From quantum88 at mail.ru  Sun Apr  1 20:04:50 2012
From: quantum88 at mail.ru (=?UTF-8?B?0J3QuNC60LjRgtCwINCS0LDQutGD0LvQsA==?=)
Date: Sun, 01 Apr 2012 22:04:50 +0400
Subject: [Pw_forum] =?utf-8?q?pseudopotential_for_silver?=
Message-ID: <E1SEP90-0006iG-C3.quantum88-mail-ru@f45.mail.ru>

Hi all!

I am new to Pwscf and to this forum. I have a question about pseudopotential for silver: if I calculate the energy of pure silver atom and its cation in vacuum then they (energies) are ok. But if I optimize the structure Ag_surface (when Ag or its cation adsorped on a dielectric surface, for example, SiO2), then the absolute value of charged Ag+_surface energy is greater than the absolute value of neutral Ag_surface energy. Could you please tell me how it could be? I used Ag.pbe-d-rrkjus.UPF.

Thank you in advance!

Best regards,
Nikita
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From Lorenzo.Paulatto at impmc.upmc.fr  Sun Apr  1 21:11:57 2012
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Sun, 01 Apr 2012 21:11:57 +0200
Subject: [Pw_forum] problem in generating pseudopotential
In-Reply-To: <b75092.229fa.136667e9c94.Coremail.ptao10b@imr.ac.cn>
References: <b75092.229fa.136667e9c94.Coremail.ptao10b@imr.ac.cn>
Message-ID: <op.wb3ox7u2xuur8c@linux-qnvk.site>

On Sat, 31 Mar 2012 04:03:55 +0200, ?? <ptao10b at imr.ac.cn> wrote:
>    lloc=1,
> ...
> 5P  2  1  0.00 -0.10  6.00  6.00

This radius is enormous, and it is larger than the radius used for the
other wavefunctions. In order to have a good pseudo the radius where the
local potential is pseudized must be smaller than the radius where the
wavefunctions are pseudized.

Please note that there are several pseudopotential for Mo in the
ps-library by Dal Corso <http://qe-forge.org/projects/pslibrary/>

bests


-- 
Lorenzo Paulatto IdR CNRS @ IMPMC/UPMC - Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www.impmc.upmc.fr/~paulatto/
mail:  23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From jiachen at princeton.edu  Tue Apr  3 06:15:00 2012
From: jiachen at princeton.edu (jia chen)
Date: Tue, 3 Apr 2012 00:15:00 -0400
Subject: [Pw_forum] electrostatic potential in CP calculation
Message-ID: <CADa2diZFd-Wkh4UA_DbduG-bYPDSdM7oj=+krHzJv3XqOrYcYw@mail.gmail.com>

Hello All,

I am trying to calculate the work function based on CP calculation. In
order to do that, I need to figure out the electrostatic potential
corresponding to cp eigenvalues in real space. I tried PP post possessing,
but the result looks consistent with pwscf, but cp eigenvalues present a
shift. I also tried to print out variable vpot, but it looks not like
electrostatic potential. I hope some one here has experience dealing with
this problem, or some one knows the origin of eigenvalue shift between cp
and pwscf and how to calculation that. Thank you in advance.

Best Wishes
-- 
Jia Chen
Chemistry Department
Princeton University
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From giannozz at democritos.it  Tue Apr  3 12:52:06 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 3 Apr 2012 12:52:06 +0200
Subject: [Pw_forum] electrostatic potential in CP calculation
In-Reply-To: <CADa2diZFd-Wkh4UA_DbduG-bYPDSdM7oj=+krHzJv3XqOrYcYw@mail.gmail.com>
References: <CADa2diZFd-Wkh4UA_DbduG-bYPDSdM7oj=+krHzJv3XqOrYcYw@mail.gmail.com>
Message-ID: <0F7428C3-0000-4CC0-971A-96122D095FB7@democritos.it>


On Apr 3, 2012, at 6:15 , jia chen wrote:

> I am trying to calculate the work function based on CP calculation.  
> In order to do that, I need to figure out the electrostatic  
> potential corresponding to cp eigenvalues in real space. I tried PP  
> post possessing, but the result looks consistent with pwscf, but cp  
> eigenvalues present a shift. I also tried to print out variable  
> vpot, but it looks not like electrostatic potential. I hope some  
> one here has experience dealing with this problem, or some one  
> knows the origin of eigenvalue shift between cp and pwscf and how  
> to calculation that.

I am not sure what "potential" exactly is actually contained in the  
potential
file written by CP. I am quite sure instead about the origin and size  
of the
shift between Kohn-Sham eigenvalues printed by CP and by PWscf. In
recent CP versions, look for "Delta V(G=0)" in the output: this is the
difference between the potential at G=0 for CP and for PWscf.  
Explanations
here: http://www.fisica.uniud.it/~giannozz/public/ewald.pdf

  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  3 19:30:56 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 3 Apr 2012 19:30:56 +0200
Subject: [Pw_forum] pseudopotential for silver
In-Reply-To: <E1SEP90-0006iG-C3.quantum88-mail-ru@f45.mail.ru>
References: <E1SEP90-0006iG-C3.quantum88-mail-ru@f45.mail.ru>
Message-ID: <0CA48BA7-055B-48DC-B708-D4EF473CE6A3@democritos.it>


On Apr 1, 2012, at 20:04 , ?????? ?????? wrote:

>  I have a question about pseudopotential for silver

your question is not related to the pseudopotential
of silver, but to the meaning of energies in charged
cells, if I understand correctly. Energies for charged
cell should be handled with care and cannot be directly
compared to the energy for the neutral cell.

P.

> if I calculate the energy of pure silver atom and its cation
> in vacuum then they (energies) are ok. But if I optimize
> the structure Ag_surface (when Ag or its cation adsorped
> on a dielectric surface, for example, SiO2), then the absolute
> value of charged Ag+_surface energy is greater than the
> absolute value of neutral Ag_surface energy. Could you
> please tell me how it could be?


---
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 amirhosseinba67 at gmail.com  Wed Apr  4 09:52:15 2012
From: amirhosseinba67 at gmail.com (Amir hosseini)
Date: Wed, 4 Apr 2012 12:22:15 +0430
Subject: [Pw_forum] (no subject)
Message-ID: <CABGPTx0bh2m4eUpXqBGm8F92dUCJFm0Cid=gUrowZWM8=M68JA@mail.gmail.com>

Dear all

Quantum Espresso can calculated polarization and piezoelectric
properties and change the dimension of a material such as carbon
nanotubes in the presence of electric field?

Thanks

From ptao10b at imr.ac.cn  Wed Apr  4 12:58:36 2012
From: ptao10b at imr.ac.cn (=?GBK?B?zNXF9A==?=)
Date: Wed, 4 Apr 2012 18:58:36 +0800 (CST)
Subject: [Pw_forum] How to plot the potential curve during pseudopotential
	generation?
Message-ID: <192cf63.2cfa.1367d0192a9.Coremail.ptao10b@imr.ac.cn>

Dear all,

When I am using the ld1.x to generate a pseudopotential, I want to plot the potential curve (pseudo V-r curve) to see how it fitting the all-electron case. However, I cannot find any file containing such potential. And could you guide me how to find it? Thank you very much?

Warmest regards,

Plato Tao



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------





From flux_ray12 at 163.com  Wed Apr  4 13:27:33 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Wed, 4 Apr 2012 19:27:33 +0800 (CST)
Subject: [Pw_forum] How to plot the potential curve during
 pseudopotential generation?
In-Reply-To: <192cf63.2cfa.1367d0192a9.Coremail.ptao10b@imr.ac.cn>
References: <192cf63.2cfa.1367d0192a9.Coremail.ptao10b@imr.ac.cn>
Message-ID: <784093f8.1489d.1367d1c13af.Coremail.flux_ray12@163.com>

The one you need may be in the name of ld1ps.wfc, you can draw it by gnuplot or xmgrace.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 



At 2012-04-04 18:58:36,"??" <ptao10b at imr.ac.cn> wrote:
>Dear all,
>
>When I am using the ld1.x to generate a pseudopotential, I want to plot the potential curve (pseudo V-r curve) to see how it fitting the all-electron case. However, I cannot find any file containing such potential. And could you guide me how to find it? Thank you very much?
>
>Warmest regards,
>
>Plato Tao
>
>
>
>--
>-------------------------------------------------------------------
>PH.D. candidate Peng Tao 
>Magnetism and Magnetic Materials Division
>National Laboratory for Material Science
>Institute of Metal Research, Chinese Academy of Sciences
>Phone  +86-024-83978751
>-------------------------------------------------------------------
>
>
>
>
>_______________________________________________
>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  Wed Apr  4 13:45:28 2012
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Wed, 04 Apr 2012 13:45:28 +0200
Subject: [Pw_forum] How to plot the potential curve during
 pseudopotential generation?
In-Reply-To: <192cf63.2cfa.1367d0192a9.Coremail.ptao10b@imr.ac.cn>
References: <192cf63.2cfa.1367d0192a9.Coremail.ptao10b@imr.ac.cn>
Message-ID: <op.wb8n92zgxuur8c@vanoxite.impmc.jussieu.fr>

I'm not 100% sure I understaood what you need, but if it is the pseudized  
local potential, it will be stored in file_screen if you set it.

The file contains 5 columns:
#   n, r(n),       aeloc(n),   psloc(n),   pscharge(n)

bests



On Wed, 04 Apr 2012 12:58:36 +0200, ?? <ptao10b at imr.ac.cn> wrote:

> Dear all,
>
> When I am using the ld1.x to generate a pseudopotential, I want to plot  
> the potential curve (pseudo V-r curve) to see how it fitting the  
> all-electron case. However, I cannot find any file containing such  
> potential. And could you guide me how to find it? Thank you very much?
>
> Warmest regards,
>
> Plato Tao
>
>
>
> --
> -------------------------------------------------------------------
> PH.D. candidate Peng Tao
> Magnetism and Magnetic Materials Division
> National Laboratory for Material Science
> Institute of Metal Research, Chinese Academy of Sciences
> Phone  +86-024-83978751
> -------------------------------------------------------------------
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 
Lorenzo Paulatto IdR @ IMPMC/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 ptao10b at imr.ac.cn  Wed Apr  4 14:02:57 2012
From: ptao10b at imr.ac.cn (=?utf-8?B?6Zm26bmP?=)
Date: Wed, 4 Apr 2012 20:02:57 +0800 (CST)
Subject: [Pw_forum] How to plot the potential curve during
 pseudopotential generation?
In-Reply-To: <op.wb8n92zgxuur8c@vanoxite.impmc.jussieu.fr>
References: <op.wb8n92zgxuur8c@vanoxite.impmc.jussieu.fr>
	<192cf63.2cfa.1367d0192a9.Coremail.ptao10b@imr.ac.cn>
Message-ID: <10cf559.2df6.1367d3c7b48.Coremail.ptao10b@imr.ac.cn>

And sorry for another question, is it possible to visualize the potential curve of each orbit?


> -----????-----
> ???: "Lorenzo Paulatto" <Lorenzo.Paulatto at impmc.upmc.fr>
> ????: 2012?4?4? ???
> ???: pw_forum at pwscf.org
> ??: 
> ??: Re: [Pw_forum] How to plot the potential curve during pseudopotential generation?
> 
> I'm not 100% sure I understaood what you need, but if it is the pseudized  
> local potential, it will be stored in file_screen if you set it.
> 
> The file contains 5 columns:
> #   n, r(n),       aeloc(n),   psloc(n),   pscharge(n)
> 
> bests
> 
> 
> 
> On Wed, 04 Apr 2012 12:58:36 +0200, ?? <ptao10b at imr.ac.cn> wrote:
> 
> > Dear all,
> >
> > When I am using the ld1.x to generate a pseudopotential, I want to plot  
> > the potential curve (pseudo V-r curve) to see how it fitting the  
> > all-electron case. However, I cannot find any file containing such  
> > potential. And could you guide me how to find it? Thank you very much?
> >
> > Warmest regards,
> >
> > Plato Tao
> >
> >
> >
> > --
> > -------------------------------------------------------------------
> > PH.D. candidate Peng Tao
> > Magnetism and Magnetic Materials Division
> > National Laboratory for Material Science
> > Institute of Metal Research, Chinese Academy of Sciences
> > Phone  +86-024-83978751
> > -------------------------------------------------------------------
> >
> >
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> -- 
> Lorenzo Paulatto IdR @ IMPMC/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



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------






From Lorenzo.Paulatto at impmc.upmc.fr  Wed Apr  4 14:17:04 2012
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Wed, 04 Apr 2012 14:17:04 +0200
Subject: [Pw_forum] How to plot the potential curve during
 pseudopotential generation?
In-Reply-To: <10cf559.2df6.1367d3c7b48.Coremail.ptao10b@imr.ac.cn>
References: <op.wb8n92zgxuur8c@vanoxite.impmc.jussieu.fr>
	<192cf63.2cfa.1367d0192a9.Coremail.ptao10b@imr.ac.cn>
	<10cf559.2df6.1367d3c7b48.Coremail.ptao10b@imr.ac.cn>
Message-ID: <op.wb8pqqf0xuur8c@vanoxite.impmc.jussieu.fr>

On Wed, 04 Apr 2012 14:02:57 +0200, ?? <ptao10b at imr.ac.cn> wrote:

> And sorry for another question, is it possible to visualize the  
> potential curve of each orbit?

I'm not sure what you mean: all the orbitals have the same local  
potential. In additions there are non-local projectors ("beta"), but they  
cannot really be considered "potential curves".

bests

-- 
Lorenzo Paulatto IdR @ IMPMC/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 ptao10b at imr.ac.cn  Thu Apr  5 10:26:28 2012
From: ptao10b at imr.ac.cn (=?GBK?B?zNXF9A==?=)
Date: Thu, 5 Apr 2012 16:26:28 +0800 (CST)
Subject: [Pw_forum] Is it possible for all-electron calculation on anions
	with ld1.x?
Message-ID: <e5c5c9.4d42.136819ca60b.Coremail.ptao10b@imr.ac.cn>

Dear all,

I am generating pseudopotential these days and happening to meet lots of unexpected problems. One of which is, when I run the all-electronic calculation on anions, the error of "errors in KS equations" appears. But when I run the program on cations, it works well. I just want to do some tests on those electronic configurations after pseudo generation. Could anyone help me, thanks.

Here are the input file:
 &input
        iswitch=1,
        atom='C',
        config="[He] 2s2 2p3 3d0"
        dft='LDA'
 /

Output file:
     Message from routine scf:
     errors in KS equations
     --------------------------- All-electron run ----------------------------                                                                         

     atomic number is  6.00
     dft =LDA   lsd =0 sic =0 latt =0  beta=0.20 tr2=1.0E-14
     mesh =1675 r(mesh) =  99.50825 xmin = -7.00 dx = 0.00800
     1 Ry =  13.60569193 eV

     n l     nl                  e(Ry)          e(Ha)          e(eV)
     1 0     1S 1( 2.00)       -18.6214        -9.3107      -253.3569
     2 0     2S 1( 2.00)        -0.0513        -0.0256        -0.6977
     2 1     2P 1( 3.00)         0.0000         0.0000         0.0000
     3 2     3D 1( 0.00)        -0.0522        -0.0261        -0.7099

As you can see, the energy of 2P is 0.

Best wishes,

Plato Tao



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------





From nicola.marzari at epfl.ch  Thu Apr  5 10:37:19 2012
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Thu, 05 Apr 2012 10:37:19 +0200
Subject: [Pw_forum] Is it possible for all-electron calculation on
 anions with ld1.x?
In-Reply-To: <e5c5c9.4d42.136819ca60b.Coremail.ptao10b@imr.ac.cn>
References: <e5c5c9.4d42.136819ca60b.Coremail.ptao10b@imr.ac.cn>
Message-ID: <4F7D59BF.3060500@epfl.ch>



It might be that LDA doesn't bind many anions (a failure of lda).

Not sure what the solution could be - maybe only a small filling on the 
last electron?

Of course, the neutral atom should give a pseudo reasonably good to 
describe also the anion, if it weren't the case that the energy of the 
last electron in the anion in lda is much higher that it should be (and
in most cases not bound).

			nicola


On 05/04/2012 10:26, ?? wrote:
> Dear all,
>
> I am generating pseudopotential these days and happening to meet lots of unexpected problems. One of which is, when I run the all-electronic calculation on anions, the error of "errors in KS equations" appears. But when I run the program on cations, it works well. I just want to do some tests on those electronic configurations after pseudo generation. Could anyone help me, thanks.
>
> Here are the input file:
>   &input
>          iswitch=1,
>          atom='C',
>          config="[He] 2s2 2p3 3d0"
>          dft='LDA'
>   /
>
> Output file:
>       Message from routine scf:
>       errors in KS equations
>       --------------------------- All-electron run ----------------------------
>
>       atomic number is  6.00
>       dft =LDA   lsd =0 sic =0 latt =0  beta=0.20 tr2=1.0E-14
>       mesh =1675 r(mesh) =  99.50825 xmin = -7.00 dx = 0.00800
>       1 Ry =  13.60569193 eV
>
>       n l     nl                  e(Ry)          e(Ha)          e(eV)
>       1 0     1S 1( 2.00)       -18.6214        -9.3107      -253.3569
>       2 0     2S 1( 2.00)        -0.0513        -0.0256        -0.6977
>       2 1     2P 1( 3.00)         0.0000         0.0000         0.0000
>       3 2     3D 1( 0.00)        -0.0522        -0.0261        -0.7099
>
> As you can see, the energy of 2P is 0.
>
> Best wishes,
>
> Plato Tao
>
>
>
> --
> -------------------------------------------------------------------
> PH.D. candidate Peng Tao
> Magnetism and Magnetic Materials Division
> National Laboratory for Material Science
> Institute of Metal Research, Chinese Academy of Sciences
> Phone  +86-024-83978751
> -------------------------------------------------------------------
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 

----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL

From ptao10b at imr.ac.cn  Thu Apr  5 10:54:43 2012
From: ptao10b at imr.ac.cn (=?UTF-8?B?6Zm26bmP?=)
Date: Thu, 5 Apr 2012 16:54:43 +0800 (CST)
Subject: [Pw_forum] Is it possible for all-electron calculation on
 anions with ld1.x?
In-Reply-To: <4F7D59BF.3060500@epfl.ch>
References: <4F7D59BF.3060500@epfl.ch>
	<e5c5c9.4d42.136819ca60b.Coremail.ptao10b@imr.ac.cn>
Message-ID: <1ba15da.4e75.13681b682d9.Coremail.ptao10b@imr.ac.cn>

Thank you for your suggestion!
This is the PBE result:

? ? ?Message from routine scf:
? ? ?warning: convergence not achieved
? ? ?--------------------------- All-electron run ----------------------------

? ? ?atomic number is ?6.00
? ? ?dft =PBE ? lsd =0 sic =0 latt =0 ?beta=0.20 tr2=1.0E-14
? ? ?mesh =1675 r(mesh) = ?99.50825 xmin = -7.00 dx = 0.00800
? ? ?1 Ry = ?13.60569193 eV

? ? ?n l ? ? nl ? ? ? ? ? ? ? ? ?e(Ry) ? ? ? ? ?e(Ha) ? ? ? ? ?e(eV)
? ? ?1 0 ? ? 1S 1( 2.00) ? ? ? -19.5752 ? ? ? ?-9.7876 ? ? ?-266.3335
? ? ?2 0 ? ? 2S 1( 2.00) ? ? ? ?-0.4269 ? ? ? ?-0.2135 ? ? ? ?-5.8089
? ? ?2 1 ? ? 2P 1( 3.00) ? ? ? ? 0.0000 ? ? ? ? 0.0000 ? ? ? ? 0.0000
? ? ?3 2 ? ? 3D 1( 0.00) ? ? ? ?-0.0519 ? ? ? ?-0.0260 ? ? ? ?-0.7064


And I did the PW91 run:

     Message from routine scf:
     warning: convergence not achieved
     --------------------------- All-electron run ----------------------------
                                                                        

     atomic number is  6.00
     dft =PW91   lsd =0 sic =0 latt =0  beta=0.20 tr2=1.0E-14
     mesh =1675 r(mesh) =  99.50825 xmin = -7.00 dx = 0.00800
     1 Ry =  13.60569193 eV

     n l     nl                  e(Ry)          e(Ha)          e(eV)
     1 0     1S 1( 2.00)       -19.5225        -9.7613      -265.6172
     2 0     2S 1( 2.00)        -0.3682        -0.1841        -5.0099
     2 1     2P 1( 3.00)         0.0000         0.0000         0.0000
     3 2     3D 1( 0.00)        -0.0522        -0.0261        -0.7100


The error turns to warning, but the problem is not solved.

> 
> 
> 
> It might be that LDA doesn't bind many anions (a failure of lda).
> 
> Not sure what the solution could be - maybe only a small filling on the 
> last electron?
> 
> Of course, the neutral atom should give a pseudo reasonably good to 
> describe also the anion, if it weren't the case that the energy of the 
> last electron in the anion in lda is much higher that it should be (and
> in most cases not bound).
> 
> 			nicola
> 
> 
> On 05/04/2012 10:26, ?? wrote:
> > Dear all,
> >
> > I am generating pseudopotential these days and happening to meet lots of unexpected problems. One of which is, when I run the all-electronic calculation on anions, the error of "errors in KS equations" appears. But when I run the program on cations, it works well. I just want to do some tests on those electronic configurations after pseudo generation. Could anyone help me, thanks.
> >
> > Here are the input file:
> >   &input
> >          iswitch=1,
> >          atom='C',
> >          config="[He] 2s2 2p3 3d0"
> >          dft='LDA'
> >   /
> >
> > Output file:
> >       Message from routine scf:
> >       errors in KS equations
> >       --------------------------- All-electron run ----------------------------
> >
> >       atomic number is  6.00
> >       dft =LDA   lsd =0 sic =0 latt =0  beta=0.20 tr2=1.0E-14
> >       mesh =1675 r(mesh) =  99.50825 xmin = -7.00 dx = 0.00800
> >       1 Ry =  13.60569193 eV
> >
> >       n l     nl                  e(Ry)          e(Ha)          e(eV)
> >       1 0     1S 1( 2.00)       -18.6214        -9.3107      -253.3569
> >       2 0     2S 1( 2.00)        -0.0513        -0.0256        -0.6977
> >       2 1     2P 1( 3.00)         0.0000         0.0000         0.0000
> >       3 2     3D 1( 0.00)        -0.0522        -0.0261        -0.7099
> >
> > As you can see, the energy of 2P is 0.
> >
> > Best wishes,
> >
> > Plato Tao
> >
> >
> >
> > --
> > -------------------------------------------------------------------
> > PH.D. candidate Peng Tao
> > Magnetism and Magnetic Materials Division
> > National Laboratory for Material Science
> > Institute of Metal Research, Chinese Academy of Sciences
> > Phone  +86-024-83978751
> > -------------------------------------------------------------------
> >
> >
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> -- 
> 
> ----------------------------------------------------------------------
> Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------






From nicola.marzari at epfl.ch  Thu Apr  5 11:29:47 2012
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Thu, 05 Apr 2012 11:29:47 +0200
Subject: [Pw_forum] Is it possible for all-electron calculation on
 anions with ld1.x?
In-Reply-To: <1ba15da.4e75.13681b682d9.Coremail.ptao10b@imr.ac.cn>
References: <4F7D59BF.3060500@epfl.ch>
	<e5c5c9.4d42.136819ca60b.Coremail.ptao10b@imr.ac.cn>
	<1ba15da.4e75.13681b682d9.Coremail.ptao10b@imr.ac.cn>
Message-ID: <4F7D660B.8030105@epfl.ch>

On 05/04/2012 10:54, ?? wrote:
> The error turns to warning, but the problem is not solved.
>


Indeed - PBE and PW91 have the same problems with anions as LDA.

Can dl1 deal with Hartree-Fock or hybrids?

But the main point is that you shouldn't have the need to generate a
pseudopotential for an anion - the neutral is transferable enough,
and studyin anions with LDA/PBE/PW91 is in any case a losing proposition.

			nicola



----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL

From giannozz at democritos.it  Thu Apr  5 11:59:40 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 5 Apr 2012 11:59:40 +0200
Subject: [Pw_forum] Is it possible for all-electron calculation on
	anions with ld1.x?
In-Reply-To: <4F7D59BF.3060500@epfl.ch>
References: <e5c5c9.4d42.136819ca60b.Coremail.ptao10b@imr.ac.cn>
	<4F7D59BF.3060500@epfl.ch>
Message-ID: <4261C68E-81E2-4852-960B-94A557FC54C2@democritos.it>


On Apr 5, 2012, at 10:37 , Nicola Marzari wrote:

> It might be that LDA doesn't bind many anions (a failure of lda).

I vaguely remember it doesn't bind any (not even F-)

> Not sure what the solution could be

self-interaction-free functionals ...

> - maybe only a small filling on the last electron?

This might work. I don't think there is any need to use a
negatively charged reference configuration to deal with
anions, though

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 susanta96 at gmail.com  Thu Apr  5 13:59:17 2012
From: susanta96 at gmail.com (susanta tripathy)
Date: Thu, 5 Apr 2012 07:59:17 -0400
Subject: [Pw_forum] Re
Message-ID: <CACEBywBndmKTboUtB=pk18aqfrV3BpBPCZAbzry6ZDfD=jqrkA@mail.gmail.com>

Dear sir,
       i want to a member of quantum espresso forum.

-- 
S.K.Tripathy
Ph.D, Indian School of Mines
Dhanbad

From alex968873 at yahoo.com.cn  Thu Apr  5 15:32:28 2012
From: alex968873 at yahoo.com.cn (=?utf-8?B?5p2O5paM?=)
Date: Thu, 5 Apr 2012 21:32:28 +0800 (CST)
Subject: [Pw_forum] Potassium Ultrasoft pseudopotential with PBE
Message-ID: <1333632748.87002.YahooMailNeo@web15102.mail.cnb.yahoo.com>

Dear All,
?
?
Recently, my calculation needs Potassium PBE Ultrasoft pseudopotential. But I?m not sure about my pseudo generated by ld1.x. So is there existing K.pbe pseudo? Thank you very much!
?
Best regards, ?
?
LiBin

From apv544 at phys.tsu.ru  Fri Apr  6 06:32:14 2012
From: apv544 at phys.tsu.ru (Pavel V. Akulov)
Date: Fri, 6 Apr 2012 11:32:14 +0700
Subject: [Pw_forum] Extractring wavefunctions from complex band calculation
Message-ID: <20120406042932.M83791@phys.tsu.ru>

Dear, all!

Is there any way to extract wavefunctions from complex band calculation using 
PWCOND.x or some other post-processing routine?

Thank you.

Pavel Akulov,
Tomsk State Univercity

From phq323 at gmail.com  Sat Apr  7 07:00:30 2012
From: phq323 at gmail.com (Hua Pan)
Date: Sat, 7 Apr 2012 13:00:30 +0800
Subject: [Pw_forum] loop and GGA
Message-ID: <CAJkYyGpqZyXXVyDXp98YiVVK2k3nT-sP+O_uiZccDfzTAykcWA@mail.gmail.com>

Hi all,

I encountered some troubles when I simulated?the structures and
lattice constants of Nickel in PWSCF.
1. Didn't use loop in PWSCF code due to reduce workload.
2. No GGA potential of Nickel.
How to deal with them?
Thanks.

Best reagards,
Pan

From phq323 at gmail.com  Sat Apr  7 09:36:05 2012
From: phq323 at gmail.com (Hua Pan)
Date: Sat, 7 Apr 2012 15:36:05 +0800
Subject: [Pw_forum]  loop and GGA
In-Reply-To: <CAH9diMUuYi5drB7cihGjsawcRx6iZtB2vxbUbf02HeOGNA8uDQ@mail.gmail.com>
References: <CAJkYyGpqZyXXVyDXp98YiVVK2k3nT-sP+O_uiZccDfzTAykcWA@mail.gmail.com>
	<CAH9diMUuYi5drB7cihGjsawcRx6iZtB2vxbUbf02HeOGNA8uDQ@mail.gmail.com>
Message-ID: <CAJkYyGrJT9fzp8muL-s7Vn1Z8QKcHyUPfNS=misBSkvrjLVpKQ@mail.gmail.com>

http://www.quantum-espresso.org/pseudo/1.3/html/Ni.html
I don't find it in the URL, only LDA and PBE pp.

---------- Forwarded message ----------
From: Yunpeng Wang <yunpengwang85 at gmail.com>
Date: 2012/4/7
Subject: Re: [Pw_forum] loop and GGA
To: Hua Pan <phq323 at gmail.com>


there must be a GGA PP for nickel. you can find it.

On Sat, Apr 7, 2012 at 1:00 PM, Hua Pan <phq323 at gmail.com> wrote:

> Hi all,
>
> I encountered some troubles when I simulated the structures and
> lattice constants of Nickel in PWSCF.
> 1. Didn't use loop in PWSCF code due to reduce workload.
> 2. No GGA potential of Nickel.
> How to deal with them?
> Thanks.
>
> Best reagards,
> Pan
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
*Yunpeng Peter Wang*
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From jamali at dena.kntu.ac.ir  Sun Apr  8 10:57:26 2012
From: jamali at dena.kntu.ac.ir (Maryam Jamali)
Date: Sun, 08 Apr 2012 13:27:26 +0430 (IRDT)
Subject: [Pw_forum] band calculation
In-Reply-To: <6c290c3d-43e5-4952-a670-9d1a7572751e@mail.kntu.ac.ir>
Message-ID: <48f850f9-5ea7-4d20-bc7a-f28177d0b64b@mail.kntu.ac.ir>


Dear all,

I have run band calculation job with pw.x. The job was truncated. Is there any instruction to restart the job?

Thank you in advance 

Maryam Jamali
phD student of physical chemistry 
K.N.T.University of technology.Tehran 

From samadzare at gmail.com  Sun Apr  8 14:57:55 2012
From: samadzare at gmail.com (samad zare)
Date: Sun, 8 Apr 2012 17:27:55 +0430
Subject: [Pw_forum] made nanowire
Message-ID: <CAJ_oS4TOwD_Eiattxm8Dk2o+KZsY=7PcJkZJ1pseM-OvQbrVFw@mail.gmail.com>

dear all pwscf user
i want simulation nanowires by pwscf  how can do it?
i know we must made supercell how to  made supercell?

-- 
With Best Regards
SAMAD ZARE, phD  Student UTM university
Nanotechnology Research Alliance
APSI, UTM 81310, Skudai,Johor Bahru, Malaysia
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From bamideleibrahim at yahoo.com  Sun Apr  8 15:08:47 2012
From: bamideleibrahim at yahoo.com (bamidele ibrahim)
Date: Sun, 8 Apr 2012 06:08:47 -0700 (PDT)
Subject: [Pw_forum] help on convergence
Message-ID: <1333890527.95645.YahooMailNeo@web39403.mail.mud.yahoo.com>

Dear all,
?I am working on TiO2 and running scf for this compound, i have not been able to get a convergence. I will be delighted if i can get help on this from any expert. I have with this mail the input file for the scf. 

?
Adetunji Bamidele Ibrahim(PhD Student)
Department of physics,University of Agriculture,
Abeokuta, Ogun State,Nigeria.
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From funmiayedun at yahoo.com  Sun Apr  8 16:00:51 2012
From: funmiayedun at yahoo.com (funmi ayedun)
Date: Sun, 8 Apr 2012 07:00:51 -0700 (PDT)
Subject: [Pw_forum] convergence for lattice parameter
Message-ID: <1333893651.47269.YahooMailClassic@web162103.mail.bf1.yahoo.com>

Dear All,

Good day all, I am a new user in quantum espresso, I am working on anatase TiO2 (with hexagonal structure) but? I have problem with convergence test? for lattice parameter for TiO2 system.? I have tried to vary celldm 1 from 8.2 to 9.0Bohr but I was unable get a convergence result. Also, I tried to vary celldm 3? from 0.2441 to 1.3441Bohr and? keeping celldm 1 constant, I was unable to get convergence as well. I have my input file below. 

&control
? calculation = 'scf',
? restart_mode='from_scratch',
? prefix='TiO2'
? pseudo_dir='/home/funmilayo/espresso-4.2.1/pseudo',
? outdir='./',
??? tprnfor = .true.
? tstress = .true.
/
&system
? ibrav=6, celldm(1)= 8.6808, celldm(3)= 0.7450,
? nat=3, ntyp=2,occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 
? ecutwfc= 25.0,
/
&electrons
?mixing_beta = 0.7
?diagonalization='davidson'
conv_thr =? 1.0d-8
/
ATOMIC_SPECIES
Ti 47.867? Ti.blyp-sp-van_ak.UPF
O? 15.994? O.blyp-van_ak.UPF
ATOMIC_POSITIONS
Ti 0.00000000?? 0.00000000?? 0.00000000 
O? 0.33333333?? 0.33333333?? 0.33333333
O? 0.80000000?? 0.20000000?? 0.50000000
K_POINTS (automatic)
6 6 6? 0? 0? 0

Can anyone please tell me where I have gone wrong.? 
Thank you all.


Ayedun Oluwafunmilayo,
PhD student,
Department of Physics,
University of Agriculture,
Abeokuta,
Nigeria.
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From akohlmey at gmail.com  Sun Apr  8 16:29:48 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Sun, 8 Apr 2012 10:29:48 -0400
Subject: [Pw_forum] made nanowire
In-Reply-To: <CAJ_oS4TOwD_Eiattxm8Dk2o+KZsY=7PcJkZJ1pseM-OvQbrVFw@mail.gmail.com>
References: <CAJ_oS4TOwD_Eiattxm8Dk2o+KZsY=7PcJkZJ1pseM-OvQbrVFw@mail.gmail.com>
Message-ID: <CADTmJ6GPtE4_VijAJUYvibquxgvMYXLUMMUQzaFipp2e4LHvkw@mail.gmail.com>

On Sun, Apr 8, 2012 at 8:57 AM, samad zare <samadzare at gmail.com> wrote:
> dear all pwscf user
> i want simulation nanowires by pwscf? how can do it?

like all other system. define the starting geometry
and have a go. to make a wire you can either compute
the positions or take a crystal and remove the positions
that don't fit with your desired shape of wire.

> i know we must made supercell how to? made supercell?

trivial. take a singe cell and replicate.

cheers,
    axel.


> --
> With Best Regards
> SAMAD ZARE, phD? Student UTM university
> Nanotechnology Research Alliance
> APSI, UTM 81310, Skudai,Johor Bahru, Malaysia
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From faccin.giovani at gmail.com  Sun Apr  8 16:46:53 2012
From: faccin.giovani at gmail.com (Giovani Faccin)
Date: Sun, 8 Apr 2012 11:46:53 -0300
Subject: [Pw_forum] convergence for lattice parameter
In-Reply-To: <1333893651.47269.YahooMailClassic@web162103.mail.bf1.yahoo.com>
References: <1333893651.47269.YahooMailClassic@web162103.mail.bf1.yahoo.com>
Message-ID: <CAK-VqZB2kFtqQaXEC+ncG7xNvXb3ZrHYHapd5TrEJGTLBo-9wg@mail.gmail.com>

Dear Ayedun,

Try using a higher ecutwfc, like 50 for example. Also a smaller degauss
value. Finally set the ecutrho to 4*ecutwfc if your pseudopotential is not
US, and to 12*ecutwfc if it is.

It`s also a good idea to specify the number of bands, to make sure you got
enough ones on the calculation. If unsure you can just use a high value and
reduce it after a test calculation to compensate for the extra empty bands.

Choose a single ibrav value (if unsure, go for the experimental value or
close to it) and play with these parameters, checking how the total energy
changes with them. Once you get convergence on the total energy, then
you'll have a reliable setup that will allow you to change the ibrav values
and obtain good curves.

Sincerely,

Giovani Faccin

UFMS/Brazil


2012/4/8 funmi ayedun <funmiayedun at yahoo.com>

> Dear All,
>
> Good day all, I am a new user in quantum espresso, I am working on anatase
> TiO2 (with hexagonal structure) but  I have problem with convergence test
> for lattice parameter for TiO2 system.  I have tried to vary celldm 1 from
> 8.2 to 9.0Bohr but I was unable get a convergence result. Also, I tried to
> vary celldm 3  from 0.2441 to 1.3441Bohr and  keeping celldm 1 constant, I
> was unable to get convergence as well. I have my input file below.
>
> &control
>   calculation = 'scf',
>   restart_mode='from_scratch',
>   prefix='TiO2'
>   pseudo_dir='/home/funmilayo/espresso-4.2.1/pseudo',
>   outdir='./',
>     tprnfor = .true.
>   tstress = .true.
> /
> &system
>   ibrav=6, celldm(1)= 8.6808, celldm(3)= 0.7450,
>   nat=3, ntyp=2,occupations='smearing', smearing='marzari-vanderbilt',
> degauss=0.02
>   ecutwfc= 25.0,
> /
> &electrons
>  mixing_beta = 0.7
>  diagonalization='davidson'
> conv_thr =  1.0d-8
> /
> ATOMIC_SPECIES
> Ti 47.867  Ti.blyp-sp-van_ak.UPF
> O  15.994  O.blyp-van_ak.UPF
> ATOMIC_POSITIONS
> Ti 0.00000000   0.00000000   0.00000000
> O  0.33333333   0.33333333   0.33333333
> O  0.80000000   0.20000000   0.50000000
> K_POINTS (automatic)
> 6 6 6  0  0  0
>
> Can anyone please tell me where I have gone wrong.
> Thank you all.
>
>
> Ayedun Oluwafunmilayo,
> PhD student,
> Department of Physics,
> University of Agriculture,
> Abeokuta,
> Nigeria.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From akohlmey at gmail.com  Sun Apr  8 16:54:34 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Sun, 8 Apr 2012 10:54:34 -0400
Subject: [Pw_forum] help on convergence
In-Reply-To: <1333890527.95645.YahooMailNeo@web39403.mail.mud.yahoo.com>
References: <1333890527.95645.YahooMailNeo@web39403.mail.mud.yahoo.com>
Message-ID: <CADTmJ6GSxGV3n9pvpMQ2b73zG4Z6Z0Q4MGAk2XX=S3+83O7=fA@mail.gmail.com>

On Sun, Apr 8, 2012 at 9:08 AM, bamidele ibrahim
<bamideleibrahim at yahoo.com> wrote:
> Dear all,
> ?I am working on TiO2 and running scf for this compound, i have not been
> able to get a convergence. I will be delighted if i can get help on this
> from any expert. I have with this mail the input file for the scf.

this input aborts with an error message.

axel.


>
> Adetunji Bamidele Ibrahim(PhD Student)
> Department of physics,University of Agriculture,
> Abeokuta, Ogun State,Nigeria.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From henod2001 at yahoo.com  Sun Apr  8 18:17:47 2012
From: henod2001 at yahoo.com (henry odhiambo)
Date: Sun, 8 Apr 2012 09:17:47 -0700 (PDT)
Subject: [Pw_forum] Phonon frequency
Message-ID: <1333901867.40794.YahooMailClassic@web121005.mail.ne1.yahoo.com>

Hello colleagues,
?
I am?calculating?the phonon frequencies for stable ( or hexagonal) GST (Ge2Sb2Te5). I am getting some?negative values (contrary to the notion of stability and literature).?I used the unrelaxed structure to do the calculations. Could this be the reason?
?
Henry Otunga
Dept. of Physics
Maseno UNiversity
Kenya? 
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From akohlmey at gmail.com  Sun Apr  8 18:21:39 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Sun, 8 Apr 2012 12:21:39 -0400
Subject: [Pw_forum] Phonon frequency
In-Reply-To: <1333901867.40794.YahooMailClassic@web121005.mail.ne1.yahoo.com>
References: <1333901867.40794.YahooMailClassic@web121005.mail.ne1.yahoo.com>
Message-ID: <CADTmJ6GH=AakD1S-abO2cwCFpWh2gLKD69cwOax89AX31JzU_A@mail.gmail.com>

On Sun, Apr 8, 2012 at 12:17 PM, henry odhiambo <henod2001 at yahoo.com> wrote:

> Hello colleagues,
>
> I am calculating the phonon frequencies for stable ( or hexagonal) GST
> (Ge2Sb2Te5). I am getting some negative values (contrary to the notion of
> stability and literature). I used the unrelaxed structure to do the
> calculations. Could this be the reason?
>

yes. check out how phonons are calculated
and then it will be evident why.

axel.



>
> Henry Otunga
> Dept. of Physics
> Maseno UNiversity
> Kenya
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com  http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.
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From flux_ray12 at 163.com  Sun Apr  8 18:37:56 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Mon, 9 Apr 2012 00:37:56 +0800 (CST)
Subject: [Pw_forum] help on convergence
In-Reply-To: <1333890527.95645.YahooMailNeo@web39403.mail.mud.yahoo.com>
References: <1333890527.95645.YahooMailNeo@web39403.mail.mud.yahoo.com>
Message-ID: <18de9c45.17d87.13692d1ac0d.Coremail.flux_ray12@163.com>

Dear Ibrahim
at least, you need to:
1, increasing your ecutwfc little bit, 25Ry is normally not good enough;
2, adding ecutrho, which should be equal to 8~12 times of ecutwfc, due to you were using ultrasoft pp
3, the most important one, you'd better add crystal after ATOMIC_POSITIONS, I remember the default one may be alat.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-04-08 21:08:47,"bamidele ibrahim" <bamideleibrahim at yahoo.com> wrote:

Dear all,
 I am working on TiO2 and running scf for this compound, i have not been able to get a convergence. I will be delighted if i can get help on this from any expert. I have with this mail the input file for the scf.
 
