explained by Dr. Giannozzi in previous posts too.


>      this has nothing to do with the bfgs procedure. it's a check to
> verify what is the impact of the deformation of the cutoff "sphere"
> induced by the cell-shape change.
>

My question is exactly about this. More specific: why deformed cutoff
"sphere" gives lower total energy compared to undeformed one?



>    if the cutoff is large enough the change should be very small. 0.5
> mRy looks small to me.
>

Is there any criteria for an energy difference to be called "small"?

-- 
Best regards, Max Popov
Ph.D. student
Materials center Leoben (MCL), Leoben, Austria.
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From b.bouaouina at gmail.com  Tue Apr 19 12:26:37 2011
From: b.bouaouina at gmail.com (boudjemaa bouaouina)
Date: Tue, 19 Apr 2011 12:26:37 +0200
Subject: [Pw_forum] radius of the sphere to calculate the projected
 density of states
In-Reply-To: <BANLkTik2oosq2y-D1Qjvx2r6pgTK1Of7kw@mail.gmail.com>
References: <BANLkTi=vcKHsx-X8dNXYSDNBLRPhNSDf2w@mail.gmail.com>
	<BAB8F75F-B155-4B83-A5CE-29848B6C19D9@democritos.it>
	<BANLkTik2oosq2y-D1Qjvx2r6pgTK1Of7kw@mail.gmail.com>
Message-ID: <BANLkTintpZ_dTXvE0yfy=D9bwwsH+cAuig@mail.gmail.com>

Dear all,
I want to plot energy band for silicon, I have the scf calculation, and now
how to plot energy band function with K
thank you
bouaouina

2011/4/19 Gianluca Giovannetti <gianluca.giovannetti at gmail.com>

> Dear Paolo,
>
> where i can find some guide-lines how this is done in PW?
>
> thank you.
>
> ciao
>
> G.
>
>
> On Tue, Apr 19, 2011 at 9:44 AM, Paolo Giannozzi <giannozz at democritos.it>wrote:
>
>>
>> On Apr 19, 2011, at 8:15 , Gianluca Giovannetti wrote:
>>
>> > i`m calculating the projected density of states of some material.
>> > this should be done integrating within a sphere.
>>
>> it isn't done that way
>>
>> P.
>> ---
>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://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 eariel99 at gmail.com  Tue Apr 19 12:56:03 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Tue, 19 Apr 2011 07:56:03 -0300
Subject: [Pw_forum] new bfgs: strange behavior doing vc-relax
Message-ID: <BANLkTimF1tTW3N20=ptvZ7vh0ut_qJJcKQ@mail.gmail.com>

>Dear Dr. Giannozzi,
>thank you for the answer! I could find it myself looking in the output file
a bit >more carefully...
>One thing, which is somehow contrary to my expectations, is that the final
scf >energy is higher
>than the last one from vc-relax. Could you, please, elaborate a bit on the
>matter?

Dear Maxim,

I followed this discussion with interest, and thanks to that I learned about
the new scf calculation with final G-vectors. Concerning your last question,

the energy is higher because the vc-relaxed energy was optimized for a
different basis set, than the final scf calculation (different G-vectors).
Hence, the energy of the final scf calculation is is made for a structure
that is slightly out of the minimum for the new basis set. Remember than the
G-vectors used in a scf calculation are all the reciprocal lattice vectors
 contained in a sphere that has a radius determined by the cutoff. These
vectors are selected at the first step of the vc-relaxation. When the unit
cell gets deformed, the G-vectors vary accordingly, and the region that the
G-vectors occupy is a deformation from the initial sphere, maybe an
elipsoid. When the vc-relax stops, the final scf calculation takes the
G-vectors contained inside a sphere. Hence, some of the old G-vectors that
were in the border of the deformed sphere may be eliminated, and some that
were absent are now included.
If you had used an (impossible) infinite cutoff, the basis set would be
complete in both cases (G-vectors contained in an infinite sphere or in an
infinite elipsoid) and there would be no difference. Usually, I repeat the
vc-relax procedure starting 'from_scratch' with the last structure
(coordinates and lattice vectors) in the new input file, until the vc-relax
procedure performs only one step. In this case there is no difference. If it
never happens that vc-relax stops at the first step, then I increase the
cutoffs. In your case, the energy difference of 0.5 mRy may be small enough
and do not need to do that. It depends on the property that you want. E.g.,
if you are interested in elastic properties,  you may need that the minimal
energy structure also gives a stress tensor below 0.1 kbar or so. If you
cannot get it, increase the cutoff.

The following link may help

http://www.quantum-espresso.org/wiki/index.php/Methodological_Background#Stress

Best regards

-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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From giovanni.cantele at spin.cnr.it  Tue Apr 19 13:10:49 2011
From: giovanni.cantele at spin.cnr.it (Giovanni Cantele)
Date: Tue, 19 Apr 2011 13:10:49 +0200
Subject: [Pw_forum] radius of the sphere to calculate the projected
	density of states (ACTUALLY BAND STRUCTURE OF Si)
In-Reply-To: <BANLkTintpZ_dTXvE0yfy=D9bwwsH+cAuig@mail.gmail.com>
References: <BANLkTi=vcKHsx-X8dNXYSDNBLRPhNSDf2w@mail.gmail.com>
	<BAB8F75F-B155-4B83-A5CE-29848B6C19D9@democritos.it>
	<BANLkTik2oosq2y-D1Qjvx2r6pgTK1Of7kw@mail.gmail.com>
	<BANLkTintpZ_dTXvE0yfy=D9bwwsH+cAuig@mail.gmail.com>
Message-ID: <CCDABAD4-8C4B-44B2-A188-D59223A6CF0E@spin.cnr.it>


On Apr 19, 2011, at 12:26 PM, boudjemaa bouaouina wrote:

> Dear all,
> I want to plot energy band for silicon, I have the scf calculation, and now how to plot energy band function with K
> thank you
> bouaouina
> 

I apologize if I'm wrong, but it seems to me that this question as nothing to do with "radius of the sphere to calculate the projected density of states"
as reported in the subject.

According to what suggested here:
http://www.quantum-espresso.org/wiki/index.php/Pw_users
you should:
i) sign your post with your name and affiliation
ii) choose a meaningful subject. Do not use "reply" to start a new thread

Mostly important (always quoting from the above link), "Before posting, please: browse or search the archives - ..... Most questions are asked over and over again. Also: make an attempt to search the available documentation, notably the FAQ, the User Guide, and the Input Data Description. The answer to most questions is already there."

In this specific case, browsing the User Guide would take you to the following link:
http://www.quantum-espresso.org/user_guide/node26.html#SECTION00061020000000000000
where, among the other things it is suggested to "See Examples 01, 05, 08"

If you now cd the espresso-x.x.x/examples directory on your PC, the README file says: 
example01:
    This example shows how to use pw.x to calculate the total energy
    and the band structure of four simple systems: Si, Al, Cu, Ni.

So, not only you get an answer, but in this specific case, browsing example01, you're so lucky that
someone already wrote all the input files  you need!!!!



Giovanni




--

**** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it

Giovanni Cantele, PhD
CNR-SPIN and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910 - Fax:   +39 081 676346
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it

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From giannozz at democritos.it  Tue Apr 19 14:07:10 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 19 Apr 2011 14:07:10 +0200
Subject: [Pw_forum] radius of the sphere to calculate the projected
	density of states
In-Reply-To: <BANLkTintpZ_dTXvE0yfy=D9bwwsH+cAuig@mail.gmail.com>
References: <BANLkTi=vcKHsx-X8dNXYSDNBLRPhNSDf2w@mail.gmail.com>
	<BAB8F75F-B155-4B83-A5CE-29848B6C19D9@democritos.it>
	<BANLkTik2oosq2y-D1Qjvx2r6pgTK1Of7kw@mail.gmail.com>
	<BANLkTintpZ_dTXvE0yfy=D9bwwsH+cAuig@mail.gmail.com>
Message-ID: <5E3E9432-940C-4A5B-8DF4-D40E21E971D4@democritos.it>


On Apr 19, 2011, at 12:26 , boudjemaa bouaouina wrote:

> I want to plot energy band for silicon, I have the scf calculation,
> and now how to plot energy band function with K

and I want you to stop using "reply" in a random way

---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From giannozz at democritos.it  Tue Apr 19 14:09:52 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 19 Apr 2011 14:09:52 +0200
Subject: [Pw_forum] radius of the sphere to calculate the projected
	density of states
In-Reply-To: <BANLkTik2oosq2y-D1Qjvx2r6pgTK1Of7kw@mail.gmail.com>
References: <BANLkTi=vcKHsx-X8dNXYSDNBLRPhNSDf2w@mail.gmail.com>
	<BAB8F75F-B155-4B83-A5CE-29848B6C19D9@democritos.it>
	<BANLkTik2oosq2y-D1Qjvx2r6pgTK1Of7kw@mail.gmail.com>
Message-ID: <BED1142A-808D-48BD-9F03-58CE82B7B1EA@democritos.it>


On Apr 19, 2011, at 11:18 , Gianluca Giovannetti wrote:

> where i can find some guide-lines how this is done in PW?

it was discussed in this mailing list no later than a few days
ago

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





From yuminqian at gmail.com  Tue Apr 19 15:59:27 2011
From: yuminqian at gmail.com (yumin qian)
Date: Tue, 19 Apr 2011 21:59:27 +0800
Subject: [Pw_forum] Difference between cartesian coordinates and crystal
	coordinates
Message-ID: <BANLkTi=Ny=qDeYL9iP9QvPVHCRS9Uv7Qng@mail.gmail.com>

Dear Pwscf user
       I am still do not very clear how to set the axes using crystal axes
in the &system  card
      ibrav  and celldm(:) define the gives the  cartesian coordinates
      ibarv and A, B,C, cosab, cosac,cosbc gives the crystal coordinates

is my understanding correct?
the following two cards are all coordinate dependent
      ATOMIC_POSITIONS
      K_POINTS
there are either in accordence with cartesian coordinates or crystal
coordinates
how to make the three cards are in the same coordinates forms? or there are
all independent and can work consistent with it self in either coordinates?
The mixture of unit(alat,borhr,angstrom) and coordinates(crystal ,cartesian
) often confuse me.


is there anyone tell me how to set the ( &system,ATOMIC_POSITIONS, K_POINTS)
for cartesian coordinates and crystal coordinates respectively

and this is my input file for crystal coordinates structure, it can not give
right symmetry, I do not know the reason.


&control
    calculation='scf'
    restart_mode='from_scratch',
    pseudo_dir = '/home1/ymqian/soft/pwscf/psudo',
    outdir='./test'
    prefix='NaFeOSe',
 /
 &system
    ibrav = 7, A=4.1105, B=4.1105, C=14.65253, cosAB=90, cosAC=90, cosBC=90
    , nat= 7, ntyp= 4,
    ecutwfc = 45.0, ecutrho = 400.0
    occupations='smearing', smearing='mv', degauss=0.02,
    nspin=1,
 /
 &electrons
    diagonalization='david'
    conv_thr = 1.0e-7
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
Na  22.98977  Na.pbe-sp-van_ak.UPF
Fe  55.845    Fe.pbe-sp-van.UPF
Se  78.96     Se.pbe-van.UPF
O   15.9994   O.pbe-van_ak.UPF
ATOMIC_POSITIONS {crystal}
Na  0.500   0.500   0.1636801516544306
Na  0.000   0.000   0.3363198483455694
Fe  0.500   0.000   0.000000000000000
Fe  0.000   0.500   0.000000000000000
Se  0.000   0.000   0.1090917831789712
Se  0.500   0.500   0.3909082168210289
O   0.500   0.500   0.000000000000000
K_POINTS automatic
 12 12 4 0 0 0



Best Regards
Sincerely Y. M. Qian (???)
Laboratory of Condensed Matter Theory and Materials Computation
Institute of Physics(IOP), Chinese Academy of Sciences(CAS)
Tel:        + 8610 8264 9827
E-Mail:    yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603   Beijing 100190
China
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From nkxirainbow at gmail.com  Tue Apr 19 16:06:41 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Tue, 19 Apr 2011 22:06:41 +0800
Subject: [Pw_forum] radius of the sphere to calculate the projected
 density of states
In-Reply-To: <BANLkTi=vcKHsx-X8dNXYSDNBLRPhNSDf2w@mail.gmail.com>
References: <BANLkTi=vcKHsx-X8dNXYSDNBLRPhNSDf2w@mail.gmail.com>
Message-ID: <BANLkTim1AooeX4stKEuPSqjr=G+GgMA75w@mail.gmail.com>

Dear Gianluca Giovannetti:
I hope this would give you some help:)
http://www.democritos.it/pipermail/pw_forum/2011-April/019891.html
<http://www.democritos.it/pipermail/pw_forum/2011-April/019891.html>

On Tue, Apr 19, 2011 at 2:15 PM, Gianluca Giovannetti <
gianluca.giovannetti at gmail.com> wrote:

> Dear All,
>
> i`m calculating the projected density of states of some material.
>
> this should be done integrating within a sphere.
>
> can i change the radius of such sphere in PW?
>
> i thank you in advance.
>
> cheers,
>
> Gianluca Giovannetti
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From gianluca.giovannetti at gmail.com  Tue Apr 19 16:11:42 2011
From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti)
Date: Tue, 19 Apr 2011 16:11:42 +0200
Subject: [Pw_forum] radius of the sphere to calculate the projected
 density of states
In-Reply-To: <BANLkTim1AooeX4stKEuPSqjr=G+GgMA75w@mail.gmail.com>
References: <BANLkTi=vcKHsx-X8dNXYSDNBLRPhNSDf2w@mail.gmail.com>
	<BANLkTim1AooeX4stKEuPSqjr=G+GgMA75w@mail.gmail.com>
Message-ID: <BANLkTik0w0sBGjR13ofM6T3b=EB1JH9ytw@mail.gmail.com>

Dear All,

i thank you for all the replies. :-)

cheers,

Gianluca

On Tue, Apr 19, 2011 at 4:06 PM, xirainbow <nkxirainbow at gmail.com> wrote:

> Dear Gianluca Giovannetti:
> I hope this would give you some help:)
> http://www.democritos.it/pipermail/pw_forum/2011-April/019891.html
> <http://www.democritos.it/pipermail/pw_forum/2011-April/019891.html>
>
> On Tue, Apr 19, 2011 at 2:15 PM, Gianluca Giovannetti <
> gianluca.giovannetti at gmail.com> wrote:
>
>> Dear All,
>>
>> i`m calculating the projected density of states of some material.
>>
>> this should be done integrating within a sphere.
>>
>> can i change the radius of such sphere in PW?
>>
>> i thank you in advance.
>>
>> cheers,
>>
>> Gianluca Giovannetti
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> ____________________________________
> Hui Wang
> School of physics, Fudan University, Shanghai, China
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From madhura at jncasr.ac.in  Tue Apr 19 16:31:26 2011
From: madhura at jncasr.ac.in (madhura at jncasr.ac.in)
Date: Tue, 19 Apr 2011 20:01:26 +0530
Subject: [Pw_forum] spin polarised STM
Message-ID: <1303223486.4dad9cbe33a65@mercury.jncasr.ac.in>

Dear all,

I have done some spin polarized calculations, and would like to get
STM image for the system. Now I have a few questions regarding this PP
tool:

1. While calculating STM image, is sum taken over both the spin
channels? Because there is no option for spin resolved calculations,
and in the subroutine I was not able to find where sum is done.? 

2. Does anyone have a subroutine to get spin-polarized STM image? If
yes, can you send it? 

3. Or if not, can anyone tell which part of code needs to be modified
to get SP-STM image? 

Thanks a lot,
Madhura.

----
PhD Student,
Theoretical Sciences Unit, 
JNCASR, Bangalore - 560064.
Ph. No. +91 80 2208 2835


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From giannozz at democritos.it  Tue Apr 19 20:34:07 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 19 Apr 2011 20:34:07 +0200
Subject: [Pw_forum] Difference between cartesian coordinates and crystal
	coordinates
In-Reply-To: <BANLkTi=Ny=qDeYL9iP9QvPVHCRS9Uv7Qng@mail.gmail.com>
References: <BANLkTi=Ny=qDeYL9iP9QvPVHCRS9Uv7Qng@mail.gmail.com>
Message-ID: <6497957E-6233-4667-95CB-432668938213@democritos.it>


On Apr 19, 2011, at 15:59 , yumin qian wrote:

> The mixture of unit(alat,borhr,angstrom) and coordinates 
> (crystal ,cartesian  ) often confuse me.

There are 1001 ways to specify input coordinates and lattices.
There is always somebody who would like the 1002-th.
Now you complain that there are too many ways to specify
input coordinates and lattices. Choose the format you want
and stick to that one.

---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From priya_johari at brown.edu  Tue Apr 19 21:26:19 2011
From: priya_johari at brown.edu (Johari, Priya Sudhir)
Date: Tue, 19 Apr 2011 15:26:19 -0400
Subject: [Pw_forum] TDDFT approach for periodic system
Message-ID: <BANLkTi=JEJyTi26LHXWkWYO8=WP_0haGSg@mail.gmail.com>

Dear Developers,

I was wondering if recently implemented TD-DFPT tool in espresso-4.3 can be
used for calculating absorption spectrum of period systems (slab or so)?

Thanks in advance.

Regards,
Dr Priya Johari.
Brown University,
Providence, RI - 02906. USA
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From ttduyle at gmail.com  Tue Apr 19 21:59:15 2011
From: ttduyle at gmail.com (Duy Le)
Date: Tue, 19 Apr 2011 15:59:15 -0400
Subject: [Pw_forum] TDDFT approach for periodic system
In-Reply-To: <BANLkTi=JEJyTi26LHXWkWYO8=WP_0haGSg@mail.gmail.com>
References: <BANLkTi=JEJyTi26LHXWkWYO8=WP_0haGSg@mail.gmail.com>
Message-ID: <BANLkTimVkfF5X-P1Zj_yy4U-4k4Kcduw8Q@mail.gmail.com>

If you do a little homework (such as googling keyword TD-DFPT), you'll
find this link
http://qe-forge.org/projects/tddfpt/
I have not read it carefully but I guess it contains some useful information.
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Tue, Apr 19, 2011 at 3:26 PM, Johari, Priya Sudhir
<priya_johari at brown.edu> wrote:
> TD-DFPT

From giannozz at democritos.it  Tue Apr 19 22:44:55 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 19 Apr 2011 22:44:55 +0200
Subject: [Pw_forum] implementation of variation of occupations and Fermi
	level with perturbations
In-Reply-To: <BANLkTi=sidNdheP906hgk2LznewjBqYkFA@mail.gmail.com>
References: <BANLkTi=sidNdheP906hgk2LznewjBqYkFA@mail.gmail.com>
Message-ID: <0E9B33A7-45CE-47E3-9642-D2EE19724EB6@democritos.it>


On Apr 8, 2011, at 20:39 , David Strubbe wrote:

> Eq. 79 refers to a quantity \Delta n_{ext} and an integral of the LDOS
> with \Delta V_{SCF} to calculate the shift in Fermi level. However in
> ef_shift it appears that the density response drhoscf is used instead
> of these quantities in the numerator, which doesn't seem like the  
> same thing.

it doesn't, but it is. The (dirty) trick is well hidden in the call  
to routine dv_of_drho:
it accepts in input the variation of the charge density, returns in  
output the
variation of the potential, overwritten on the former. It was done a  
looong time
ago in order to spare some memory, when machines had much less ram and
the code was much simpler and smaller (occasional dirty tricks were  
under
control, sort of). A comment in the code would have spared you (and me)
some time. Unfortunately comments in code tend to belong to one of the
following categories: 1) useless, 2) misleading, 3) obsolete, 4)  
nonexistent

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




From priya_johari at brown.edu  Tue Apr 19 23:02:11 2011
From: priya_johari at brown.edu (Johari, Priya Sudhir)
Date: Tue, 19 Apr 2011 17:02:11 -0400
Subject: [Pw_forum] TDDFT approach for periodic system
In-Reply-To: <BANLkTimVkfF5X-P1Zj_yy4U-4k4Kcduw8Q@mail.gmail.com>
References: <BANLkTi=JEJyTi26LHXWkWYO8=WP_0haGSg@mail.gmail.com>
	<BANLkTimVkfF5X-P1Zj_yy4U-4k4Kcduw8Q@mail.gmail.com>
Message-ID: <BANLkTin8wXSGr7FnGzyJSE_JwfXYs183iQ@mail.gmail.com>

Thanks Duy, but the link does not give sufficient information. However, I
found a discussion on forum's archive itself where Giuseppe Mattioli has
mentioned that TDDPFT does not work for periodic systems* :-(

*Dr Priya Johari.
Brown University,
Providence, RI - 02906. USA
*
*

On Tue, Apr 19, 2011 at 3:59 PM, Duy Le <ttduyle at gmail.com> wrote:

> If you do a little homework (such as googling keyword TD-DFPT), you'll
> find this link
> http://qe-forge.org/projects/tddfpt/
> I have not read it carefully but I guess it contains some useful
> information.
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
>
> On Tue, Apr 19, 2011 at 3:26 PM, Johari, Priya Sudhir
> <priya_johari at brown.edu> wrote:
> > TD-DFPT
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From vormar at gmail.com  Tue Apr 19 23:40:32 2011
From: vormar at gmail.com (Marci)
Date: Tue, 19 Apr 2011 23:40:32 +0200
Subject: [Pw_forum] TDDFT approach for periodic system
In-Reply-To: <BANLkTin8wXSGr7FnGzyJSE_JwfXYs183iQ@mail.gmail.com>
References: <BANLkTi=JEJyTi26LHXWkWYO8=WP_0haGSg@mail.gmail.com>
	<BANLkTimVkfF5X-P1Zj_yy4U-4k4Kcduw8Q@mail.gmail.com>
	<BANLkTin8wXSGr7FnGzyJSE_JwfXYs183iQ@mail.gmail.com>
Message-ID: <BANLkTi=+CH7HMf3_V=yTWmw_FcOG3RYS5w@mail.gmail.com>

Dear Priya,

Though I have never tried, it should work with periodic systems if you
sample the Brillouin zone only with the gamma point. Keep in mind that
the usual adiabatic approximations with (semi)local functionals might
not work very well for calculating the absorption of periodic systems.

Marton

--
Marton Voros
PhD student
Department of Atomic Physics
Budapest University of Technology and Economics
Budafoki ?t 8., H-1111, Budapest, Hungary
www.fat.bme.hu/MartonVoros

On Tue, Apr 19, 2011 at 11:02 PM, Johari, Priya Sudhir
<priya_johari at brown.edu> wrote:
> Thanks Duy, but the link does not give sufficient information. However, I
> found a discussion on forum's archive itself where Giuseppe Mattioli has
> mentioned that TDDPFT does not work for periodic systems :-(
>
> Dr Priya Johari.
> Brown University,
> Providence, RI - 02906. USA
>
>
>
> On Tue, Apr 19, 2011 at 3:59 PM, Duy Le <ttduyle at gmail.com> wrote:
>>
>> If you do a little homework (such as googling keyword TD-DFPT), you'll
>> find this link
>> http://qe-forge.org/projects/tddfpt/
>> I have not read it carefully but I guess it contains some useful
>> information.
>> --------------------------------------------------
>> Duy Le
>> PhD Student
>> Department of Physics
>> University of Central Florida.
>>
>> "Men don't need hand to do things"
>>
>>
>>
>> On Tue, Apr 19, 2011 at 3:26 PM, Johari, Priya Sudhir
>> <priya_johari at brown.edu> wrote:
>> > TD-DFPT
>> _______________________________________________
>> 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 dstrubbe at berkeley.edu  Wed Apr 20 00:08:09 2011
From: dstrubbe at berkeley.edu (David Strubbe)
Date: Tue, 19 Apr 2011 15:08:09 -0700
Subject: [Pw_forum] implementation of variation of occupations and Fermi
 level with perturbations
In-Reply-To: <0E9B33A7-45CE-47E3-9642-D2EE19724EB6@democritos.it>
References: <BANLkTi=sidNdheP906hgk2LznewjBqYkFA@mail.gmail.com>
	<0E9B33A7-45CE-47E3-9642-D2EE19724EB6@democritos.it>
Message-ID: <BANLkTinTJ5BHnKiDgefuo4SVas7XTcLhMw@mail.gmail.com>

Paolo,

Thanks for the response. This gives me some more insight into what is going
on, but I still don't understand.

As far as I can tell, the drhoscf in ef_shift is still the change in the
density rather than the change in the potential, because the calls in
solve_linter to dv_of_drho are using a copy of the density response rather
than drhoscf itself:

        call zcopy
(nrxx*nspin_mag,drhoscfh(1,1,ipert),1,dvscfout(1,1,ipert),1)
        call dv_of_drho (imode0+ipert, dvscfout(1,1,ipert), .true.)

The heart of the matter is the lines in ef_shift:

delta_n = delta_n + omega*drhoscf(nl(1),is,ipert)
def (ipert) = - delta_n / dos_ef

delta_n does not seem to refer to \Delta n_{ext} or the integral of the LDOS
with \Delta V_{SCF}, as in the numerator of Eq. 79. Do those quantities
exist in the calculation here?

Thanks,
David Strubbe
UC Berkeley

On Tue, Apr 19, 2011 at 1:44 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Apr 8, 2011, at 20:39 , David Strubbe wrote:
>
> > Eq. 79 refers to a quantity \Delta n_{ext} and an integral of the LDOS
> > with \Delta V_{SCF} to calculate the shift in Fermi level. However in
> > ef_shift it appears that the density response drhoscf is used instead
> > of these quantities in the numerator, which doesn't seem like the
> > same thing.
>
> it doesn't, but it is. The (dirty) trick is well hidden in the call
> to routine dv_of_drho:
> it accepts in input the variation of the charge density, returns in
> output the
> variation of the potential, overwritten on the former. It was done a
> looong time
> ago in order to spare some memory, when machines had much less ram and
> the code was much simpler and smaller (occasional dirty tricks were
> under
> control, sort of). A comment in the code would have spared you (and me)
> some time. Unfortunately comments in code tend to belong to one of the
> following categories: 1) useless, 2) misleading, 3) obsolete, 4)
> nonexistent
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From priya_johari at brown.edu  Wed Apr 20 03:00:41 2011
From: priya_johari at brown.edu (Johari, Priya Sudhir)
Date: Tue, 19 Apr 2011 21:00:41 -0400
Subject: [Pw_forum] TDDFT approach for periodic system
In-Reply-To: <BANLkTi=+CH7HMf3_V=yTWmw_FcOG3RYS5w@mail.gmail.com>
References: <BANLkTi=JEJyTi26LHXWkWYO8=WP_0haGSg@mail.gmail.com>
	<BANLkTimVkfF5X-P1Zj_yy4U-4k4Kcduw8Q@mail.gmail.com>
	<BANLkTin8wXSGr7FnGzyJSE_JwfXYs183iQ@mail.gmail.com>
	<BANLkTi=+CH7HMf3_V=yTWmw_FcOG3RYS5w@mail.gmail.com>
Message-ID: <BANLkTi=ATF7Ge_xy50FRdb5aOVsiXKd_wQ@mail.gmail.com>

Thanks Marton, its working.


On Tue, Apr 19, 2011 at 5:40 PM, Marci <vormar at gmail.com> wrote:

> Dear Priya,
>
> Though I have never tried, it should work with periodic systems if you
> sample the Brillouin zone only with the gamma point. Keep in mind that
> the usual adiabatic approximations with (semi)local functionals might
> not work very well for calculating the absorption of periodic systems.
>
> Marton
>
> --
> Marton Voros
> PhD student
> Department of Atomic Physics
> Budapest University of Technology and Economics
> Budafoki ?t 8., H-1111, Budapest, Hungary
> www.fat.bme.hu/MartonVoros
>
> On Tue, Apr 19, 2011 at 11:02 PM, Johari, Priya Sudhir
> <priya_johari at brown.edu> wrote:
> > Thanks Duy, but the link does not give sufficient information. However, I
> > found a discussion on forum's archive itself where Giuseppe Mattioli has
> > mentioned that TDDPFT does not work for periodic systems :-(
> >
> > Dr Priya Johari.
> > Brown University,
> > Providence, RI - 02906. USA
> >
> >
> >
> > On Tue, Apr 19, 2011 at 3:59 PM, Duy Le <ttduyle at gmail.com> wrote:
> >>
> >> If you do a little homework (such as googling keyword TD-DFPT), you'll
> >> find this link
> >> http://qe-forge.org/projects/tddfpt/
> >> I have not read it carefully but I guess it contains some useful
> >> information.
> >> --------------------------------------------------
> >> Duy Le
> >> PhD Student
> >> Department of Physics
> >> University of Central Florida.
> >>
> >> "Men don't need hand to do things"
> >>
> >>
> >>
> >> On Tue, Apr 19, 2011 at 3:26 PM, Johari, Priya Sudhir
> >> <priya_johari at brown.edu> wrote:
> >> > TD-DFPT
> >> _______________________________________________
> >> 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
>
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From hqzhou at nju.edu.cn  Wed Apr 20 05:00:53 2011
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Wed, 20 Apr 2011 11:00:53 +0800
Subject: [Pw_forum] Shirley interpolation
References: <BANLkTinJifvUkmcJ8AOTjwe2v74Ujuo-qw@mail.gmail.com>
Message-ID: <2B1321E28DEF41C599792C01E4FC1040@solarflare>

It's provided only internally to the "Molecular Foundry" users, I think.


zhou huiqun
@earth sciences, nanjing university, china

  ----- Original Message ----- 
  From: Mingxing Chen 
  To: pw_forum at pwscf.org 
  Sent: Tuesday, April 19, 2011 2:34 PM
  Subject: [Pw_forum] Shirley interpolation


  Dear all,

  As stated in PRB 80, 235126 (2009) by David Prendergast, the Shirley's interpolation scheme has been implemented as a post processing tool in QE. However, I did not find it in the latest version of QE, i.e., Version 4.3. Does anyone know that? Any suggestion would be appreciated. Thanks a lot.

  Best regards,

  Mingxing Chen

  -- 

Mingxing Chen,Institute for Physical ChemistryUniversity of ViennaEmail: mxchen.2011 at gmail.com




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


  _______________________________________________
  Pw_forum mailing list
  Pw_forum at pwscf.org
  http://www.democritos.it/mailman/listinfo/pw_forum
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From germaneau at gucas.ac.cn  Wed Apr 20 21:29:36 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Wed, 20 Apr 2011 15:29:36 -0400
Subject: [Pw_forum] Graphene band structure
In-Reply-To: <503193425.21667@test1.gucas.ac.cn>
References: <503193425.21667@test1.gucas.ac.cn>
Message-ID: <4DAF3420.2050500@gucas.ac.cn>

Your path is certainly different than your reference.

On 04/19/2011 02:17 AM, Mahdi Faqieh nasiri wrote:
> Dear all,
> I'm trying to draw Graphene band structure.
> i do "calculation= "scf" "bands'" and a define a K-path.
> Then execute bands.x. and plotband.x.
> but the graph in M-K is Completely different with TB graph.
> please take a look to this files.
>
>
> Mahdi Faghih nasiri
> MSC,
> Guilan University,
> Rasht, Iran.
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
/Be the change you wish to see in the world
/ ? Mahatma Gandhi ?

Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/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 degironc at sissa.it  Wed Apr 20 10:12:29 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 20 Apr 2011 10:12:29 +0200
Subject: [Pw_forum] implementation of variation of occupations and Fermi
 level with perturbations
In-Reply-To: <BANLkTinTJ5BHnKiDgefuo4SVas7XTcLhMw@mail.gmail.com>
References: <BANLkTi=sidNdheP906hgk2LznewjBqYkFA@mail.gmail.com>	<0E9B33A7-45CE-47E3-9642-D2EE19724EB6@democritos.it>
	<BANLkTinTJ5BHnKiDgefuo4SVas7XTcLhMw@mail.gmail.com>
Message-ID: <4DAE956D.4000402@sissa.it>

Dear David Strubbe,

eq. 79 is a general formula; in the phonon code Delta n_ext(q=0) is 
always vanishing because the perturbation is neutral (atoms are 
displaced but their charge is not changed), still Delta Vscf is in 
general non zero so one has to do something

Let's look at the scf variation of rho that is something like

Delta rho(r) = sum_i  f_i (phi_i* Delta_phi_i +cc) + d f_i/de *(Delta 
e_i - Delta e_F) |phi|^2

As said, eq. 79 is the condition of charge neutrality of the 
perturbation which is due ONLY to the last term involving changes in 
occupation of states (remember that Delta phi is always orthogonal to 
the unperturbed phi so in no case Delta phi can contribute to the total 
charge variation)

if you work out the expression ...

total charge = Delta n_ext + Delta_n induced by Delta e_i (defined in 
terms of the potential change) + Delta_n induced by the Fermi energy shift..

and the neutrality condition reads

0 = Delta_n_ext + \int n(e_F,r) Delta Vscf - n(e_F) * Delta e_F

which is eq. 79.

HOWEVER, delta rho that enters ef_shift has been computed without the 
contribution coming from the (then unknown) Fermi energy shift Delta e_F 
that is (see above)

- n(e_F,r) * Delta e_F

this is how ef_shift routine icomputes Delta e_F:  it calculates the G=0 
component of Delta rho before the shift ( which amount to be \int 
n(e_F,r) Delta Vscf ) and define Delta e_F in such a way that after the 
term  - n(e_F,r) * Delta e_F is added the final Delta rho is neutral.

I hope the procedure is a bit clearer now.

stefano


On 04/20/2011 12:08 AM, David Strubbe wrote:
> Paolo,
>
> Thanks for the response. This gives me some more insight into what is going
> on, but I still don't understand.
>
> As far as I can tell, the drhoscf in ef_shift is still the change in the
> density rather than the change in the potential, because the calls in
> solve_linter to dv_of_drho are using a copy of the density response rather
> than drhoscf itself:
>
>          call zcopy
> (nrxx*nspin_mag,drhoscfh(1,1,ipert),1,dvscfout(1,1,ipert),1)
>          call dv_of_drho (imode0+ipert, dvscfout(1,1,ipert), .true.)
>
> The heart of the matter is the lines in ef_shift:
>
> delta_n = delta_n + omega*drhoscf(nl(1),is,ipert)
> def (ipert) = - delta_n / dos_ef
>
> delta_n does not seem to refer to \Delta n_{ext} or the integral of the LDOS
> with \Delta V_{SCF}, as in the numerator of Eq. 79. Do those quantities
> exist in the calculation here?
>
> Thanks,
> David Strubbe
> UC Berkeley
>
> On Tue, Apr 19, 2011 at 1:44 PM, Paolo Giannozzi<giannozz at democritos.it>wrote:
>
>> On Apr 8, 2011, at 20:39 , David Strubbe wrote:
>>
>>> Eq. 79 refers to a quantity \Delta n_{ext} and an integral of the LDOS
>>> with \Delta V_{SCF} to calculate the shift in Fermi level. However in
>>> ef_shift it appears that the density response drhoscf is used instead
>>> of these quantities in the numerator, which doesn't seem like the
>>> same thing.
>> it doesn't, but it is. The (dirty) trick is well hidden in the call
>> to routine dv_of_drho:
>> it accepts in input the variation of the charge density, returns in
>> output the
>> variation of the potential, overwritten on the former. It was done a
>> looong time
>> ago in order to spare some memory, when machines had much less ram and
>> the code was much simpler and smaller (occasional dirty tricks were
>> under
>> control, sort of). A comment in the code would have spared you (and me)
>> some time. Unfortunately comments in code tend to belong to one of the
>> following categories: 1) useless, 2) misleading, 3) obsolete, 4)
>> nonexistent
>>
>> P.
>> ---
>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://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 giuseppe.mattioli at mlib.ism.cnr.it  Wed Apr 20 11:21:45 2011
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Wed, 20 Apr 2011 11:21:45 +0200
Subject: [Pw_forum] TDDFT approach for periodic system
In-Reply-To: <BANLkTi=ATF7Ge_xy50FRdb5aOVsiXKd_wQ@mail.gmail.com>
References: <BANLkTi=JEJyTi26LHXWkWYO8=WP_0haGSg@mail.gmail.com>
	<BANLkTi=+CH7HMf3_V=yTWmw_FcOG3RYS5w@mail.gmail.com>
	<BANLkTi=ATF7Ge_xy50FRdb5aOVsiXKd_wQ@mail.gmail.com>
Message-ID: <201104201121.45702.giuseppe.mattioli@mlib.ism.cnr.it>

Dear all
I did not say that TDDFPT does not work with periodic system, but you cannot 
have a realistic absorption spectra of a slab (or bulk crystal) if you sample 
the Brillouin zone by using Gamma only... TDDFPT works fine with finite 
systems, i.e., which do not show a (strong) k dependence of the psi_n,k 
eigenvalues.

Giuseppe

On Wednesday 20 April 2011 03:00:41 Johari, Priya Sudhir wrote:
> Thanks Marton, its working.
>
> On Tue, Apr 19, 2011 at 5:40 PM, Marci <vormar at gmail.com> wrote:
> > Dear Priya,
> >
> > Though I have never tried, it should work with periodic systems if you
> > sample the Brillouin zone only with the gamma point. Keep in mind that
> > the usual adiabatic approximations with (semi)local functionals might
> > not work very well for calculating the absorption of periodic systems.
> >
> > Marton
> >
> > --
> > Marton Voros
> > PhD student
> > Department of Atomic Physics
> > Budapest University of Technology and Economics
> > Budafoki ?t 8., H-1111, Budapest, Hungary
> > www.fat.bme.hu/MartonVoros
> >
> > On Tue, Apr 19, 2011 at 11:02 PM, Johari, Priya Sudhir
> >
> > <priya_johari at brown.edu> wrote:
> > > Thanks Duy, but the link does not give sufficient information. However,
> > > I found a discussion on forum's archive itself where Giuseppe Mattioli
> > > has mentioned that TDDPFT does not work for periodic systems :-(
> > >
> > > Dr Priya Johari.
> > > Brown University,
> > > Providence, RI - 02906. USA
> > >
> > > On Tue, Apr 19, 2011 at 3:59 PM, Duy Le <ttduyle at gmail.com> wrote:
> > >> If you do a little homework (such as googling keyword TD-DFPT), you'll
> > >> find this link
> > >> http://qe-forge.org/projects/tddfpt/
> > >> I have not read it carefully but I guess it contains some useful
> > >> information.
> > >> --------------------------------------------------
> > >> Duy Le
> > >> PhD Student
> > >> Department of Physics
> > >> University of Central Florida.
> > >>
> > >> "Men don't need hand to do things"
> > >>
> > >>
> > >>
> > >> On Tue, Apr 19, 2011 at 3:26 PM, Johari, Priya Sudhir
> > >>
> > >> <priya_johari at brown.edu> wrote:
> > >> > TD-DFPT
> > >>
> > >> _______________________________________________
> > >> 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



-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? 
? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ?
? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ?
? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ?
? ?E-mail: <giuseppe.mattioli at ism.cnr.it>

From max.n.popov at gmail.com  Wed Apr 20 11:25:46 2011
From: max.n.popov at gmail.com (=?KOI8-R?B?7cHL08nNIPDP0M/X?=)
Date: Wed, 20 Apr 2011 11:25:46 +0200
Subject: [Pw_forum] new bfgs: strange behavior doing vc-relax
In-Reply-To: <BANLkTimF1tTW3N20=ptvZ7vh0ut_qJJcKQ@mail.gmail.com>
References: <BANLkTimF1tTW3N20=ptvZ7vh0ut_qJJcKQ@mail.gmail.com>
Message-ID: <BANLkTinTvmvO8s7eb8cyXe-dDboFcYMN8w@mail.gmail.com>

Dear Eduardo,

thank you very much for expanded answer and sharing the practical tricks.
I've done some computational experiments on bulk Si (cubic conventional
cell) vc-relaxation.