Adetunji Bamidele Ibrahim(PhD Student)
Department of physics,University of Agriculture,
Abeokuta, Ogun State,Nigeria.
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From bahadira at buffalo.edu  Sun Apr  8 21:42:34 2012
From: bahadira at buffalo.edu (bahadir)
Date: Sun, 08 Apr 2012 15:42:34 -0400
Subject: [Pw_forum] ekphon q-points and kpoint.x mesh does not match
Message-ID: <4F81EA2A.9030106@buffalo.edu>

Hi,

i am calculating elphon interactions for MgH12 which has S_6 pint group 
with spacegroup 148(due to findsym results) my k-grid is 16x16x16 and 
coarse q-mesh is 4x4x4. It gives 14 q-points in elphon output file and 
produces 14 elph. XXXXX.XXXXX.XXXXX. also output shows it has S_6 symmetry.
when i try to generate k-points from kpoints.x for this sytstem (bravais 
lattice=5 and celldm(4)=0) it generates 13 points. so i can not 
calculate lambda coefficiant with lambda.x due to mismatch of generated 
points and points in elphon output.

is there something wrong with my symmetry or with kpoint.x?

thank you

-- 
Dr.Bahadir Altintas

* Dept. of Chemistry
  SUNY Buffalo
  NY,USA

* Abant Izzet Baysal University
   Dept. of Computer Education
   Bolu,Turkey


From merilege at gmail.com  Sun Apr  8 21:57:29 2012
From: merilege at gmail.com (merilege at gmail.com)
Date: Sun, 8 Apr 2012 20:57:29 +0100
Subject: [Pw_forum] Pw_forum Digest, Vol 58, Issue 9
In-Reply-To: <mailman.2022.1333901870.9401.pw_forum@pwscf.org>
References: <mailman.2022.1333901870.9401.pw_forum@pwscf.org>
Message-ID: <CB41096A-ED4A-4607-B6FF-4C1BA6251254@gmail.com>


Eliasberhe73 at yahoo.or
Sent from my iPod

On 8 Apr 2012, at 17:17, 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. band calculation (Maryam Jamali)
>   2. made nanowire (samad zare)
>   3. help on convergence (bamidele ibrahim)
>   4. convergence for lattice parameter (funmi ayedun)
>   5. Re: made nanowire (Axel Kohlmeyer)
>   6. Re: convergence for lattice parameter (Giovani Faccin)
>   7. Re: help on convergence (Axel Kohlmeyer)
>   8. Phonon frequency (henry odhiambo)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sun, 08 Apr 2012 13:27:26 +0430 (IRDT)
> From: Maryam Jamali <jamali at dena.kntu.ac.ir>
> Subject: [Pw_forum] band calculation
> To: pw_forum at pwscf.org
> Message-ID: <48f850f9-5ea7-4d20-bc7a-f28177d0b64b at mail.kntu.ac.ir>
> Content-Type: text/plain; charset=utf-8
> 
> 
> Dear all,
> 
> I have run band calculation job with pw.x. The job was truncated. Is there any instruction to restart the job?
> 
> Thank you in advance 
> 
> Maryam Jamali
> phD student of physical chemistry 
> K.N.T.University of technology.Tehran 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Sun, 8 Apr 2012 17:27:55 +0430
> From: samad zare <samadzare at gmail.com>
> Subject: [Pw_forum] made nanowire
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
>    <CAJ_oS4TOwD_Eiattxm8Dk2o+KZsY=7PcJkZJ1pseM-OvQbrVFw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> dear all pwscf user
> i want simulation nanowires by pwscf  how can do it?
> i know we must made supercell how to  made supercell?
> 
> -- 
> With Best Regards
> SAMAD ZARE, phD  Student UTM university
> Nanotechnology Research Alliance
> APSI, UTM 81310, Skudai,Johor Bahru, Malaysia
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> 
> ------------------------------
> 
> Message: 3
> Date: Sun, 8 Apr 2012 06:08:47 -0700 (PDT)
> From: bamidele ibrahim <bamideleibrahim at yahoo.com>
> Subject: [Pw_forum] help on convergence
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
>    <1333890527.95645.YahooMailNeo at web39403.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear all,
> ?I am working on TiO2 and running scf for this compound, i have not been able to get a convergence. I will be delighted if i can get help on this from any expert. I have with this mail the input file for the scf. 
> 
> ?
> Adetunji Bamidele Ibrahim(PhD Student)
> Department of physics,University of Agriculture,
> Abeokuta, Ogun State,Nigeria.
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> 
> ------------------------------
> 
> Message: 4
> Date: Sun, 8 Apr 2012 07:00:51 -0700 (PDT)
> From: funmi ayedun <funmiayedun at yahoo.com>
> Subject: [Pw_forum] convergence for lattice parameter
> To: pw_forum at pwscf.org
> Message-ID:
>    <1333893651.47269.YahooMailClassic at web162103.mail.bf1.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear All,
> 
> Good day all, I am a new user in quantum espresso, I am working on anatase TiO2 (with hexagonal structure) but? I have problem with convergence test? for lattice parameter for TiO2 system.? I have tried to vary celldm 1 from 8.2 to 9.0Bohr but I was unable get a convergence result. Also, I tried to vary celldm 3? from 0.2441 to 1.3441Bohr and? keeping celldm 1 constant, I was unable to get convergence as well. I have my input file below. 
> 
> &control
> ? calculation = 'scf',
> ? restart_mode='from_scratch',
> ? prefix='TiO2'
> ? pseudo_dir='/home/funmilayo/espresso-4.2.1/pseudo',
> ? outdir='./',
> ??? tprnfor = .true.
> ? tstress = .true.
> /
> &system
> ? ibrav=6, celldm(1)= 8.6808, celldm(3)= 0.7450,
> ? nat=3, ntyp=2,occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 
> ? ecutwfc= 25.0,
> /
> &electrons
> ?mixing_beta = 0.7
> ?diagonalization='davidson'
> conv_thr =? 1.0d-8
> /
> ATOMIC_SPECIES
> Ti 47.867? Ti.blyp-sp-van_ak.UPF
> O? 15.994? O.blyp-van_ak.UPF
> ATOMIC_POSITIONS
> Ti 0.00000000?? 0.00000000?? 0.00000000 
> O? 0.33333333?? 0.33333333?? 0.33333333
> O? 0.80000000?? 0.20000000?? 0.50000000
> K_POINTS (automatic)
> 6 6 6? 0? 0? 0
> 
> Can anyone please tell me where I have gone wrong.? 
> Thank you all.
> 
> 
> Ayedun Oluwafunmilayo,
> PhD student,
> Department of Physics,
> University of Agriculture,
> Abeokuta,
> Nigeria.
> -------------- next part --------------
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> 
> ------------------------------
> 
> Message: 5
> Date: Sun, 8 Apr 2012 10:29:48 -0400
> From: Axel Kohlmeyer <akohlmey at gmail.com>
> Subject: Re: [Pw_forum] made nanowire
> To: samad zare <samadzare at gmail.com>
> Cc: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
>    <CADTmJ6GPtE4_VijAJUYvibquxgvMYXLUMMUQzaFipp2e4LHvkw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> On Sun, Apr 8, 2012 at 8:57 AM, samad zare <samadzare at gmail.com> wrote:
>> dear all pwscf user
>> i want simulation nanowires by pwscf? how can do it?
> 
> like all other system. define the starting geometry
> and have a go. to make a wire you can either compute
> the positions or take a crystal and remove the positions
> that don't fit with your desired shape of wire.
> 
>> i know we must made supercell how to? made supercell?
> 
> trivial. take a singe cell and replicate.
> 
> cheers,
>    axel.
> 
> 
>> --
>> With Best Regards
>> SAMAD ZARE, phD? Student UTM university
>> Nanotechnology Research Alliance
>> APSI, UTM 81310, Skudai,Johor Bahru, Malaysia
>> 
>> 
>> 
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>> 
> 
> 
> 
> -- 
> Dr. Axel Kohlmeyer
> akohlmey at gmail.com ?http://goo.gl/1wk0
> 
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
> 
> 
> ------------------------------
> 
> Message: 6
> Date: Sun, 8 Apr 2012 11:46:53 -0300
> From: Giovani Faccin <faccin.giovani at gmail.com>
> Subject: Re: [Pw_forum] convergence for lattice parameter
> To: funmi ayedun <funmiayedun at yahoo.com>
> Cc: pw_forum at pwscf.org
> Message-ID:
>    <CAK-VqZB2kFtqQaXEC+ncG7xNvXb3ZrHYHapd5TrEJGTLBo-9wg at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear Ayedun,
> 
> Try using a higher ecutwfc, like 50 for example. Also a smaller degauss
> value. Finally set the ecutrho to 4*ecutwfc if your pseudopotential is not
> US, and to 12*ecutwfc if it is.
> 
> It`s also a good idea to specify the number of bands, to make sure you got
> enough ones on the calculation. If unsure you can just use a high value and
> reduce it after a test calculation to compensate for the extra empty bands.
> 
> Choose a single ibrav value (if unsure, go for the experimental value or
> close to it) and play with these parameters, checking how the total energy
> changes with them. Once you get convergence on the total energy, then
> you'll have a reliable setup that will allow you to change the ibrav values
> and obtain good curves.
> 
> Sincerely,
> 
> Giovani Faccin
> 
> UFMS/Brazil
> 
> 
> 2012/4/8 funmi ayedun <funmiayedun at yahoo.com>
> 
>> Dear All,
>> 
>> Good day all, I am a new user in quantum espresso, I am working on anatase
>> TiO2 (with hexagonal structure) but  I have problem with convergence test
>> for lattice parameter for TiO2 system.  I have tried to vary celldm 1 from
>> 8.2 to 9.0Bohr but I was unable get a convergence result. Also, I tried to
>> vary celldm 3  from 0.2441 to 1.3441Bohr and  keeping celldm 1 constant, I
>> was unable to get convergence as well. I have my input file below.
>> 
>> &control
>>  calculation = 'scf',
>>  restart_mode='from_scratch',
>>  prefix='TiO2'
>>  pseudo_dir='/home/funmilayo/espresso-4.2.1/pseudo',
>>  outdir='./',
>>    tprnfor = .true.
>>  tstress = .true.
>> /
>> &system
>>  ibrav=6, celldm(1)= 8.6808, celldm(3)= 0.7450,
>>  nat=3, ntyp=2,occupations='smearing', smearing='marzari-vanderbilt',
>> degauss=0.02
>>  ecutwfc= 25.0,
>> /
>> &electrons
>> mixing_beta = 0.7
>> diagonalization='davidson'
>> conv_thr =  1.0d-8
>> /
>> ATOMIC_SPECIES
>> Ti 47.867  Ti.blyp-sp-van_ak.UPF
>> O  15.994  O.blyp-van_ak.UPF
>> ATOMIC_POSITIONS
>> Ti 0.00000000   0.00000000   0.00000000
>> O  0.33333333   0.33333333   0.33333333
>> O  0.80000000   0.20000000   0.50000000
>> K_POINTS (automatic)
>> 6 6 6  0  0  0
>> 
>> Can anyone please tell me where I have gone wrong.
>> Thank you all.
>> 
>> 
>> Ayedun Oluwafunmilayo,
>> PhD student,
>> Department of Physics,
>> University of Agriculture,
>> Abeokuta,
>> Nigeria.
>> 
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>> 
>> 
> -------------- next part --------------
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> 
> ------------------------------
> 
> Message: 7
> Date: Sun, 8 Apr 2012 10:54:34 -0400
> From: Axel Kohlmeyer <akohlmey at gmail.com>
> Subject: Re: [Pw_forum] help on convergence
> To: bamidele ibrahim <bamideleibrahim at yahoo.com>
> Cc: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
>    <CADTmJ6GSxGV3n9pvpMQ2b73zG4Z6Z0Q4MGAk2XX=S3+83O7=fA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> On Sun, Apr 8, 2012 at 9:08 AM, bamidele ibrahim
> <bamideleibrahim at yahoo.com> wrote:
>> Dear all,
>> ?I am working on TiO2 and running scf for this compound, i have not been
>> able to get a convergence. I will be delighted if i can get help on this
>> from any expert. I have with this mail the input file for the scf.
> 
> this input aborts with an error message.
> 
> axel.
> 
> 
>> 
>> Adetunji Bamidele Ibrahim(PhD Student)
>> Department of physics,University of Agriculture,
>> Abeokuta, Ogun State,Nigeria.
>> 
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>> 
> 
> 
> 
> -- 
> Dr. Axel Kohlmeyer
> akohlmey at gmail.com ?http://goo.gl/1wk0
> 
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
> 
> 
> ------------------------------
> 
> Message: 8
> Date: Sun, 8 Apr 2012 09:17:47 -0700 (PDT)
> From: henry odhiambo <henod2001 at yahoo.com>
> Subject: [Pw_forum] Phonon frequency
> To: pw_forum at pwscf.org
> Message-ID:
>    <1333901867.40794.YahooMailClassic at web121005.mail.ne1.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hello colleagues,
> ?
> I am?calculating?the phonon frequencies for stable ( or hexagonal) GST (Ge2Sb2Te5). I am getting some?negative values (contrary to the notion of stability and literature).?I used the unrelaxed structure to do the calculations. Could this be the reason?
> ?
> Henry Otunga
> Dept. of Physics
> Maseno UNiversity
> Kenya? 
> -------------- 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 58, Issue 9
> ***************************************

From pankajsahota at gmail.com  Mon Apr  9 07:36:01 2012
From: pankajsahota at gmail.com (pankaj sahota)
Date: Mon, 9 Apr 2012 11:06:01 +0530
Subject: [Pw_forum] Error in running the pwcond.x
Message-ID: <CADww=10n0FnsTL7C1YZswwMP50jvCt__4nu1u4mQU0Kd_7D9dw@mail.gmail.com>

Hi,

I am running the transport calculation of carbon chains. I am gettig the
following error with espresso-4.3.2:
########################################################################################################################
# FROM IOTK LIBRARY, VERSION 1.2.0
# UNRECOVERABLE ERROR (ierr=1)
# ERROR IN: iotk_scan_dat_aux (iotk_dat+REAL2_0.f90:1403)
# CVS Revision: 1.27
# ERROR IN: iotk_scan_dat (iotk_dat+REAL2_0.f90:1582)
# CVS Revision: 1.27
# Error reading data
name=z.1
rkind=8
rlen=-1
########################################################################################################################
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec has exited due to process rank 0 with PID 23750 on
node c2411.tusker.hcc.unl.edu exiting improperly. There are two reasons
this could occur:

1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.

2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"

This may have caused other processes in the application to be
terminated by signals sent by mpiexec (as reported here).


But I the program runs perfectly fine with espresso-4.2.

Please help me to resolve the problem.
Thanks in advance.
Pankaj.

-- 
Pankaj Kumar
DST Project Fellow(Ph.D.)
Department of Physics
The LNM IIT Jaipur
Mob. No. +91 9736694726
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From pankajsahota at gmail.com  Mon Apr  9 09:23:10 2012
From: pankajsahota at gmail.com (pankaj sahota)
Date: Mon, 9 Apr 2012 12:53:10 +0530
Subject: [Pw_forum] Error in running the pwcond.x
In-Reply-To: <CADww=10n0FnsTL7C1YZswwMP50jvCt__4nu1u4mQU0Kd_7D9dw@mail.gmail.com>
References: <CADww=10n0FnsTL7C1YZswwMP50jvCt__4nu1u4mQU0Kd_7D9dw@mail.gmail.com>
Message-ID: <CADww=13UiYvtSYMBOYUkxP2xRSRpoigi0oE4QKnr+8kath2BDw@mail.gmail.com>

Hi

while looking at the problem of pwcond.x , I found the the calculation runs
for ifospin=1 but it shows this error for ifspin=2. I also tried with the
provided examples. I got the following output of example12 of
espresso-4.3.2. I just want to know that to find the transmission of down
spin states, do i have some other tag or it this iofspin=2.


/home/sellmyer/sahota/softwares/espresso-4.3.2/examples/example12 : starting

This example shows how to use pw.x and pwcond.x to calculate the
complex bands and the transmission coefficient of an open quantum
system.

  executables directory: /home/sellmyer/sahota/softwares/espresso-4.3.2/bin
  pseudo directory:
/home/sellmyer/sahota/softwares/espresso-4.3.2/pseudo
  temporary directory:   /home/sellmyer/sahota/tmp
  checking that needed directories and files exist... done

  running pw.x as:
/home/sellmyer/sahota/softwares/espresso-4.3.2/bin/pw.x
  running pwcond.x as:
/home/sellmyer/sahota/softwares/espresso-4.3.2/bin/pwcond.x

  cleaning /home/sellmyer/sahota/tmp... done
  running the scf calculation for Al... done
  running pwcond.x to calculate the complex bands of Al... done
  running the scf calculation for Al monatomic wire... done
  running pwcond.x to calculate the complex bands of Al wire... done
  running the scf calculation for Ni bulk... done
  running pwcond.x to calculate the complex bands of Ni... done
  running the scf calculation for Al monatomic wire... done
  running the scf calculation for Al wire with H impurity... done
  running pwcond.x to calculate transmission of a perfect Al wire
...########################################################################################################################
# FROM IOTK LIBRARY, VERSION 1.2.0
# UNRECOVERABLE ERROR (ierr=1)
# ERROR IN: iotk_scan_dat_aux (iotk_dat+REAL2_0.f90:1403)
# CVS Revision: 1.27
# ERROR IN: iotk_scan_dat (iotk_dat+REAL2_0.f90:1582)
# CVS Revision: 1.27
# Error reading data
name=z.1
rkind=8
rlen=-1
########################################################################################################################
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
Error condition encountered during test: exit status = 1
Aborting


On Mon, Apr 9, 2012 at 11:06 AM, pankaj sahota <pankajsahota at gmail.com>wrote:

> Hi,
>
> I am running the transport calculation of carbon chains. I am gettig the
> following error with espresso-4.3.2:
>
> ########################################################################################################################
> # FROM IOTK LIBRARY, VERSION 1.2.0
> # UNRECOVERABLE ERROR (ierr=1)
> # ERROR IN: iotk_scan_dat_aux (iotk_dat+REAL2_0.f90:1403)
> # CVS Revision: 1.27
> # ERROR IN: iotk_scan_dat (iotk_dat+REAL2_0.f90:1582)
> # CVS Revision: 1.27
> # Error reading data
> name=z.1
> rkind=8
> rlen=-1
>
> ########################################################################################################################
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> mpiexec has exited due to process rank 0 with PID 23750 on
> node c2411.tusker.hcc.unl.edu exiting improperly. There are two reasons
> this could occur:
>
> 1. this process did not call "init" before exiting, but others in
> the job did. This can cause a job to hang indefinitely while it waits
> for all processes to call "init". By rule, if one process calls "init",
> then ALL processes must call "init" prior to termination.
>
> 2. this process called "init", but exited without calling "finalize".
> By rule, all processes that call "init" MUST call "finalize" prior to
> exiting or it will be considered an "abnormal termination"
>
> This may have caused other processes in the application to be
> terminated by signals sent by mpiexec (as reported here).
>
>
> But I the program runs perfectly fine with espresso-4.2.
>
> Please help me to resolve the problem.
> Thanks in advance.
> Pankaj.
>
> --
> Pankaj Kumar
> DST Project Fellow(Ph.D.)
> Department of Physics
> The LNM IIT Jaipur
> Mob. No. +91 9736694726
>
>
>


-- 
Pankaj Kumar
DST Project Fellow(Ph.D.)
Department of Physics
The LNM IIT Jaipur
Mob. No. +91 9736694726
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From eariel99 at gmail.com  Mon Apr  9 12:05:50 2012
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Mon, 9 Apr 2012 12:05:50 +0200
Subject: [Pw_forum] Ba pseudopotential for spin-orbit calculations
Message-ID: <CAM5Vcw_TX=zh6PxPmoVoPF2UPc1uTxjtrY4No-rUWuJyfEfSfg@mail.gmail.com>

Hi,
Is there any Ba pseudopotential available that can be used for spin-orbit
calculations (generated with fully relativistic hamiltonian).
Thanks,
-- 


Eduardo Menendez Proupin
Departamento de Qu?mica Fisica Aplicada
Facultad de Ciencias
Universidad Aut?noma de Madrid
28049 Madrid, Spain
Phone: +34 91 497 6706

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

"...man never knows for who he suffers and waits. He suffers and waits and
works for peoples he will never meet, and who at the same time will suffer
and wait and work for others who will also not be happy, as man always
desires a happiness that is beyond the lot that he is given. But the
greatness of man is precisely in wanting to improve what he is. In
assigning himself Tasks. In the Kingdom of Heaven there is no greatness to
conquer, for everything there is an established hierarchy, the unknown is
unobscured, existence is without end, sacrifice, rest, and delight are
impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful
within his misery, capable of loving in the middle of calamity, man can
only find his greatness, his full self-realization, in the Kingdom of this
World." - Alejo Carpentier
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From trambui at u.boisestate.edu  Tue Apr 10 00:39:38 2012
From: trambui at u.boisestate.edu (Tram Bui)
Date: Mon, 9 Apr 2012 16:39:38 -0600
Subject: [Pw_forum] problem with average.x (average potential) calculation
Message-ID: <CANzxBn_qEVbvBonEnkGm2C2_HTO2Z+M7tPwqdUrOAYr1uMGD1g@mail.gmail.com>

Dear All QE Users,

    I did an average.x calculation for my bulk SiC structure. I know the
process includes: scf calculation, pp.x to obtain 3D potential, then
average.x to obtain macroscopic 1D potential. For an input file of
average.x calculation, and I defined the nfile=1, since I have only one
data file from pp.x calculation. I got an error say: "nfile value is
wrong". Would you please give me some suggestion on what might be the issue?

Thank you very much,

Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From mansourehp at gmail.com  Tue Apr 10 09:51:30 2012
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Tue, 10 Apr 2012 12:21:30 +0430
Subject: [Pw_forum] GW
Message-ID: <CAAZPSteyCtJJL7_nQ8LmuXWLRRYSkL1ou7DQTcaOSbd-1KStXA@mail.gmail.com>

Dear pwscf users,
I would like to know  can one use GW approximation to obtain  bandstructure
of a system?
considering GWW-examples I find that the GW quasi-particle energies can be
calculated but what about GWA in bandstructure.
I look forward to hear from you,
M. Pashangpour
IIAU, Tehran,Iran
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From abmus007 at gmail.com  Tue Apr 10 15:06:52 2012
From: abmus007 at gmail.com (Abolore Musari)
Date: Tue, 10 Apr 2012 08:06:52 -0500
Subject: [Pw_forum] xcrysden
In-Reply-To: <1332928401.14514.12.camel@catalyst.ijs.si>
References: <BAY151-W638C03AAC77A95724F0CC6A34A0@phx.gbl>
	<1332928401.14514.12.camel@catalyst.ijs.si>
Message-ID: <CAOP21kJx1rPEm78BFwauRu8bODAUZWZ2Nu+XaewctgTWNhDxqw@mail.gmail.com>

Dear ramzi
You can view this structure using xcrysden by using the following command
xcrysden --pwi filename

On 3/28/12, Tone Kokalj <tone.kokalj at ijs.si> wrote:
> On Tue, 2012-03-27 at 11:38 +0100, ramzi alaya wrote:
>> Dear all,
>>
>>
>> I have a file input structure Zinc blenbe relaxed, do I draw this
>> structure with xcrysden?
>> Can you help me out?
>
> You would like to visualize the structure from your pw.x input file or
> what?
>
> If so you may try with: xcrysden --pwi filename
>
> 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
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From Max.Lawson at unige.ch  Tue Apr 10 16:26:31 2012
From: Max.Lawson at unige.ch (=?ISO-8859-1?Q?Lat=E9vi_Max_LAWSON_DAKU?=)
Date: Tue, 10 Apr 2012 16:26:31 +0200
Subject: [Pw_forum] ph.x on BG/P: does not seem to be functional
Message-ID: <4F844317.7040805@unige.ch>

Dear QE developers and users,

I would like to run some phonons calculations on a BG/P,
with QE-4.3.2.

I have therefore compiled the code using a make.sys file which
is adapted from $TOPDIR/INSTALL/Make.BGP (please see the
attached make.sys file): tThe compilation went fine (excepts
warning about the sizes of the symbols _pow, _acos, _asin and
_log, which are not the same in libmass.a and in libxlfmath.a).

I have then tried to run testcases taken from examples
15 (alas.{sch,ph}.in) and 24 (ni.{scf,phG}.in). In both cases,
the preliminaries SCF calculation completed successfully
(inferred from the comparison with the reference data),
while the phonon calculations systematically fail with

     [...]    BE_MPI (ERROR): "killed with signal 11"  [...]


The calculation was submitted using a command line like

$ mpirun -partition R00-M0-03 -np 128 -mode VN -cwd $PWD  \
    -exe $PH_EXE -args "-npool 4 -in ni.phG.in" > ni.phG.out


I have tried also with QE-4.3.1: same behavior.

Did someone succeed in running a BG/P-mpixlf90-compiled ph.x
executable? If so can she/he share his compilation setup with me?

Except recompiling with debugging turned on (which supposes being
confident about the compilation setup), I am somehow at loss on
how to deal with this issue. I thank you in advance for your advices
and suggestions are warmly welcome.

Best regards,
Max

-- 
Latevi Max LAWSON DAKU
Universite de Geneve - Sciences II
Quai Ernest-Ansermet 30                            Tel: (41) 22/379 6548
CH-1211 Geneve 4                                   Fax: (41) 22/379 6103



-------------- next part --------------
# make.sys.  Generated from make.sys.in by configure.

# compilation rules

.SUFFIXES :
.SUFFIXES : .o .c .f .f90

# most fortran compilers can directly preprocess c-like directives: use
# 	$(MPIF90) $(F90FLAGS) -c $<
# if explicit preprocessing by the C preprocessor is needed, use:
# 	$(CPP) $(CPPFLAGS) $< -o $*.F90 
#	$(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o
# remember the tabulator in the first column !!!

.f90.o:
	$(MPIF90) $(F90FLAGS) -c $<

# .f.o and .c.o: do not modify

.f.o:
	$(F77) $(FFLAGS) -c $<

.c.o:
	$(CC) $(CFLAGS)  -c $<


# DFLAGS  = precompilation options (possible arguments to -D and -U)
#           used by the C compiler and preprocessor
# FDFLAGS = as DFLAGS, for the f90 compiler
# See include/defs.h.README for a list of options and their meaning
# With the exception of IBM xlf, FDFLAGS = $(DFLAGS)
# For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas 

DFLAGS         = -D__AIX -D__XLF -D__ESSL -D__FFTW3 -D__MASS -D__MPI -D__PARA -D__SCALAPACK -D__WALLTIME
FDFLAGS        = -D__AIX,-D__XLF,-D__ESSL,-D__FFTW3,-D__MASS,-D__MPI,-D__PARA,-D__SCALAPACK,-D__WALLTIME

# IFLAGS = how to locate directories where files to be included are
# In most cases, IFLAGS = -I../include

IFLAGS         = -I../include

# MOD_FLAGS = flag used by f90 compiler to locate modules
# Each Makefile defines the list of needed modules in MODFLAGS

MOD_FLAG      = -I

# Compilers: fortran-90, fortran-77, C
# If a parallel compilation is desired, MPIF90 should be a fortran-90 
# compiler that produces executables for parallel execution using MPI
# (such as for instance mpif90, mpf90, mpxlf90,...);
# otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...)
# If you have a parallel machine but no suitable candidate for MPIF90,
# try to specify the directory containing "mpif.h" in IFLAGS
# and to specify the location of MPI libraries in MPI_LIBS

MPIF90         = mpixlf90_r
#F90           = bgxlf90_r
CC             = bgxlc_r
F77            = bgxlf_r

# C preprocessor and preprocessing flags - for explicit preprocessing, 
# if needed (see the compilation rules above)
# preprocessing flags must include DFLAGS and IFLAGS

CPP            = cpp
CPPFLAGS       = -P -traditional $(DFLAGS) $(IFLAGS)

# compiler flags: C, F90, F77
# C flags must include DFLAGS and IFLAGS
# F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax

CFLAGS         = -O2 $(DFLAGS) $(IFLAGS)
FFLAGS         = -qalias=noaryovrlp:nointptr -O2 -qstrict -qdpc=e -qtune=450 -qarch=450d 
F90FLAGS       = $(FFLAGS) -qsuffix=cpp=f90 -WF,$(FDFLAGS) $(IFLAGS) $(MODFLAGS)

# compiler flags without optimization for fortran-77
# the latter is NEEDED to properly compile dlamch.f, used by lapack

FFLAGS_NOOPT   = -O0

# compiler flag needed by some compilers when the main is not fortran
# Currently used for Yambo

FFLAGS_NOMAIN   = 

# Linker, linker-specific flags (if any)
# Typically LD coincides with F90 or MPIF90, LD_LIBS is empty

LD             = mpixlf90_r
LDFLAGS        = -Wl,--allow-multiple-definition
LD_LIBS        = 

# External Libraries (if any) : blas, lapack, fft, MPI

# If you have nothing better, use the local copy :
# BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a
# BLAS_LIBS_SWITCH = internal

BLAS_LIBS      = -L/bgsys/ibm_essl/sles10/prod/opt/ibmmath/essl/4.4/lib/ -lesslbg
BLAS_LIBS_SWITCH = external

# If you have nothing better, use the local copy :
# LAPACK_LIBS = /your/path/to/espresso/lapack-3.2/lapack.a
# LAPACK_LIBS_SWITCH = internal
# For IBM machines with essl (-D__ESSL): load essl BEFORE lapack !
# remember that LAPACK_LIBS precedes BLAS_LIBS in loading order

LAPACK_LIBS    = /home/lawson/apps/netlib/liblapack.a 
LAPACK_LIBS_SWITCH = external

SCALAPACK_LIBS = /home/lawson/apps/netlib/libscalapack.a 

# nothing needed here if the the internal copy of FFTW is compiled
# (needs -D__FFTW in DFLAGS)

FFT_LIBS       = -L/bgsys/local/fftw-3.2.2/lib -lfftw3 

# For parallel execution, the correct path to MPI libraries must
# be specified in MPI_LIBS (except for IBM if you use mpxlf)

MPI_LIBS       = 

# IBM-specific: MASS libraries, if available and if -D__MASS is defined in FDFLAGS

MASS_LIBS      =  -lmassv -lmass

# ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv

AR             = ar
ARFLAGS        = ruv

# ranlib command. If ranlib is not needed (it isn't in most cases) use
# RANLIB = echo

RANLIB         = ranlib

# all internal and external libraries - do not modify

FLIB_TARGETS   = all

LIBOBJS        = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a 
LIBS           = $(SCALAPACK_LIBS) $(LAPACK_LIBS) $(FFT_LIBS) $(BLAS_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(LD_LIBS)

# topdir for linking espresso libs with plugins
TOPDIR = /home/lawson/bgscratch/espresso-4.3.2

From Max.Lawson at unige.ch  Tue Apr 10 18:03:58 2012
From: Max.Lawson at unige.ch (=?ISO-8859-1?Q?Lat=E9vi_Max_LAWSON_DAKU?=)
Date: Tue, 10 Apr 2012 18:03:58 +0200
Subject: [Pw_forum] ph.x on BG/P: does not seem to be functional
In-Reply-To: <4F844317.7040805@unige.ch>
References: <4F844317.7040805@unige.ch>
Message-ID: <4F8459EE.3080907@unige.ch>

Please find attached the outputs of the SCF and
(aborted) phonon calculations (Ni case). These
are 4.3.1 results; using 4.3.2, similar results are
obtained.

Max

On 10. 04. 12 16:26, Lat?vi Max LAWSON DAKU wrote:
> Dear QE developers and users,
>
> I would like to run some phonons calculations on a BG/P,
> with QE-4.3.2.
>
> I have therefore compiled the code using a make.sys file which
> is adapted from $TOPDIR/INSTALL/Make.BGP (please see the
> attached make.sys file): tThe compilation went fine (excepts
> warning about the sizes of the symbols _pow, _acos, _asin and
> _log, which are not the same in libmass.a and in libxlfmath.a).
>
> I have then tried to run testcases taken from examples
> 15 (alas.{sch,ph}.in) and 24 (ni.{scf,phG}.in). In both cases,
> the preliminaries SCF calculation completed successfully
> (inferred from the comparison with the reference data),
> while the phonon calculations systematically fail with
>
>     [...]    BE_MPI (ERROR): "killed with signal 11"  [...]
>
>
> The calculation was submitted using a command line like
>
> $ mpirun -partition R00-M0-03 -np 128 -mode VN -cwd $PWD  \
>    -exe $PH_EXE -args "-npool 4 -in ni.phG.in" > ni.phG.out
>
>
> I have tried also with QE-4.3.1: same behavior.
>
> Did someone succeed in running a BG/P-mpixlf90-compiled ph.x
> executable? If so can she/he share his compilation setup with me?
>
> Except recompiling with debugging turned on (which supposes being
> confident about the compilation setup), I am somehow at loss on
> how to deal with this issue. I thank you in advance for your advices
> and suggestions are warmly welcome.
>
> Best regards,
> Max
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
Latevi Max LAWSON DAKU
Universite de Geneve - Sciences II
Quai Ernest-Ansermet 30                            Tel: (41) 22/379 6548
CH-1211 Geneve 4                                   Fax: (41) 22/379 6103



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     Program PHONON v.4.3.1     starts on 10Apr2012 at 14:16:29 

     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   128 processors
     K-points division:     npool     =    4
     R & G space division:  proc/pool =   32

     Ultrasoft (Vanderbilt) Pseudopotentials

   Info: using nr1, nr2, nr3 values from input

   Info: using nr1s, nr2s, nr3s values from input
     file Ni.pbe-nd-rrkjus.UPF: wavefunction(s)  4S renormalized
 
   Stick Mesh
   ----------
   nst =   451,  nstw =    61, nsts =   163
               n.st   n.stw   n.sts    n.g    n.gw   n.gs
   min          14       1       5     199       8      39
   max          15       2       6     202      11      46
        451      61     163    6423     331    1411
 

     Check: negative/imaginary core charge=   -0.000020    0.000000

     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )
<Apr 10 16:16:52.450087> BE_MPI (ERROR): The error message in the job record is as follows:
<Apr 10 16:16:52.450180> BE_MPI (ERROR):   "killed with signal 11"
-------------- next part --------------

     Program PWSCF v.4.3.1      starts on 10Apr2012 at 13:36:23 

     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   128 processors
     K-points division:     npool     =    4
     R & G space division:  proc/pool =   32

     Current dimensions of program PWSCF are:
     Max number of different atomic species (ntypx) = 10
     Max number of k-points (npk) =  40000
     Max angular momentum in pseudopotentials (lmaxx) =  3
     Waiting for input...
     file Ni.pbe-nd-rrkjus.UPF: wavefunction(s)  4S renormalized

     Fixed quantization axis for GGA:     0.000000    1.000000    0.000000

     Subspace diagonalization in iterative solution of the eigenvalue problem:
     parallel, distributed-memory algorithm (size of sub-group:  4*  4 procs)


   Info: using nr1, nr2, nr3 values from input
 
   Stick Mesh
   ----------
   nst =   451,  nstw =    61, nsts =   163
               n.st   n.stw   n.sts    n.g    n.gw   n.gs
   min          14       1       5     199       8      39
   max          15       2       6     202      11      46
        451      61     163    6423     331    1411
 
     Generating pointlists ...
     new r_m :   0.2917 (alat units)  1.9397 (a.u.) for type    1
     Message from routine sym_rho_init:
     likely internal error: no G-vectors found


     bravais-lattice index     =            2
     lattice parameter (alat)  =       6.6500  a.u.
     unit-cell volume          =      73.5199 (a.u.)^3
     number of atoms/cell      =            1
     number of atomic types    =            1
     number of electrons       =        10.00
     number of Kohn-Sham states=           18
     kinetic-energy cutoff     =      27.0000  Ry
     charge density cutoff     =     300.0000  Ry
     convergence threshold     =      1.0E-12
     mixing beta               =       0.7000
     number of iterations used =            8  plain     mixing
     Exchange-correlation      =  SLA  PW   PBE  PBE ( 1 4 3 4 0)
     EXX-fraction              =        0.00
     Noncollinear calculation without spin-orbit


     celldm(1)=   6.650000  celldm(2)=   0.000000  celldm(3)=   0.000000
     celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=   0.000000

     crystal axes: (cart. coord. in units of alat)
               a(1) = (  -0.500000   0.000000   0.500000 )  
               a(2) = (   0.000000   0.500000   0.500000 )  
               a(3) = (  -0.500000   0.500000   0.000000 )  

     reciprocal axes: (cart. coord. in units 2 pi/alat)
               b(1) = ( -1.000000 -1.000000  1.000000 )  
               b(2) = (  1.000000  1.000000  1.000000 )  
               b(3) = ( -1.000000  1.000000 -1.000000 )  


     PseudoPot. # 1 for Ni read from file Ni.pbe-nd-rrkjus.UPF
     MD5 check sum: 8081f0a005c9a5470caab1a58e82ecb2
     Pseudo is Ultrasoft + core correction, Zval = 10.0
     Generated by new atomic code, or converted to UPF format
     Using radial grid of 1203 points,  6 beta functions with: 
                l(1) =   0
                l(2) =   0
                l(3) =   1
                l(4) =   1
                l(5) =   2
                l(6) =   2
     Q(r) pseudized with 0 coefficients 


     atomic species   valence    mass     pseudopotential
        Ni            10.00    58.69340     Ni( 1.00)

     16 Sym.Ops. (with inversion)


   Cartesian axes

     site n.     atom                  positions (alat units)
         1           Ni  tau(  1) = (   0.0000000   0.0000000   0.0000000  )

     number of k points=    20  Methfessel-Paxton smearing, width (Ry)=  0.0200
                       cart. coord. in units 2pi/alat
        k(    1) = (  -0.1250000   0.1250000   0.1250000), wk =   0.0312500
        k(    2) = (  -0.3750000   0.3750000  -0.1250000), wk =   0.0625000
        k(    3) = (   0.3750000  -0.3750000   0.6250000), wk =   0.0625000
        k(    4) = (   0.1250000  -0.1250000   0.3750000), wk =   0.0625000
        k(    5) = (  -0.1250000   0.6250000   0.1250000), wk =   0.0312500
        k(    6) = (   0.6250000  -0.1250000   0.8750000), wk =   0.0625000
        k(    7) = (   0.3750000   0.1250000   0.6250000), wk =   0.0625000
        k(    8) = (  -0.1250000  -0.8750000   0.1250000), wk =   0.0312500
        k(    9) = (  -0.3750000   0.3750000   0.3750000), wk =   0.0312500
        k(   10) = (   0.3750000  -0.3750000   1.1250000), wk =   0.0625000
        k(   11) = (   0.3750000  -0.1250000  -0.3750000), wk =   0.0312500
        k(   12) = (  -0.3750000   0.6250000   0.3750000), wk =   0.0312500
        k(   13) = (  -0.1250000   0.3750000   0.1250000), wk =   0.0312500
        k(   14) = (   0.6250000   0.1250000  -0.1250000), wk =   0.0625000
        k(   15) = (  -0.1250000   0.8750000   0.6250000), wk =   0.0625000
        k(   16) = (   0.8750000   0.6250000  -0.1250000), wk =   0.0625000
        k(   17) = (   0.1250000   0.6250000   0.3750000), wk =   0.0625000
        k(   18) = (   0.6250000   0.3750000   0.1250000), wk =   0.0625000
        k(   19) = (  -0.8750000   0.1250000  -0.1250000), wk =   0.0625000
        k(   20) = (  -0.3750000   1.1250000   0.3750000), wk =   0.0312500

     G cutoff =  336.0507  (   6423 G-vectors)     FFT grid: ( 28, 28, 28)
     G cutoff =  120.9783  (   1411 G-vectors)  smooth grid: ( 16, 16, 16)

     Largest allocated arrays     est. size (Mb)     dimensions
        Kohn-Sham Wavefunctions         0.00 Mb     (     12,  18)
        NL pseudopotentials             0.00 Mb     (      6,  18)
        Each V/rho on FFT grid          0.01 Mb     (    784)
        Each G-vector array             0.00 Mb     (    201)
        G-vector shells                 0.00 Mb     (     92)
     Largest temporary arrays     est. size (Mb)     dimensions
        Auxiliary wavefunctions         0.01 Mb     (     12,  72)
        Each subspace H/S matrix        0.08 Mb     (     72,  72)
        Each <psi_i|beta_j> matrix      0.01 Mb     (     18,   2,  18)
        Arrays for rho mixing           0.10 Mb     (    784,   8)

     Check: negative/imaginary core charge=   -0.000020    0.000000

     Initial potential from superposition of free atoms

     starting charge    9.99954, renormalised to   10.00000

     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )

 ==============================================================================
     atom number    1 relative position :    0.0000   0.0000   0.0000
     charge :     8.915455
     magnetization :          0.000000    4.457727    0.000000
     magnetization/charge:    0.000000    0.500000    0.000000
     polar coord.: r, theta, phi [deg] :     4.457727   90.000000   90.000000

 ==============================================================================
     Starting wfc are   12 atomic +    6 random wfc

     total cpu time spent up to now is      4.04 secs

     per-process dynamical memory:     2.8 Mb

     Self-consistent Calculation

     iteration #  1     ecut=    27.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.00E-02,  avg # of iterations =  4.7

     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )

 ==============================================================================
     atom number    1 relative position :    0.0000   0.0000   0.0000
     charge :     8.527281
     magnetization :          0.000000    2.473206    0.000000
     magnetization/charge:    0.000000    0.290035    0.000000
     polar coord.: r, theta, phi [deg] :     2.473206   90.000000   90.000000

 ==============================================================================

     total cpu time spent up to now is      6.18 secs

     total energy              =     -85.61972888 Ry
     Harris-Foulkes estimate   =     -85.78377605 Ry
     estimated scf accuracy    <       0.59971619 Ry

     total magnetization       =     0.00     1.62     0.00 Bohr mag/cell
     absolute magnetization    =     1.64 Bohr mag/cell

     iteration #  2     ecut=    27.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  6.00E-03,  avg # of iterations =  2.0

     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )

 ==============================================================================
     atom number    1 relative position :    0.0000   0.0000   0.0000
     charge :     8.729440
     magnetization :          0.000000    1.915161    0.000000
     magnetization/charge:    0.000000    0.219391    0.000000
     polar coord.: r, theta, phi [deg] :     1.915161   90.000000   90.000000

 ==============================================================================

     total cpu time spent up to now is      7.35 secs

     total energy              =     -85.74820616 Ry
     Harris-Foulkes estimate   =     -86.04363635 Ry
     estimated scf accuracy    <       0.80814526 Ry

     total magnetization       =     0.00     0.69     0.00 Bohr mag/cell
     absolute magnetization    =     0.75 Bohr mag/cell

     iteration #  3     ecut=    27.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  6.00E-03,  avg # of iterations =  1.1

     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )

 ==============================================================================
     atom number    1 relative position :    0.0000   0.0000   0.0000
     charge :     8.735738
     magnetization :          0.000000    0.685818    0.000000
     magnetization/charge:    0.000000    0.078507    0.000000
     polar coord.: r, theta, phi [deg] :     0.685818   90.000000   90.000000

 ==============================================================================

     total cpu time spent up to now is      8.27 secs

     total energy              =     -85.88840936 Ry
     Harris-Foulkes estimate   =     -85.86948298 Ry
     estimated scf accuracy    <       0.02469543 Ry

     total magnetization       =     0.00     0.86     0.00 Bohr mag/cell
     absolute magnetization    =     1.01 Bohr mag/cell

     iteration #  4     ecut=    27.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  2.47E-04,  avg # of iterations =  1.6

     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )

 ==============================================================================
     atom number    1 relative position :    0.0000   0.0000   0.0000
     charge :     8.736741
     magnetization :          0.000000    0.727951    0.000000
     magnetization/charge:    0.000000    0.083321    0.000000
     polar coord.: r, theta, phi [deg] :     0.727951   90.000000   90.000000

 ==============================================================================

     total cpu time spent up to now is      9.32 secs

     total energy              =     -85.89653436 Ry
     Harris-Foulkes estimate   =     -85.89641137 Ry
     estimated scf accuracy    <       0.00055014 Ry

     total magnetization       =     0.00     0.69     0.00 Bohr mag/cell
     absolute magnetization    =     0.82 Bohr mag/cell

     iteration #  5     ecut=    27.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  5.50E-06,  avg # of iterations =  2.8

     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )

 ==============================================================================
     atom number    1 relative position :    0.0000   0.0000   0.0000
     charge :     8.740437
     magnetization :          0.000000    0.733680    0.000000
     magnetization/charge:    0.000000    0.083941    0.000000
     polar coord.: r, theta, phi [deg] :     0.733680   90.000000   90.000000

 ==============================================================================

     total cpu time spent up to now is     10.68 secs

     total energy              =     -85.89675013 Ry
     Harris-Foulkes estimate   =     -85.89669724 Ry
     estimated scf accuracy    <       0.00002031 Ry

     total magnetization       =     0.00     0.69     0.00 Bohr mag/cell
     absolute magnetization    =     0.80 Bohr mag/cell

     iteration #  6     ecut=    27.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  2.03E-07,  avg # of iterations =  2.4

     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )

 ==============================================================================
     atom number    1 relative position :    0.0000   0.0000   0.0000
     charge :     8.740156
     magnetization :          0.000000    0.729250    0.000000
     magnetization/charge:    0.000000    0.083437    0.000000
     polar coord.: r, theta, phi [deg] :     0.729250   90.000000   90.000000

 ==============================================================================

     total cpu time spent up to now is     12.08 secs

     total energy              =     -85.89677066 Ry
     Harris-Foulkes estimate   =     -85.89676730 Ry
     estimated scf accuracy    <       0.00000483 Ry

     total magnetization       =     0.00     0.69     0.00 Bohr mag/cell
     absolute magnetization    =     0.79 Bohr mag/cell

     iteration #  7     ecut=    27.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  4.83E-08,  avg # of iterations =  1.9

     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )

 ==============================================================================
     atom number    1 relative position :    0.0000   0.0000   0.0000
     charge :     8.739967
     magnetization :          0.000000    0.733793    0.000000
     magnetization/charge:    0.000000    0.083958    0.000000
     polar coord.: r, theta, phi [deg] :     0.733793   90.000000   90.000000

 ==============================================================================

     total cpu time spent up to now is     13.14 secs

     total energy              =     -85.89677271 Ry
     Harris-Foulkes estimate   =     -85.89677201 Ry
     estimated scf accuracy    <       0.00000117 Ry

     total magnetization       =     0.00     0.69     0.00 Bohr mag/cell
     absolute magnetization    =     0.79 Bohr mag/cell

     iteration #  8     ecut=    27.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.17E-08,  avg # of iterations =  2.0

     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )

 ==============================================================================
     atom number    1 relative position :    0.0000   0.0000   0.0000
     charge :     8.740181
     magnetization :          0.000000    0.730161    0.000000
     magnetization/charge:    0.000000    0.083541    0.000000
     polar coord.: r, theta, phi [deg] :     0.730161   90.000000   90.000000

 ==============================================================================

     total cpu time spent up to now is     14.19 secs

     total energy              =     -85.89677287 Ry
     Harris-Foulkes estimate   =     -85.89677299 Ry
     estimated scf accuracy    <       0.00000005 Ry

     total magnetization       =     0.00     0.69     0.00 Bohr mag/cell
     absolute magnetization    =     0.79 Bohr mag/cell

     iteration #  9     ecut=    27.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  4.93E-10,  avg # of iterations =  2.0

     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )

 ==============================================================================
     atom number    1 relative position :    0.0000   0.0000   0.0000
     charge :     8.740016
     magnetization :          0.000000    0.732993    0.000000
     magnetization/charge:    0.000000    0.083866    0.000000
     polar coord.: r, theta, phi [deg] :     0.732993   90.000000   90.000000

 ==============================================================================

     total cpu time spent up to now is     15.30 secs

     total energy              =     -85.89677303 Ry
     Harris-Foulkes estimate   =     -85.89677291 Ry
     estimated scf accuracy    <       0.00000024 Ry

     total magnetization       =     0.00     0.69     0.00 Bohr mag/cell
     absolute magnetization    =     0.79 Bohr mag/cell

     iteration # 10     ecut=    27.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  4.93E-10,  avg # of iterations =  2.0

     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )

 ==============================================================================
     atom number    1 relative position :    0.0000   0.0000   0.0000
     charge :     8.740036
     magnetization :          0.000000    0.732665    0.000000
     magnetization/charge:    0.000000    0.083829    0.000000
     polar coord.: r, theta, phi [deg] :     0.732665   90.000000   90.000000

 ==============================================================================

     total cpu time spent up to now is     16.44 secs

     total energy              =     -85.89677305 Ry
     Harris-Foulkes estimate   =     -85.89677305 Ry
     estimated scf accuracy    <          4.4E-09 Ry

     total magnetization       =     0.00     0.69     0.00 Bohr mag/cell
     absolute magnetization    =     0.79 Bohr mag/cell

     iteration # 11     ecut=    27.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  4.35E-11,  avg # of iterations =  1.0

     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )

 ==============================================================================
     atom number    1 relative position :    0.0000   0.0000   0.0000
     charge :     8.740037
     magnetization :          0.000000    0.732648    0.000000
     magnetization/charge:    0.000000    0.083827    0.000000
     polar coord.: r, theta, phi [deg] :     0.732648   90.000000   90.000000

 ==============================================================================

     total cpu time spent up to now is     17.35 secs

     total energy              =     -85.89677306 Ry
     Harris-Foulkes estimate   =     -85.89677306 Ry
     estimated scf accuracy    <          2.7E-12 Ry

     total magnetization       =     0.00     0.69     0.00 Bohr mag/cell
     absolute magnetization    =     0.79 Bohr mag/cell

     iteration # 12     ecut=    27.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  2.72E-14,  avg # of iterations =  3.5

     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )

 ==============================================================================
     atom number    1 relative position :    0.0000   0.0000   0.0000
     charge :     8.740036
     magnetization :          0.000000    0.732674    0.000000
     magnetization/charge:    0.000000    0.083830    0.000000
     polar coord.: r, theta, phi [deg] :     0.732674   90.000000   90.000000

 ==============================================================================

     total cpu time spent up to now is     18.95 secs

     total energy              =     -85.89677306 Ry
     Harris-Foulkes estimate   =     -85.89677306 Ry
     estimated scf accuracy    <          3.0E-11 Ry

     total magnetization       =     0.00     0.69     0.00 Bohr mag/cell
     absolute magnetization    =     0.79 Bohr mag/cell

     iteration # 13     ecut=    27.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  2.72E-14,  avg # of iterations =  3.0

     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )

 ==============================================================================
     atom number    1 relative position :    0.0000   0.0000   0.0000
     charge :     8.740036
     magnetization :          0.000000    0.732673    0.000000
     magnetization/charge:    0.000000    0.083830    0.000000
     polar coord.: r, theta, phi [deg] :     0.732673   90.000000   90.000000

 ==============================================================================

     total cpu time spent up to now is     20.47 secs

     End of self-consistent calculation

          k =-0.1250 0.1250 0.1250 (   172 PWs)   bands (ev):

     5.8247   5.8691  11.5861  11.8446  11.8446  12.4414  12.7266  12.7266
    12.8768  12.8768  13.5944  13.5944  35.2155  35.2398  38.9860  39.1151
    41.0572  41.0572

          k =-0.3750 0.3750-0.1250 (   171 PWs)   bands (ev):

     8.5760   8.6215  11.2604  11.8473  11.9889  12.1423  12.5911  12.7666
    12.9254  13.5913  13.6869  14.4942  27.1067  27.2784  32.6469  32.7148
    39.6091  39.6746

          k = 0.3750-0.3750 0.6250 (   172 PWs)   bands (ev):

     9.6700  10.1807  11.5294  11.9963  12.1362  12.2060  12.7457  12.7903
    13.5685  14.4653  15.4906  15.8885  20.5038  20.9015  33.7472  33.7530
    36.0292  36.0976

          k = 0.1250-0.1250 0.3750 (   169 PWs)   bands (ev):

     7.3339   7.3628  11.1872  11.9948  12.0405  12.1507  12.7076  12.8315
    13.0158  13.1524  13.4830  13.9136  31.2714  31.3759  36.2548  36.3335
    36.7661  36.8254

          k =-0.1250 0.6250 0.1250 (   178 PWs)   bands (ev):

     9.3898   9.5394  10.5911  11.3396  12.0588  12.7031  12.7242  13.4952
    13.5715  13.7975  14.3252  14.5127  28.1586  28.2787  31.5090  31.5784
    32.3304  32.3844

          k = 0.6250-0.1250 0.8750 (   179 PWs)   bands (ev):

    10.3964  10.6512  10.8788  11.3192  11.6342  12.3414  12.9297  13.5295
    13.6406  14.5087  19.0431  19.3203  22.3296  22.5345  26.0133  26.1701
    28.3127  28.4085

          k = 0.3750 0.1250 0.6250 (   174 PWs)   bands (ev):

    10.0200  10.3484  11.0651  11.4389  11.6737  12.1542  12.5046  13.2468
    13.2530  14.1294  15.3184  15.9156  24.0962  24.3090  29.7578  29.8493
    32.8996  32.9696

          k =-0.1250-0.8750 0.1250 (   176 PWs)   bands (ev):

     9.7869  10.1747  10.2063  10.8927  12.8809  13.3188  13.6374  13.6497
    14.1047  14.5799  16.7913  17.0377  24.9832  25.1827  26.3769  26.4724
    30.0889  30.1027

          k =-0.3750 0.3750 0.3750 (   174 PWs)   bands (ev):

     9.0496   9.3302  11.8388  11.8388  12.3406  12.5971  12.5971  12.6755
    13.3546  13.3546  14.2217  14.2217  23.0056  23.2884  36.9019  37.0641
    39.2803  39.2804

          k = 0.3750-0.3750 1.1250 (   176 PWs)   bands (ev):

    10.3743  10.9676  11.0277  11.5078  11.5680  12.2770  12.5162  13.2422
    13.2830  14.2140  17.7604  18.1049  21.2406  21.5392  27.2400  27.3702
    34.3340  34.3961

          k = 0.3750-0.1250-0.3750 (   171 PWs)   bands (ev):

     8.5760   8.6215  11.2604  11.8473  11.9889  12.1423  12.5911  12.7666
    12.9254  13.5913  13.6869  14.4942  27.1067  27.2784  32.6469  32.7148
    39.6091  39.6746

          k =-0.3750 0.6250 0.3750 (   172 PWs)   bands (ev):

     9.6700  10.1807  11.5294  11.9963  12.1362  12.2060  12.7457  12.7903
    13.5685  14.4653  15.4906  15.8885  20.5038  20.9015  33.7472  33.7530
    36.0292  36.0976

          k =-0.1250 0.3750 0.1250 (   169 PWs)   bands (ev):

     7.3339   7.3628  11.1872  11.9948  12.0405  12.1507  12.7076  12.8315
    13.0158  13.1524  13.4830  13.9136  31.2714  31.3759  36.2548  36.3335
    36.7661  36.8254

          k = 0.6250 0.1250-0.1250 (   178 PWs)   bands (ev):

     9.3898   9.5394  10.5911  11.3396  12.0588  12.7031  12.7242  13.4952
    13.5715  13.7975  14.3252  14.5127  28.1586  28.2787  31.5090  31.5784
    32.3303  32.3844

          k =-0.1250 0.8750 0.6250 (   179 PWs)   bands (ev):

    10.3964  10.6512  10.8788  11.3192  11.6342  12.3414  12.9297  13.5295
    13.6406  14.5087  19.0431  19.3203  22.3296  22.5345  26.0133  26.1701
    28.3127  28.4085

          k = 0.8750 0.6250-0.1250 (   179 PWs)   bands (ev):

    10.3964  10.6512  10.8788  11.3192  11.6342  12.3414  12.9297  13.5295
    13.6406  14.5087  19.0431  19.3203  22.3296  22.5345  26.0133  26.1701
    28.3127  28.4085

          k = 0.1250 0.6250 0.3750 (   174 PWs)   bands (ev):

    10.0200  10.3484  11.0651  11.4389  11.6737  12.1542  12.5046  13.2468
    13.2530  14.1294  15.3184  15.9156  24.0962  24.3090  29.7578  29.8493
    32.8996  32.9696

          k = 0.6250 0.3750 0.1250 (   174 PWs)   bands (ev):

    10.0200  10.3484  11.0651  11.4389  11.6737  12.1542  12.5046  13.2468
    13.2530  14.1294  15.3184  15.9156  24.0962  24.3090  29.7578  29.8493
    32.8996  32.9696

          k =-0.8750 0.1250-0.1250 (   176 PWs)   bands (ev):

     9.7869  10.1747  10.2063  10.8927  12.8809  13.3188  13.6374  13.6497
    14.1047  14.5799  16.7913  17.0377  24.9832  25.1827  26.3769  26.4724
    30.0889  30.1027

          k =-0.3750 1.1250 0.3750 (   176 PWs)   bands (ev):

    10.3743  10.9676  11.0277  11.5078  11.5680  12.2770  12.5162  13.2422
    13.2830  14.2140  17.7604  18.1049  21.2406  21.5392  27.2400  27.3702
    34.3340  34.3961

     the Fermi energy is    14.2797 ev

!    total energy              =     -85.89677306 Ry
     Harris-Foulkes estimate   =     -85.89677306 Ry
     estimated scf accuracy    <          1.6E-13 Ry

     The total energy is the sum of the following terms:

     one-electron contribution =      -2.06721471 Ry
     hartree contribution      =      15.23682292 Ry
     xc contribution           =     -30.12085021 Ry
     ewald contribution        =     -68.94529435 Ry
     smearing contrib. (-TS)   =      -0.00023671 Ry

     total magnetization       =     0.00     0.69     0.00 Bohr mag/cell
     absolute magnetization    =     0.79 Bohr mag/cell

     convergence has been achieved in  13 iterations

     Forces acting on atoms (Ry/au):


     GGA quantization axis: (  0.0000,  1.0000,  0.0000  )
     atom   1 type  1   force =     0.00000000    0.00000000    0.00000000

     Total force =     0.000000     Total SCF correction =     0.000000

     Writing output data file ni.save
 
     init_run     :      1.52s CPU      1.52s WALL (       1 calls)
     electrons    :     17.10s CPU     17.10s WALL (       1 calls)
     forces       :      0.20s CPU      0.20s WALL (       1 calls)

     Called by init_run:
     wfcinit      :      0.25s CPU      0.25s WALL (       1 calls)
     potinit      :      0.10s CPU      0.10s WALL (       1 calls)

     Called by electrons:
     c_bands      :     12.31s CPU     12.31s WALL (      13 calls)
     sum_band     :      1.42s CPU      1.42s WALL (      13 calls)
     v_of_rho     :      0.34s CPU      0.34s WALL (      14 calls)
     newd         :      0.17s CPU      0.17s WALL (      14 calls)
     mix_rho      :      0.05s CPU      0.05s WALL (      13 calls)

     Called by c_bands:
     init_us_2    :      0.01s CPU      0.01s WALL (     140 calls)
     cegterg      :     10.51s CPU     10.51s WALL (      65 calls)

     Called by *egterg:
     h_psi        :      2.56s CPU      2.56s WALL (     227 calls)
     s_psi        :      0.07s CPU      0.07s WALL (     227 calls)
     g_psi        :      0.01s CPU      0.01s WALL (     157 calls)
     cdiaghg      :      7.16s CPU      7.16s WALL (     222 calls)

     Called by h_psi:
     add_vuspsi   :      0.09s CPU      0.09s WALL (     227 calls)

     General routines
     calbec       :      0.16s CPU      0.16s WALL (     297 calls)
     fft          :      0.33s CPU      0.33s WALL (     687 calls)
     ffts         :      0.02s CPU      0.02s WALL (     108 calls)
     fftw         :      2.61s CPU      2.61s WALL (   13968 calls)
     interpolate  :      0.07s CPU      0.07s WALL (     108 calls)
     davcio       :      1.07s CPU      1.07s WALL (     205 calls)
 
     Parallel routines
     fft_scatter  :      1.85s CPU      1.90s WALL (   14763 calls)
 
     PWSCF        :    22.74s CPU        22.74s WALL

 
   This run was terminated on:  13:36:45  10Apr2012            

=------------------------------------------------------------------------------=
   JOB DONE.
=------------------------------------------------------------------------------=

From giannozz at democritos.it  Tue Apr 10 18:48:50 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 10 Apr 2012 18:48:50 +0200
Subject: [Pw_forum] ph.x on BG/P: does not seem to be functional
In-Reply-To: <4F844317.7040805@unige.ch>
References: <4F844317.7040805@unige.ch>
Message-ID: <4A19EEEC-C7DA-4A43-8B59-FF2194B4D5C7@democritos.it>


On Apr 10, 2012, at 16:26 , Lat?vi Max LAWSON DAKU wrote:

> Did someone succeed in running a BG/P-mpixlf90-compiled ph.x
> executable? If so can she/he share his compilation setup with me?

the compilation setup that is fine for pw.x is fine for ph.x as well.
Not sure if and how well it works on the BG, though. Anyway:
before attempting to run anything on 128 BG cores, you should
first learn to run on a few processors on more conventional machines.

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 10 19:30:13 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 10 Apr 2012 19:30:13 +0200
Subject: [Pw_forum] problem with average.x (average potential)
	calculation
In-Reply-To: <CANzxBn_qEVbvBonEnkGm2C2_HTO2Z+M7tPwqdUrOAYr1uMGD1g@mail.gmail.com>
References: <CANzxBn_qEVbvBonEnkGm2C2_HTO2Z+M7tPwqdUrOAYr1uMGD1g@mail.gmail.com>
Message-ID: <4BF32928-9BDC-41B4-9756-94CE76B4CA57@democritos.it>


On Apr 10, 2012, at 24:39 , Tram Bui wrote:

> For an input file of average.x calculation, and I defined the nfile=1,
> since I have only one data file from pp.x calculation. I got an error
> say: "nfile value is wrong". Would you please give me some
> suggestion on what might be the issue?

the issue is that you gave a wrong input. Please look in
examples/WorkFct/ for a case where "average.x" is used

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 10 19:40:52 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 10 Apr 2012 19:40:52 +0200
Subject: [Pw_forum] Error in running the pwcond.x
In-Reply-To: <CADww=13UiYvtSYMBOYUkxP2xRSRpoigi0oE4QKnr+8kath2BDw@mail.gmail.com>
References: <CADww=10n0FnsTL7C1YZswwMP50jvCt__4nu1u4mQU0Kd_7D9dw@mail.gmail.com>
	<CADww=13UiYvtSYMBOYUkxP2xRSRpoigi0oE4QKnr+8kath2BDw@mail.gmail.com>
Message-ID: <6B9A7359-FFF9-4205-BFCD-BB28E0EC3AB2@democritos.it>


On Apr 9, 2012, at 9:23 , pankaj sahota wrote:

> I also tried with the provided examples. I got the following output  
> of example12
> of espresso-4.3.2.
> [....]
> # FROM IOTK LIBRARY, VERSION 1.2.0
> # UNRECOVERABLE ERROR (ierr=1)

with very high probability: buggy compiler

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 wparker at anl.gov  Tue Apr 10 22:36:57 2012
From: wparker at anl.gov (William Parker)
Date: Tue, 10 Apr 2012 15:36:57 -0500
Subject: [Pw_forum] How to parallelize phonons
In-Reply-To: <8683BB35-5EEF-4F84-A2C9-3574B645A230@anl.gov>
References: <e967ad85c1044e18684862e4830023ee.squirrel@webmail.uic.edu>
	<348C4E21-9C24-4E10-A46A-D3437F65AF66@anl.gov>
	<FE1A9531-37F1-4B76-9CED-5015B2831098@democritos.it>
	<8683BB35-5EEF-4F84-A2C9-3574B645A230@anl.gov>
Message-ID: <09A8485D-19E6-4C03-B3F4-E3952864E084@anl.gov>

I want to follow up on my last mailing.  I have since found, thanks to some discussion with Alejandro R?bola, that, if I copy only the data-file.*.*.xml files from the _ph* directories into _ph0, the recover step works correctly.

So my script goes something like this (using one processor per k-point pool):

mpirun -n $npool         pw.x                 -npool $npool -inp $pw_input         >& $pw_output
mpirun -n $npool*$nimage ph.x -nimage $nimage -npool $npool -inp $ph_input         >& $ph_output
i=1
while [ "$i" -lt "$nimage" ]
do
        cp _ph$i/$prefix.phsave/data-file.*.*.xml _ph0/$prefix.phsave/
        i=`expr $i + 1`
done
mpirun -n $npool         ph.x                 -npool $npool -inp $ph_recover_input >& $ph_recover_output

$ph_recover_input and $ph_input differ only in that the former contains the additional line:
recover=.true.

This procedure produces $prefix.dyn* files containing all of the expected eigenvalues and eigenvectors. 
I imagine a more fluent person could write the copy stage better.  May I update the documentation for ph.x to indicate this vital copy step?  

--William


On Mar 28, 2012, at 10:16 PM, William Parker wrote:

> Thanks for the followup, Paolo.
> 
> The recover step happens, producing the appropriate "Restart after Phonon calculation" message, but the output insists the representations calculated on other images are still "To be done."  ph.x produces a new .dyn file for the first q-point but no others.  So, the remaining .dyn files from the other images are incorrect because they are incomplete, even though all the data are correctly stored in the data-file.*.xml files in the _ph*/(prefix).phsave/ directories.   Any ideas?  Need any more information?
> 
> --William
> 
> On Mar 28, 2012, at 4:08 PM, Paolo Giannozzi wrote:
> 
>> 
>> On Mar 28, 2012, at 21:47 , William Parker wrote:
>> 
>>> The second step does generate all of the right dynamical matrix entries,
>>> but I have been unable to get the recover step to complete successfully
>>> yet, though I am currently working on this (if anyone else on the list has
>>> any comments on this, please speak up).
>> 
>> why have you been unable to perform the last step? what happens?
>> 
>> 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
>> 
>> 
>> 
>> 
> 
> *********************************************************
>  William D. Parker                 phone: (630) 252-4834
>  Computational Postdoctoral Fellow   fax: (630) 252-4798
>  MSD-212, Rm. C-215
>  Argonne National Laboratory
>  9700 S. Cass Ave.
>  Argonne, IL 60439
> *********************************************************
> 
> 
> 
> 
> 

*********************************************************
  William D. Parker                 phone: (630) 252-4834
  Computational Postdoctoral Fellow   fax: (630) 252-4798
  MSD-212, Rm. C-215
  Argonne National Laboratory
  9700 S. Cass Ave.
  Argonne, IL 60439
*********************************************************






From Max.Lawson at unige.ch  Tue Apr 10 22:51:34 2012
From: Max.Lawson at unige.ch (=?ISO-8859-1?Q?Lat=E9vi_Max_LAWSON_DAKU?=)
Date: Tue, 10 Apr 2012 22:51:34 +0200
Subject: [Pw_forum] ph.x on BG/P: does not seem to be functional
In-Reply-To: <4A19EEEC-C7DA-4A43-8B59-FF2194B4D5C7@democritos.it>
References: <4F844317.7040805@unige.ch>
	<4A19EEEC-C7DA-4A43-8B59-FF2194B4D5C7@democritos.it>
Message-ID: <4F849D56.3030208@unige.ch>



On 10. 04. 12 18:48, Paolo Giannozzi wrote:
> On Apr 10, 2012, at 16:26 , Lat?vi Max LAWSON DAKU wrote:
>
>> Did someone succeed in running a BG/P-mpixlf90-compiled ph.x
>> executable? If so can she/he share his compilation setup with me?
> the compilation setup that is fine for pw.x is fine for ph.x as well.
> Not sure if and how well it works on the BG, though. Anyway:
> before attempting to run anything on 128 BG cores, you should
> first learn to run on a few processors on more conventional machines.

Dear Paolo,

Many thanks for your kind e-mail and your indication regarding
the compilation setup. I will recompile the code with debugging
turn on and see if I can locate the origin of the problem... let's see

Thanks, again, for your time.

Best,
Max

>
> 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
>

-- 
Latevi Max LAWSON DAKU
Universite de Geneve - Sciences II
Quai Ernest-Ansermet 30                            Tel: (41) 22/379 6548
CH-1211 Geneve 4                                   Fax: (41) 22/379 6103




From janette.wong at mail.utoronto.ca  Tue Apr 10 23:17:46 2012
From: janette.wong at mail.utoronto.ca (Janet Wong)
Date: Tue, 10 Apr 2012 21:17:46 +0000
Subject: [Pw_forum] problems modeling H2 adsorption on boron doped graphene
	sheet
Message-ID: <6D3C4797C791254CB5D576BF880C82A60F784E5D@BY2PRD0310MB388.namprd03.prod.outlook.com>

Dear QE users,

I am currently in the process of learning how to model hydrogen adsorption on a graphene sheet. So, as a starting point I tried to calculate the adsorption energy of hydrogen on boron doped graphene. However, I am unable to obtain values close to those that were stated in papers with similar DFT calculations. Does anyone have any suggestions as to what I might be doing incorrectly? My calculated value was -0.74 eV (please refer to below for input file used) while other papers stated -0.014 eV. I've tried different orientations for the hydrogen molecule (vertical vs horizontal to the graphene sheet) but my final value doesn't change by much (~0.01eV).

  &control
    prefix='h2ads_BG'
    calculation='relax'
    outdir = './out'
    pseudo_dir = '/scratch/Hydrogen_Adsorption/pseudo/'
    forc_conv_thr=1D-3
 /
 &system
    ibrav=0, nat=34, ntyp=3,
    ecutwfc=25, ecutrho=200
    occupations='smearing', smearing='methfessel-paxton', degauss=0.01
 /
 &electrons
    mixing_mode='local-TF'
 /
 &ions
 /
CELL_PARAMETERS
18.65816237 0.000000000 0.000000000
9.329081185 16.15844260 0.000000000
0.000000000 0.000000000 28.34588983
ATOMIC_SPECIES
 C 12.01  C.pbe-van_bm.UPF
 H 1.001  H.pbe-van_bm.UPF
 B 10.81  B.pbe-n-van.UPF
ATOMIC_POSITIONS angstrom
 C         1.728024        0.709000        0.001000
 C         4.184072        0.709000        0.001000
 C         6.640120        0.709000        0.001000
 C         9.096169        0.709000        0.001000
 C         1.728024        2.127000        0.001000
 C         4.184072        2.127000        0.001000
 C         6.640120        2.127000        0.001000
 C         9.096169        2.127000        0.001000
 C         2.931405        2.793323        0.001000
 C         5.436735        2.793328        0.001000
 C         7.892783        2.793323        0.001000
 C        10.324192        2.793323        0.001000
 C         2.956048        4.254000        0.001000
 C         5.412096        4.254000        0.001000
 B         7.868144        4.254000        0.001000
 H         7.483935        4.254000        1.220000
 H         8.252353        4.254000        1.220000
 C        10.324192        4.254000        0.001000
 C         4.184072        4.963000        0.001000
 C         6.640120        4.963000        0.001000
 C         9.096169        4.963000        0.001000
 C        11.601494        4.963000        0.001000
 C         4.184072        6.381000        0.001000
 C         6.640120        6.381000        0.001000
 C         9.096169        6.381000        0.001000
 C        11.601494        6.381000        0.001000
 C         5.412096        7.090000        0.001000
 C         7.868144        7.090000        0.001000
 C        10.373470        7.090000        0.001000
 C        12.829518        7.090000        0.001000
 C         5.412096        8.508000        0.001000
 C         7.868144        8.508000        0.001000
 C        10.373470        8.508000        0.001000
 C        12.829518        8.508000        0.001000
K_POINTS automatic
5 5 1 1 1 1

Thank you all in advance.

Regards,
Janet Wong
Graduate Student
University of Toronto
Canada
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From avallabh at purdue.edu  Wed Apr 11 06:06:15 2012
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Wed, 11 Apr 2012 00:06:15 -0400 (EDT)
Subject: [Pw_forum] Query on band crossing
Message-ID: <1348646176.101593.1334117175526.JavaMail.root@mailhub016.itcs.purdue.edu>

Dear Users and developers,

                 I have a question regarding the crossing of branches in electron and phonon dispersion plots. Since the no. of elec bands vary from 1 to nbnd and phonon branches vary from 1 to 3*nat, in the output files they are written usually from the minimum to maximum. 

   I want to make sure whether for different points in the BZ, the bands are always considered in the same order (from min to max) without considering any crossing of bands in both scf and also e-ph calculations. What is the best way to distinguish or track one band across the entire BZ? I believe for phonons, the eigen vectors could help to some extent, then what about electrons? 


Thanks
Ajit


         

From pankajsahota at gmail.com  Wed Apr 11 09:14:44 2012
From: pankajsahota at gmail.com (pankaj sahota)
Date: Wed, 11 Apr 2012 12:44:44 +0530
Subject: [Pw_forum] Querry abou the kpoints in transport calculations
Message-ID: <CADww=110Paam7D5zWDmj=xTnqU81J7V0G=o5s775L+N87eZxNQ@mail.gmail.com>

Hi,

Can anybody tell me that if I want to calculate the transport properties of
a wire then do I have to take the same kpoints for the scattering region
and electrode or they can be chosen differently because kpoints for both of
them will be generated differently due to the different length along the
z-direction.

Thanks and regards.
Pankaj

-- 
Pankaj Kumar
DST Project Fellow(Ph.D.)
Department of Physics
The LNM IIT Jaipur
Mob. No. +91 9736694726
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From nicola.marzari at epfl.ch  Wed Apr 11 09:30:20 2012
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Wed, 11 Apr 2012 09:30:20 +0200
Subject: [Pw_forum] Query on band crossing
In-Reply-To: <1348646176.101593.1334117175526.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <1348646176.101593.1334117175526.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <4F85330C.2050103@epfl.ch>



Dear Ajit,


it's not a trivial question to answer; probably the best solution is to
use Wannier functions as interpolators - see e.g. the
discussion here (http://arxiv.org/abs/1112.5411).

				nicola



On 11/04/2012 06:06, Ajit Vallabhaneni wrote:
> Dear Users and developers,
>
>                   I have a question regarding the crossing of branches in electron and phonon dispersion plots. Since the no. of elec bands vary from 1 to nbnd and phonon branches vary from 1 to 3*nat, in the output files they are written usually from the minimum to maximum.
>
>     I want to make sure whether for different points in the BZ, the bands are always considered in the same order (from min to max) without considering any crossing of bands in both scf and also e-ph calculations. What is the best way to distinguish or track one band across the entire BZ? I believe for phonons, the eigen vectors could help to some extent, then what about electrons?
>
>
> Thanks
> Ajit
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 

----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL

From fratesi at mater.unimib.it  Wed Apr 11 09:49:47 2012
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Wed, 11 Apr 2012 09:49:47 +0200
Subject: [Pw_forum] Potassium Ultrasoft pseudopotential with PBE
In-Reply-To: <1333632748.87002.YahooMailNeo@web15102.mail.cnb.yahoo.com>
References: <1333632748.87002.YahooMailNeo@web15102.mail.cnb.yahoo.com>
Message-ID: <4F85379B.3080907@mater.unimib.it>

Dear LiBin,

please notice that list rules ask posts to be signed with affiliation.

> Recently, my calculation needs Potassium PBE Ultrasoft pseudopotential. But I?m not sure about my pseudo generated by ld1.x. So is there existing K.pbe pseudo? Thank you very much!

I have a PBE K pseudo which I used to compute K adsorption properties on 
Cu with good agreement with experimental workfunction changes and 
diffusion energy barriers. That was generated with the Vanderbilt code, 
then converted, starting from a CA-LDA pseudo distributed with 
Vanderbilt's USPP code. In more detail, I have:

1)  taken input files for CA-LDA in USPP-7.3.5 distribution:
   uspp-735/Work/019-K/019-K-ca-sp-vgrp/k_ae_s1.adat
   uspp-735/Work/019-K/019-K-ca-sp-vgrp/k_ps.adat

2) changed:
   exfact 0 -> 5 (PBE)
   ifqopt 2 -> 3 (different augfun pseudiz; 2 not allowed for GGA)
   rinner 0.8 -> 0.95 (Determines the inner radii that are used
                                 for pseudizing the q-functions)

3) run the code
  $ make

4) converted to UPF
    $ echo k_ps.uspp | upftools/uspp2upf.x

I'm sending you the generated file in a separate email to not clutter 
the list. Please report whether that matches your needs, and especially 
if not, why.

HTH, Guido

-- 
Guido Fratesi

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

From ramzialaya at hotmail.fr  Wed Apr 11 14:09:06 2012
From: ramzialaya at hotmail.fr (ramzi alaya)
Date: Wed, 11 Apr 2012 13:09:06 +0100
Subject: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation
Message-ID: <BAY151-W5650027C992A2D7A791F1CA3350@phx.gbl>


Dear all;
 
I checked the Pwscf for US Bi PZ relativitic pseudopotential but could not find or generate it myself . Thus could you please send me Bi US pseudopotential with PZ approximation.
 
Thank you.
Regards.
 
 
**********************************************************************************
Ramzi Alaya
E-mail : ramzialaya at hotmail.fr
Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie
Unit? de Recherche sur les H?t?ro-Epitaxies et Applications

  		 	   		  
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From ptao10b at imr.ac.cn  Thu Apr 12 02:23:17 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Thu, 12 Apr 2012 08:23:17 +0800 (CST)
Subject: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation
In-Reply-To: <BAY151-W5650027C992A2D7A791F1CA3350@phx.gbl>
References: <BAY151-W5650027C992A2D7A791F1CA3350@phx.gbl>
Message-ID: <1e6f453.85d.136a3eecb2f.Coremail.ptao10b@imr.ac.cn>

It's really a pity that pwscf has so few pseudopotentials. T_T 


-----????-----
???: "ramzi alaya" <ramzialaya at hotmail.fr>
????: 2012?4?11? ???
???: pw_forum at pwscf.org
??:
??: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation


Dear all;
 
I checked the Pwscf for US Bi PZ relativitic pseudopotential but could not find or generate it myself . Thus could you please send me Bi US pseudopotential with PZ approximation.
 
Thank you.
Regards.
 
 


**********************************************************************************
Ramzi Alaya

E-mail : ramzialaya at hotmail.fr
Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie
Unit? de Recherche sur les H?t?ro-Epitaxies et Applications


 



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------


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From akohlmey at gmail.com  Thu Apr 12 03:02:22 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Wed, 11 Apr 2012 21:02:22 -0400
Subject: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation
In-Reply-To: <1e6f453.85d.136a3eecb2f.Coremail.ptao10b@imr.ac.cn>
References: <BAY151-W5650027C992A2D7A791F1CA3350@phx.gbl>
	<1e6f453.85d.136a3eecb2f.Coremail.ptao10b@imr.ac.cn>
Message-ID: <CADTmJ6GXbVe43L2sDZRH_7vjHGetUqpvLy2ZQPSO9opEgFX96g@mail.gmail.com>

On Wed, Apr 11, 2012 at 8:23 PM, Peng Tao <ptao10b at imr.ac.cn> wrote:
> It's really a pity that pwscf has so few pseudopotentials. T_T

here is a business opportunity:

p-bay

where people can bid on custom pseudopotentials.

all that is need would be a suitable currency. i could
imagine that if something valuable enough was offered
in exchange, some people might become interested
in specializing on generating custom potentials.

<evil grin>,
    axel.


> -----????-----
> ???: "ramzi alaya" <ramzialaya at hotmail.fr>
> ????: 2012?4?11? ???
> ???: pw_forum at pwscf.org
> ??:
> ??: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation
>
>
> Dear all;
>
> I checked the Pwscf for US Bi?PZ relativitic?pseudopotential but could not
> find or generate it myself . Thus could you please send me Bi US
> pseudopotential with PZ approximation.
>
> Thank you.
> Regards.
>
>
>
> **********************************************************************************
> Ramzi Alaya
>
> E-mail?: ramzialaya at hotmail.fr
> Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie
> Unit? de Recherche sur les H?t?ro-Epitaxies et Applications
>
>
>
>
>
>
> --
> -------------------------------------------------------------------
> PH.D. candidate Peng Tao
> Magnetism and Magnetic Materials Division
> National Laboratory for Material Science
> Institute of Metal Research, Chinese Academy of Sciences
> Phone ?+86-024-83978751
> -------------------------------------------------------------------
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From nicola.marzari at epfl.ch  Thu Apr 12 03:10:02 2012
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Thu, 12 Apr 2012 03:10:02 +0200
Subject: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation
In-Reply-To: <CADTmJ6GXbVe43L2sDZRH_7vjHGetUqpvLy2ZQPSO9opEgFX96g@mail.gmail.com>
References: <BAY151-W5650027C992A2D7A791F1CA3350@phx.gbl>
	<1e6f453.85d.136a3eecb2f.Coremail.ptao10b@imr.ac.cn>
	<CADTmJ6GXbVe43L2sDZRH_7vjHGetUqpvLy2ZQPSO9opEgFX96g@mail.gmail.com>
Message-ID: <4F862B6A.2000809@epfl.ch>



I wondered about this for some time! In my opinion, it could be
an interesting challenge to issue, but one would need to
have a competition, and only the "best" pseudo for each element
would get prize money.

Now, the issue is what is best - we would need solid-state all-electron
data to test against, and that is what is missing right now... (of 
course, we could have a double competition, and hope the best match
is for good reasons).

				nicola




On 12/04/2012 03:02, Axel Kohlmeyer wrote:
> On Wed, Apr 11, 2012 at 8:23 PM, Peng Tao<ptao10b at imr.ac.cn>  wrote:
>> It's really a pity that pwscf has so few pseudopotentials. T_T
>
> here is a business opportunity:
>
> p-bay
>
> where people can bid on custom pseudopotentials.
>
> all that is need would be a suitable currency. i could
> imagine that if something valuable enough was offered
> in exchange, some people might become interested
> in specializing on generating custom potentials.
>
> <evil grin>,
>      axel.
>
>
>> -----????-----
>> ???: "ramzi alaya"<ramzialaya at hotmail.fr>
>> ????: 2012?4?11? ???
>> ???: pw_forum at pwscf.org
>> ??:
>> ??: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation
>>
>>
>> Dear all;
>>
>> I checked the Pwscf for US Bi PZ relativitic pseudopotential but could not
>> find or generate it myself . Thus could you please send me Bi US
>> pseudopotential with PZ approximation.
>>
>> Thank you.
>> Regards.
>>
>>
>>
>> **********************************************************************************
>> Ramzi Alaya
>>
>> E-mail : ramzialaya at hotmail.fr
>> Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie
>> Unit? de Recherche sur les H?t?ro-Epitaxies et Applications
>>
>>
>>
>>
>>
>>
>> --
>> -------------------------------------------------------------------
>> PH.D. candidate Peng Tao
>> Magnetism and Magnetic Materials Division
>> National Laboratory for Material Science
>> Institute of Metal Research, Chinese Academy of Sciences
>> Phone  +86-024-83978751
>> -------------------------------------------------------------------
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>


-- 

----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL

From ptao10b at imr.ac.cn  Thu Apr 12 03:33:41 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Thu, 12 Apr 2012 09:33:41 +0800 (CST)
Subject: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation
In-Reply-To: <CADTmJ6GXbVe43L2sDZRH_7vjHGetUqpvLy2ZQPSO9opEgFX96g@mail.gmail.com>
References: <CADTmJ6GXbVe43L2sDZRH_7vjHGetUqpvLy2ZQPSO9opEgFX96g@mail.gmail.com>
	<BAY151-W5650027C992A2D7A791F1CA3350@phx.gbl>
	<1e6f453.85d.136a3eecb2f.Coremail.ptao10b@imr.ac.cn>
Message-ID: <78fcd9.c78.136a42f3e04.Coremail.ptao10b@imr.ac.cn>

It's a nice idea but the generation of pseudo is a boring and complicated work. The most important point is the market is too limited and researchers have the choice changing pwscf to VASP or win2k. Thus I am not sure about this deal. It is just my personal view and hope there would be pseudos available as many as possible. 

Plato Tao
> -----????-----
> ???: "Axel Kohlmeyer" <akohlmey at gmail.com>
> ????: 2012?4?12? ???
> ???: "Peng Tao" <ptao10b at imr.ac.cn>
> ??: "ramzi alaya" <ramzialaya at hotmail.fr>, pw_forum <pw_forum at pwscf.org>
> ??: Re: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation
> 
> On Wed, Apr 11, 2012 at 8:23 PM, Peng Tao <ptao10b at imr.ac.cn> wrote:
> > It's really a pity that pwscf has so few pseudopotentials. T_T
> 
> here is a business opportunity:
> 
> p-bay
> 
> where people can bid on custom pseudopotentials.
> 
> all that is need would be a suitable currency. i could
> imagine that if something valuable enough was offered
> in exchange, some people might become interested
> in specializing on generating custom potentials.
> 
> <evil grin>,
>     axel.
> 
> 
> > -----????-----
> > ???: "ramzi alaya" <ramzialaya at hotmail.fr>
> > ????: 2012?4?11? ???
> > ???: pw_forum at pwscf.org
> > ??:
> > ??: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation
> >
> >
> > Dear all;
> >
> > I checked the Pwscf for US Bi?PZ relativitic?pseudopotential but could not
> > find or generate it myself . Thus could you please send me Bi US
> > pseudopotential with PZ approximation.
> >
> > Thank you.
> > Regards.
> >
> >
> >
> > **********************************************************************************
> > Ramzi Alaya
> >
> > E-mail?: ramzialaya at hotmail.fr
> > Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie
> > Unit? de Recherche sur les H?t?ro-Epitaxies et Applications
> >
> >
> >
> >
> >
> >
> > --
> > -------------------------------------------------------------------
> > PH.D. candidate Peng Tao
> > Magnetism and Magnetic Materials Division
> > National Laboratory for Material Science
> > Institute of Metal Research, Chinese Academy of Sciences
> > Phone ?+86-024-83978751
> > -------------------------------------------------------------------
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> 
> 
> 
> -- 
> Dr. Axel Kohlmeyer
> akohlmey at gmail.com ?http://goo.gl/1wk0
> 
> College of Science and Technology
> Temple University, Philadelphia PA, USA.



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------






From degironc at sissa.it  Thu Apr 12 08:25:49 2012
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 12 Apr 2012 08:25:49 +0200
Subject: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation
In-Reply-To: <4F862B6A.2000809@epfl.ch>
References: <BAY151-W5650027C992A2D7A791F1CA3350@phx.gbl>	<1e6f453.85d.136a3eecb2f.Coremail.ptao10b@imr.ac.cn>	<CADTmJ6GXbVe43L2sDZRH_7vjHGetUqpvLy2ZQPSO9opEgFX96g@mail.gmail.com>
	<4F862B6A.2000809@epfl.ch>
Message-ID: <4F86756D.6080608@sissa.it>

I agree with Nicola that an important issue is what to compare with and 
this requires good all electron calculations. There is some work going 
on on that line and we'll see where it'll take us.
stefano

On 04/12/2012 03:10 AM, Nicola Marzari wrote:
>
> I wondered about this for some time! In my opinion, it could be
> an interesting challenge to issue, but one would need to
> have a competition, and only the "best" pseudo for each element
> would get prize money.
>
> Now, the issue is what is best - we would need solid-state all-electron
> data to test against, and that is what is missing right now... (of
> course, we could have a double competition, and hope the best match
> is for good reasons).
>
> 				nicola
>
>
>
>
> On 12/04/2012 03:02, Axel Kohlmeyer wrote:
>> On Wed, Apr 11, 2012 at 8:23 PM, Peng Tao<ptao10b at imr.ac.cn>   wrote:
>>> It's really a pity that pwscf has so few pseudopotentials. T_T
>> here is a business opportunity:
>>
>> p-bay
>>
>> where people can bid on custom pseudopotentials.
>>
>> all that is need would be a suitable currency. i could
>> imagine that if something valuable enough was offered
>> in exchange, some people might become interested
>> in specializing on generating custom potentials.
>>
>> <evil grin>,
>>       axel.
>>
>>
>>> -----????-----
>>> ???: "ramzi alaya"<ramzialaya at hotmail.fr>
>>> ????: 2012?4?11? ???
>>> ???: pw_forum at pwscf.org
>>> ??:
>>> ??: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation
>>>
>>>
>>> Dear all;
>>>
>>> I checked the Pwscf for US Bi PZ relativitic pseudopotential but could not
>>> find or generate it myself . Thus could you please send me Bi US
>>> pseudopotential with PZ approximation.
>>>
>>> Thank you.
>>> Regards.
>>>
>>>
>>>
>>> **********************************************************************************
>>> Ramzi Alaya
>>>
>>> E-mail : ramzialaya at hotmail.fr
>>> Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie
>>> Unit? de Recherche sur les H?t?ro-Epitaxies et Applications
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> -------------------------------------------------------------------
>>> PH.D. candidate Peng Tao
>>> Magnetism and Magnetic Materials Division
>>> National Laboratory for Material Science
>>> Institute of Metal Research, Chinese Academy of Sciences
>>> Phone  +86-024-83978751
>>> -------------------------------------------------------------------
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>
>>
>


From sheleonzhang at gmail.com  Thu Apr 12 08:55:34 2012
From: sheleonzhang at gmail.com (Sheleon Zhang)
Date: Thu, 12 Apr 2012 14:55:34 +0800
Subject: [Pw_forum] Any Norm-conserved PP database for Pwscf?
Message-ID: <4F867C66.30203@gmail.com>

Hello,
Recently,i am going to perform the photon calulations for some crystal,
but most of the pp for atoms are not nc formatted. at first, i want to
covert the abinit nc-pp to pwscf using phi2upf.x, but when it read the
second line of nc-pp file contains znatom, zion, pspdat,programme failed
with 'Fortran runtime error: Bad real number in item 1 of list input' or
'forrtl: severe (59): list-directed I/O syntax error, unit 1,'. i check
the code,but cant find anything wierd.Please guide me how to solve this
promblem.
Thanks in advanced



Best regards!

Sheleon

From nicola.marzari at epfl.ch  Thu Apr 12 10:15:40 2012
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Thu, 12 Apr 2012 10:15:40 +0200
Subject: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation
In-Reply-To: <78fcd9.c78.136a42f3e04.Coremail.ptao10b@imr.ac.cn>
References: <CADTmJ6GXbVe43L2sDZRH_7vjHGetUqpvLy2ZQPSO9opEgFX96g@mail.gmail.com>
	<BAY151-W5650027C992A2D7A791F1CA3350@phx.gbl>
	<1e6f453.85d.136a3eecb2f.Coremail.ptao10b@imr.ac.cn>
	<78fcd9.c78.136a42f3e04.Coremail.ptao10b@imr.ac.cn>
Message-ID: <4F868F2C.5000402@epfl.ch>



Dear Plato,


the point is that QE is a free, open-source community project, a bit
like Linux (as opposed to, say, Windows or Mac) - the spirit is to try
and empower people to become electronic-structure researchers,
rather than users.

Becoming an expert in pseudopotential generation (or any other
complex task of one's choice) makes someone a better scientist,
in this field. Of course, time is limited, and goals can be
different, so everyone is welcome to make whatever use of the
tool they wish for.

Still, the world will be a more interesting place if everyone
asks oneself what they can do for the community, rather than
what the community can do for them (JFK, more or less).

			nicola


On 12/04/2012 03:33, Peng Tao wrote:
> It's a nice idea but the generation of pseudo is a boring and complicated work. The most important point is the market is too limited and researchers have the choice changing pwscf to VASP or win2k. Thus I am not sure about this deal. It is just my personal view and hope there would be pseudos available as many as possible.
>
> Plato Tao

----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL

From giannozz at democritos.it  Thu Apr 12 10:52:27 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 12 Apr 2012 10:52:27 +0200
Subject: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation
In-Reply-To: <BAY151-W5650027C992A2D7A791F1CA3350@phx.gbl>
References: <BAY151-W5650027C992A2D7A791F1CA3350@phx.gbl>
Message-ID: <5E3B2FBE-7476-4937-B995-7F9729AE4464@democritos.it>


On Apr 11, 2012, at 14:09 , ramzi alaya wrote:

> I checked the Pwscf for US Bi PZ relativitic pseudopotential but  
> could not find
> or generate it myself

have you had a look at the PSlibrary project?
http://qe-forge.org/projects/pslibrary/

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  Thu Apr 12 10:40:50 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Thu, 12 Apr 2012 16:40:50 +0800 (CST)
Subject: [Pw_forum] Any Norm-conserved PP database for Pwscf?
In-Reply-To: <4F867C66.30203@gmail.com>
References: <4F867C66.30203@gmail.com>
Message-ID: <1232ff36.21942.136a5b6502b.Coremail.flux_ray12@163.com>

I remember that ph.x can deal with ultrasoft pseudo-potential (may not work with PAW pseudo-potential)~ According to my own experience, since NCPP alway requires high cut-off energy, it will cost more time for phonon calculation~
Or, this website: http://www.sas.upenn.edu/rappegroup/htdocs/Research/psp_gga.html, provides norm-conserving pseudo-potential parameters for certain elements (a little big harder pp, so the cut-off around 100Ry is required). You can use opium code to generate UPF format pp based on the parameters.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 



At 2012-04-12 14:55:34,"Sheleon Zhang" <sheleonzhang at gmail.com> wrote:
>Hello,
>Recently,i am going to perform the photon calulations for some crystal,
>but most of the pp for atoms are not nc formatted. at first, i want to
>covert the abinit nc-pp to pwscf using phi2upf.x, but when it read the
>second line of nc-pp file contains znatom, zion, pspdat,programme failed
>with 'Fortran runtime error: Bad real number in item 1 of list input' or
>'forrtl: severe (59): list-directed I/O syntax error, unit 1,'. i check
>the code,but cant find anything wierd.Please guide me how to solve this
>promblem.
>Thanks in advanced
>
>
>
>Best regards!
>
>Sheleon
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
-------------- next part --------------
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From giannozz at democritos.it  Thu Apr 12 11:07:52 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 12 Apr 2012 11:07:52 +0200
Subject: [Pw_forum] Any Norm-conserved PP database for Pwscf?
In-Reply-To: <4F867C66.30203@gmail.com>
References: <4F867C66.30203@gmail.com>
Message-ID: <AFC3622C-507F-49BC-A599-DFC691924973@democritos.it>


On Apr 12, 2012, at 8:55 , Sheleon Zhang wrote:

> at first, i want to covert the abinit nc-pp to pwscf using fhi2upf.x

which abinit nc-pp exactly?