Here is the result (V is volume of initial unit cell, and V0 is equilibrium
volume):

1) starting from V > V0, i.e. 1/V < 1/V0 -> more G-vectors for vc-relax:

G cutoff =  837.7995  ( 101505 G-vectors)     FFT grid: ( 60, 60, 60) -
vc-relax
G cutoff =  837.7995  (  97137 G-vectors)     FFT grid: ( 60, 60, 60)  -
post-scf

!    total energy              =    -372.89634728 Ry - the last energy in
the course of vc-relax
!    total energy              =    -372.89587589 Ry - post-scf energy

NB1: # of G-vectors (vc-relax) > # G-vectors(post-scf), and E(the last point
vc-relax) < E(post-scf).

1) starting from V < V0, i.e. 1/V > 1/V0 -> more G-vectors for post-scf:

G cutoff =  775.1830  (  90447 G-vectors)     FFT grid: ( 60, 60, 60) -
vc-relax
G cutoff =  775.1830  (  97137 G-vectors)     FFT grid: ( 60, 60, 60) -
post-scf

!    total energy              =    -372.89498529 Ry - the last energy in
the course of vc-relax
!    total energy              =    -372.89587142 Ry - post-scf energy

NB2: # of G-vectors(vc-relax) < # G-vectors(post-scf), and E(the last point
vc-relax) > E(post-scf).

Comparing these two experiments, one can make a preliminary conclusion: the
more G-vectors, the lower
the total Energy, provided all other parameters to be fixed.
This is easy to understand: plane-wave basis set is complete, that means 2
things (when dealing with truncated bases):
1) E(N+M) < E(N), where N,M - number of plane waves(G-vectors);
2) lim N->infinity of [ E(N+M)-E(N)] = 0.

Now it seems to be more clear for me :)
Correct me if I'm wrong somewhere.

-- 
Best regards, Max Popov
Ph.D. student
Materials center Leoben (MCL), Leoben, Austria.

2011/4/19 Eduardo Ariel Menendez Proupin <eariel99 at gmail.com>

> >Dear Dr. Giannozzi,
> >thank you for the answer! I could find it myself looking in the output
> file a bit >more carefully...
> >One thing, which is somehow contrary to my expectations, is that the final
> scf >energy is higher
> >than the last one from vc-relax. Could you, please, elaborate a bit on the
> >matter?
>
> Dear Maxim,
>
> I followed this discussion with interest, and thanks to that I learned
> about the new scf calculation with final G-vectors. Concerning your last
> question,
> the energy is higher because the vc-relaxed energy was optimized for a
> different basis set, than the final scf calculation (different G-vectors).
> Hence, the energy of the final scf calculation is is made for a structure
> that is slightly out of the minimum for the new basis set. Remember than the
> G-vectors used in a scf calculation are all the reciprocal lattice vectors
>  contained in a sphere that has a radius determined by the cutoff. These
> vectors are selected at the first step of the vc-relaxation. When the unit
> cell gets deformed, the G-vectors vary accordingly, and the region that the
> G-vectors occupy is a deformation from the initial sphere, maybe an
> elipsoid. When the vc-relax stops, the final scf calculation takes the
> G-vectors contained inside a sphere. Hence, some of the old G-vectors that
> were in the border of the deformed sphere may be eliminated, and some that
> were absent are now included.
> If you had used an (impossible) infinite cutoff, the basis set would be
> complete in both cases (G-vectors contained in an infinite sphere or in an
> infinite elipsoid) and there would be no difference. Usually, I repeat the
> vc-relax procedure starting 'from_scratch' with the last structure
> (coordinates and lattice vectors) in the new input file, until the vc-relax
> procedure performs only one step. In this case there is no difference. If it
> never happens that vc-relax stops at the first step, then I increase the
> cutoffs. In your case, the energy difference of 0.5 mRy may be small enough
> and do not need to do that. It depends on the property that you want. E.g.,
> if you are interested in elastic properties,  you may need that the minimal
> energy structure also gives a stress tensor below 0.1 kbar or so. If you
> cannot get it, increase the cutoff.
>
> The following link may help
>
>
> http://www.quantum-espresso.org/wiki/index.php/Methodological_Background#Stress
>
> Best regards
>
> --
>
>
> Eduardo Menendez
> Departamento de Fisica
> Facultad de Ciencias
> Universidad de Chile
> Phone: (56)(2)9787439
> URL: http://fisica.ciencias.uchile.cl/~emenendez
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From hannu.komsa at epfl.ch  Wed Apr 20 12:50:11 2011
From: hannu.komsa at epfl.ch (hannu.komsa at epfl.ch)
Date: Wed, 20 Apr 2011 12:50:11 +0200
Subject: [Pw_forum] Bug in NEB calculation with hybrid functionals
Message-ID: <20110420125011.90604oqxyt60sggz@webmail.epfl.ch>

Hi

I am trying to do a NEB-calculation using hybrid functionals (HSE).  
The first calculation, the first image, is calculated fine, but when  
starting the second image, QE crashed with the following error message:

   At line 228 of file exx.f90
   Fortran runtime error: Attempting to allocate already allocated array
    'index_xkq'

This line reads as:
      allocate ( index_xkq(nkstot,nqs) )
I could just add if(.not.allocated()) etc.. However, even with this,  
if the images have different number of k-points the calculation will  
end with a segmentation fault. So I guess it would be better to  
deallocate the arrays somewhere, but I don't know how to do this the  
best way.

The error was reproduced with intel and gnu compiler, with 4.3 and CVS  
version, and run in parallel or serial. Input file demonstrating the  
bug for an unrealistic system included below.


Best regards,
   Hannu-Pekka Komsa
   EPFL, Switzerland


BEGIN
BEGIN_PATH_INPUT
  &path
   restart_mode      = 'from_scratch'
   string_method     = 'neb',
   nstep_path        = 20,
   ds                = 2.D0,
   opt_scheme        = "broyden",
   num_of_images     = 5,
  /
END_PATH_INPUT
BEGIN_ENGINE_INPUT
  &control
     prefix='Si',
     pseudo_dir = './',
     outdir='./'
  /
  &system
     ibrav=  1, A = 5.465 , nat=  8, ntyp= 1,
     ecutwfc = 20,  nbnd =20,
     input_dft='hse', nqx1 = 1, nqx2 = 1, nqx3 = 1,
     exx_fraction = 0.25,
  /
  &electrons
     conv_thr = 1e-5,
  /
ATOMIC_SPECIES
  Si  28.086  Si.pbe-rrkj.UPF
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS crystal
     Si    0.00 0.00 0.00 0 0 0
     Si    0.50 0.50 0.00 0 0 0
     Si    0.00 0.50 0.50 0 0 0
     Si    0.50 0.00 0.50 0 0 0
     Si    0.25 0.25 0.25
     Si    0.75 0.75 0.25 0 0 0
     Si    0.25 0.75 0.75 0 0 0
     Si    0.75 0.25 0.75 0 0 0
LAST_IMAGE
ATOMIC_POSITIONS crystal
Si       0.000000000   0.000000000   0.000000000    0   0   0
Si       0.500000000   0.500000000   0.000000000    0   0   0
Si       0.000000000   0.500000000   0.500000000    0   0   0
Si       0.500000000   0.000000000   0.500000000    0   0   0
Si       0.386058672   0.386058672   0.386058672
Si       0.750000000   0.750000000   0.250000000    0   0   0
Si       0.250000000   0.750000000   0.750000000    0   0   0
Si       0.750000000   0.250000000   0.750000000    0   0   0
END_POSITIONS
K_POINTS automatic
  2 2 2 1 1 1
END_ENGINE_INPUT
END



From lmartinsamos at gmail.com  Wed Apr 20 15:25:40 2011
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Wed, 20 Apr 2011 15:25:40 +0200
Subject: [Pw_forum] Bug in NEB calculation with hybrid functionals
In-Reply-To: <20110420125011.90604oqxyt60sggz@webmail.epfl.ch>
References: <20110420125011.90604oqxyt60sggz@webmail.epfl.ch>
Message-ID: <BANLkTimo=xoy53OB5nqoykBVnkXP6bd9Dg@mail.gmail.com>

Dear Hannu, in the previous neb implementation it was NOT allowed to have
different numbers of k points for different images, as pw was reading
kpoints card only once. In the present implemention, the input is read
n_input_image time however iosys is called just once, so for averything but
the atomic positions ONLY what is readed at the end is savec. So, if you set
a different number of kpoints for each image in any case the code will
assume that the number of kpoint is the one of the LAST input_image. Your
comment will be very useful when we will maybe change pw and cp for
computing for the same parallel run "different systems". For the moment, the
"best thing" (quick and dirty thing) is that you change with
if(.not.allocated) allocate(index_xkq(nkstot)) etc.

thank you very much for repporting the bug.

cheers

Layla

2011/4/20 <hannu.komsa at epfl.ch>

> Hi
>
> I am trying to do a NEB-calculation using hybrid functionals (HSE).
> The first calculation, the first image, is calculated fine, but when
> starting the second image, QE crashed with the following error message:
>
>   At line 228 of file exx.f90
>   Fortran runtime error: Attempting to allocate already allocated array
>    'index_xkq'
>
> This line reads as:
>      allocate ( index_xkq(nkstot,nqs) )
> I could just add if(.not.allocated()) etc.. However, even with this,
> if the images have different number of k-points the calculation will
> end with a segmentation fault. So I guess it would be better to
> deallocate the arrays somewhere, but I don't know how to do this the
> best way.
>
> The error was reproduced with intel and gnu compiler, with 4.3 and CVS
> version, and run in parallel or serial. Input file demonstrating the
> bug for an unrealistic system included below.
>
>
> Best regards,
>   Hannu-Pekka Komsa
>   EPFL, Switzerland
>
>
> BEGIN
> BEGIN_PATH_INPUT
>  &path
>   restart_mode      = 'from_scratch'
>   string_method     = 'neb',
>   nstep_path        = 20,
>   ds                = 2.D0,
>   opt_scheme        = "broyden",
>   num_of_images     = 5,
>  /
> END_PATH_INPUT
> BEGIN_ENGINE_INPUT
>  &control
>     prefix='Si',
>     pseudo_dir = './',
>     outdir='./'
>  /
>  &system
>     ibrav=  1, A = 5.465 , nat=  8, ntyp= 1,
>     ecutwfc = 20,  nbnd =20,
>     input_dft='hse', nqx1 = 1, nqx2 = 1, nqx3 = 1,
>     exx_fraction = 0.25,
>  /
>  &electrons
>     conv_thr = 1e-5,
>  /
> ATOMIC_SPECIES
>  Si  28.086  Si.pbe-rrkj.UPF
> BEGIN_POSITIONS
> FIRST_IMAGE
> ATOMIC_POSITIONS crystal
>     Si    0.00 0.00 0.00 0 0 0
>     Si    0.50 0.50 0.00 0 0 0
>     Si    0.00 0.50 0.50 0 0 0
>     Si    0.50 0.00 0.50 0 0 0
>     Si    0.25 0.25 0.25
>     Si    0.75 0.75 0.25 0 0 0
>     Si    0.25 0.75 0.75 0 0 0
>     Si    0.75 0.25 0.75 0 0 0
> LAST_IMAGE
> ATOMIC_POSITIONS crystal
> Si       0.000000000   0.000000000   0.000000000    0   0   0
> Si       0.500000000   0.500000000   0.000000000    0   0   0
> Si       0.000000000   0.500000000   0.500000000    0   0   0
> Si       0.500000000   0.000000000   0.500000000    0   0   0
> Si       0.386058672   0.386058672   0.386058672
> Si       0.750000000   0.750000000   0.250000000    0   0   0
> Si       0.250000000   0.750000000   0.750000000    0   0   0
> Si       0.750000000   0.250000000   0.750000000    0   0   0
> END_POSITIONS
> K_POINTS automatic
>  2 2 2 1 1 1
> END_ENGINE_INPUT
> END
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From baris.malcioglu at gmail.com  Wed Apr 20 15:25:40 2011
From: baris.malcioglu at gmail.com (O. Baris Malcioglu)
Date: Wed, 20 Apr 2011 15:25:40 +0200
Subject: [Pw_forum] TDDFT approach for periodic system
In-Reply-To: <201104201121.45702.giuseppe.mattioli@mlib.ism.cnr.it>
References: <BANLkTi=JEJyTi26LHXWkWYO8=WP_0haGSg@mail.gmail.com>
	<BANLkTi=+CH7HMf3_V=yTWmw_FcOG3RYS5w@mail.gmail.com>
	<BANLkTi=ATF7Ge_xy50FRdb5aOVsiXKd_wQ@mail.gmail.com>
	<201104201121.45702.giuseppe.mattioli@mlib.ism.cnr.it>
Message-ID: <BANLkTimbp8JKoEyPKi6JjMK07kA5okg4vw@mail.gmail.com>

Dear All,
The current implementation of TDDFPT in Q-E is intended for "standalone"
systems (i.e. non bulk, solvated or encapsulated in dielectric systems are
ok). You will see confinement effects in lower dimensional systems
(including 1D and 2D systems) in the non-extended dimensionality(-ies) save
excitations with strong Mott-Wannier like character (CT excitations in
theoretical chemistry) since the oscillator strength for them in the current
implementation goes to zero due to ALDA (working on that). For the extended
dimensions you'll see no accountable difference from run-of-the-mill DFT-RPA
save if there is an extraordinarily strongly bound exciton at gamma point
(i.e. strongly ionic materials) (please see how TDDFT is formulated through
response -charge-, and how K points may come into play). For "ordinary" bulk
materials, frequency dependence and long range tail of the kernel is
generally mandatory for a bound exciton, which is quite "tricky" to add I
would say (beware of EXX and TD-HF, they tend to have quite wrong exciton
binding energies, personally I think this is due to lack of inclusion of a
proper generalised dielectric function in their formulation).  If you want
to study "ordinary bulk materials" I would recommend you BSP or TD-CFT
whenever GW can not save the day. Did you try SAX?
Best,
Baris
P.S.
(There are many books on the topic, especially regarding what to expect and
what not to expect from TDDFT, my personal opinion is that TDDFT thrives in
the realm between theoretical chemistry and bulk materials, i.e. large
molecules, nanocrystals, etc. Then again, this is my personal opinion)
I would recommend you to start with M.A.L. Marques, C.A. Ullrich, F.
Nogueira, A. Rubio, K. Burke, and E.K.U. Gross (eds.), Time-Dependent
Density Functional Theory (Springer-Verlag, 2006). )

2011/4/20 Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>

> Dear all
> I did not say that TDDFPT does not work with periodic system, but you
> cannot
> have a realistic absorption spectra of a slab (or bulk crystal) if you
> sample
> the Brillouin zone by using Gamma only... TDDFPT works fine with finite
> systems, i.e., which do not show a (strong) k dependence of the psi_n,k
> eigenvalues.
>
> Giuseppe
>
> On Wednesday 20 April 2011 03:00:41 Johari, Priya Sudhir wrote:
> > Thanks Marton, its working.
> >
> > On Tue, Apr 19, 2011 at 5:40 PM, Marci <vormar at gmail.com> wrote:
> > > Dear Priya,
> > >
> > > Though I have never tried, it should work with periodic systems if you
> > > sample the Brillouin zone only with the gamma point. Keep in mind that
> > > the usual adiabatic approximations with (semi)local functionals might
> > > not work very well for calculating the absorption of periodic systems.
> > >
> > > Marton
> > >
> > > --
> > > Marton Voros
> > > PhD student
> > > Department of Atomic Physics
> > > Budapest University of Technology and Economics
> > > Budafoki ?t 8., H-1111, Budapest, Hungary
> > > www.fat.bme.hu/MartonVoros
> > >
> > > On Tue, Apr 19, 2011 at 11:02 PM, Johari, Priya Sudhir
> > >
> > > <priya_johari at brown.edu> wrote:
> > > > Thanks Duy, but the link does not give sufficient information.
> However,
> > > > I found a discussion on forum's archive itself where Giuseppe
> Mattioli
> > > > has mentioned that TDDPFT does not work for periodic systems :-(
> > > >
> > > > Dr Priya Johari.
> > > > Brown University,
> > > > Providence, RI - 02906. USA
> > > >
> > > > On Tue, Apr 19, 2011 at 3:59 PM, Duy Le <ttduyle at gmail.com> wrote:
> > > >> If you do a little homework (such as googling keyword TD-DFPT),
> you'll
> > > >> find this link
> > > >> http://qe-forge.org/projects/tddfpt/
> > > >> I have not read it carefully but I guess it contains some useful
> > > >> information.
> > > >> --------------------------------------------------
> > > >> Duy Le
> > > >> PhD Student
> > > >> Department of Physics
> > > >> University of Central Florida.
> > > >>
> > > >> "Men don't need hand to do things"
> > > >>
> > > >>
> > > >>
> > > >> On Tue, Apr 19, 2011 at 3:26 PM, Johari, Priya Sudhir
> > > >>
> > > >> <priya_johari at brown.edu> wrote:
> > > >> > TD-DFPT
> > > >>
> > > >> _______________________________________________
> > > >> 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
>
>
>
> --
> ********************************************************
> - Article premier - Les hommes naissent et demeurent
> libres et ?gaux en droits. Les distinctions sociales
> ne peuvent ?tre fond?es que sur l'utilit? commune
> - Article 2 - Le but de toute association politique
> est la conservation des droits naturels et
> imprescriptibles de l'homme. Ces droits sont la libert?,
> la propri?t?, la s?ret? et la r?sistance ? l'oppression.
> ********************************************************
>
>    Giuseppe Mattioli
>    CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
>    v. Salaria Km 29,300 - C.P. 10
>    I 00015 - Monterotondo Stazione (RM)
>    Tel + 39 06 90672836 - Fax +39 06 90672316
>    E-mail: <giuseppe.mattioli at ism.cnr.it>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From baris.malcioglu at gmail.com  Wed Apr 20 15:38:02 2011
From: baris.malcioglu at gmail.com (O. Baris Malcioglu)
Date: Wed, 20 Apr 2011 15:38:02 +0200
Subject: [Pw_forum] TDDFT approach for periodic system
In-Reply-To: <BANLkTimbp8JKoEyPKi6JjMK07kA5okg4vw@mail.gmail.com>
References: <BANLkTi=JEJyTi26LHXWkWYO8=WP_0haGSg@mail.gmail.com>
	<BANLkTi=+CH7HMf3_V=yTWmw_FcOG3RYS5w@mail.gmail.com>
	<BANLkTi=ATF7Ge_xy50FRdb5aOVsiXKd_wQ@mail.gmail.com>
	<201104201121.45702.giuseppe.mattioli@mlib.ism.cnr.it>
	<BANLkTimbp8JKoEyPKi6JjMK07kA5okg4vw@mail.gmail.com>
Message-ID: <BANLkTikG5uuctLOacYfUG9gO=JQS1mPNCw@mail.gmail.com>

A further addition and good reading why adding k-points to TDDFT might not
be that straightforward:

THE JOURNAL OF CHEMICAL PHYSICS 129, 034101
"Why are time-dependent density functional theory excitations in solids
equal to band structure energy gaps for semilocal functionals, and how does
nonlocal Hartree?Fock-type exchange introduce excitonic effects?"
Artur F. Izmaylov and Gustavo E. Scuseriaa

2011/4/20 O. Baris Malcioglu <baris.malcioglu at gmail.com>

> Dear All,
> The current implementation of TDDFPT in Q-E is intended for "standalone"
> systems (i.e. non bulk, solvated or encapsulated in dielectric systems are
> ok). You will see confinement effects in lower dimensional systems
> (including 1D and 2D systems) in the non-extended dimensionality(-ies) save
> excitations with strong Mott-Wannier like character (CT excitations in
> theoretical chemistry) since the oscillator strength for them in the current
> implementation goes to zero due to ALDA (working on that). For the extended
> dimensions you'll see no accountable difference from run-of-the-mill DFT-RPA
> save if there is an extraordinarily strongly bound exciton at gamma point
> (i.e. strongly ionic materials) (please see how TDDFT is formulated through
> response -charge-, and how K points may come into play). For "ordinary" bulk
> materials, frequency dependence and long range tail of the kernel is
> generally mandatory for a bound exciton, which is quite "tricky" to add I
> would say (beware of EXX and TD-HF, they tend to have quite wrong exciton
> binding energies, personally I think this is due to lack of inclusion of a
> proper generalised dielectric function in their formulation).  If you want
> to study "ordinary bulk materials" I would recommend you BSP or TD-CFT
> whenever GW can not save the day. Did you try SAX?
> Best,
> Baris
> P.S.
> (There are many books on the topic, especially regarding what to expect and
> what not to expect from TDDFT, my personal opinion is that TDDFT thrives in
> the realm between theoretical chemistry and bulk materials, i.e. large
> molecules, nanocrystals, etc. Then again, this is my personal opinion)
> I would recommend you to start with M.A.L. Marques, C.A. Ullrich, F.
> Nogueira, A. Rubio, K. Burke, and E.K.U. Gross (eds.), Time-Dependent
> Density Functional Theory (Springer-Verlag, 2006). )
>
> 2011/4/20 Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>
>
>> Dear all
>> I did not say that TDDFPT does not work with periodic system, but you
>> cannot
>> have a realistic absorption spectra of a slab (or bulk crystal) if you
>> sample
>> the Brillouin zone by using Gamma only... TDDFPT works fine with finite
>> systems, i.e., which do not show a (strong) k dependence of the psi_n,k
>> eigenvalues.
>>
>> Giuseppe
>>
>> On Wednesday 20 April 2011 03:00:41 Johari, Priya Sudhir wrote:
>> > Thanks Marton, its working.
>> >
>> > On Tue, Apr 19, 2011 at 5:40 PM, Marci <vormar at gmail.com> wrote:
>> > > Dear Priya,
>> > >
>> > > Though I have never tried, it should work with periodic systems if you
>> > > sample the Brillouin zone only with the gamma point. Keep in mind that
>> > > the usual adiabatic approximations with (semi)local functionals might
>> > > not work very well for calculating the absorption of periodic systems.
>> > >
>> > > Marton
>> > >
>> > > --
>> > > Marton Voros
>> > > PhD student
>> > > Department of Atomic Physics
>> > > Budapest University of Technology and Economics
>> > > Budafoki ?t 8., H-1111, Budapest, Hungary
>> > > www.fat.bme.hu/MartonVoros
>> > >
>> > > On Tue, Apr 19, 2011 at 11:02 PM, Johari, Priya Sudhir
>> > >
>> > > <priya_johari at brown.edu> wrote:
>> > > > Thanks Duy, but the link does not give sufficient information.
>> However,
>> > > > I found a discussion on forum's archive itself where Giuseppe
>> Mattioli
>> > > > has mentioned that TDDPFT does not work for periodic systems :-(
>> > > >
>> > > > Dr Priya Johari.
>> > > > Brown University,
>> > > > Providence, RI - 02906. USA
>> > > >
>> > > > On Tue, Apr 19, 2011 at 3:59 PM, Duy Le <ttduyle at gmail.com> wrote:
>> > > >> If you do a little homework (such as googling keyword TD-DFPT),
>> you'll
>> > > >> find this link
>> > > >> http://qe-forge.org/projects/tddfpt/
>> > > >> I have not read it carefully but I guess it contains some useful
>> > > >> information.
>> > > >> --------------------------------------------------
>> > > >> Duy Le
>> > > >> PhD Student
>> > > >> Department of Physics
>> > > >> University of Central Florida.
>> > > >>
>> > > >> "Men don't need hand to do things"
>> > > >>
>> > > >>
>> > > >>
>> > > >> On Tue, Apr 19, 2011 at 3:26 PM, Johari, Priya Sudhir
>> > > >>
>> > > >> <priya_johari at brown.edu> wrote:
>> > > >> > TD-DFPT
>> > > >>
>> > > >> _______________________________________________
>> > > >> 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
>>
>>
>>
>> --
>> ********************************************************
>> - Article premier - Les hommes naissent et demeurent
>> libres et ?gaux en droits. Les distinctions sociales
>> ne peuvent ?tre fond?es que sur l'utilit? commune
>> - Article 2 - Le but de toute association politique
>> est la conservation des droits naturels et
>> imprescriptibles de l'homme. Ces droits sont la libert?,
>> la propri?t?, la s?ret? et la r?sistance ? l'oppression.
>> ********************************************************
>>
>>    Giuseppe Mattioli
>>    CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
>>    v. Salaria Km 29,300 - C.P. 10
>>    I 00015 - Monterotondo Stazione (RM)
>>    Tel + 39 06 90672836 - Fax +39 06 90672316
>>    E-mail: <giuseppe.mattioli at ism.cnr.it>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
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From eariel99 at gmail.com  Wed Apr 20 16:02:41 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Wed, 20 Apr 2011 10:02:41 -0400
Subject: [Pw_forum] new bfgs: strange behavior doing vc-relax
Message-ID: <BANLkTinqvDinA8rCJO8M5U=wHUmq4Np0Qg@mail.gmail.com>

Dear Max,
Thanks for your tests. Your  experiments looks nice to be included in a QE
tutorial.
I think your reasoning is correct. Moreover, the energy should always
decrease when you enlarge de basis set (adding G-vectors) because the
calculation is variational (within a given density functional). I am not
sure if the calculation is still variational with ultrasoft
pseudopotentials, or even if the Hohenberg-Kohn lemma is valid with non
local pseudopotentials. With QE I have always seen the energy to decrease
when the cutoffs are increased, but with VASP, I always see an oscillation
in the total energy when the cutoff is incremented. I hope one of our
professors can clarify this point.
Best regards
Eduardo



Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez

---------- Mensaje reenviado ----------
From: "?????? ?????" <max.n.popov at gmail.com>
To: PWSCF Forum <pw_forum at pwscf.org>
Date: Wed, 20 Apr 2011 11:25:46 +0200
Subject: Re: [Pw_forum] new bfgs: strange behavior doing vc-relax
Dear Eduardo,

thank you very much for expanded answer and sharing the practical tricks.
I've done some computational experiments on bulk Si (cubic conventional
cell) vc-relaxation.

Here is the result (V is volume of initial unit cell, and V0 is equilibrium
volume):

1) starting from V > V0, i.e. 1/V < 1/V0 -> more G-vectors for vc-relax:

G cutoff =  837.7995  ( 101505 G-vectors)     FFT grid: ( 60, 60, 60) -
vc-relax
G cutoff =  837.7995  (  97137 G-vectors)     FFT grid: ( 60, 60, 60)  -
post-scf

!    total energy              =    -372.89634728 Ry - the last energy in
the course of vc-relax
!    total energy              =    -372.89587589 Ry - post-scf energy

NB1: # of G-vectors (vc-relax) > # G-vectors(post-scf), and E(the last point
vc-relax) < E(post-scf).

1) starting from V < V0, i.e. 1/V > 1/V0 -> more G-vectors for post-scf:

G cutoff =  775.1830  (  90447 G-vectors)     FFT grid: ( 60, 60, 60) -
vc-relax
G cutoff =  775.1830  (  97137 G-vectors)     FFT grid: ( 60, 60, 60) -
post-scf

!    total energy              =    -372.89498529 Ry - the last energy in
the course of vc-relax
!    total energy              =    -372.89587142 Ry - post-scf energy

NB2: # of G-vectors(vc-relax) < # G-vectors(post-scf), and E(the last point
vc-relax) > E(post-scf).

Comparing these two experiments, one can make a preliminary conclusion: the
more G-vectors, the lower
the total Energy, provided all other parameters to be fixed.
This is easy to understand: plane-wave basis set is complete, that means 2
things (when dealing with truncated bases):
1) E(N+M) < E(N), where N,M - number of plane waves(G-vectors);
2) lim N->infinity of [ E(N+M)-E(N)] = 0.

Now it seems to be more clear for me :)
Correct me if I'm wrong somewhere.

-- 
Best regards, Max Popov
Ph.D. student
Materials center Leoben (MCL), Leoben, Austria.

--
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From giannozz at democritos.it  Wed Apr 20 17:46:18 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 20 Apr 2011 17:46:18 +0200
Subject: [Pw_forum] new bfgs: strange behavior doing vc-relax
In-Reply-To: <BANLkTinqvDinA8rCJO8M5U=wHUmq4Np0Qg@mail.gmail.com>
References: <BANLkTinqvDinA8rCJO8M5U=wHUmq4Np0Qg@mail.gmail.com>
Message-ID: <BFEAD9D5-B76C-4FDD-94CA-E738B5016814@democritos.it>


On Apr 20, 2011, at 16:02 , Eduardo Ariel Menendez Proupin wrote:

> I am not sure if the calculation is still variational with  
> ultrasoft pseudopotentials

it should be

> or even if the Hohenberg-Kohn lemma is valid with non local  
> pseudopotentials

there is some old work by Gilbert on this subject: http://prb.aps.org/ 
abstract/PRB/v12/i6/p2111_1

> With QE I have always seen the energy to decrease when the cutoffs are
> increased, but with VASP, I always see an oscillation in the total  
> energy
> when the cutoff is incremented.

just guessing: it might be a consequence of real-space treatment of  
augmentation
functions.

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





From dstrubbe at berkeley.edu  Wed Apr 20 21:51:56 2011
From: dstrubbe at berkeley.edu (David Strubbe)
Date: Wed, 20 Apr 2011 12:51:56 -0700
Subject: [Pw_forum] implementation of variation of occupations and Fermi
 level with perturbations
In-Reply-To: <4DAE956D.4000402@sissa.it>
References: <BANLkTi=sidNdheP906hgk2LznewjBqYkFA@mail.gmail.com>
	<0E9B33A7-45CE-47E3-9642-D2EE19724EB6@democritos.it>
	<BANLkTinTJ5BHnKiDgefuo4SVas7XTcLhMw@mail.gmail.com>
	<4DAE956D.4000402@sissa.it>
Message-ID: <BANLkTi=LfMazNDDe+XuB+nDawXU2D_uRoQ@mail.gmail.com>

Stefano,

Thank you for the explanation. Things are clear now. Is there a circumstance
in which Delta n_ext(q=0) is nonzero?

David Strubbe
UC Berkeley

On Wed, Apr 20, 2011 at 1:12 AM, Stefano de Gironcoli <degironc at sissa.it>wrote:

>  Dear David Strubbe,
>
> eq. 79 is a general formula; in the phonon code Delta n_ext(q=0) is always
> vanishing because the perturbation is neutral (atoms are displaced but their
> charge is not changed), still Delta Vscf is in general non zero so one has
> to do something
>
> Let's look at the scf variation of rho that is something like
>
> Delta rho(r) = sum_i  f_i (phi_i* Delta_phi_i +cc) + d f_i/de *(Delta e_i -
> Delta e_F) |phi|^2
>
> As said, eq. 79 is the condition of charge neutrality of the perturbation
> which is due ONLY to the last term involving changes in occupation of states
> (remember that Delta phi is always orthogonal to the unperturbed phi so in
> no case Delta phi can contribute to the total charge variation)
>
> if you work out the expression ...
>
> total charge = Delta n_ext + Delta_n induced by Delta e_i (defined in terms
> of the potential change) + Delta_n induced by the Fermi energy shift..
>
> and the neutrality condition reads
>
> 0 = Delta_n_ext + \int n(e_F,r) Delta Vscf - n(e_F) * Delta e_F
>
> which is eq. 79.
>
> HOWEVER, delta rho that enters ef_shift has been computed without the
> contribution coming from the (then unknown) Fermi energy shift Delta e_F
> that is (see above)
>
> - n(e_F,r) * Delta e_F
>
> this is how ef_shift routine icomputes Delta e_F:  it calculates the G=0
> component of Delta rho before the shift ( which amount to be \int n(e_F,r)
> Delta Vscf ) and define Delta e_F in such a way that after the term  -
> n(e_F,r) * Delta e_F is added the final Delta rho is neutral.
>
> I hope the procedure is a bit clearer now.
>
> stefano
>
>
>
> On 04/20/2011 12:08 AM, David Strubbe wrote:
>
> Paolo,
>
> Thanks for the response. This gives me some more insight into what is going
> on, but I still don't understand.
>
> As far as I can tell, the drhoscf in ef_shift is still the change in the
> density rather than the change in the potential, because the calls in
> solve_linter to dv_of_drho are using a copy of the density response rather
> than drhoscf itself:
>
>         call zcopy
> (nrxx*nspin_mag,drhoscfh(1,1,ipert),1,dvscfout(1,1,ipert),1)
>         call dv_of_drho (imode0+ipert, dvscfout(1,1,ipert), .true.)
>
> The heart of the matter is the lines in ef_shift:
>
> delta_n = delta_n + omega*drhoscf(nl(1),is,ipert)
> def (ipert) = - delta_n / dos_ef
>
> delta_n does not seem to refer to \Delta n_{ext} or the integral of the LDOS
> with \Delta V_{SCF}, as in the numerator of Eq. 79. Do those quantities
> exist in the calculation here?
>
> Thanks,
> David Strubbe
> UC Berkeley
>
> On Tue, Apr 19, 2011 at 1:44 PM, Paolo Giannozzi <giannozz at democritos.it> <giannozz at democritos.it>wrote:
>
>
>  On Apr 8, 2011, at 20:39 , David Strubbe wrote:
>
>
>  Eq. 79 refers to a quantity \Delta n_{ext} and an integral of the LDOS
> with \Delta V_{SCF} to calculate the shift in Fermi level. However in
> ef_shift it appears that the density response drhoscf is used instead
> of these quantities in the numerator, which doesn't seem like the
> same thing.
>
>  it doesn't, but it is. The (dirty) trick is well hidden in the call
> to routine dv_of_drho:
> it accepts in input the variation of the charge density, returns in
> output the
> variation of the potential, overwritten on the former. It was done a
> looong time
> ago in order to spare some memory, when machines had much less ram and
> the code was much simpler and smaller (occasional dirty tricks were
> under
> control, sort of). A comment in the code would have spared you (and me)
> some time. Unfortunately comments in code tend to belong to one of the
> following categories: 1) useless, 2) misleading, 3) obsolete, 4)
> nonexistent
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> _______________________________________________
> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum
>
>
> _______________________________________________
> Pw_forum mailing listPw_forum at pwscf.orghttp://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 degironc at sissa.it  Wed Apr 20 22:11:58 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 20 Apr 2011 22:11:58 +0200
Subject: [Pw_forum] implementation of variation of occupations and Fermi
 level with perturbations
In-Reply-To: <BANLkTi=LfMazNDDe+XuB+nDawXU2D_uRoQ@mail.gmail.com>
References: <BANLkTi=sidNdheP906hgk2LznewjBqYkFA@mail.gmail.com>	<0E9B33A7-45CE-47E3-9642-D2EE19724EB6@democritos.it>	<BANLkTinTJ5BHnKiDgefuo4SVas7XTcLhMw@mail.gmail.com>	<4DAE956D.4000402@sissa.it>
	<BANLkTi=LfMazNDDe+XuB+nDawXU2D_uRoQ@mail.gmail.com>
Message-ID: <4DAF3E0E.7000109@sissa.it>

It might happen if you transform one atom into another like in the 
"computational alchemy" approach [PRL 66 2116( 1991)]
stefano

On 04/20/2011 09:51 PM, David Strubbe wrote:
> Stefano,
>
> Thank you for the explanation. Things are clear now. Is there a circumstance
> in which Delta n_ext(q=0) is nonzero?
>
> David Strubbe
> UC Berkeley
>
> On Wed, Apr 20, 2011 at 1:12 AM, Stefano de Gironcoli<degironc at sissa.it>wrote:
>
>>   Dear David Strubbe,
>>
>> eq. 79 is a general formula; in the phonon code Delta n_ext(q=0) is always
>> vanishing because the perturbation is neutral (atoms are displaced but their
>> charge is not changed), still Delta Vscf is in general non zero so one has
>> to do something
>>
>> Let's look at the scf variation of rho that is something like
>>
>> Delta rho(r) = sum_i  f_i (phi_i* Delta_phi_i +cc) + d f_i/de *(Delta e_i -
>> Delta e_F) |phi|^2
>>
>> As said, eq. 79 is the condition of charge neutrality of the perturbation
>> which is due ONLY to the last term involving changes in occupation of states
>> (remember that Delta phi is always orthogonal to the unperturbed phi so in
>> no case Delta phi can contribute to the total charge variation)
>>
>> if you work out the expression ...
>>
>> total charge = Delta n_ext + Delta_n induced by Delta e_i (defined in terms
>> of the potential change) + Delta_n induced by the Fermi energy shift..
>>
>> and the neutrality condition reads
>>
>> 0 = Delta_n_ext + \int n(e_F,r) Delta Vscf - n(e_F) * Delta e_F
>>
>> which is eq. 79.
>>
>> HOWEVER, delta rho that enters ef_shift has been computed without the
>> contribution coming from the (then unknown) Fermi energy shift Delta e_F
>> that is (see above)
>>
>> - n(e_F,r) * Delta e_F
>>
>> this is how ef_shift routine icomputes Delta e_F:  it calculates the G=0
>> component of Delta rho before the shift ( which amount to be \int n(e_F,r)
>> Delta Vscf ) and define Delta e_F in such a way that after the term  -
>> n(e_F,r) * Delta e_F is added the final Delta rho is neutral.
>>
>> I hope the procedure is a bit clearer now.
>>
>> stefano
>>
>>
>>
>> On 04/20/2011 12:08 AM, David Strubbe wrote:
>>
>> Paolo,
>>
>> Thanks for the response. This gives me some more insight into what is going
>> on, but I still don't understand.
>>
>> As far as I can tell, the drhoscf in ef_shift is still the change in the
>> density rather than the change in the potential, because the calls in
>> solve_linter to dv_of_drho are using a copy of the density response rather
>> than drhoscf itself:
>>
>>          call zcopy
>> (nrxx*nspin_mag,drhoscfh(1,1,ipert),1,dvscfout(1,1,ipert),1)
>>          call dv_of_drho (imode0+ipert, dvscfout(1,1,ipert), .true.)
>>
>> The heart of the matter is the lines in ef_shift:
>>
>> delta_n = delta_n + omega*drhoscf(nl(1),is,ipert)
>> def (ipert) = - delta_n / dos_ef
>>
>> delta_n does not seem to refer to \Delta n_{ext} or the integral of the LDOS
>> with \Delta V_{SCF}, as in the numerator of Eq. 79. Do those quantities
>> exist in the calculation here?
>>
>> Thanks,
>> David Strubbe
>> UC Berkeley
>>
>> On Tue, Apr 19, 2011 at 1:44 PM, Paolo Giannozzi<giannozz at democritos.it>  <giannozz at democritos.it>wrote:
>>
>>
>>   On Apr 8, 2011, at 20:39 , David Strubbe wrote:
>>
>>
>>   Eq. 79 refers to a quantity \Delta n_{ext} and an integral of the LDOS
>> with \Delta V_{SCF} to calculate the shift in Fermi level. However in
>> ef_shift it appears that the density response drhoscf is used instead
>> of these quantities in the numerator, which doesn't seem like the
>> same thing.
>>
>>   it doesn't, but it is. The (dirty) trick is well hidden in the call
>> to routine dv_of_drho:
>> it accepts in input the variation of the charge density, returns in
>> output the
>> variation of the potential, overwritten on the former. It was done a
>> looong time
>> ago in order to spare some memory, when machines had much less ram and
>> the code was much simpler and smaller (occasional dirty tricks were
>> under
>> control, sort of). A comment in the code would have spared you (and me)
>> some time. Unfortunately comments in code tend to belong to one of the
>> following categories: 1) useless, 2) misleading, 3) obsolete, 4)
>> nonexistent
>>
>> P.
>> ---
>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>> _______________________________________________
>> Pw_forum mailing listPw_forum at pwscf.orghttp://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

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From degironc at sissa.it  Wed Apr 20 22:21:56 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 20 Apr 2011 22:21:56 +0200
Subject: [Pw_forum] new bfgs: strange behavior doing vc-relax
In-Reply-To: <BFEAD9D5-B76C-4FDD-94CA-E738B5016814@democritos.it>
References: <BANLkTinqvDinA8rCJO8M5U=wHUmq4Np0Qg@mail.gmail.com>
	<BFEAD9D5-B76C-4FDD-94CA-E738B5016814@democritos.it>
Message-ID: <4DAF4064.4090002@sissa.it>

On 04/20/2011 05:46 PM, Paolo Giannozzi wrote:
> On Apr 20, 2011, at 16:02 , Eduardo Ariel Menendez Proupin wrote:
>
>> I am not sure if the calculation is still variational with
>> ultrasoft pseudopotentials
> it should be
>
>> or even if the Hohenberg-Kohn lemma is valid with non local
>> pseudopotentials
> there is some old work by Gilbert on this subject: http://prb.aps.org/
> abstract/PRB/v12/i6/p2111_1
>
>> With QE I have always seen the energy to decrease when the cutoffs are
>> increased, but with VASP, I always see an oscillation in the total
>> energy
>> when the cutoff is incremented.
> just guessing: it might be a consequence of real-space treatment of
> augmentation
> functions.

actually it can happen for US pseudo, if the cutoff for the density is 
not large enough, that the energy increases with increasing cutoff.. 
just because the augmentation charges are not integrated correctly and 
the error can have any sign. If ecutrho is sufficient to integrate 
correctly augmentation charges the energy should be variational w.r.t. 
ecutwfc .

stefano



> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From trambui at u.boisestate.edu  Thu Apr 21 00:25:55 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Wed, 20 Apr 2011 16:25:55 -0600
Subject: [Pw_forum] Generating ultra soft pseudopotential
In-Reply-To: <BANLkTi=pmuBY4W3_84vsE_m1okCtMSg0rQ@mail.gmail.com>
References: <BANLkTi=pmuBY4W3_84vsE_m1okCtMSg0rQ@mail.gmail.com>
Message-ID: <BANLkTinK7+Vb-YXotPFN2Z2a4eVKt00mgg@mail.gmail.com>

Dear Everyone,
     I'm trying to complete my process of generating the Cesium PP
(extremely hard for a total new and have no experience with QE like me!!!).
So far I have been helped with many other issues, and I'm very much getting
there. I still have couple more questions and hope you can spare me some
time to help me out. my questions are :
 -------the number of logarithmic derivatives to be calculated, the "nld"
value, how does it determine?
--------Angular momentum of the local channel, the "lloc" value, how does it
determine?
 my atom is : Cs with electron config. [Xe] 6s1, and i'm doing ultra-soft
PP. I have checked and it does have the bound state on the p orbital. so I
guess my electron config. should be "[Xe] 6s1 6p-1 ".

I appreciate any input you have for me!
Tram Bui

On Tue, Apr 5, 2011 at 3:42 PM, Tram Bui <trambui at u.boisestate.edu> wrote:

> Dear Folks,
>      I'm trying to build an input file for generating the Cs
> pseudopotential. when I run the ld1.x on my input file. I got an error
> message saying that i'm using the wrong core. would you help me with extra
> information of where I can find the help for how to choose the right core
> for some atoms such as in my case it is Cs.
>
> Thank you very much,
>
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
>
>


-- 
Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From eariel99 at gmail.com  Thu Apr 21 01:35:39 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Wed, 20 Apr 2011 19:35:39 -0400
Subject: [Pw_forum] why are there two Fermi energies?
Message-ID: <BANLkTimdDHniPCQ5pyx6BQWxce=ZbMmpRg@mail.gmail.com>

Hi,
Why are there two Fermi energies in certain spin-polarized calculations ?

input             starting_magnetization(1) = 0.0,
                    starting_magnetization(2) = 0.5,
output      the Fermi energy is     6.1598 ev
               !    total energy              =    -502.92538790 Ry

input           tot_magnetization = 1
output     the spin up/dw Fermi energies are     6.3821    6.1598 ev
              !    total energy              =    -502.92538790 Ry

What is the meaning of the spin up Fermi level in the second case?

This numbers are for a 64 atoms Si unit cell with one Si replaced by Al, and
only one k-point, but the same happens with more k-points. I also used Fermi
smearing with a very low smearing.
 There is a difference if I set the starting magnetization or the total
magnetization, with pw.x version 4.2.1. However, despite reporting different
Fermi levels, the total energy and magnetization are equal. Also are equal
KS energies, at least around the Fermi levels.

Thanks,

Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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From sclauzer at sissa.it  Thu Apr 21 09:50:34 2011
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Thu, 21 Apr 2011 09:50:34 +0200
Subject: [Pw_forum] Generating ultra soft pseudopotential
In-Reply-To: <BANLkTinK7+Vb-YXotPFN2Z2a4eVKt00mgg@mail.gmail.com>
References: <BANLkTi=pmuBY4W3_84vsE_m1okCtMSg0rQ@mail.gmail.com>
	<BANLkTinK7+Vb-YXotPFN2Z2a4eVKt00mgg@mail.gmail.com>
Message-ID: <A1D45CED-ED2D-463E-AFA1-2F3B4244F2AB@sissa.it>

Dear Tram Bui,

Il giorno 21/apr/2011, alle ore 00.25, Tram Bui ha scritto:

> Dear Everyone,
>      I'm trying to complete my process of generating the Cesium PP (extremely hard for a total new and have no experience with QE like me!!!).

Have you tried with those available on the internet, before trying to generate it by yourself?

> So far I have been helped with many other issues, and I'm very much getting there. I still have couple more questions and hope you can spare me some time to help me out. my questions are :
>  -------the number of logarithmic derivatives to be calculated, the "nld" value, how does it determine? 

You determine. In principle it depends on how many angular momenta you include in the non-local part of the PP (i.e., if you include s and p, then choose nld=1, if you include also d then you need nld=2, ...). This does not influence the final PP data, but it helps you to understand if your PP is a good one or not.

> --------Angular momentum of the local channel, the "lloc" value, how does it determine?

You determine. This flag is used to select how the local part of the PP is built (either from the smoothed all-electron KS potential - the default - or from a smoothed KS wavefunction - if lloc>=0). Different choices are possible here, it is not easy to give a general advice (you might have a look into Paolo's notes, there should be something:
http://www.fisica.uniud.it/~giannozz/Atom/doc.pdf)

>  my atom is : Cs with electron config. [Xe] 6s1, and i'm doing ultra-soft PP. I have checked and it does have the bound state on the p orbital. so I guess my electron config. should be "[Xe] 6s1 6p-1 ".

What about 5d and 4f?


Regards


GS

> 
> I appreciate any input you have for me!
> Tram Bui
> 
> On Tue, Apr 5, 2011 at 3:42 PM, Tram Bui <trambui at u.boisestate.edu> wrote:
> Dear Folks,

P.S.: of course this forum is quite friendly and informal, but maybe not to this point :)

>      I'm trying to build an input file for generating the Cs pseudopotential. when I run the ld1.x on my input file. I got an error message saying that i'm using the wrong core. would you help me with extra information of where I can find the help for how to choose the right core for some atoms such as in my case it is Cs.
>  
> Thank you very much,
> 
> Tram Bui
> 
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
> 
> 
> 
> 
> -- 
> Tram Bui
> 
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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

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From Lorenzo.Paulatto at impmc.upmc.fr  Thu Apr 21 11:00:49 2011
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Thu, 21 Apr 2011 11:00:49 +0200
Subject: [Pw_forum] why are there two Fermi energies?
In-Reply-To: <BANLkTimdDHniPCQ5pyx6BQWxce=ZbMmpRg@mail.gmail.com>
References: <BANLkTimdDHniPCQ5pyx6BQWxce=ZbMmpRg@mail.gmail.com>
Message-ID: <op.vt95znr7xuur8c@vanoxite.impmc.jussieu.fr>


On Thu, 21 Apr 2011 01:35:39 +0200, Eduardo Ariel Menendez Proupin  
<eariel99 at gmail.com> wrote:
> Why are there two Fermi energies in certain spin-polarized calculations ?
>
> input             starting_magnetization(1) = 0.0,
>                     starting_magnetization(2) = 0.5,
> output      the Fermi energy is     6.1598 ev
>                !    total energy              =    -502.92538790 Ry
>
> input           tot_magnetization = 1
> output     the spin up/dw Fermi energies are     6.3821    6.1598 ev
>               !    total energy              =    -502.92538790 Ry
>
> What is the meaning of the spin up Fermi level in the second case?

Dear Eduardo, if you force the system to have a certain magnetization  
(i.e. setting tot_magnetization) you are actually asking to occupy the  
"up" spin orbital more then the "down" spin ones, i.e. you have more up  
electrons then down electrons. This is achieved by filling the up orbitals  
up to a higher energy than the down orbitals, by setting two distinct  
Fermi energies.

On the other hand, if you only set starting magnetization, you get the  
computational ground state, where up and down orbitals are be filled up to  
the same level; what changes is the KS eigenvalues.

hth, lorenzo


>
> This numbers are for a 64 atoms Si unit cell with one Si replaced by Al,  
> and
> only one k-point, but the same happens with more k-points. I also used  
> Fermi
> smearing with a very low smearing.
>  There is a difference if I set the starting magnetization or the total
> magnetization, with pw.x version 4.2.1. However, despite reporting  
> different
> Fermi levels, the total energy and magnetization are equal. Also are  
> equal
> KS energies, at least around the Fermi levels.
>
> Thanks,
>
> Eduardo Menendez
> Departamento de Fisica
> Facultad de Ciencias
> Universidad de Chile
> Phone: (56)(2)9787439
> URL: http://fisica.ciencias.uchile.cl/~emenendez


-- 
Lorenzo Paulatto (IdR)
IMPMC - CNRS UMR 7590 & Universit? P&M Curie
T23-C23/24-4e16 - 4 place Jussieu - 75252 Paris Cedex5
phone: +33 (0)144 27 5211
www:   http://www-int.impmc.upmc.fr/~paulatto/

From giannozz at democritos.it  Thu Apr 21 11:04:21 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 21 Apr 2011 11:04:21 +0200
Subject: [Pw_forum] Generating ultra soft pseudopotential
In-Reply-To: <A1D45CED-ED2D-463E-AFA1-2F3B4244F2AB@sissa.it>
References: <BANLkTi=pmuBY4W3_84vsE_m1okCtMSg0rQ@mail.gmail.com>
	<BANLkTinK7+Vb-YXotPFN2Z2a4eVKt00mgg@mail.gmail.com>
	<A1D45CED-ED2D-463E-AFA1-2F3B4244F2AB@sissa.it>
Message-ID: <1303376661.17194.7.camel@fe12lx.fisica.uniud.it>

On Thu, 2011-04-21 at 09:50 +0200, Gabriele Sclauzero wrote:

> (you might have a look into Paolo's notes, there should be something:
> http://www.fisica.uniud.it/~giannozz/Atom/doc.pdf)

an updated version of this document is in atomic_doc/pseudo-gen.pdf

P.

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



From sclauzer at sissa.it  Thu Apr 21 11:28:51 2011
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Thu, 21 Apr 2011 11:28:51 +0200
Subject: [Pw_forum] why are there two Fermi energies?
In-Reply-To: <BANLkTimdDHniPCQ5pyx6BQWxce=ZbMmpRg@mail.gmail.com>
References: <BANLkTimdDHniPCQ5pyx6BQWxce=ZbMmpRg@mail.gmail.com>
Message-ID: <0CD095EE-2EC8-4E33-9F7F-334812E8089C@sissa.it>

Hello, 

   I'm also interested in going deeper into this topic. I tell what (I think) I've understood, so maybe we can trigger a discussion with Paolo or Stefano ;)

Il giorno 21/apr/2011, alle ore 01.35, Eduardo Ariel Menendez Proupin ha scritto:

> Hi, 
> Why are there two Fermi energies in certain spin-polarized calculations ? 

It's just a practical way to deal with spin polarized calculations when you fix a net non-zero total magnetization in the unit cell. Since you know the total charge and the total magnetization, you can determine univocally the number of spin up and of spin down electrons. This in turns allows you to treat the up and down Fermi energies independently, using the same techniques for spin-unpolarized calculations to determine the two Fermi energies.

> 
> input             starting_magnetization(1) = 0.0,
>                     starting_magnetization(2) = 0.5,
> output      the Fermi energy is     6.1598 ev
>                !    total energy              =    -502.92538790 Ry
> 
> input           tot_magnetization = 1
> output     the spin up/dw Fermi energies are     6.3821    6.1598 ev
>               !    total energy              =    -502.92538790 Ry
> 
> What is the meaning of the spin up Fermi level in the second case? 

Did you get this with smearing? Otherwise the Fermi energy should not be printed.
Specifying starting_magnetization or tot_magnetization is not equivalent, the former is just used to break the symmetry. You might end with a different magnetization, if that set by 
tot_magnetization does not correspond to the ground state. In your case it looks like the GS has M_tot=1, since you got exactly the same energy. What do you get as total magnetization in the first case?
At first glance I don't see why in the first case you get the lowest of the two Fermi energies, I would rather expect the other. What changes between the two calculations is how the occupations are computed (see PW/weights.f90). You can print them on output by specifying verbosity='high'.


> 
> This numbers are for a 64 atoms Si unit cell with one Si replaced by Al, and only one k-point, but the same happens with more k-points. I also used Fermi smearing with a very low smearing. 
>  There is a difference if I set the starting magnetization or the total magnetization, with pw.x version 4.2.1. However, despite reporting different Fermi levels, the total energy and magnetization are equal. Also are equal KS energies, at least around the Fermi levels.

Yes, I know there have been some changes in the last versions. I think Paolo can be more helpful here.


HTH

GS

> 
> Thanks,
> 
> Eduardo Menendez
> Departamento de Fisica
> Facultad de Ciencias
> Universidad de Chile
> Phone: (56)(2)9787439
> URL: http://fisica.ciencias.uchile.cl/~emenendez
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


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

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From cyrille.barreteau at cea.fr  Thu Apr 21 11:14:44 2011
From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille)
Date: Thu, 21 Apr 2011 11:14:44 +0200
Subject: [Pw_forum] =?iso-8859-1?q?RE=A0=3A__why_are_there_two_Fermi_energ?=
	=?iso-8859-1?q?ies=3F?=
References: <BANLkTimdDHniPCQ5pyx6BQWxce=ZbMmpRg@mail.gmail.com>
	<op.vt95znr7xuur8c@vanoxite.impmc.jussieu.fr>
Message-ID: <18E4AC9C2FAC504E994A6759DE5ABE8DE315B8@DIODON.extra.cea.fr>

Dear Eduardo
 
Let me precise a little this point.
If you do a fixed total moment calculation as explained by Lorenzo you get two different Fermi energies.
You can also plot E(M) ie the total energy with respect to the total magnetization. You will then find a minimum of energy (or several ones if you have metastable solutions) for a given M0. This M0 corresponds to the true ground state and for this particular case the two Fermi energies are aligned..
 