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 d.tiana at bath.ac.uk  Thu Apr 12 12:49:08 2012
From: d.tiana at bath.ac.uk (Davide Tiana)
Date: Thu, 12 Apr 2012 11:49:08 +0100
Subject: [Pw_forum] pp.x problem and doubts related to the point keyword
Message-ID: <20120412114908.Horde.DvlrFVLxr25PhrMk0orQFLA@webmail.bath.ac.uk>

I am trying to write a xsf file with the LUMO electron charge density  
using pp.x. I am in doubt with the meaning of kpoint option. Indeed if  
I don't put that keyword (or if I chose gamma point) the program crash.

"
      Calling punch_plot, plot_num =   7

      Plotting k_point =   0  band = 49

   
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      from local_dos : error #         1
      wrong kpoint specified
   
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

      stopping ...
"

Everything works fine if I put kpoint=1 or 2
what is the correct meaning of this keyword?
What I think is that, using kpoint=X, the properties is calculated at  
a specific point instead of in all the reciprocal space (i.e. all the  
point used during pw.x calc). Is this correct? if yes, how Can I  
calculate a properties over all the reciprocal space?

Thanks a lot


From ptao10b at imr.ac.cn  Thu Apr 12 13:46:28 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Thu, 12 Apr 2012 19:46:28 +0800 (CST)
Subject: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation
In-Reply-To: <4F868F2C.5000402@epfl.ch>
References: <4F868F2C.5000402@epfl.ch>
	<CADTmJ6GXbVe43L2sDZRH_7vjHGetUqpvLy2ZQPSO9opEgFX96g@mail.gmail.com>
	<BAY151-W5650027C992A2D7A791F1CA3350@phx.gbl>
	<1e6f453.85d.136a3eecb2f.Coremail.ptao10b@imr.ac.cn>
	<78fcd9.c78.136a42f3e04.Coremail.ptao10b@imr.ac.cn>
Message-ID: <14b2336.2ab2.136a6604482.Coremail.ptao10b@imr.ac.cn>

Sorry for my misleading words.(-? I was just insisting that it's better be free, for the commercialization is a bit like VASP or win2k.

Plato


> -----????-----
> ???: "Nicola Marzari" <nicola.marzari at epfl.ch>
> ????: 2012?4?12? ???
> ???: "Peng Tao" <ptao10b at imr.ac.cn>
> ??: pw_forum <pw_forum at pwscf.org>
> ??: Re: [Pw_forum] relativitic pseudopotential for Bi, PZ approximation
> 
> 
> 
> Dear Plato,
> 
> 
> the point is that QE is a free, open-source community project, a bit
> like Linux (as opposed to, say, Windows or Mac) - the spirit is to try
> and empower people to become electronic-structure researchers,
> rather than users.
> 
> Becoming an expert in pseudopotential generation (or any other
> complex task of one's choice) makes someone a better scientist,
> in this field. Of course, time is limited, and goals can be
> different, so everyone is welcome to make whatever use of the
> tool they wish for.
> 
> Still, the world will be a more interesting place if everyone
> asks oneself what they can do for the community, rather than
> what the community can do for them (JFK, more or less).
> 
> 			nicola
> 
> 
> On 12/04/2012 03:33, Peng Tao wrote:
> > It's a nice idea but the generation of pseudo is a boring and complicated work. The most important point is the market is too limited and researchers have the choice changing pwscf to VASP or win2k. Thus I am not sure about this deal. It is just my personal view and hope there would be pseudos available as many as possible.
> >
> > Plato Tao
> 
> ----------------------------------------------------------------------
> Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL



--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------






From Lorenzo.Paulatto at impmc.upmc.fr  Thu Apr 12 14:00:53 2012
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Thu, 12 Apr 2012 14:00:53 +0200
Subject: [Pw_forum] Any Norm-conserved PP database for Pwscf?
In-Reply-To: <1232ff36.21942.136a5b6502b.Coremail.flux_ray12@163.com>
References: <4F867C66.30203@gmail.com>
	<1232ff36.21942.136a5b6502b.Coremail.flux_ray12@163.com>
Message-ID: <op.wcnibr08xuur8c@vanoxite.impmc.jussieu.fr>

On Thu, 12 Apr 2012 10:40:50 +0200, GAO Zhe <flux_ray12 at 163.com> wrote:
> I remember that ph.x can deal with ultrasoft pseudo-potential (may not  
> work with PAW pseudo-potential

PAW dataset are supported by the phonon code.


bests
-- 
Lorenzo Paulatto IdR @ IMPMC/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 flux_ray12 at 163.com  Thu Apr 12 14:13:11 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Thu, 12 Apr 2012 20:13:11 +0800 (CST)
Subject: [Pw_forum] Any Norm-conserved PP database for Pwscf?
In-Reply-To: <op.wcnibr08xuur8c@vanoxite.impmc.jussieu.fr>
References: <4F867C66.30203@gmail.com>
	<1232ff36.21942.136a5b6502b.Coremail.flux_ray12@163.com>
	<op.wcnibr08xuur8c@vanoxite.impmc.jussieu.fr>
Message-ID: <5593f462.24fa2.136a678b9c8.Coremail.flux_ray12@163.com>

Oh, that is nice, thank you very much for providing this information.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 



At 2012-04-12 20:00:53,"Lorenzo Paulatto" <Lorenzo.Paulatto at impmc.upmc.fr> wrote:
>On Thu, 12 Apr 2012 10:40:50 +0200, GAO Zhe <flux_ray12 at 163.com> wrote:
>> I remember that ph.x can deal with ultrasoft pseudo-potential (may not  
>> work with PAW pseudo-potential
>
>PAW dataset are supported by the phonon code.
>
>
>bests
>-- 
>Lorenzo Paulatto IdR @ IMPMC/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
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From giuseppe.mattioli at ism.cnr.it  Thu Apr 12 14:41:14 2012
From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli)
Date: Thu, 12 Apr 2012 14:41:14 +0200
Subject: [Pw_forum] pp.x problem and doubts related to the point keyword
In-Reply-To: <20120412114908.Horde.DvlrFVLxr25PhrMk0orQFLA@webmail.bath.ac.uk>
References: <20120412114908.Horde.DvlrFVLxr25PhrMk0orQFLA@webmail.bath.ac.uk>
Message-ID: <201204121441.15276.giuseppe.mattioli@ism.cnr.it>


Dear Davide
Please remember always to properly sign your post (name, affiliation...)
in the case of Gamma calculations and nspin=2, k_point=1 indicates the first k point printed in pw.x 
output (i.e., Gamma, spin up), k_point=2 is Gamma, spin down instead. If you want to plot the whole 
LUMO orbital (spin up + spin down) you must export both the spin densities and sum them when 
producing the xsf (or cube) file, in this way

export INPFILE=$FILEA-LUMOu.inp
export OUTFILE=$FILEA-LUMOu.out
echo " $FILEA"
echo " $INPFILE"
echo " $OUTFILE"
cat > $INPFILE << EOF
 &inputpp
    prefix  = '$FILEA'
    outdir = '$TMP_DIR/'
    filplot = '$FILEA-LUMOu.dat'
    plot_num= 7
    kpoint=1
    kband=406
 /
EOF
$PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE

export INPFILE=$FILEA-LUMOd.inp
export OUTFILE=$FILEA-LUMOd.out
echo " $FILEA"
echo " $INPFILE"
echo " $OUTFILE"
cat > $INPFILE << EOF
 &inputpp
    prefix  = '$FILEA'
    outdir = '$TMP_DIR/'
    filplot = '$FILEA-LUMOd.dat'
    plot_num= 7
    kpoint=2
    kband=405
 /
EOF
$PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE

export INPFILE=$FILEA-LUMO.inp
export OUTFILE=$FILEA-LUMO.out
echo " $FILEA"
echo " $INPFILE"
echo " $OUTFILE"
cat > $INPFILE << EOF
 &inputpp
 /
 &plot
    nfile = 2
    filepp(1) = '$FILEA-LUMOu.dat'
    weight(1) = 1.0
    filepp(2) = '$FILEA-LUMOd.dat'
    weight(2) = 1.0
    iflag = 3
    output_format = 5
    fileout = '$FILEA-LUMO.plot'
    e1(1) =1.0, e1(2)=1.0, e1(3) = 0.0,
    e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
    nx=56, ny=40
 /
EOF
$PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE


HTH

Giuseppe

On Thursday 12 April 2012 12:49:08 Davide Tiana wrote:
> I am trying to write a xsf file with the LUMO electron charge density
> using pp.x. I am in doubt with the meaning of kpoint option. Indeed if
> I don't put that keyword (or if I chose gamma point) the program crash.
> 
> "
>       Calling punch_plot, plot_num =   7
> 
>       Plotting k_point =   0  band = 49
> 
> 
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%% from local_dos : error #         1
>       wrong kpoint specified
> 
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%
> 
>       stopping ...
> "
> 
> Everything works fine if I put kpoint=1 or 2
> what is the correct meaning of this keyword?
> What I think is that, using kpoint=X, the properties is calculated at
> a specific point instead of in all the reciprocal space (i.e. all the
> point used during pw.x calc). Is this correct? if yes, how Can I
> calculate a properties over all the reciprocal space?
> 
> Thanks a lot
> 
> _______________________________________________
> 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 giuseppe.mattioli at ism.cnr.it  Thu Apr 12 14:44:29 2012
From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli)
Date: Thu, 12 Apr 2012 14:44:29 +0200
Subject: [Pw_forum] hybrid phonons
In-Reply-To: <20120412114908.Horde.DvlrFVLxr25PhrMk0orQFLA@webmail.bath.ac.uk>
References: <20120412114908.Horde.DvlrFVLxr25PhrMk0orQFLA@webmail.bath.ac.uk>
Message-ID: <201204121444.29752.giuseppe.mattioli@ism.cnr.it>


Dear all
Is it possible to perform hybrid (HF-DFT) phonon (well, actually molecular vibrational modes at 
Gamma) calculations?
Giuseppe

-- 
********************************************************
- 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 PCJ994 at bham.ac.uk  Thu Apr 12 14:06:07 2012
From: PCJ994 at bham.ac.uk (Paul Jennings)
Date: Thu, 12 Apr 2012 13:06:07 +0100
Subject: [Pw_forum] Serial Diagonalization
Message-ID: <86CAF89B0E5A344E90835C7D6EEFCF47039A75CC8C52@mbx5.adf.bham.ac.uk>

Dear QE Users,

I am trying to run a relaxation with Davidson diagonalization in serial using QE 4.3.2. I have set the submission script up with the run command utilising "-ndiag 1" as stated in QE Wiki: 

  aprun -n $NPROC -N $NTASK pw.x    -npool 1 -ndiag 1 -inp < Ti8_0_2.in > Ti8_0_2.out

However, my calculations are still running with parallel diagonalization: 


From payam.norouzzadeh at gmail.com  Thu Apr 12 17:03:19 2012
From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh)
Date: Thu, 12 Apr 2012 10:03:19 -0500
Subject: [Pw_forum] Force criteria for relaxation
Message-ID: <CAND4gJE+CT8B-znkrp726_KC=3tb4qhOh-56J6Vph-_s6T1CeA@mail.gmail.com>

Dear QE users

I have a quick question:
I set
etot_conv_thr = 1.0E-9
forc_conv_thr = 1.0D-4 ,
in vc-relax procedure but the job ended when
 Total force =     0.016813     Total SCF correction =     0.000067

How is it possible? Do I have to add some other flags to reach smaller
forces?

Best regards,
Payam Norouzzadeh
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From fratesi at mater.unimib.it  Thu Apr 12 17:59:30 2012
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Thu, 12 Apr 2012 17:59:30 +0200
Subject: [Pw_forum] Force criteria for relaxation
In-Reply-To: <CAND4gJE+CT8B-znkrp726_KC=3tb4qhOh-56J6Vph-_s6T1CeA@mail.gmail.com>
References: <CAND4gJE+CT8B-znkrp726_KC=3tb4qhOh-56J6Vph-_s6T1CeA@mail.gmail.com>
Message-ID: <4F86FBE2.7000006@mater.unimib.it>

Dear Payam,

"the job ended"... have you reached the maximum number of steps, or some 
other event occurred? did the program printed "bfgs converged" or the like?

Then, how many atoms are in your system? The threshold forc_conv_thr is 
on the components, not on the total force which will in general be larger.

HTH,
Guido

Il 04/12/2012 05:03 PM, Payam Norouzzadeh ha scritto:
> Dear QE users
>
> I have a quick question:
> I set
> etot_conv_thr = 1.0E-9
> forc_conv_thr = 1.0D-4 ,
> in vc-relax procedure but the job ended when
>   Total force =     0.016813     Total SCF correction =     0.000067
>
> How is it possible? Do I have to add some other flags to reach smaller
> forces?
>
> Best regards,
> Payam Norouzzadeh
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
Guido Fratesi

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

From sohailphysics at yahoo.co.in  Thu Apr 12 20:55:49 2012
From: sohailphysics at yahoo.co.in (Sohail Ahmad)
Date: Fri, 13 Apr 2012 02:55:49 +0800 (SGT)
Subject: [Pw_forum] PWgui utility
Message-ID: <1334256949.36228.YahooMailClassic@web192202.mail.sg3.yahoo.com>

Dear All
Can we perform calculation of band structure/Density of states/.... from PWgui or it just creates input file
--------------------------------------------------------------------- 

Sohail AhmadKing Khalid UniversityAbha, Saudi Arabia--------------------------------------------------------------------
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From giannozz at democritos.it  Thu Apr 12 21:34:16 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 12 Apr 2012 21:34:16 +0200
Subject: [Pw_forum] Serial Diagonalization
In-Reply-To: <86CAF89B0E5A344E90835C7D6EEFCF47039A75CC8C52@mbx5.adf.bham.ac.uk>
References: <86CAF89B0E5A344E90835C7D6EEFCF47039A75CC8C52@mbx5.adf.bham.ac.uk>
Message-ID: <710CF4ED-D752-4AFF-BE25-82F0D2FB1DB2@democritos.it>


On Apr 12, 2012, at 14:06 , Paul Jennings wrote:

> I have set the submission script up with the run command utilising  
> "-ndiag 1"
> [...] However, my calculations are still running with parallel  
> diagonalization:


is the code compiled using ScaLAPACK?

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 xrhino at gmail.com  Thu Apr 12 22:07:24 2012
From: xrhino at gmail.com (YY)
Date: Thu, 12 Apr 2012 16:07:24 -0400
Subject: [Pw_forum] ecutrho in phonon calculations
Message-ID: <CAKr8hj0y1tGHXy_E7k3ehU3yR-b=gfp8auXUszgp=M2aU8BbPw@mail.gmail.com>

Dear all,

I am now calculating the phonon with ph.x (US-PP, off gamma point).
As recommended by the manual, ecutrho should be 8-10 times of ecutwfc.
 But I find there is no simple convergence trend while increasing
ecutrho.  When I use 35 Ry ecutwfc, and fix all the other parameters,
the results are like this:

   ecutrho       f1(cm-1)      ....  f12(cm-1)
   420            40.475                324.062
   600           123.746               350.727
   900           -251.876              306.721

I also increase ecutwfc, test the convergence of ecutrho, but get the
same trend.  So I don't know how to choose a "proper" ecutrho.

I attached the input files as following, and thanks for your help.

Yuyang,Ph.D student
RPI, USA


inputfile for the ph.x calculation:
 phonon
 &inputph
  tr2_ph=1.0d-14,
  prefix='yytest',
  amass(1)=55.845
  amass(2)=78.96
  outdir='./tmp'
  fildyn='yytest.dyn'
 /
0.000000000   0.200000000   0.000000000

inputfile for the SCF calculation
 &control
    calculation='scf'
    restart_mode='from_scratch',
    pseudo_dir='./'
    outdir='./tmp'
    prefix='yytest',
    tprnfor=.TRUE.
    tstress = .TRUE.
    wf_collect=.true.
 /
 &system
    ibrav=8, celldm(1)=7.18092, celldm(2)=1.000, celldm(3)= 1.515622236,
    nat= 4, ntyp=2,
    ecutwfc = 35
    ecutrho = 420
!    nbnd    = 24
    occupations = 'smearing',  smearing = 'gaussian',  degauss = 0.000736
 /
 &electrons
    conv_thr =  1.0d-10
 /
ATOMIC_SPECIES
 Fe  55.845   Fe.UPF
 Se  78.96    Se.UPF
ATOMIC_POSITIONS (crystal)
Fe       0.000000000   0.500000000   0.500000000
Fe       0.500000000   0.000000000   0.500000000
Se       0.000000000   0.000000000   0.726479503
Se       0.500000000   0.500000000   0.273520497
K_POINTS automatic
5 5 4 1 1 1

From trambui at u.boisestate.edu  Fri Apr 13 00:21:18 2012
From: trambui at u.boisestate.edu (Tram Bui)
Date: Thu, 12 Apr 2012 16:21:18 -0600
Subject: [Pw_forum] error in average.x calculation
Message-ID: <CANzxBn9yVDHgCtd_Oq3nwvs9wcFrf6F0SBw3xV7dm9ciZ_X31A@mail.gmail.com>

Dear QE users,

    I'm trying to run the average.x calculation for my bulk SiC system. I
got the calculations to work by re-running the WorkFct-examples. However,
when I apply the same procedure to my bulk SiC system, I got the error of
"nfile is wrong". Even though I ran everything with the same QE version
(4.3.2).Would you please take a look at what I have here and help me fix
the issue? I have a zincblend cubic structure of 64 atoms and
celldm(1)=16.56 Bohr, and FFT grid (81 81 81).
 Here is my bulkpp.in file:
           &inputpp
              prefix='bulk'
              outdir='./bulk',
              filplot='potential'
              plot_num=11
           /
           &plot
              iflag=3,
              output_format=3
           /
Here is the very top of my "potential" file:

      81      81      81      81      81      81      64       2
     0       16.56000000      0.00000000      0.00000000
0.00000000      0.00000000      0.00000000
   1.00000000000000       0.000000000000000E+000  0.000000000000000E+000
  0.000000000000000E+000   1.00000000000000       0.000000000000000E+000
  0.000000000000000E+000  0.000000000000000E+000   1.00000000000000
     1667.1403767900        8.0000000000       30.0000000000    11
   1   Si    4.00
   2   C     4.00
   1       0.000000000    0.000000000    0.000000000    1
   2       0.500000000    0.000000000    0.000000000    1
   3       0.000000000    0.500000000    0.000000000    1
   4       0.000000000    0.000000000    0.500000000    1
   5       0.500000000    0.500000000    0.000000000    1
   6       0.500000000    0.000000000    0.500000000    1
   7       0.000000000    0.500000000    0.500000000    1
And here is my average.in file:
          1
          potential
          1.D0
          81
          3
          16.56

And I keep getting the error of "nfile is wrong". Please help me out! If
you need additional information. Please let me know


Best regards,

Tram Bui

-- 
Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From payam.norouzzadeh at gmail.com  Fri Apr 13 00:32:44 2012
From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh)
Date: Thu, 12 Apr 2012 17:32:44 -0500
Subject: [Pw_forum] Force criteria for relaxation
Message-ID: <CAND4gJE+9o66fR_sN+L3Lb-724pm0D79qfhpNzY+uUrSvtMzqA@mail.gmail.com>

Dear Dr.Fratesi

Thank you for your attention.
It reached to max number of steps while I set it 1000 and it is wired.
The number of atoms in the system is 54.
These lines are before the last SCF in output:

The maximum number of steps has been reached.
 End of BFGS Geometry Optimization

Best regards,Payam Norouzzadeh
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From chenhanghuipwscf at gmail.com  Fri Apr 13 04:53:52 2012
From: chenhanghuipwscf at gmail.com (Hanghui Chen)
Date: Thu, 12 Apr 2012 22:53:52 -0400
Subject: [Pw_forum] offset in QE 4.2 and QE 4.3
Message-ID: <CAOE2MOyqo-uH9wkn_ZykucAmS59CeewsEk67t8es=nkNiPUuAA@mail.gmail.com>

Dear QE developers,
     I notice a change in the subroutine offset_atom_wfc.f90 from QE 4.2 to
QE 4.3. At line 60, in QE 4.3 an additional condition upf(nt)%oc(n) > 0 is
present while such a condition does not exist in QE 4.2. For a particular
case of BaO, I want to turn on Hubbard U on Ba empty 5d state. Ba is NOT
included in the default setting of QE. So I modified the file
set_hubbard_l.f90 and tabd.f90. In tabd.f90, I set hubbard_occ = 0.0 for
Ba. But in QE 4.3 it seems that hubbard_occ must be larger than 0.
Otherwise the code crashes.
     In fact, I am a little bit confused that in the subroutine
offset_atom_wfc.f90, at line 40, upf(nt)%oc(n)>=0.0. So the occupancy of d
orbital could be larger or equal to zero. Then why at line 60, we must have
the addition condition that upf(nt)%oc(n)>0, which is absent in QE 4.2? How
about upf(nt)%oc(n) = 0?
    Thank you very much.

Hanghui Chen
Department of Physics
Yale University
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From fratesi at mater.unimib.it  Fri Apr 13 09:36:10 2012
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Fri, 13 Apr 2012 09:36:10 +0200
Subject: [Pw_forum] Force criteria for relaxation
In-Reply-To: <CAND4gJE+9o66fR_sN+L3Lb-724pm0D79qfhpNzY+uUrSvtMzqA@mail.gmail.com>
References: <CAND4gJE+9o66fR_sN+L3Lb-724pm0D79qfhpNzY+uUrSvtMzqA@mail.gmail.com>
Message-ID: <4F87D76A.6090605@mater.unimib.it>

Il 04/13/2012 12:32 AM, Payam Norouzzadeh ha scritto:

> The maximum number of steps has been reached.
>   End of BFGS Geometry Optimization

Then, your system is either
  1) lowering energy and forces rather slowly
  2) unable to find the local energy minimum and wandering around

It could help to have a look if:
  i) is the total energy decreasing between the various BFGS steps?
  ii) are forces decreasing?

If (not (i)) there might be some difficulty in the minimization 
procedure, but if (i) and (not(ii)) you could have started far from the 
minimum in a system with a shallow potential energy surface.

Best,
Guido

-- 
Guido Fratesi

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

From giannozz at democritos.it  Fri Apr 13 10:02:18 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 13 Apr 2012 10:02:18 +0200
Subject: [Pw_forum] error in average.x calculation
In-Reply-To: <CANzxBn9yVDHgCtd_Oq3nwvs9wcFrf6F0SBw3xV7dm9ciZ_X31A@mail.gmail.com>
References: <CANzxBn9yVDHgCtd_Oq3nwvs9wcFrf6F0SBw3xV7dm9ciZ_X31A@mail.gmail.com>
Message-ID: <1334304138.23516.6.camel@fe12lx.fisica.uniud.it>

On Thu, 2012-04-12 at 16:21 -0600, Tram Bui wrote:

> And I keep getting the error of "nfile is wrong". 
> Please help me out! 

at line 120 of average.f90:

     READ (inunit, *, err = 1100, iostat = ios) nfile
     IF (nfile<=0.or.nfile>nfilemax) CALL errore ('average ', &
          'nfile is wrong ', 1)

Add  some "print *, .." and you will see what happens and why

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



From lmartinsamos at gmail.com  Fri Apr 13 10:14:25 2012
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Fri, 13 Apr 2012 10:14:25 +0200
Subject: [Pw_forum] hybrid phonons
In-Reply-To: <201204121444.29752.giuseppe.mattioli@ism.cnr.it>
References: <20120412114908.Horde.DvlrFVLxr25PhrMk0orQFLA@webmail.bath.ac.uk>
	<201204121444.29752.giuseppe.mattioli@ism.cnr.it>
Message-ID: <CAGCSmJQXyeXRbUb+ibsRHvszKjfpOtf95Q1WDA+TzvcTEbUh2A@mail.gmail.com>

Dear Giuseppe, not at the moment. But we are thinking in implementing it.
The biggest issue is the time and hands!! Do you have some skilled PhD that
could be interested in participating?

bests

Layla

Le 12 avril 2012 14:44, Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it> a
?crit :

>
> Dear all
> Is it possible to perform hybrid (HF-DFT) phonon (well, actually molecular
> vibrational modes at
> Gamma) calculations?
> Giuseppe
>
> --
> ********************************************************
> - 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 avallabh at purdue.edu  Fri Apr 13 10:25:25 2012
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Fri, 13 Apr 2012 04:25:25 -0400 (EDT)
Subject: [Pw_forum] Query on band crossing
In-Reply-To: <4F85330C.2050103@epfl.ch>
Message-ID: <1642870996.109401.1334305525816.JavaMail.root@mailhub016.itcs.purdue.edu>

Dr. Marzari,


            I have a question regarding the order of the bands in the scf and elph calculations. In the scf output, the energies at every K point
 are arranged from lowest to highest. I want to know if that order holds true in el-ph calculations as well. Like in elphon.f90 file, the variables ibnd,jbnd vary from 1 to nbnd; do they have the same increasing order as in the scf ? 


Thanks
Ajit

From halin at ifm.liu.se  Fri Apr 13 11:26:44 2012
From: halin at ifm.liu.se (Hans Lind)
Date: Fri, 13 Apr 2012 11:26:44 +0200
Subject: [Pw_forum] Phonon LO-TO splitting in semiconductor with smearing
Message-ID: <CAMBdDSNHKMH54Dz5VsxGna+hidei5+gw8NkTCiJXwFhw+vi3iw@mail.gmail.com>

Dear QE users

I am trying to do phonon calculations on AlN at non-zero fermi temperature
to get forces recalculated for higher temperatures. But since I need to use
smearing for that the code won't do LO-TO splitting as is needed in a
semiconductor. Normally to get LO-TO splitting handled correctly all I need
to do is omit the smearing keyword, but since I can't do it now, is there
anything that I can do to get the splitting even while using smearing?
Grateful for any suggestions.

Hans Lind
PhD student
Link?ping University, Link?ping, Sweden
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From PCJ994 at bham.ac.uk  Fri Apr 13 12:17:58 2012
From: PCJ994 at bham.ac.uk (Paul Jennings)
Date: Fri, 13 Apr 2012 11:17:58 +0100
Subject: [Pw_forum] Serial Diagonalization
In-Reply-To: <710CF4ED-D752-4AFF-BE25-82F0D2FB1DB2@democritos.it>
References: <86CAF89B0E5A344E90835C7D6EEFCF47039A75CC8C52@mbx5.adf.bham.ac.uk>,
	<710CF4ED-D752-4AFF-BE25-82F0D2FB1DB2@democritos.it>
Message-ID: <86CAF89B0E5A344E90835C7D6EEFCF47039A75CC8C5A@mbx5.adf.bham.ac.uk>

Yes,

It is linked against ScaLAPACK from Cray's libsci.

Many thanks,
Paul Jennings


________________________________________
From: Paolo Giannozzi [giannozz at democritos.it]
Sent: 12 April 2012 20:34
To: Paul Jennings
Cc: pw_forum at pwscf.org
Subject: Re: [Pw_forum] Serial Diagonalization

On Apr 12, 2012, at 14:06 , Paul Jennings wrote:

> I have set the submission script up with the run command utilising
> "-ndiag 1"
> [...] However, my calculations are still running with parallel
> diagonalization:


is the code compiled using ScaLAPACK?

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



******************************************************
Paul Jennings

Centre for Hydrogen and Fuel Cell Research
PEMFC Research group
School of Chemical Engineering
The University of Birmingham
Edgbaston, Birmingham B15 2TT (U.K.)

E:  PCJ994 at bham.ac.uk
T:  07816644583
W: www.fuelcells.bham.ac.uk

******************************************************

From giannozz at democritos.it  Fri Apr 13 12:33:30 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 13 Apr 2012 12:33:30 +0200
Subject: [Pw_forum] Serial Diagonalization
In-Reply-To: <86CAF89B0E5A344E90835C7D6EEFCF47039A75CC8C5A@mbx5.adf.bham.ac.uk>
References: <86CAF89B0E5A344E90835C7D6EEFCF47039A75CC8C52@mbx5.adf.bham.ac.uk>
	, <710CF4ED-D752-4AFF-BE25-82F0D2FB1DB2@democritos.it>
	<86CAF89B0E5A344E90835C7D6EEFCF47039A75CC8C5A@mbx5.adf.bham.ac.uk>
Message-ID: <1334313210.25277.5.camel@fe12lx.fisica.uniud.it>

On Fri, 2012-04-13 at 11:17 +0100, Paul Jennings wrote:

> It is linked against ScaLAPACK from Cray's libsci.

in Modules/mp_global.f90, lines 575 and following, try to replace
this piece of code:

#if defined __SCALAPACK
       nproc_ortho_try = MAX( parent_nproc/2, 1 )
#else
       nproc_ortho_try = 1
#endif

with

       nproc_ortho_try = 1

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



From giannozz at democritos.it  Fri Apr 13 14:11:41 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 13 Apr 2012 14:11:41 +0200
Subject: [Pw_forum] Query on band crossing
In-Reply-To: <1642870996.109401.1334305525816.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <1642870996.109401.1334305525816.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <1334319101.28218.1.camel@fe12lx.fisica.uniud.it>

On Fri, 2012-04-13 at 04:25 -0400, Ajit Vallabhaneni wrote:

>  In the scf output, the energies at every K point
>  are arranged from lowest to highest. I want to know 
> if that order holds true in el-ph calculations as well

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



From gabriele.sclauzero at epfl.ch  Fri Apr 13 18:20:46 2012
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Fri, 13 Apr 2012 18:20:46 +0200
Subject: [Pw_forum] Querry abou the kpoints in transport calculations
In-Reply-To: <CADww=110Paam7D5zWDmj=xTnqU81J7V0G=o5s775L+N87eZxNQ@mail.gmail.com>
References: <CADww=110Paam7D5zWDmj=xTnqU81J7V0G=o5s775L+N87eZxNQ@mail.gmail.com>
Message-ID: <4F88525E.8070000@epfl.ch>

Dear Pankaj,

     if you are speaking about the k-points in the scf calculations, 
then the correct thing to do is the second.
The optimal number of k-points depends on the band structure and on the 
size of the BZ. The latter in turn depends on the size of the simulation 
cell. Since this is usually much shorter for the electrode, then the 
corresponding number of k-points along the transport direction must be 
larger.
     Regarding the k-points in the transport calculations, if you are 
simulating a one-dimensional system then you just need one k-point in 
the perpendicular directions xy (because the transmission does not 
depend on k_perp, in principle). If the system has extended leads 
instead, you need to choose a k_perp-points set that integrates the 
transmission in the 2D-BZ with sufficient accuracy. This set might be 
larger than that of the scf calculation.

HTH

GS

On 04/11/2012 09:14 AM, pankaj sahota wrote:
> Hi,
>
> Can anybody tell me that if I want to calculate the transport 
> properties of a wire then do I have to take the same kpoints for the 
> scattering region and electrode or they can be chosen differently 
> because kpoints for both of them will be generated differently due to 
> the different length along the z-direction.
>
> Thanks and regards.
> Pankaj
>
> -- 
> Pankaj Kumar
> DST Project Fellow(Ph.D.)
> Department of Physics
> The LNM IIT Jaipur
> Mob. No. +91 9736694726
>
-- 

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

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From mourad_fsm at yahoo.fr  Fri Apr 13 19:30:03 2012
From: mourad_fsm at yahoo.fr (debbichi mourad)
Date: Fri, 13 Apr 2012 18:30:03 +0100 (BST)
Subject: [Pw_forum] (no subject)
Message-ID: <1334338203.33622.YahooMailNeo@web29506.mail.ird.yahoo.com>

Dear PWScf Users, 
I try to do the dielectric function calculations. At first I did the
scf-calculation. After using the code epsilon.x, I gives the following error message :

running epsilon.x ...Cannot match namelist object name calculation
namelist read: missplaced = sign
Cannot match namelist object name eps'

?Why such a problem occurs?

?My input files is as following:

cat > MgO.scf.in << EOF
&control
calculation='scf'
restart_mode='from_scratch',
prefix='MgO'
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
tstress=.true.
/

&SYSTEM
ibrav = 4,
celldm(1) =6.11,
celldm(3) = 1.611, 
nat = 4,
ntyp = 2,
ecutwfc =50,
nspin = 2,
starting_magnetization(1)=0.7, starting_magnetization(2)=0.5,
occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02,
/
&ELECTRONS
conv_thr = 1.0d-10 ,
mixing_mode = 'plain' ,
mixing_beta = 0.6,
diagonalization = 'david' ,
/
ATOMIC_SPECIES
Mg   24.3050  Mg.pz-n-vbc.UPF 
O   15.99940   O.pz-mt.UPF

ATOMIC_POSITIONS Crystal
Mg     0.666666667    0.333333333    0.000000000
Mg     0.333333333    0.666666667    0.500000000
O      0.666666667    0.333333333    0.380000000
O      0.333333333    0.666666667    0.880000000

K_POINTS automatic
9 9 3 1 1 1 

EOF
$ECHO "  running the scf calculation...\c"
$PW_COMMAND < MgO.scf.in > MgO.scf.out
check_failure $?
$ECHO " done"
#########################################################
cat> MgO_eps.in << EOF
&inputpp
outdir='$TMP_DIR/'
prefix='MgO'
calculation='eps'
/
&energy_grid
smeartype='gauss'
intersmear=0.15d0
wmin     = 0.0d0
wmax=30.0d0
nw=1000
shift=0.0d0
intrasmear   = 0.0d0
/
EOF

$ECHO "  running epsilon.x ...\c"
$PROJWFC_COMMAND <  MgO_eps.in > MgO_eps.out
check_failure $?
$ECHO " done"

Sincerely


?
DEBBICHI Mourad
Unit? de Recherche Physique des Solides,99/UR/13-19,
D?partement de Physique, Facult? des Science de Monastir,
Avenue de l'Environnement 5019, Monastir Tunisie.
t?l:+21697487042
mourad_fsm at yahoo.fr
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From giannozz at democritos.it  Fri Apr 13 19:39:20 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 13 Apr 2012 19:39:20 +0200
Subject: [Pw_forum] (no subject)
In-Reply-To: <1334338203.33622.YahooMailNeo@web29506.mail.ird.yahoo.com>
References: <1334338203.33622.YahooMailNeo@web29506.mail.ird.yahoo.com>
Message-ID: <4F86B18D-E22A-4868-8755-5686900E4149@democritos.it>


On Apr 13, 2012, at 19:30 , debbichi mourad wrote:

> Cannot match namelist object name calculation
> namelist read: missplaced = sign
> Cannot match namelist object name eps'
>
>  Why such a problem occurs?

for the reason explained above. Look carefully this line:

> calculation='eps'

there is something wrong there

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  Fri Apr 13 22:41:04 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 13 Apr 2012 22:41:04 +0200
Subject: [Pw_forum] offset in QE 4.2 and QE 4.3
In-Reply-To: <CAOE2MOyqo-uH9wkn_ZykucAmS59CeewsEk67t8es=nkNiPUuAA@mail.gmail.com>
References: <CAOE2MOyqo-uH9wkn_ZykucAmS59CeewsEk67t8es=nkNiPUuAA@mail.gmail.com>
Message-ID: <0D290833-0BC8-4A47-956B-8872EA90530E@democritos.it>


On Apr 13, 2012, at 4:53 , Hanghui Chen wrote:

> I notice a change in the subroutine offset_atom_wfc.f90 from QE 4.2  
> to QE 4.3.
> At line 60, in QE 4.3 an additional condition upf(nt)%oc(n) > 0 is  
> present while
> such a condition does not exist in QE 4.2.

please see http://www.democritos.it/pipermail/pw_forum/2010-July/ 
017622.html
and the relative thread. Apparently this change was introduced as a  
workaround
for cases in which two states with same value of angular momentum  
were present.

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 halin at ifm.liu.se  Sat Apr 14 13:09:43 2012
From: halin at ifm.liu.se (Hans Lind)
Date: Sat, 14 Apr 2012 13:09:43 +0200
Subject: [Pw_forum] Phonon LO-TO splitting in semiconductor with smearing
In-Reply-To: <64287682-EFF6-4F5C-AE5E-CB915C81750C@democritos.it>
References: <CAMBdDSNHKMH54Dz5VsxGna+hidei5+gw8NkTCiJXwFhw+vi3iw@mail.gmail.com>
	<64287682-EFF6-4F5C-AE5E-CB915C81750C@democritos.it>
Message-ID: <CAMBdDSPqfpe8Z7hRir7s0m-pw7XNs3EpirJDsQHt3n_cdbcX=A@mail.gmail.com>

Thanks for the response, but not sure how useful it is.
To get the fermi smearing I set the following input lines

occupations='smearing'
smearing='fermi-dirac'
degauss=0.01 (fermi temperature in Ry, about 1500K, I want to set it higher
also)

The smearing would ensure that states are no longer either fully occupied
or empty. And I am not sure either of what you mean by commenting out check
on LO-TO splitting and smearing. As I have used it before, as long as I
don't specify smearing I get the LO-TO splitting automatically.

2012/4/13 Paolo Giannozzi <giannozz at democritos.it>

>
> On Apr 13, 2012, at 11:26 , Hans Lind wrote:
>
>  I am trying to do phonon calculations on AlN at non-zero fermi temperature
>> to get forces recalculated for higher temperatures. But since I need to
>> use
>> smearing for that the code won't do LO-TO splitting as is needed in a
>> semiconductor.
>>
>
> if you comment out the check on LO-TO splitting and smearing, and if all
> states are
> either fully occupied or empty, you should still get a LO-TO splitting.
> Not sure what
> it means, though. The phonon formalism is supposed to work at zero
> temperature.
> Not sure what it takes to extend the formalism to cover finite-temperature
> effects.
>
> 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 jptrinastic at phys.ufl.edu  Sat Apr 14 14:56:40 2012
From: jptrinastic at phys.ufl.edu (Jonathan Trinastic)
Date: Sat, 14 Apr 2012 08:56:40 -0400
Subject: [Pw_forum] Tunneling density of states using pwcond
Message-ID: <4F897408.8080108@phys.ufl.edu>

Hi all,

I'm performing pwcond calculations on a magnetic tunnel junction 
structure, and I'm interested in creating a figure that shows the change 
in the tunneling density of states as a function of the monolayer of the 
barrier for each different orbital (delta1, delta2, etc). In this way, I 
can show the the different decay rates of each.  I understand how to 
find the tunneling density of states using projwfc.x on the sfc 
structure using the command tdosboxes, but my understanding is that this 
is done on the sfc structure and would not give the tunneling results.  
I'm wondering if there is a way to extract information from the pwcond 
output to show these tunneling states?  I'm not able to find any 
relevant choices in the help menu.

Thanks for your help,
Jonathan

-- 
Jonathan Trinastic, M.S.
Graduate Student
Department of Physics
University of Florida


From nicola.marzari at epfl.ch  Sat Apr 14 20:38:52 2012
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Sat, 14 Apr 2012 20:38:52 +0200
Subject: [Pw_forum] Phonon LO-TO splitting in semiconductor with smearing
In-Reply-To: <CAMBdDSNHKMH54Dz5VsxGna+hidei5+gw8NkTCiJXwFhw+vi3iw@mail.gmail.com>
References: <CAMBdDSNHKMH54Dz5VsxGna+hidei5+gw8NkTCiJXwFhw+vi3iw@mail.gmail.com>
Message-ID: <4F89C43C.7050104@epfl.ch>



Dear Hans,


for a semiconductor/insulator at finite temperature you have free
electrons in the conduction band that will screen the electric field
of the LO phonons - in the adiabatic limit of the PWSCF/phonon
calculations you have no macroscopic electric field, and no LO/TO 
splitting, but in the real world you might have non-adiabatic effects.

Depending on the material you'll have a wavevector/frequency
/temperature dependent dielectric function epsilon(q,omega,T) for your
electronic system that will screen more or less successfully the
electric field of the LO phonons - in the limit of very little screening
you have the full LO/TO phonon splitting of the zero-temperature 
semiconductor, and in the limit of very effective screening you'll have
no splitting.

Some related ab-initio work has been done in the group of Mauri:
http://prl.aps.org/pdf/PRL/v100/i22/e226401
http://prl.aps.org/pdf/PRL/v97/i26/e266407

It would be interesting to see experimental data for LO/TO phonons
in III-V as a function of temperature or doping, to see if the screening
is really effective or not. If you search and find them, please share!

			nicola


On 13/04/2012 11:26, Hans Lind wrote:
> Dear QE users
>
> I am trying to do phonon calculations on AlN at non-zero fermi
> temperature to get forces recalculated for higher temperatures. But
> since I need to use smearing for that the code won't do LO-TO splitting
> as is needed in a semiconductor. Normally to get LO-TO splitting handled
> correctly all I need to do is omit the smearing keyword, but since I
> can't do it now, is there anything that I can do to get the splitting
> even while using smearing?
> Grateful for any suggestions.
>
> Hans Lind
> PhD student
> Link?ping University, Link?ping, Sweden
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 

----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL

From elie.moujaes at hotmail.co.uk  Sat Apr 14 21:28:31 2012
From: elie.moujaes at hotmail.co.uk (Elie M)
Date: Sat, 14 Apr 2012 20:28:31 +0100
Subject: [Pw_forum] visualizing results of molecular dynamics using XCRYSDEN
Message-ID: <DUB110-W59A544D299A8DCFCC2DFECD3380@phx.gbl>


Dear all,
I am testing the molecular dynamics package on monolayer graphene: the molecular dynamics I am doing is simply "calculation= 'md', using pw.x; Is there a way to visualize the output using XCrySDEN or is this option only for  calculation='cp'?
Thanks
Elie MoukaeaUniversity of NottinghamNG7 2RDUK 		 	   		  
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From pandey.bramha at gmail.com  Sun Apr 15 11:50:18 2012
From: pandey.bramha at gmail.com (bramha pandey)
Date: Sun, 15 Apr 2012 15:20:18 +0530
Subject: [Pw_forum] problem regrading convergence
Message-ID: <CAC2dNGEnYX-gJ_H9EcZw-cQFccF-F-SY-sB8i84WSPkdjgr-1A@mail.gmail.com>

Dear all PW users,
I m facing convergence problem with my LiInTe2 system. I have reduced the
scf threshold, mixing from 0.7 to 0.8, ecut from 110Ry to 150Ry
But i could not find my convergence after 100 iterations it was stop with
message, convergence not achieved as my system it should not take much
iteration might be i am  wrong. Also i was using Gamma point for fast
convergence with CG diagonalization mehod
Please look my input file....
&control
    calculation = 'scf'
    restart_mode='from_scratch',
    pseudo_dir = '  ',
    outdir=' '
    prefix = 'lit' ,
    tprnfor = .true. ,
 /
&SYSTEM
                       ibrav = 4,
                   celldm(1) = 12.13,
                   celldm(3) = 2.0,
                         nat = 4,
                        ntyp = 3,
                     ecutwfc = 150,
                     ecutrho = 550 ,
 /
 &ELECTRONS
                    conv_thr = 1.0d-9 ,
                 mixing_beta = 0.8 ,
        mixing_ndim = 16,
        diagonalization = 'cg',
 /
 &IONS
                ion_dynamics = 'bfgs' ,

 /
 &CELL
               cell_dynamics = 'bfgs' ,
                       press = 0 ,
                       wmass = 40 ,
            cell_factor = 2.0D0,
 /
ATOMIC_SPECIES
   Li    6.94100  Li.pz-n-vbc.UPF
   In  114.82000  In.pz-bhs.UPF
   Te  127.60000  Te.pz-bhs.UPF

ATOMIC_POSITIONS crystal
   Li      0.000000000    0.000000000    0.000000000
   In      0.50000000    0.50000000      0.50000000
   Te      0.500000000    0.000000000    0.75
   Te      1.0000000      0.50000000     0.25
K_POINTS gamma

Any valuable comment will be highly appreciated.

-- 
Thanks and Regards
Bramha Prasad Pandey
GLA University, Mathura.
INDIA.
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From lmartinsamos at gmail.com  Sun Apr 15 16:36:18 2012
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Sun, 15 Apr 2012 16:36:18 +0200
Subject: [Pw_forum] problem regrading convergence
In-Reply-To: <CAC2dNGEnYX-gJ_H9EcZw-cQFccF-F-SY-sB8i84WSPkdjgr-1A@mail.gmail.com>
References: <CAC2dNGEnYX-gJ_H9EcZw-cQFccF-F-SY-sB8i84WSPkdjgr-1A@mail.gmail.com>
Message-ID: <CAGCSmJTJObPa07e5tZtsEoqV-CtRMV0bepWFijac7hGBCS7z=g@mail.gmail.com>

Dear Bramha, infortunately this kin of behavior could happen, in particular
if the elctronic groundstate could have  two solutions. You can try
wdeducing to 0.1 mixing_beta and choosing mixing_mode="local-TF".