hth
 
  cyrille
 
================================================================== 
Cyrille Barreteau                                                      phone : +33 (0)1 69 08 29 51 
CEA Saclay                                                             fax :      +33 (0)1 69 08 84 46 
IRAMIS, SPCSI,    Batiment 462                            email     cyrille.barreteau at cea.fr 
91191 Gif sur Yvette Cedex 
FRANCE 
~~~~~~~~~~~~~~~~~~~~~~~~ 
Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ 
==================================================================

________________________________

De: pw_forum-bounces at pwscf.org de la part de Lorenzo Paulatto
Date: jeu. 21/04/2011 11:00
?: PWSCF Forum
Objet : Re: [Pw_forum] why are there two Fermi energies?




On Thu, 21 Apr 2011 01:35:39 +0200, Eduardo Ariel Menendez Proupin 
<eariel99 at gmail.com> wrote:
> Why are there two Fermi energies in certain spin-polarized calculations ?
>
> input             starting_magnetization(1) = 0.0,
>                     starting_magnetization(2) = 0.5,
> output      the Fermi energy is     6.1598 ev
>                !    total energy              =    -502.92538790 Ry
>
> input           tot_magnetization = 1
> output     the spin up/dw Fermi energies are     6.3821    6.1598 ev
>               !    total energy              =    -502.92538790 Ry
>
> What is the meaning of the spin up Fermi level in the second case?

Dear Eduardo, if you force the system to have a certain magnetization 
(i.e. setting tot_magnetization) you are actually asking to occupy the 
"up" spin orbital more then the "down" spin ones, i.e. you have more up 
electrons then down electrons. This is achieved by filling the up orbitals 
up to a higher energy than the down orbitals, by setting two distinct 
Fermi energies.

On the other hand, if you only set starting magnetization, you get the 
computational ground state, where up and down orbitals are be filled up to 
the same level; what changes is the KS eigenvalues.

hth, lorenzo


>
> This numbers are for a 64 atoms Si unit cell with one Si replaced by Al, 
> and
> only one k-point, but the same happens with more k-points. I also used 
> Fermi
> smearing with a very low smearing.
>  There is a difference if I set the starting magnetization or the total
> magnetization, with pw.x version 4.2.1. However, despite reporting 
> different
> Fermi levels, the total energy and magnetization are equal. Also are 
> equal
> KS energies, at least around the Fermi levels.
>
> Thanks,
>
> Eduardo Menendez
> Departamento de Fisica
> Facultad de Ciencias
> Universidad de Chile
> Phone: (56)(2)9787439
> URL: http://fisica.ciencias.uchile.cl/~emenendez


--
Lorenzo Paulatto (IdR)
IMPMC - CNRS UMR 7590 & Universit? P&M Curie
T23-C23/24-4e16 - 4 place Jussieu - 75252 Paris Cedex5
phone: +33 (0)144 27 5211
www:   http://www-int.impmc.upmc.fr/~paulatto/
_______________________________________________
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  Thu Apr 21 12:32:20 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 21 Apr 2011 12:32:20 +0200
Subject: [Pw_forum] why are there two Fermi energies?
In-Reply-To: <0CD095EE-2EC8-4E33-9F7F-334812E8089C@sissa.it>
References: <BANLkTimdDHniPCQ5pyx6BQWxce=ZbMmpRg@mail.gmail.com>
	<0CD095EE-2EC8-4E33-9F7F-334812E8089C@sissa.it>
Message-ID: <1303381940.17194.27.camel@fe12lx.fisica.uniud.it>

On Thu, 2011-04-21 at 11:28 +0200, Gabriele Sclauzero wrote:

> Yes, I know there have been some changes in the last versions. 
> I think Paolo can be more helpful here.

I don't think so. There are no substantial differences in the
last version wrt the previous one in this case. I do not see 
anything anomalous in Eduardo's results, by the way. The
results with constrained and unconstrained magnetizations
are the same => the constrained-magnetization result is the
ground state. The "two Fermi energies" of the constrained 
case need not to be exactly the same as the (single)
Fermi energy of the unconstrained case, as long as the
occupancies for spin-up and spin-down are the same in the
two cases.

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



From m_pazoki at physics.sharif.edu  Thu Apr 21 13:04:47 2011
From: m_pazoki at physics.sharif.edu (meysam pazoki)
Date: Thu, 21 Apr 2011 15:34:47 +0430
Subject: [Pw_forum] A problem with average.x
Message-ID: <BANLkTiniwb3LCMqbbG26Lj2oy3Ze2eFrmg@mail.gmail.com>

Dear Pwscf users

I have a problem in using average.x,
after DFT ground state calculations i use pp.x for saving  the V_bare + V_H
potential in  "fermipot.dat" file.
I want to use average.x for average the data saved in the file for obtaining
the fermi level(follow the instruction of work_FCT example of espresso)
i use the following input file for average.in:


1
fermirefpot
1.D0
500
3
55.809


where if i am not wrong,*55.809 is my lattice constant in bohr and i want to
get 500 data finally.
but the program average.x is steel running after two  days for a 16
processor server and in .out file i see:

Reading header from file  fermirefpot.dat

the cpu is fully engaged but the memory usage is 0%!
i think there is something wrong in my input file.*I try to change some
parameters like "3->2 or 1"  and "500->1000 or 300" but the result is the
same.

i would be really grateful *if you could help me,
Thanks indeed for your time and kindness
Meysam*
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From rajanpandey at gmail.com  Thu Apr 21 13:56:07 2011
From: rajanpandey at gmail.com (Rajan Pandey)
Date: Thu, 21 Apr 2011 17:26:07 +0530
Subject: [Pw_forum] A problem with average.x
In-Reply-To: <BANLkTiniwb3LCMqbbG26Lj2oy3Ze2eFrmg@mail.gmail.com>
References: <BANLkTiniwb3LCMqbbG26Lj2oy3Ze2eFrmg@mail.gmail.com>
Message-ID: <BANLkTim9W+tdy0MK2JAen4+1MfGK+PHxiA@mail.gmail.com>

Hi,
My understanding is that average.x needs to be run on single processor
(serial submission) and not multiple CPUs in parallel.
So if you run average.x  as mpirun -np 1 path/to/average.x ......it should
work.

Hope it helps!

Regards,

Rajan

Rajan K. Pandey, Ph.D.

Advisory Research Engineer,
Semiconductor Research & Development Center
India Systems & Technology Engineering Lab
IBM India Pvt. Ltd.
MD3 1F B354
Manyata Embassy  Business Park
Nagawara, Outer Ring Road
Bangalore - 560045, India
Phone: +91-80-28061262
Mobile: +91-9901850981
Email: rajapand at in.ibm.com
            rajanpandey at gmail.com


On Thu, Apr 21, 2011 at 4:34 PM, meysam pazoki
<m_pazoki at physics.sharif.edu>wrote:

> Dear Pwscf users
>
> I have a problem in using average.x,
> after DFT ground state calculations i use pp.x for saving  the V_bare + V_H
> potential in  "fermipot.dat" file.
> I want to use average.x for average the data saved in the file for
> obtaining the fermi level(follow the instruction of work_FCT example of
> espresso)
> i use the following input file for average.in:
>
>
> 1
> fermirefpot
> 1.D0
> 500
> 3
> 55.809
>
>
> where if i am not wrong,*55.809 is my lattice constant in bohr and i want
> to get 500 data finally.
> but the program average.x is steel running after two  days for a 16
> processor server and in .out file i see:
>
> Reading header from file  fermirefpot.dat
>
> the cpu is fully engaged but the memory usage is 0%!
> i think there is something wrong in my input file.*I try to change some
> parameters like "3->2 or 1"  and "500->1000 or 300" but the result is the
> same.
>
> i would be really grateful *if you could help me,
> Thanks indeed for your time and kindness
> Meysam*
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From baroni at sissa.it  Thu Apr 21 14:05:33 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 21 Apr 2011 14:05:33 +0200
Subject: [Pw_forum] TDDFT approach for periodic system
In-Reply-To: <201104201121.45702.giuseppe.mattioli@mlib.ism.cnr.it>
References: <BANLkTi=JEJyTi26LHXWkWYO8=WP_0haGSg@mail.gmail.com>
	<BANLkTi=+CH7HMf3_V=yTWmw_FcOG3RYS5w@mail.gmail.com>
	<BANLkTi=ATF7Ge_xy50FRdb5aOVsiXKd_wQ@mail.gmail.com>
	<201104201121.45702.giuseppe.mattioli@mlib.ism.cnr.it>
Message-ID: <5BB7A50A-C21A-4AC3-ADC5-B049519E79EE@sissa.it>

Just a couple of further comments.
1) The ability (or lack thereof) of (adiabatic) tddft to properly describe optical excitations in extended systems does not depend on the code's ability to sample the whole BZ using special k-points. The current version of the tddfpt code distributed with QE is only apt to sample k=0 Bloch state, but periodic systems can nevertheless be treated (admittedly not very efficiently) to arbitrary numerical accuracy, by using suitable supercells.
2) adiabatic XC functionals miss excitonic effects in periodic systems (irrespective of the number of k-points used to sample the BZ) for the same reason why they miss Rydberg series in molecular systems. Always be suspicious of statements such as "TDDFT works for molecules, but it fails for crystals". This is nonsense: any crystal is nothing but a "big molecule". TDDFT works for both, and it fails for both. Only the failures manifest themselves in different ways, according to the size of the system.
Cheers - SB


On Apr 20, 2011, at 11:21 AM, Giuseppe Mattioli wrote:

> Dear all
> I did not say that TDDFPT does not work with periodic system, but you cannot 
> have a realistic absorption spectra of a slab (or bulk crystal) if you sample 
> the Brillouin zone by using Gamma only... TDDFPT works fine with finite 
> systems, i.e., which do not show a (strong) k dependence of the psi_n,k 
> eigenvalues.
> 
> Giuseppe
> 
> On Wednesday 20 April 2011 03:00:41 Johari, Priya Sudhir wrote:
>> Thanks Marton, its working.
>> 
>> On Tue, Apr 19, 2011 at 5:40 PM, Marci <vormar at gmail.com> wrote:
>>> Dear Priya,
>>> 
>>> Though I have never tried, it should work with periodic systems if you
>>> sample the Brillouin zone only with the gamma point. Keep in mind that
>>> the usual adiabatic approximations with (semi)local functionals might
>>> not work very well for calculating the absorption of periodic systems.
>>> 
>>> Marton
>>> 
>>> --
>>> Marton Voros
>>> PhD student
>>> Department of Atomic Physics
>>> Budapest University of Technology and Economics
>>> Budafoki ?t 8., H-1111, Budapest, Hungary
>>> www.fat.bme.hu/MartonVoros
>>> 
>>> On Tue, Apr 19, 2011 at 11:02 PM, Johari, Priya Sudhir
>>> 
>>> <priya_johari at brown.edu> wrote:
>>>> Thanks Duy, but the link does not give sufficient information. However,
>>>> I found a discussion on forum's archive itself where Giuseppe Mattioli
>>>> has mentioned that TDDPFT does not work for periodic systems :-(
>>>> 
>>>> Dr Priya Johari.
>>>> Brown University,
>>>> Providence, RI - 02906. USA
>>>> 
>>>> On Tue, Apr 19, 2011 at 3:59 PM, Duy Le <ttduyle at gmail.com> wrote:
>>>>> If you do a little homework (such as googling keyword TD-DFPT), you'll
>>>>> find this link
>>>>> http://qe-forge.org/projects/tddfpt/
>>>>> I have not read it carefully but I guess it contains some useful
>>>>> information.
>>>>> --------------------------------------------------
>>>>> Duy Le
>>>>> PhD Student
>>>>> Department of Physics
>>>>> University of Central Florida.
>>>>> 
>>>>> "Men don't need hand to do things"
>>>>> 
>>>>> 
>>>>> 
>>>>> On Tue, Apr 19, 2011 at 3:26 PM, Johari, Priya Sudhir
>>>>> 
>>>>> <priya_johari at brown.edu> wrote:
>>>>>> TD-DFPT
>>>>> 
>>>>> _______________________________________________
>>>>> 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
> 
> 
> 
> -- 
> ********************************************************
> - Article premier - Les hommes naissent et demeurent
> libres et ?gaux en droits. Les distinctions sociales
> ne peuvent ?tre fond?es que sur l'utilit? commune
> - Article 2 - Le but de toute association politique
> est la conservation des droits naturels et 
> imprescriptibles de l'homme. Ces droits sont la libert?,
> la propri?t?, la s?ret? et la r?sistance ? l'oppression.
> ********************************************************
> 
>    Giuseppe Mattioli                            
>    CNR - ISTITUTO DI STRUTTURA DELLA MATERIA   
>    v. Salaria Km 29,300 - C.P. 10                
>    I 00015 - Monterotondo Stazione (RM)          
>    Tel + 39 06 90672836 - Fax +39 06 90672316    
>    E-mail: <giuseppe.mattioli at ism.cnr.it>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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



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From baroni at sissa.it  Thu Apr 21 14:17:07 2011
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 21 Apr 2011 14:17:07 +0200
Subject: [Pw_forum] new bfgs: strange behavior doing vc-relax
In-Reply-To: <4DAF4064.4090002@sissa.it>
References: <BANLkTinqvDinA8rCJO8M5U=wHUmq4Np0Qg@mail.gmail.com>
	<BFEAD9D5-B76C-4FDD-94CA-E738B5016814@democritos.it>
	<4DAF4064.4090002@sissa.it>
Message-ID: <CDF1DD25-3A17-4802-8BD8-A45D0C4240F4@sissa.it>


On Apr 20, 2011, at 10:21 PM, Stefano de Gironcoli wrote:

>>> With QE I have always seen the energy to decrease when the cutoffs are
>>> increased, but with VASP, I always see an oscillation in the total
>>> energy
>>> when the cutoff is incremented.
>> just guessing: it might be a consequence of real-space treatment of
>> augmentation
>> functions.
> 
> actually it can happen for US pseudo, if the cutoff for the density is 
> not large enough, that the energy increases with increasing cutoff.. 
> just because the augmentation charges are not integrated correctly and 
> the error can have any sign. If ecutrho is sufficient to integrate 
> correctly augmentation charges the energy should be variational w.r.t. 
> ecutwfc .

Just a short, half-philosphoc comment, in the hope to make the whole issue even more clear. DFT is variational with respect to the size of the 1-electron basis set (irrespective of the fact that ionic potentials are local or not), if the numerics of the calculation is otherwise well converged with respect to any possible parameter of the calculation. When it is not, no guarantee of variational bounds. This is obvious in a sense. Stealthy problems may arise when some of the auxiliary numerical parameters of the calculations are surreptitiously correlated with the size of the basis set (such as, e.g. the number of plane waves in the Fourier expansion of the [augmented] charge density or the number of mesh points used for the real-space integration of different functions).

Hope this halps
Stefano

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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



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From giannozz at democritos.it  Thu Apr 21 14:32:30 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 21 Apr 2011 14:32:30 +0200
Subject: [Pw_forum] One minor bug, one not minor and two questions
In-Reply-To: <BANLkTimpo976SxfyDctMvwAg8U8bSAo+9A@mail.gmail.com>
References: <BANLkTimpo976SxfyDctMvwAg8U8bSAo+9A@mail.gmail.com>
Message-ID: <1303389150.17194.42.camel@fe12lx.fisica.uniud.it>

On Sun, 2011-04-10 at 16:13 -0500, Laurence Marks wrote:

> Another quick one: line 1766 of install/configure.ac nulls out
> scalapack_libs and the lines below look like they are special tests,
> which seems to be inconsistent with line 150 and standard protocols of
> letting the user define input variables. 

(hopefully) fixed in the development version:
http://qe-forge.org/scm/browser.php?group_id=10

> at least on the cluster where I have PWSCF installed it complains that
> at configure.ac:30 the language is set as C not Fortran. 

this happens on my macintosh as well, after some recent change. It must
be somethiing related to the version of "autoconf"

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



From eariel99 at gmail.com  Thu Apr 21 15:01:31 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Thu, 21 Apr 2011 09:01:31 -0400
Subject: [Pw_forum] why are there two Fermi energies?
Message-ID: <BANLkTinDuigVbPM-gKgPtB4QDeeyyM3NGA@mail.gmail.com>

Hi,
Let me clarify that I found no difference between version 4.2.1 and others.
I have used only 4.2.1.

I suspected that the Fermi level was a way to control the occupations.
However, using different fermi levels will produce different charge
densities because the occupation numbers will be different. If both types of
calculations produce the same energy, then the ground state is degenerate,
but the one with two Fermi energies seems incompatible with thermodynamics.
I used Fermi smearing, by the way.

I am committed to teaching duties today. Thanks for your answers, and I will
come back tomorrow, or maybe late today, and I will look at the occupations
using verbosity = .true.

Mathematically it seems logical that to control  the number of electron (one
degree of freedom) one needs one parameter, which is the Fermi level. To
control an additional degree of freedom, the magnetization, one needs an
additional parameter, then it is reasonable to use two Fermi levels or an
equivalent set of two parameters.
For example, one could define a single Fermi level and apply a shift to the
spin down eigenvalues. This needs a physical interpretation, as well as
having to Fermi levels.

Moreover, reversing the reasoning, I wonder why or how one gets the same
number of electrons and magnetization using only one parameter (Fermi level)
in the case of not using tot_magnetization. Is it a hazard or is there a
trick that bias the calculation to the integer magnetization?

Best regards
-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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From asmogunov at gmail.com  Thu Apr 21 16:36:53 2011
From: asmogunov at gmail.com (Alex Smogunov)
Date: Thu, 21 Apr 2011 16:36:53 +0200
Subject: [Pw_forum] why are there two Fermi energies?
In-Reply-To: <BANLkTinDuigVbPM-gKgPtB4QDeeyyM3NGA@mail.gmail.com>
References: <BANLkTinDuigVbPM-gKgPtB4QDeeyyM3NGA@mail.gmail.com>
Message-ID: <BANLkTi=Lzdw_XREQ2rYQZbKQXcouXp8QTQ@mail.gmail.com>

Hello

2011/4/21 Eduardo Ariel Menendez Proupin <eariel99 at gmail.com>

> Hi,
> Let me clarify that I found no difference between version 4.2.1 and others.
> I have used only 4.2.1.
>
> I suspected that the Fermi level was a way to control the occupations.
> However, using different fermi levels will produce different charge
> densities because the occupation numbers will be different. If both types of
> calculations produce the same energy, then the ground state is degenerate,
> but the one with two Fermi energies seems incompatible with thermodynamics.
> I used Fermi smearing, by the way.
>
> I am committed to teaching duties today. Thanks for your answers, and I
> will come back tomorrow, or maybe late today, and I will look at the
> occupations using verbosity = .true.
>
> Mathematically it seems logical that to control  the number of electron
> (one degree of freedom) one needs one parameter, which is the Fermi level.
> To control an additional degree of freedom, the magnetization, one needs an
> additional parameter, then it is reasonable to use two Fermi levels or an
> equivalent set of two parameters.
> For example, one could define a single Fermi level and apply a shift to the
> spin down eigenvalues. This needs a physical interpretation, as well as
> having to Fermi levels.
>

Shift in eigenvalues can be seen as produced by external magnetic fiels (a
Zeeman term) then the state with two different Fermi energies may be thought
of a true ground state with only one Fermi level but in the presence of this
stabilizing magnetic field proportional to the difference in Fermi energies.
The true ground state with equal Efs do not need of course this magnetic
field.

regards,
Alexander



>
> Moreover, reversing the reasoning, I wonder why or how one gets the same
> number of electrons and magnetization using only one parameter (Fermi level)
> in the case of not using tot_magnetization. Is it a hazard or is there a
> trick that bias the calculation to the integer magnetization?
>
> Best regards
> --
>
>
> Eduardo Menendez
> Departamento de Fisica
> Facultad de Ciencias
> Universidad de Chile
> Phone: (56)(2)9787439
> URL: http://fisica.ciencias.uchile.cl/~emenendez
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From virginie.trinite at thalesgroup.com  Fri Apr 22 09:30:37 2011
From: virginie.trinite at thalesgroup.com (TRINITE Virginie)
Date: Fri, 22 Apr 2011 09:30:37 +0200
Subject: [Pw_forum] questions about PWCOND
In-Reply-To: <BANLkTik_D0V6NV38TKYBu+X4k5Tw11iuOQ@mail.gmail.com>
References: <29121_1303121870_4DAC0FCE_29121_220_1_908CBC9017354841B2F32BBEC70A05A101C154717C33@THSONEA01CMS01P.one.grp>
	<BANLkTik_D0V6NV38TKYBu+X4k5Tw11iuOQ@mail.gmail.com>
Message-ID: <24679_1303457437_4DB12E9D_24679_4905_1_908CBC9017354841B2F32BBEC70A05A101C154827529@THSONEA01CMS01P.one.grp>

Dear Alexander

Thanks for your reply.
Your are right, it was just that no enough digit was print out.
Now I obtain 11.6 e-7 transmission and you publish 11.82 e-7, this seems correct to me.

Best regards

Virginie

De : pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] De la part de Alex Smogunov
Envoy? : mardi 19 avril 2011 11:14
? : PWSCF Forum
Objet : Re: [Pw_forum] questions about PWCOND

Dear Virginie.

2011/4/18 TRINITE Virginie <virginie.trinite at thalesgroup.com<mailto:virginie.trinite at thalesgroup.com>>
Dear all,
I try to use PWCOND, and I have two questions:
>In which units are the boundary in the input file (bdl, bds, bdr)?


  They are in alat units.

>I have run the two examples 12 and 22 without problem and found results in agreement with the publications but when
I try a more heavy system, I obtain zero conductance.
The example that I have used, is the Magnetic Tunnel Junction given in Alexandre Smogounov's home page.
The program finished normally without error or complain but all the transmission are nearly zero.
I didn't check any convergence, because I want only to test the program. Did I miss something?


  I think it is normal since here you have a tunneling through an insulating spacer and TMR effects.
 The conductances should get larger if you decrease the number of isolating layers.

All the best,
Alexander
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org>
http://www.democritos.it/mailman/listinfo/pw_forum

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From eariel99 at gmail.com  Fri Apr 22 17:10:28 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Fri, 22 Apr 2011 11:10:28 -0400
Subject: [Pw_forum] why are there two Fermi energies?
Message-ID: <BANLkTimWtmXLNCvh+--kEb77QwQRJScNLg@mail.gmail.com>

Alexander
>Shift in eigenvalues can be seen as produced by external magnetic fiels (a
>Zeeman term) then the state with two different Fermi energies may be
thought of a >true ground state with only one Fermi level but in the
presence of this stabilizing >magnetic field proportional to the difference
in Fermi energies.

Why not a true ground state with one Fermi level and an external plus an
internal magnetic field that is due to the spin polarization, causes a shift
ib the KS energies, and is self adjusted to have  thermodynamical
equilibrium, i.e., one Fermi level.

Fixing total magnetization would be equivalent to setting and external
magnetic field, and shifting the eigenvalues would be equivalent to an
internal magnetic field.

By the way, what are the physical restrictions to the values of
tot_magnetization ?
In my system, having 255 electrons, I can fix tehe tot_magnetization  to
0.5, 0.7, 1, 1.2, 1.3, 3.0

For 1.5 <= tot_magnetization<2.5 I get error

     from  set_nelup_neldw  : error #         2
     tot_magnetization is inconsistent with total number of electrons

well I see the restriction is in this piece of code
the restriction is in this code
         if ( ((MOD(NINT(tot_magnetization_),2) == 0) .and.
(MOD(NINT(nelec_),2)==1)) .or.   &
              ((MOD(NINT(tot_magnetization_),2) == 1) .and.
(MOD(NINT(nelec_),2)==0))      ) &
              CALL errore(' set_nelup_neldw ',                          &
             'tot_magnetization is inconsistent with total number of
electrons ', 2 )

I understand that with integer occupations the magnetization could have only
even or odd integer values values depending on the number of electrons. But,
with smearing, allowing real occupations, what is the problem with having
even magnetization with odd number of electrons or close real values?


Best wishes

-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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From padmaja_patnaik at yahoo.co.uk  Fri Apr 22 20:59:04 2011
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Fri, 22 Apr 2011 19:59:04 +0100 (BST)
Subject: [Pw_forum] Doubt in celldm(1)
Message-ID: <759508.96996.qm@web28516.mail.ukl.yahoo.com>

Hi all

I have a doubt regarding the value of celldm(1) in the input file for a supercell calculations. Celldm(1) is the lattice constant value. If I am using a supercell constructed by expanding the original lattice constant 'a'? 2 times in all direction, then what will be the value of celldm(1) now? Will it be the original lattice constant 'a' or '2a'?

Thanks in advance
Regards
Padmaja Patnaik

Research Scholar

Dept of Physics

IIT Bombay

Mumbai, India
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From sxu2 at ncsu.edu  Fri Apr 22 21:00:41 2011
From: sxu2 at ncsu.edu (shu xu)
Date: Fri, 22 Apr 2011 15:00:41 -0400
Subject: [Pw_forum] Doubt in celldm(1)
In-Reply-To: <759508.96996.qm@web28516.mail.ukl.yahoo.com>
References: <759508.96996.qm@web28516.mail.ukl.yahoo.com>
Message-ID: <BANLkTikv7ZV4fdtyvjSwzh=Zf3GvhvnTgA@mail.gmail.com>

2a

On Fri, Apr 22, 2011 at 2:59 PM, Padmaja Patnaik <
padmaja_patnaik at yahoo.co.uk> wrote:

>   Hi all
>
> I have a doubt regarding the value of celldm(1) in the input file for a
> supercell calculations. Celldm(1) is the lattice constant value. If I am
> using a supercell constructed by expanding the original lattice constant
> 'a'  2 times in all direction, then what will be the value of celldm(1) now?
> Will it be the original lattice constant 'a' or '2a'?
>
> Thanks in advance
> Regards
> Padmaja Patnaik
> Research Scholar
> Dept of Physics
> IIT Bombay
> Mumbai, India
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From bliu520 at gmail.com  Sat Apr 23 00:13:45 2011
From: bliu520 at gmail.com (Baowei Liu)
Date: Fri, 22 Apr 2011 18:13:45 -0400
Subject: [Pw_forum] Charge density inside the core
Message-ID: <BANLkTi=PgemMr-X3N4+r1k+iNpynhNWv7Q@mail.gmail.com>

Dear all,

pp.x can save the charge density outside the core. Is there a way to
get the charge density inside the core?

Thanks in advance!

Baowei Liu

From giannozz at democritos.it  Sat Apr 23 10:06:30 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 23 Apr 2011 10:06:30 +0200
Subject: [Pw_forum] why are there two Fermi energies?
In-Reply-To: <BANLkTimWtmXLNCvh+--kEb77QwQRJScNLg@mail.gmail.com>
References: <BANLkTimWtmXLNCvh+--kEb77QwQRJScNLg@mail.gmail.com>
Message-ID: <6A97382A-1992-43BC-B637-2CF65F4B253B@democritos.it>


On Apr 22, 2011, at 17:10 , Eduardo Ariel Menendez Proupin wrote:

> the restriction is in this code
>          if ( ((MOD(NINT(tot_magnetization_),2) == 0) .and. (MOD 
> (NINT(nelec_),2)==1)) .or.   &
>               ((MOD(NINT(tot_magnetization_),2) == 1) .and. (MOD 
> (NINT(nelec_),2)==0))      ) &
>               CALL errore(' set_nelup_neldw  
> ',                          &
>              'tot_magnetization is inconsistent with total number  
> of electrons ', 2 )

in the new version, this restriction (now a warning, no longer an  
error) applies only if the
number of electrons is integer and if the magnetization is integer.  
For noninteger charge
or magnetization, it doesn't make sense.

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





From bliu520 at gmail.com  Sat Apr 23 11:05:05 2011
From: bliu520 at gmail.com (Baowei Liu)
Date: Sat, 23 Apr 2011 05:05:05 -0400
Subject: [Pw_forum] Charge density inside the core
In-Reply-To: <BANLkTi=PgemMr-X3N4+r1k+iNpynhNWv7Q@mail.gmail.com>
References: <BANLkTi=PgemMr-X3N4+r1k+iNpynhNWv7Q@mail.gmail.com>
Message-ID: <BANLkTik6yuQTe-_rqOjOiuW0-5=g_5j0zA@mail.gmail.com>

Well, maybe this is not a well-formulated question. But what I want is
charge density both inside and outside the core. If I understand
correctly, gipaw.x can get reconstructed all-electron wavefunctions
(so the all-electron charge density?) from the pseudopotential
wavefunctions. Is it possible to save and extract the data (other than
induced current and magnetic field) like wavefunctions and charge
density.

On Fri, Apr 22, 2011 at 6:13 PM, Baowei Liu <bliu520 at gmail.com> wrote:
> Dear all,
>
> pp.x can save the charge density outside the core. Is there a way to
> get the charge density inside the core?
>
> Thanks in advance!
>
> Baowei Liu
>

From dsagfds at 163.com  Sat Apr 23 14:18:52 2011
From: dsagfds at 163.com (dsagfds)
Date: Sat, 23 Apr 2011 20:18:52 +0800 (CST)
Subject: [Pw_forum] confirm the subscription
In-Reply-To: <mailman.1.1303543938.27446.pw_forum@pwscf.org>
References: <mailman.1.1303543938.27446.pw_forum@pwscf.org>
Message-ID: <468d9c42.44f4.12f824c5a62.Coremail.dsagfds@163.com>

Dear Sir,


I write to confirm the apply for join the PW_forum. I am a undergraduate student in China and do some first principle calculation with quantum-espresso, I really want to subscribe the mailing list to post my problems and answer the problems of others. Thanks so much for patience.


Yours, sincerely
Chris




At 2011-04-23 15:32:18?pw_forum-request at pwscf.org wrote:

>Send Pw_forum mailing list submissions to
>	pw_forum at pwscf.org
>
>To subscribe or unsubscribe via the World Wide Web, visit
>	http://www.democritos.it/mailman/listinfo/pw_forum
>or, via email, send a message with subject or body 'help' to
>	pw_forum-request at pwscf.org
>
>You can reach the person managing the list at
>	pw_forum-owner at pwscf.org
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of Pw_forum digest..."
>
>
>Today's Topics:
>
>   1. Re: why are there two Fermi energies?
>      (Eduardo Ariel Menendez Proupin)
>   2. Doubt in celldm(1) (Padmaja Patnaik)
>   3. Re: Doubt in celldm(1) (shu xu)
>   4. Charge density inside the core (Baowei Liu)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Fri, 22 Apr 2011 11:10:28 -0400
>From: Eduardo Ariel Menendez Proupin <eariel99 at gmail.com>
>Subject: Re: [Pw_forum] why are there two Fermi energies?
>To: pw_forum at pwscf.org
>Message-ID: <BANLkTimWtmXLNCvh+--kEb77QwQRJScNLg at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Alexander
>>Shift in eigenvalues can be seen as produced by external magnetic fiels (a
>>Zeeman term) then the state with two different Fermi energies may be
>thought of a >true ground state with only one Fermi level but in the
>presence of this stabilizing >magnetic field proportional to the difference
>in Fermi energies.
>
>Why not a true ground state with one Fermi level and an external plus an
>internal magnetic field that is due to the spin polarization, causes a shift
>ib the KS energies, and is self adjusted to have  thermodynamical
>equilibrium, i.e., one Fermi level.
>
>Fixing total magnetization would be equivalent to setting and external
>magnetic field, and shifting the eigenvalues would be equivalent to an
>internal magnetic field.
>
>By the way, what are the physical restrictions to the values of
>tot_magnetization ?
>In my system, having 255 electrons, I can fix tehe tot_magnetization  to
>0.5, 0.7, 1, 1.2, 1.3, 3.0
>
>For 1.5 <= tot_magnetization<2.5 I get error
>
>     from  set_nelup_neldw  : error #         2
>     tot_magnetization is inconsistent with total number of electrons
>
>well I see the restriction is in this piece of code
>the restriction is in this code
>         if ( ((MOD(NINT(tot_magnetization_),2) == 0) .and.
>(MOD(NINT(nelec_),2)==1)) .or.   &
>              ((MOD(NINT(tot_magnetization_),2) == 1) .and.
>(MOD(NINT(nelec_),2)==0))      ) &
>              CALL errore(' set_nelup_neldw ',                          &
>             'tot_magnetization is inconsistent with total number of
>electrons ', 2 )
>
>I understand that with integer occupations the magnetization could have only
>even or odd integer values values depending on the number of electrons. But,
>with smearing, allowing real occupations, what is the problem with having
>even magnetization with odd number of electrons or close real values?
>
>
>Best wishes
>
>-- 
>
>
>Eduardo Menendez
>Departamento de Fisica
>Facultad de Ciencias
>Universidad de Chile
>Phone: (56)(2)9787439
>URL: http://fisica.ciencias.uchile.cl/~emenendez
>-------------- next part --------------
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>
>------------------------------
>
>Message: 2
>Date: Fri, 22 Apr 2011 19:59:04 +0100 (BST)
>From: Padmaja Patnaik <padmaja_patnaik at yahoo.co.uk>
>Subject: [Pw_forum] Doubt in celldm(1)
>To: pw_forum at pwscf.org
>Message-ID: <759508.96996.qm at web28516.mail.ukl.yahoo.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hi all
>
>I have a doubt regarding the value of celldm(1) in the input file for a supercell calculations. Celldm(1) is the lattice constant value. If I am using a supercell constructed by expanding the original lattice constant 'a'? 2 times in all direction, then what will be the value of celldm(1) now? Will it be the original lattice constant 'a' or '2a'?
>
>Thanks in advance
>Regards
>Padmaja Patnaik
>
>Research Scholar
>
>Dept of Physics
>
>IIT Bombay
>
>Mumbai, India
>-------------- next part --------------
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>URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110422/603f9c08/attachment-0001.htm 
>
>------------------------------
>
>Message: 3
>Date: Fri, 22 Apr 2011 15:00:41 -0400
>From: shu xu <sxu2 at ncsu.edu>
>Subject: Re: [Pw_forum] Doubt in celldm(1)
>To: PWSCF Forum <pw_forum at pwscf.org>
>Message-ID: <BANLkTikv7ZV4fdtyvjSwzh=Zf3GvhvnTgA at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>2a
>
>On Fri, Apr 22, 2011 at 2:59 PM, Padmaja Patnaik <
>padmaja_patnaik at yahoo.co.uk> wrote:
>
>>   Hi all
>>
>> I have a doubt regarding the value of celldm(1) in the input file for a
>> supercell calculations. Celldm(1) is the lattice constant value. If I am
>> using a supercell constructed by expanding the original lattice constant
>> 'a'  2 times in all direction, then what will be the value of celldm(1) now?
>> Will it be the original lattice constant 'a' or '2a'?
>>
>> Thanks in advance
>> Regards
>> Padmaja Patnaik
>> Research Scholar
>> Dept of Physics
>> IIT Bombay
>> Mumbai, India
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
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>
>------------------------------
>
>Message: 4
>Date: Fri, 22 Apr 2011 18:13:45 -0400
>From: Baowei Liu <bliu520 at gmail.com>
>Subject: [Pw_forum] Charge density inside the core
>To: PWSCF Forum <pw_forum at pwscf.org>
>Message-ID: <BANLkTi=PgemMr-X3N4+r1k+iNpynhNWv7Q at mail.gmail.com>
>Content-Type: text/plain; charset=ISO-8859-1
>
>Dear all,
>
>pp.x can save the charge density outside the core. Is there a way to
>get the charge density inside the core?
>
>Thanks in advance!
>
>Baowei Liu
>
>
>------------------------------
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>End of Pw_forum Digest, Vol 46, Issue 73
>****************************************
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From abmus007 at gmail.com  Sun Apr 24 11:31:49 2011
From: abmus007 at gmail.com (Abolore Musari)
Date: Sun, 24 Apr 2011 04:31:49 -0500
Subject: [Pw_forum] cell(dm)
Message-ID: <BANLkTinnBUQansbWXqwNbrB89JR1SMf_qA@mail.gmail.com>

Dear QE User, l want to ask if for instance am workn on orthorhombic
sys r we going to perform lattice constant optimization for b and c
also afer performing for a. THANKS  MUSARI, A. A DEPT OF PHY UNAAB

From degironc at sissa.it  Sun Apr 24 15:06:14 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Sun, 24 Apr 2011 15:06:14 +0200
Subject: [Pw_forum] cell(dm)
In-Reply-To: <BANLkTinnBUQansbWXqwNbrB89JR1SMf_qA@mail.gmail.com>
References: <BANLkTinnBUQansbWXqwNbrB89JR1SMf_qA@mail.gmail.com>
Message-ID: <20110424150614.kvw50iurokccswwc@webmail.sissa.it>

the simplest way to optimize the cell of your system would be to use  
vc-relax choosing bfgs or damp dynamics. as a default I would begin  
with bfgs

stefano

Quoting Abolore Musari <abmus007 at gmail.com>:

> Dear QE User, l want to ask if for instance am workn on orthorhombic
> sys r we going to perform lattice constant optimization for b and c
> also afer performing for a. THANKS  MUSARI, A. A DEPT OF PHY UNAAB
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



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From abmus007 at gmail.com  Sun Apr 24 18:37:24 2011
From: abmus007 at gmail.com (Abolore Musari)
Date: Sun, 24 Apr 2011 11:37:24 -0500
Subject: [Pw_forum] cell(dm)
In-Reply-To: <20110424150614.kvw50iurokccswwc@webmail.sissa.it>
References: <BANLkTinnBUQansbWXqwNbrB89JR1SMf_qA@mail.gmail.com>
	<20110424150614.kvw50iurokccswwc@webmail.sissa.it>
Message-ID: <BANLkTi=LATvnMV6fbXj_tK-Qav5+8WDwVA@mail.gmail.com>

Dear sir, am glad for the info thanks, but first if my celldm(4) =
-0.7724 Sir is d -ve sign allowed note that i got this from cos(ab)
where a and b r in bohr, secondly hw do l locate my answer? afta d vc
relax cos ve done it using example03 of the expresso. THANKS

On 4/24/11, Stefano de Gironcoli <degironc at sissa.it> wrote:
> the simplest way to optimize the cell of your system would be to use
> vc-relax choosing bfgs or damp dynamics. as a default I would begin
> with bfgs
>
> stefano
>
> Quoting Abolore Musari <abmus007 at gmail.com>:
>
>> Dear QE User, l want to ask if for instance am workn on orthorhombic
>> sys r we going to perform lattice constant optimization for b and c
>> also afer performing for a. THANKS  MUSARI, A. A DEPT OF PHY UNAAB
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
> ----------------------------------------------------------------
>    SISSA Webmail https://webmail.sissa.it/
>    Powered by Horde http://www.horde.org/
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From swapnil.chandratre at gmail.com  Mon Apr 25 02:14:00 2011
From: swapnil.chandratre at gmail.com (swapnil chandratre)
Date: Sun, 24 Apr 2011 19:14:00 -0500
Subject: [Pw_forum] Error computing Cholesky
Message-ID: <BANLkTin821WPCc5chAmwUJSAnM7OYNwYbg@mail.gmail.com>

Hi,

I get the following error for Graphene Ribbon with porosity, can anyone
help.

 from  cdiaghg  : error #       426
      problems computing cholesky


-- 
Regards,
Swapnil Chandratre
Graduate Student
Dept. of Mechanical Engineering,
University of Houston,
Houston, TX
(M)-713-294-9546
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From zhaohscas at yahoo.com.cn  Mon Apr 25 07:06:10 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Mon, 25 Apr 2011 13:06:10 +0800
Subject: [Pw_forum] Should we use a double bond or 2 H atoms to saturate the
	system?
Message-ID: <1637883071.20110425130610@yahoo.com.cn>

Dear All,

This issues is somehow not so pertained to the PWSCF, but a gerneral DFT modelling problem, sorry for this request on this list. 

We all know that the H atoms is often used to saturate the dangling bonds in the system's edge, say, for graphene nanoribbon.  My issue is: as far as the passivation results is concerned, adding 2 atoms is equivalent to introduce a double bond between the two adjacent ions in the system, am I right?  If so, Should we use a double bond or 2 H atoms to saturate the system?

Regards.
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn> 
School of Physics and Electrical Information Science, 
Ningxia University, Yinchuan 750021, China
GnuPG DSA: 0xD108493
2011-4-25


From degironc at sissa.it  Mon Apr 25 10:39:51 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Mon, 25 Apr 2011 10:39:51 +0200
Subject: [Pw_forum] cell(dm)
In-Reply-To: <BANLkTi=LATvnMV6fbXj_tK-Qav5+8WDwVA@mail.gmail.com>
References: <BANLkTinnBUQansbWXqwNbrB89JR1SMf_qA@mail.gmail.com>
	<20110424150614.kvw50iurokccswwc@webmail.sissa.it>
	<BANLkTi=LATvnMV6fbXj_tK-Qav5+8WDwVA@mail.gmail.com>
Message-ID: <20110425103951.jujhk2yrswckog8k@webmail.sissa.it>

Dear Abolore Musari ,
   I'm not sure I understood your question... it would help if you  
would write in English.
stefano

Quoting Abolore Musari <abmus007 at gmail.com>:

> Dear sir, am glad for the info thanks, but first if my celldm(4) =
> -0.7724 Sir is d -ve sign allowed note that i got this from cos(ab)
> where a and b r in bohr, secondly hw do l locate my answer? afta d vc
> relax cos ve done it using example03 of the expresso. THANKS
>
> On 4/24/11, Stefano de Gironcoli <degironc at sissa.it> wrote:
>> the simplest way to optimize the cell of your system would be to use
>> vc-relax choosing bfgs or damp dynamics. as a default I would begin
>> with bfgs
>>
>> stefano
>>
>> Quoting Abolore Musari <abmus007 at gmail.com>:
>>
>>> Dear QE User, l want to ask if for instance am workn on orthorhombic
>>> sys r we going to perform lattice constant optimization for b and c
>>> also afer performing for a. THANKS  MUSARI, A. A DEPT OF PHY UNAAB
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>
>>
>>
>> ----------------------------------------------------------------
>>    SISSA Webmail https://webmail.sissa.it/
>>    Powered by Horde http://www.horde.org/
>>
>>
>> _______________________________________________
>> 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 kucukben at sissa.it  Mon Apr 25 10:58:03 2011
From: kucukben at sissa.it (Emine Kucukbenli)
Date: Mon, 25 Apr 2011 10:58:03 +0200
Subject: [Pw_forum] cell(dm)
In-Reply-To: <BANLkTi=LATvnMV6fbXj_tK-Qav5+8WDwVA@mail.gmail.com>
References: <BANLkTinnBUQansbWXqwNbrB89JR1SMf_qA@mail.gmail.com>
	<20110424150614.kvw50iurokccswwc@webmail.sissa.it>
	<BANLkTi=LATvnMV6fbXj_tK-Qav5+8WDwVA@mail.gmail.com>
Message-ID: <20110425105803.otrlndpgggkww8w4@webmail.sissa.it>

Dear Abolore,
Sorry I couldnt  understand your first question.Please rephrase it.
For the second one:
During the vc-relax run, at each step towards convergence, new cell  
parameters are written on the output. Look for CELL_PARAMETERS (a 3x3  
matrix) values.The final one should be the relaxed one. (Please verify  
this before progressing further, check stress, pressure )

You may want to examine the VCSexample directory and examples therein,  
before dong anything , actually. (It is different than example03,  
which you have been dong similar calculations till now, in which only  
the atomic positions are relaxed)
best,
emine kucukbenli, phd student, sissa, it

Quoting Abolore Musari <abmus007 at gmail.com>:

> Dear sir, am glad for the info thanks, but first if my celldm(4) =
> -0.7724 Sir is d -ve sign allowed note that i got this from cos(ab)
> where a and b r in bohr, secondly hw do l locate my answer? afta d vc
> relax cos ve done it using example03 of the expresso. THANKS
>


----------------------------------------------------------------
   SISSA Webmail https://webmail.sissa.it/
   Powered by Horde http://www.horde.org/



From baris.malcioglu at gmail.com  Mon Apr 25 12:29:37 2011
From: baris.malcioglu at gmail.com (O. Baris Malcioglu)
Date: Mon, 25 Apr 2011 12:29:37 +0200
Subject: [Pw_forum] TDDFT approach for periodic system
In-Reply-To: <5BB7A50A-C21A-4AC3-ADC5-B049519E79EE@sissa.it>
References: <BANLkTi=JEJyTi26LHXWkWYO8=WP_0haGSg@mail.gmail.com>
	<BANLkTi=+CH7HMf3_V=yTWmw_FcOG3RYS5w@mail.gmail.com>
	<BANLkTi=ATF7Ge_xy50FRdb5aOVsiXKd_wQ@mail.gmail.com>
	<201104201121.45702.giuseppe.mattioli@mlib.ism.cnr.it>
	<5BB7A50A-C21A-4AC3-ADC5-B049519E79EE@sissa.it>
Message-ID: <BANLkTik_=gGOtxnuD=W2uuZ0SuzSVKqS2g@mail.gmail.com>

I completely agree, one should focus on excitonic characters in these
kind of discussions

For archival purposes and for not risking being esoteric to the
newcomers to the field,
I would like to mention some commonly used references
regarding the tests performed in the theoretical chemistry literature
comparing TDDFT with other methods.

The summary is that: When you are sure the type of excitons in your
system is covered by the "kernel" at hand, TDDFT results are on par
with some higher level wavefunction based methods at a fraction of the
computational cost.

The current implementation in QE 4.3 is ALDA only, thus it is good for
systems with -no- charge transfer or -no- zwitterionic character.
(if I may risk a adumbrate use of
nomenclature, I would say it works better for excitons with more
Frenkel-like character, and that seems to be the usual argument used
to discuss why quantum confinement tends to work in
favor of the accuracy of TDDFT-ALDA in size constrained isolated
systems, for example in quantum dots etc.
). The problem resides in the locality of the kernel, which is being
worked on for the next version.

and here are the references:
M Parac et al. Chem. Phys. 292, 11 (2003);
A. Rosa et al. Structure and Bonding, 112, 49 (2004)
I. Tavernelli et al. Molecular Physics 103, 963 (2005)





2011/4/21 Stefano Baroni <baroni at sissa.it>:
> Just a couple of further comments.
> 1) The ability (or lack thereof) of (adiabatic) tddft to properly describe
> optical excitations in extended systems does not depend on the code's
> ability to sample the whole BZ using special k-points. The current version
> of the tddfpt code distributed with QE is only apt to sample k=0 Bloch
> state, but periodic systems can nevertheless be treated (admittedly not very
> efficiently) to arbitrary numerical accuracy, by using suitable supercells.
> 2) adiabatic XC functionals miss excitonic effects in periodic systems
> (irrespective of the number of k-points used to sample the BZ) for the same
> reason why they miss Rydberg series in molecular systems. Always be
> suspicious of statements such as "TDDFT works for molecules, but it fails
> for crystals". This is nonsense: any crystal is nothing but a "big
> molecule". TDDFT works for both, and it fails for both. Only the failures
> manifest themselves in different ways, according to the size of the system.
> Cheers - SB
>
> On Apr 20, 2011, at 11:21 AM, Giuseppe Mattioli wrote:
>
> Dear all
> I did not say that TDDFPT does not work with periodic system, but you cannot
> have a realistic absorption spectra of a slab (or bulk crystal) if you
> sample
> the Brillouin zone by using Gamma only... TDDFPT works fine with finite
> systems, i.e., which do not show a (strong) k dependence of the psi_n,k
> eigenvalues.
>
> Giuseppe
>
> On Wednesday 20 April 2011 03:00:41 Johari, Priya Sudhir wrote:
>
> Thanks Marton, its working.
>
> On Tue, Apr 19, 2011 at 5:40 PM, Marci <vormar at gmail.com> wrote:
>
> Dear Priya,
>
> Though I have never tried, it should work with periodic systems if you
>
> sample the Brillouin zone only with the gamma point. Keep in mind that
>
> the usual adiabatic approximations with (semi)local functionals might
>
> not work very well for calculating the absorption of periodic systems.
>
> Marton
>
> --
>
> Marton Voros
>
> PhD student
>
> Department of Atomic Physics
>
> Budapest University of Technology and Economics
>
> Budafoki ?t 8., H-1111, Budapest, Hungary
>
> www.fat.bme.hu/MartonVoros
>
> On Tue, Apr 19, 2011 at 11:02 PM, Johari, Priya Sudhir
>
> <priya_johari at brown.edu> wrote:
>
> Thanks Duy, but the link does not give sufficient information. However,
>
> I found a discussion on forum's archive itself where Giuseppe Mattioli
>
> has mentioned that TDDPFT does not work for periodic systems :-(
>
> Dr Priya Johari.
>
> Brown University,
>
> Providence, RI - 02906. USA
>
> On Tue, Apr 19, 2011 at 3:59 PM, Duy Le <ttduyle at gmail.com> wrote:
>
> If you do a little homework (such as googling keyword TD-DFPT), you'll
>
> find this link
>
> http://qe-forge.org/projects/tddfpt/
>
> I have not read it carefully but I guess it contains some useful
>
> information.
>
> --------------------------------------------------
>
> Duy Le
>
> PhD Student
>
> Department of Physics
>
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
>
> On Tue, Apr 19, 2011 at 3:26 PM, Johari, Priya Sudhir
>
> <priya_johari at brown.edu> wrote:
>
> TD-DFPT
>
> _______________________________________________
>
> 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
>
>
>
> --
> ********************************************************
> - Article premier - Les hommes naissent et demeurent
> libres et ?gaux en droits. Les distinctions sociales
> ne peuvent ?tre fond?es que sur l'utilit? commune
> - Article 2 - Le but de toute association politique
> est la conservation des droits naturels et
> imprescriptibles de l'homme. Ces droits sont la libert?,
> la propri?t?, la s?ret? et la r?sistance ? l'oppression.
> ********************************************************
>
> ? ?Giuseppe Mattioli
> ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> ? ?v. Salaria Km 29,300 - C.P. 10
> ? ?I 00015 - Monterotondo Stazione (RM)
> ? ?Tel + 39 06 90672836 - Fax +39 06 90672316
> ? ?E-mail: <giuseppe.mattioli at ism.cnr.it>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
> ---
> Stefano Baroni - SISSA??&??DEMOCRITOS National Simulation Center - Trieste
> http://stefano.baroni.me?[+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni
> (skype)
> La morale est une logique de l'action comme la logique est une morale de la
> pens?e - Jean Piaget
> Please, if possible, don't??send me MS Word or PowerPoint attachments
> Why? See:??http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

From baris.malcioglu at gmail.com  Mon Apr 25 13:04:05 2011
From: baris.malcioglu at gmail.com (O. Baris Malcioglu)
Date: Mon, 25 Apr 2011 13:04:05 +0200
Subject: [Pw_forum] Should we use a double bond or 2 H atoms to saturate
 the system?
In-Reply-To: <1637883071.20110425130610@yahoo.com.cn>
References: <1637883071.20110425130610@yahoo.com.cn>
Message-ID: <BANLkTinbukNnYgRXj3Je65fESV7GDt3F5g@mail.gmail.com>

Dear Hongsheng Zhao,

Unless you are asking if someone ever tried forcing a particular
"bond" or aromaticity in PW explicitly (one can try to constrain some
number of KS states trying to estimate a particular bond, but I don't
think this is a good idea to do in a pw DFT code), I think you might
be a little confused by the concepts.

Beware that in literature they tend to do assume hydrogens implicitly
in order not to complicate figure presentation. Also, please notice
that you add hydrogens not just to saturate, but to put the atom in a
particular "bonding state" (i.e. sp3 or sp2 hybridization etc.). That
"bonding state" is handled by PW with no additional constraints (i.e.
when you input the coordinates of Carbon and Hydrogen atoms in
Benzene, with a suitable XC kernel, the electronic structure will
assume aromaticity without you explicitly mentioning it, and if you
want to see explicit proof of aromaticity using the nomenclature of
theoretical chemistry, you can, for example, project the ks states in
terms of atom centered pi levels)

Best,
Baris

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Dr. O. Baris Malcioglu,
University of Liege,
B?t. B5 Physique de la mati?re condens?e
all?e du 6 Ao?t 17
4000 Li?ge 1
Belgique
Tel:+32 4366 3612
Fax: +32 4366 3629
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=



2011/4/25 Hongsheng Zhao <zhaohscas at yahoo.com.cn>:
> Dear All,
>
> This issues is somehow not so pertained to the PWSCF, but a gerneral DFT modelling problem, sorry for this request on this list.
>
> We all know that the H atoms is often used to saturate the dangling bonds in the system's edge, say, for graphene nanoribbon. ?My issue is: as far as the passivation results is concerned, adding 2 atoms is equivalent to introduce a double bond between the two adjacent ions in the system, am I right? ?If so, Should we use a double bond or 2 H atoms to saturate the system?
>
> Regards.
> --
> Hongsheng Zhao <zhaohscas at yahoo.com.cn>
> School of Physics and Electrical Information Science,
> Ningxia University, Yinchuan 750021, China
> GnuPG DSA: 0xD108493
> 2011-4-25
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From daijiayu at nudt.edu.cn  Mon Apr 25 14:29:45 2011
From: daijiayu at nudt.edu.cn (jiayudai)
Date: Mon, 25 Apr 2011 20:29:45 +0800
Subject: [Pw_forum] fft error in XSPECTRA of 4.3 version
In-Reply-To: <503716237.26045@eyou.net>
References: <503716237.26045@eyou.net>
Message-ID: <110425202945a03ae2d1d0a7b4772cf067a1ec2e0def@nudt.edu.cn>


Dear developers,

I met a error message when i used xspectra code, which is

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from  fft_dlay_set  : error #         2
      wrong fft dimensions
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 I knew it from the reason of nr1<nr1x ... However, there is no error when i changed to use the version of 4.2.1. So, could you tell me what's the problem? Or is it a bug in the new version?

Best regards.

Jiayu
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From eariel99 at gmail.com  Mon Apr 25 15:10:35 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Mon, 25 Apr 2011 09:10:35 -0400
Subject: [Pw_forum]  why are there two Fermi energies?
Message-ID: <BANLkTi=MCfQnkfcEmSfmHNzbBuq=qVGKMA@mail.gmail.com>

Hi Paolo,



>>* the restriction is in this code
*>>*          if ( ((MOD(NINT(tot_magnetization_),2) == 0) .and. (MOD
*>>* (NINT(nelec_),2)==1)) .or.   &
*>>*               ((MOD(NINT(tot_magnetization_),2) == 1) .and. (MOD
*>>* (NINT(nelec_),2)==0))      ) &
*>>*               CALL errore(' set_nelup_neldw
*>>* ',                          &
*>>*              'tot_magnetization is inconsistent with total number
*>>* of electrons ', 2 )
*
>in the new version, this restriction (now a warning, no longer an
>error) applies only if the
>number of electrons is integer and if the magnetization is integer.
>For noninteger charge
>or magnetization, it doesn't make sense.


In fact, increasing the k-point sampling, the unrestricted calculation
converges towards
0 total magnetization, with a lower energy than magnetization =1, but
setting tot_magnetization=0, or 0.1, 0.2, etc, stops due to the above
instruction in versiom 4.2.1.
This is one more reason to change to the newest version.


*You stated something in a previous post*
<pw_forum%40pwscf.org?Subject=%5BPw_forum%5D%20why%20are%20there%20two%20Fermi%20energies%3F&In-Reply-To=0CD095EE-2EC8-4E33-9F7F-334812E8089C%40sissa.it>
>The "two Fermi energies" of the constrained
>case need not to be exactly the same as the (single)
>Fermi energy of the unconstrained case, as long as the
>occupancies for spin-up and spin-down are the same in the
>two cases.

Why not? Aren't the the energies and occupations related by
the Fermi-Dirac function? I verified that the occupations are the
same, then I do not understand
why it is possible with different Fermi energies.
These are my KS energies and the occupations, using degauss=0.00019. I
think the differences are just numerical noise.

1)  tot_magnetization unset
     the Fermi energy is     6.1614 ev
!    total energy              =    -502.92571441 Ry     total
magnetization       =     1.00 Bohr mag/cell
up: 4.8593   4.8594   5.2221   5.2221   5.2222   6.1335   6.1336   6.1338


      1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   1.0000

dw: 4.8796   4.8796   5.2528   5.2530   5.2531   6.1595   6.1596   6.1596
      1.0000   1.0000   1.0000   1.0000   1.0000   0.6709   0.6661   0.6631

2) tot_magnetization=1
     the spin up/dw Fermi energies are     6.3853    6.1614 ev
!    total energy              =    -502.92571439 Ry     total
magnetization       =     1.00 Bohr mag/cell
up: 4.8593   4.8594   5.2221   5.2221   5.2221   6.1335   6.1337   6.1338


      1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   1.0000

dw: 4.8796   4.8796   5.2528   5.2530   5.2531   6.1595   6.1596   6.1596
      1.0000   1.0000   1.0000   1.0000   1.0000   0.6715   0.6660   0.6625

Finally, I plotted Energy vs magnetization. Indeed, I have a minimum
at total magnetization equal 1. However, the
behavior is strange. The plot of E vs M is linear at each side of the
minimum, with a kink at M=1. Should'n it be rather like a parable ?
Please, see the plots here

http://www.gnm.cl/emenendez/pmwiki.php/Temp/Plots?action=upload&upname=impurity-energy.eps

http://www.gnm.cl/emenendez/pmwiki.php/Temp/Plots?action=upload&upname=impurity-fermi.eps


This was using gamma point fo sample the Brillouin zone. That is not
converged, using a 3x3x3 grid the lowest energy seems to be
for null magnetization (I am doing more calculations). Maybe the kinks
are due to insufficient Brillouin zone sampling.



Best regards


-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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From eariel99 at gmail.com  Mon Apr 25 15:19:34 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Mon, 25 Apr 2011 09:19:34 -0400
Subject: [Pw_forum]  why are there two Fermi energies?
Message-ID: <BANLkTikLJwaLLrtoVgfFawdds6ZgR7hSbw@mail.gmail.com>

I am sorry, Murphy's law has just acted. Find the figures here

http://www.gnm.cl/emenendez/uploads/Temp/impurity-energy.eps
http://www.gnm.cl/emenendez/uploads/Temp/impurity-fermi.eps

Finally, I plotted Energy vs magnetization. Indeed, I have a minimum
at total magnetization equal 1. However, the
behavior is strange. The plot of E vs M is linear at each side of the

minimum, with a kink at M=1. Should'n it be rather like a parable ?
Please, see the plots here (above)




Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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From giannozz at democritos.it  Mon Apr 25 21:22:33 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 25 Apr 2011 21:22:33 +0200
Subject: [Pw_forum] why are there two Fermi energies?
In-Reply-To: <BANLkTi=MCfQnkfcEmSfmHNzbBuq=qVGKMA@mail.gmail.com>
References: <BANLkTi=MCfQnkfcEmSfmHNzbBuq=qVGKMA@mail.gmail.com>
Message-ID: <F80CB5E4-729C-452D-BE85-64DB62C056BC@democritos.it>


On Apr 25, 2011, at 15:10 , Eduardo Ariel Menendez Proupin wrote:
>
> >The "two Fermi energies" of the constrained
> >case need not to be exactly the same as the (single)
> >Fermi energy of the unconstrained case, as long as the
> >occupancies for spin-up and spin-down are the same in the
> >two cases.
>
> Why not? Aren't the the energies and occupations related by
> the Fermi-Dirac function?

they are (Fermi-Dirac or whatever function applies), but if you have a
gap and a small broadening, the occupancies will do not (visibly)
depend upon Ef for some interval of values

> 2) tot_magnetization=1
>      the spin up/dw Fermi energies are     6.3853    6.1614 ev

> up: 4.8593   4.8594   5.2221   5.2221   5.2221   6.1335   6.1337    
> 6.1338
>       1.0000   1.0000   1.0000   1.0000   1.0000   1.0000    
> 1.0000   1.0000

Ef=6.3853eV is perfectly consistent with these occupations, as long  
as there
are no states between 6.14eV and 6.40eV or so

>
> dw: 4.8796   4.8796   5.2528   5.2530   5.2531   6.1595   6.1596    
> 6.1596
>       1.0000   1.0000   1.0000   1.0000   1.0000   0.6715    
> 0.6660   0.6625

this is quite the same as case with spin magnetization not set

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





From giannozz at democritos.it  Mon Apr 25 21:25:31 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 25 Apr 2011 21:25:31 +0200
Subject: [Pw_forum] fft error in XSPECTRA of 4.3 version
In-Reply-To: <110425202945a03ae2d1d0a7b4772cf067a1ec2e0def@nudt.edu.cn>
References: <503716237.26045@eyou.net>
	<110425202945a03ae2d1d0a7b4772cf067a1ec2e0def@nudt.edu.cn>
Message-ID: <37085ED8-2835-41F8-B4B9-8D37B685B17C@democritos.it>


On Apr 25, 2011, at 14:29 , jiayudai wrote:

> I met a error message when i used xspectra code, which is
>
...the same as this:

http://www.democritos.it/pipermail/pw_forum/2011-April/019999.html
>      from  fft_dlay_set  : error #         2      wrong fft dimensions
>

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





From giannozz at democritos.it  Mon Apr 25 21:33:49 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 25 Apr 2011 21:33:49 +0200
Subject: [Pw_forum] Error computing Cholesky
In-Reply-To: <BANLkTin821WPCc5chAmwUJSAnM7OYNwYbg@mail.gmail.com>
References: <BANLkTin821WPCc5chAmwUJSAnM7OYNwYbg@mail.gmail.com>
Message-ID: <438D2C9A-1CD3-42ED-A939-E8D0978894BF@democritos.it>


On Apr 25, 2011, at 2:14 , swapnil chandratre wrote:

> I get the following error for Graphene Ribbon with porosity, can  
> anyone help.
>
>  from  cdiaghg  : error #       426
>       problems computing cholesky

what about searching the mailing list for "cholesky" ?

http://www.quantum-espresso.org/user_guide/ 
node52.html#SECTION000121070000000000000
>


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





From abmus007 at gmail.com  Mon Apr 25 23:54:46 2011
From: abmus007 at gmail.com (Abolore Musari)
Date: Mon, 25 Apr 2011 16:54:46 -0500
Subject: [Pw_forum] cell(dm)
In-Reply-To: <20110425105803.otrlndpgggkww8w4@webmail.sissa.it>
References: <BANLkTinnBUQansbWXqwNbrB89JR1SMf_qA@mail.gmail.com>
	<20110424150614.kvw50iurokccswwc@webmail.sissa.it>
	<BANLkTi=LATvnMV6fbXj_tK-Qav5+8WDwVA@mail.gmail.com>
	<20110425105803.otrlndpgggkww8w4@webmail.sissa.it>
Message-ID: <BANLkTinKoXwjshQ_6ORQKap0y3dOb_Ln5Q@mail.gmail.com>

Dear Sir,
I am really glad for the assistance u have rendered so far in fact i has
been really helpful, Thanks a lot
I am having another problem as regard (k-point)
I am working on monoclinic system, and am using xcrysden to get my k-point
and my question is how do I know the special points (k-points) to select
from the Brillion zone in the xcrysden k path selection?

Thanks in anticipation of your favourable assistance

Musari Abolore
Dept Of Physics
University of Agriculture, Abeokuta
Nigeria


On Mon, Apr 25, 2011 at 3:58 AM, Emine Kucukbenli <kucukben at sissa.it> wrote:

> Dear Abolore,
> Sorry I couldnt  understand your first question.Please rephrase it.
> For the second one:
> During the vc-relax run, at each step towards convergence, new cell
> parameters are written on the output. Look for CELL_PARAMETERS (a 3x3
> matrix) values.The final one should be the relaxed one. (Please verify
> this before progressing further, check stress, pressure )
>
> You may want to examine the VCSexample directory and examples therein,
> before dong anything , actually. (It is different than example03,
> which you have been dong similar calculations till now, in which only
> the atomic positions are relaxed)
> best,
> emine kucukbenli, phd student, sissa, it
>
> Quoting Abolore Musari <abmus007 at gmail.com>:
>
> > Dear sir, am glad for the info thanks, but first if my celldm(4) =
> > -0.7724 Sir is d -ve sign allowed note that i got this from cos(ab)
> > where a and b r in bohr, secondly hw do l locate my answer? afta d vc
> > relax cos ve done it using example03 of the expresso. THANKS
> >
>
>
> ----------------------------------------------------------------
>   SISSA Webmail https://webmail.sissa.it/
>   Powered by Horde http://www.horde.org/
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From abmus007 at gmail.com  Mon Apr 25 23:57:21 2011
From: abmus007 at gmail.com (Abolore Musari)
Date: Mon, 25 Apr 2011 16:57:21 -0500
Subject: [Pw_forum] k-point
Message-ID: <BANLkTik=J=4dmqTo1O06MK_K8wcA1tjgUQ@mail.gmail.com>

Dear QE User,
I am having a problem as regard (k-point)
I am working on monoclinic system, and am using xcrysden to get my k-point
and my question is how do I know the special points (k-points) to select
from the Brillion zone in the xcrysden k path selection?

Thanks in anticipation of your favourable assistance

Musari Abolore
Dept Of Physics
University of Agriculture, Abeokuta
Nigeria
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From eariel99 at gmail.com  Tue Apr 26 01:46:15 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Mon, 25 Apr 2011 19:46:15 -0400
Subject: [Pw_forum]  k-point
Message-ID: <BANLkTimjs1i7wiQbCyf38-6qk=MECWTyKA@mail.gmail.com>

Abolore,I do not know any standard set of k-points for monoclinic system.
Chose the points that you think are representative, e.g, half of every
reciprocal lattice vectors, and path between them. I suggest you first
calculate the DOS, locate the points of the valence band maximum and
conduction band minimum, and be sure that they are in included in the
k-points path of the band diagram. Some maxima of the DOS are related to
lines were some bands are flat. Assure that these lines are included in the
path. A good method is to explain the DOS features with the band diagram. If
some feature cannot be explained with the band diagram, investigate the
reason.
It is like choosing 4 or 5 cities to visit in a tour by Italy, with a good
choice you will get some idea about the country and you can explain some of
the history from the monuments and museum, or the cafes that you visited.
As there is no convention for the letters that design the k-points in a
monoclinic crystal, PLEASE, indicate the coordinates of the points in the
figure caption or in the text.  [Pw_forum] k-point
*Abolore Musari* abmus007 at gmail.com
<pw_forum%40pwscf.org?Subject=%5BPw_forum%5D%20k-point&In-Reply-To=>
*Mon Apr 25 23:57:21 CEST 2011*

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

Dear QE User,
I am having a problem as regard (k-point)
I am working on monoclinic system, and am using xcrysden to get my k-point
and my question is how do I know the special points (k-points) to select
from the Brillion zone in the xcrysden k path selection?

Thanks in anticipation of your favourable assistance

Musari Abolore
Dept Of Physics
University of Agriculture, Abeokuta
Nigeria
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-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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From zhaohscas at yahoo.com.cn  Tue Apr 26 14:15:36 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Tue, 26 Apr 2011 08:15:36 -0400
Subject: [Pw_forum] Should we use a double bond or 2 H atoms to saturate
 the system?
In-Reply-To: <BANLkTinbukNnYgRXj3Je65fESV7GDt3F5g@mail.gmail.com>
References: <1637883071.20110425130610@yahoo.com.cn>
	<BANLkTinbukNnYgRXj3Je65fESV7GDt3F5g@mail.gmail.com>
Message-ID: <4DB6B768.2080909@yahoo.com.cn>

On 04/25/2011 07:04 AM, O. Baris Malcioglu wrote:
> Dear Hongsheng Zhao,
>
> Unless you are asking if someone ever tried forcing a particular
> "bond" or aromaticity in PW explicitly (one can try to constrain some
> number of KS states trying to estimate a particular bond, but I don't
> think this is a good idea to do in a pw DFT code), I think you might
> be a little confused by the concepts.
>
> Beware that in literature they tend to do assume hydrogens implicitly
> in order not to complicate figure presentation. Also, please notice
> that you add hydrogens not just to saturate, but to put the atom in a
> particular "bonding state" (i.e. sp3 or sp2 hybridization etc.). That
> "bonding state" is handled by PW with no additional constraints (i.e.
> when you input the coordinates of Carbon and Hydrogen atoms in
> Benzene, with a suitable XC kernel, the electronic structure will
> assume aromaticity without you explicitly mentioning it, and if you
> want to see explicit proof of aromaticity using the nomenclature of
> theoretical chemistry, you can, for example, project the ks states in
> terms of atom centered pi levels)
Thanks a lot for your kindly reply.  In fact, I want to know how to do 
the corresponding adding operations in the input file for pwscf.

Say, for example, the following is the model input file for graphene 
nanoribbon including 7 primitive unit cell of armchair graphene 
nanoribbon (8), which is described and used in the following paper: 
http://tinyurl.com/3nz3xz9 ,

---------------
&CONTROL
calculation = 'scf'
prefix='block_1'
pseudo_dir = './'
outdir='./'
tstress=.true.
tprnfor = .true.
forc_conv_thr=1.0d-4
nstep=200
/
&SYSTEM
ibrav=0
celldm(1)=1.889726
nat=112
ntyp=1
ecutwfc=36
/
&ELECTRONS
mixing_beta=0.7
conv_thr =  1.0d-8
electron_maxstep=200
/
&IONS
trust_radius_max=0.2
/
&CELL
cell_dynamics='bfgs'
/
ATOMIC_SPECIES
    C  12.0110   C.UPF

CELL_PARAMETERS (alat)
   16.5000000000    0.0000000000    0.0000000000
    0.0000000000    8.0000000000    0.0000000000
    0.0000000000    0.0000000000   30.8203000000

ATOMIC_POSITIONS (crystal)
  C       0.128008000     0.500000000     0.050828000
  C       0.128008000     0.500000000     0.092030000
  C       0.197928000     0.500000000     0.023239000
  C       0.197929000     0.500000000     0.119619000
  C       0.273757000     0.500000000     0.047731000
  C       0.273757000     0.500000000     0.095127000
  C       0.349589000     0.500000000     0.023674000
  C       0.349589000     0.500000000     0.119183000
  C       0.425569000     0.500000000     0.047753000
  C       0.425570000     0.500000000     0.095104000
  C       0.501414000     0.500000000     0.023700000
  C       0.501414000     0.500000000     0.119157000
  C       0.577255000     0.500000000     0.048189000
  C       0.577255000     0.500000000     0.094668000
  C       0.647174000     0.500000000     0.020600000
  C       0.647174000     0.500000000     0.122256000
  C       0.128008000     0.500000000     0.193686000
  C       0.128008000     0.500000000     0.234887000
  C       0.197928000     0.500000000     0.166096000
  C       0.197929000     0.500000000     0.262476000
  C       0.273757000     0.500000000     0.190588000
  C       0.273757000     0.500000000     0.237984000
  C       0.349589000     0.500000000     0.166531000
  C       0.349589000     0.500000000     0.262040000
  C       0.425569000     0.500000000     0.190611000
  C       0.425570000     0.500000000     0.237961000
  C       0.501414000     0.500000000     0.166557000
  C       0.501414000     0.500000000     0.262014000
  C       0.577255000     0.500000000     0.191046000
  C       0.577255000     0.500000000     0.237525000
  C       0.647174000     0.500000000     0.163457000
  C       0.647174000     0.500000000     0.265113000
  C       0.128008000     0.500000000     0.336543000
  C       0.128008000     0.500000000     0.377744000
  C       0.197928000     0.500000000     0.308953000
  C       0.197929000     0.500000000     0.405334000
  C       0.273757000     0.500000000     0.333445000
  C       0.273757000     0.500000000     0.380842000
  C       0.349589000     0.500000000     0.309389000
  C       0.349589000     0.500000000     0.404897000
  C       0.425569000     0.500000000     0.333468000
  C       0.425570000     0.500000000     0.380818000
  C       0.501414000     0.500000000     0.309414000
  C       0.501414000     0.500000000     0.404871000
  C       0.577255000     0.500000000     0.333903000
  C       0.577255000     0.500000000     0.380382000
  C       0.647174000     0.500000000     0.306315000
  C       0.647174000     0.500000000     0.407970000
  C       0.128008000     0.500000000     0.479400000
  C       0.128008000     0.500000000     0.520601000
  C       0.197928000     0.500000000     0.451810000
  C       0.197929000     0.500000000     0.548191000
  C       0.273757000     0.500000000     0.476302000
  C       0.273757000     0.500000000     0.523699000
  C       0.349589000     0.500000000     0.452246000
  C       0.349589000     0.500000000     0.547755000
  C       0.425569000     0.500000000     0.476325000
  C       0.425570000     0.500000000     0.523675000
  C       0.501414000     0.500000000     0.452271000
  C       0.501414000     0.500000000     0.547729000
  C       0.577255000     0.500000000     0.476760000
  C       0.577255000     0.500000000     0.523239000
  C       0.647174000     0.500000000     0.449172000
  C       0.647174000     0.500000000     0.550827000
  C       0.128008000     0.500000000     0.622257000
  C       0.128008000     0.500000000     0.663458000
  C       0.197928000     0.500000000     0.594667000
  C       0.197929000     0.500000000     0.691048000
  C       0.273757000     0.500000000     0.619159000
  C       0.273757000     0.500000000     0.666556000
  C       0.349589000     0.500000000     0.595103000
  C       0.349589000     0.500000000     0.690612000
  C       0.425569000     0.500000000     0.619182000
  C       0.425570000     0.500000000     0.666532000
  C       0.501414000     0.500000000     0.595128000
  C       0.501414000     0.500000000     0.690586000
  C       0.577255000     0.500000000     0.619617000
  C       0.577255000     0.500000000     0.666096000
  C       0.647174000     0.500000000     0.592029000
  C       0.647174000     0.500000000     0.693684000
  C       0.128008000     0.500000000     0.765114000
  C       0.128008000     0.500000000     0.806316000
  C       0.197928000     0.500000000     0.737525000
  C       0.197929000     0.500000000     0.833905000
  C       0.273757000     0.500000000     0.762016000
  C       0.273757000     0.500000000     0.809413000
  C       0.349589000     0.500000000     0.737960000
  C       0.349589000     0.500000000     0.833469000
  C       0.425569000     0.500000000     0.762039000
  C       0.425570000     0.500000000     0.809389000
  C       0.501414000     0.500000000     0.737985000
  C       0.501414000     0.500000000     0.833443000
  C       0.577255000     0.500000000     0.762475000
  C       0.577255000     0.500000000     0.808953000
  C       0.647174000     0.500000000     0.734886000
  C       0.647174000     0.500000000     0.836542000
  C       0.128008000     0.500000000     0.907971000
  C       0.128008000     0.500000000     0.949173000
  C       0.197928000     0.500000000     0.880382000
  C       0.197929000     0.500000000     0.976762000
  C       0.273757000     0.500000000     0.904873000
  C       0.273757000     0.500000000     0.952270000
  C       0.349589000     0.500000000     0.880817000
  C       0.349589000     0.500000000     0.976326000
  C       0.425569000     0.500000000     0.904896000
  C       0.425570000     0.500000000     0.952246000
  C       0.501414000     0.500000000     0.880842000
  C       0.501414000     0.500000000     0.976300000
  C       0.577255000     0.500000000     0.905332000
  C       0.577255000     0.500000000     0.951810000
  C       0.647174000     0.500000000     0.877743000
  C       0.647174000     0.500000000     0.979399000
K_POINTS {automatic}
  4 4 4  1 1 1
---------------

In that paper, we can find the following description on page two:

---------
The carbon atoms at the edges are saturated with H atoms.
----------

So, according to the above description, what should I revise the input 
file in order to saturating the edges with H atoms?

Attached please find the snapshot for this structure.

Regards.
-- 

Hongsheng Zhao<zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

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From flux_ray12 at 163.com  Tue Apr 26 05:47:44 2011
From: flux_ray12 at 163.com (=?UTF-8?Q?GAO=C2=A0Zhe?=)
Date: Tue, 26 Apr 2011 11:47:44 +0800 (CST)
Subject: [Pw_forum] file reading error while using pp.x
Message-ID: <7883ea16.5419.12f8feb790c.Coremail.flux_ray12@163.com>

Dear QE developers and users:
I used pp.x to show the charge density of my structure: TiC (100) surface with one layer of Ni.
Of course, this model may not good enough, but, after pw.x running, pp.x gave an error and stopped.
The error is:
Calling punch_plot, plot_num =   0
Writing data to file  edensity
Reading data from file  1
%%%%%%%%%%%%%%%%%%
from plot_io : error #         2
opening file 1
%%%%%%%%%%%%%%%%%%
I also calculated for TiC cell without vacuum slab, every thing went right in this case. The difference is that the charge density file we obtained from filplot = '' in surface case was much larger (3.0MiB) than the one in cell case (smaller than 500KiB).
The version of QE I am using is 4.3, this problem occurred both in Red Hat, Mandriva and Ubuntu system.
My calculation script:
#!/bin/sh

cat >TiC.scf.in <<EOF
&control
   calculation = 'scf' ,
   prefix = 'TiC_Ni' ,
   pseudo_dir = '$PseudoDIR/' ,
   outdir = '$TempDIR/' ,
   disk_io = 'low' ,
/
&system
   ibrav = 6 ,
   celldm(1) = 8.17873408 ,
   celldm(3) = 2.0 ,
   nat = 14 ,
   ntyp = 3 ,
   ecutwfc = 25.52 ,
   ecutrho = 255.2 ,
   occupations = 'smearing' ,
   smearing = 'mp' ,
   degauss = 0.015 ,
/
&electrons
   startingpot = 'atomic' ,
   startingwfc = 'atomic+random' ,
   diagonalization = 'david' ,
/
ATOMIC_SPECIES
  Ti  47.900  Ti.pbe-sp-van_ak.UPF
   C  12.011  C.pbe-van_ak.UPF
  Ni  58.690  Ni.pbe-nd-rrkjus.UPF
ATOMIC_POSITIONS crystal
  Ti  0.00  0.00  0.00
  Ti  0.50  0.50  0.00
  Ti  0.50  0.00  0.25
  Ti  0.00  0.50  0.25
  Ti  0.00  0.00  0.50
  Ti  0.50  0.50  0.50
   C  0.50  0.00  0.00
   C  0.00  0.50  0.00
   C  0.00  0.00  0.25
   C  0.50  0.50  0.25
   C  0.00  0.50  0.50
   C  0.50  0.00  0.50
  Ni  0.00  0.00  0.75
  Ni  0.50  0.50  0.75
K_POINTS automatic
5 5 1 0 0 0
EOF
echo "  SCF processing...\c"
mpirun -n $1 pw.x -npool $2 <TiC.scf.in >TiC.scf.out
echo "done"

cat >TiC.pp.in <<EOF
&inputpp
   prefix = 'TiC_Ni' ,
   outdir = '$TempDIR/' ,
   filplot = 'edensity' ,
   plot_num = 0 ,
/
&plot
   nfile = 1 ,
   filepp(1) = 1 ,
   iflag = 2 ,
   output_format = 3 ,
   fileout = 'TiC_Ni_cd.xsf' ,
   e1(1)=0.0,e1(2)=1.0,e1(3)=0.0,
   e2(1)=0.0,e2(2)=0.0,e2(3)=1.0,
   x0(1)=0.5,x0(2)=0.0,x0(3)=0.0,
   nx=52,ny=52,
/
EOF
echo "  PP processing...\c"
mpirun -n $1 pp.x -npool $2 <TiC.pp.in >TiC.pp.out
echo "done"
Is this problem cased by huge size of charge density file? How could I overcome this problem?
Best Regards.



--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea
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From flux_ray12 at 163.com  Tue Apr 26 07:16:51 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Tue, 26 Apr 2011 13:16:51 +0800 (CST)
Subject: [Pw_forum] (Solved) Re: file reading error while using pp.x
In-Reply-To: <7883ea16.5419.12f8feb790c.Coremail.flux_ray12@163.com>
References: <7883ea16.5419.12f8feb790c.Coremail.flux_ray12@163.com>
Message-ID: <46835238.7039.12f903d10a8.Coremail.flux_ray12@163.com>

I am sorry about previous e-mail. The problem was caused by mycareless~ I should set the parameterfilepp(1) as a file name instead of 1~


At 2011-04-26 11:47:44?"GAO Zhe" <flux_ray12 at 163.com> wrote:
Dear QE developers and users:
I used pp.x to show the charge density of my structure: TiC (100) surface with one layer of Ni.
Of course, this model may not good enough, but, after pw.x running, pp.x gave an error and stopped.
The error is:
Calling punch_plot, plot_num =   0
Writing data to file  edensity
Reading data from file  1
%%%%%%%%%%%%%%%%%%
from plot_io : error #         2
opening file 1
%%%%%%%%%%%%%%%%%%
I also calculated for TiC cell without vacuum slab, every thing went right in this case. The difference is that the charge density file we obtained from filplot = '' in surface case was much larger (3.0MiB) than the one in cell case (smaller than 500KiB).
The version of QE I am using is 4.3, this problem occurred both in Red Hat, Mandriva and Ubuntu system.
My calculation script:
#!/bin/sh

cat >TiC.scf.in <<EOF
&control
   calculation = 'scf' ,
   prefix = 'TiC_Ni' ,
   pseudo_dir = '$PseudoDIR/' ,
   outdir = '$TempDIR/' ,
   disk_io = 'low' ,
/
&system
   ibrav = 6 ,
   celldm(1) = 8.17873408 ,
   celldm(3) = 2.0 ,
   nat = 14 ,
   ntyp = 3 ,
   ecutwfc = 25.52 ,
   ecutrho = 255.2 ,
   occupations = 'smearing' ,
   smearing = 'mp' ,
   degauss = 0.015 ,
/
&electrons
   startingpot = 'atomic' ,
   startingwfc = 'atomic+random' ,
   diagonalization = 'david' ,
/
ATOMIC_SPECIES
  Ti  47.900  Ti.pbe-sp-van_ak.UPF
   C  12.011  C.pbe-van_ak.UPF
  Ni  58.690  Ni.pbe-nd-rrkjus.UPF
ATOMIC_POSITIONS crystal
  Ti  0.00  0.00  0.00
  Ti  0.50  0.50  0.00
  Ti  0.50  0.00  0.25
  Ti  0.00  0.50  0.25
  Ti  0.00  0.00  0.50
  Ti  0.50  0.50  0.50
   C  0.50  0.00  0.00
   C  0.00  0.50  0.00
   C  0.00  0.00  0.25
   C  0.50  0.50  0.25
   C  0.00  0.50  0.50
   C  0.50  0.00  0.50
  Ni  0.00  0.00  0.75
  Ni  0.50  0.50  0.75
K_POINTS automatic
5 5 1 0 0 0
EOF
echo "  SCF processing...\c"
mpirun -n $1 pw.x -npool $2 <TiC.scf.in >TiC.scf.out
echo "done"

cat >TiC.pp.in <<EOF
&inputpp
   prefix = 'TiC_Ni' ,
   outdir = '$TempDIR/' ,
   filplot = 'edensity' ,
   plot_num = 0 ,
/
&plot
   nfile = 1 ,
   filepp(1) = 1 ,
   iflag = 2 ,
   output_format = 3 ,
   fileout = 'TiC_Ni_cd.xsf' ,
   e1(1)=0.0,e1(2)=1.0,e1(3)=0.0,
   e2(1)=0.0,e2(2)=0.0,e2(3)=1.0,
   x0(1)=0.5,x0(2)=0.0,x0(3)=0.0,
   nx=52,ny=52,
/
EOF
echo "  PP processing...\c"
mpirun -n $1 pp.x -npool $2 <TiC.pp.in >TiC.pp.out
echo "done"
Is this problem cased by huge size of charge density file? How could I overcome this problem?
Best Regards.



--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea




??????2G????????????????????3?!
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From lorenzo.paulatto at impmc.upmc.fr  Tue Apr 26 08:49:57 2011
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Tue, 26 Apr 2011 08:49:57 +0200
Subject: [Pw_forum] Should we use a double bond or 2 H atoms to saturate
 the system?
In-Reply-To: <4DB6B768.2080909@yahoo.com.cn>
References: <1637883071.20110425130610@yahoo.com.cn>
	<BANLkTinbukNnYgRXj3Je65fESV7GDt3F5g@mail.gmail.com>
	<4DB6B768.2080909@yahoo.com.cn>
Message-ID: <op.vui89jou5jfbqb@paulax>

In data 26 aprile 2011 alle ore 14:15:36, Hongsheng Zhao  
<zhaohscas at yahoo.com.cn> ha scritto:
> ---------
> The carbon atoms at the edges are saturated with H atoms.
> ----------
>
> So, according to the above description, what should I revise the input
> file in order to saturating the edges with H atoms?

Dear Hongsheng Zhao,
there are many ways to saturate the bonds, and not all of them actually  
make sense in experimental conditions. The matter is discussed quite in  
depth in Phys. Rev. Lett. 101, 096402 (2008).

best regards

-- 
Lorenzo Paulatto
post-doc @ IMPMC/UPMC - Universit? Paris 6
phone: +33 (0)1 44 27 74 89
www:   http://www-int.impmc.upmc.fr/~paulatto/

previously (take note of the change!):
phd student @ SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
www:   http://people.sissa.it/~paulatto/

From wonvein at gmail.com  Tue Apr 26 10:00:59 2011
From: wonvein at gmail.com (WANG Wei)
Date: Tue, 26 Apr 2011 17:00:59 +0900
Subject: [Pw_forum] vdW functional not implemented for spin polarized runs
Message-ID: <BANLkTik77RKMOm-KUviZaki_hpUnP4Brtw@mail.gmail.com>

Dear everyone,

I want to investigate the vdW systems with spin polarized calculations.
However, I found that the vdW functional is not implemented for spin
polarized calculations yet. It would be better if it will be supported in
the near future. Thank you.

Sincerely yours,
WANG


+---------------------------------------------------------+

Kawazoe's Lab
Institute for Materials Research (IMR),
Tohoku University2-1-1 Katahira, Aoba-ku, Sendai,
Japan
+---------------------------------------------------------+
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From abmus007 at gmail.com  Tue Apr 26 10:24:42 2011
From: abmus007 at gmail.com (Abolore Musari)
Date: Tue, 26 Apr 2011 03:24:42 -0500
Subject: [Pw_forum] k-point
Message-ID: <BANLkTi=-ZU0VHiWy+_TEFOU+ygHUzt-_og@mail.gmail.com>

Dear QE User,
I am having a problem as regard (k-point)
I am working on monoclinic system, and am using xcrysden to get my k-point
and my question is how do I know the special points (k-points) to select

from the Brillion zone in the xcrysden k path selection?

Thanks in anticipation of your favourable assistance

Musari Abolore
Dept Of Physics
University of Agriculture, Abeokuta
Nigeria
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From wonvein at gmail.com  Tue Apr 26 12:49:33 2011
From: wonvein at gmail.com (WANG Wei)
Date: Tue, 26 Apr 2011 19:49:33 +0900
Subject: [Pw_forum] Error in the NEB calculations using QE 4.3
Message-ID: <BANLkTi=w8Pr=vXkCp=r081HLG=5ZEhvfVA@mail.gmail.com>

Dear QE users,

I have no idea about calculating NEB with QE 4.3.

I used the following commands to perform NEB calculations, but error
occurred

*~/bin/neb.x <neb.in> log.neb*

error information is:

* NO input file found, assuming nothing to parse.
 Searching argument -input_images or --input_images
 Number of input images:             0
[0] MPI Abort by user Aborting program !
[0] Aborting program!*


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
BEGIN
BEGIN_PATH_INPUT
&PATH
  restart_mode      = 'from_scratch'
  string_method     = 'neb',
  nstep_path        = 20,
  ds                = 2.D0,
  opt_scheme        = "broyden",
  num_of_images     = 7,