I hope it helps

bests

Layla

2012/4/15 bramha pandey <pandey.bramha at gmail.com>

> Dear all PW users,
> I m facing convergence problem with my LiInTe2 system. I have reduced the
> scf threshold, mixing from 0.7 to 0.8, ecut from 110Ry to 150Ry
> But i could not find my convergence after 100 iterations it was stop with
> message, convergence not achieved as my system it should not take much
> iteration might be i am  wrong. Also i was using Gamma point for fast
> convergence with CG diagonalization mehod
> Please look my input file....
> &control
>     calculation = 'scf'
>     restart_mode='from_scratch',
>     pseudo_dir = '  ',
>     outdir=' '
>     prefix = 'lit' ,
>     tprnfor = .true. ,
>  /
> &SYSTEM
>                        ibrav = 4,
>                    celldm(1) = 12.13,
>                    celldm(3) = 2.0,
>                          nat = 4,
>                         ntyp = 3,
>                      ecutwfc = 150,
>                      ecutrho = 550 ,
>  /
>  &ELECTRONS
>                     conv_thr = 1.0d-9 ,
>                  mixing_beta = 0.8 ,
>         mixing_ndim = 16,
>         diagonalization = 'cg',
>  /
>  &IONS
>                 ion_dynamics = 'bfgs' ,
>
>  /
>  &CELL
>                cell_dynamics = 'bfgs' ,
>                        press = 0 ,
>                        wmass = 40 ,
>             cell_factor = 2.0D0,
>  /
> ATOMIC_SPECIES
>    Li    6.94100  Li.pz-n-vbc.UPF
>    In  114.82000  In.pz-bhs.UPF
>    Te  127.60000  Te.pz-bhs.UPF
>
> ATOMIC_POSITIONS crystal
>    Li      0.000000000    0.000000000    0.000000000
>    In      0.50000000    0.50000000      0.50000000
>    Te      0.500000000    0.000000000    0.75
>    Te      1.0000000      0.50000000     0.25
> K_POINTS gamma
>
> Any valuable comment will be highly appreciated.
>
> --
> Thanks and Regards
> Bramha Prasad Pandey
> GLA University, Mathura.
> INDIA.
>
>
> _______________________________________________
> 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  Sun Apr 15 19:38:17 2012
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Sun, 15 Apr 2012 19:38:17 +0200
Subject: [Pw_forum] problem regrading convergence
In-Reply-To: <CAC2dNGEnYX-gJ_H9EcZw-cQFccF-F-SY-sB8i84WSPkdjgr-1A@mail.gmail.com>
References: <CAC2dNGEnYX-gJ_H9EcZw-cQFccF-F-SY-sB8i84WSPkdjgr-1A@mail.gmail.com>
Message-ID: <op.wcthk2fcxuur8c@linux-qnvk.site>

On Sun, 15 Apr 2012 11:50:18 +0200, bramha pandey  
<pandey.bramha at gmail.com> wrote:
> LiInTe2

If this crystal is metallic, at least in DFT and at the specific unit cell  
volume you are using, it will probably not converge without a smearing.

> mixing_beta = 0.8

If you have problems with convergence you should *reduce* not increase  
this parameter (take something like 0.3)

>  diagonalization = 'cg',

this controls the diagonalization performed at each scf step, not the scf  
step iteself, use the default algorithm instead wich is faster.

bests


-- 
Lorenzo Paulatto IdR CNRS @ IMPMC/UPMC - Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www.impmc.upmc.fr/~paulatto/
mail:  23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From elie.moujaes at hotmail.co.uk  Mon Apr 16 05:15:01 2012
From: elie.moujaes at hotmail.co.uk (Elie M)
Date: Mon, 16 Apr 2012 04:15:01 +0100
Subject: [Pw_forum] vizualizing the molecular dynamics of graphene
Message-ID: <DUB110-W86550842B140B613DC78FCD33E0@phx.gbl>


Dear all,
I am testing the molecular dynamics package on monolayer graphene: the molecular dynamics I am doing is simply "calculation= 'md', using pw.x; Is there a way to visualize the output using XCrySDEN or is this option only for  calculation='cp'?
Thanks
Elie MoukaeaUniversity of NottinghamNG7 2RDUK 		 	   		  
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From marcos.verissimo.alves at gmail.com  Mon Apr 16 08:41:47 2012
From: marcos.verissimo.alves at gmail.com (=?ISO-8859-1?Q?Marcos_Ver=EDssimo_Alves?=)
Date: Mon, 16 Apr 2012 03:41:47 -0300
Subject: [Pw_forum] freeing memory after end of pw.x calculation
Message-ID: <CAOm7q=CQ4Qh63t5X0gGvk=3qN7-H0oGherR=YpUEx2Z5yw+g4g@mail.gmail.com>

Hi all,

Maybe this is a silly question that has come up before, and probably it has
nothing to do with QE, but I could not find anything about it. I have
recently compiled QE in parallel with mpich, all compiled with ifort 10.1
and mkl. Now I am running a series of many many (luckily small) jobs on my
personal machine through a shell script, and I notice that after each of
the small runs, the used memory (as seen with the top command) does not go
down. Instead, it goes up steadily at the end of each pw.x run, and I can
only conclude that, for whatever reason, the memory used is not being freed
at the end of the runs. Has anyone seen this behavior before? Could it be a
bug of the intel compiler, or an OS-related (Ubuntu 11.10) problem?

Best regards,

Marcos
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From Lorenzo.Paulatto at impmc.upmc.fr  Mon Apr 16 08:48:25 2012
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Mon, 16 Apr 2012 08:48:25 +0200
Subject: [Pw_forum] freeing memory after end of pw.x calculation
In-Reply-To: <CAOm7q=CQ4Qh63t5X0gGvk=3qN7-H0oGherR=YpUEx2Z5yw+g4g@mail.gmail.com>
References: <CAOm7q=CQ4Qh63t5X0gGvk=3qN7-H0oGherR=YpUEx2Z5yw+g4g@mail.gmail.com>
Message-ID: <op.wcuiizrexuur8c@linux-qnvk.site>

On Mon, 16 Apr 2012 08:41:47 +0200, Marcos Ver?ssimo Alves  
<marcos.verissimo.alves at gmail.com> wrote:
> Instead, it goes up steadily at the end of each pw.x run, and I can
> only conclude that, for whatever reason, the memory used is not being  
> freed at the end of the runs.

Dear Marco,
are you sure you do not fall in this case <http://www.linuxatemyram.com/>?

bests

-- 
Lorenzo Paulatto IdR CNRS @ IMPMC/UPMC - Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www.impmc.upmc.fr/~paulatto/
mail:  23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From marcos.verissimo.alves at gmail.com  Mon Apr 16 09:02:29 2012
From: marcos.verissimo.alves at gmail.com (=?ISO-8859-1?Q?Marcos_Ver=EDssimo_Alves?=)
Date: Mon, 16 Apr 2012 04:02:29 -0300
Subject: [Pw_forum] freeing memory after end of pw.x calculation
In-Reply-To: <op.wcuiizrexuur8c@linux-qnvk.site>
References: <CAOm7q=CQ4Qh63t5X0gGvk=3qN7-H0oGherR=YpUEx2Z5yw+g4g@mail.gmail.com>
	<op.wcuiizrexuur8c@linux-qnvk.site>
Message-ID: <CAOm7q=AFop0DNL=g2T4B47MO2A975gWpej7hqa6i35Sjg8a9uA@mail.gmail.com>

Hi Lorenzo.

Doesn't seem to be the case, unfortunately. During one run of pw.x:

mverissi at rocknroll:~/pseudo_ape/Carbono/pbe/brute_force/rcs_1.20_rcp_1.20/bmod$
free -m
             total       used       free     shared    buffers     cached
Mem:          7934       2636       5297          0        165       1323
-/+ buffers/cache:       1147       6786
Swap:        11444          0      11444

In the one immediately following it:

mverissi at rocknroll:~/pseudo_ape/Carbono/pbe/brute_force/rcs_1.20_rcp_1.20/bmod$
free -m
             total       used       free     shared    buffers     cached
Mem:          7934       2705       5228          0        165       1387
-/+ buffers/cache:       1151       6782
Swap:        11444          0      11444

Even though the runs eat little RAM at a time, I have a few hundred runs to
perform - I suppose by the end of the runs I'll have my ram all gobbled :(

Marcos

On Mon, Apr 16, 2012 at 3:48 AM, Lorenzo Paulatto <
Lorenzo.Paulatto at impmc.upmc.fr> wrote:

> On Mon, 16 Apr 2012 08:41:47 +0200, Marcos Ver?ssimo Alves
> <marcos.verissimo.alves at gmail.com> wrote:
> > Instead, it goes up steadily at the end of each pw.x run, and I can
> > only conclude that, for whatever reason, the memory used is not being
> > freed at the end of the runs.
>
> Dear Marco,
> are you sure you do not fall in this case <http://www.linuxatemyram.com/>?
>
> bests
>
> --
> Lorenzo Paulatto IdR CNRS @ IMPMC/UPMC - Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www:   http://www.impmc.upmc.fr/~paulatto/
> mail:  23-24/4?14 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
>
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From marcos.verissimo.alves at gmail.com  Mon Apr 16 09:10:32 2012
From: marcos.verissimo.alves at gmail.com (=?ISO-8859-1?Q?Marcos_Ver=EDssimo_Alves?=)
Date: Mon, 16 Apr 2012 04:10:32 -0300
Subject: [Pw_forum] freeing memory after end of pw.x calculation
In-Reply-To: <CAOm7q=AFop0DNL=g2T4B47MO2A975gWpej7hqa6i35Sjg8a9uA@mail.gmail.com>
References: <CAOm7q=CQ4Qh63t5X0gGvk=3qN7-H0oGherR=YpUEx2Z5yw+g4g@mail.gmail.com>
	<op.wcuiizrexuur8c@linux-qnvk.site>
	<CAOm7q=AFop0DNL=g2T4B47MO2A975gWpej7hqa6i35Sjg8a9uA@mail.gmail.com>
Message-ID: <CAOm7q=APHJD6oBoTehuQjiNoGtnTjCP40S8m80K4K-EB7JQTug@mail.gmail.com>

Sorry - my mistake. The second column of the line with buffers/cache is
fairly constant, as I see now. Working late... Sorry for taking your time,
and many thanks for the tip.

Marcos

On Mon, Apr 16, 2012 at 4:02 AM, Marcos Ver?ssimo Alves <
marcos.verissimo.alves at gmail.com> wrote:

> Hi Lorenzo.
>
> Doesn't seem to be the case, unfortunately. During one run of pw.x:
>
> mverissi at rocknroll:~/pseudo_ape/Carbono/pbe/brute_force/rcs_1.20_rcp_1.20/bmod$
> free -m
>              total       used       free     shared    buffers     cached
> Mem:          7934       2636       5297          0        165       1323
> -/+ buffers/cache:       1147       6786
> Swap:        11444          0      11444
>
> In the one immediately following it:
>
> mverissi at rocknroll:~/pseudo_ape/Carbono/pbe/brute_force/rcs_1.20_rcp_1.20/bmod$
> free -m
>              total       used       free     shared    buffers     cached
> Mem:          7934       2705       5228          0        165       1387
> -/+ buffers/cache:       1151       6782
> Swap:        11444          0      11444
>
> Even though the runs eat little RAM at a time, I have a few hundred runs
> to perform - I suppose by the end of the runs I'll have my ram all gobbled
> :(
>
> Marcos
>
> On Mon, Apr 16, 2012 at 3:48 AM, Lorenzo Paulatto <
> Lorenzo.Paulatto at impmc.upmc.fr> wrote:
>
>> On Mon, 16 Apr 2012 08:41:47 +0200, Marcos Ver?ssimo Alves
>> <marcos.verissimo.alves at gmail.com> wrote:
>> > Instead, it goes up steadily at the end of each pw.x run, and I can
>> > only conclude that, for whatever reason, the memory used is not being
>> > freed at the end of the runs.
>>
>> Dear Marco,
>> are you sure you do not fall in this case <http://www.linuxatemyram.com/
>> >?
>>
>> bests
>>
>> --
>> Lorenzo Paulatto IdR CNRS @ IMPMC/UPMC - Paris 6
>> phone: +33 (0)1 44275 084 / skype: paulatz
>> www:   http://www.impmc.upmc.fr/~paulatto/
>> mail:  23-24/4?14 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
>>
>
>
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From lukuilin at gmail.com  Mon Apr 16 09:19:19 2012
From: lukuilin at gmail.com (kuilin lu)
Date: Mon, 16 Apr 2012 15:19:19 +0800
Subject: [Pw_forum] two program logic questions in TDDFPT
In-Reply-To: <CAH5A=bC0SaVBR4vqVGQf11rC=_av1A=CsBXAWC+AG19SA4OPPw@mail.gmail.com>
References: <CAH5A=bC0SaVBR4vqVGQf11rC=_av1A=CsBXAWC+AG19SA4OPPw@mail.gmail.com>
Message-ID: <CAGL+XK9eqkOMLGp1+zuQg=U2ozY_x6v=47Lyg7uYXLdDEkTYeA@mail.gmail.com>

Dear QE users and developers:
   I have two program logic questions in TDDFPT.  The questions are
about lr_lanczos.f90.

-----------------------
place 1:
/-----------------------------------------------------------------------------------------------------------\
place 1
273     IF(.not.ltammd) THEN
274     !
275     IF ( mod(LR_iteration,2)==0 ) THEN
276        CALL
lr_apply_liouvillian(evc1(1,1,1,1),evc1_new(1,1,1,1),sevc1_new(1,1,1,1),.false.)
277        CALL
lr_apply_liouvillian(evc1(1,1,1,2),evc1_new(1,1,1,2),sevc1_new(1,1,1,2),.true.)
278     ELSE
279        CALL
lr_apply_liouvillian(evc1(1,1,1,1),evc1_new(1,1,1,1),sevc1_new(1,1,1,1),.true.)
280        CALL
lr_apply_liouvillian(evc1(1,1,1,2),evc1_new(1,1,1,2),sevc1_new(1,1,1,2),.false.)
281     ENDIF
282     !
283     ELSE
284        CALL
lr_apply_liouvillian(evc1(1,1,1,1),evc1_new(1,1,1,1),sevc1_new(1,1,1,1),.true.)
285        CALL zcopy(size_evc,evc1(:,:,:,1),1,evc1(:,:,:,2),1)
!evc1(,1) = evc1(,2)
286        CALL
zcopy(size_evc,evc1_new(:,:,:,1),1,evc1_new(:,:,:,2),1) !evc1_new(,1)
= evc1_new(,2)
287        CALL
zcopy(size_evc,evc1_new(:,:,:,1),1,evc1_new(:,:,:,2),1) !evc1_new(,1)
= evc1_new(,2)
288
289     ENDIF
\-----------------------------------------------------------------------------------------------------------/
at line 287, it is
  CALL zcopy(size_evc,evc1_new(:,:,:,1),1,evc1_new(:,:,:,2),1)
!evc1_new(,1) = evc1_new(,2)
should here be the following?
  CALL zcopy(size_evc,sevc1_new(:,:,:,1),1,sevc1_new(:,:,:,2),1)
!sevc1_new(,1) = sevc1_new(,2)

  since it is a waste to copy evc1_new(:,:,:,1) two times and missing
setting value of sevc1_new(:,:,:,2)
\

-----------------------
place 2:
/-----------------------------------------------------------------------------------------------------------\
place 2
217     IF ( abs(beta)<1.0d-12 ) THEN
218        !
219        WRITE(stdout,'(5x,"lr_lanczos: Left and right Lanczos
vectors are orthogonal, this is a violation of oblique projection")')
220        !
221     ELSEIF ( beta<0.0d0 ) THEN
222        !
223        beta=sqrt(-beta)
224        gamma=-beta
225        !
226     ELSEIF ( beta>0.0d0 ) THEN
227        !
228        beta=sqrt(beta)
229        gamma=beta
230        !
231     ENDIF
\-----------------------------------------------------------------------------------------------------------
/
at line 217

  if beta is by accidently small, it just print a warning
?lr_lanczos: Left and right Lanczos vectors are orthogonal, this is a
violation of oblique projection?
then exit the IF structure. So variable gamma is actually not
computed, it will use the value of last step.  It might cause NaN
error later since beta and gamma are not same in this step and
different from lanczos algorithm
(http://www.cs.utk.edu/~dongarra/etemplates/node245.html) which is
mentioned in the code.

 Should here be the following?

!------
    IF ( abs(beta)<1.0d-12 ) THEN
       !
       WRITE(stdout,'(5x,"lr_lanczos: Left and right Lanczos vectors
are orthogonal, this is a violation of oblique projection")')
       !
    ENDIF
    IF ( beta<0.0d0 ) THEN
       !
       beta=sqrt(-beta)
       gamma=-beta
       !
    ELSEIF ( beta>0.0d0 ) THEN
       !
       beta=sqrt(beta)
       gamma=beta
       !
    ENDIF
!------
    I met this problem when I wrote my program based on Siesta (which
is a DFT software),  finding that  variable beta can be small, and get
NaN later.  My  program could get reasonable result after using my
changed logic. The test result is in accessory of this mail.  So I
doubt there is some problem here. If the original logic is right,  is
there some reason to do so? Thanks in advance.
 \

Best Wishes
Kuilin Lu
-- 
----------------------------------------------------------------------
Kuilin Lu, Ph.D student
College of Materials Science and Engineering
Hunan University
Changsha 410082
China
E-Mail: lukuilin at gmail.com
----------------------------------------------------------------------
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From asmogunov at gmail.com  Mon Apr 16 09:33:29 2012
From: asmogunov at gmail.com (Alex Smogunov)
Date: Mon, 16 Apr 2012 09:33:29 +0200
Subject: [Pw_forum] Tunneling density of states using pwcond
In-Reply-To: <4F897408.8080108@phys.ufl.edu>
References: <4F897408.8080108@phys.ufl.edu>
Message-ID: <CAHuemf9Ki7FyWYp7oM39ay_2Anm13R_zvcjd1=-ofZU4cyMgZw@mail.gmail.com>

Dear Jonathan.
There is an option (lorb, lorb3d) to plot in real space all the scattering
states for both directions of propagation. Probably you can just look at
the wave functions (not LDOS) if you need decay rates for them separately.
regards,
A.

Le 14 avril 2012 14:56, Jonathan Trinastic <jptrinastic at phys.ufl.edu> a
?crit :

> Hi all,
>
> I'm performing pwcond calculations on a magnetic tunnel junction
> structure, and I'm interested in creating a figure that shows the change
> in the tunneling density of states as a function of the monolayer of the
> barrier for each different orbital (delta1, delta2, etc). In this way, I
> can show the the different decay rates of each.  I understand how to
> find the tunneling density of states using projwfc.x on the sfc
> structure using the command tdosboxes, but my understanding is that this
> is done on the sfc structure and would not give the tunneling results.
> I'm wondering if there is a way to extract information from the pwcond
> output to show these tunneling states?  I'm not able to find any
> relevant choices in the help menu.
>
> Thanks for your help,
> Jonathan
>
> --
> Jonathan Trinastic, M.S.
> Graduate Student
> Department of Physics
> University of Florida
>
> _______________________________________________
> 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  Mon Apr 16 17:52:40 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 16 Apr 2012 17:52:40 +0200
Subject: [Pw_forum] ecutrho in phonon calculations
In-Reply-To: <CAKr8hj0y1tGHXy_E7k3ehU3yR-b=gfp8auXUszgp=M2aU8BbPw@mail.gmail.com>
References: <CAKr8hj0y1tGHXy_E7k3ehU3yR-b=gfp8auXUszgp=M2aU8BbPw@mail.gmail.com>
Message-ID: <1334591560.11882.66.camel@fe12lx.fisica.uniud.it>

On Thu, 2012-04-12 at 16:07 -0400, YY wrote:

> But I find there is no simple convergence trend while increasing
> ecutrho.  When I use 35 Ry ecutwfc, and fix all the other parameters,
> the results are like this:
> 
>    ecutrho       f1(cm-1)      ....  f12(cm-1)
>    420            40.475                324.062
>    600           123.746               350.727
>    900           -251.876              306.721

unfortunately in at least some [ and I am afraid, in many ] cases,
a rather high cutoff is needed anyway to get decent phonons. If 
this happens, the advantage of using USPP becomes dubious, given 
their significant computational overhead wrt Norm-Conserving PPs. 
Which USPP did you use ?

P.

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



From giannozz at democritos.it  Mon Apr 16 17:54:13 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 16 Apr 2012 17:54:13 +0200
Subject: [Pw_forum] PWgui utility
In-Reply-To: <1334256949.36228.YahooMailClassic@web192202.mail.sg3.yahoo.com>
References: <1334256949.36228.YahooMailClassic@web192202.mail.sg3.yahoo.com>
Message-ID: <1334591653.11882.69.camel@fe12lx.fisica.uniud.it>

On Fri, 2012-04-13 at 02:55 +0800, Sohail Ahmad wrote:


Can we perform calculation of band structure/Density of states/.... 
from PWgui or it just creates input file

you can create input files and run some selected codes directly
from the PWgui, but nothing more than this.

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



From tone.kokalj at ijs.si  Mon Apr 16 18:01:47 2012
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 16 Apr 2012 18:01:47 +0200
Subject: [Pw_forum] visualizing results of molecular dynamics using
 XCRYSDEN
In-Reply-To: <DUB110-W59A544D299A8DCFCC2DFECD3380@phx.gbl>
References: <DUB110-W59A544D299A8DCFCC2DFECD3380@phx.gbl>
Message-ID: <1334592107.29462.41.camel@catalyst.ijs.si>

On Sat, 2012-04-14 at 20:28 +0100, Elie M wrote:
> Dear all,
> 
> 
> I am testing the molecular dynamics package on monolayer graphene: the
> molecular dynamics I am doing is simply "calculation= 'md', using
> pw.x; Is there a way to visualize the output using XCrySDEN or is this
> option only for  calculation='cp'?

You can visualize structures from the pw.x output file as:

xcrysden --pwo filename

(if the number of structures in the output file ss huge than consider
using the "lighting off" mode (click the corresponding radiobutton on
the right toolbox)

Regards,
-- 
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 pandey.bramha at gmail.com  Mon Apr 16 18:08:18 2012
From: pandey.bramha at gmail.com (bramha pandey)
Date: Mon, 16 Apr 2012 21:38:18 +0530
Subject: [Pw_forum] problem regrading convergence
In-Reply-To: <op.wcthk2fcxuur8c@linux-qnvk.site>
References: <CAC2dNGEnYX-gJ_H9EcZw-cQFccF-F-SY-sB8i84WSPkdjgr-1A@mail.gmail.com>
	<op.wcthk2fcxuur8c@linux-qnvk.site>
Message-ID: <CAC2dNGFHOoUn_Dh8dxmLWrHy6w-WvScmjuvxv+X78W4ufEnxWw@mail.gmail.com>

Thank you very much Dear Sir Lorenzo Paulatto and Layla for your kind help.

it was converged in 23 iteration when i put smearing with degauss 0.001,
mixing beta=0.3 with mixing mode = plain.
Sir i wondered my system is semiconductor in nature so how much smearing
should i take?

Also i got mixing mode with 'TF' and 'Local-TF' with 'highly homogeneous'
and 'highly non homogeneous'  system respectively. so how can one decide
when we should use it?
i know this is very trivial  question which i was asking due to my less
knowledge in this field.

Thanks in advanced.

On Sun, Apr 15, 2012 at 11:08 PM, Lorenzo Paulatto <
Lorenzo.Paulatto at impmc.upmc.fr> wrote:

> On Sun, 15 Apr 2012 11:50:18 +0200, bramha pandey
> <pandey.bramha at gmail.com> wrote:
> > LiInTe2
>
> If this crystal is metallic, at least in DFT and at the specific unit cell
> volume you are using, it will probably not converge without a smearing.
>
> > mixing_beta = 0.8
>
> If you have problems with convergence you should *reduce* not increase
> this parameter (take something like 0.3)
>
> >  diagonalization = 'cg',
>
> this controls the diagonalization performed at each scf step, not the scf
> step iteself, use the default algorithm instead wich is faster.
>
> bests
>
>
> --
> Lorenzo Paulatto IdR CNRS @ IMPMC/UPMC - Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www:   http://www.impmc.upmc.fr/~paulatto/
> mail:  23-24/4?14 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
>



-- 
Thanks and Regards
Bramha Prasad Pandey
GLA University, Mathura.
INDIA.
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From giannozz at democritos.it  Mon Apr 16 18:13:42 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 16 Apr 2012 18:13:42 +0200
Subject: [Pw_forum] problems modeling H2 adsorption on boron
	doped	graphene sheet
In-Reply-To: <6D3C4797C791254CB5D576BF880C82A60F784E5D@BY2PRD0310MB388.namprd03.prod.outlook.com>
References: <6D3C4797C791254CB5D576BF880C82A60F784E5D@BY2PRD0310MB388.namprd03.prod.outlook.com>
Message-ID: <1334592822.12869.5.camel@fe12lx.fisica.uniud.it>

On Tue, 2012-04-10 at 21:17 +0000, Janet Wong wrote:


> as a starting point I tried to calculate the adsorption energy 
> of hydrogen on boron doped graphene. 

if you ever publish a paper on this, please list me as undesired
referee: I am fed up of receiving papers dealing with adsorption 
of something on graphene

> However, I am unable to obtain values close to those that were 
> stated in papers with similar DFT calculations.

you should compare results: E[graphene+H2]-E[graphene]-E[H2],
obtained with the same cell, same cutoff, same k-points. 

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



From giuseppe.mattioli at ism.cnr.it  Mon Apr 16 22:05:41 2012
From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli)
Date: Mon, 16 Apr 2012 22:05:41 +0200
Subject: [Pw_forum] neb.x and -ndiag option
In-Reply-To: <1334591560.11882.66.camel@fe12lx.fisica.uniud.it>
References: <CAKr8hj0y1tGHXy_E7k3ehU3yR-b=gfp8auXUszgp=M2aU8BbPw@mail.gmail.com>
	<1334591560.11882.66.camel@fe12lx.fisica.uniud.it>
Message-ID: <20120416220541.6omgrw454wgco4cs@webmail.sic.rm.cnr.it>



Dear all
I've succesfully compiled the 4.99 QE version against scalapack, and  
pw.x performs very well when invoked together with the "-ndiag N"  
option.
Is it possible to make the neb.x wrapper able to "pass the -ndiag  
option" to the pw.x engine?
Yours
Giuseppe

Giuseppe Mattioli
ISM-CNR
Italy



From giannozz at democritos.it  Mon Apr 16 22:07:13 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 16 Apr 2012 22:07:13 +0200
Subject: [Pw_forum] neb.x and -ndiag option
In-Reply-To: <20120416220541.6omgrw454wgco4cs@webmail.sic.rm.cnr.it>
References: <CAKr8hj0y1tGHXy_E7k3ehU3yR-b=gfp8auXUszgp=M2aU8BbPw@mail.gmail.com>
	<1334591560.11882.66.camel@fe12lx.fisica.uniud.it>
	<20120416220541.6omgrw454wgco4cs@webmail.sic.rm.cnr.it>
Message-ID: <97FE8F05-1412-447B-B9EA-8104D88BDDD8@democritos.it>


On Apr 16, 2012, at 22:05 , Giuseppe Mattioli wrote:

> Is it possible to make the neb.x wrapper able to "pass the -ndiag
> option" to the pw.x engine?

doesn't it work? neb.x -ndiag N ...

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 giuseppe.mattioli at ism.cnr.it  Mon Apr 16 22:18:58 2012
From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli)
Date: Mon, 16 Apr 2012 22:18:58 +0200
Subject: [Pw_forum] neb.x and -ndiag option
In-Reply-To: <97FE8F05-1412-447B-B9EA-8104D88BDDD8@democritos.it>
References: <CAKr8hj0y1tGHXy_E7k3ehU3yR-b=gfp8auXUszgp=M2aU8BbPw@mail.gmail.com>
	<1334591560.11882.66.camel@fe12lx.fisica.uniud.it>
	<20120416220541.6omgrw454wgco4cs@webmail.sic.rm.cnr.it>
	<97FE8F05-1412-447B-B9EA-8104D88BDDD8@democritos.it>
Message-ID: <20120416221858.483yb5pm8sw8os48@webmail.sic.rm.cnr.it>


Dear Paolo
Was not sure. The calculation is horribly big, thus I asked before trying.
I will report if something goes wrong.
Thanks
Giuseppe

Quoting Paolo Giannozzi <giannozz at democritos.it>:

>
> On Apr 16, 2012, at 22:05 , Giuseppe Mattioli wrote:
>
>> Is it possible to make the neb.x wrapper able to "pass the -ndiag
>> option" to the pw.x engine?
>
> doesn't it work? neb.x -ndiag N ...
>
> 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 akohlmey at gmail.com  Mon Apr 16 22:32:20 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Mon, 16 Apr 2012 16:32:20 -0400
Subject: [Pw_forum] neb.x and -ndiag option
In-Reply-To: <20120416221858.483yb5pm8sw8os48@webmail.sic.rm.cnr.it>
References: <CAKr8hj0y1tGHXy_E7k3ehU3yR-b=gfp8auXUszgp=M2aU8BbPw@mail.gmail.com>
	<1334591560.11882.66.camel@fe12lx.fisica.uniud.it>
	<20120416220541.6omgrw454wgco4cs@webmail.sic.rm.cnr.it>
	<97FE8F05-1412-447B-B9EA-8104D88BDDD8@democritos.it>
	<20120416221858.483yb5pm8sw8os48@webmail.sic.rm.cnr.it>
Message-ID: <CADTmJ6EUR0xEHQ2PkRzi2cXGygwhMffA6f8aZzrHMCejYDwYjA@mail.gmail.com>

On Mon, Apr 16, 2012 at 4:18 PM, Giuseppe Mattioli
<giuseppe.mattioli at ism.cnr.it> wrote:
>
> Dear Paolo
> Was not sure. The calculation is horribly big, thus I asked before trying.

the reasonable thing to do then would be
to first run a (much) smaller test job.

axel.

> I will report if something goes wrong.
> Thanks
> Giuseppe
>
> Quoting Paolo Giannozzi <giannozz at democritos.it>:
>
>>
>> On Apr 16, 2012, at 22:05 , Giuseppe Mattioli wrote:
>>
>>> Is it possible to make the neb.x wrapper able to "pass the -ndiag
>>> option" to the pw.x engine?
>>
>> doesn't it work? neb.x -ndiag N ...
>>
>> 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



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From 200210qb at gmail.com  Tue Apr 17 00:01:33 2012
From: 200210qb at gmail.com (Bo Qiu)
Date: Mon, 16 Apr 2012 18:01:33 -0400
Subject: [Pw_forum] phonon dynamical matrix and eigenvectors
Message-ID: <4F8C96BD.4060307@gmail.com>

Dear Developers and Users,

I'm new to Quantum Espresso and I want to compute phonon dynamical 
matrix and eigenvectors for silicon. I can use the eigenvectors to 
construct normal mode amplitudes based on independent molecular dynamics 
simulated atomic velocities.

q^dot (k,\nu) =sum v_\alpha^{b,l}(t)e_\alpha^{b,*}(k,\nu)exp(-ik r_0^l)
here v is the alpha (=x,y,z) component of atomic velocity, e is the 
alpha-th portion of the eigenvector of dynamical matrix D(k) and branch \nu

I tried to compare the dynamical matrix and eigenvectors for silicon at 
q=(-0.333333000  -0.333333000  -0.666667000) from both Quantum Espresso 
and GULP (a lattice dynamics code based on classical interatomic 
potentials, chosen to be SW silicon). However, I found the dynamical 
matrices do not agree. The eigenvectors are also completely different.
As a result, if I use the eigenvector e*(k,\nu) from GULP to construct 
q^dot, its Fourier transform shows single peak at the corresponding 
phonon mode frequency, which is expected for single mode (k,\nu). 
However, if I use the eigenvector e'*(k,\nu) from QE, the FT shows 
multiple peaks, with peak positions corresponding to frequencies of 
multiple branches (\nu, \nu', \nu'', etc), which is incorrect.

I first thought maybe there is some discrepancy in the definition of 
coordinate systems so e'*(k,\nu) from QE may be linear combinations of 
e*(k,\nu) from GULP. However I made sure the primitive cell vectors for 
both computation is
cubic
       0.000000000    0.500000000    0.500000000
       0.500000000    0.000000000    0.500000000
       0.500000000    0.500000000    0.000000000
and the internal coordinates for both are:
     1    1      0.0000000      0.0000000      0.0000000
     2    1      0.2500000      0.2500000      0.2500000

I suppose when the dynamical matrices are defined under the same 
coordinate systems and they should be very similar (despite inaccuracy 
of classical SW potential), so should the corresponding eigenvectors. I 
don't quite understand what went wrong or if there is some hidden 
transformation to the dynamical matrix/ eigenvectors in QE. Could you 
please help me with that? Sorry for the lengthy email!

===========================
QE:
dynamical matrix:
     1    1
   0.26584460  0.00000000    0.01095706  0.00000000    0.01178255  
0.00797619
   0.01095706  0.00000000    0.26584460  0.00000000    0.01178255  
0.00797619
   0.01178255 -0.00797619    0.01178255 -0.00797619    0.29527850  
0.00000000
     1    2
   0.10051503 -0.05636929   -0.11838412 -0.03489786   -0.07026611  
0.03761305
  -0.11838412 -0.03489786    0.10051503 -0.05636929   -0.07026611  
0.03761305
  -0.07026611  0.03761305   -0.07026611  0.03761305    0.11544724 
-0.05301088
     2    1
   0.10051503  0.05636929   -0.11838412  0.03489786   -0.07026611 
-0.03761305
  -0.11838412  0.03489786    0.10051503  0.05636929   -0.07026611 
-0.03761305
  -0.07026611 -0.03761305   -0.07026611 -0.03761305    0.11544724  
0.05301088
     2    2
   0.26584460  0.00000000    0.01095706  0.00000000    0.01178255 
-0.00797619
   0.01095706  0.00000000    0.26584460  0.00000000    0.01178255 
-0.00797619
   0.01178255  0.00797619    0.01178255  0.00797619    0.29527850  
0.00000000

GULP:
dynamical matrix:
   Real Dynamical matrix :

    0.612757   0.007542   0.000000  -0.162617   0.306835   0.000000
    0.007542   0.612757   0.000000   0.306835  -0.162617   0.000000
    0.000000   0.000000   0.650468   0.000000   0.000000  -0.162617
   -0.162617   0.306835   0.000000   0.612757   0.007542   0.000000
    0.306835  -0.162617   0.000000   0.007542   0.612757   0.000000
    0.000000   0.000000  -0.162617   0.000000   0.000000   0.650468

   Imaginary Dynamical matrix :

    0.000000   0.000000  -0.026128   0.000001   0.000000   0.177151
    0.000000   0.000000  -0.026128   0.000000   0.000001   0.177151
    0.026128   0.026128   0.000000   0.177151   0.177151   0.000001
   -0.000001   0.000000  -0.177151   0.000000   0.000000   0.026128
    0.000000  -0.000001  -0.177151   0.000000   0.000000   0.026128
   -0.177151  -0.177151  -0.000001  -0.026128  -0.026128   0.000000

====================================

The corresponding eigenvectors:
QE:
      omega( 1) =       3.843790 [THz] =     128.215027 [cm-1]
  ( -0.466622  0.179622  0.466622 -0.179622  0.000000  0.000000 )
  (  0.481928 -0.133213 -0.481928  0.133213  0.000000  0.000000 )
      omega( 2) =       5.191233 [THz] =     173.160893 [cm-1]
  (  0.240380 -0.225674  0.240380 -0.225674 -0.500138  0.180108 )
  ( -0.302624 -0.130882 -0.302624 -0.130882  0.531580  0.000000 )
      omega( 3) =       9.773114 [THz] =     325.995997 [cm-1]
  ( -0.301588 -0.275885 -0.301588 -0.275885 -0.088915 -0.397439 )
  ( -0.335073 -0.234081 -0.335073 -0.234081 -0.407264  0.000000 )
      omega( 4) =      12.316327 [THz] =     410.828451 [cm-1]
  ( -0.266508 -0.236976 -0.266508 -0.236976 -0.152029 -0.471719 )
  (  0.307303  0.180967  0.307303  0.180967  0.495612  0.000000 )
      omega( 5) =      14.170455 [THz] =     472.675510 [cm-1]
  ( -0.445864  0.226286  0.445864 -0.226286  0.000000  0.000000 )
  ( -0.465825  0.181680  0.465825 -0.181680  0.000000  0.000000 )
      omega( 6) =      14.480825 [THz] =     483.028344 [cm-1]
  (  0.214285 -0.226094  0.214285 -0.226094 -0.551429  0.043056 )
  (  0.231234  0.208727  0.231234  0.208727 -0.553107  0.000000 )


GULP:
  Frequency     192.1405                 270.1120                    
368.8443
                 Real    Imaginary           Real    Imaginary          
Real    Imaginary

      1 x      -0.473100 -0.161793  0.000000  0.358390  0.000002  0.368133
      1 y       0.473100  0.161793  0.000000  0.358390  0.000002  0.368133
      1 z       0.000000  0.000000  0.493066  0.000003 -0.478494 -0.000001
      2 x      -0.473100 -0.161792  0.000002 -0.358390 -0.000002  0.368133
      2 y       0.473100  0.161792  0.000002 -0.358390 -0.000002  0.368133
      2 z       0.000000  0.000000  0.493066  0.000000  0.478494  0.000000
  Frequency     434.9274                     540.5867                    
541.2499
                Real    Imaginary               Real    Imaginary        
Real    Imaginary

      1 x      -0.000002 -0.348650 -0.018584 -0.499655  0.000000  0.338346
      1 y      -0.000002 -0.348650  0.018584  0.499655  0.000000  0.338346
      1 z       0.506840  0.000000  0.000000  0.000000  0.520618  0.000001
      2 x      -0.000001  0.348650  0.018585  0.499654 -0.000001  0.338346
      2 y      -0.000001  0.348650 -0.018585 -0.499654 -0.000001  0.338346
      2 z       0.506840  0.000000  0.000000  0.000000 -0.520618  0.000000

From elie.moujaes at hotmail.co.uk  Tue Apr 17 05:22:22 2012
From: elie.moujaes at hotmail.co.uk (Elie M)
Date: Tue, 17 Apr 2012 04:22:22 +0100
Subject: [Pw_forum] forming supercell for a (10,
 0) nanotube attached to polymers and oligomers
Message-ID: <DUB110-W7105C68CF17C5B597BFF63D33F0@phx.gbl>


Dear all,
I am trying to study the dynamics of a (10,0) nanotube attached to a polymer. Does anyone know of any code that forms supercells for such systems? Any examples on that?
Thanks
Regards
Elie MoujaesUniversity of NottsNG7 2RDNottsUK
 		 	   		  
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From lmartinsamos at gmail.com  Tue Apr 17 09:31:58 2012
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Tue, 17 Apr 2012 09:31:58 +0200
Subject: [Pw_forum] neb.x and -ndiag option
In-Reply-To: <20120416220541.6omgrw454wgco4cs@webmail.sic.rm.cnr.it>
References: <CAKr8hj0y1tGHXy_E7k3ehU3yR-b=gfp8auXUszgp=M2aU8BbPw@mail.gmail.com>
	<1334591560.11882.66.camel@fe12lx.fisica.uniud.it>
	<20120416220541.6omgrw454wgco4cs@webmail.sic.rm.cnr.it>
Message-ID: <CAGCSmJTUY_NLjm4SdXRLontE+hVMbUHUCdrTMYCQ9Y1UDk7B4g@mail.gmail.com>

Dear Giuseppe, in principle it does, as neb calls the same getarg as pw.
Try it and if you find any problem please let us know.

best regards

Layla

2012/4/16 Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>

>
>
> Dear all
> I've succesfully compiled the 4.99 QE version against scalapack, and
> pw.x performs very well when invoked together with the "-ndiag N"
> option.
> Is it possible to make the neb.x wrapper able to "pass the -ndiag
> option" to the pw.x engine?
> Yours
> Giuseppe
>
> Giuseppe Mattioli
> ISM-CNR
> Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From sbinnie at sissa.it  Tue Apr 17 11:05:49 2012
From: sbinnie at sissa.it (Simon Binnie)
Date: Tue, 17 Apr 2012 11:05:49 +0200
Subject: [Pw_forum] two program logic questions in TDDFPT
In-Reply-To: <CAGL+XK9eqkOMLGp1+zuQg=U2ozY_x6v=47Lyg7uYXLdDEkTYeA@mail.gmail.com>
References: <CAH5A=bC0SaVBR4vqVGQf11rC=_av1A=CsBXAWC+AG19SA4OPPw@mail.gmail.com>
	<CAGL+XK9eqkOMLGp1+zuQg=U2ozY_x6v=47Lyg7uYXLdDEkTYeA@mail.gmail.com>
Message-ID: <op.wcwjjzjjb4z88i@mugon.cm.sissa.it>

Thanks. You are right about the duplicated zcopy line, it is rather  
pointless to perform the same copy twice in a row. It's not necessary to  
copy sevc1_new though as far as I can see, since this is only really used  
as a workspace within lr_apply_liovillian. The only thing that is  
important is to make sure that evc1_new gets copied so evc1_old can then  
be properly updated.

Best regards,

Simon

On Mon, 16 Apr 2012 09:19:19 +0200, kuilin lu <lukuilin at gmail.com> wrote:

> Dear QE users and developers:
>    I have two program logic questions in TDDFPT.  The questions are
> about lr_lanczos.f90.


-- 
Simon Binnie | Post Doc, Condensed Matter Sector
Scuola Internazionale di Studi Avanzati (SISSA)
Via Bonomea 256 | 34100 Trieste | sbinnie at sissa.it

From neumann at if.ufrj.br  Tue Apr 17 16:01:22 2012
From: neumann at if.ufrj.br (Rodrigo Neumann)
Date: Tue, 17 Apr 2012 16:01:22 +0200
Subject: [Pw_forum] DLASCL error on some architectures/QE versions
Message-ID: <CAO6DZYBQJ1LbLAK+Cq3NiV+GjBmtT=eU=eCota2L5ZpUxdx3=A@mail.gmail.com>

Dear QE users and developers,

Not having found any mention to execution-time DLASCL errors in the forum
archives, I though it would be helpful to share my latest experiences with
you. The minimal input file required to run the calculation (and to see the
error) is attached. It's a simple bulk cell calculation with noncollinear
magnetism and spin-orbit coupling using one of the relativistic PPs
provided in the website.

I *sometimes* (the situations in which the error occurs will be detailed
afterwards) get the following error in less than 30 seconds of execution
time:

     Starting wfc are   36 atomic wfcs
 ** On entry to DLASCL parameter number  4 had an illegal value

I'm not at all an expert on BLAS/LAPACK functions but from what I've found
on the online documentation, what DLASCL does is to multiply a M x N real
matrix by a real scalar that is given in the form of a ration CTO/CFROM.
The DLASCL parameter #4 is the double precision variable CFROM which, of
course, should be nonzero. Apparently (both from obvious arithmetic and
the DLASCL manual entry) that is exactly what happens.

What intrigues me is why this error only shows up in specific Architecture
/ QE version pairs...

Situations in which the error ALWAYS shows up:
- IBM/SP6 @ CINECA (AIX 6.1) running QE 4.3.1 with more than 8 processors
- IBM/SP6 @ CINECA (AIX 6.1) running QE 4.2    with more than 8 processors

Situations in which the error NEVER shows up:
- IBM/SP6 @ CINECA (AIX 6.1) running QE 4.1 (tried with up to 32 processors)
- IBM/SP6 @ CINECA (AIX 6.1) running QE 4.3.1 if I set angle1(1)=0 (tried
with up to 32 processors)
- IBM/SP6 @ CINECA (AIX 6.1) running QE 4.2    if I set angle1(1)=0 (tried
with up to 32 processors)
- Argo Linux cluster @ ICTP (CentOS 6) running QE 4.3.2 (tried with up
to 12 processors)
- TMC Linux cluster @ UFRJ (Scientific Linux) running QE 4.1 (tried with up
to 6 processors)

Of course I am already crunching numbers and getting my so-desired results
just by switching to the 4.1 version of pw.x (instead of using the newest
version as I usually do), but then my last 2 days and nights trying to map
the origins of the error would have been useless have I not shared this
with you, with the hope someone might have a clue of what's happening.
Because I don't have the slightest.

Thanks in advance!

With my best regards,
Rodrigo

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

 Rodrigo Neumann Barros Ferreira
Ph.D. Student
Departamento de F?sica dos S?lidos - Instituto de F?sica
Universidade Federal do Rio de Janeiro
Cx.Postal 68.528
21945-972, Rio de Janeiro - RJ - BRASIL

Tel: [+55] (21) 2562-7341
http://www.if.ufrj.br/~neumann/
http://tmc.if.ufrj.br/
--------------------------------------------------------
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From pandey.bramha at gmail.com  Tue Apr 17 16:40:08 2012
From: pandey.bramha at gmail.com (bramha pandey)
Date: Tue, 17 Apr 2012 20:10:08 +0530
Subject: [Pw_forum] Regarding GAMMA kpoint
Message-ID: <CAC2dNGGB5iqhhKdzYk9ff6k3GF8PBWDLg7HqW+1RLftu+wHhfw@mail.gmail.com>

Dear all PW users and Developers,

I have a one quick question.

I am interested to calculate the PHDOS of LiInTe2. I have found the
convergence with gamma point.
So, is it right way to calculate the PHDOS at gamma point for caalculation
of  all the thermodynamical property (Like Cv, Temperature dependent
property bulk modulus and lattice parameter)???

Thanks in advanced for your valuable time to read and answering to this
mail.

-- 
Thanks and Regards
Bramha Prasad Pandey
GLA University, Mathura.
INDIA.
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From elie.moujaes at hotmail.co.uk  Tue Apr 17 17:19:32 2012
From: elie.moujaes at hotmail.co.uk (Elie M)
Date: Tue, 17 Apr 2012 16:19:32 +0100
Subject: [Pw_forum] forming a supercell for a (10,
	0) nanotube attached to a polymer
Message-ID: <DUB110-W5770537174E2625E530EEBD33F0@phx.gbl>


Dear all,
I am trying to study the dynamics of a (10,0) nanotube attached to a polymer. Does anyone know of any code that forms supercells for such systems? Any examples on that?
Thanks
Regards
Elie MoujaesUniversity of NottsNG7 2RDNottsUK 		 	   		  
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From akohlmey at gmail.com  Tue Apr 17 17:31:15 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Tue, 17 Apr 2012 11:31:15 -0400
Subject: [Pw_forum] forming a supercell for a (10,
 0) nanotube attached to a polymer
In-Reply-To: <DUB110-W5770537174E2625E530EEBD33F0@phx.gbl>
References: <DUB110-W5770537174E2625E530EEBD33F0@phx.gbl>
Message-ID: <CADTmJ6Gg5ejp_vkhtoCBjJLUH6-dJZf7runUqj8OVqcbzrhx-Q@mail.gmail.com>

On Tue, Apr 17, 2012 at 11:19 AM, Elie M <elie.moujaes at hotmail.co.uk> wrote:
> Dear all,
>
> I am trying to study the dynamics of a (10,0) nanotube attached to a
> polymer. Does anyone know of any code that forms supercells for such
> systems? Any examples on that?

are you sure you are posting to the right forum?
as a q-e calculation, this would likely be very demanding.

what kind of polymer and how much of it?

i've written some plugins for VMD that can
combine coordinate files and remove overlap.
there also is a plugin that can generate a
(10,0)-SWCNT. also, i don't think you want
to start a q-e calculation on this right away,
but do a good equilibration with a classical
model first, or else you'd be wasting a serious
amount of CPU time.

axel.

>
> Thanks
>
> Regards
>
> Elie Moujaes
> University of Notts
> NG7 2RD
> Notts
> UK
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From bangj at rpi.edu  Tue Apr 17 17:33:07 2012
From: bangj at rpi.edu (Junhyeok Bang)
Date: Tue, 17 Apr 2012 11:33:07 -0400
Subject: [Pw_forum] serial or parallel computation in electron-phonon matrix
	integration
Message-ID: <CAEfM_1ENS4rGg5QgeNtcQRrWfiJ0SUOBw4n3b3t=tFg4CXAcKw@mail.gmail.com>

Hello, everyone.

After the phonon calculation, the electron-phonon matrix calculation takes
very long time. Thus, I wonder if the quantum-espresso performs a parallel
calculation or a serial calculation in the electron-phonon matrix
calculation. If yes, how does the code parallelize?

Junhyeok Bang
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From elie.moujaes at hotmail.co.uk  Wed Apr 18 04:50:11 2012
From: elie.moujaes at hotmail.co.uk (Elie M)
Date: Wed, 18 Apr 2012 03:50:11 +0100
Subject: [Pw_forum] forming a supercell for a (10,
 0) nanotube attached to a polymer
In-Reply-To: <CADTmJ6Gg5ejp_vkhtoCBjJLUH6-dJZf7runUqj8OVqcbzrhx-Q@mail.gmail.com>
References: <DUB110-W5770537174E2625E530EEBD33F0@phx.gbl>,
	<CADTmJ6Gg5ejp_vkhtoCBjJLUH6-dJZf7runUqj8OVqcbzrhx-Q@mail.gmail.com>
Message-ID: <DUB110-W497E71D9E84CFC12FA44DDD33C0@phx.gbl>


Hello,
Thanks for the reply..actually I am trying to reproduce the Molecular dynamics obtained in the paper entitled" Helical Wrapping of SWNT by water soluble Poly (--phenyleneethynylene) , nano letters, 2009, Vol 9 No 4, 1414-1418 where did the MD of 10,0 nanotube with a polymer called PPES. I was able to build the 10,0 nantube but have no idea how to attach the polymer; in other words how to get the positions of the several atoms in the molecule and to attach it to the nanotube to build the supercell which will be ready for calculations..This is the software  am looking for..

Regards
Elie

> Date: Tue, 17 Apr 2012 11:31:15 -0400
> Subject: Re: [Pw_forum] forming a supercell for a (10, 0) nanotube attached to a polymer
> From: akohlmey at gmail.com
> To: elie.moujaes at hotmail.co.uk
> CC: pw_forum at pwscf.org
> 
> On Tue, Apr 17, 2012 at 11:19 AM, Elie M <elie.moujaes at hotmail.co.uk> wrote:
> > Dear all,
> >
> > I am trying to study the dynamics of a (10,0) nanotube attached to a
> > polymer. Does anyone know of any code that forms supercells for such
> > systems? Any examples on that?
> 
> are you sure you are posting to the right forum?
> as a q-e calculation, this would likely be very demanding.
> 
> what kind of polymer and how much of it?
> 
> i've written some plugins for VMD that can
> combine coordinate files and remove overlap.
> there also is a plugin that can generate a
> (10,0)-SWCNT. also, i don't think you want
> to start a q-e calculation on this right away,
> but do a good equilibration with a classical
> model first, or else you'd be wasting a serious
> amount of CPU time.
> 
> axel.
> 
> >
> > Thanks
> >
> > Regards
> >
> > Elie Moujaes
> > University of Notts
> > NG7 2RD
> > Notts
> > UK
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> 
> 
> 
> -- 
> Dr. Axel Kohlmeyer
> akohlmey at gmail.com  http://goo.gl/1wk0
> 
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
 		 	   		  
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From akohlmey at gmail.com  Wed Apr 18 05:09:21 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Tue, 17 Apr 2012 23:09:21 -0400
Subject: [Pw_forum] forming a supercell for a (10,
 0) nanotube attached to a polymer
In-Reply-To: <DUB110-W497E71D9E84CFC12FA44DDD33C0@phx.gbl>
References: <DUB110-W5770537174E2625E530EEBD33F0@phx.gbl>
	<CADTmJ6Gg5ejp_vkhtoCBjJLUH6-dJZf7runUqj8OVqcbzrhx-Q@mail.gmail.com>
	<DUB110-W497E71D9E84CFC12FA44DDD33C0@phx.gbl>
Message-ID: <CADTmJ6GE0801tEOC9zyrTo4PdmruzNEXPdJno=Eb8q0oTRvC6Q@mail.gmail.com>

On Tue, Apr 17, 2012 at 10:50 PM, Elie M <elie.moujaes at hotmail.co.uk> wrote:

>  Hello,
>
> Thanks for the reply..actually I am trying to reproduce the Molecular
> dynamics obtained in the paper entitled" Helical Wrapping of SWNT by water
> soluble Poly (--phenyleneethynylene) , nano letters, 2009, Vol 9 No 4,
> 1414-1418 where did the MD of 10,0 nanotube with a polymer called PPES. I
> was able to build the 10,0 nantube but have no idea how to attach the
> polymer; in other words how to get the positions of the several atoms in
> the molecule and to attach it to the nanotube to build the supercell which
> will be ready for calculations..This is the software  am looking for..
>

well, again, this is *definitely* the wrong forum.
the paper is about classical MD. i actually know
a few of the authors personally.

you don't really need to get a perfect position.

you can pretty much build the polymer with
a simple molecule editor to be a straight chain,
move it somewhere in space, merge it with the
CNT structure and a suitably sized pre-equilibrated
water box while removing the overlaps. then
carefully relax the structure and equilibrate to
the proper density. this is all pretty straightforward
classical MD protocol for multi-component systems.

using quantum espresso programs on
any of this will just be a massive waste
of time. i strongly suggest you pick a
more suitable forum to get advice, and
looks at tutorials, e.g. for proteins embedded
in lipid bilayers (which require a similar
setup and equilibration protocol).

axel.



>
> Regards
>
> Elie
>
> > Date: Tue, 17 Apr 2012 11:31:15 -0400
> > Subject: Re: [Pw_forum] forming a supercell for a (10, 0) nanotube
> attached to a polymer
> > From: akohlmey at gmail.com
> > To: elie.moujaes at hotmail.co.uk
> > CC: pw_forum at pwscf.org
>
> >
> > On Tue, Apr 17, 2012 at 11:19 AM, Elie M <elie.moujaes at hotmail.co.uk>
> wrote:
> > > Dear all,
> > >
> > > I am trying to study the dynamics of a (10,0) nanotube attached to a
> > > polymer. Does anyone know of any code that forms supercells for such
> > > systems? Any examples on that?
> >
> > are you sure you are posting to the right forum?
> > as a q-e calculation, this would likely be very demanding.
> >
> > what kind of polymer and how much of it?
> >
> > i've written some plugins for VMD that can
> > combine coordinate files and remove overlap.
> > there also is a plugin that can generate a
> > (10,0)-SWCNT. also, i don't think you want
> > to start a q-e calculation on this right away,
> > but do a good equilibration with a classical
> > model first, or else you'd be wasting a serious
> > amount of CPU time.
> >
> > axel.
> >
> > >
> > > Thanks
> > >
> > > Regards
> > >
> > > Elie Moujaes
> > > University of Notts
> > > NG7 2RD
> > > Notts
> > > UK
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer
> > akohlmey at gmail.com  http://goo.gl/1wk0
> >
> > College of Science and Technology
> > Temple University, Philadelphia PA, USA.
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com  http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.
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From elie.moujaes at hotmail.co.uk  Wed Apr 18 06:29:28 2012
From: elie.moujaes at hotmail.co.uk (Elie M)
Date: Wed, 18 Apr 2012 05:29:28 +0100
Subject: [Pw_forum] forming a supercell for a (10,
 0) nanotube attached to a polymer
In-Reply-To: <CADTmJ6GE0801tEOC9zyrTo4PdmruzNEXPdJno=Eb8q0oTRvC6Q@mail.gmail.com>
References: <DUB110-W5770537174E2625E530EEBD33F0@phx.gbl>,
	<CADTmJ6Gg5ejp_vkhtoCBjJLUH6-dJZf7runUqj8OVqcbzrhx-Q@mail.gmail.com>,
	<DUB110-W497E71D9E84CFC12FA44DDD33C0@phx.gbl>,
	<CADTmJ6GE0801tEOC9zyrTo4PdmruzNEXPdJno=Eb8q0oTRvC6Q@mail.gmail.com>
Message-ID: <DUB110-W673D15A3E336FE520E449CD33C0@phx.gbl>


 I will have a look at the suggested tutorials. Many thanks
Elie

Date: Tue, 17 Apr 2012 23:09:21 -0400
Subject: Re: [Pw_forum] forming a supercell for a (10, 0) nanotube attached to a polymer
From: akohlmey at gmail.com
To: elie.moujaes at hotmail.co.uk
CC: pw_forum at pwscf.org



On Tue, Apr 17, 2012 at 10:50 PM, Elie M <elie.moujaes at hotmail.co.uk> wrote:





Hello,
Thanks for the reply..actually I am trying to reproduce the Molecular dynamics obtained in the paper entitled" Helical Wrapping of SWNT by water soluble Poly (--phenyleneethynylene) , nano letters, 2009, Vol 9 No 4, 1414-1418 where did the MD of 10,0 nanotube with a polymer called PPES. I was able to build the 10,0 nantube but have no idea how to attach the polymer; in other words how to get the positions of the several atoms in the molecule and to attach it to the nanotube to build the supercell which will be ready for calculations..This is the software  am looking for..

well, again, this is *definitely* the wrong forum.the paper is about classical MD. i actually knowa few of the authors personally. 

you don't really need to get a perfect position.
you can pretty much build the polymer witha simple molecule editor to be a straight chain,move it somewhere in space, merge it with the
CNT structure and a suitably sized pre-equilibratedwater box while removing the overlaps. then carefully relax the structure and equilibrate tothe proper density. this is all pretty straightforward
classical MD protocol for multi-component systems.
using quantum espresso programs onany of this will just be a massive wasteof time. i strongly suggest you pick a
more suitable forum to get advice, and looks at tutorials, e.g. for proteins embeddedin lipid bilayers (which require a similar setup and equilibration protocol).

axel.



Regards

Elie

> Date: Tue, 17 Apr 2012 11:31:15 -0400
> Subject: Re: [Pw_forum] forming a supercell for a (10, 0) nanotube attached to a polymer
> From: akohlmey at gmail.com

> To: elie.moujaes at hotmail.co.uk
> CC: pw_forum at pwscf.org
> 
> On Tue, Apr 17, 2012 at 11:19 AM, Elie M <elie.moujaes at hotmail.co.uk> wrote:

> > Dear all,
> >
> > I am trying to study the dynamics of a (10,0) nanotube attached to a
> > polymer. Does anyone know of any code that forms supercells for such
> > systems? Any examples on that?

> 
> are you sure you are posting to the right forum?
> as a q-e calculation, this would likely be very demanding.
> 
> what kind of polymer and how much of it?
> 
> i've written some plugins for VMD that can

> combine coordinate files and remove overlap.
> there also is a plugin that can generate a
> (10,0)-SWCNT. also, i don't think you want
> to start a q-e calculation on this right away,
> but do a good equilibration with a classical

> model first, or else you'd be wasting a serious
> amount of CPU time.
> 
> axel.
> 
> >
> > Thanks
> >
> > Regards
> >
> > Elie Moujaes

> > University of Notts
> > NG7 2RD
> > Notts
> > UK
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org

> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> 
> 
> 
> -- 
> Dr. Axel Kohlmeyer

> akohlmey at gmail.com  http://goo.gl/1wk0
> 
> College of Science and Technology
> Temple University, Philadelphia PA, USA.

 		 	   		  


-- 
Dr. Axel Kohlmeyer   
akohlmey at gmail.com  http://goo.gl/1wk0


College of Science and Technology
Temple University, Philadelphia PA, USA.
 		 	   		  
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From giannozz at democritos.it  Wed Apr 18 08:54:10 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 18 Apr 2012 08:54:10 +0200
Subject: [Pw_forum] Quantum Espresso Workshop (Jun 25 - Jun 29 /2012,
	Penn State Univ., PA, USA)
Message-ID: <CEE3C6FC-B660-4803-AE0E-636E01B8D137@democritos.it>

Reminder: a workshop/tutorial on Quantum Espresso will be held in
Penn State University, Philadelphia, USA, from Jun 25 to June 29.
More info can be found at the url:
    http://rcc.its.psu.edu/education/workshops/pages/ 
quantum_espresso_2012/
Hoping to see you in Pennsylvania for the QE 2012 Workshop

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





From giannozz at democritos.it  Wed Apr 18 09:24:52 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 18 Apr 2012 09:24:52 +0200
Subject: [Pw_forum] serial or parallel computation in electron-phonon
	matrix integration
In-Reply-To: <CAEfM_1ENS4rGg5QgeNtcQRrWfiJ0SUOBw4n3b3t=tFg4CXAcKw@mail.gmail.com>
References: <CAEfM_1ENS4rGg5QgeNtcQRrWfiJ0SUOBw4n3b3t=tFg4CXAcKw@mail.gmail.com>
Message-ID: <969F0EB2-C4CE-4EEB-B4DE-DBA6219919D0@democritos.it>


On Apr 17, 2012, at 17:33 , Junhyeok Bang wrote:

> I wonder if the quantum-espresso performs a parallel calculation
> or a serial calculation in the electron-phonon matrix calculation.

the caalculations of matrix elements is parallelized, but I don't think
you can use the most interesting parallelization for this case, i.e.
over k-points

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 mourad_fsm at yahoo.fr  Wed Apr 18 10:40:45 2012
From: mourad_fsm at yahoo.fr (debbichi mourad)
Date: Wed, 18 Apr 2012 09:40:45 +0100 (BST)
Subject: [Pw_forum] (no subject)
Message-ID: <1334738445.34114.YahooMailNeo@web29502.mail.ird.yahoo.com>

Dear PWScf Users,

I try to do the dielectric function calculations. At first I did the
scf-calculation. After using the code epsilon.x, I gives the following error message :

running epsilon.x ...Cannot match namelist object name calculation
namelist read: missplaced = sign
Cannot match namelist object name eps'

?Why such a problem occurs?

?My input files is as following: 

cat > MgO.scf.in << EOF
&control
calculation='scf'
restart_mode='from_scratch',
prefix='MgO'
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
tstress=.true.
/

&SYSTEM
ibrav = 4,
celldm(1) =6.11,
celldm(3) = 1.611, 
nat = 4,
ntyp = 2,

ecutwfc =50,
nspin = 2,
starting_magnetization(1)=0.7, starting_magnetization(2)=0.5,
occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02,
/
&ELECTRONS
conv_thr = 1.0d-10 ,
mixing_mode = 'plain' ,
mixing_beta = 0.6,
diagonalization = 'david' ,
/
ATOMIC_SPECIES
Mg   24.3050  Mg.pz-n-vbc.UPF 
O   15.99940   O.pz-mt.UPF

ATOMIC_POSITIONS Crystal
Mg     0.666666667    0.333333333    0.000000000
Mg     0.333333333    0.666666667    0.500000000
O      0.666666667    0.333333333    0.380000000
O      0.333333333    0.666666667    0.880000000

K_POINTS automatic
9 9 3 1 1 1 

EOF
$ECHO "  running the scf calculation...\c"
$PW_COMMAND < MgO.scf.in > MgO.scf.out
check_failure $?
$ECHO "
done"
#########################################################
cat> MgO_eps.in << EOF
&inputpp
outdir='$TMP_DIR/'
prefix='MgO'
calculation='eps'
/
&energy_grid
smeartype='gauss'
intersmear=0.15d0
wmin     = 0.0d0
wmax=30.0d0
nw=1000
shift=0.0d0
intrasmear   = 0.0d0
/
EOF

$ECHO "  running epsilon.x ...\c"
$PROJWFC_COMMAND <  MgO_eps.in > MgO_eps.out
check_failure $?
$ECHO " done"

Sincerely

?
DEBBICHI Mourad
Unit? de Recherche Physique des Solides,99/UR/13-19,
D?partement de Physique, Facult? des Science de Monastir,
Avenue de l'Environnement 5019, Monastir Tunisie.
t?l:+21697487042
mourad_fsm at yahoo.fr
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From mourad_fsm at yahoo.fr  Wed Apr 18 10:41:30 2012
From: mourad_fsm at yahoo.fr (debbichi mourad)
Date: Wed, 18 Apr 2012 09:41:30 +0100 (BST)
Subject: [Pw_forum] epsilon.x
Message-ID: <1334738490.77674.YahooMailNeo@web29501.mail.ird.yahoo.com>

Dear PWScf Users,

I try to do the dielectric function calculations. At first I did the
scf-calculation. After using the code epsilon.x, I gives the following error message :

running epsilon.x ...Cannot match namelist object name calculation
namelist read: missplaced = sign
Cannot match namelist object name eps'

?Why such a problem occurs?

?My input files is as following: 

cat > MgO.scf.in << EOF
&control
calculation='scf'
restart_mode='from_scratch',
prefix='MgO'
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
tstress=.true.
/

&SYSTEM
ibrav = 4,
celldm(1) =6.11,
celldm(3) = 1.611, 
nat = 4,
ntyp = 2,

ecutwfc =50,
nspin = 2,
starting_magnetization(1)=0.7, starting_magnetization(2)=0.5,
occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02,
/
&ELECTRONS
conv_thr = 1.0d-10 ,
mixing_mode = 'plain' ,
mixing_beta = 0.6,
diagonalization = 'david' ,
/
ATOMIC_SPECIES
Mg   24.3050  Mg.pz-n-vbc.UPF 
O   15.99940   O.pz-mt.UPF

ATOMIC_POSITIONS Crystal
Mg     0.666666667    0.333333333    0.000000000
Mg     0.333333333    0.666666667    0.500000000
O      0.666666667    0.333333333    0.380000000
O      0.333333333    0.666666667    0.880000000

K_POINTS automatic
9 9 3 1 1 1 

EOF
$ECHO "  running the scf calculation...\c"
$PW_COMMAND < MgO.scf.in > MgO.scf.out
check_failure $?
$ECHO "
done"
#########################################################
cat> MgO_eps.in << EOF
&inputpp
outdir='$TMP_DIR/'
prefix='MgO'
calculation='eps'
/
&energy_grid
smeartype='gauss'
intersmear=0.15d0
wmin     = 0.0d0
wmax=30.0d0
nw=1000
shift=0.0d0
intrasmear   = 0.0d0
/
EOF

$ECHO "  running epsilon.x ...\c"
$PROJWFC_COMMAND <  MgO_eps.in > MgO_eps.out
check_failure $?
$ECHO " done"

Sincerely

?
DEBBICHI Mourad
Unit? de Recherche Physique des Solides,99/UR/13-19,
D?partement de Physique, Facult? des Science de Monastir,
Avenue de l'Environnement 5019, Monastir Tunisie.
t?l:+21697487042
mourad_fsm at yahoo.fr
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From lmartinsamos at gmail.com  Wed Apr 18 11:00:57 2012
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Wed, 18 Apr 2012 11:00:57 +0200
Subject: [Pw_forum] epsilon.x
In-Reply-To: <1334738490.77674.YahooMailNeo@web29501.mail.ird.yahoo.com>
References: <1334738490.77674.YahooMailNeo@web29501.mail.ird.yahoo.com>
Message-ID: <CAGCSmJRkekY51nGCuYzh36+M8ciKF0QH=X7U0FZ-tR3W4a-48w@mail.gmail.com>

The code is telling that he is not recognizing the input variable
"calculation", are you sure that you are running epsilon.x and not
projwfc.x?

becouse in your job you wrote:

$PROJWFC_COMMAND <  MgO_eps.in > MgO_eps.out

best regards

Layla

2012/4/18 debbichi mourad <mourad_fsm at yahoo.fr>

> Dear PWScf Users,
>
> I try to do the dielectric function calculations. At first I did the
> scf-calculation. After using the code epsilon.x, *I gives the following error message* :
>
> running epsilon.x ...Cannot match namelist object name calculation
> namelist read: missplaced = sign
> Cannot match namelist object name eps'
>
>  Why such a problem occurs?
>
>  My input files is as following:
>
> cat > MgO.scf.in << EOF
>  &control
>     calculation='scf'
>  restart_mode='from_scratch',
>        prefix='MgO'
>     pseudo_dir = '$PSEUDO_DIR/',
>     outdir='$TMP_DIR/'
> tstress=.true.
>
>  /
>
> &SYSTEM
>                        ibrav = 4,
>                     celldm(1) =6.11,
>                    celldm(3) = 1.611,
>                         nat = 4,
>                         ntyp = 2,
>
>   ecutwfc =50,
>                           nspin = 2,
>  starting_magnetization(1)=0.7, starting_magnetization(2)=0.5,
>   occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02,
>  /
>  &ELECTRONS
>                     conv_thr = 1.0d-10 ,
>                  mixing_mode = 'plain' ,
>                  mixing_beta = 0.6,
>              diagonalization = 'david' ,
>  /
> ATOMIC_SPECIES
>  Mg   24.3050  Mg.pz-n-vbc.UPF
>  O   15.99940   O.pz-mt.UPF
>
> ATOMIC_POSITIONS Crystal
>     Mg     0.666666667    0.333333333    0.000000000
>     Mg     0.333333333    0.666666667    0.500000000
>     O      0.666666667    0.333333333    0.380000000
>     O      0.333333333    0.666666667
>  0.880000000
>
> K_POINTS automatic
>  9 9 3 1 1 1
>
> EOF
> $ECHO "  running the scf calculation...\c"
> $PW_COMMAND < MgO.scf.in > MgO.scf.out
> check_failure $?
> $ECHO "
>  done"
> #########################################################
>  cat> MgO_eps.in << EOF
>  &inputpp
>      outdir='$TMP_DIR/'
>      prefix='MgO'
>      calculation='eps'
>   /
>   &energy_grid
>      smeartype='gauss'
>      intersmear=0.15d0
>       wmin     = 0.0d0
>      wmax=30.0d0
>      nw=1000
>      shift=0.0d0
>       intrasmear   = 0.0d0
>   /
> EOF
>
> $ECHO "  running epsilon.x ...\c"
> $PROJWFC_COMMAND <  MgO_eps.in > MgO_eps.out
> check_failure $?
> $ECHO " done"
>
> Sincerely
>
>
> DEBBICHI Mourad
> Unit? de Recherche Physique des Solides,99/UR/13-19,
> D?partement de Physique, Facult? des Science de Monastir,
> Avenue de l'Environnement 5019, Monastir Tunisie.
> t?l:+21697487042
> mourad_fsm at yahoo.fr
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From lmartinsamos at gmail.com  Wed Apr 18 11:24:40 2012
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Wed, 18 Apr 2012 11:24:40 +0200
Subject: [Pw_forum] Fwd:  epsilon.x
In-Reply-To: <CAGCSmJRkekY51nGCuYzh36+M8ciKF0QH=X7U0FZ-tR3W4a-48w@mail.gmail.com>
References: <1334738490.77674.YahooMailNeo@web29501.mail.ird.yahoo.com>
	<CAGCSmJRkekY51nGCuYzh36+M8ciKF0QH=X7U0FZ-tR3W4a-48w@mail.gmail.com>
Message-ID: <CAGCSmJRjvbNTFBUOfzgDJDYkjoaQKdKM9GYW8O+dYZwBJR205A@mail.gmail.com>

Dear Mourad, Are you sure that you are running epsilon.x? because the error
message indicates that the code is not recognizing the input variable
"calculation". I have noticed that in your scritp you use PROJWFC_COMMAND.

best regards

Layla


2012/4/18 debbichi mourad <mourad_fsm at yahoo.fr>

> Dear PWScf Users,
>
> I try to do the dielectric function calculations. At first I did the
> scf-calculation. After using the code epsilon.x, *I gives the following error message* :
>
> running epsilon.x ...Cannot match namelist object name calculation
> namelist read: missplaced = sign
> Cannot match namelist object name eps'
>
>  Why such a problem occurs?
>
>  My input files is as following:
>
> cat > MgO.scf.in << EOF
>
>  &control
>     calculation='scf'
>  restart_mode='from_scratch',
>        prefix='MgO'
>     pseudo_dir = '$PSEUDO_DIR/',
>     outdir='$TMP_DIR/'
> tstress=.true.
>
>  /
>
> &SYSTEM
>                        ibrav = 4,
>                     celldm(1) =6.11,
>                    celldm(3) = 1.611,
>                         nat = 4,
>                         ntyp = 2,
>
>
>   ecutwfc =50,
>                           nspin = 2,
>  starting_magnetization(1)=0.7, starting_magnetization(2)=0.5,
>   occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02,
>  /
>  &ELECTRONS
>
>                     conv_thr = 1.0d-10 ,
>                  mixing_mode = 'plain' ,
>                  mixing_beta = 0.6,
>              diagonalization = 'david' ,
>  /
> ATOMIC_SPECIES
>  Mg   24.3050  Mg.pz-n-vbc.UPF
>
>  O   15.99940   O.pz-mt.UPF
>
> ATOMIC_POSITIONS Crystal
>     Mg     0.666666667    0.333333333    0.000000000
>     Mg     0.333333333    0.666666667    0.500000000
>     O      0.666666667    0.333333333    0.380000000
>
>     O      0.333333333    0.666666667
>  0.880000000
>
> K_POINTS automatic
>  9 9 3 1 1 1
>
> EOF
> $ECHO "  running the scf calculation...\c"
> $PW_COMMAND < MgO.scf.in > MgO.scf.out
>
> check_failure $?
> $ECHO "
>  done"
> #########################################################
>  cat> MgO_eps.in << EOF
>  &inputpp
>      outdir='$TMP_DIR/'
>      prefix='MgO'
>
>      calculation='eps'
>   /
>   &energy_grid
>      smeartype='gauss'
>      intersmear=0.15d0
>       wmin     = 0.0d0
>      wmax=30.0d0
>      nw=1000
>      shift=0.0d0
>       intrasmear   = 0.0d0
>
>   /
> EOF
>
> $ECHO "  running epsilon.x ...\c"
> $PROJWFC_COMMAND <  MgO_eps.in > MgO_eps.out
> check_failure $?
> $ECHO " done"
>
> Sincerely
>
>
> DEBBICHI Mourad
> Unit? de Recherche Physique des Solides,99/UR/13-19,
> D?partement de Physique, Facult? des Science de Monastir,
> Avenue de l'Environnement 5019, Monastir Tunisie.
> t?l:+21697487042
> mourad_fsm at yahoo.fr
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From amirhosseinba67 at gmail.com  Wed Apr 18 11:35:50 2012
From: amirhosseinba67 at gmail.com (Amir hosseini)
Date: Wed, 18 Apr 2012 14:05:50 +0430
Subject: [Pw_forum] piezoelectric
Message-ID: <CABGPTx1Zi5Co8s5YhAf=WqLjb0=V-_RJiVbF70Oi+HGDYypm0g@mail.gmail.com>

Quantum Espresso can calculated polarization and piezoelectric
properties and change the dimension of a material such as carbon
nanotubes in the presence of electric field?

Thanks

From chenjianyong0223 at 126.com  Wed Apr 18 11:27:50 2012
From: chenjianyong0223 at 126.com (=?GBK?B?s8K9qNPC?=)
Date: Wed, 18 Apr 2012 17:27:50 +0800 (CST)
Subject: [Pw_forum] bismuth fully relativistic  pseudopotential  needed
Message-ID: <77bf0c8b.24104.136c4c77e82.Coremail.chenjianyong0223@126.com>

Hi ,all

       I  want to  calculate   properties of  Bi2Se3 concerning  spin orbit coupling  ,  however attempt  to find the  full relativistic  ultrasoft  PBE  pseudopotential  of  bismuth  failed .

       Will   you   be  kind enough to supply me with the pseudopotential    file ???

 
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From pankajsahota at gmail.com  Wed Apr 18 13:06:15 2012
From: pankajsahota at gmail.com (pankaj sahota)
Date: Wed, 18 Apr 2012 16:36:15 +0530
Subject: [Pw_forum] Error in getting the transmission while doing the
	transport calculation
Message-ID: <CADww=12CrgBNJb-ApwqqJohc1xKiWBgv8KQ12uuNo+Zo1v=RBA@mail.gmail.com>

Hello,

I am trying to reproduce the results of one paper on carbon chains. while
doing the conductance calculations, I am getting the following output

 Total T_j, R_j =  *********115.69580

I cannot understand wheather I am doing something wrong.   Please help me.

-- 
Pankaj Kumar
DST Project Fellow(Ph.D.)
Department of Physics
The LNM IIT Jaipur
Mob. No. +91 9736694726
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From babraram at yahoo.com  Wed Apr 18 13:51:34 2012
From: babraram at yahoo.com (babr aram)
Date: Wed, 18 Apr 2012 04:51:34 -0700 (PDT)
Subject: [Pw_forum] supercell in matdyn.x
Message-ID: <1334749894.12512.YahooMailNeo@web161306.mail.bf1.yahoo.com>

Dear all, I would like to use matdyn.x?to calculatephonon dos but i don't know the difference between?
(1): making a 2*2*2 supercell and running?ph.x calculation for?supercell and then?running?matdyn.x to calculte phonon dos
?and
(2):??running?ph.x calculation for?unit cell?(or?primitive cell) and then matdyn.x for supercell (for l1=2, l2=2, l3=2).(first needs more time and second is very fast)
what is  the difference between them?

thanks a lot

babraram
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From lukuilin at gmail.com  Wed Apr 18 14:21:03 2012
From: lukuilin at gmail.com (kuilin lu)
Date: Wed, 18 Apr 2012 20:21:03 +0800
Subject: [Pw_forum] two program logic questions in TDDFPT
Message-ID: <CAGL+XK9kxAV6nJEkNJ9k2SfkHp9LnWkkE5WMmefoJJsHwBhP1A@mail.gmail.com>

Dear Simon,

   Thanks a lot for your explanation, it really makes me more
understanding of the program.  I'm lucky to have my question solved.

Best Wishes,
Kuilin Lu

On 4/17/12, Simon Binnie <sbinnie at sissa.it> wrote:
> Thanks. You are right about the duplicated zcopy line, it is rather
> pointless to perform the same copy twice in a row. It's not necessary to
> copy sevc1_new though as far as I can see, since this is only really used
> as a workspace within lr_apply_liovillian. The only thing that is
> important is to make sure that evc1_new gets copied so evc1_old can then
> be properly updated.
>
> Best regards,
>
> Simon
>

- Hide quoted text -
--
----------------------------------------------------------------------
Kuilin Lu, Ph.D student
College of Materials Science and Engineering
Hunan University
Changsha 410082
China
E-Mail: lukuilin at gmail.com
----------------------------------------------------------------------

From flux_ray12 at 163.com  Wed Apr 18 16:12:09 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Wed, 18 Apr 2012 22:12:09 +0800 (CST)
Subject: [Pw_forum] bismuth fully relativistic  pseudopotential  needed
In-Reply-To: <77bf0c8b.24104.136c4c77e82.Coremail.chenjianyong0223@126.com>
References: <77bf0c8b.24104.136c4c77e82.Coremail.chenjianyong0223@126.com>
Message-ID: <4c9db38d.232a4.136c5cbcc44.Coremail.flux_ray12@163.com>

The PSLibrary contents the pseudo-potential of ultrasoft full-rel Bi as:
&input
 title='Bi',
 zed=83,
 rel=$nrel,
 config='[Xe] 4f14 5d10 6s2 6p3 6d-2',
 iswitch=3,
 dft='$gfun',
/
&inputp
 pseudotype=3,
 file_pseudopw='Bi.$fct-dn-rrkjus.UPF',
 author='ADC',
 lloc=-2,
 rcloc=2.2,
 which_augfun='PSQ',
 rmatch_augfun_nc=.true.,
 nlcc=.true.,
 new_core_ps=.true.,
 nlcc=.true.,
 new_core_ps=.true.,
 rcore=1.4,
 tm=.true.,
/
6
6S 1 0 2 0 1.6 2.2 0
6S 1 0 0 0.2 1.6 2.2 0
6P 2 1 3 0 1.6 2.3 0
6P 2 1 0 0.2 1.6 2.3 0
5D 3 2 10 0 0.9 2 0
5D 3 2 0 2.5 0.9 2 0


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-04-18 17:27:50,"???" <chenjianyong0223 at 126.com> wrote:


Hi ,all

       I  want to  calculate   properties of  Bi2Se3 concerning  spin orbit coupling  ,  however attempt  to find the  full relativistic  ultrasoft  PBE  pseudopotential  of  bismuth  failed .

       Will   you   be  kind enough to supply me with the pseudopotential    file ???

 


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From saidasma1987 at yahoo.fr  Wed Apr 18 16:42:21 2012
From: saidasma1987 at yahoo.fr (Said Asma)
Date: Wed, 18 Apr 2012 15:42:21 +0100 (BST)
Subject: [Pw_forum] (no subject)
References: <mailman.2198.1334741082.9401.pw_forum@pwscf.org> 
Message-ID: <1334760141.69824.YahooMailNeo@web29008.mail.ird.yahoo.com>



Dear PWScf Users,

I did the band structure of?BN(zinc blende) with two atoms and I found aindirectgap? (like literature) Gamma-X. But when I did it with 8 atoms I found direct gap Gamma -Gamma.

Why such a problem occurs?

My input files is as following:
?
?*With TWO ATOMS:

cat > bn.band.in << EOF
?&control
??? calculation='bands'
??? pseudo_dir = '$PSEUDO_DIR/',
??? outdir='$TMP_DIR/',
??? prefix='bn'
?/
?&system
??? ibrav=? 2, celldm(1) = 6.76, nat=? 2, ntyp= 2,
??? ecutwfc = 60.0,
??? occupations ='smearing',
??? smearing = 'methfessel-paxton',
??? degauss= 0.03,
?/
?&electrons
???????????????? conv_thr = 1.0d-7 ,
???????????????? mixing_mode = 'plain' ,
???????????????? mixing_beta = 0.2 ,
???????????????? diagonalization = 'david' ,
?/
ATOMIC_SPECIES
?B? 10.811? B.pz-vbc.UPF
?N? 14.007? N.pz-vbc.UPF
ATOMIC_POSITIONS
? B 0.00 0.00 0.00
? N 0.25 0.25 0.25
K_POINTS {crystal_b}
5
0.5? 0.5? 0.5? 400
0??? 0??? 0??? 400
1.0? 0??? 0??? 400
0.75 0.75 0??? 400
0??? 0??? 0??? 400
EOF
$ECHO "? running the band-structure calculation for bn...\c"
$PW_COMMAND < bn.band.in > bn.band.out
check_failure $?
$ECHO " done"



*and WITH 8 ATOMS:

cat > bn.band.in << EOF
?&control
??? calculation='bands'
??? pseudo_dir = '$PSEUDO_DIR/',
??? outdir='$TMP_DIR/',
??? prefix='bn'
?/
?&system
??? ibrav= 1, celldm(1) = 6.82, nat=8, ntyp= 2,
??? ecutwfc = 40.0, nbnd = 40,
??? occupations ='smearing',
??? smearing = 'methfessel-paxton',
??? degauss= 0.02,
?/
?&electrons
? conv_thr =? 1.0d-7,
??? mixing_beta = 0.2,
?/

ATOMIC_SPECIES
?B? 10.811? B.pz-vbc.UPF
?N? 14.007? N.pz-vbc.UPF
ATOMIC_POSITIONS
?B????? 0.000???? 0.000???? 0.000
?N????? 0.250???? 0.250???? 0.250
?B????? 0.000???? 0.500???? 0.500
?N????? 0.250???? 0.750???? 0.750
?B????? 0.500???? 0.500???? 0.000
?N????? 0.750???? 0.250???? 0.750
?B????? 0.500???? 0.000???? 0.500
?N????? 0.750???? 0.750???? 0.250

K_POINTS {crystal_b}
4
0??? 0??? 0??? 40
0.5? 0??? 0??? 40
0.5? 0.5? 0??? 40
0??? 0??? 0??? 40
EOF
$ECHO "? running the band-structure calculation for bn...\c"
$PW_COMMAND < bn.band.in > bn.band.out
check_failure $?
$ECHO " done"

Any help would be appreciated.
Best regards,
Said Asma
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From lmartinsamos at gmail.com  Wed Apr 18 16:45:48 2012
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Wed, 18 Apr 2012 16:45:48 +0200
Subject: [Pw_forum] (no subject)
In-Reply-To: <1334760141.69824.YahooMailNeo@web29008.mail.ird.yahoo.com>
References: <mailman.2198.1334741082.9401.pw_forum@pwscf.org>
	<1334760141.69824.YahooMailNeo@web29008.mail.ird.yahoo.com>
Message-ID: <CAGCSmJRyZqFn3fkBb7zqAxUmaVv2Z-TAV3vvMoJ-jJhomXMUoA@mail.gmail.com>

Dear Said, it is not a problem, I think, as increasing the number of atoms
will fold the Brillouin zone into gamma.

bests

Layla

2012/4/18 Said Asma <saidasma1987 at yahoo.fr>

>
> Dear PWScf Users,
>
> I did the band structure of  BN (zinc blende) with two atoms and I found aindirect
> gap  (like literature) Gamma-X. But when I did it with 8 atoms I found direct
> gap Gamma -Gamma.
>
> Why such a problem occurs?
>
> My input files is as following:
>
>  *With TWO ATOMS:
>
> cat > bn.band.in << EOF
>  &control
>     calculation='bands'
>     pseudo_dir = '$PSEUDO_DIR/',
>     outdir='$TMP_DIR/',
>     prefix='bn'
>  /
>  &system
>     ibrav=  2, celldm(1) = 6.76, nat=  2, ntyp= 2,
>     ecutwfc = 60.0,
>     occupations ='smearing',
>     smearing = 'methfessel-paxton',
>     degauss= 0.03,
>  /
>  &electrons
>                  conv_thr = 1.0d-7 ,
>                  mixing_mode = 'plain' ,
>                  mixing_beta = 0.2 ,
>                  diagonalization = 'david' ,
>  /
> ATOMIC_SPECIES
>  B  10.811  B.pz-vbc.UPF
>  N  14.007  N.pz-vbc.UPF
> ATOMIC_POSITIONS
>   B 0.00 0.00 0.00
>   N 0.25 0.25 0.25
> K_POINTS {crystal_b}
> 5
> 0.5  0.5  0.5  400
> 0    0    0    400
> 1.0  0    0    400
> 0.75 0.75 0    400
> 0    0    0    400
> EOF
> $ECHO "  running the band-structure calculation for bn...\c"
> $PW_COMMAND < bn.band.in > bn.band.out
> check_failure $?
> $ECHO " done"
>
>
>
> *and WITH 8 ATOMS:
>
> cat > bn.band.in << EOF
>  &control
>     calculation='bands'
>     pseudo_dir = '$PSEUDO_DIR/',
>     outdir='$TMP_DIR/',
>     prefix='bn'
>  /
>  &system
>     ibrav= 1, celldm(1) = 6.82, nat=8, ntyp= 2,
>     ecutwfc = 40.0, nbnd = 40,
>     occupations ='smearing',
>     smearing = 'methfessel-paxton',
>     degauss= 0.02,
>  /
>  &electrons
>   conv_thr =  1.0d-7,
>     mixing_beta = 0.2,
>  /
>
> ATOMIC_SPECIES
>  B  10.811  B.pz-vbc.UPF
>  N  14.007  N.pz-vbc.UPF
> ATOMIC_POSITIONS
>  B      0.000     0.000     0.000
>  N      0.250     0.250     0.250
>  B      0.000     0.500     0.500
>  N      0.250     0.750     0.750
>  B      0.500     0.500     0.000
>  N      0.750     0.250     0.750
>  B      0.500     0.000     0.500
>  N      0.750     0.750     0.250
>
> K_POINTS {crystal_b}
> 4
> 0    0    0    40
> 0.5  0    0    40
> 0.5  0.5  0    40
> 0    0    0    40
> EOF
> $ECHO "  running the band-structure calculation for bn...\c"
> $PW_COMMAND < bn.band.in > bn.band.out
> check_failure $?
> $ECHO " done"
>
> Any help would be appreciated.
> Best regards,
> Said Asma
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From saidasma1987 at yahoo.fr  Wed Apr 18 17:10:15 2012
From: saidasma1987 at yahoo.fr (Said Asma)
Date: Wed, 18 Apr 2012 16:10:15 +0100 (BST)
Subject: [Pw_forum] Re :  Band gap of BN (zinc blende)
In-Reply-To: <CAGCSmJRyZqFn3fkBb7zqAxUmaVv2Z-TAV3vvMoJ-jJhomXMUoA@mail.gmail.com>
References: <mailman.2198.1334741082.9401.pw_forum@pwscf.org>
	<1334760141.69824.YahooMailNeo@web29008.mail.ird.yahoo.com>
	<CAGCSmJRyZqFn3fkBb7zqAxUmaVv2Z-TAV3vvMoJ-jJhomXMUoA@mail.gmail.com>
Message-ID: <1334761815.9985.YahooMailNeo@web29005.mail.ird.yahoo.com>

Dear Layla,
Thank you for your answer, normally if we change (nat = 2, ibrav = 2) to (nat = 8, ibrav = 1),we find the same nature of gap.
If such we have the composition B0.25Ga0.75N how we can determine the nature of gap?

bests

Said Asma



________________________________
 De?: Layla Martin-Samos <lmartinsamos at gmail.com>
??: Said Asma <saidasma1987 at yahoo.fr> 
Cc?: "pw_forum at pwscf.org" <pw_forum at pwscf.org> 
Envoy? le : Mercredi 18 avril 2012 15h45
Objet?: Re: [Pw_forum] (no subject)
 

Dear Said, it is not a problem, I think, as increasing the number of atoms will fold the Brillouin zone into gamma. 

bests

Layla


2012/4/18 Said Asma <saidasma1987 at yahoo.fr>


>
>Dear PWScf Users,
>
>I did the band structure of?BN(zinc blende) with two atoms and I found aindirectgap? (like literature) Gamma-X. But when I did it with 8 atoms I found direct gap Gamma -Gamma.
>
>Why such a problem occurs?
>
>My input files is as following:
>?
>?*With TWO ATOMS:
>
>cat > bn.band.in << EOF
>?&control
>??? calculation='bands'
>??? pseudo_dir = '$PSEUDO_DIR/',
>??? outdir='$TMP_DIR/',
>??? prefix='bn'
>?/
>?&system
>??? ibrav=? 2, celldm(1) = 6.76, nat=? 2, ntyp= 2,
>??? ecutwfc = 60.0,
>??? occupations ='smearing',
>??? smearing = 'methfessel-paxton',
>??? degauss= 0.03,
>?/
>?&electrons
>???????????????? conv_thr = 1.0d-7 ,
>???????????????? mixing_mode = 'plain' ,
>???????????????? mixing_beta = 0.2
 ,
>???????????????? diagonalization = 'david' ,
>?/
>ATOMIC_SPECIES
>?B? 10.811? B.pz-vbc.UPF
>?N? 14.007? N.pz-vbc.UPF
>ATOMIC_POSITIONS
>? B 0.00 0.00 0.00
>? N 0.25 0.25 0.25
>K_POINTS {crystal_b}
>5
>0.5? 0.5? 0.5? 400
>0??? 0??? 0??? 400
>1.0? 0??? 0??? 400
>0.75 0.75 0??? 400
>0??? 0??? 0??? 400
>EOF
>$ECHO "? running the band-structure calculation for bn...\c"
>$PW_COMMAND < bn.band.in > bn.band.out
>check_failure $?
>$ECHO " done"
>
>
>
>*and WITH 8 ATOMS:
>
>cat > bn.band.in << EOF
>?&control
>??? calculation='bands'
>??? pseudo_dir = '$PSEUDO_DIR/',
>??? outdir='$TMP_DIR/',
>??? prefix='bn'
>?/
>?&system
>??? ibrav= 1, celldm(1) = 6.82, nat=8, ntyp= 2,
>??? ecutwfc = 40.0, nbnd = 40,
>??? occupations ='smearing',
>??? smearing = 'methfessel-paxton',
>??? degauss= 0.02,
>?/
>?&electrons
>? conv_thr =? 1.0d-7,
>??? mixing_beta = 0.2,
>?/
>
>ATOMIC_SPECIES
>?B? 10.811? B.pz-vbc.UPF
>?N? 14.007? N.pz-vbc.UPF
>ATOMIC_POSITIONS
>?B????? 0.000???? 0.000???? 0.000
>?N????? 0.250???? 0.250???? 0.250
>?B????? 0.000???? 0.500???? 0.500
>?N????? 0.250???? 0.750???? 0.750
>?B????? 0.500???? 0.500???? 0.000
>?N????? 0.750???? 0.250???? 0.750
>?B????? 0.500???? 0.000???? 0.500
>?N????? 0.750???? 0.750???? 0.250
>
>K_POINTS {crystal_b}
>4
>0??? 0??? 0??? 40
>0.5? 0??? 0??? 40
>0.5? 0.5? 0??? 40
>0??? 0??? 0??? 40
>EOF
>$ECHO "? running the band-structure calculation for bn...\c"
>$PW_COMMAND < bn.band.in > bn.band.out
>check_failure $?
>$ECHO " done"
>
>Any help would be appreciated.
>Best regards,
>Said Asma
>
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From xrhino at gmail.com  Wed Apr 18 17:26:28 2012
From: xrhino at gmail.com (YY)
Date: Wed, 18 Apr 2012 11:26:28 -0400
Subject: [Pw_forum] ecutrho in phonon calculations
In-Reply-To: <1334591560.11882.66.camel@fe12lx.fisica.uniud.it>
References: <CAKr8hj0y1tGHXy_E7k3ehU3yR-b=gfp8auXUszgp=M2aU8BbPw@mail.gmail.com>
	<1334591560.11882.66.camel@fe12lx.fisica.uniud.it>
Message-ID: <CAKr8hj1XNEjsGgEpVrWSwwHMYYSJsUTo2VCoGiy5kL7D3cR1tQ@mail.gmail.com>

Hi Paolo,

Thanks for your reply.  For the phonon calculation, I use a PBE-US PP
(Fe.pbe-sp-van_ak.UPF, and Se.pbe-van.UPF).
According to your suggestion, I increase the ecutwfc, and do several
tests.  Unfortunately, it seems there are still convergence problem:

ecutwfc  ecutrho  f1(cm-1) ... f12(cm-1)
100        1200      106.5    ...  329.5
100        2400      127.2    ...  339.8
200        2400      127.8    ...  341.2
200        4800        32.9    ...  319.8

Could there be any other reasons to cause this convergence problem?