  k_max             = 0.3D0,
  k_min             = 0.2D0,
  CI_scheme         = "auto",
  path_thr          = 0.1D0,
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT
&CONTROL
  prefix         = "H2+H"
  outdir         = "./",
  pseudo_dir   = "/home/wangvei/works/quantum-espresso/pseudo",
/
&SYSTEM
  ibrav                  = 0,
  celldm(1)              = 1.D0,
  nat                    = 3,
  ntyp                   = 1,
  ecutwfc                = 20.0D0,
  ecutrho                = 100.0D0,
  nspin                  = 2,
  starting_magnetization = 0.5D0,
  occupations            = "smearing",
  degauss                = 0.03D0,
/
&ELECTRONS
  conv_thr    = 1.D-8,
  mixing_beta = 0.3D0,
/
&IONS
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
/
ATOMIC_SPECIES
H  1.00794  HUSPBE.RRKJ3
K_POINTS { gamma }
CELL_PARAMETERS { cubic }
  12.00000  0.00000  0.00000
   0.00000  5.00000  0.00000
   0.00000  0.00000  5.00000
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS { bohr }
H   -4.56670009      0.00000000      0.00000000  1  0  0
H    0.00000000      0.00000000      0.00000000  0  0  0
H    1.55776676      0.00000000      0.00000000  1  0  0
LAST_IMAGE
ATOMIC_POSITIONS { bohr }
H   -1.55776676      0.00000000      0.00000000
H    0.00000000      0.00000000      0.00000000
H    4.56670009      0.00000000      0.00000000
END_POSITIONS
END_ENGINE_INPUT
END

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

+---------------------------------------------------------+
Kawazoe's Lab
Institute for Materials Research (IMR),
Tohoku University2-1-1 Katahira, Aoba-ku, Sendai, Japan
Phone: +81-022-215-2057
Fax:   +81-022-215-2052
+---------------------------------------------------------+
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From zhaohscas at yahoo.com.cn  Wed Apr 27 02:07:28 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Tue, 26 Apr 2011 20:07:28 -0400
Subject: [Pw_forum] Should we use a double bond or 2 H atoms to saturate
 the system?
In-Reply-To: <op.vui89jou5jfbqb@paulax>
References: <1637883071.20110425130610@yahoo.com.cn>	<BANLkTinbukNnYgRXj3Je65fESV7GDt3F5g@mail.gmail.com>	<4DB6B768.2080909@yahoo.com.cn>
	<op.vui89jou5jfbqb@paulax>
Message-ID: <4DB75E40.2000807@yahoo.com.cn>

On 04/26/2011 02:49 AM, Lorenzo Paulatto wrote:
> Dear Hongsheng Zhao,
> there are many ways to saturate the bonds, and not all of them actually
> make sense in experimental conditions. The matter is discussed quite in
> depth in Phys. Rev. Lett. 101, 096402 (2008).
Thanks a lot for all the helps from here.

Regards.
-- 

Hongsheng Zhao<zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China


From giannozz at democritos.it  Tue Apr 26 14:16:27 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 26 Apr 2011 14:16:27 +0200
Subject: [Pw_forum] Error in the NEB calculations using QE 4.3
In-Reply-To: <BANLkTi=w8Pr=vXkCp=r081HLG=5ZEhvfVA@mail.gmail.com>
References: <BANLkTi=w8Pr=vXkCp=r081HLG=5ZEhvfVA@mail.gmail.com>
Message-ID: <DBBFE287-0994-4346-837C-75F2D2A220EE@democritos.it>


On Apr 26, 2011, at 12:49 , WANG Wei wrote:

> I have no idea about calculating NEB with QE 4.3.

so why are you using NEB if you have "no idea"?

> I used the following commands to perform NEB calculations, but  
> error occurred
>
> ~/bin/neb.x <neb.in> log.neb

you cannot use this syntax any longer:
http://www.quantum-espresso.org/user_guide/node29.html
Use "~/bin/neb.x -inp neb.in"

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





From L-marks at northwestern.edu  Tue Apr 26 14:29:23 2011
From: L-marks at northwestern.edu (Laurence Marks)
Date: Tue, 26 Apr 2011 07:29:23 -0500
Subject: [Pw_forum] Should we use a double bond or 2 H atoms to saturate
 the system?
In-Reply-To: <4DB75E40.2000807@yahoo.com.cn>
References: <1637883071.20110425130610@yahoo.com.cn>
	<BANLkTinbukNnYgRXj3Je65fESV7GDt3F5g@mail.gmail.com>
	<4DB6B768.2080909@yahoo.com.cn> <op.vui89jou5jfbqb@paulax>
	<4DB75E40.2000807@yahoo.com.cn>
Message-ID: <BANLkTinct6FCXZK0B5L_uA1d4S=W8VCBEw@mail.gmail.com>

A personal opinion: saturating "bonds" with hydrogen is bad science,
just as "fixing atoms" is also bad science. These are relics of the
days when it was hard to calculate a big system, but 100's (1000's) of
atoms are no longer particularly difficult. Do it right.

On Tue, Apr 26, 2011 at 7:07 PM, Hongsheng Zhao <zhaohscas at yahoo.com.cn> wrote:
> On 04/26/2011 02:49 AM, Lorenzo Paulatto wrote:
>> Dear Hongsheng Zhao,
>> there are many ways to saturate the bonds, and not all of them actually
>> make sense in experimental conditions. The matter is discussed quite in
>> depth in Phys. Rev. Lett. 101, 096402 (2008).
> Thanks a lot for all the helps from here.
>
> Regards.
> --
>
> Hongsheng Zhao<zhaohscas at yahoo.com.cn>
> School of Physics and Electrical Information Science,
> Ningxia University, Yinchuan 750021, China
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Research is to see what everybody else has seen, and to think what
nobody else has thought
Albert Szent-Gyorgi

From Lorenzo.Paulatto at impmc.upmc.fr  Tue Apr 26 14:33:55 2011
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Tue, 26 Apr 2011 14:33:55 +0200
Subject: [Pw_forum] Should we use a double bond or 2 H atoms to saturate
 the system?
In-Reply-To: <BANLkTinct6FCXZK0B5L_uA1d4S=W8VCBEw@mail.gmail.com>
References: <1637883071.20110425130610@yahoo.com.cn>
	<BANLkTinbukNnYgRXj3Je65fESV7GDt3F5g@mail.gmail.com>
	<4DB6B768.2080909@yahoo.com.cn> <op.vui89jou5jfbqb@paulax>
	<4DB75E40.2000807@yahoo.com.cn>
	<BANLkTinct6FCXZK0B5L_uA1d4S=W8VCBEw@mail.gmail.com>
Message-ID: <op.vujo6tvaxuur8c@vanoxite.impmc.jussieu.fr>

On Tue, 26 Apr 2011 14:29:23 +0200, Laurence Marks  
<L-marks at northwestern.edu> wrote:
> A personal opinion: saturating "bonds" with hydrogen is bad science,
> just as "fixing atoms" is also bad science. These are relics of the
> days when it was hard to calculate a big system, but 100's (1000's) of
> atoms are no longer particularly difficult. Do it right.

yet, if you study graphene nano-ribbons, the saturating hydrogens are  
actually there


-- 
Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From L-marks at northwestern.edu  Tue Apr 26 14:36:30 2011
From: L-marks at northwestern.edu (Laurence Marks)
Date: Tue, 26 Apr 2011 07:36:30 -0500
Subject: [Pw_forum] Should we use a double bond or 2 H atoms to saturate
 the system?
In-Reply-To: <op.vujo6tvaxuur8c@vanoxite.impmc.jussieu.fr>
References: <1637883071.20110425130610@yahoo.com.cn>
	<BANLkTinbukNnYgRXj3Je65fESV7GDt3F5g@mail.gmail.com>
	<4DB6B768.2080909@yahoo.com.cn> <op.vui89jou5jfbqb@paulax>
	<4DB75E40.2000807@yahoo.com.cn>
	<BANLkTinct6FCXZK0B5L_uA1d4S=W8VCBEw@mail.gmail.com>
	<op.vujo6tvaxuur8c@vanoxite.impmc.jussieu.fr>
Message-ID: <BANLkTi=fWiuiMyAFkvocNZ_iZVqkuLjDcw@mail.gmail.com>

This is the exception, but then this is not "saturating" this is
calculating the thermodynamics of wet/hydrogenated graphene.
Saturating is, for instance, calculating a silicon surface and
terminating with hydrogen to model the bulk rather than using a big,
centro-symmetric slab.

On Tue, Apr 26, 2011 at 7:33 AM, Lorenzo Paulatto
<Lorenzo.Paulatto at impmc.upmc.fr> wrote:
> On Tue, 26 Apr 2011 14:29:23 +0200, Laurence Marks
> <L-marks at northwestern.edu> wrote:
>> A personal opinion: saturating "bonds" with hydrogen is bad science,
>> just as "fixing atoms" is also bad science. These are relics of the
>> days when it was hard to calculate a big system, but 100's (1000's) of
>> atoms are no longer particularly difficult. Do it right.
>
> yet, if you study graphene nano-ribbons, the saturating hydrogens are
> actually there
>
>
> --
> Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www: ? http://www-int.impmc.upmc.fr/~paulatto/
> mail: ?23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Research is to see what everybody else has seen, and to think what
nobody else has thought
Albert Szent-Gyorgi

From zhaohscas at yahoo.com.cn  Wed Apr 27 03:01:35 2011
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Tue, 26 Apr 2011 21:01:35 -0400
Subject: [Pw_forum] Should we use a double bond or 2 H atoms to saturate
 the system?
In-Reply-To: <BANLkTi=fWiuiMyAFkvocNZ_iZVqkuLjDcw@mail.gmail.com>
References: <1637883071.20110425130610@yahoo.com.cn>	<BANLkTinbukNnYgRXj3Je65fESV7GDt3F5g@mail.gmail.com>	<4DB6B768.2080909@yahoo.com.cn>
	<op.vui89jou5jfbqb@paulax>	<4DB75E40.2000807@yahoo.com.cn>	<BANLkTinct6FCXZK0B5L_uA1d4S=W8VCBEw@mail.gmail.com>	<op.vujo6tvaxuur8c@vanoxite.impmc.jussieu.fr>
	<BANLkTi=fWiuiMyAFkvocNZ_iZVqkuLjDcw@mail.gmail.com>
Message-ID: <4DB76AEF.8010006@yahoo.com.cn>

On 04/26/2011 08:36 AM, Laurence Marks wrote:
> This is the exception, but then this is not "saturating" this is
> calculating the thermodynamics of wet/hydrogenated graphene.
> Saturating is, for instance, calculating a silicon surface and
> terminating with hydrogen to model the bulk rather than using a big,
> centro-symmetric slab.
But, in my mind, some times, people use a big slab with

hydrogen to terminating the dangling bond.



-- 
Hongsheng Zhao<zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China


From wonvein at gmail.com  Tue Apr 26 15:05:35 2011
From: wonvein at gmail.com (WANG Wei)
Date: Tue, 26 Apr 2011 22:05:35 +0900
Subject: [Pw_forum] Error in the NEB calculations using QE 4.3
In-Reply-To: <DBBFE287-0994-4346-837C-75F2D2A220EE@democritos.it>
References: <BANLkTi=w8Pr=vXkCp=r081HLG=5ZEhvfVA@mail.gmail.com>
	<DBBFE287-0994-4346-837C-75F2D2A220EE@democritos.it>
Message-ID: <BANLkTim7q781DRO0rKKHWf0t1FjC-cnjew@mail.gmail.com>

Dear Prof. Giannozzi,

I mean that I have no idea about the error methioned above. I do not the
reason for it . Thank you.


On 26 April 2011 21:16, Paolo Giannozzi <giannozz at democritos.it> wrote:

>
> On Apr 26, 2011, at 12:49 , WANG Wei wrote:
>
> > I have no idea about calculating NEB with QE 4.3.
>
> so why are you using NEB if you have "no idea"?
>
> > I used the following commands to perform NEB calculations, but
> > error occurred
> >
> > ~/bin/neb.x <neb.in> log.neb
>
> you cannot use this syntax any longer:
> http://www.quantum-espresso.org/user_guide/node29.html
> Use "~/bin/neb.x -inp neb.in"
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
+---------------------------------------------------------+
Vei WANG
Kawazoe's Lab
Institute for Materials Research (IMR),
Tohoku University2-1-1 Katahira, Aoba-ku, Sendai, Japan
Phone: +81-022-215-2057
Fax:   +81-022-215-2052
+---------------------------------------------------------+
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From degironc at sissa.it  Tue Apr 26 19:00:53 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Tue, 26 Apr 2011 19:00:53 +0200
Subject: [Pw_forum] vdW functional not implemented for spin
	polarized	runs
In-Reply-To: <BANLkTik77RKMOm-KUviZaki_hpUnP4Brtw@mail.gmail.com>
References: <BANLkTik77RKMOm-KUviZaki_hpUnP4Brtw@mail.gmail.com>
Message-ID: <20110426190053.jklki05r4g044wc0@webmail.sissa.it>

Dear  WANG Wei
   the vdw-DF functional form is not defined for spin polarized system...
   if you define, implement and test it, you could even get a nice  
publication out of it. thank you.
stefano


Quoting WANG Wei <wonvein at gmail.com>:

> Dear everyone,
>
> I want to investigate the vdW systems with spin polarized calculations.
> However, I found that the vdW functional is not implemented for spin
> polarized calculations yet. It would be better if it will be supported in
> the near future. Thank you.
>
> Sincerely yours,
> WANG
>
>
> +---------------------------------------------------------+
>
> Kawazoe's Lab
> Institute for Materials Research (IMR),
> Tohoku University2-1-1 Katahira, Aoba-ku, Sendai,
> Japan
> +---------------------------------------------------------+
>



----------------------------------------------------------------
   SISSA Webmail https://webmail.sissa.it/
   Powered by Horde http://www.horde.org/



From baris.malcioglu at gmail.com  Tue Apr 26 19:52:40 2011
From: baris.malcioglu at gmail.com (O. Baris Malcioglu)
Date: Tue, 26 Apr 2011 19:52:40 +0200
Subject: [Pw_forum] Should we use a double bond or 2 H atoms to saturate
 the system?
In-Reply-To: <4DB6B768.2080909@yahoo.com.cn>
References: <1637883071.20110425130610@yahoo.com.cn>
	<BANLkTinbukNnYgRXj3Je65fESV7GDt3F5g@mail.gmail.com>
	<4DB6B768.2080909@yahoo.com.cn>
Message-ID: <BANLkTin2J2MQ1uJBSy-dY=m4dXYyeii_8w@mail.gmail.com>

Well, you literally add the coordinates of H atoms, and the definition
of H atom itself...

If you are asking how I do it, depending on the system, I either write
a simple script, or, if it is small enough, I extract the coordinates
to a standart from, and then use a freely available "geometry editor"
(I tend to use accelrys discovery studio viewer for such tasks, since
it is quite well equipped (the free version is available in accelrys
web site), with somewhat a guilty conscience because it is not GPL).

By the way, I beg to differ from "Hydrogen saturation is bad science".
Actually, I do fail to see your point in this generalisation.  Would
you, for a very simple example, consider studying the difference
between cyclohexane and benzene as bad science? I think this kind of
generalisations are quite dangerous to make without proper context,
after all, it all depends on what you want to study.

From m_pazoki at physics.sharif.edu  Tue Apr 26 20:29:50 2011
From: m_pazoki at physics.sharif.edu (meysam pazoki)
Date: Tue, 26 Apr 2011 22:59:50 +0430
Subject: [Pw_forum] Average.x planar vs macroscopic average
Message-ID: <BANLkTi=cumWwciVJzytk8A3a-T1PekTo=Q@mail.gmail.com>

Dear all

I follow the trend used in Work_Fct example of espresso for obtaining the
work function of my super cell.
I increase the vaccum layer of my super cell and by PP.x save the  V_bare +
V_H potential and use average.x for averaging.
But the  macroscopic and planar averages is not match at the borders of
supercell.(each of them converge to a different constant at the border)
Could you help me that my results is true or not?
and What is the diference between macroscopic and planar averages?
Thanks indeed for your consideration
Regards
Meysam Pazoki
SUT
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From swapnil.chandratre at gmail.com  Tue Apr 26 23:28:02 2011
From: swapnil.chandratre at gmail.com (swapnil chandratre)
Date: Tue, 26 Apr 2011 16:28:02 -0500
Subject: [Pw_forum] Error computing Cholesky
In-Reply-To: <438D2C9A-1CD3-42ED-A939-E8D0978894BF@democritos.it>
References: <BANLkTin821WPCc5chAmwUJSAnM7OYNwYbg@mail.gmail.com>
	<438D2C9A-1CD3-42ED-A939-E8D0978894BF@democritos.it>
Message-ID: <BANLkTinmBTSVJkbJ1hVaoutQPvgzcqp1-w@mail.gmail.com>

I couldnt find anything pertaining to error 426.

On Mon, Apr 25, 2011 at 2:33 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Apr 25, 2011, at 2:14 , swapnil chandratre wrote:
>
> > I get the following error for Graphene Ribbon with porosity, can
> > anyone help.
> >
> >  from  cdiaghg  : error #       426
> >       problems computing cholesky
>
> what about searching the mailing list for "cholesky" ?
>
> http://www.quantum-espresso.org/user_guide/
> node52.html#SECTION000121070000000000000
> >
>
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Regards,
Swapnil Chandratre
Graduate Student
Dept. of Mechanical Engineering,
University of Houston,
Houston, TX
(M)-713-294-9546
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From shruba at gmail.com  Wed Apr 27 02:15:34 2011
From: shruba at gmail.com (Shruba Gangopadhyay)
Date: Tue, 26 Apr 2011 20:15:34 -0400
Subject: [Pw_forum] Error computing Cholesky
In-Reply-To: <BANLkTinmBTSVJkbJ1hVaoutQPvgzcqp1-w@mail.gmail.com>
References: <BANLkTin821WPCc5chAmwUJSAnM7OYNwYbg@mail.gmail.com>
	<438D2C9A-1CD3-42ED-A939-E8D0978894BF@democritos.it>
	<BANLkTinmBTSVJkbJ1hVaoutQPvgzcqp1-w@mail.gmail.com>
Message-ID: <BANLkTik0iCg2UMauw1RaHrUGkJxJ7hu-Hg@mail.gmail.com>

Dear Swapnil,
                    Its always better to send the input file here. Because
without your input its very difficult for anybody to understand whats going
wrong. From my experience I can suggest you one thing to check if your
supercell length along anyone of the axis having much high value (like
length of x axis/length along z ~20 or more). I suspect it because you have
a nanoribbon.  In that case you might reduce the ratio and see if you still
getting the error.
                   Cheers
                   Shruba

On Tue, Apr 26, 2011 at 5:28 PM, swapnil chandratre <
swapnil.chandratre at gmail.com> wrote:

> I couldnt find anything pertaining to error 426.
>
>
> On Mon, Apr 25, 2011 at 2:33 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:
>
>>
>> On Apr 25, 2011, at 2:14 , swapnil chandratre wrote:
>>
>> > I get the following error for Graphene Ribbon with porosity, can
>> > anyone help.
>> >
>> >  from  cdiaghg  : error #       426
>> >       problems computing cholesky
>>
>> what about searching the mailing list for "cholesky" ?
>>
>> http://www.quantum-espresso.org/user_guide/
>> node52.html#SECTION000121070000000000000
>> >
>>
>>
>> P.
>> ---
>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
>  --
> Regards,
> Swapnil Chandratre
> Graduate Student
> Dept. of Mechanical Engineering,
> University of Houston,
> Houston, TX
> (M)-713-294-9546
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Shruba Gangopadhyay
PhD candidate
Department of Chemistry, NanoScience Technology Center
12424 Research Parkway, Suite 400
University of Central Florida
Orlando, FL-32826
'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
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From wonvein at gmail.com  Wed Apr 27 02:30:02 2011
From: wonvein at gmail.com (WANG Wei)
Date: Wed, 27 Apr 2011 09:30:02 +0900
Subject: [Pw_forum] vdW functional not implemented for spin polarized
	runs
In-Reply-To: <20110426190053.jklki05r4g044wc0@webmail.sissa.it>
References: <BANLkTik77RKMOm-KUviZaki_hpUnP4Brtw@mail.gmail.com>
	<20110426190053.jklki05r4g044wc0@webmail.sissa.it>
Message-ID: <BANLkTimZjkewZNWX+NbEe5+UtX7vna3BTw@mail.gmail.com>

Dear stefano,

Thank you for your reply.  That's OK.

WANG

On 27 April 2011 02:00, Stefano de Gironcoli <degironc at sissa.it> wrote:

> Dear  WANG Wei
>   the vdw-DF functional form is not defined for spin polarized system...
>   if you define, implement and test it, you could even get a nice
> publication out of it. thank you.
> stefano
>
>
> Quoting WANG Wei <wonvein at gmail.com>:
>
> > Dear everyone,
> >
> > I want to investigate the vdW systems with spin polarized calculations.
> > However, I found that the vdW functional is not implemented for spin
> > polarized calculations yet. It would be better if it will be supported in
> > the near future. Thank you.
> >
> > Sincerely yours,
> > WANG
> >
> >
> > +---------------------------------------------------------+
> >
> > Kawazoe's Lab
> > Institute for Materials Research (IMR),
> > Tohoku University2-1-1 Katahira, Aoba-ku, Sendai,
> > Japan
> > +---------------------------------------------------------+
> >
>
>
>
> ----------------------------------------------------------------
>   SISSA Webmail https://webmail.sissa.it/
>   Powered by Horde http://www.horde.org/
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
+---------------------------------------------------------+
Vei WANG
Kawazoe's Lab
Institute for Materials Research (IMR),
Tohoku University2-1-1 Katahira, Aoba-ku, Sendai, Japan
Phone: +81-022-215-2057
Fax:   +81-022-215-2052
+---------------------------------------------------------+
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From tanycimr at gmail.com  Wed Apr 27 03:21:59 2011
From: tanycimr at gmail.com (=?Big5?B?zuu0xqbB?=)
Date: Wed, 27 Apr 2011 09:21:59 +0800
Subject: [Pw_forum] phonon dispersion
Message-ID: <BANLkTikOdseAksS5PxXMcNzEiVwuaUwoUQ@mail.gmail.com>

 Dear all

I want to calculate the phonon dispersion of B12 at the first Brillouin Zone
. i don't know which program should I use ? Please give me some advice . And
if it's possible ,please give me a example ?

thanks in advance .


Tanyci
Nankai university , tianjin
china
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From nicola.marzari at materials.ox.ac.uk  Wed Apr 27 03:29:09 2011
From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari)
Date: Wed, 27 Apr 2011 02:29:09 +0100
Subject: [Pw_forum] phonon dispersion
In-Reply-To: <BANLkTikOdseAksS5PxXMcNzEiVwuaUwoUQ@mail.gmail.com>
References: <BANLkTikOdseAksS5PxXMcNzEiVwuaUwoUQ@mail.gmail.com>
Message-ID: <4DB77165.4010904@materials.ox.ac.uk>

On 4/27/11 2:21 AM, ??? wrote:
> Dear all
> I want to calculate the phonon dispersion of B12 at the first Brillouin 
> Zone . i don't know which program should I use ? Please give me some 
> advice . And if it's possible ,please give me a example ?
> 
> thanks in advance .
> Tanyci
> Nankai university , tianjin
> china

Der Tanyci,

all the answers to your questions are on the website, including
e.g. extensive video lectures and tutorials: www.quantum-espresso.org

			nicola

-- 
----------------------------------------------------------------------
Prof Nicola Marzari    Department of Materials    University of Oxford
Chair of Materials Modelling  Director, Materials Modelling Laboratory
nicola.marzari at materials.ox.ac.uk     http://mml.materials.ox.ac.uk/NM

From germaneau at gucas.ac.cn  Wed Apr 27 15:31:00 2011
From: germaneau at gucas.ac.cn (Eric Germaneau)
Date: Wed, 27 Apr 2011 09:31:00 -0400
Subject: [Pw_forum] phonon dispersion
In-Reply-To: <503866732.22923@test1.gucas.ac.cn>
References: <503866732.22923@test1.gucas.ac.cn>
Message-ID: <4DB81A94.4050806@gucas.ac.cn>

Hey Tanyci,

You'd better take look to the examples first.

            ?ric.

On 04/26/2011 09:21 PM, ??? wrote:
> Dear all
> I want to calculate the phonon dispersion of B12 at the first 
> Brillouin Zone . i don't know which program should I use ? Please give 
> me some advice . And if it's possible ,please give me a example ?
>
> thanks in advance .
> Tanyci
> Nankai university , tianjin
> china
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn>

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/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 tfcao at theory.issp.ac.cn  Wed Apr 27 04:52:12 2011
From: tfcao at theory.issp.ac.cn (=?utf-8?B?5pu56IW+6aOe?=)
Date: Wed, 27 Apr 2011 10:52:12 +0800
Subject: [Pw_forum] =?utf-8?q?How_to_choose_the_supercell_=3F____=28cao_te?=
	=?utf-8?q?ngfei=29?=
Message-ID: <20110427025212.30026.qmail@ms.hfcas.ac.cn>

Dear QE users:
 I want to construct  a supercell   of graphene with one Hydrogen absorbed on it , and my question is  how can I choose the supercell properly so that the interaction between Hydrogens can be neglected .  Any suggestions will be greatly appreciated .
   

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From faccin.giovani at gmail.com  Wed Apr 27 05:21:30 2011
From: faccin.giovani at gmail.com (Giovani Faccin)
Date: Tue, 26 Apr 2011 23:21:30 -0400
Subject: [Pw_forum] How to choose the supercell ? (cao tengfei)
In-Reply-To: <20110427025212.30026.qmail@ms.hfcas.ac.cn>
References: <20110427025212.30026.qmail@ms.hfcas.ac.cn>
Message-ID: <BANLkTi==iiJze2w78B7Bsjda=yROdGHxUQ@mail.gmail.com>

Dear ???,

One possibility that comes to my mind is to proceed as follows:

1 - First make a few supercells of pure graphene, each with a different
size, all without the hydrogen atom, and evaluate their total energies per
atom and/or bands, in order to make sure that the cell you'll use on step 2
is large enough to remove spurious border effects.

2 - Once you get a cell that's large enough, then evaluate it with the
hydrogen atom and check the forces acting on the H atom.

3 - Now try to use a larger cell with the hydrogen, and evaluate the forces
again on the H atom.

4 - If the cell is large enough so that no border effects are present and
the hydrogens are not interfering with each other, then the forces on step 2
and 3 should be the same.

Hope it helps.

Giovani M. Faccin
UFMS - Brazil




2011/4/26 ??? <tfcao at theory.issp.ac.cn>

>  Dear QE users:
> I want to construct a supercell of graphene with one Hydrogen absorbed on
> it , and my question is how can I choose the supercell properly so that the
> interaction between Hydrogens can be neglected . Any suggestions will be
> greatly appreciated .
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Giovani
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From ttduyle at gmail.com  Wed Apr 27 05:34:56 2011
From: ttduyle at gmail.com (Duy Le)
Date: Tue, 26 Apr 2011 23:34:56 -0400
Subject: [Pw_forum] vdW functional not implemented for spin polarized
	runs
In-Reply-To: <20110426190053.jklki05r4g044wc0@webmail.sissa.it>
References: <BANLkTik77RKMOm-KUviZaki_hpUnP4Brtw@mail.gmail.com>
	<20110426190053.jklki05r4g044wc0@webmail.sissa.it>
Message-ID: <BANLkTiniCjVY5GFStON8zkAQi6Wk3eyocw@mail.gmail.com>

--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Tue, Apr 26, 2011 at 1:00 PM, Stefano de Gironcoli <degironc at sissa.it> wrote:
> Dear ?WANG Wei
> ? the vdw-DF functional form is not defined for spin polarized system...
Or it does mean that non-local energy is not spin-dependent but
charge-density-dependent only.
> ? if you define, implement and test it, you could even get a nice
> publication out of it. thank you.
The spin-polarized vdW-DF has been implemented in GPAW.
> stefano
>
>
> Quoting WANG Wei <wonvein at gmail.com>:
>
>> Dear everyone,
>>
>> I want to investigate the vdW systems with spin polarized calculations.
>> However, I found that the vdW functional is not implemented for spin
>> polarized calculations yet. It would be better if it will be supported in
>> the near future. Thank you.
>>
>> Sincerely yours,
>> WANG
>>
>>
>> +---------------------------------------------------------+
>>
>> Kawazoe's Lab
>> Institute for Materials Research (IMR),
>> Tohoku University2-1-1 Katahira, Aoba-ku, Sendai,
>> Japan
>> +---------------------------------------------------------+
>>
>
>
>
> ----------------------------------------------------------------
> ? SISSA Webmail https://webmail.sissa.it/
> ? Powered by Horde http://www.horde.org/
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From wonvein at gmail.com  Wed Apr 27 06:35:35 2011
From: wonvein at gmail.com (WANG Wei)
Date: Wed, 27 Apr 2011 13:35:35 +0900
Subject: [Pw_forum] vdW functional not implemented for spin polarized
	runs
In-Reply-To: <BANLkTiniCjVY5GFStON8zkAQi6Wk3eyocw@mail.gmail.com>
References: <BANLkTik77RKMOm-KUviZaki_hpUnP4Brtw@mail.gmail.com>
	<20110426190053.jklki05r4g044wc0@webmail.sissa.it>
	<BANLkTiniCjVY5GFStON8zkAQi6Wk3eyocw@mail.gmail.com>
Message-ID: <BANLkTine4_GTeSpziWgMUgJHxpn+ZFakcA@mail.gmail.com>

Thank you for your advice, Deu. Yes, the non-local energy is independent the
spin density.


On 27 April 2011 12:34, Duy Le <ttduyle at gmail.com> wrote:

> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
>
> On Tue, Apr 26, 2011 at 1:00 PM, Stefano de Gironcoli <degironc at sissa.it>
> wrote:
> > Dear  WANG Wei
> >   the vdw-DF functional form is not defined for spin polarized system...
> Or it does mean that non-local energy is not spin-dependent but
> charge-density-dependent only.
> >   if you define, implement and test it, you could even get a nice
> > publication out of it. thank you.
> The spin-polarized vdW-DF has been implemented in GPAW.
> > stefano
> >
> >
>
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From eyvaz_isaev at yahoo.com  Wed Apr 27 07:14:25 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 26 Apr 2011 22:14:25 -0700 (PDT)
Subject: [Pw_forum] phonon dispersion
In-Reply-To: <BANLkTikOdseAksS5PxXMcNzEiVwuaUwoUQ@mail.gmail.com>
References: <BANLkTikOdseAksS5PxXMcNzEiVwuaUwoUQ@mail.gmail.com>
Message-ID: <396696.22896.qm@web65708.mail.ac4.yahoo.com>

Hi, 

I suppose, the best way to plot phonons is PlotPhon utility in  QE.
What you need is IFC-matrix (*.fc file).
See examples in /PlotPhon/Examples how to launch them.

Bests,
Eyvaz.

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

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

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




________________________________
From: ??? <tanycimr at gmail.com>
To: pw_forum at pwscf.org
Sent: Wed, April 27, 2011 5:21:59 AM
Subject: [Pw_forum] phonon dispersion


Dear all 
 
I want to calculate the phonon dispersion of B12 at the first Brillouin  Zone . 
i don't know which program should I use ? Please give me some advice . And if 
it's possible ,please give me a example ?

thanks in advance .
 
 
Tanyci
Nankai university , tianjin
china
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From padmaja_patnaik at yahoo.co.uk  Wed Apr 27 07:24:34 2011
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Wed, 27 Apr 2011 06:24:34 +0100 (BST)
Subject: [Pw_forum] Doubt in band structure output
Message-ID: <86292.76616.qm@web28515.mail.ukl.yahoo.com>

Hi All

I have a query. When we are plotting band structure, in the output ps file the code doesn't mention the high symmetry points Gamma, K, L etc. along the X axis. How to do that?

Thanks in advance
Regards
Padmaja Patnaik

Research Scholar

Dept of Physics

IIT Bombay

Mumbai, India
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From mehrnooshhazrati at gmail.com  Wed Apr 27 08:35:51 2011
From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati)
Date: Wed, 27 Apr 2011 10:05:51 +0330
Subject: [Pw_forum] dos vs. pdos.tot
Message-ID: <BANLkTimpdf9SA-1oiU_pihNSKZ4v=WaxhA@mail.gmail.com>

Hi dear QE users,

I have a question about DOS diagram : what is the difference between DOS
gained of the dos.x code and PDOS_tot gained of projwfc.x code output ?!

Regards

-- 
*

*
*
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
**** Mehrnoosh Kh. Hazrati ****
**** Master Student of Computational Physical Chemistry,KNTU,Tehran ****
 *** Phone : +989123436300 ***
*** Mail : mehrnooshhazrati at gmail.com ***
*
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
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From degironc at sissa.it  Wed Apr 27 09:29:41 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 27 Apr 2011 09:29:41 +0200
Subject: [Pw_forum] vdW functional not implemented for spin polarized
 runs
In-Reply-To: <BANLkTine4_GTeSpziWgMUgJHxpn+ZFakcA@mail.gmail.com>
References: <BANLkTik77RKMOm-KUviZaki_hpUnP4Brtw@mail.gmail.com>	<20110426190053.jklki05r4g044wc0@webmail.sissa.it>	<BANLkTiniCjVY5GFStON8zkAQi6Wk3eyocw@mail.gmail.com>
	<BANLkTine4_GTeSpziWgMUgJHxpn+ZFakcA@mail.gmail.com>
Message-ID: <4DB7C5E5.4090903@sissa.it>

the vdW energy depends on the local polarizability of the electron gas ..
does it depend on the spin density ? I would say so.
Is it taken into account in the current definition of vdw-DF ? I would 
say no...
how is it implemented in GPAW ? just blindly or with some argument ?
stefano

On 04/27/2011 06:35 AM, WANG Wei wrote:
> Thank you for your advice, Deu. Yes, the non-local energy is independent the
> spin density.
>
>
> On 27 April 2011 12:34, Duy Le<ttduyle at gmail.com>  wrote:
>
>> --------------------------------------------------
>> Duy Le
>> PhD Student
>> Department of Physics
>> University of Central Florida.
>>
>> "Men don't need hand to do things"
>>
>>
>>
>> On Tue, Apr 26, 2011 at 1:00 PM, Stefano de Gironcoli<degironc at sissa.it>
>> wrote:
>>> Dear  WANG Wei
>>>    the vdw-DF functional form is not defined for spin polarized system...
>> Or it does mean that non-local energy is not spin-dependent but
>> charge-density-dependent only.
>>>    if you define, implement and test it, you could even get a nice
>>> publication out of it. thank you.
>> The spin-polarized vdW-DF has been implemented in GPAW.
>>> stefano
>>>
>>>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From padmaja_patnaik at yahoo.co.uk  Wed Apr 27 12:27:47 2011
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Wed, 27 Apr 2011 11:27:47 +0100 (BST)
Subject: [Pw_forum] Another doubt in band plot
Message-ID: <581419.27884.qm@web28513.mail.ukl.yahoo.com>

Hi All

While plotting band structure for a supercell it shows some lines connecting from the valence bad to conduction band points. Why so? I am doing this for SiC with a 16 atoms supercell which is obtained by exapnding the lattice parameter 2 times in all directions. Attaching the band plot ps file here.? Please suggest.
Thanking you in advance.
Regards

Padmaja Patnaik

Research Scholar

Dept of Physics

IIT Bombay

Mumbai, India
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From sxu2 at ncsu.edu  Wed Apr 27 13:06:42 2011
From: sxu2 at ncsu.edu (shu xu)
Date: Wed, 27 Apr 2011 07:06:42 -0400
Subject: [Pw_forum] Another doubt in band plot
In-Reply-To: <581419.27884.qm@web28513.mail.ukl.yahoo.com>
References: <581419.27884.qm@web28513.mail.ukl.yahoo.com>
Message-ID: <BANLkTikoUNR5kOh+cPyRXeKfhwSnqWSngQ@mail.gmail.com>

in bands.in file. add no_overlap = true,

On Wed, Apr 27, 2011 at 6:27 AM, Padmaja Patnaik <
padmaja_patnaik at yahoo.co.uk> wrote:

>   Hi All
>
> While plotting band structure for a supercell it shows some lines
> connecting from the valence bad to conduction band points. Why so? I am
> doing this for SiC with a 16 atoms supercell which is obtained by exapnding
> the lattice parameter 2 times in all directions. Attaching the band plot ps
> file here.  Please suggest.
> Thanking you in advance.
> Regards
>
> Padmaja Patnaik
> Research Scholar
> Dept of Physics
> IIT Bombay
> Mumbai, India
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From masoudnahali at gmail.com  Wed Apr 27 13:20:41 2011
From: masoudnahali at gmail.com (Masoud Nahali)
Date: Wed, 27 Apr 2011 15:50:41 +0430
Subject: [Pw_forum] dos vs. pdos.tot
Message-ID: <BANLkTi=+RtykiY_on629KYRN-MDVwKrJbw@mail.gmail.com>

*Dear Mehrnoosh

I think that a**tomic states on different atoms are not orthonormal
which makes PDOS-tot different from DOS. I hope it helps.


*

Best Wishes

 Masoud

--------------
Masoud Nahali, Ph.D Student at Sharif University of Technology


*>Mehrnoosh Hazrati* Wrote on W*ed Apr 27 08:35:51 CEST 2011*

>Hi dear QE users,

>I have a question about DOS diagram : what is the difference between DOS
>gained of the dos.x code and PDOS_tot gained of projwfc.x code output ?!

>Regards
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From fratesi at mater.unimib.it  Wed Apr 27 14:07:44 2011
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Wed, 27 Apr 2011 14:07:44 +0200 (CEST)
Subject: [Pw_forum] spin polarised STM
In-Reply-To: <1303223486.4dad9cbe33a65@mercury.jncasr.ac.in>
References: <1303223486.4dad9cbe33a65@mercury.jncasr.ac.in>
Message-ID: <alpine.DEB.2.00.1104271357090.3628@localhost.localdomain,>

Dear Madhura,

> 1. While calculating STM image, is sum taken over both the spin
> channels? Because there is no option for spin resolved calculations,
> and in the subroutine I was not able to find where sum is done.?

Yes it is. The sum is taken over all k-points, regardless of the spin this 
kpoint correspond to (as you know, in pwscf spin "up" and spin "down" are 
treated as two sets of kpoints).

> 2. Does anyone have a subroutine to get spin-polarized STM image? If
> yes, can you send it?

You might consider using again pp.x to plot the ILDOS in the corresponding 
energy range, for which you can specify the spin component. Although the 
weight of states contributing to ILDOS and STM is not computed exactly in 
the same way by pp.x, you should expect the results to become equivalent 
as the number of relevant states falling in the energy interval is 
sufficiently large (see, number of kpoints & slab thickness).

> 3. Or if not, can anyone tell which part of code needs to be modified
> to get SP-STM image?

At line 150 of PP/stm.f90, "DO ik = 1, nks". You could restrict this 
summation to states with wanted spin, or accumulate the two sums 
independently. The spin of each kpoint is stored in isk(ik). See its use 
in projwfc.f90 for examples.

HTH

-- 
Guido Fratesi

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

From ttduyle at gmail.com  Wed Apr 27 16:45:16 2011
From: ttduyle at gmail.com (Duy Le)
Date: Wed, 27 Apr 2011 10:45:16 -0400
Subject: [Pw_forum] vdW functional not implemented for spin polarized
	runs
In-Reply-To: <4DB7C5E5.4090903@sissa.it>
References: <BANLkTik77RKMOm-KUviZaki_hpUnP4Brtw@mail.gmail.com>
	<20110426190053.jklki05r4g044wc0@webmail.sissa.it>
	<BANLkTiniCjVY5GFStON8zkAQi6Wk3eyocw@mail.gmail.com>
	<BANLkTine4_GTeSpziWgMUgJHxpn+ZFakcA@mail.gmail.com>
	<4DB7C5E5.4090903@sissa.it>
Message-ID: <BANLkTik8Kv-KeqDxr22yzgEwGi+H6z8_tA@mail.gmail.com>

--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Wed, Apr 27, 2011 at 3:29 AM, Stefano de Gironcoli <degironc at sissa.it> wrote:
> the vdW energy depends on the local polarizability of the electron gas ..
> does it depend on the spin density ? I would say so.

I would depend as we expected, however, from the formalism of vdW-DF,
spin is not taken into account. So, I think in the limit of vdW-DF,
the spin-dependence is ignored.

> Is it taken into account in the current definition of vdw-DF ? I would say
> no...
> how is it implemented in GPAW ? just blindly or with some argument ?

I am not sure. Did not have a chance to look at it and there is no
found document about this.

> stefano
>
> On 04/27/2011 06:35 AM, WANG Wei wrote:
>
> Thank you for your advice, Deu. Yes, the non-local energy is independent the
> spin density.
>
>
> On 27 April 2011 12:34, Duy Le <ttduyle at gmail.com> wrote:
>
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
>
> On Tue, Apr 26, 2011 at 1:00 PM, Stefano de Gironcoli <degironc at sissa.it>
> wrote:
>
> Dear  WANG Wei
>   the vdw-DF functional form is not defined for spin polarized system...
>
> Or it does mean that non-local energy is not spin-dependent but
> charge-density-dependent only.
>
>   if you define, implement and test it, you could even get a nice
> publication out of it. thank you.
>
> The spin-polarized vdW-DF has been implemented in GPAW.
>
> stefano
>
>
>
> _______________________________________________
> 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 kangbugy at lycos.co.kr  Wed Apr 27 16:41:22 2011
From: kangbugy at lycos.co.kr (=?UTF-8?B?a2FuZ2J1Z3lAbHljb3MuY28ua3I=?=)
Date: Wed, 27 Apr 2011 23:41:22 +0900
Subject: [Pw_forum] =?utf-8?q?Drawing_the_DOS?=
Message-ID: <e0d9fbdace8203c8538eda6448b0020f$5c6718fe@pcmail3.nate.com>

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From giovanni.cantele at spin.cnr.it  Wed Apr 27 17:03:16 2011
From: giovanni.cantele at spin.cnr.it (Giovanni Cantele)
Date: Wed, 27 Apr 2011 17:03:16 +0200
Subject: [Pw_forum] Drawing the DOS
In-Reply-To: <e0d9fbdace8203c8538eda6448b0020f$5c6718fe@pcmail3.nate.com>
References: <e0d9fbdace8203c8538eda6448b0020f$5c6718fe@pcmail3.nate.com>
Message-ID: <61B66173-CA88-4168-9937-AE0704A3495E@spin.cnr.it>


On Apr 27, 2011, at 4:41 PM, kangbugy at lycos.co.kr wrote:

> Hi.
>  
> I have a poor probelm.
> I want to draw a density of state.
> How can I draw DOS.
>  
> In advance, thank your for your reply.
> 

Please follow the following links:
http://www.quantum-espresso.org/wiki/index.php/Bugs
http://www.quantum-espresso.org/user_guide/node38.html
http://www.quantum-espresso.org/input-syntax/INPUT_DOS.html

as well as have a look to:
examples/example08
within your Quantum-ESPRESSO directory.

All what you need is already there.

Giovanni




--

**** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it

Giovanni Cantele, PhD
CNR-SPIN and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910 - Fax:   +39 081 676346
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it

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From ismotochi at gmail.com  Wed Apr 27 17:05:02 2011
From: ismotochi at gmail.com (isaac motochi)
Date: Wed, 27 Apr 2011 17:05:02 +0200
Subject: [Pw_forum] Drawing the DOS
In-Reply-To: <e0d9fbdace8203c8538eda6448b0020f$5c6718fe@pcmail3.nate.com>
References: <e0d9fbdace8203c8538eda6448b0020f$5c6718fe@pcmail3.nate.com>
Message-ID: <BANLkTimBcSRjt4L6V4+nuEP45GT7bnzA6A@mail.gmail.com>

>
> If you have your output you can use either Xmgrace or gnuplot
>
>
>
Motochi
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From chenhanghuipwscf at gmail.com  Wed Apr 27 18:45:13 2011
From: chenhanghuipwscf at gmail.com (hanghui chen)
Date: Wed, 27 Apr 2011 12:45:13 -0400
Subject: [Pw_forum] Ultrasoft Pseudopotential of Eu
Message-ID: <BANLkTiniB2gAWaTngh-OP4ALontfGMzWJA@mail.gmail.com>

Dear PWscf community,
     I am wondering if any one has succeeded in generating the ultrasoft
pseudopotential of Eu, using uspp-736. Now in the literature, for most of
the work that involves Eu, the calculation is done with VASP where the
pseudopotential is provided in its own library.
     Thank you very much indeed.

Hanghui Chen
Department of Physics,
Yale University
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From swapnil.chandratre at gmail.com  Wed Apr 27 19:28:09 2011
From: swapnil.chandratre at gmail.com (swapnil chandratre)
Date: Wed, 27 Apr 2011 12:28:09 -0500
Subject: [Pw_forum] Error computing Cholesky
In-Reply-To: <BANLkTik0iCg2UMauw1RaHrUGkJxJ7hu-Hg@mail.gmail.com>
References: <BANLkTin821WPCc5chAmwUJSAnM7OYNwYbg@mail.gmail.com>
	<438D2C9A-1CD3-42ED-A939-E8D0978894BF@democritos.it>
	<BANLkTinmBTSVJkbJ1hVaoutQPvgzcqp1-w@mail.gmail.com>
	<BANLkTik0iCg2UMauw1RaHrUGkJxJ7hu-Hg@mail.gmail.com>
Message-ID: <BANLkTikNf4HmO8N7jvGW-TSLzB10kkDihw@mail.gmail.com>

Hi Shruba,

I think what you are suggesting is very close to my problem, I started using
espresso just a week back so I am not very familiar with it. I am sending
you the input file, Its a porous graphene ribbon, periodic in y and z
direction with some atoms deleted. I think the error may be somewhere in
defining the system, could you help ?

On Tue, Apr 26, 2011 at 7:15 PM, Shruba Gangopadhyay <shruba at gmail.com>wrote:

> Dear Swapnil,
>                     Its always better to send the input file here. Because
> without your input its very difficult for anybody to understand whats going
> wrong. From my experience I can suggest you one thing to check if your
> supercell length along anyone of the axis having much high value (like
> length of x axis/length along z ~20 or more). I suspect it because you have
> a nanoribbon.  In that case you might reduce the ratio and see if you still
> getting the error.
>                    Cheers
>                    Shruba
>
> On Tue, Apr 26, 2011 at 5:28 PM, swapnil chandratre <
> swapnil.chandratre at gmail.com> wrote:
>
>> I couldnt find anything pertaining to error 426.
>>
>>
>> On Mon, Apr 25, 2011 at 2:33 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:
>>
>>>
>>> On Apr 25, 2011, at 2:14 , swapnil chandratre wrote:
>>>
>>> > I get the following error for Graphene Ribbon with porosity, can
>>> > anyone help.
>>> >
>>> >  from  cdiaghg  : error #       426
>>> >       problems computing cholesky
>>>
>>> what about searching the mailing list for "cholesky" ?
>>>
>>> http://www.quantum-espresso.org/user_guide/
>>> node52.html#SECTION000121070000000000000
>>> >
>>>
>>>
>>> P.
>>> ---
>>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>>> Phone +39-0432-558216, fax +39-0432-558222
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>
>>
>>
>>  --
>> Regards,
>> Swapnil Chandratre
>> Graduate Student
>> Dept. of Mechanical Engineering,
>> University of Houston,
>> Houston, TX
>> (M)-713-294-9546
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> Shruba Gangopadhyay
> PhD candidate
> Department of Chemistry, NanoScience Technology Center
> 12424 Research Parkway, Suite 400
> University of Central Florida
> Orlando, FL-32826
> 'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Regards,
Swapnil Chandratre
Graduate Student
Dept. of Mechanical Engineering,
University of Houston,
Houston, TX
(M)-713-294-9546
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From nicola.marzari at materials.ox.ac.uk  Wed Apr 27 19:30:58 2011
From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari)
Date: Wed, 27 Apr 2011 18:30:58 +0100
Subject: [Pw_forum] Ultrasoft Pseudopotential of Eu
In-Reply-To: <BANLkTiniB2gAWaTngh-OP4ALontfGMzWJA@mail.gmail.com>
References: <BANLkTiniB2gAWaTngh-OP4ALontfGMzWJA@mail.gmail.com>
Message-ID: <4DB852D2.4070809@materials.ox.ac.uk>

On 4/27/11 5:45 PM, hanghui chen wrote:
> Dear PWscf community,
>       I am wondering if any one has succeeded in generating the
> ultrasoft pseudopotential of Eu, using uspp-736. Now in the literature,
> for most of the work that involves Eu, the calculation is done with VASP
> where the pseudopotential is provided in its own library.
>       Thank you very much indeed.
>
> Hanghui Chen
> Department of Physics,
> Yale University


Dear Hanghui,

we have a test one normconserving, with f electrons in the valence, and
an ultrasoft one, with f electrons in the core. This is part of a 
project developing and testing lanthanides pseudos, to be released later
on, but if you want to give them a try, I can send them to you (would
be great to have some test feedback).

			nicola


-- 
----------------------------------------------------------------------
Prof Nicola Marzari    Department of Materials    University of Oxford
Chair of Materials Modelling  Director, Materials Modelling Laboratory
nicola.marzari at materials.ox.ac.uk     http://mml.materials.ox.ac.uk/NM

From mehrnooshhazrati at gmail.com  Wed Apr 27 20:32:00 2011
From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati)
Date: Wed, 27 Apr 2011 22:02:00 +0330
Subject: [Pw_forum] dos vs. pdos.tot
In-Reply-To: <BANLkTi=+RtykiY_on629KYRN-MDVwKrJbw@mail.gmail.com>
References: <BANLkTi=+RtykiY_on629KYRN-MDVwKrJbw@mail.gmail.com>
Message-ID: <BANLkTik_NS83=y2E5j1ufOsmqgzJS8qcgg@mail.gmail.com>

Dear Masoud

Thank you very much for your reply.

Mehrnoosh



On Wed, Apr 27, 2011 at 2:50 PM, Masoud Nahali <masoudnahali at gmail.com>wrote:

> *Dear Mehrnoosh
>
> I think that a**tomic states on  different atoms are not orthonormal which makes PDOS-tot different from DOS. I hope it helps.
>
>
> *
>
>  Best Wishes
>
>  Masoud
>
> --------------
> Masoud Nahali, Ph.D Student at Sharif University of Technology
>
>
> *>Mehrnoosh Hazrati* Wrote on W*ed Apr 27 08:35:51 CEST 2011*
>
> >Hi dear QE users,
>
> >I have a question about DOS diagram : what is the difference between DOS
> >gained of the dos.x code and PDOS_tot gained of projwfc.x code output ?!
>
> >Regards
>
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
*

*
*
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
**** Mehrnoosh Kh. Hazrati ****
**** Master Student of Computational Physical Chemistry,KNTU,Tehran ****
 *** Phone : +989123436300 ***
*** Mail : mehrnooshhazrati at gmail.com ***
*
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
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From mehrnooshhazrati at gmail.com  Wed Apr 27 20:40:48 2011
From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati)
Date: Wed, 27 Apr 2011 22:10:48 +0330
Subject: [Pw_forum] Drawing the DOS
In-Reply-To: <e0d9fbdace8203c8538eda6448b0020f$5c6718fe@pcmail3.nate.com>
References: <e0d9fbdace8203c8538eda6448b0020f$5c6718fe@pcmail3.nate.com>
Message-ID: <BANLkTim3986ahVgj8e13Jtuizc0=JHRY6w@mail.gmail.com>

use the output with the suffix '.dos' , then you should draw the column
E(eV) vs. dos(E) with a drawing program as Excel or Matlab or ... !



On Wed, Apr 27, 2011 at 6:11 PM, kangbugy at lycos.co.kr
<kangbugy at lycos.co.kr>wrote:

>  Hi.
>
> I have a poor probelm.
> I want to draw a density of state.
> How can I draw DOS.
>
> In advance, thank your for your reply.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
*

*
*
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
**** Mehrnoosh Kh. Hazrati ****
**** Master Student of Computational Physical Chemistry,KNTU,Tehran ****
 *** Phone : +989123436300 ***
*** Mail : mehrnooshhazrati at gmail.com ***
*
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
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From Trinh.Vo at jpl.nasa.gov  Wed Apr 27 20:48:29 2011
From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Wed, 27 Apr 2011 11:48:29 -0700
Subject: [Pw_forum] Ultrasoft Pseudopotential of Eu
In-Reply-To: <4DB852D2.4070809@materials.ox.ac.uk>
Message-ID: <C9DDB30D.5E6F%Trinh.Vo@jpl.nasa.gov>

Dear Nicola,

I am working on generating pseudo potentials for a few elements of
Lanthanides too, but so far I am not successful yet (it is still bad).  I
appreciate if you could share with me your parameter input.

Thank you very much in advance,

Trinh


On 4/27/11 10:30 AM, "Nicola Marzari" <nicola.marzari at materials.ox.ac.uk>
wrote:

> On 4/27/11 5:45 PM, hanghui chen wrote:
>> Dear PWscf community,
>>       I am wondering if any one has succeeded in generating the
>> ultrasoft pseudopotential of Eu, using uspp-736. Now in the literature,
>> for most of the work that involves Eu, the calculation is done with VASP
>> where the pseudopotential is provided in its own library.
>>       Thank you very much indeed.
>> 
>> Hanghui Chen
>> Department of Physics,
>> Yale University
> 
> 
> Dear Hanghui,
> 
> we have a test one normconserving, with f electrons in the valence, and
> an ultrasoft one, with f electrons in the core. This is part of a
> project developing and testing lanthanides pseudos, to be released later
> on, but if you want to give them a try, I can send them to you (would
> be great to have some test feedback).
> 
> nicola
> 


From padmaja_patnaik at yahoo.co.uk  Thu Apr 28 06:34:15 2011
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Thu, 28 Apr 2011 05:34:15 +0100 (BST)
Subject: [Pw_forum] About band plot
Message-ID: <380461.67515.qm@web28511.mail.ukl.yahoo.com>

Hi All
I had put this query last tuesday but didnt get any response. Thats why asking it again. While plotting band structure, in
the output ps file the code doesn't mention the high symmetry points
Gamma, K, L etc. along the X axis. How to do that? 

Thanks in advance

Padmaja Patnaik

Research Scholar

Dept of Physics

IIT Bombay

Mumbai, India
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From flux_ray12 at 163.com  Thu Apr 28 08:01:39 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Thu, 28 Apr 2011 14:01:39 +0800 (CST)
Subject: [Pw_forum] Drawing the DOS
In-Reply-To: <e0d9fbdace8203c8538eda6448b0020f$5c6718fe@pcmail3.nate.com>
References: <e0d9fbdace8203c8538eda6448b0020f$5c6718fe@pcmail3.nate.com>
Message-ID: <b9ce58e.16996.12f9ab2cbda.Coremail.flux_ray12@163.com>

Please read the example 05 for both DOS and PDOS~

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-04-27 22:41:22?"kangbugy"<kangbugy at lycos.co.kr> wrote:

Hi.
 
I have a poor probelm.
I want to draw a density of state.
How can I draw DOS.
 
In advance, thank your for your reply.
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From flux_ray12 at 163.com  Thu Apr 28 08:06:18 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Thu, 28 Apr 2011 14:06:18 +0800 (CST)
Subject: [Pw_forum] dos vs. pdos.tot
In-Reply-To: <BANLkTimpdf9SA-1oiU_pihNSKZ4v=WaxhA@mail.gmail.com>
References: <BANLkTimpdf9SA-1oiU_pihNSKZ4v=WaxhA@mail.gmail.com>
Message-ID: <235bf526.16ad6.12f9ab70f47.Coremail.flux_ray12@163.com>

DOS gives you the DOS status of total model, but pDOS gives you more detailed info about the DOS on each atom and its orbitals.


At 2011-04-27 14:35:51?"Mehrnoosh Hazrati" <mehrnooshhazrati at gmail.com> wrote:

Hi dear QE users,
 
I have a question about DOS diagram : what is the difference between DOS gained of the dos.x code and PDOS_tot gained of projwfc.x code output ?!
 
Regards

--

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
***Mehrnoosh Kh. Hazrati***
***Master Student of Computational Physical Chemistry,KNTU,Tehran***
 ***Phone : +989123436300***
***Mail :mehrnooshhazrati at gmail.com***
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 
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From flux_ray12 at 163.com  Thu Apr 28 08:08:04 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Thu, 28 Apr 2011 14:08:04 +0800 (CST)
Subject: [Pw_forum] Drawing the DOS
In-Reply-To: <b9ce58e.16996.12f9ab2cbda.Coremail.flux_ray12@163.com>
References: <b9ce58e.16996.12f9ab2cbda.Coremail.flux_ray12@163.com>
	<e0d9fbdace8203c8538eda6448b0020f$5c6718fe@pcmail3.nate.com>
Message-ID: <36629f20.16b50.12f9ab8aa54.Coremail.flux_ray12@163.com>

Sorry, it should be example08, which is about DOS, PDOS and Fermi Surface calculation for Ni.


At 2011-04-28 14:01:39?"GAO Zhe" <flux_ray12 at 163.com> wrote:
Please read the example 05 for both DOS and PDOS~

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-04-27 22:41:22?"kangbugy"<kangbugy at lycos.co.kr> wrote:

Hi.
 
I have a poor probelm.
I want to draw a density of state.
How can I draw DOS.
 
In advance, thank your for your reply.



??????2G????????????????????3?!
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From bipulrr at gmail.com  Thu Apr 28 09:27:11 2011
From: bipulrr at gmail.com (Bipul Rakshit)
Date: Thu, 28 Apr 2011 12:57:11 +0530
Subject: [Pw_forum] LO-TO splitting in dynmat.x
Message-ID: <BANLkTi=tXraf2Ni5LeFbbFQHmYttBsoNgg@mail.gmail.com>

Dear users,
I want to get LO-TO splitting, using dynmat.x. Following is my input file (
dynmat.in).

 &input
    fildyn='ZnO.dyn1',
    asr='crystal',  amass(1)=65.39, amass(2)=15.9994,
     q(1)=0.0, q(2)=0.0, q(3)=0.00,
     filout='dynmat.out',
     filxsf='dynmat.axsf',
 /

After running dynmat.x < dynmat.in
command it gives the output something like that

     Reading Dynamical Matrix from file ZnO.dyn1
     ...Force constants read
     ...epsilon and Z* read
     Acoustic Sum Rule: || Z*(ASR) - Z*(orig)|| =    0.750479E-03
     Acoustic Sum Rule: ||dyn(ASR) - dyn(orig)||=    0.660223E-02
     A direction for q was not specified:TO-LO splitting will be absent

So plz tell me where to specify the direction in dynmat.in file, to get the
LO-TO splitting.
-- 
 Bipul Rakshit
Research Associate,
S N Bose Centre for Basic Sciences,
Salt Lake,
Kolkata 700 098
India
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From lorenzo.paulatto at impmc.upmc.fr  Thu Apr 28 09:33:39 2011
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Thu, 28 Apr 2011 09:33:39 +0200
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <BANLkTi=tXraf2Ni5LeFbbFQHmYttBsoNgg@mail.gmail.com>
References: <BANLkTi=tXraf2Ni5LeFbbFQHmYttBsoNgg@mail.gmail.com>
Message-ID: <op.vum0mdm35jfbqb@paulax>

In data 28 aprile 2011 alle ore 09:27:11, Bipul Rakshit  
<bipulrr at gmail.com> ha scritto:
>  &input
>     fildyn='ZnO.dyn1',
>     asr='crystal',  amass(1)=65.39, amass(2)=15.9994,
>      q(1)=0.0, q(2)=0.0, q(3)=0.00,
>      filout='dynmat.out',
>      filxsf='dynmat.axsf',
>  /
>
> [...]
> So plz tell me where to specify the direction in dynmat.in file, to get  
> the
> LO-TO splitting.


Dear Bipul,
Please note that the q-point (phonon wavevector) at which dynmat is  
working is determined by the fildyn file, not by the q specified in input,  
which you set to (0,0,0). Just set q(1),q(2) and q(3) to any non-zero  
value to have the splitting along the direction of q.

-- 
Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From eyvaz_isaev at yahoo.com  Thu Apr 28 10:04:47 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 28 Apr 2011 01:04:47 -0700 (PDT)
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <BANLkTi=tXraf2Ni5LeFbbFQHmYttBsoNgg@mail.gmail.com>
References: <BANLkTi=tXraf2Ni5LeFbbFQHmYttBsoNgg@mail.gmail.com>
Message-ID: <539141.86586.qm@web65708.mail.ac4.yahoo.com>

Hi, 

You should specify  q-point like 


 q(1)=0.01, q(2)=0.0, q(3)=0.00

but not the Gamma-point.

Bests,
Eyvaz.

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

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

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




________________________________
From: Bipul Rakshit <bipulrr at gmail.com>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Thu, April 28, 2011 11:27:11 AM
Subject: [Pw_forum] LO-TO splitting in dynmat.x

Dear users,
I want to get LO-TO splitting, using dynmat.x. Following is my input file 
(dynmat.in).

 &input
    fildyn='ZnO.dyn1',
    asr='crystal',  amass(1)=65.39, amass(2)=15.9994,
     q(1)=0.0, q(2)=0.0, q(3)=0.00,
     filout='dynmat.out',
     filxsf='dynmat.axsf',
 /

After running dynmat.x < dynmat.in 
command it gives the output something like that

     Reading Dynamical Matrix from file ZnO.dyn1
     ...Force constants read
     ...epsilon and Z* read
     Acoustic Sum Rule: || Z*(ASR) - Z*(orig)|| =    0.750479E-03
     Acoustic Sum Rule: ||dyn(ASR) - dyn(orig)||=    0.660223E-02
     A direction for q was not specified:TO-LO splitting will be absent

So plz tell me where to specify the direction in dynmat.in file, to get the 
LO-TO splitting.
-- 
 Bipul Rakshit
Research Associate,
S N Bose Centre for Basic Sciences,
Salt Lake,
Kolkata 700 098
India
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From mehrnooshhazrati at gmail.com  Thu Apr 28 10:14:28 2011
From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati)
Date: Thu, 28 Apr 2011 11:44:28 +0330
Subject: [Pw_forum] About band plot
In-Reply-To: <380461.67515.qm@web28511.mail.ukl.yahoo.com>
References: <380461.67515.qm@web28511.mail.ukl.yahoo.com>
Message-ID: <BANLkTinz08PCx2q8q3ko-OyTbHEg1WAUyQ@mail.gmail.com>

Actually you yourself give the high symmetry point in the input calculation
= 'bands'  by determining the K-points. Then you can recognize in output .ps
or .pdf which line belongs to which high symmetry point.

I hope that it helps.


On Thu, Apr 28, 2011 at 8:04 AM, Padmaja Patnaik <
padmaja_patnaik at yahoo.co.uk> wrote:

>   Hi All
> I had put this query last tuesday but didnt get any response. Thats why
> asking it again. While plotting band structure, in the output ps file the
> code doesn't mention the high symmetry points Gamma, K, L etc. along the X
> axis. How to do that?
>
> Thanks in advance
>
> 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
>
>


-- 
*

*
*
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
**** Mehrnoosh Kh. Hazrati ****
**** Master Student of Computational Physical Chemistry,KNTU,Tehran ****
 *** Phone : +989123436300 ***
*** Mail : mehrnooshhazrati at gmail.com ***
*
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
*
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From bipulrr at gmail.com  Thu Apr 28 10:17:20 2011
From: bipulrr at gmail.com (Bipul Rakshit)
Date: Thu, 28 Apr 2011 13:47:20 +0530
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <539141.86586.qm@web65708.mail.ac4.yahoo.com>
References: <BANLkTi=tXraf2Ni5LeFbbFQHmYttBsoNgg@mail.gmail.com>
	<539141.86586.qm@web65708.mail.ac4.yahoo.com>
Message-ID: <BANLkTikaHmgWKYM0BSJzWqB+d2rNJn5dEw@mail.gmail.com>

Thanks Eyvaz and Paulatto,
Now it works.


On Thu, Apr 28, 2011 at 1:34 PM, Eyvaz Isaev <eyvaz_isaev at yahoo.com> wrote:

> Hi,
>
> You should specify  q-point like
>
>   q(1)=0.01, q(2)=0.0, q(3)=0.00
>
> but not the Gamma-point.
>
> Bests,
> Eyvaz.
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
> Sweden
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
> Russia,
> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
> ------------------------------
> *From:* Bipul Rakshit <bipulrr at gmail.com>
> *To:* PWSCF Forum <pw_forum at pwscf.org>
> *Sent:* Thu, April 28, 2011 11:27:11 AM
> *Subject:* [Pw_forum] LO-TO splitting in dynmat.x
>
> Dear users,
> I want to get LO-TO splitting, using dynmat.x. Following is my input file (
> dynmat.in).
>
>  &input
>     fildyn='ZnO.dyn1',
>     asr='crystal',  amass(1)=65.39, amass(2)=15.9994,
>      q(1)=0.0, q(2)=0.0, q(3)=0.00,
>      filout='dynmat.out',
>      filxsf='dynmat.axsf',
>  /
>
> After running dynmat.x < dynmat.in
> command it gives the output something like that
>
>      Reading Dynamical Matrix from file ZnO.dyn1
>      ...Force constants read
>      ...epsilon and Z* read
>      Acoustic Sum Rule: || Z*(ASR) - Z*(orig)|| =    0.750479E-03
>      Acoustic Sum Rule: ||dyn(ASR) - dyn(orig)||=    0.660223E-02
>      A direction for q was not specified:TO-LO splitting will be absent
>
> So plz tell me where to specify the direction in dynmat.in file, to get
> the LO-TO splitting.
> --
>  Bipul Rakshit
> Research Associate,
> S N Bose Centre for Basic Sciences,
> Salt Lake,
> Kolkata 700 098
> India
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
 Bipul Rakshit
Research Associate,
S N Bose Centre for Basic Sciences,
Salt Lake,
Kolkata 700 098
India
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From sks.jnc at gmail.com  Thu Apr 28 13:04:28 2011
From: sks.jnc at gmail.com (S. K. S.)
Date: Thu, 28 Apr 2011 13:04:28 +0200
Subject: [Pw_forum] epsilon_0
Message-ID: <BANLkTinebriAnucVfCFxYz_7bpMiH-_iKw@mail.gmail.com>

Dear QE USERS,

What QE calculates is the dielectric tensor at clamped ions
(often referred to as \epsilon_\infty). The ionic contribution
must be calculated and added to this in order to obtain the
static dielectric tensor (\epsilon_0). Does the most recent
version of QE print "\epsilon_0" somewhere in the output file ?


Thanking you and with my best regards,

Saha SK
R&D Assistant
JNCASR, Jakkur,
Bangalore 560064
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From nkxirainbow at gmail.com  Thu Apr 28 16:30:22 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Thu, 28 Apr 2011 22:30:22 +0800
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <BANLkTikaHmgWKYM0BSJzWqB+d2rNJn5dEw@mail.gmail.com>
References: <BANLkTi=tXraf2Ni5LeFbbFQHmYttBsoNgg@mail.gmail.com>
	<539141.86586.qm@web65708.mail.ac4.yahoo.com>
	<BANLkTikaHmgWKYM0BSJzWqB+d2rNJn5dEw@mail.gmail.com>
Message-ID: <BANLkTinyt=HSeNsAs_=Fx2sv19LEYz98fw@mail.gmail.com>

Dear all:
Is there LO-TO splitting far away from Gamma point?
How large is the influence range of LO-TO splitting in Brillouin zone? One
hundred percent?
Thanks in advance;)



-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From giannozz at democritos.it  Thu Apr 28 17:34:06 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 28 Apr 2011 17:34:06 +0200
Subject: [Pw_forum] About band plot
In-Reply-To: <380461.67515.qm@web28511.mail.ukl.yahoo.com>
References: <380461.67515.qm@web28511.mail.ukl.yahoo.com>
Message-ID: <01DFF761-FA18-421E-8307-7BD92EDE48F1@democritos.it>


On Apr 28, 2011, at 6:34 , Padmaja Patnaik wrote:

> the code doesn't mention the high symmetry points
> Gamma, K, L etc. along the X axis. How to do that?

with group theory: see item 12.4.0.3 in
http://www.quantum-espresso.org/user_guide/node61.html

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





From eyvaz_isaev at yahoo.com  Thu Apr 28 18:00:35 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 28 Apr 2011 09:00:35 -0700 (PDT)
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <BANLkTinyt=HSeNsAs_=Fx2sv19LEYz98fw@mail.gmail.com>
References: <BANLkTi=tXraf2Ni5LeFbbFQHmYttBsoNgg@mail.gmail.com>
	<539141.86586.qm@web65708.mail.ac4.yahoo.com>
	<BANLkTikaHmgWKYM0BSJzWqB+d2rNJn5dEw@mail.gmail.com>
	<BANLkTinyt=HSeNsAs_=Fx2sv19LEYz98fw@mail.gmail.com>
Message-ID: <47190.88201.qm@web65714.mail.ac4.yahoo.com>

From: xirainbow <nkxirainbow at gmail.com>


> Is there LO-TO splitting far away from Gamma point?

No.


>How large is the influence range of LO-TO splitting in Brillouin zone? One 
>hundred percent?

It depends on the macroscopic dielectric constant and  Born effective charge, 
see  any good solid state physics textbook 

or review paper Rev.Mod.Phys. 73, 515 (2001). 
It is clear that the effect is more pronounced for (polar) insulators (large 
band gap). 



Bests,
Eyvaz.


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

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

isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
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From swapnil.chandratre at gmail.com  Thu Apr 28 18:08:37 2011
From: swapnil.chandratre at gmail.com (swapnil chandratre)
Date: Thu, 28 Apr 2011 11:08:37 -0500
Subject: [Pw_forum] Error computing Cholesky
In-Reply-To: <BANLkTikNf4HmO8N7jvGW-TSLzB10kkDihw@mail.gmail.com>
References: <BANLkTin821WPCc5chAmwUJSAnM7OYNwYbg@mail.gmail.com>
	<438D2C9A-1CD3-42ED-A939-E8D0978894BF@democritos.it>
	<BANLkTinmBTSVJkbJ1hVaoutQPvgzcqp1-w@mail.gmail.com>
	<BANLkTik0iCg2UMauw1RaHrUGkJxJ7hu-Hg@mail.gmail.com>
	<BANLkTikNf4HmO8N7jvGW-TSLzB10kkDihw@mail.gmail.com>
Message-ID: <BANLkTinocfYb+EB-USXZ5vSoJYhvxU6ddQ@mail.gmail.com>

Hi,

The structure is periodic in only z direction, I made a mistake saying its
periodic in 2 directions.

On Wed, Apr 27, 2011 at 12:28 PM, swapnil chandratre <
swapnil.chandratre at gmail.com> wrote:

> Hi Shruba,
>
> I think what you are suggesting is very close to my problem, I started
> using espresso just a week back so I am not very familiar with it. I am
> sending you the input file, Its a porous graphene ribbon, periodic in y and
> z direction with some atoms deleted. I think the error may be somewhere in
> defining the system, could you help ?
>
>
> On Tue, Apr 26, 2011 at 7:15 PM, Shruba Gangopadhyay <shruba at gmail.com>wrote:
>
>> Dear Swapnil,
>>                     Its always better to send the input file here. Because
>> without your input its very difficult for anybody to understand whats going
>> wrong. From my experience I can suggest you one thing to check if your
>> supercell length along anyone of the axis having much high value (like
>> length of x axis/length along z ~20 or more). I suspect it because you have
>> a nanoribbon.  In that case you might reduce the ratio and see if you still
>> getting the error.
>>                    Cheers
>>                    Shruba
>>
>> On Tue, Apr 26, 2011 at 5:28 PM, swapnil chandratre <
>> swapnil.chandratre at gmail.com> wrote:
>>
>>> I couldnt find anything pertaining to error 426.
>>>
>>>
>>> On Mon, Apr 25, 2011 at 2:33 PM, Paolo Giannozzi <giannozz at democritos.it
>>> > wrote:
>>>
>>>>
>>>> On Apr 25, 2011, at 2:14 , swapnil chandratre wrote:
>>>>
>>>> > I get the following error for Graphene Ribbon with porosity, can
>>>> > anyone help.
>>>> >
>>>> >  from  cdiaghg  : error #       426
>>>> >       problems computing cholesky
>>>>
>>>> what about searching the mailing list for "cholesky" ?
>>>>
>>>> http://www.quantum-espresso.org/user_guide/
>>>> node52.html#SECTION000121070000000000000
>>>> >
>>>>
>>>>
>>>> P.
>>>> ---
>>>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>>>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>>>> Phone +39-0432-558216, fax +39-0432-558222
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Pw_forum mailing list
>>>> Pw_forum at pwscf.org
>>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>>
>>>
>>>
>>>
>>>  --
>>> Regards,
>>> Swapnil Chandratre
>>> Graduate Student
>>> Dept. of Mechanical Engineering,
>>> University of Houston,
>>> Houston, TX
>>> (M)-713-294-9546
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>>
>>
>> --
>> Shruba Gangopadhyay
>> PhD candidate
>> Department of Chemistry, NanoScience Technology Center
>> 12424 Research Parkway, Suite 400
>> University of Central Florida
>> Orlando, FL-32826
>> 'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> Regards,
> Swapnil Chandratre
> Graduate Student
> Dept. of Mechanical Engineering,
> University of Houston,
> Houston, TX
> (M)-713-294-9546
>



-- 
Regards,
Swapnil Chandratre
Graduate Student
Dept. of Mechanical Engineering,
University of Houston,
Houston, TX
(M)-713-294-9546
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From eariel99 at gmail.com  Thu Apr 28 18:33:54 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Thu, 28 Apr 2011 12:33:54 -0400
Subject: [Pw_forum]  About band plot
Message-ID: <BANLkTi=kjz_aXj+soD+SwPZxRpV-x3L-3Q@mail.gmail.com>

Hi Padmaja,

Please, study the example05
example05:
    This example shows how to use pw.x and postprocessing codes to
    make a contour plot in the [110] plane of the charge density for
    Si, and to plot the band structure of Si.


The code is not aware of the name of the symmetry points (as far as I know).
You should. If you are studying a cubic material, you can find the names and
coordinates of the high symmetry points in a solid state physics or
semiconductor textbook or in one of the hundreds of articles on band
calculations.
If your crystal  has a not so usual lattice, you can use the names defined
in the book
The Mathematical Theory of Symmetry in Solids: Representation Theory for
Point Groups and Space Groups
[image: Cubierta
delantera]<http://books.google.com/books?id=lMdNv_wbu2IC&printsec=frontcover&hl=es&source=gbs_ge_summary_r&cad=0>
Christopher Bradley<http://www.google.com/search?hl=es&tbo=p&tbm=bks&q=+inauthor:%22Christopher+Bradley%22>,
Arthur Cracknell<http://www.google.com/search?hl=es&tbo=p&tbm=bks&q=+inauthor:%22Arthur+Cracknell%22>

http://books.google.com/books?id=lMdNv_wbu2IC&printsec=frontcover&dq=bradley+symmetry&source=bl&ots=Nle4sptJFT&sig=68EASNmZCFBcppbWHbe3_1gSq0c&hl=es&ei=X5W5TYDRBIfe0QGLsaTgDw&sa=X&oi=book_result&ct=result&resnum=1&ved=0CBYQ6AEwAA#v=onepage&q&f=false

or define your own names, i.e, A,B,C, ... , specifying the coordinates of
the points.

Personally I do not like the postscript file generated with plot bands. I
generally use the data file, and make my band diagram with gnuplot (a heavy
of work). If you just want to add the letters, you may edit the postcript
file.

pstoedit - f xfig file.ps file.fig

edit it with xfig, and export to EPS.


---------- Mensaje reenviado ----------
From: Padmaja Patnaik <padmaja_patnaik at yahoo.co.uk>
To: pw_forum at pwscf.org
Date: Thu, 28 Apr 2011 05:34:15 +0100 (BST)
Subject: [Pw_forum] About band plot
Hi All
I had put this query last tuesday but didnt get any response. Thats why
asking it again. While plotting band structure, in the output ps file the
code doesn't mention the high symmetry points Gamma, K, L etc. along the X
axis. How to do that?

Thanks in advance

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

-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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From giannozz at democritos.it  Thu Apr 28 18:37:56 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 28 Apr 2011 18:37:56 +0200
Subject: [Pw_forum] epsilon_0
In-Reply-To: <BANLkTinebriAnucVfCFxYz_7bpMiH-_iKw@mail.gmail.com>
References: <BANLkTinebriAnucVfCFxYz_7bpMiH-_iKw@mail.gmail.com>
Message-ID: <66EC9F68-7680-4211-ABED-481F27046DCE@democritos.it>


On Apr 28, 2011, at 13:04 , S. K. S. wrote:

> What QE calculates is the dielectric tensor at clamped ions
> (often referred to as \epsilon_\infty). The ionic contribution
> must be calculated and added to this in order to obtain the
> static dielectric tensor (\epsilon_0). Does the most recent
> version of QE print "\epsilon_0" somewhere in the output file ?

not that I know. Writing a piece of code that does the calculation
could be a good exercise for a student. Also for a professor.

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





From zafartariq2003 at yahoo.com  Thu Apr 28 18:45:23 2011
From: zafartariq2003 at yahoo.com (zafar rasheed)
Date: Thu, 28 Apr 2011 09:45:23 -0700 (PDT)
Subject: [Pw_forum] Problems about QHA
Message-ID: <281720.98983.qm@web65410.mail.ac4.yahoo.com>











Dear Eyvaz Isaev
?
We have just started use Quantum Espresso (since one years ago) . We want to calculat thermal properties (coefficient of thermal expansion, Cp, Cv etc.). But we can not create *.x? files of QHA folder. We are using Fedora core 7 (on Simple P4 computer having 2GHz processor , 256 RAM) having gfortran compiler. We change FC in Makefile ( ifort to gfortran) but *.x? files does not work. Please help us in this aspect.?
?
Best Regards
?
Zafar Rasheed
?
PhD Student
Department of Physics
?
The Islamia University of Bahawalpur, Pakistan
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From eyvaz_isaev at yahoo.com  Thu Apr 28 19:25:25 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 28 Apr 2011 10:25:25 -0700 (PDT)
Subject: [Pw_forum] Problems about QHA
In-Reply-To: <281720.98983.qm@web65410.mail.ac4.yahoo.com>
References: <281720.98983.qm@web65410.mail.ac4.yahoo.com>
Message-ID: <483636.30130.qm@web65713.mail.ac4.yahoo.com>

Dear Zafar,

OK, I will contact you as soon as possible.

Best regards,
Eyvaz.

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

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

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




________________________________
From: zafar rasheed <zafartariq2003 at yahoo.com>
To: pw_forum at pwscf.org
Cc: pw_forum-request at pwscf.org
Sent: Thu, April 28, 2011 8:45:23 PM
Subject: [Pw_forum] Problems about QHA






>Dear Eyvaz Isaev
> 
>We have just started use Quantum Espresso (since one years ago) . We want to 
>calculat thermal properties (coefficient of thermal expansion, Cp, Cv etc.). But 
>we can not create *.x  files of QHA folder. We are using Fedora core 7 (on 
>Simple P4 computer having 2GHz processor , 256 RAM) having gfortran compiler. We 
>change FC in Makefile ( ifort to gfortran) but*.x  files does not work. Please 
>help us in this aspect. 
> 
>Best Regards
> 
>Zafar Rasheed
> 
>PhD Student
>Department of Physics
> 
>The Islamia University of Bahawalpur, Pakistan  
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From Michael.Mehl at nrl.navy.mil  Thu Apr 28 19:32:31 2011
From: Michael.Mehl at nrl.navy.mil (Mike Mehl)
Date: Thu, 28 Apr 2011 13:32:31 -0400
Subject: [Pw_forum] About band plot
In-Reply-To: <BANLkTi=kjz_aXj+soD+SwPZxRpV-x3L-3Q@mail.gmail.com>
References: <BANLkTi=kjz_aXj+soD+SwPZxRpV-x3L-3Q@mail.gmail.com>
Message-ID: <4DB9A4AF.7080601@nrl.navy.mil>

If you know the space group of your system (for the diamond structure 
it's 227), you can find all the high symmetry points at

http://www.cryst.ehu.es/cryst/get_kvec.html

along with a labeled picture of the first Brillouin zone.

On 04/28/2011 12:33 PM, Eduardo Ariel Menendez Proupin wrote:
> Hi Padmaja,
>
> Please, study the example05
> example05:
>      This example shows how to use pw.x and postprocessing codes to
>      make a contour plot in the [110] plane of the charge density for
>      Si, and to plot the band structure of Si.
>
>
> The code is not aware of the name of the symmetry points (as far as I
> know). You should. If you are studying a cubic material, you can find
> the names and coordinates of the high symmetry points in a solid state
> physics or semiconductor textbook or in one of the hundreds of articles
> on band calculations.
> If your crystal  has a not so usual lattice, you can use the names
> defined in the book
>
>
>   The Mathematical Theory of Symmetry in Solids:
>

-- 
Michael J. Mehl
Head, Center for Computational Materials Science
Naval Research Laboratory Code 6390
Washington DC

From trambui at u.boisestate.edu  Thu Apr 28 21:01:18 2011
From: trambui at u.boisestate.edu (Tram Bui)
Date: Thu, 28 Apr 2011 13:01:18 -0600
Subject: [Pw_forum] cesium PP generation regarding semicore state
Message-ID: <BANLkTikb=JEfQmvp9wmE2bFc_CQXeWJ6vA@mail.gmail.com>

Hi Everyone,
     The Cs has electron configuartion of [Xe] 6s1. So would you give me
some information on how to determine if the semicore state need to be
included in the valence?

Regard,

Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From padmaja_patnaik at yahoo.co.uk  Thu Apr 28 22:23:06 2011
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Thu, 28 Apr 2011 21:23:06 +0100 (BST)
Subject: [Pw_forum] Supercell totlal energy
Message-ID: <243686.75678.qm@web28509.mail.ukl.yahoo.com>

Dear All

My calculation involves a zinc blend structure . To generate a supercell I have expanded the lattice constant 'a' twice in all direction. This I have done using Exciting code (also known as Elk code). Which gives the primitive cell involving 54 atoms out of this expanded cell. The scf calculation in Quantum Espresso gives the total energy for this cell. If I want total energy/unit cell then dividing the value with 8 (since supercell has 8 unit cells) will give the correct total energy per unit cell. Am I right?

Thanking you in advance,
Regards
Padmaja Patnaik

Research Scholar

Dept of Physics

IIT Bombay

Mumbai, India
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From wumindt2 at zju.edu.cn  Fri Apr 29 01:42:51 2011
From: wumindt2 at zju.edu.cn (wumindt2)
Date: Fri, 29 Apr 2011 07:42:51 +0800
Subject: [Pw_forum] dos calculation
Message-ID: <TNSIIXYFYRPIXKCZPOUXMDBPQPOA.wumindt2@zju.edu.cn>

Dear All,

I meet a problem with the Dos calculation using projwfc.x.
Due to the limit of the disk quota, i need to store the wf files to other directory.
So i set the 'outdir' and 'wfcdir' with two different directories.
In the discription of projwfc.x, it said that wavefunciton files are needed to calculate the DOS.
Since i didn't collect the wavefunctions, the wavefunction files and the *.save file are in two different
directory.
To do the dos calculation, i set the 'outdir' as the directory of wavefunctions. But then i got an error saying 
that the *.save file was not found.
Does it mean that the 'outdir' and 'wfcdir' should have the same directories? Or otherwise i need to collect
the wavefunctions to the *.save file ?

Looking forward to your reply. Thanks so much!

Min Wu
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From flux_ray12 at 163.com  Fri Apr 29 01:49:58 2011
From: flux_ray12 at 163.com (GAO Zhe)
Date: Fri, 29 Apr 2011 07:49:58 +0800 (CST)
Subject: [Pw_forum] Problems about QHA
In-Reply-To: <281720.98983.qm@web65410.mail.ac4.yahoo.com>
References: <281720.98983.qm@web65410.mail.ac4.yahoo.com>
Message-ID: <239af5e4.789.12f9e84def6.Coremail.flux_ray12@163.com>

There is two problems as I known.
First, gfortran cannot deal with the non-integer temperature step, so you would receive some warnings.
Second, try to ignore the compiling option '-static' in makefile, since both of ifort 2011 and gfortran is not seemed to support '-static' parameter.


At 2011-04-29 00:45:23?"zafar rasheed" <zafartariq2003 at yahoo.com> wrote:





Dear Eyvaz Isaev
 
We have just started use Quantum Espresso (since one years ago) . We want to calculat thermal properties (coefficient of thermal expansion, Cp, Cv etc.). But we can not create*.x  files of QHA folder. We are using Fedora core 7 (on Simple P4 computer having 2GHz processor , 256 RAM) having gfortran compiler. We change FC in Makefile ( ifort to gfortran) but*.x  files does not work. Please help us in this aspect. 
 
Best Regards
 
Zafar Rasheed
 
PhD Student
Department of Physics
 
The Islamia University of Bahawalpur, Pakistan
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From lfhuang at theory.issp.ac.cn  Fri Apr 29 02:31:01 2011
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Fri, 29 Apr 2011 8:31:01 +0800
Subject: [Pw_forum] =?utf-8?q?LO-TO_splitting_in_dynmat=2Ex?=
Message-ID: <20110429003101.14706.qmail@ms.hfcas.ac.cn>

Dear Wang, H.:
     LO-TO splitting always exists in Brillouin zone, but two points are worth noting:
(1) it is caused by short-range interactions, which are calculated directly from DFPT. The splitting at Gamma point is due to long-range dipolar interaction, which needs postprocessing with Born charge;
(2) only cubic crystals has LO and TO braches.

Best Wishes!
Yours Sincerely
L. F. Huang

> From: xirainbow 
> Subject: Re: [Pw_forum] LO-TO splitting in dynmat.x
> To: PWSCF Forum 
> Message-ID: 
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear all:
> Is there LO-TO splitting far away from Gamma point?
> How large is the influence range of LO-TO splitting in Brillouin zone? One
> hundred percent?
> Thanks in advance;)
> 
> -- 
> ____________________________________
> Hui Wang
> School of physics, Fudan University, Shanghai, China



------
======================================================================
L.F.Huang(???) DFT and phonon physics
======================================================================
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: 86-551-5591464-326(office)
Fax: 86-551-5591434
Our group: http://theory.issp.ac.cn
======================================================================


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From nkxirainbow at gmail.com  Fri Apr 29 05:00:47 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Fri, 29 Apr 2011 11:00:47 +0800
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <20110429003101.14706.qmail@ms.hfcas.ac.cn>
References: <20110429003101.14706.qmail@ms.hfcas.ac.cn>
Message-ID: <BANLkTinaoaRO0-rLdU3UGu=dYYaBMXgk1A@mail.gmail.com>

Dear Huang:
Thanks very much for your help:)

 LO-TO splitting always exists in Brillouin zone, but two points are worth
> noting:
>
I do not think so. I do not find any LO-TO splitting at the X and R point of
Brillouin zone of cubic.
Because I use finite difference method, I do not know LO-TO splitting
persists at other part.


> (2) only cubic crystals has LO and TO braches.
>
The LO-TO splitting exists also in uniaxial crystal(direction dispersion in
Raman).
-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From nkxirainbow at gmail.com  Fri Apr 29 05:05:15 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Fri, 29 Apr 2011 11:05:15 +0800
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <47190.88201.qm@web65714.mail.ac4.yahoo.com>
References: <BANLkTi=tXraf2Ni5LeFbbFQHmYttBsoNgg@mail.gmail.com>
	<539141.86586.qm@web65708.mail.ac4.yahoo.com>
	<BANLkTikaHmgWKYM0BSJzWqB+d2rNJn5dEw@mail.gmail.com>
	<BANLkTinyt=HSeNsAs_=Fx2sv19LEYz98fw@mail.gmail.com>
	<47190.88201.qm@web65714.mail.ac4.yahoo.com>
Message-ID: <BANLkTimgkd0gXKy9g+P4MXG-tveoOGAP_A@mail.gmail.com>

Dear Eyvaz:
Thank you very much;)

> Is there LO-TO splitting far away from Gamma point?
> No.
>

Does LO-TO splitting must disappear at the boundary of Brillouin zone?

-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From tanycimr at gmail.com  Fri Apr 29 05:28:43 2011
From: tanycimr at gmail.com (tanycimr at gmail.com)
Date: Fri, 29 Apr 2011 11:28:43 +0800
Subject: [Pw_forum] phonon dispersion
References: <BANLkTikOdseAksS5PxXMcNzEiVwuaUwoUQ@mail.gmail.com>
	<4DB77165.4010904@materials.ox.ac.uk>
Message-ID: <4DBA306B.000001.02428@LBDZ-12271421>

 
Dear Nicola

Thanks , I have find the answer . I need ph.x & q2r.x & matdyn,x to get what
I want .

tanyci
 
 
 
-------Original Message-------
 
From: Nicola Marzari
Date: 2011-4-27 9:29:31
To: PWSCF Forum
Subject: Re: [Pw_forum] phonon dispersion
 
On 4/27/11 2:21 AM, ??? wrote:
> Dear all
> I want to calculate the phonon dispersion of B12 at the first Brillouin
> Zone . i don't know which program should I use ? Please give me some
> advice . And if it's possible ,please give me a example ?
>
> thanks in advance .
> Tanyci
> Nankai university , tianjin
> china
 
Der Tanyci,
 
all the answers to your questions are on the website, including
e.g. extensive video lectures and tutorials: www.quantum-espresso.org
 
    nicola
 
--
----------------------------------------------------------------------
Prof Nicola Marzari    Department of Materials    University of Oxford
Chair of Materials Modelling  Director, Materials Modelling Laboratory
nicola.marzari at materials.ox.ac.uk     http://mml.materials.ox.ac.uk/NM
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
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From lfhuang at theory.issp.ac.cn  Fri Apr 29 05:50:35 2011
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Fri, 29 Apr 2011 11:50:35 +0800
Subject: [Pw_forum] =?utf-8?q?LO-TO_splitting_in_dynmat=2Ex?=
Message-ID: <20110429035035.2859.qmail@ms.hfcas.ac.cn>

Dear Wang:
     
>  LO-TO splitting always exists in Brillouin zone, but two points are worth
> > noting:
> >
> I do not think so. I do not find any LO-TO splitting at the X and R point of
> Brillouin zone of cubic.

This could depend on the definition of "LO-TO splitting", which I meant "the reduction of the LO-TO degeneracy".
If it is defined to be the splitting due to the long-range electric force on LO,  it will disappear in BZ zone.   

Best Wishes!
Yours Sincerely
L. F. Huang
------
======================================================================
L.F.Huang(???) DFT and phonon physics
======================================================================
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: 86-551-5591464-326(office)
Fax: 86-551-5591434
Our group: http://theory.issp.ac.cn
======================================================================