Yuyang at RPI

On Mon, Apr 16, 2012 at 11:52 AM, Paolo Giannozzi
<giannozz at democritos.it> wrote:
> On Thu, 2012-04-12 at 16:07 -0400, YY wrote:
>
>> But I find there is no simple convergence trend while increasing
>> ecutrho. ?When I use 35 Ry ecutwfc, and fix all the other parameters,
>> the results are like this:
>>
>> ? ?ecutrho ? ? ? f1(cm-1) ? ? ?.... ?f12(cm-1)
>> ? ?420 ? ? ? ? ? ?40.475 ? ? ? ? ? ? ? ?324.062
>> ? ?600 ? ? ? ? ? 123.746 ? ? ? ? ? ? ? 350.727
>> ? ?900 ? ? ? ? ? -251.876 ? ? ? ? ? ? ?306.721
>
> unfortunately in at least some [ and I am afraid, in many ] cases,
> a rather high cutoff is needed anyway to get decent phonons. If
> this happens, the advantage of using USPP becomes dubious, given
> their significant computational overhead wrt Norm-Conserving PPs.
> Which USPP did you use ?
>
> P.
>
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>

From elbuesta at icqmail.com  Wed Apr 18 17:48:55 2012
From: elbuesta at icqmail.com (elbuesta at icqmail.com)
Date: Wed, 18 Apr 2012 11:48:55 -0400 (EDT)
Subject: [Pw_forum] ecutrho in phonon calculations
In-Reply-To: <CAKr8hj1XNEjsGgEpVrWSwwHMYYSJsUTo2VCoGiy5kL7D3cR1tQ@mail.gmail.com>
References: <CAKr8hj0y1tGHXy_E7k3ehU3yR-b=gfp8auXUszgp=M2aU8BbPw@mail.gmail.com><1334591560.11882.66.camel@fe12lx.fisica.uniud.it>
	<CAKr8hj1XNEjsGgEpVrWSwwHMYYSJsUTo2VCoGiy5kL7D3cR1tQ@mail.gmail.com>
Message-ID: <8CEEB91E5232ABB-1ABC-2EAC@webmail-m166.sysops.aol.com>


 Dear Yuyang, 

If I may ask (I did not follow the discussion, only now I saw your e-mail, so I don't know what was discussed previously), what are the values of the "conv_thr" and "tr2_ph" parameters used in your case? I never did phonon calculations for your specific case, but using USPP for Ag/Cu/Au/Pt, the phonon frequencies are already converged at wfc and charge cutoffs of 40/480, as long as one performs a very accurate scf and phonon calculation. For silver, for example, I had to use a "conv_thr" as low as 10-12, and tr2_ph about 10-19.

Fabio Negreiros Ribeiro
Post-doc at CNR
Pisa - Italy
 

-----Original Message-----
From: YY <xrhino at gmail.com>
To: Paolo Giannozzi <giannozz at democritos.it>
Cc: pw_forum <pw_forum at pwscf.org>
Sent: Wed, Apr 18, 2012 5:26 pm
Subject: Re: [Pw_forum] ecutrho in phonon calculations


Hi Paolo,

Thanks for your reply.  For the phonon calculation, I use a PBE-US PP
(Fe.pbe-sp-van_ak.UPF, and Se.pbe-van.UPF).
According to your suggestion, I increase the ecutwfc, and do several
tests.  Unfortunately, it seems there are still convergence problem:

ecutwfc  ecutrho  f1(cm-1) ... f12(cm-1)
100        1200      106.5    ...  329.5
100        2400      127.2    ...  339.8
200        2400      127.8    ...  341.2
200        4800        32.9    ...  319.8

Could there be any other reasons to cause this convergence problem?

Yuyang at RPI

On Mon, Apr 16, 2012 at 11:52 AM, Paolo Giannozzi
<giannozz at democritos.it> wrote:
> On Thu, 2012-04-12 at 16:07 -0400, YY wrote:
>
>> But I find there is no simple convergence trend while increasing
>> ecutrho.  When I use 35 Ry ecutwfc, and fix all the other parameters,
>> the results are like this:
>>
>>    ecutrho       f1(cm-1)      ....  f12(cm-1)
>>    420            40.475                324.062
>>    600           123.746               350.727
>>    900           -251.876              306.721
>
> unfortunately in at least some [ and I am afraid, in many ] cases,
> a rather high cutoff is needed anyway to get decent phonons. If
> this happens, the advantage of using USPP becomes dubious, given
> their significant computational overhead wrt Norm-Conserving PPs.
> Which USPP did you use ?
>
> 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


 
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From pankajsahota at gmail.com  Wed Apr 18 19:10:48 2012
From: pankajsahota at gmail.com (pankaj sahota)
Date: Wed, 18 Apr 2012 22:40:48 +0530
Subject: [Pw_forum] About the size of electrode
Message-ID: <CADww=10kBq2VZjjxCeRk6gEd2uecnOHu-+KHMgCjHBQjYuyvQg@mail.gmail.com>

Hi,

Is it possible that an electrode can contain vacuum on x and y directions,
The size of electrode to be used remain as the size of layers of electrode
attached to the lead. Because from the reference (A. Smogunov, A. Dal
Corso, E. Tosatti, Phys. Rev. B 70, 045417 (2004)) given for the PWCOND, it
is looking like that. But according to the book by Supriyo Datta, the
electrode size should be large.

-- 
Pankaj Kumar
DST Project Fellow(Ph.D.)
Department of Physics
The LNM IIT Jaipur
Mob. No. +91 9736694726
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From bahadira at buffalo.edu  Wed Apr 18 20:35:07 2012
From: bahadira at buffalo.edu (bahadir)
Date: Wed, 18 Apr 2012 14:35:07 -0400
Subject: [Pw_forum] lambda(omega)
Message-ID: <4F8F095B.1010603@buffalo.edu>

how to get values of lambda(omega) from el-phon calculations?

thanks

-- 
Dr.Bahadir Altintas

* Dept. of Chemistry
  SUNY Buffalo
  NY,USA

* Abant Izzet Baysal University
   Dept. of Computer Education
   Bolu,Turkey


From bahadira at buffalo.edu  Wed Apr 18 20:37:11 2012
From: bahadira at buffalo.edu (bahadir)
Date: Wed, 18 Apr 2012 14:37:11 -0400
Subject: [Pw_forum] lambda(omega)
In-Reply-To: <4F8F095B.1010603@buffalo.edu>
References: <4F8F095B.1010603@buffalo.edu>
Message-ID: <4F8F09D7.7090207@buffalo.edu>

On 04/18/2012 02:35 PM, bahadir wrote:
> how to get values of lambda(omega) from el-phon calculations?
>
> thanks
>
i meant lambda as a function of omega. (lambda values for each frequency)

-- 
Dr.Bahadir Altintas

* Dept. of Chemistry
  SUNY Buffalo
  NY,USA

* Abant Izzet Baysal University
   Dept. of Computer Education
   Bolu,Turkey


From giannozz at democritos.it  Wed Apr 18 22:21:29 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 18 Apr 2012 22:21:29 +0200
Subject: [Pw_forum] supercell in matdyn.x
In-Reply-To: <1334749894.12512.YahooMailNeo@web161306.mail.bf1.yahoo.com>
References: <1334749894.12512.YahooMailNeo@web161306.mail.bf1.yahoo.com>
Message-ID: <85F45C4E-8513-4BC0-958E-D9544E94B71E@democritos.it>


On Apr 18, 2012, at 13:51 , babr aram wrote:

> Dear all, I would like to use matdyn.x to calculate phonon dos
> but i don't know the difference between
> (1): making a 2*2*2 supercell and running ph.x calculation
> for supercell and then running matdyn.x to calculate phonon dos and
> (2):  running ph.x calculation for unit cell (or primitive cell)  
> and then
> matdyn.x for supercell (for l1=2, l2=2, l3=2)

they should actually yield the same result, provided the latter option
still works. It was written 20 years ago or so to implement the so- 
called
"effective-mass approximation" in GaAs/AlAs superlattices and alloys.
Several years ago it was still working, but I doubt it has been used
since.

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 18 22:40:37 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 18 Apr 2012 22:40:37 +0200
Subject: [Pw_forum] Quantum Espresso Workshop (Jun 25 - Jun 29 /2012,
	Penn State Univ., PA, USA)
In-Reply-To: <CEE3C6FC-B660-4803-AE0E-636E01B8D137@democritos.it>
References: <CEE3C6FC-B660-4803-AE0E-636E01B8D137@democritos.it>
Message-ID: <804F8008-53E2-4A03-9F07-DC59DEE27D23@democritos.it>


On Apr 18, 2012, at 8:54 , Paolo Giannozzi wrote:

> Reminder: a workshop/tutorial on Quantum Espresso will be held in
> Penn State University, Philadelphia

oops...not really: Penn State University, State College, PA (sorry)

> USA, from Jun 25 to June 29. More info can be found at the url:
>     http://rcc.its.psu.edu/education/workshops/pages/
> quantum_espresso_2012/
> Hoping to see you in Pennsylvania for the QE 2012 Workshop

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



From giannozz at democritos.it  Wed Apr 18 22:46:40 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 18 Apr 2012 22:46:40 +0200
Subject: [Pw_forum] lambda(omega)
In-Reply-To: <4F8F09D7.7090207@buffalo.edu>
References: <4F8F095B.1010603@buffalo.edu> <4F8F09D7.7090207@buffalo.edu>
Message-ID: <06B8BD45-3DC0-4CCB-840C-24CE2F2C572C@democritos.it>


On Apr 18, 2012, at 20:37 , bahadir wrote:

> On 04/18/2012 02:35 PM, bahadir wrote:
>> how to get values of lambda(omega) from el-phon calculations?
>>
>> thanks
>>
> i meant lambda as a function of omega. (lambda values for each  
> frequency)

what do you mean? the electron-phonon coefficient lambda as usually  
defined
is not a funciton of omega. All you can get is lambda(q,nu) for each  
phonon
mode nu and wavevector q. These are hidden somewhere in data file

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 18 22:49:18 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 18 Apr 2012 22:49:18 +0200
Subject: [Pw_forum] phonon dynamical matrix and eigenvectors
In-Reply-To: <4F8C96BD.4060307@gmail.com>
References: <4F8C96BD.4060307@gmail.com>
Message-ID: <73F2BECF-E252-4EE4-B461-4E2627CDE1D0@democritos.it>


On Apr 17, 2012, at 24:01 , Bo Qiu wrote:

> However, I found the dynamical matrices do not agree.
> The eigenvectors are also completely different.

all I can say is that properly computed dynamical matrices
produced by QE are correct and should compare well with
properly computed dynamical matrices produced by other
packages

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 bahadira at buffalo.edu  Thu Apr 19 00:05:30 2012
From: bahadira at buffalo.edu (bahadir)
Date: Wed, 18 Apr 2012 18:05:30 -0400
Subject: [Pw_forum] lambda(omega)
In-Reply-To: <06B8BD45-3DC0-4CCB-840C-24CE2F2C572C@democritos.it>
References: <4F8F095B.1010603@buffalo.edu> <4F8F09D7.7090207@buffalo.edu>
	<06B8BD45-3DC0-4CCB-840C-24CE2F2C572C@democritos.it>
Message-ID: <4F8F3AAA.6060604@buffalo.edu>

On 04/18/2012 04:46 PM, Paolo Giannozzi wrote:
>
> On Apr 18, 2012, at 20:37 , bahadir wrote:
>
>> On 04/18/2012 02:35 PM, bahadir wrote:
>>> how to get values of lambda(omega) from el-phon calculations?
>>>
>>> thanks
>>>
>> i meant lambda as a function of omega. (lambda values for each 
>> frequency)
>
> what do you mean? the electron-phonon coefficient lambda as usually 
> defined
> is not a funciton of omega. All you can get is lambda(q,nu) for each 
> phonon
> mode nu and wavevector q. These are hidden somewhere in data file
>
> 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
>
>
>
>
>
ok, got it!
  thank you very much.

-- 
Dr.Bahadir Altintas

* Dept. of Chemistry
  SUNY Buffalo
  NY,USA

* Abant Izzet Baysal University
   Dept. of Computer Education
   Bolu,Turkey


From jagaran_acharya at yahoo.com  Thu Apr 19 07:47:53 2012
From: jagaran_acharya at yahoo.com (jagaran Acharya)
Date: Thu, 19 Apr 2012 11:32:53 +0545
Subject: [Pw_forum] regarding problem in bands structure calculation
Message-ID: <1334814473.4927.6.camel@localhost.localdomain>

Dear All,
I have the input and output files for calculation of
band structure.
The problem is while running band by pw.x command and further other
calculation,
But, the scf calculation is done successfully.
The error also give a message like this on computer screen.
############################################################
# FROM IOTK LIBRARY, VERSION 1.2.0
# UNRECOVERABLE ERROR (ierr=1)
# ERROR IN: iotk_scan_end (iotk_scan.spp:233)
# CVS Revision: 1.23
# foundl
# ERROR IN: iotk_close_read (iotk_files.spp:645)
# CVS Revision: 1.20
########################################################################################################################

&control
 calculation = 'bands',
 restart_mode = 'from_scratch',
 outdir= './tmp',
 pseudo_dir= '/home/narayan/Documents/Jagaran/pseudo',
 prefix='ch4_p21_P50_band',
 tstress= .TRUE.,
 tprnfor= .TRUE.,
 wf_collect = .true.,
/
&system
  ibrav = 8,
  celldm(1)= 12.263840883,
  celldm(2) = 0.870281589,
  celldm(3) = 0.545153917,
  nat = 20,
  ntyp = 2,
  ecutwfc= 40.0,
  ecutrho = 520.0,
  smearing='methfessel-paxton',
  degauss=0.02,
  nbnd = 20,
/
&electrons
  diagonalization = 'david',
  mixing_beta = 0.4,
  conv_thr = 1.0e-7,
 mixing_mode = 'local-TF',
/
ATOMIC_SPECIES
H  1.0d0    H.pbe-rrkjus.UPF
C  12.0107  C.pbe-van_ak.UPF
ATOMIC_POSITIONS {angstrom}
C       -2.554371943  -4.199340405   4.960395658
C        5.799300165   4.199319625   3.191400598
H        0.461056440   2.092045365   1.326808649
H        3.039177321   1.632544047   0.828387676
H        5.019098732   4.603264031   2.543617201
H        5.458730610   3.265083430   0.102821724
H        2.783838047  -2.091991228   3.095860797
H        0.205732363  -1.632560899   2.597393883
H       -1.774165453  -4.603343474   4.312665777
H       -2.213819232  -3.265082688   1.871809597
C       -5.799259711   7.023352572  -1.422499686
H       -0.461051736   4.916033675   0.442040272
H       -3.039136444   4.456590010   0.940495554
H       -5.019052763   7.427368467  -0.774808659
H       -5.458696766   6.089105143   1.666051280
C        9.044189608  -1.375259842  -3.191421589
H        3.705946906   0.732033020  -1.326826300
H        6.284043568   1.191530305  -0.828399573
H        8.263944006  -1.779191588  -2.543626825
H        8.703608683  -0.441012607  -0.102827879
K_POINTS
41
0.0000000 0.0000000 0.0000000  1.0000000
0.0500000 0.0500000 0.0000000  1.0000000
0.1000000 0.1000000 0.0000000  1.0000000
0.1500000 0.1500000 0.0000000  1.0000000
0.2000000 0.2000000 0.0000000  1.0000000
0.2500000 0.2500000 0.0000000  1.0000000
0.3000000 0.3000000 0.0000000  1.0000000
0.3500000 0.3500000 0.0000000  1.0000000
0.4000000 0.4000000 0.0000000  1.0000000
0.4500000 0.4500000 0.0000000  1.0000000
0.5000000 0.5000000 0.0000000  1.0000000
0.5500000 0.5000000 0.0500000  1.0000000
0.6000000 0.5000000 0.1000000  1.0000000
0.6500000 0.5000000 0.1500000  1.0000000
0.7000000 0.5000000 0.2000000  1.0000000
0.7500000 0.5000000 0.2500000  1.0000000
0.7000000 0.5000000 0.3000000  1.0000000
0.6500000 0.5000000 0.3500000  1.0000000
0.6000000 0.5000000 0.4000000  1.0000000
0.5500000 0.5000000 0.4500000  1.0000000
0.5000000 0.5000000 0.5000000  1.0000000
0.4500000 0.4500000 0.4500000  1.0000000
0.4000000 0.4000000 0.4000000  1.0000000
0.3500000 0.3500000 0.3500000  1.0000000
0.3000000 0.3000000 0.3000000  1.0000000
0.2500000 0.2500000 0.2500000  1.0000000
0.2000000 0.2000000 0.2000000  1.0000000
0.1500000 0.1500000 0.1500000  1.0000000
0.1000000 0.1000000 0.1000000  1.0000000
0.0500000 0.0500000 0.0500000  1.0000000
0.0000000 0.0000000 0.0000000  1.0000000
0.0750000 0.0375000 0.0375000  1.0000000
0.1500000 0.0750000 0.0750000  1.0000000
0.2250000 0.1125000 0.1125000  1.0000000
0.3000000 0.1500000 0.1500000  1.0000000
0.3750000 0.1875000 0.1875000  1.0000000
0.4500000 0.2250000 0.2250000  1.0000000
0.5250000 0.2625000 0.2625000  1.0000000
0.6000000 0.3000000 0.3000000  1.0000000
0.6750000 0.3375000 0.3375000  1.0000000
0.7500000 0.3750000 0.3750000  1.0000000





Please can anyone help me to find solutions.
This is getting me in great trouble,
Sincerely Yours
Jagaran Acharya
Tribhuvan university
Kathmandu Nepal

From asmogunov at gmail.com  Thu Apr 19 10:28:27 2012
From: asmogunov at gmail.com (Alex Smogunov)
Date: Thu, 19 Apr 2012 10:28:27 +0200
Subject: [Pw_forum] About the size of electrode
In-Reply-To: <CADww=10kBq2VZjjxCeRk6gEd2uecnOHu-+KHMgCjHBQjYuyvQg@mail.gmail.com>
References: <CADww=10kBq2VZjjxCeRk6gEd2uecnOHu-+KHMgCjHBQjYuyvQg@mail.gmail.com>
Message-ID: <CAHuemf8eFfxsm4XmQfp0HfWb=JsgSK9OVDzBSumFp1YfTXpmKw@mail.gmail.com>

Dear  Pankaj.
It is not a problem, you can have vacuum in the XY plane, it is
the case of infinite monatomic wires with some adatom, for example.
The important point is to have long enough scattering region, with
many "lead" atoms on the right and on the left to match from both
sides to the bulk-like potential of the leads.
You can see some our examples.
HTH,
Alexander



As electrodes you can h

Le 18 avril 2012 19:10, pankaj sahota <pankajsahota at gmail.com> a ?crit :

> Hi,
>
> Is it possible that an electrode can contain vacuum on x and y directions,
> The size of electrode to be used remain as the size of layers of electrode
> attached to the lead. Because from the reference (A. Smogunov, A. Dal
> Corso, E. Tosatti, Phys. Rev. B 70, 045417 (2004)) given for the PWCOND,
> it is looking like that. But according to the book by Supriyo Datta, the
> electrode size should be large.
>
> --
> Pankaj Kumar
> DST Project Fellow(Ph.D.)
> Department of Physics
> The LNM IIT Jaipur
> Mob. No. +91 9736694726
>
>
>
> _______________________________________________
> 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 19 10:36:43 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 19 Apr 2012 10:36:43 +0200
Subject: [Pw_forum] regarding problem in bands structure calculation
In-Reply-To: <1334814473.4927.6.camel@localhost.localdomain>
References: <1334814473.4927.6.camel@localhost.localdomain>
Message-ID: <E67B7073-D22A-447D-9DC7-43310A98862D@democritos.it>


On Apr 19, 2012, at 7:47 , jagaran Acharya wrote:
>
> # FROM IOTK LIBRARY, VERSION 1.2.0

it's a known problem that has been discussed no less thamn
1001 times. Unless you have evidence of the opposite, it is
due to a compiler bug

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 solayinka at biu.edu.ng  Thu Apr 19 11:20:28 2012
From: solayinka at biu.edu.ng (Olayinka, Samson A.)
Date: Thu, 19 Apr 2012 10:20:28 +0100
Subject: [Pw_forum] How to get atomic positions for TiO2
Message-ID: <CAEMJ76guAWNzANe7hrSCbL4N-B9sJMVvbuSubqqykUphVH4yyQ@mail.gmail.com>

Dear all,
Please I need help on how to determine atomic positions for Rutile and Anatase.

Thanks in advance

Olayinka A. S

From Lorenzo.Paulatto at impmc.upmc.fr  Thu Apr 19 11:32:41 2012
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Thu, 19 Apr 2012 11:32:41 +0200
Subject: [Pw_forum] How to get atomic positions for TiO2
In-Reply-To: <CAEMJ76guAWNzANe7hrSCbL4N-B9sJMVvbuSubqqykUphVH4yyQ@mail.gmail.com>
References: <CAEMJ76guAWNzANe7hrSCbL4N-B9sJMVvbuSubqqykUphVH4yyQ@mail.gmail.com>
Message-ID: <op.wcz94roixuur8c@vanoxite.impmc.jussieu.fr>

On Thu, 19 Apr 2012 11:20:28 +0200, Olayinka, Samson A.  
<solayinka at biu.edu.ng> wrote:
> Please I need help on how to determine atomic positions for Rutile and  
> Anatase.


You could find them with google in 5 minutes, anyway, here they are:
Rutile: <http://cst-www.nrl.navy.mil/lattice/struk/c4.html>
Anatase: <http://cst-www.nrl.navy.mil/lattice/struk/c5.html>

and before you come back asking for Brookite here it is as well:
<http://cst-www.nrl.navy.mil/lattice/struk/c21.html>


bests
-- 
Lorenzo Paulatto IdR @ IMPMC/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 saidasma1987 at yahoo.fr  Thu Apr 19 11:37:37 2012
From: saidasma1987 at yahoo.fr (Said Asma)
Date: Thu, 19 Apr 2012 10:37:37 +0100 (BST)
Subject: [Pw_forum] Error band structure
In-Reply-To: <mailman.2211.1334762790.9401.pw_forum@pwscf.org>
References: <mailman.2211.1334762790.9401.pw_forum@pwscf.org>
Message-ID: <1334828257.36755.YahooMailNeo@web29009.mail.ird.yahoo.com>



?Dear PWScf Users,

I did the band structure of? BN (zinc blende) with two atoms and I found a indirect gap? (like literature) Gamma-X. But when I did it with 8 atoms I found direct gap Gamma -Gamma.
Normally if we change (nat = 2, ibrav = 2) to (nat = 8, ibrav = 1),we find the same nature of gap.
If such we have the composition B0.25Ga0.75N how we can determine the nature of gap?

?Why such a problem occurs?

?My input files is as following:

? *With TWO ATOMS:

?cat > bn.band.in << EOF
? &control
? ?  calculation='bands'
? ?  pseudo_dir = '$PSEUDO_DIR/',
? ?  outdir='$TMP_DIR/',
? ?  prefix='bn'
? /
? &system
? ?  ibrav=? 2, celldm(1) = 6.76, nat=? 2, ntyp= 2,
? ?  ecutwfc = 60.0,
? ?  occupations ='smearing',
? ?  smearing = 'methfessel-paxton',
? ?  degauss= 0.03,
? /
? &electrons
? ? ? ? ? ? ? ? ? conv_thr = 1.0d-7 ,
? ? ? ? ? ? ? ? ? mixing_mode = 'plain' ,
? ? ? ? ? ? ? ? ? mixing_beta = 0.2 ,
? ? ? ? ? ? ? ? ? diagonalization = 'david' ,
? /
ATOMIC_SPECIES
? B? 10.811? B.pz-vbc.UPF
? N? 14.007? N.pz-vbc.UPF
ATOMIC_POSITIONS
?  B 0.00 0.00 0.00
?  N 0.25 0.25 0.25
K_POINTS {crystal_b}
?5
0.5? 0.5? 0.5? 400
0? ? 0? ? 0? ? 400
1.0? 0? ? 0? ? 400
0.75 0.75 0? ? 400
0? ? 0? ? 0? ? 400
EOF
$ECHO "? running the band-structure calculation for bn...\c"
$PW_COMMAND < bn.band.in > bn.band.out
check_failure $?
$ECHO " done"



*and WITH 8 ATOMS:

?cat > bn.band.in << EOF
? &control
? ?  calculation='bands'
? ?  pseudo_dir = '$PSEUDO_DIR/',
? ?  outdir='$TMP_DIR/',
? ?  prefix='bn'
? /
?&system
? ?  ibrav= 1, celldm(1) = 6.82, nat=8, ntyp= 2,
? ?  ecutwfc = 40.0, nbnd = 40,
? ?  occupations ='smearing',
? ?  smearing = 'methfessel-paxton',
? ?  degauss= 0.02,
? /
? &electrons
?  conv_thr =? 1.0d-7,
? ?  mixing_beta = 0.2,
? /

ATOMIC_SPECIES
? B? 10.811? B.pz-vbc.UPF
? N? 14.007? N.pz-vbc.UPF
ATOMIC_POSITIONS
? B? ? ? 0.000? ?  0.000? ?  0.000
? N? ? ? 0.250? ?  0.250? ?  0.250
? B? ? ? 0.000? ?  0.500? ?  0.500
? N? ? ? 0.250? ?  0.750? ?  0.750
? B? ? ? 0.500? ?  0.500? ?  0.000
? N? ? ? 0.750? ?  0.250? ?  0.750
? B? ? ? 0.500? ?  0.000? ?  0.500
? N? ? ? 0.750? ?  0.750? ?  0.250

?K_POINTS {crystal_b}
?4
?0? ? 0? ? 0? ? 40
?0.5? 0? ? 0? ? 40
?0.5? 0.5? 0? ? 40
?0? ? 0? ? 0? ? 40
?EOF
?$ECHO "? running the band-structure calculation for bn...\c"
?$PW_COMMAND < bn.band.in > bn.band.out
?check_failure $?
?$ECHO " done"

?Any help would be appreciated.
?Best regards,
?Said Asma



bests

Said Asma



________________________________
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From ytaghipour at aeoi.org.ir  Thu Apr 19 11:57:29 2012
From: ytaghipour at aeoi.org.ir (Yavar Taghipour Azar)
Date: Thu, 19 Apr 2012 14:27:29 +0430
Subject: [Pw_forum] on the way of approximating a large slab
Message-ID: <84834F3F94064E63B61958E8D2F8C3D9@yavarpc>

Dear QE users

 

I want to model adsorption of a large molecule on a relatively large slab. After test convergence on the number of layers for clean surface, I found 14 layers are needed, but for well-known technical reasons (time and memory limitation), I am thinking on how can one take into account the atoms of just some 3 topmost layers of the slab, and the effects of the remaining layers of the slab as an external potential. 

Is it a meaningful question and what about its feasibility in the context of QE?

Thanks in advance.



 

-------------------------------------------
Yavar Taghipour
PhD Student
Physics Group, AEOI
Tehran-Iran

Email: ytaghipour at aeoi.org.ir
Phone: +98 (0) 21 82064556
-----------------------------------------------------------
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From fratesi at mater.unimib.it  Thu Apr 19 12:25:48 2012
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Thu, 19 Apr 2012 12:25:48 +0200
Subject: [Pw_forum] on the way of approximating a large slab
In-Reply-To: <84834F3F94064E63B61958E8D2F8C3D9@yavarpc>
References: <84834F3F94064E63B61958E8D2F8C3D9@yavarpc>
Message-ID: <4F8FE82C.30804@mater.unimib.it>

Dear Yavar,

I hope a comment on your question (unfortunately not an answer) could be 
helpful.
Notice that the properties of the adsorbed species may converge faster 
than those of the clean surface alone. So, if you are interested in the 
distance of the molecule from the surface, or the adsorption energy, 
these may be described with a thin slab better than the interlayer 
relaxation or the surface energy of the clean substrate (or even worse, 
the surface electronic structure). You could practice by adsorbing a 
smaller molecule or a fragment. I'd expect that much less than 14 layers 
could be sufficient rather often.

(then, I remember about an "Effective Screening Medium Method" 
implemented in QE, there's also an example, but I don't know much about it)

HTH
Guido

Il 04/19/2012 11:57 AM, Yavar Taghipour Azar ha scritto:
> Dear QE users
>
> I want to model adsorption of a large molecule on a relatively large
> slab. After test convergence on the number of layers for clean surface,
> I found 14 layers are needed, but for well-known technical reasons (time
> and memory limitation), I am thinking on how can one take into account
> the atoms of just some 3 topmost layers of the slab, and the effects of
> the remaining layers of the slab as an external potential.
>
> Is it a meaningful question and what about its feasibility in the
> context of QE?
>
> Thanks in advance.
>
> -------------------------------------------
> Yavar Taghipour
> PhD Student
> Physics Group, AEOI
> Tehran-Iran
> Email: ytaghipour at aeoi.org.ir <mailto:ytaghipour at aeoi.org.ir>
> Phone: +98 (0) 21 82064556
> -----------------------------------------------------------
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
Guido Fratesi

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

From pandey.bramha at gmail.com  Thu Apr 19 15:30:03 2012
From: pandey.bramha at gmail.com (bramha pandey)
Date: Thu, 19 Apr 2012 19:00:03 +0530
Subject: [Pw_forum] error in volume calculation in ibrav=7
Message-ID: <CAC2dNGFCwyqUFmzF5y-yjddkLB6ApBaWRFW9e9ZonjhBBwJ1oA@mail.gmail.com>

Dear all PW usres..

I was dealing with the LIT(LiInTe2) system in chalcopyrite structure with
&SYSTEM
                       ibrav = 7,
                   celldm(1) = 9.854,
                   celldm(3) = 2,

and i was obtaning the volume after pw.x run as 956.8364 (a.u.)^3 which is
the simply celldm(1)^3=(9.854)^3.
Here i wondered why i am not obtaning the volume as 2*(9.854)^3? Am i
somewhere wrong in conceptual basis?

Thanks in advanced .

-- 
Thanks and Regards
Bramha Prasad Pandey
GLA University, Mathura.
INDIA.
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From fratesi at mater.unimib.it  Thu Apr 19 16:03:51 2012
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Thu, 19 Apr 2012 16:03:51 +0200
Subject: [Pw_forum] error in volume calculation in ibrav=7
In-Reply-To: <CAC2dNGFCwyqUFmzF5y-yjddkLB6ApBaWRFW9e9ZonjhBBwJ1oA@mail.gmail.com>
References: <CAC2dNGFCwyqUFmzF5y-yjddkLB6ApBaWRFW9e9ZonjhBBwJ1oA@mail.gmail.com>
Message-ID: <4F901B47.6040203@mater.unimib.it>

Is it because ibrav=7 stands for body-centered tetragonal?
Regards,
Guido

Il 04/19/2012 03:30 PM, bramha pandey ha scritto:
> Dear all PW usres..
>
> I was dealing with the LIT(LiInTe2) system in chalcopyrite structure with
> &SYSTEM
>                         ibrav = 7,
>                     celldm(1) = 9.854,
>                     celldm(3) = 2,
>
> and i was obtaning the volume after pw.x run as 956.8364 (a.u.)^3 which
> is the simply celldm(1)^3=(9.854)^3.
> Here i wondered why i am not obtaning the volume as 2*(9.854)^3? Am i
> somewhere wrong in conceptual basis?
>
> Thanks in advanced .
>
> --
> Thanks and Regards
> Bramha Prasad Pandey
> GLA University, Mathura.
> INDIA.
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
Guido Fratesi

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

From xrhino at gmail.com  Thu Apr 19 22:00:31 2012
From: xrhino at gmail.com (YY)
Date: Thu, 19 Apr 2012 16:00:31 -0400
Subject: [Pw_forum] Pw_forum Digest, Vol 58, Issue 33
In-Reply-To: <mailman.2219.1334817153.9401.pw_forum@pwscf.org>
References: <mailman.2219.1334817153.9401.pw_forum@pwscf.org>
Message-ID: <CAKr8hj3HqUSF1Gtsa2pKvSoOunXKOc2VD63pgvcA=AkUdVrMXw@mail.gmail.com>

Hi Fabio,

Thanks for your reply.  In my previous calculations, I set the
threshold to 10^-10/10^-14 for scf/phonon calculation respectively.
According to your suggestion, I increase the precision to
10^-13/10^-19.  The results indicate the previous threshold is enough.

Yuyang at RPI


> ?Dear Yuyang,
>
> If I may ask (I did not follow the discussion, only now I saw your e-mail, so I don't know what was discussed previously), what are the values of the "conv_thr" and "tr2_ph" parameters used in your case? I never did phonon calculations for your specific case, but using USPP for Ag/Cu/Au/Pt, the phonon frequencies are already converged at wfc and charge cutoffs of 40/480, as long as one performs a very accurate scf and phonon calculation. For silver, for example, I had to use a "conv_thr" as low as 10-12, and tr2_ph about 10-19.
>
> Fabio Negreiros Ribeiro
> Post-doc at CNR
> Pisa - Italy

From lmartinsamos at gmail.com  Fri Apr 20 10:00:31 2012
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Fri, 20 Apr 2012 10:00:31 +0200
Subject: [Pw_forum] Re :  Band gap of BN (zinc blende)
In-Reply-To: <1334761815.9985.YahooMailNeo@web29005.mail.ird.yahoo.com>
References: <mailman.2198.1334741082.9401.pw_forum@pwscf.org>
	<1334760141.69824.YahooMailNeo@web29008.mail.ird.yahoo.com>
	<CAGCSmJRyZqFn3fkBb7zqAxUmaVv2Z-TAV3vvMoJ-jJhomXMUoA@mail.gmail.com>
	<1334761815.9985.YahooMailNeo@web29005.mail.ird.yahoo.com>
Message-ID: <CAGCSmJQYff4-=OeOsV+z0ZjRxuO8GMFED78QG1dAzSnZC4-HFw@mail.gmail.com>

Dear Said, I have not a big experience in crystals but as long as I
understand, the "nature" of the gap is defined by its "nature" calculated
with the unit cell of your crystal. If instead of the unit cell you are
using bigger cells then you need to make a careful analysis of the
symmetries to unfold your brilloin zone by hand. When you use dopants, is
the same mechanism. To be safe and avoid manual unfoldings, you need to
build the unit cell corresponding to B0.25Ga075N. I have no idea of what is
the unit cell for your system. Maybe you can find more info in
crystallographic tables.

best regards

Layla

2012/4/18 Said Asma <saidasma1987 at yahoo.fr>

> Dear Layla,
> Thank you for your answer, normally if we change (nat = 2, ibrav = 2) to (
> nat = 8, ibrav = 1),we find the same nature of gap.
> If such we have the composition B0.25Ga0.75N how we can determine the
> nature of gap?
>
> bests
>
> Said Asma
>
>   ------------------------------
> *De :* Layla Martin-Samos <lmartinsamos at gmail.com>
> *? :* Said Asma <saidasma1987 at yahoo.fr>
> *Cc :* "pw_forum at pwscf.org" <pw_forum at pwscf.org>
> *Envoy? le :* Mercredi 18 avril 2012 15h45
> *Objet :* Re: [Pw_forum] (no subject)
>
> Dear Said, it is not a problem, I think, as increasing the number of atoms
> will fold the Brillouin zone into gamma.
>
> bests
>
> Layla
>
> 2012/4/18 Said Asma <saidasma1987 at yahoo.fr>
>
>
> Dear PWScf Users,
>
> I did the band structure of  BN (zinc blende) with two atoms and I found aindirect
> gap  (like literature) Gamma-X. But when I did it with 8 atoms I found direct
> gap Gamma -Gamma.
>
> Why such a problem occurs?
>
> My input files is as following:
>
>  *With TWO ATOMS:
>
> cat > bn.band.in << EOF
>  &control
>     calculation='bands'
>     pseudo_dir = '$PSEUDO_DIR/',
>     outdir='$TMP_DIR/',
>     prefix='bn'
>  /
>  &system
>     ibrav=  2, celldm(1) = 6.76, nat=  2, ntyp= 2,
>     ecutwfc = 60.0,
>     occupations ='smearing',
>     smearing = 'methfessel-paxton',
>     degauss= 0.03,
>  /
>  &electrons
>                  conv_thr = 1.0d-7 ,
>                  mixing_mode = 'plain' ,
>                  mixing_beta = 0.2 ,
>                  diagonalization = 'david' ,
>  /
> ATOMIC_SPECIES
>  B  10.811  B.pz-vbc.UPF
>  N  14.007  N.pz-vbc.UPF
> ATOMIC_POSITIONS
>   B 0.00 0.00 0.00
>   N 0.25 0.25 0.25
> K_POINTS {crystal_b}
> 5
> 0.5  0.5  0.5  400
> 0    0    0    400
> 1.0  0    0    400
> 0.75 0.75 0    400
> 0    0    0    400
> EOF
> $ECHO "  running the band-structure calculation for bn...\c"
> $PW_COMMAND < bn.band.in > bn.band.out
> check_failure $?
> $ECHO " done"
>
>
>
> *and WITH 8 ATOMS:
>
> cat > bn.band.in << EOF
>  &control
>     calculation='bands'
>     pseudo_dir = '$PSEUDO_DIR/',
>     outdir='$TMP_DIR/',
>     prefix='bn'
>  /
>  &system
>     ibrav= 1, celldm(1) = 6.82, nat=8, ntyp= 2,
>     ecutwfc = 40.0, nbnd = 40,
>     occupations ='smearing',
>     smearing = 'methfessel-paxton',
>     degauss= 0.02,
>  /
>  &electrons
>   conv_thr =  1.0d-7,
>     mixing_beta = 0.2,
>  /
>
> ATOMIC_SPECIES
>  B  10.811  B.pz-vbc.UPF
>  N  14.007  N.pz-vbc.UPF
> ATOMIC_POSITIONS
>  B      0.000     0.000     0.000
>  N      0.250     0.250     0.250
>  B      0.000     0.500     0.500
>  N      0.250     0.750     0.750
>  B      0.500     0.500     0.000
>  N      0.750     0.250     0.750
>  B      0.500     0.000     0.500
>  N      0.750     0.750     0.250
>
> K_POINTS {crystal_b}
> 4
> 0    0    0    40
> 0.5  0    0    40
> 0.5  0.5  0    40
> 0    0    0    40
> EOF
> $ECHO "  running the band-structure calculation for bn...\c"
> $PW_COMMAND < bn.band.in > bn.band.out
> check_failure $?
> $ECHO " done"
>
> Any help would be appreciated.
> Best regards,
> Said Asma
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
>
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From ali.allam2 at hotmail.com  Fri Apr 20 10:09:20 2012
From: ali.allam2 at hotmail.com (Ali ALLAM)
Date: Fri, 20 Apr 2012 10:09:20 +0200
Subject: [Pw_forum] Problem in vc-relax, radial FFT
Message-ID: <BAY154-W371C1368F9E3C195281551DA220@phx.gbl>



Dear all
I want to perform a vc-relax calculation for NbSi2 :
First i use the following input : 

?&CONTROLtitle = 'NbSi2',calculation = 'vc-relax',nstep = 100,etot_conv_thr = 1.d-7,forc_conv_thr = 1.d-5,
tstress = .true.,
prefix = 'NbSi2',
verbosity = 'high',
disk_io = 'low',
tprnfor = .true.,
/
&SYSTEM
celldm(1) = 1.d0,
ibrav = 0, 
nat = 9,
ntyp = 2,
ecutwfc = 30.d0,
ecutrho = 300.d0,
nspin = 1,
occupations = 'smearing',degauss = 0.005d0,
/
&ELECTRONS
conv_thr = 1.d-7,
mixing_beta = 0.1d0,
diagonalization = 'cg',
/
&IONS
ion_dynamics = 'bfgs',
bfgs_ndim = 1,
/
&CELL
cell_dynamics = 'bfgs',
press = 0.d0,
press_conv_thr = 0.200d0,
cell_dofree = 'xyz',
/
ATOMIC_SPECIES
Si 28.0855d0 Si.pbe-n-van.UPF
Nb 92.90638d0 Nb.pbe-nsp-van.UPF

K_POINTS automatic
6 6 1 0 0 0

ATOMIC_POSITIONS crystal
Nb 0.50000 0.00000 0.00000 
Si 0.16578 0.33156 0.00000
Nb 0.00000 0.50000 0.66667 
Si 0.66844 0.83422 0.66667 
Nb 0.50000 0.50000 0.33333 
Si 0.16578 0.83422 0.33333 
Si 0.83422 0.66844 0.00000 
Si 0.33156 0.16578 0.66667 
Si 0.83422 0.16578 0.33333 

CELL_PARAMETERS
9.053677211    0.000000000    0.000000000
0.000000000    9.053677211    0.000000000
0.000000000    0.000000000  12.449514813


During convergence, the error was : Not enough space allocated for radial FFT: try restarting with a larger cell_factor
So, i use a cell_factor = 2 , then the structure was converged, but the cell parameters of the relaxed structure differs so much from the cell-parameters of the begining.
relaxed cell parameters :10.94171211    0.000000000    0.0000000000.000000000    10.94171211    0.0000000000.000000000    0.000000000   9.245414256
I try to decrease ecutwfc for 25 Ry and ecutrho = 200 Ry, and to change the 'smearing' , but always i converge the structure with a big difference between cell_parameters.the difference between cell-parameters is about 20%.
So my question is : What is the real problem in my input ?
Thanks a lot for your helping 
best regards
Ali ALLAMPhysics of materials - 2nd year PhDAix-Marseille UniversityMarseille 13013FRANCE
 		 	   		  
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From max.n.popov at gmail.com  Fri Apr 20 11:03:54 2012
From: max.n.popov at gmail.com (Maxim Popov)
Date: Fri, 20 Apr 2012 11:03:54 +0200
Subject: [Pw_forum] Problem in vc-relax, radial FFT
In-Reply-To: <BAY154-W371C1368F9E3C195281551DA220@phx.gbl>
References: <BAY154-W371C1368F9E3C195281551DA220@phx.gbl>
Message-ID: <CAORFTiH-PT+YrwH2df3zO7OUzPTT62GhHb0WDyQTB8fzNegThA@mail.gmail.com>

Dear Ali,

>
> During convergence, the error was : Not enough space allocated for radial
> FFT: try restarting with a larger cell_factor
> .
> So my question is : What is the real problem in my input ?
>

the real problem in your input is that the initial lattice parameters are
way too far from the equilibrium.
Usually, to use the experimental data as the initial guess for
relax/vc-relax is quite a good idea, and leads
to no troubles.