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From nkxirainbow at gmail.com  Fri Apr 29 05:54:31 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Fri, 29 Apr 2011 11:54:31 +0800
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <20110429035035.2859.qmail@ms.hfcas.ac.cn>
References: <20110429035035.2859.qmail@ms.hfcas.ac.cn>
Message-ID: <BANLkTimkFU+SJjd=S+wRxDUdw2uUKtTkpw@mail.gmail.com>

Dear Huang:
I think you are right;)
Thanks a lot :P



On Fri, Apr 29, 2011 at 11:50 AM, lfhuang <lfhuang at theory.issp.ac.cn> wrote:

>  Dear Wang:
>
> > LO-TO splitting always exists in Brillouin zone, but two points are worth
>
> > > noting:
> > >
> > I do not think so. I do not find any LO-TO splitting at the X and R point
> of
> > Brillouin zone of cubic.
>
> This could depend on the definition of "LO-TO splitting", which I meant
> "the reduction of the LO-TO degeneracy".
> If it is defined to be the splitting due to the long-range electric force
> on LO, it will disappear in BZ zone.
>
> Best Wishes!
> Yours Sincerely
> L. F. Huang
> ------
> ======================================================================
> L.F.Huang(???) DFT and phonon physics
> ======================================================================
> 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: 86-551-5591464-326(office)
> Fax: 86-551-5591434
> Our group: http://theory.issp.ac.cn
> ======================================================================
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From nkxirainbow at gmail.com  Fri Apr 29 06:53:51 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Fri, 29 Apr 2011 12:53:51 +0800
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <20110429035035.2859.qmail@ms.hfcas.ac.cn>
References: <20110429035035.2859.qmail@ms.hfcas.ac.cn>
Message-ID: <BANLkTikwMpiwAt6DWz6HJ+jaFZAeUe4_pQ@mail.gmail.com>

Dear Huang:

This could depend on the definition of "LO-TO splitting", which I meant "the
> reduction of the LO-TO degeneracy".
>

I still have another question  ??
 Suppose a uniaxial crystal(no cubic): c>a=b. Suppose there is a
double-degenerate polar E_u mode, in which all atoms move in the a-b plane.
If the wavevector around Gamma point is in the a-b plane, the degenerate E
mode will split into LO and TO mode.
Am I right?

-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From 1009ukumar at gmail.com  Fri Apr 29 07:18:07 2011
From: 1009ukumar at gmail.com (sonu kumar)
Date: Fri, 29 Apr 2011 10:48:07 +0530
Subject: [Pw_forum] Pw_forum Digest, Vol 46, Issue 89
In-Reply-To: <mailman.11782.1304037484.1814.pw_forum@pwscf.org>
References: <mailman.11782.1304037484.1814.pw_forum@pwscf.org>
Message-ID: <BANLkTimM6iLj7AsHKvfMBCsSN+hhLAApyQ@mail.gmail.com>

Dear All QE users,

> (2) only cubic crystals has LO and TO braches.
>

crystals ( having considerable values of macroscopic dielectric constant [ i
suppose
epsilon infinity] and born effective charges, as pointed  out by Prof. Eyvaz
Isaev) with low symmetry can, also, have LO-TO splitting. But this can be
 different in different symmetry directions, so one has to search all
symmetry directions for this splitting.

For cubic crystals splitting is equal in all directions.

with regards,
-- 
Sonu Kumar

Phd Student
Physics Department
Indian Institute of Technology
Delhi-110016, India
web:-http://www.iitd.ac.in/
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From 1009ukumar at gmail.com  Fri Apr 29 07:21:44 2011
From: 1009ukumar at gmail.com (sonu kumar)
Date: Fri, 29 Apr 2011 10:51:44 +0530
Subject: [Pw_forum] LO-TO splitting in dynmat.x
Message-ID: <BANLkTinQ1ToXegqM-Od0mQGz64U0mG5aow@mail.gmail.com>

Dear All QE users,

i am sorry again, as i havn't corrected the subject title.

(2) only cubic crystals has LO and TO braches.
>

crystals ( having considerable values of macroscopic dielectric constant [ i
suppose
epsilon infinity] and born effective charges, as pointed  out by Prof. Eyvaz
Isaev) with low symmetry can, also, have LO-TO splitting. But this can be
 different in different symmetry directions, so one has to search all
symmetry directions for this splitting.

For cubic crystals splitting is equal in all directions.

with regards,

-- 
Sonu Kumar

Phd Student
Physics Department
Indian Institute of Technology
Delhi-110016, India
web:-http://www.iitd.ac.in/
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From nkxirainbow at gmail.com  Fri Apr 29 07:30:31 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Fri, 29 Apr 2011 13:30:31 +0800
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <BANLkTinQ1ToXegqM-Od0mQGz64U0mG5aow@mail.gmail.com>
References: <BANLkTinQ1ToXegqM-Od0mQGz64U0mG5aow@mail.gmail.com>
Message-ID: <BANLkTikNhSKOC=A-ETjHu7FUbbt=OH5QNQ@mail.gmail.com>

Dear Sonu Kumar
What you said is reasonable;)

I have two little questions.
One:
Does LO-TO splitting must disappear at the boundary of Brillouin zone?

Two:
I can understand the LO-TO splitting near Gamma point.
However, at Gamma point(not  near Gamma point), q=0. When q is zero, there
is no longitude and transverse mode. Why are there LO-TO splitting at Gamma
point?

Thanks:)



On Fri, Apr 29, 2011 at 1:21 PM, sonu kumar <1009ukumar at gmail.com> wrote:

> Dear All QE users,
>
> i am sorry again, as i havn't corrected the subject title.
>
>
> (2) only cubic crystals has LO and TO braches.
>>
>
> crystals ( having considerable values of macroscopic dielectric constant [
> i suppose
> epsilon infinity] and born effective charges, as pointed  out by Prof.
> Eyvaz Isaev) with low symmetry can, also, have LO-TO splitting. But this can
> be  different in different symmetry directions, so one has to search all
> symmetry directions for this splitting.
>
> For cubic crystals splitting is equal in all directions.
>
> with regards,
>
> --
> Sonu Kumar
>
> Phd Student
> Physics Department
> Indian Institute of Technology
> Delhi-110016, India
> web:-http://www.iitd.ac.in/
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From degironc at sissa.it  Fri Apr 29 08:58:36 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 29 Apr 2011 08:58:36 +0200
Subject: [Pw_forum] Supercell totlal energy
In-Reply-To: <243686.75678.qm@web28509.mail.ukl.yahoo.com>
References: <243686.75678.qm@web28509.mail.ukl.yahoo.com>
Message-ID: <4DBA619C.1050005@sissa.it>

Dear Padmaja Patnaik
  if your cell contains 54 [=2*(3^3)] atoms it is likely a cell with an 
"a" constant three times the original one.
   then you should divide by 27 and if you want good matching with the 
original calculation your k-point grid should also be reduced by a 
factor of three.

stefano

On 04/28/2011 10:23 PM, Padmaja Patnaik wrote:
> Dear All
>
> My calculation involves a zinc blend structure . To generate a supercell I have expanded the lattice constant 'a' twice in all direction. This I have done using Exciting code (also known as Elk code). Which gives the primitive cell involving 54 atoms out of this expanded cell. The scf calculation in Quantum Espresso gives the total energy for this cell. If I want total energy/unit cell then dividing the value with 8 (since supercell has 8 unit cells) will give the correct total energy per unit cell. Am I right?
>
> Thanking you in advance,
> Regards
> Padmaja Patnaik
>
> Research Scholar
>
> Dept of Physics
>
> IIT Bombay
>
> Mumbai, India
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From degironc at sissa.it  Fri Apr 29 09:16:13 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 29 Apr 2011 09:16:13 +0200
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <BANLkTimgkd0gXKy9g+P4MXG-tveoOGAP_A@mail.gmail.com>
References: <BANLkTi=tXraf2Ni5LeFbbFQHmYttBsoNgg@mail.gmail.com>	<539141.86586.qm@web65708.mail.ac4.yahoo.com>	<BANLkTikaHmgWKYM0BSJzWqB+d2rNJn5dEw@mail.gmail.com>	<BANLkTinyt=HSeNsAs_=Fx2sv19LEYz98fw@mail.gmail.com>	<47190.88201.qm@web65714.mail.ac4.yahoo.com>
	<BANLkTimgkd0gXKy9g+P4MXG-tveoOGAP_A@mail.gmail.com>
Message-ID: <4DBA65BD.5020709@sissa.it>

the electristatic interaction at the origin of LO-TO splitting is always 
present...

for any q<>0 (even very small) it is included in the calculation.

in the limit of q->0 in non-metallic systems it gives origin to a non 
analytic behavior that must be calculate separately.

If you want to Fourier interpolate the phonon dispersions calculated on 
a regular grid of q-points
you are in trouble because non analyticity of the phonon dispersion 
implyes long-range (1/R^3) interatomic force constants and so you need to

1) evaluate Z* and epsilon_infty in the limit of q->0 that determine the 
non-analyticity
2) remove from dynamical matrix in every q point in you grid an 
electrostatic model that gives the correct non-analyticity for q->0 and 
is smooth elsewhere
3) Fourier interpolate  the modified (hopefully short-range) dynamical 
matrices
4) add back the model in any q-point you want to study.

This is what the sequence ph.x -> q2r.x -> matdyn.x does (in example06 
for instance)

thete is some discussion of these issues in Review of Modern Physics 73, 
515 (2001) and in Phys Rev 43, 7231 (1991)

stefano

On 04/29/2011 05:05 AM, xirainbow wrote:
> Dear Eyvaz:
> Thank you very much;)
>
>> Is there LO-TO splitting far away from Gamma point?
>> No.
>>
> Does LO-TO splitting must disappear at the boundary of Brillouin zone?
>
>
>
> _______________________________________________
> 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  Fri Apr 29 09:28:05 2011
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 29 Apr 2011 09:28:05 +0200
Subject: [Pw_forum] dos calculation
In-Reply-To: <TNSIIXYFYRPIXKCZPOUXMDBPQPOA.wumindt2@zju.edu.cn>
References: <TNSIIXYFYRPIXKCZPOUXMDBPQPOA.wumindt2@zju.edu.cn>
Message-ID: <2A55CFF7-6EF6-427A-AAA3-32BA02727A8F@democritos.it>

On Apr 29, 2011, at 1:42 , wumindt2 wrote:

> Since i didn't collect the wavefunctions, the wavefunction files
> and the *.save file are in two different directory.
> To do the dos calculation, i set the 'outdir' as the directory of
> wavefunctions. But then i got an error saying  that the *.save
> file was not found.

if you have problems with the disk quota on the other directory,
just move the *.save directory into "outdir"

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





From eyvaz_isaev at yahoo.com  Fri Apr 29 09:41:54 2011
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 29 Apr 2011 00:41:54 -0700 (PDT)
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <BANLkTikNhSKOC=A-ETjHu7FUbbt=OH5QNQ@mail.gmail.com>
References: <BANLkTinQ1ToXegqM-Od0mQGz64U0mG5aow@mail.gmail.com>
	<BANLkTikNhSKOC=A-ETjHu7FUbbt=OH5QNQ@mail.gmail.com>
Message-ID: <843971.37633.qm@web65712.mail.ac4.yahoo.com>

Dear Wang,

Let me reiterate: LO-TO splitting takes place ONLY at the Gamma point.  Why? 
It is the physics. Please read at least the review paper I mentioned in my 
previous mail.
Or take a good textbook.


>For cubic crystals splitting is equal in all directions.
So, for non-cubic LO-TO splitting  also occurs and the splitting is different 
for different directions. That is 

why one can see a discontinuity near the Gamma point in phonon dispersion 
relations.  


>When q is zero, there is no longitude and transverse mode. 
Really? How about optical modes? Did you pay attention to "O"?  

Bests,
Eyvaz.

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

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

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




________________________________
From: xirainbow <nkxirainbow at gmail.com>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Fri, April 29, 2011 9:30:31 AM
Subject: Re: [Pw_forum] LO-TO splitting in dynmat.x


Dear Sonu Kumar
What you said is reasonable;)

I have two little questions.
One:
Does LO-TO splitting must disappear at the boundary of Brillouin zone?

Two:
I can understand the LO-TO splitting near Gamma point.
However, at Gamma point(not  near Gamma point), q=0. When q is zero, there is no 
longitude and transverse mode. Why are there LO-TO splitting at Gamma point?

Thanks:)



On Fri, Apr 29, 2011 at 1:21 PM, sonu kumar <1009ukumar at gmail.com> wrote:

Dear All QE users,
>
>i am sorry again, as i havn't corrected the subject title.
>
>
>
>(2) only cubic crystals has LO and TO braches.
>>
 
>crystals ( having considerable values of macroscopic dielectric constant [ i 
>suppose
>epsilon infinity] and born effective charges, as pointed  out by Prof. Eyvaz 
>Isaev) with low symmetry can, also, have LO-TO splitting. But this can be 
> different in different symmetry directions, so one has to search all symmetry 
>directions for this splitting.
>
>For cubic crystals splitting is equal in all directions.
>
>with regards,
>
>-- 
>Sonu Kumar
>
>Phd Student
>Physics Department
>Indian Institute of Technology 
>Delhi-110016, India
>web:-http://www.iitd.ac.in/
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From degironc at sissa.it  Fri Apr 29 09:49:42 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 29 Apr 2011 09:49:42 +0200
Subject: [Pw_forum] vdW functional not implemented for spin polarized
 runs
In-Reply-To: <BANLkTik8Kv-KeqDxr22yzgEwGi+H6z8_tA@mail.gmail.com>
References: <BANLkTik77RKMOm-KUviZaki_hpUnP4Brtw@mail.gmail.com>	<20110426190053.jklki05r4g044wc0@webmail.sissa.it>	<BANLkTiniCjVY5GFStON8zkAQi6Wk3eyocw@mail.gmail.com>	<BANLkTine4_GTeSpziWgMUgJHxpn+ZFakcA@mail.gmail.com>	<4DB7C5E5.4090903@sissa.it>
	<BANLkTik8Kv-KeqDxr22yzgEwGi+H6z8_tA@mail.gmail.com>
Message-ID: <4DBA6D96.80208@sissa.it>

Dear all,

     I inquired Timo Thonhauser (now Wake Forest  University), the main 
character behind the vdW-DF functional implementation in Quantum 
ESPRESSO,  about the issue of the spin-polarized version of vdW-DF.

I'm reporting his opinion below:

"In general, at the moment there exists NO true extension of vdW-DF for 
spin-polarized cases. Several groups have expressed interest in working 
on it, but nothing has been published yet. Note that just evaluating 
vdW-DF for the two spin densities separately, while simple to implement, 
is an approximation which is difficult to justify: there is no 
quantitative measure of the error being made, other than hand waving 
arguments that it has to be small. Also, we did not implement that 
simple fix, because we were afraid that people would use it as a 
black-box for spin-polarized calculations, not knowing that there is no 
spin-polarized vdW-DF"

hope this helps to clarify the situation.

stefano



On 04/27/2011 04:45 PM, Duy Le wrote:
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
>
> On Wed, Apr 27, 2011 at 3:29 AM, Stefano de Gironcoli<degironc at sissa.it>  wrote:
>> the vdW energy depends on the local polarizability of the electron gas ..
>> does it depend on the spin density ? I would say so.
> I would depend as we expected, however, from the formalism of vdW-DF,
> spin is not taken into account. So, I think in the limit of vdW-DF,
> the spin-dependence is ignored.
>
>> Is it taken into account in the current definition of vdw-DF ? I would say
>> no...
>> how is it implemented in GPAW ? just blindly or with some argument ?
> I am not sure. Did not have a chance to look at it and there is no
> found document about this.
>
>> stefano
>>
>> On 04/27/2011 06:35 AM, WANG Wei wrote:
>>
>> Thank you for your advice, Deu. Yes, the non-local energy is independent the
>> spin density.
>>
>>
>> On 27 April 2011 12:34, Duy Le<ttduyle at gmail.com>  wrote:
>>
>> --------------------------------------------------
>> Duy Le
>> PhD Student
>> Department of Physics
>> University of Central Florida.
>>
>> "Men don't need hand to do things"
>>
>>
>>
>> On Tue, Apr 26, 2011 at 1:00 PM, Stefano de Gironcoli<degironc at sissa.it>
>> wrote:
>>
>> Dear  WANG Wei
>>    the vdw-DF functional form is not defined for spin polarized system...
>>
>> Or it does mean that non-local energy is not spin-dependent but
>> charge-density-dependent only.
>>
>>    if you define, implement and test it, you could even get a nice
>> publication out of it. thank you.
>>
>> The spin-polarized vdW-DF has been implemented in GPAW.
>>
>> stefano
>>
>>
>>
>> _______________________________________________
>> 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 lfhuang at theory.issp.ac.cn  Fri Apr 29 11:20:07 2011
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Fri, 29 Apr 2011 17:20:07 +0800
Subject: [Pw_forum] =?utf-8?q?LO-TO_splitting_in_dynmat=2Ex?=
Message-ID: <20110429092007.5946.qmail@ms.hfcas.ac.cn>


Dear Wang, H:
>  Suppose a uniaxial crystal(no cubic): c>a=b. Suppose there is a
> double-degenerate polar E_u mode, in which all atoms move in the a-b plane.
> If the wavevector around Gamma point is in the a-b plane, the degenerate E
> mode will split into LO and TO mode.
> Am I right?
It is probable for some ionic crystals, but still depends.
Maybe the Equ. 98 (nonanalytic part of the dynamical matrix) in Rev. Mod. Phys. 73, 515 (2001) by prof. S. Baroni etc. and the related parts in the book "Dynamical Theory of Crystal Lattices" by M. Born & K. Huang can give you much information if these things are important/interesting to you.
In addition, is the method "finite difference" you mentioned exactly the "frozen phonon" or "small displacement" method? If so, the treatment like that in PWSCF should be good to obtain a satisfied LO/TO splitting, although honestly I haven't done this in the "frozen phonon" method. Some people propose other methods, like using a prolonged supercell, which I think, could not fully describe the long-range dipolar interaction, because of its long-range character (as prof. Stefano de Gironcoli said ~1/R^3).  
Best Wishes!
Yours Sincerely
L. F. Huang
------
======================================================================
L.F.Huang(???) DFT and phonon physics
======================================================================
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: 86-551-5591464-326(office)
Fax: 86-551-5591434
Our group: http://theory.issp.ac.cn
======================================================================


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From nkxirainbow at gmail.com  Fri Apr 29 12:17:56 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Fri, 29 Apr 2011 18:17:56 +0800
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <4DBA65BD.5020709@sissa.it>
References: <BANLkTi=tXraf2Ni5LeFbbFQHmYttBsoNgg@mail.gmail.com>
	<539141.86586.qm@web65708.mail.ac4.yahoo.com>
	<BANLkTikaHmgWKYM0BSJzWqB+d2rNJn5dEw@mail.gmail.com>
	<BANLkTinyt=HSeNsAs_=Fx2sv19LEYz98fw@mail.gmail.com>
	<47190.88201.qm@web65714.mail.ac4.yahoo.com>
	<BANLkTimgkd0gXKy9g+P4MXG-tveoOGAP_A@mail.gmail.com>
	<4DBA65BD.5020709@sissa.it>
Message-ID: <BANLkTinEciWRgbRU_YLwhNVcDvekRvtt9A@mail.gmail.com>

Dear Professor Stefano:
Thanks very much for your patient instruction.
I will read your mentioned paper carefully.
And now, I imagine that the phonon dispersion near Gamma point may look
like:

                                ^ Frequency
                                 |
                                 |
            *@@@@@* |*@@@@@**    **LO*
                                 |
                                 |
*           **$$$$$$$$$**@$$$$$$$$$   TO*
                                 |
  <-----------------------|------------------------->
                          Gamma         wavevector near Gamma

When q->0, there is  LO-TO splitting.
When q=0,  q has no direction. Therefore, optical modes can not be
classified into longitude or transverse ones. As a result, at q=0,  *$*=*@.*
However, there is not infinite crystal; and electric-static interaction
always occurs for finite crystal.
Therefore, in experiment, LO-TO splitting exists at the q=0.

On Fri, Apr 29, 2011 at 3:16 PM, Stefano de Gironcoli <degironc at sissa.it>wrote:

>  the electristatic interaction at the origin of LO-TO splitting is always
> present...
>
> for any q<>0 (even very small) it is included in the calculation.
>
> in the limit of q->0 in non-metallic systems it gives origin to a non
> analytic behavior that must be calculate separately.
>
> If you want to Fourier interpolate the phonon dispersions calculated on a
> regular grid of q-points
> you are in trouble because non analyticity of the phonon dispersion implyes
> long-range (1/R^3) interatomic force constants and so you need to
>
> 1) evaluate Z* and epsilon_infty in the limit of q->0 that determine the
> non-analyticity
> 2) remove from dynamical matrix in every q point in you grid an
> electrostatic model that gives the correct non-analyticity for q->0 and is
> smooth elsewhere
> 3) Fourier interpolate  the modified (hopefully short-range) dynamical
> matrices
> 4) add back the model in any q-point you want to study.
>
> This is what the sequence ph.x -> q2r.x -> matdyn.x does (in example06 for
> instance)
>
> thete is some discussion of these issues in Review of Modern Physics 73,
> 515 (2001) and in Phys Rev 43, 7231 (1991)
>
> stefano
>
> On 04/29/2011 05:05 AM, xirainbow wrote:
>
> Dear Eyvaz:
> Thank you very much;)
>
>
>  Is there LO-TO splitting far away from Gamma point?
> No.
>
>
>  Does LO-TO splitting must disappear at the boundary of Brillouin zone?
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From nkxirainbow at gmail.com  Fri Apr 29 12:23:45 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Fri, 29 Apr 2011 18:23:45 +0800
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <843971.37633.qm@web65712.mail.ac4.yahoo.com>
References: <BANLkTinQ1ToXegqM-Od0mQGz64U0mG5aow@mail.gmail.com>
	<BANLkTikNhSKOC=A-ETjHu7FUbbt=OH5QNQ@mail.gmail.com>
	<843971.37633.qm@web65712.mail.ac4.yahoo.com>
Message-ID: <BANLkTikdZz6GY5FkuU8VpL64nSAt+29zgA@mail.gmail.com>

Dear Professor Eyvaz:
Thank you very much for your instruction:)

>When q is zero, there is no longitude and transverse mode.
> Really? How about optical modes? Did you pay attention to "O"?
>
I do not express myself clearly.
When q=0,  q has no direction. Therefore, optical modes can not be
classified into longitude or transverse ones. As a result, at q=0,  these
optical phonon should be still degenerate( LO=TO ).



> Bests,
> Eyvaz.
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
> Sweden
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
> Russia,
> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
> ------------------------------
> *From:* xirainbow <nkxirainbow at gmail.com>
> *To:* PWSCF Forum <pw_forum at pwscf.org>
> *Sent:* Fri, April 29, 2011 9:30:31 AM
>
> *Subject:* Re: [Pw_forum] LO-TO splitting in dynmat.x
>
> Dear Sonu Kumar
> What you said is reasonable;)
>
> I have two little questions.
> One:
> Does LO-TO splitting must disappear at the boundary of Brillouin zone?
>
> Two:
> I can understand the LO-TO splitting near Gamma point.
> However, at Gamma point(not  near Gamma point), q=0. When q is zero, there
> is no longitude and transverse mode. Why are there LO-TO splitting at Gamma
> point?
>
> Thanks:)
>
>
>
> On Fri, Apr 29, 2011 at 1:21 PM, sonu kumar <1009ukumar at gmail.com> wrote:
>
>> Dear All QE users,
>>
>> i am sorry again, as i havn't corrected the subject title.
>>
>>
>> (2) only cubic crystals has LO and TO braches.
>>>
>>
>> crystals ( having considerable values of macroscopic dielectric constant [
>> i suppose
>> epsilon infinity] and born effective charges, as pointed  out by Prof.
>> Eyvaz Isaev) with low symmetry can, also, have LO-TO splitting. But this can
>> be  different in different symmetry directions, so one has to search all
>> symmetry directions for this splitting.
>>
>> For cubic crystals splitting is equal in all directions.
>>
>> with regards,
>>
>> --
>> Sonu Kumar
>>
>> Phd Student
>> Physics Department
>> Indian Institute of Technology
>> Delhi-110016, India
>> web:-http://www.iitd.ac.in/
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> ____________________________________
> Hui Wang
> School of physics, Fudan University, Shanghai, China
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From nkxirainbow at gmail.com  Fri Apr 29 12:25:47 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Fri, 29 Apr 2011 18:25:47 +0800
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <20110429092007.5946.qmail@ms.hfcas.ac.cn>
References: <20110429092007.5946.qmail@ms.hfcas.ac.cn>
Message-ID: <BANLkTim-v1hbRj5UWP3NXuD5YOCsq3DBhA@mail.gmail.com>

Dear Huang:
Thanks very much for your valuable discussion.
I are reading your mentioned paper:)

On Fri, Apr 29, 2011 at 5:20 PM, lfhuang <lfhuang at theory.issp.ac.cn> wrote:

>  Dear Wang, H:
> > Suppose a uniaxial crystal(no cubic): c>a=b. Suppose there is a
> > double-degenerate polar E_u mode, in which all atoms move in the a-b
> plane.
> > If the wavevector around Gamma point is in the a-b plane, the degenerate
> E
> > mode will split into LO and TO mode.
> > Am I right?
>
> It is probable for some ionic crystals, but still depends.
> Maybe the Equ. 98 (nonanalytic part of the dynamical matrix) in Rev. Mod.
> Phys. 73, 515 (2001) by prof. S. Baroni etc. and the related parts in the
> book "Dynamical Theory of Crystal Lattices" by M. Born & K. Huang can give
> you much information if these things are important/interesting to you.
>
> In addition, is the method "finite difference" you mentioned exactly the
> "frozen phonon" or "small displacement" method? If so, the treatment like
> that in PWSCF should be good to obtain a satisfied LO/TO splitting, although
> honestly I haven't done this in the "frozen phonon" method. Some people
> propose other methods, like using a prolonged supercell, which I think,
> could not fully describe the long-range dipolar interaction, because of its
> long-range character (as prof. Stefano de Gironcoli said ~1/R^3).
>
> Best Wishes!
> Yours Sincerely
> L. F. Huang
> ------
> ======================================================================
> L.F.Huang(???) DFT and phonon physics
> ======================================================================
> 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: 86-551-5591464-326(office)
> Fax: 86-551-5591434
> Our group: http://theory.issp.ac.cn
> ======================================================================
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From degironc at sissa.it  Fri Apr 29 13:16:58 2011
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 29 Apr 2011 13:16:58 +0200
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <BANLkTikdZz6GY5FkuU8VpL64nSAt+29zgA@mail.gmail.com>
References: <BANLkTinQ1ToXegqM-Od0mQGz64U0mG5aow@mail.gmail.com>	<BANLkTikNhSKOC=A-ETjHu7FUbbt=OH5QNQ@mail.gmail.com>	<843971.37633.qm@web65712.mail.ac4.yahoo.com>
	<BANLkTikdZz6GY5FkuU8VpL64nSAt+29zgA@mail.gmail.com>
Message-ID: <4DBA9E2A.2070105@sissa.it>

if you really want to know what happens close to gamma... look for the 
theory of polaritons.
also of interest can be to look for derivation of Lyddane-Sachs-Teller 
relationship.
stefano


On 04/29/2011 12:23 PM, xirainbow wrote:
> Dear Professor Eyvaz:
> Thank you very much for your instruction:)
>
>> When q is zero, there is no longitude and transverse mode.
>> Really? How about optical modes? Did you pay attention to "O"?
>>
> I do not express myself clearly.
> When q=0,  q has no direction. Therefore, optical modes can not be
> classified into longitude or transverse ones. As a result, at q=0,  these
> optical phonon should be still degenerate( LO=TO ).
>
>
>
>> Bests,
>> Eyvaz.
>>
>> -------------------------------------------------------------------
>> Prof. Eyvaz Isaev,
>> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
>> Sweden
>> Theoretical Physics Department, Moscow State Institute of Steel&  Alloys,
>> Russia,
>> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>>
>>
>> ------------------------------
>> *From:* xirainbow<nkxirainbow at gmail.com>
>> *To:* PWSCF Forum<pw_forum at pwscf.org>
>> *Sent:* Fri, April 29, 2011 9:30:31 AM
>>
>> *Subject:* Re: [Pw_forum] LO-TO splitting in dynmat.x
>>
>> Dear Sonu Kumar
>> What you said is reasonable;)
>>
>> I have two little questions.
>> One:
>> Does LO-TO splitting must disappear at the boundary of Brillouin zone?
>>
>> Two:
>> I can understand the LO-TO splitting near Gamma point.
>> However, at Gamma point(not  near Gamma point), q=0. When q is zero, there
>> is no longitude and transverse mode. Why are there LO-TO splitting at Gamma
>> point?
>>
>> Thanks:)
>>
>>
>>
>> On Fri, Apr 29, 2011 at 1:21 PM, sonu kumar<1009ukumar at gmail.com>  wrote:
>>
>>> Dear All QE users,
>>>
>>> i am sorry again, as i havn't corrected the subject title.
>>>
>>>
>>> (2) only cubic crystals has LO and TO braches.
>>> crystals ( having considerable values of macroscopic dielectric constant [
>>> i suppose
>>> epsilon infinity] and born effective charges, as pointed  out by Prof.
>>> Eyvaz Isaev) with low symmetry can, also, have LO-TO splitting. But this can
>>> be  different in different symmetry directions, so one has to search all
>>> symmetry directions for this splitting.
>>>
>>> For cubic crystals splitting is equal in all directions.
>>>
>>> with regards,
>>>
>>> --
>>> Sonu Kumar
>>>
>>> Phd Student
>>> Physics Department
>>> Indian Institute of Technology
>>> Delhi-110016, India
>>> web:-http://www.iitd.ac.in/
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>>
>> --
>> ____________________________________
>> Hui Wang
>> School of physics, Fudan University, Shanghai, China
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From nkxirainbow at gmail.com  Fri Apr 29 13:40:22 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Fri, 29 Apr 2011 19:40:22 +0800
Subject: [Pw_forum] LO-TO splitting in dynmat.x
In-Reply-To: <4DBA9E2A.2070105@sissa.it>
References: <BANLkTinQ1ToXegqM-Od0mQGz64U0mG5aow@mail.gmail.com>
	<BANLkTikNhSKOC=A-ETjHu7FUbbt=OH5QNQ@mail.gmail.com>
	<843971.37633.qm@web65712.mail.ac4.yahoo.com>
	<BANLkTikdZz6GY5FkuU8VpL64nSAt+29zgA@mail.gmail.com>
	<4DBA9E2A.2070105@sissa.it>
Message-ID: <BANLkTinxk9VEOxPXgUus-sW_hf7tPwD8WA@mail.gmail.com>

Dear Professor Stefano:
You mean when q->0, the polar phonon is described by Huang-equation?
If so, I know the answer:)
Thank you very much;)

On Fri, Apr 29, 2011 at 7:16 PM, Stefano de Gironcoli <degironc at sissa.it>wrote:

>  if you really want to know what happens close to gamma... look for the
> theory of polaritons.
> also of interest can be to look for derivation of Lyddane-Sachs-Teller
> relationship.
> stefano
>
>
>
> On 04/29/2011 12:23 PM, xirainbow wrote:
>
> Dear Professor Eyvaz:
> Thank you very much for your instruction:)
>
>
>  When q is zero, there is no longitude and transverse mode.
> Really? How about optical modes? Did you pay attention to "O"?
>
>
>  I do not express myself clearly.
> When q=0,  q has no direction. Therefore, optical modes can not be
> classified into longitude or transverse ones. As a result, at q=0,  these
> optical phonon should be still degenerate( LO=TO ).
>
>
>
>
>  Bests,
> Eyvaz.
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
> Sweden
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
> Russia,isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
> ------------------------------
> *From:* xirainbow <nkxirainbow at gmail.com> <nkxirainbow at gmail.com>
> *To:* PWSCF Forum <pw_forum at pwscf.org> <pw_forum at pwscf.org>
> *Sent:* Fri, April 29, 2011 9:30:31 AM
>
> *Subject:* Re: [Pw_forum] LO-TO splitting in dynmat.x
>
> Dear Sonu Kumar
> What you said is reasonable;)
>
> I have two little questions.
> One:
> Does LO-TO splitting must disappear at the boundary of Brillouin zone?
>
> Two:
> I can understand the LO-TO splitting near Gamma point.
> However, at Gamma point(not  near Gamma point), q=0. When q is zero, there
> is no longitude and transverse mode. Why are there LO-TO splitting at Gamma
> point?
>
> Thanks:)
>
>
>
> On Fri, Apr 29, 2011 at 1:21 PM, sonu kumar <1009ukumar at gmail.com> <1009ukumar at gmail.com> wrote:
>
>
>  Dear All QE users,
>
> i am sorry again, as i havn't corrected the subject title.
>
>
> (2) only cubic crystals has LO and TO braches.
>
>   crystals ( having considerable values of macroscopic dielectric constant [
> i suppose
> epsilon infinity] and born effective charges, as pointed  out by Prof.
> Eyvaz Isaev) with low symmetry can, also, have LO-TO splitting. But this can
> be  different in different symmetry directions, so one has to search all
> symmetry directions for this splitting.
>
> For cubic crystals splitting is equal in all directions.
>
> with regards,
>
> --
> Sonu Kumar
>
> Phd Student
> Physics Department
> Indian Institute of Technology
> Delhi-110016, India
> web:-http://www.iitd.ac.in/
>
> _______________________________________________
> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum
>
>  --
> ____________________________________
> Hui Wang
> School of physics, Fudan University, Shanghai, China
>
> _______________________________________________
> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum
>
>
> _______________________________________________
> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From eariel99 at gmail.com  Fri Apr 29 15:57:24 2011
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Fri, 29 Apr 2011 10:57:24 -0300
Subject: [Pw_forum]  LO-TO splitting in dynmat.x
Message-ID: <BANLkTinCBygKgxcTqaAF=oYBM0YLhBW7eA@mail.gmail.com>

Just to add a reference, an analysis of the polaritons in non cubic crystals
can be found in this article.

R. Loudon, Advances in Physics, 2001, Vol. 50, No. 7, 813-864



This article was originall y published in Advances in Physics, volume 13,
1964 . It attracted 1147 citations by October 2001, and is ranked 2 in the
index of articles attracting more than 100 citations.

-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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From ttduyle at gmail.com  Fri Apr 29 16:38:55 2011
From: ttduyle at gmail.com (Duy Le)
Date: Fri, 29 Apr 2011 10:38:55 -0400
Subject: [Pw_forum] vdW functional not implemented for spin polarized
	runs
In-Reply-To: <4DBA6D96.80208@sissa.it>
References: <BANLkTik77RKMOm-KUviZaki_hpUnP4Brtw@mail.gmail.com>
	<20110426190053.jklki05r4g044wc0@webmail.sissa.it>
	<BANLkTiniCjVY5GFStON8zkAQi6Wk3eyocw@mail.gmail.com>
	<BANLkTine4_GTeSpziWgMUgJHxpn+ZFakcA@mail.gmail.com>
	<4DB7C5E5.4090903@sissa.it>
	<BANLkTik8Kv-KeqDxr22yzgEwGi+H6z8_tA@mail.gmail.com>
	<4DBA6D96.80208@sissa.it>
Message-ID: <BANLkTi=bCPe69N40cdLMF1zWGtosx8AEVg@mail.gmail.com>

On Fri, Apr 29, 2011 at 3:49 AM, Stefano de Gironcoli <degironc at sissa.it> wrote:
> Dear all,
>
> ? ? I inquired Timo Thonhauser (now Wake Forest ?University), the main
> character behind the vdW-DF functional implementation in Quantum
> ESPRESSO, ?about the issue of the spin-polarized version of vdW-DF.
>
> I'm reporting his opinion below:
>
> "In general, at the moment there exists NO true extension of vdW-DF for
> spin-polarized cases. Several groups have expressed interest in working
> on it, but nothing has been published yet. Note that just evaluating
> vdW-DF for the two spin densities separately, while simple to implement,
> is an approximation which is difficult to justify: there is no
> quantitative measure of the error being made, other than hand waving
> arguments that it has to be small. Also, we did not implement that
> simple fix, because we were afraid that people would use it as a
> black-box for spin-polarized calculations, not knowing that there is no
> spin-polarized vdW-DF"
>
> hope this helps to clarify the situation.
>
> stefano

Thank you Stefano and Thonhauser Timo for the clarification.

--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"

>
>
>
> On 04/27/2011 04:45 PM, Duy Le wrote:
>> --------------------------------------------------
>> Duy Le
>> PhD Student
>> Department of Physics
>> University of Central Florida.
>>
>> "Men don't need hand to do things"
>>
>>
>>
>> On Wed, Apr 27, 2011 at 3:29 AM, Stefano de Gironcoli<degironc at sissa.it> ?wrote:
>>> the vdW energy depends on the local polarizability of the electron gas ..
>>> does it depend on the spin density ? I would say so.
>> I would depend as we expected, however, from the formalism of vdW-DF,
>> spin is not taken into account. So, I think in the limit of vdW-DF,
>> the spin-dependence is ignored.
>>
>>> Is it taken into account in the current definition of vdw-DF ? I would say
>>> no...
>>> how is it implemented in GPAW ? just blindly or with some argument ?
>> I am not sure. Did not have a chance to look at it and there is no
>> found document about this.
>>
>>> stefano
>>>
>>> On 04/27/2011 06:35 AM, WANG Wei wrote:
>>>
>>> Thank you for your advice, Deu. Yes, the non-local energy is independent the
>>> spin density.
>>>
>>>
>>> On 27 April 2011 12:34, Duy Le<ttduyle at gmail.com> ?wrote:
>>>
>>> --------------------------------------------------
>>> Duy Le
>>> PhD Student
>>> Department of Physics
>>> University of Central Florida.
>>>
>>> "Men don't need hand to do things"
>>>
>>>
>>>
>>> On Tue, Apr 26, 2011 at 1:00 PM, Stefano de Gironcoli<degironc at sissa.it>
>>> wrote:
>>>
>>> Dear ?WANG Wei
>>> ? ?the vdw-DF functional form is not defined for spin polarized system...
>>>
>>> Or it does mean that non-local energy is not spin-dependent but
>>> charge-density-dependent only.
>>>
>>> ? ?if you define, implement and test it, you could even get a nice
>>> publication out of it. thank you.
>>>
>>> The spin-polarized vdW-DF has been implemented in GPAW.
>>>
>>> stefano
>>>
>>>
>>>
>>> _______________________________________________
>>> 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 izaakw89 at yahoo.com  Fri Apr 29 23:33:10 2011
From: izaakw89 at yahoo.com (Izaak Williamson)
Date: Fri, 29 Apr 2011 14:33:10 -0700 (PDT)
Subject: [Pw_forum] Oscillations in macroscopic average of VH+Vbare
In-Reply-To: <BANLkTinzry6grqXy8ofWreXJn49ioHEgYQ@mail.gmail.com>
References: <BANLkTinzry6grqXy8ofWreXJn49ioHEgYQ@mail.gmail.com>
Message-ID: <695642.11777.qm@web43412.mail.sp1.yahoo.com>

Dear all,


I am trying to calculate the work function for Cu(100) surface with and without 
bulk reference. The equations used are as follows:

work function w/o bulkref  -->  wf1 = Vvac - EF,slab 
work function with bulkref  -->  wf2 = Vvac - Vslab,int + Vbulk,macro - EF,bulk

The problem is that the macroscopic average of VH+Vbare for the slab is 
oscillating as a function of z (see 05.png). I do not understand why the 
macroscopic average is oscillating. We want to see the convergence of the work 
function with the number of atomic layers in the slab. Due to the oscillation in 
macroscopic average,  the work function dramatically changes when we go from 5 
to 6 layers (4.86641 eV to 3.62728 eV, respectively). This makes it hard to see 
the convergence of wf with number of layers.

Would it be correct to use the average of the macroscopic average of the peaks 
and troughs in calculating wf2? Even if we calculate the average of upper 
oscillations (05.png), I don't know what to do with the trough that comes up 
just before the vacuum region? 

 
Thank you for any help.

-- 
Izaak Williamson
Research Assistant
Physics Department
Boise State University
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From iphyboy at gmail.com  Sat Apr 30 05:34:13 2011
From: iphyboy at gmail.com (wenmei ming)
Date: Fri, 29 Apr 2011 21:34:13 -0600
Subject: [Pw_forum] bulk projected band structure
Message-ID: <BANLkTimPG1+Grb564c8FW7O8guX=o2D2ow@mail.gmail.com>

Dear all,

I'm going to plot bulk projected band structure on a 2D BZ. I'm
guessing(take x-y plane 2D for example) for every k point in xy plane (K_x,
k_y, 0.0) I have to calculate all other energies with different k_z. By this
way the final energy band structure with K index only on xy plane is
so-called bulk projected band structure. But one problem for this I need to
specify too much k-points, so I am wondering if there is a more efficient
way to do this? Can someone share your experience in this?

Thanks so much in advance.

Jack Ming
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From nkxirainbow at gmail.com  Sat Apr 30 05:40:32 2011
From: nkxirainbow at gmail.com (xirainbow)
Date: Sat, 30 Apr 2011 11:40:32 +0800
Subject: [Pw_forum] bulk projected band structure
In-Reply-To: <BANLkTimPG1+Grb564c8FW7O8guX=o2D2ow@mail.gmail.com>
References: <BANLkTimPG1+Grb564c8FW7O8guX=o2D2ow@mail.gmail.com>
Message-ID: <BANLkTim3ytc_CNEYZVt2-+WPo9pqqCVhgw@mail.gmail.com>

Dear Ming:
I have less experience in bulk projected band structure.
I think you can do scf calculation with less k-points in three directions.
Then switch to nscf calculation for dense k-points in z-direction, similar
with dos calculation.

On Sat, Apr 30, 2011 at 11:34 AM, wenmei ming <iphyboy at gmail.com> wrote:

> Dear all,
>
> I'm going to plot bulk projected band structure on a 2D BZ. I'm
> guessing(take x-y plane 2D for example) for every k point in xy plane (K_x,
> k_y, 0.0) I have to calculate all other energies with different k_z. By this
> way the final energy band structure with K index only on xy plane is
> so-called bulk projected band structure. But one problem for this I need to
> specify too much k-points, so I am wondering if there is a more efficient
> way to do this? Can someone share your experience in this?
>
> Thanks so much in advance.
>
> Jack Ming
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
____________________________________
Hui Wang
School of physics, Fudan University, Shanghai, China
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From mirnezhad.mm at gmail.com  Sat Apr 30 10:27:36 2011
From: mirnezhad.mm at gmail.com (Mahdi Mirnezhad)
Date: Sat, 30 Apr 2011 01:27:36 -0700
Subject: [Pw_forum] About time dependent
Message-ID: <BANLkTikHWQsBR-=S_7Ck22fggWn9yxaX4g@mail.gmail.com>

Dear users,
Can quantum espresso simulate the time-dependent phenomena? for
example i want to calculate the position of atoms t second after an
external force. It is a non-equilibrium phenomena and the total energy
does not minimum. Is there any way to simulate such phenomena with QE?
I think in principle we could do such a work. If we have the initial
position (wave function) the wave function after t simply could be
written as A0*exp(-ien t), is it correct?
Best Regards


Mahdi Mirnezhad
Guilan University,