-- 
Best regards, Max Popov
Ph.D. student
Materials center Leoben (MCL), Leoben, Austria.
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From Lorenzo.Paulatto at impmc.upmc.fr  Fri Apr 20 11:28:48 2012
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Fri, 20 Apr 2012 11:28:48 +0200
Subject: [Pw_forum] Problem in vc-relax, radial FFT
In-Reply-To: <BAY154-W371C1368F9E3C195281551DA220@phx.gbl>
References: <BAY154-W371C1368F9E3C195281551DA220@phx.gbl>
Message-ID: <op.wc14may7xuur8c@linux-qnvk.site>

On Fri, 20 Apr 2012 10:09:20 +0200, Ali ALLAM <ali.allam2 at hotmail.com>
wrote:
> mixing_beta = 0.1d0,diagonalization = 'cg',

These 2 parameters are making you waste a lot of time: use the default
values unless you have some serious reason to change them.

> I try to decrease ecutwfc for 25 Ry and ecutrho = 200 Ry,

Decrease? Why do you think that making convergence worst would improve? I  
assume you tested the pseudopotentials for convergence with respect to  
ecutwfc and ecutrho. If you did not, do it now: set up a small calculation  
for bulk Nb (BCC, alat~6.23bohr) and Silicon (diamond structure,  
alat~10.20bohr) and increase the cutoff until they converge to 0.001Ry or  
best. Then take the higher cutoff of the 2 calculations (very likely the  
Niobium one).

> and to change the 'smearing' ,

Your smearing is very small, especially compared with a number of k-points
which is not so large. I assume you tested it properly for convergence; if  
you did not take any reasonable volume, set smearing='mv' and degauss=0.01  
or 0.02 and try to increase the number of kpoints until the energy  
converges to ~0.001Ry

> but always i converge the structure with a big difference between  
> cell_parameters.the difference between cell-parameters is about 20%.

Why is this a problem? Maybe your initial guess was not very good, where
did you get it from? Why are you relaxing at constant volume instead of  
letting the volume change?

> So my question is : What is the real problem in my input ?

To be honest, I donnot see which is your problem. Maybe your initial
crystal structure in just not very close to the optimal one. Or your  
calcution is not properly converged.

     		


-- 
Lorenzo Paulatto IdR CNRS @ IMPMC/UPMC - Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www.impmc.upmc.fr/~paulatto/
mail:  23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From physics.skgupta at gmail.com  Fri Apr 20 13:48:24 2012
From: physics.skgupta at gmail.com (Sanjeev Gupta)
Date: Fri, 20 Apr 2012 17:18:24 +0530
Subject: [Pw_forum] LDA+U with phonon
Message-ID: <CAB4TLPKEETphffgUs1=ciUV_R-cDaoyNskKgMb3Pjkt-xxYbjw@mail.gmail.com>

Dear PWSCF users.

I would like to know the present status of use LDA+U in phonon calculation.
Further, the problem in rare-earth materials due to f-electron need
justification, how we overcome this issue in phonon calculations?

Please suggest me.
Best Regards
Sanjeev

-- 
*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 lmartinsamos at gmail.com  Fri Apr 20 14:08:29 2012
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Fri, 20 Apr 2012 14:08:29 +0200
Subject: [Pw_forum] LDA+U with phonon
In-Reply-To: <CAB4TLPKEETphffgUs1=ciUV_R-cDaoyNskKgMb3Pjkt-xxYbjw@mail.gmail.com>
References: <CAB4TLPKEETphffgUs1=ciUV_R-cDaoyNskKgMb3Pjkt-xxYbjw@mail.gmail.com>
Message-ID: <CAGCSmJRLZ07FfsDc3Lfp3FW=mv0Q_Z-YxVaHGOuFX1DyphrtcQ@mail.gmail.com>

Dear Sanjeev, for what concerns LDA+U and phonon, there is a version not
public available that needs re-alignement with the main development line.
We would like to do it as soon a s possible, unfortunately all of us are
very busy. Maybe Stefano De Gironcoli could give you a more precise view on
what is going on.

best regards

Layla

2012/4/20 Sanjeev Gupta <physics.skgupta at gmail.com>

> Dear PWSCF users.
>
> I would like to know the present status of use LDA+U in phonon calculation.
> Further, the problem in rare-earth materials due to f-electron need
> justification, how we overcome this issue in phonon calculations?
>
> Please suggest me.
> Best Regards
> Sanjeev
>
> --
> *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
>
>
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From pchen at ion.chem.utk.edu  Fri Apr 20 19:12:03 2012
From: pchen at ion.chem.utk.edu (Peng Chen)
Date: Fri, 20 Apr 2012 13:12:03 -0400
Subject: [Pw_forum] Fe pseudopotential (pslibrary) test failed
Message-ID: <CAP_5U0f-pkm6zHsdSqPLGRMKaX3Bmi9164_jsRwPwH-f5Nx39A@mail.gmail.com>

Dear All,

Recently, I tested Fe.pz-spn-rrkjus.in and Fe.rel-pz-spn-rrkjus.in from
pslibrary. There are two "problems" in the output:

1. the energy in the test with spherical waves is  a little lower than that
from all electron calculation. Is it reasonable?
part of output:
     n l     nl             e AE (Ry)        e PS (Ry)    De AE-PS (Ry)
     1 0     3S   1( 2.00)       -6.87296       -6.87292       -0.00004
     2 1     3P   1( 6.00)       -4.40452       -4.40448       -0.00004
     2 0     4S   1( 2.00)       -0.40342       -0.40341       -0.00001
     3 2     3D   1( 6.00)       -0.56965       -0.56961       -0.00003
     3 1     4P   1( 0.00)       -0.10550       -0.10550       -0.00000

 Cutoff (Ry) :  110.0
                           N = 1       N = 2       N = 3
     E(L=0) =        -6.8963 Ry   -0.4136 Ry   -0.0008 Ry
     E(L=1) =        -4.4514 Ry   -0.1311 Ry    0.0203 Ry
     E(L=2) =        -0.5736 Ry    0.0340 Ry    0.0747 Ry

Here -6.8963 < -6.87296, -4.4514 < -4.40452.

2. For some test configurations, the difference of PS and AE are very
large. And some configuration tests even failed and give error  "from
chargeps : error #         1      negative rho".

     n l     nl             e AE (Ry)        e PS (Ry)    De AE-PS (Ry)
     1 0     3S   1( 2.00)       -9.60696      -12.19076        2.58380
     2 1     3P   1( 6.00)       -7.12183       -7.12183        0.00000
     2 0     4S   1( 0.00)       -2.30301       -2.30301        0.00000
     3 2     3D   1( 5.00)       -3.19807       -0.29435       -2.90371
     3 1     4P   1( 0.00)       -1.76774       -1.76774        0.00000

The inputs for Fe pseudopotential and my test are shown below, I am not
sure if there is something wrong with my test input. Please let me know if
it is not correct.

Fe.pz-spn-rrkjus.in:

&input
   title='Fe',
   zed=26.,
   rel=1,
   config='[Ar] 4s2.0 3d6.0 4p0',
   iswitch=3,
   dft='LDA'
 /
 &inputp
   pseudotype=3,
   file_pseudopw='Fe.pz-spn-rrkjus.UPF',
   author='ADC',
   lloc=-2,
   rcloc=1.8,
   which_augfun='PSQ',
   rmatch_augfun=0.68,
   nlcc=.true.,
   new_core_ps=.true.,
   rcore=0.6,
   tm=.true.
 /
6
3S  1  0  2.00  0.00  1.10  1.30  0.0
4S  2  0  2.00  0.00  0.80  1.40  0.0
3P  2  1  6.00  0.00  1.00  1.30  0.0
4P  3  1  0.00  0.00  1.00  1.60  0.0
3D  3  2  6.00  0.00  1.40  2.00  0.0
3D  3  2  0.00 -0.40  1.40  2.00  0.0

Fe.testpz-spn-rrkjus.in:

 &input
        iswitch=2,

        rel=1,
        zed=26.0,
        config="[Ne] 3s2 3p6 4s2 3d6 4p0"
        dft='LDA',
 /
 &test
        file_pseudo="Fe.pz-spn-rrkjus.UPF",
        nconf=8,
        configts(1)="3s2 3p6 4s2 3d6 4p0",
        configts(2)="3s2 3p6 4s2 3d5 4p0",
        configts(3)="3s2 3p6 4s2 3d4 4p0",
        configts(4)="3s2 3p6 4s2 3d3 4p0",
        configts(5)="3s2 3p6 4s1 3d6 4p0",
        configts(6)="3s2 3p6 4s0 3d6 4p0",
        configts(7)="3s2 3p6 4s0 3d5 4p0",
        configts(8)="3s2 3p6 4s0 3d4 4p0",
       ecutmin=30,ecutmax=110,decut=20
 /

P.S. I didn't find Tb and Dy  pseudopotential  for Quantum Espresso, please
kindly let me know if someone can provide or know  where to find them. I
actually tried to create them using ld1.x, but the result is very bad and
it is frustrating.

-- 
  Best Regards.
        Peng
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From giannozz at democritos.it  Fri Apr 20 23:08:32 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 20 Apr 2012 23:08:32 +0200
Subject: [Pw_forum] Fe pseudopotential (pslibrary) test failed
In-Reply-To: <CAP_5U0f-pkm6zHsdSqPLGRMKaX3Bmi9164_jsRwPwH-f5Nx39A@mail.gmail.com>
References: <CAP_5U0f-pkm6zHsdSqPLGRMKaX3Bmi9164_jsRwPwH-f5Nx39A@mail.gmail.com>
Message-ID: <689E3F35-AE0C-4CCE-9CE8-0AEDF8D027AD@democritos.it>


On Apr 20, 2012, at 19:12 , Peng Chen wrote:

> the energy in the test with spherical waves is  a little lower than
> that from all electron calculation. Is it reasonable?

I also noticed this. It only happens when you have deep d or f states.
I have never been able to figure out why.

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 dalcorso at sissa.it  Sat Apr 21 16:21:50 2012
From: dalcorso at sissa.it (Andrea Dal Corso)
Date: Sat, 21 Apr 2012 16:21:50 +0200
Subject: [Pw_forum] Fe pseudopotential (pslibrary) test failed
In-Reply-To: <CAP_5U0f-pkm6zHsdSqPLGRMKaX3Bmi9164_jsRwPwH-f5Nx39A@mail.gmail.com>
References: <CAP_5U0f-pkm6zHsdSqPLGRMKaX3Bmi9164_jsRwPwH-f5Nx39A@mail.gmail.com>
Message-ID: <1335018110.2132.9.camel@localhost.localdomain>

On Fri, 2012-04-20 at 13:12 -0400, Peng Chen wrote:
> Dear All,
> 
> 
> Recently, I tested Fe.pz-spn-rrkjus.in and Fe.rel-pz-spn-rrkjus.in
> from pslibrary. There are two "problems" in the output:
> 
> 
> 1. the energy in the test with spherical waves is  a little lower than
> that from all electron calculation. Is it reasonable?   
> part of output:
>      n l     nl             e AE (Ry)        e PS (Ry)    De AE-PS
> (Ry)
>      1 0     3S   1( 2.00)       -6.87296       -6.87292
> -0.00004
>      2 1     3P   1( 6.00)       -4.40452       -4.40448
> -0.00004
>      2 0     4S   1( 2.00)       -0.40342       -0.40341
> -0.00001
>      3 2     3D   1( 6.00)       -0.56965       -0.56961
> -0.00003
>      3 1     4P   1( 0.00)       -0.10550       -0.10550
> -0.00000
> 
> 
>  Cutoff (Ry) :  110.0
>                            N = 1       N = 2       N = 3
>      E(L=0) =        -6.8963 Ry   -0.4136 Ry   -0.0008 Ry
>      E(L=1) =        -4.4514 Ry   -0.1311 Ry    0.0203 Ry
>      E(L=2) =        -0.5736 Ry    0.0340 Ry    0.0747 Ry
> 
> 
> Here -6.8963 < -6.87296, -4.4514 < -4.40452.
> 
> 
> 2. For some test configurations, the difference of PS and AE are very
> large. And some configuration tests even failed and give error  "from
> chargeps : error #         1      negative rho".
> 
> 
>      n l     nl             e AE (Ry)        e PS (Ry)    De AE-PS
> (Ry)
>      1 0     3S   1( 2.00)       -9.60696      -12.19076
>  2.58380
>      2 1     3P   1( 6.00)       -7.12183       -7.12183
>  0.00000
>      2 0     4S   1( 0.00)       -2.30301       -2.30301
>  0.00000
>      3 2     3D   1( 5.00)       -3.19807       -0.29435
> -2.90371
>      3 1     4P   1( 0.00)       -1.76774       -1.76774
>  0.00000
>  
> The inputs for Fe pseudopotential and my test are shown below, I am
> not sure if there is something wrong with my test input. Please let me
> know if it is not correct.
> 
Thank you for reporting this. Actually the Fe PP was tested for
configurations with 6 or 7 d electrons. Configurations with less
electrons in the d shell are not converging. This seems to be due to the
3p core radius. Decreasing it to 1.0 or 0.9 seems to work better
although the wavefunction cut-off increases, and the PP must be tested
again. Note however that for any PP, if your test configuration is too
far in energy from the configuration used to generate the PP, the test
will fail.


> 
> Fe.pz-spn-rrkjus.in:
> 
> 
> &input
>    title='Fe',
>    zed=26.,
>    rel=1,
>    config='[Ar] 4s2.0 3d6.0 4p0',
>    iswitch=3,
>    dft='LDA'
>  /
>  &inputp
>    pseudotype=3,
>    file_pseudopw='Fe.pz-spn-rrkjus.UPF',
>    author='ADC',
>    lloc=-2,
>    rcloc=1.8,
>    which_augfun='PSQ',
>    rmatch_augfun=0.68,
>    nlcc=.true.,
>    new_core_ps=.true.,
>    rcore=0.6,
>    tm=.true.
>  /
> 6
> 3S  1  0  2.00  0.00  1.10  1.30  0.0
> 4S  2  0  2.00  0.00  0.80  1.40  0.0
> 3P  2  1  6.00  0.00  1.00  1.30  0.0
> 4P  3  1  0.00  0.00  1.00  1.60  0.0
> 3D  3  2  6.00  0.00  1.40  2.00  0.0
> 3D  3  2  0.00 -0.40  1.40  2.00  0.0
> 
> 
> Fe.testpz-spn-rrkjus.in:
> 
> 
>  &input
>         iswitch=2,
> 
> 
>         rel=1,
>         zed=26.0,
>         config="[Ne] 3s2 3p6 4s2 3d6 4p0"
>         dft='LDA',
>  /
>  &test
>         file_pseudo="Fe.pz-spn-rrkjus.UPF",
>         nconf=8,
>         configts(1)="3s2 3p6 4s2 3d6 4p0",
>         configts(2)="3s2 3p6 4s2 3d5 4p0",
>         configts(3)="3s2 3p6 4s2 3d4 4p0",
>         configts(4)="3s2 3p6 4s2 3d3 4p0",
>         configts(5)="3s2 3p6 4s1 3d6 4p0",
>         configts(6)="3s2 3p6 4s0 3d6 4p0",
>         configts(7)="3s2 3p6 4s0 3d5 4p0",
>         configts(8)="3s2 3p6 4s0 3d4 4p0",
>        ecutmin=30,ecutmax=110,decut=20
>  /
> 
> 
> P.S. I didn't find Tb and Dy  pseudopotential  for Quantum Espresso,
> please kindly let me know if someone can provide or know  where to
> find them. I actually tried to create them using ld1.x, but the result
> is very bad and it is frustrating. 
> 
> 
We are still trying to tune the spd PPs. Those for f electron are not
yet available, at least within pslibrary.

HTH,

Andrea


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



From ytaghipour at aeoi.org.ir  Sun Apr 22 07:41:46 2012
From: ytaghipour at aeoi.org.ir (Yavar Taghipour Azar)
Date: Sun, 22 Apr 2012 10:11:46 +0430
Subject: [Pw_forum] on the way of approximating a large slab
References: <84834F3F94064E63B61958E8D2F8C3D9@yavarpc>
	<4F8FE82C.30804@mater.unimib.it>
Message-ID: <69E7D1D84C8847819A072B844CC25759@yavarpc>

Dear Guido,

Thanks for your consideration and very instructive comments.



Bests.
-------------------------------------------
Yavar Taghipour
PhD Student
Physics Group, AEOI
Tehran-Iran

Email: ytaghipour at aeoi.org.ir
Phone: +98 (0) 21 82064556
-----------------------------------------------------------
----- Original Message ----- 
From: "Guido Fratesi" <fratesi at mater.unimib.it>
To: <pw_forum at pwscf.org>
Sent: Thursday, April 19, 2012 2:55 PM
Subject: Re: [Pw_forum] on the way of approximating a large slab


> Dear Yavar,
>
> I hope a comment on your question (unfortunately not an answer) could be
> helpful.
> Notice that the properties of the adsorbed species may converge faster
> than those of the clean surface alone. So, if you are interested in the
> distance of the molecule from the surface, or the adsorption energy,
> these may be described with a thin slab better than the interlayer
> relaxation or the surface energy of the clean substrate (or even worse,
> the surface electronic structure). You could practice by adsorbing a
> smaller molecule or a fragment. I'd expect that much less than 14 layers
> could be sufficient rather often.
>
> (then, I remember about an "Effective Screening Medium Method"
> implemented in QE, there's also an example, but I don't know much about 
> it)
>
> HTH
> Guido
>
> Il 04/19/2012 11:57 AM, Yavar Taghipour Azar ha scritto:
>> Dear QE users
>>
>> I want to model adsorption of a large molecule on a relatively large
>> slab. After test convergence on the number of layers for clean surface,
>> I found 14 layers are needed, but for well-known technical reasons (time
>> and memory limitation), I am thinking on how can one take into account
>> the atoms of just some 3 topmost layers of the slab, and the effects of
>> the remaining layers of the slab as an external potential.
>>
>> Is it a meaningful question and what about its feasibility in the
>> context of QE?
>>
>> Thanks in advance.
>>
>> -------------------------------------------
>> Yavar Taghipour
>> PhD Student
>> Physics Group, AEOI
>> Tehran-Iran
>> Email: ytaghipour at aeoi.org.ir <mailto:ytaghipour at aeoi.org.ir>
>> Phone: +98 (0) 21 82064556
>> -----------------------------------------------------------
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
> -- 
> Guido Fratesi
>
> Dipartimento di Scienza dei Materiali
> Universita` degli Studi di Milano-Bicocca
> via Cozzi 53, 20125 Milano, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
> 




From farzad_c81 at yahoo.com  Sun Apr 22 10:44:16 2012
From: farzad_c81 at yahoo.com (Farzad Molani)
Date: Sun, 22 Apr 2012 01:44:16 -0700 (PDT)
Subject: [Pw_forum] mp vs mv
Message-ID: <1335084256.8544.YahooMailClassic@web125903.mail.ne1.yahoo.com>

Hi pwscf users,
My system is consists of boron, nitrogen and carbon, when I want to get the best structure for my systems, I get different results from mp-smearing and mv-smearing, you suppose I have a, b and c structures. When I used?mv -smearing I get this trend for stability a>b>c but, from mp I get this trend c>b>a why? which of them is true??
thanks in advance.

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 nicola.marzari at epfl.ch  Sun Apr 22 12:28:44 2012
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Sun, 22 Apr 2012 12:28:44 +0200
Subject: [Pw_forum] mp vs mv
In-Reply-To: <1335084256.8544.YahooMailClassic@web125903.mail.ne1.yahoo.com>
References: <1335084256.8544.YahooMailClassic@web125903.mail.ne1.yahoo.com>
Message-ID: <4F93DD5C.4040707@epfl.ch>



Both should give roughly similar results, so either your input
is different in the two cases, or you are using a very very large
smearing, or in some of the calculations something went wrong.


nicola

On 22/04/2012 10:44, Farzad Molani wrote:
> Hi pwscf users,
> My system is consists of boron, nitrogen and carbon, when I want to get
> the best structure for my systems, I get different results from
> mp-smearing and mv-smearing, you suppose I have a, b and c structures.
> When I used mv -smearing I get this trend for stability a>b>c but, from
> mp I get this trend c>b>a why? which of them is true?
> thanks in advance.
>
> 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


-- 

----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL

From farzad_c81 at yahoo.com  Sun Apr 22 12:40:57 2012
From: farzad_c81 at yahoo.com (Farzad Molani)
Date: Sun, 22 Apr 2012 03:40:57 -0700 (PDT)
Subject: [Pw_forum] mp vs mv
Message-ID: <1335091257.58562.YahooMailClassic@web125906.mail.ne1.yahoo.com>

Hi,
in both cases?a, b and c are semilar, just smearing is different, in both case I used 0.01 for smearing. so why I get differnt results for total energy?

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 giuseppe.mattioli at ism.cnr.it  Sun Apr 22 18:57:02 2012
From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli)
Date: Sun, 22 Apr 2012 18:57:02 +0200
Subject: [Pw_forum] XSPECTRA calculations of molecules
Message-ID: <20120422185702.4bawqft9c0ss0s4w@webmail.sic.rm.cnr.it>


Dear all
I've two questions regarding XSPECTRA calculations of molecules. Can I  
safely compare intensities related to different scattering atoms (same  
species, e.g., carbon)? Is there any particular reason for which I  
should not perform XSPECTRA calculations on the top of hybrid  
calculations?
Thanks in advance

Giuseppe

Giuseppe Mattioli
ISM-CNR
Italy



From akohlmey at gmail.com  Sun Apr 22 19:55:16 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Sun, 22 Apr 2012 13:55:16 -0400
Subject: [Pw_forum] mp vs mv
In-Reply-To: <1335091257.58562.YahooMailClassic@web125906.mail.ne1.yahoo.com>
References: <1335091257.58562.YahooMailClassic@web125906.mail.ne1.yahoo.com>
Message-ID: <CADTmJ6GhSjkSiLXjrV7Qrgk=7YK6jqNXzB-ZA-ZdjKV31Xhj3Q@mail.gmail.com>

On Sun, Apr 22, 2012 at 6:40 AM, Farzad Molani <farzad_c81 at yahoo.com> wrote:

> Hi,
> in both cases a, b and c are semilar, just smearing is different, in both
> case I used 0.01 for smearing. so why I get differnt results for total
> energy?
>

are your calculations converged with respect to the number of k-points?

axel.



>
> 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
>
>


-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com  http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.
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From pmoreira at ifi.unicamp.br  Sat Apr 21 18:07:43 2012
From: pmoreira at ifi.unicamp.br (Pedro Augusto F. P. Moreira)
Date: Sat, 21 Apr 2012 13:07:43 -0300
Subject: [Pw_forum] Home page: problem to load
Message-ID: <4F92DB4F.8060901@ifi.unicamp.br>

      Dear,

is there any problem with quantum-espresso.org site? I cannot load it.

  Thanks,

  Pedro

-- 
Pedro Moreira

IFGW - Unicamp - Brazil


From faccin.giovani at gmail.com  Sun Apr 22 22:16:01 2012
From: faccin.giovani at gmail.com (Giovani Faccin)
Date: Sun, 22 Apr 2012 16:16:01 -0400
Subject: [Pw_forum] Home page: problem to load
In-Reply-To: <4F92DB4F.8060901@ifi.unicamp.br>
References: <4F92DB4F.8060901@ifi.unicamp.br>
Message-ID: <CAK-VqZB39S_4hdaiMMmSgxR==W=u1MX2em1DBu0KdisSKW=CyA@mail.gmail.com>

Pedro,

I had the same problem back on Saturday. Right now it's working fine, tough.

Giovani Faccin
UFMS / Brazil


2012/4/21 Pedro Augusto F. P. Moreira <pmoreira at ifi.unicamp.br>

>      Dear,
>
> is there any problem with quantum-espresso.org site? I cannot load it.
>
>  Thanks,
>
>  Pedro
>
> --
> Pedro Moreira
>
> IFGW - Unicamp - Brazil
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From farzad_c81 at yahoo.com  Mon Apr 23 08:19:41 2012
From: farzad_c81 at yahoo.com (Farzad Molani)
Date: Sun, 22 Apr 2012 23:19:41 -0700 (PDT)
Subject: [Pw_forum] Fw: Re:  mp vs mv
Message-ID: <1335161981.15595.YahooMailClassic@web125905.mail.ne1.yahoo.com>








Hi Dr. Axel Kohlmeyer,
Yes, I converged my system respect to k-point. for differnt configrations?I used same K-point (119-111).
thank you for your cooperation.

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:/

--- On Sun, 4/22/12, Axel Kohlmeyer <akohlmey at gmail.com> wrote:


From: Axel Kohlmeyer <akohlmey at gmail.com>
Subject: Re: [Pw_forum] mp vs mv
To: "Farzad Molani" <farzad_c81 at yahoo.com>
Cc: "pwscf" <pw_forum at pwscf.org>
Date: Sunday, April 22, 2012, 10:25 PM





On Sun, Apr 22, 2012 at 6:40 AM, Farzad Molani <farzad_c81 at yahoo.com> wrote:






Hi,
in both cases?a, b and c are semilar, just smearing is different, in both case I used 0.01 for smearing. so why I get differnt results for total energy?



are your calculations converged with respect to the number of k-points?


axel.


?






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





-- 
Dr. Axel Kohlmeyer? ?
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.
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From pasianot at cnea.gov.ar  Mon Apr 23 13:59:32 2012
From: pasianot at cnea.gov.ar (R.C.Pasianot)
Date: Mon, 23 Apr 2012 08:59:32 -0300 (ART)
Subject: [Pw_forum] Testing subscription
In-Reply-To: <20111110064214.Horde.FlLwUh8V4mxOu2Q2iwfjf4A@webmail.sissa.it>
References: <1320902478.53447.YahooMailNeo@web28507.mail.ukl.yahoo.com>
	<20111110064214.Horde.FlLwUh8V4mxOu2Q2iwfjf4A@webmail.sissa.it>
Message-ID: <Pine.LNX.4.64.1204230853170.3196@tdmc6>


  Hello

  Please disregard this if you're not the list administrator.
  Since some time ago I stopped receiving posts to the list, should
  I re-subscribe ?.
  Thanks for your attention,

  Roberto


From pmoreira at ifi.unicamp.br  Mon Apr 23 16:34:48 2012
From: pmoreira at ifi.unicamp.br (Pedro Augusto F. P. Moreira)
Date: Mon, 23 Apr 2012 11:34:48 -0300
Subject: [Pw_forum] Home page: problem to load
In-Reply-To: <CAK-VqZB39S_4hdaiMMmSgxR==W=u1MX2em1DBu0KdisSKW=CyA@mail.gmail.com>
References: <4F92DB4F.8060901@ifi.unicamp.br>
	<CAK-VqZB39S_4hdaiMMmSgxR==W=u1MX2em1DBu0KdisSKW=CyA@mail.gmail.com>
Message-ID: <4F956888.5050306@ifi.unicamp.br>

  Thanks. I think they were updating it.

  Pedro

Em 22-04-2012 17:16, Giovani Faccin escreveu:
> Pedro,
>
> I had the same problem back on Saturday. Right now it's working fine, 
> tough.
>
> Giovani Faccin
> UFMS / Brazil
>
>
> 2012/4/21 Pedro Augusto F. P. Moreira <pmoreira at ifi.unicamp.br 
> <mailto:pmoreira at ifi.unicamp.br>>
>
>          Dear,
>
>     is there any problem with quantum-espresso.org
>     <http://quantum-espresso.org> site? I cannot load it.
>
>      Thanks,
>
>      Pedro
>
>     --
>     Pedro Moreira
>
>     IFGW - Unicamp - Brazil
>
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>

-- 
Pedro Moreira

IFGW - Unicamp - Brazil

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From meghdad_saeedian at yahoo.com  Mon Apr 23 19:13:57 2012
From: meghdad_saeedian at yahoo.com (meghdad saeedian)
Date: Mon, 23 Apr 2012 10:13:57 -0700 (PDT)
Subject: [Pw_forum] using Octave or GDIS to make the surface
Message-ID: <1335201237.89687.YahooMailClassic@web161405.mail.bf1.yahoo.com>

Dear All
?
I want to make [1010]?the surface from the?ZnO (hegzagonal) unit cell (the plane which contain c and b parameters). ?I?have installed the?Octave and GDIS softwares,I but can not use them to make this surface.
can anyone guide me?
?
Thanx in advance
?
Meghdad. Saeedian
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From masoudnahali at gmail.com  Tue Apr 24 10:26:26 2012
From: masoudnahali at gmail.com (m)
Date: Tue, 24 Apr 2012 12:56:26 +0430
Subject: [Pw_forum] using Octave or GDIS to make the surface
Message-ID: <CAM-1hSusPxy0A828kkYRrtZ-mygE0RQzJ7GTwUwedWhiRzgyGA@mail.gmail.com>

Dear Meghdad

Not bad doing it with a pencil, a paper, and may be a simple modal once in
your life ! Best Wishes

ps.
please sign your letter with your affiliation. many thanks.



:)


m



----------------------------------------
Masoud Nahali, Ph. D Student
International School for Advanced Studies (SISSA)
Sharif University of Technology



On Tue, Apr 24, 2012 at 12:15 PM, meghdad saeedian wrote:

>
>
> Dear All
> ?
> I want to make [1010]?the surface from the?ZnO (hegzagonal) unit cell (the
> plane which contain c and b parameters). ?I?have installed the?Octave and
> GDIS softwares,I but can not use them to make this surface.
> can anyone guide me?
> ?
> Thanx in advance
> ?
> Meghdad. Saeedian
>
>
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From lmartinsamos at gmail.com  Tue Apr 24 13:27:04 2012
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Tue, 24 Apr 2012 13:27:04 +0200
Subject: [Pw_forum] Testing subscription
In-Reply-To: <Pine.LNX.4.64.1204230853170.3196@tdmc6>
References: <1320902478.53447.YahooMailNeo@web28507.mail.ukl.yahoo.com>
	<20111110064214.Horde.FlLwUh8V4mxOu2Q2iwfjf4A@webmail.sissa.it>
	<Pine.LNX.4.64.1204230853170.3196@tdmc6>
Message-ID: <CAGCSmJTmdYSEJc2EUZv0n6Kiyb8j1GpaaupfcW1oH3iDutRSmg@mail.gmail.com>

Dear Roberto, we have controlled the server and apparently there is nothing
strange with your subscription to pw_forum. The server indicates that the
emails are sent to you. Maybe you could control on your side if your server
is considering the emails as spam.

keep us informed

best regards

Layla and Moreno

2012/4/23 R.C.Pasianot <pasianot at cnea.gov.ar>

>
>  Hello
>
>  Please disregard this if you're not the list administrator.
>  Since some time ago I stopped receiving posts to the list, should
>  I re-subscribe ?.
>  Thanks for your attention,
>
>  Roberto
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From meghdad_saeedian at yahoo.com  Tue Apr 24 15:25:09 2012
From: meghdad_saeedian at yahoo.com (meghdad saeedian)
Date: Tue, 24 Apr 2012 06:25:09 -0700 (PDT)
Subject: [Pw_forum] using Octave or GDIS to make the surface
In-Reply-To: <CAM-1hSusPxy0A828kkYRrtZ-mygE0RQzJ7GTwUwedWhiRzgyGA@mail.gmail.com>
Message-ID: <1335273909.73617.YahooMailClassic@web161403.mail.bf1.yahoo.com>


Dear Masoud
Thanks :)
?
Meghdad Saeedian
MSc graduated from the University Of Tehran Departemant Of Physics 

--- On Tue, 4/24/12, m <masoudnahali at gmail.com> wrote:

From: m <masoudnahali at gmail.com>
Subject: Re: [Pw_forum] using Octave or GDIS to make the surface
To: pw_forum at pwscf.org
Date: Tuesday, April 24, 2012, 12:56 PM


Dear?Meghdad
Not bad doing it with a pencil, a paper, and may be a simple modal once in your life ! Best Wishes
ps.please sign your letter with your?affiliation. many thanks.


? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? :)

? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? m
?


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

Masoud Nahali, Ph. D Student
International School for Advanced Studies (SISSA)
Sharif University of Technology




On Tue, Apr 24, 2012 at 12:15 PM,?meghdad saeedian?wrote:


? ??

Dear All

?

I want to make [1010]?the surface from the?ZnO (hegzagonal) unit cell (the plane which contain c and b parameters). ?I?have installed the?Octave and GDIS softwares,I but can not use them to make this surface.

can anyone guide me?

?

Thanx in advance

?

Meghdad. Saeedian





-----Inline Attachment Follows-----

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Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
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From avallabh at purdue.edu  Wed Apr 25 08:10:33 2012
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Wed, 25 Apr 2012 02:10:33 -0400 (EDT)
Subject: [Pw_forum] query on kpoints.x
In-Reply-To: <1441868817.144717.1335333836715.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <302199868.144731.1335334233685.JavaMail.root@mailhub016.itcs.purdue.edu>

Dear users,

            I want to know whether the format for k points output by kpoints.x is tpiba or not ? 


Thanks
Ajit

From d.tiana at bath.ac.uk  Wed Apr 25 09:43:54 2012
From: d.tiana at bath.ac.uk (Davide Tiana)
Date: Wed, 25 Apr 2012 08:43:54 +0100
Subject: [Pw_forum] Contents of Pw_forum Digest, Vol 58,
 Issue 41Re: using Octave or GDIS to make the surface (m)
In-Reply-To: <mailman.1.1335339370.4354.pw_forum@pwscf.org>
References: <mailman.1.1335339370.4354.pw_forum@pwscf.org>
Message-ID: <20120425084354.Horde.WNjfRqIjMRlPl6s6ksiVkiA@webmail.bath.ac.uk>

Agree and, by the way, I always thought this was the Quantum Espresso  
forum not the Octave or "the how to calculate a surface" one

:-)

>
> Message: 1
> Date: Tue, 24 Apr 2012 12:56:26 +0430
> From: m <masoudnahali at gmail.com>
> Subject: Re: [Pw_forum] using Octave or GDIS to make the surface
> To: pw_forum at pwscf.org
> Message-ID:
> 	<CAM-1hSusPxy0A828kkYRrtZ-mygE0RQzJ7GTwUwedWhiRzgyGA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Meghdad
>
> Not bad doing it with a pencil, a paper, and may be a simple modal once in
> your life ! Best Wishes
>
> ps.
> please sign your letter with your affiliation. many thanks.
>
>
>
> :)
>
>
> m
>
>
>
> ----------------------------------------
> Masoud Nahali, Ph. D Student
> International School for Advanced Studies (SISSA)
> Sharif University of Technology
>
>
>
> On Tue, Apr 24, 2012 at 12:15 PM, meghdad saeedian wrote:
>
>>
>>
>> Dear All
>> ?
>> I want to make [1010]?the surface from the?ZnO (hegzagonal) unit cell (the
>> plane which contain c and b parameters). ?I?have installed the?Octave and
>> GDIS softwares,I but can not use them to make this surface.
>> can anyone guide me?
>> ?
>> Thanx in advance
>> ?
>> Meghdad. Saeedian
>>
>>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:  
> http://www.democritos.it/pipermail/pw_forum/attachments/20120424/e3959df9/attachment.html
>
> ------------------------------
>
> Message: 2
> Date: Tue, 24 Apr 2012 13:27:04 +0200
> From: Layla Martin-Samos <lmartinsamos at gmail.com>
> Subject: Re: [Pw_forum] Testing subscription
> To: pasianot at cnea.gov.ar
> Cc: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> 	<CAGCSmJTmdYSEJc2EUZv0n6Kiyb8j1GpaaupfcW1oH3iDutRSmg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Roberto, we have controlled the server and apparently there is nothing
> strange with your subscription to pw_forum. The server indicates that the
> emails are sent to you. Maybe you could control on your side if your server
> is considering the emails as spam.
>
> keep us informed
>
> best regards
>
> Layla and Moreno
>
> 2012/4/23 R.C.Pasianot <pasianot at cnea.gov.ar>
>
>>
>>  Hello
>>
>>  Please disregard this if you're not the list administrator.
>>  Since some time ago I stopped receiving posts to the list, should
>>  I re-subscribe ?.
>>  Thanks for your attention,
>>
>>  Roberto
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:  
> http://www.democritos.it/pipermail/pw_forum/attachments/20120424/cc0a44bb/attachment-0001.htm
>
> ------------------------------
>
> Message: 3
> Date: Tue, 24 Apr 2012 06:25:09 -0700 (PDT)
> From: meghdad saeedian <meghdad_saeedian at yahoo.com>
> Subject: Re: [Pw_forum] using Octave or GDIS to make the surface
> To: PWscf <pw_forum at pwscf.org>
> Message-ID:
> 	<1335273909.73617.YahooMailClassic at web161403.mail.bf1.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Dear Masoud
> Thanks :)
> ?
> Meghdad Saeedian
> MSc graduated from the University Of Tehran Departemant Of Physics
>
> --- On Tue, 4/24/12, m <masoudnahali at gmail.com> wrote:
>
> From: m <masoudnahali at gmail.com>
> Subject: Re: [Pw_forum] using Octave or GDIS to make the surface
> To: pw_forum at pwscf.org
> Date: Tuesday, April 24, 2012, 12:56 PM
>
>
> Dear?Meghdad
> Not bad doing it with a pencil, a paper, and may be a simple modal  
> once in your life ! Best Wishes
> ps.please sign your letter with your?affiliation. many thanks.
>
>
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?  
> ? ? ? ? :)
>
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? m
> ?
>
>
> ----------------------------------------
>
> Masoud Nahali, Ph. D Student
> International School for Advanced Studies (SISSA)
> Sharif University of Technology
>
>
>
>
> On Tue, Apr 24, 2012 at 12:15 PM,?meghdad saeedian?wrote:
>
>
> ? ??
>
> Dear All
>
> ?
>
> I want to make [1010]?the surface from the?ZnO (hegzagonal) unit  
> cell (the plane which contain c and b parameters). ?I?have installed  
> the?Octave and GDIS softwares,I but can not use them to make this  
> surface.
>
> can anyone guide me?
>
> ?
>
> Thanx in advance
>
> ?
>
> Meghdad. Saeedian
>
>
>
>
>
> -----Inline Attachment Follows-----
>
> _______________________________________________
> 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/20120424/3340a6cc/attachment-0001.htm
>
> ------------------------------
>
>
>
>
> End of Pw_forum Digest, Vol 58, Issue 41
> ****************************************




From saidasma1987 at yahoo.fr  Wed Apr 25 18:07:54 2012
From: saidasma1987 at yahoo.fr (Said Asma)
Date: Wed, 25 Apr 2012 17:07:54 +0100 (BST)
Subject: [Pw_forum] Error band structure
In-Reply-To: <1334828257.36755.YahooMailNeo@web29009.mail.ird.yahoo.com>
References: <mailman.2211.1334762790.9401.pw_forum@pwscf.org>
	<1334828257.36755.YahooMailNeo@web29009.mail.ird.yahoo.com>
Message-ID: <1335370074.23583.YahooMailNeo@web29007.mail.ird.yahoo.com>





?Dear Giannozzi ,

I did the band structure of? BN (zinc blende) with two atoms and I found a indirect gap? (like literature) Gamma-X. But when I did it with 8 atoms I found direct gap Gamma -Gamma.
Normally if we change (nat = 2, ibrav = 2) to (nat = 8, ibrav = 1),we find the same nature of gap (the unit cell has changed to simple cubic).
If such we have the composition B0.25Ga0.75N how we can determine the nature of gap?

?Why such a problem occurs?

?My input files is as following:

? *With TWO ATOMS:

?cat > bn.band.in << EOF
? &control
? ?  calculation='bands'
?
 ?  pseudo_dir = '$PSEUDO_DIR/',
? ?  outdir='$TMP_DIR/',
? ?  prefix='bn'
? /
? &system
? ?  ibrav=? 2, celldm(1) = 6.76, nat=? 2, ntyp= 2,
? ?  ecutwfc = 60.0,
? ?  occupations ='smearing',
? ?  smearing = 'methfessel-paxton',
? ?  degauss= 0.03,
? /
? &electrons
? ? ? ? ? ? ? ? ? conv_thr = 1.0d-7 ,
? ? ? ? ? ? ? ? ? mixing_mode = 'plain' ,
? ? ? ? ? ? ? ? ? mixing_beta = 0.2 ,
? ? ? ? ? ? ? ? ? diagonalization = 'david' ,
? /
ATOMIC_SPECIES
? B? 10.811? B.pz-vbc.UPF
? N? 14.007? N.pz-vbc.UPF
ATOMIC_POSITIONS
?  B 0.00 0.00 0.00
?  N 0.25 0.25 0.25
K_POINTS {crystal_b}
?5
0.5? 0.5? 0.5? 400
0? ? 0? ? 0? ? 400
1.0? 0? ? 0? ? 400
0.75 0.75 0? ? 400
0? ? 0? ? 0? ? 400
EOF
$ECHO "? running the band-structure calculation for bn...\c"
$PW_COMMAND < bn.band.in > bn.band.out
check_failure $?
$ECHO " done"



*and WITH 8 ATOMS:

?cat > bn.band.in << EOF
? &control
? ?  calculation='bands'
? ?  pseudo_dir = '$PSEUDO_DIR/',
? ?  outdir='$TMP_DIR/',
? ?  prefix='bn'
? /
?&system
? ?  ibrav= 1, celldm(1) = 6.82, nat=8, ntyp= 2,
? ?  ecutwfc = 40.0, nbnd = 40,
? ?  occupations ='smearing',
? ?  smearing = 'methfessel-paxton',
? ?  degauss= 0.02,
? /
?
 &electrons
?  conv_thr =? 1.0d-7,
? ?  mixing_beta = 0.2,
? /

ATOMIC_SPECIES
? B? 10.811? B.pz-vbc.UPF
? N? 14.007? N.pz-vbc.UPF
ATOMIC_POSITIONS
? B? ? ? 0.000? ?  0.000? ?  0.000
? N? ? ? 0.250? ?  0.250? ?  0.250
? B? ? ? 0.000? ?  0.500? ?  0.500
? N? ? ? 0.250? ?  0.750? ?  0.750
? B? ? ? 0.500? ?  0.500? ?  0.000
? N? ? ? 0.750? ?  0.250? ?  0.750
? B? ? ? 0.500? ?  0.000? ?  0.500
? N? ? ? 0.750? ?  0.750? ?  0.250

?K_POINTS {crystal_b}
?4
?0? ? 0? ? 0? ?
 40
?0.5? 0? ? 0? ? 40
?0.5? 0.5? 0? ? 40
?0? ? 0? ? 0? ? 40
?EOF
?$ECHO "? running the band-structure calculation for bn...\c"
?$PW_COMMAND < bn.band.in > bn.band.out
?check_failure $?
?$ECHO " done"

?Any help would be appreciated.
?Best regards,
?Said Asma



bests

Said Asma



________________________________
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From degironc at sissa.it  Wed Apr 25 19:05:34 2012
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 25 Apr 2012 19:05:34 +0200
Subject: [Pw_forum] Error band structure
In-Reply-To: <1335370074.23583.YahooMailNeo@web29007.mail.ird.yahoo.com>
References: <mailman.2211.1334762790.9401.pw_forum@pwscf.org>	<1334828257.36755.YahooMailNeo@web29009.mail.ird.yahoo.com>
	<1335370074.23583.YahooMailNeo@web29007.mail.ird.yahoo.com>
Message-ID: <4F982EDE.9060901@sissa.it>

Dear Said
   when you use a supercell many k-point of the original BZ are folded 
in the same point of the supercell BZ.  If you use a SC supercell for a 
crystal that would have an FCC Bravais lattice (using a cell which has a 
4 times larger volume) 4 kpoints of the FCC BZ are folded in any point 
of the SC BZ.
   In particular Gamma plus the 3 X points of the FCC BZ are folded into 
Gamma of the SC.
   A good exercise would be to compare the band structure of the two 
equivalent systems and find the correspondence of each band of the FCC 
in the band structure of the SC. You should find perfect matching.
   Best regards,

stefano


On 04/25/2012 06:07 PM, Said Asma wrote:
>
>
>
>   Dear Giannozzi ,
>
> I did the band structure of  BN (zinc blende) with two atoms and I found a indirect gap  (like literature) Gamma-X. But when I did it with 8 atoms I found direct gap Gamma -Gamma.
> Normally if we change (nat = 2, ibrav = 2) to (nat = 8, ibrav = 1),we find the same nature of gap (the unit cell has changed to simple cubic).
> If such we have the composition B0.25Ga0.75N how we can determine the nature of gap?
>
>   Why such a problem occurs?
>
>   My input files is as following:
>
>    *With TWO ATOMS:
>
>   cat>  bn.band.in<<  EOF
>    &control
>       calculation='bands'
>   
>      pseudo_dir = '$PSEUDO_DIR/',
>       outdir='$TMP_DIR/',
>       prefix='bn'
>    /
>    &system
>       ibrav=  2, celldm(1) = 6.76, nat=  2, ntyp= 2,
>       ecutwfc = 60.0,
>       occupations ='smearing',
>       smearing = 'methfessel-paxton',
>       degauss= 0.03,
>    /
>    &electrons
>                    conv_thr = 1.0d-7 ,
>                    mixing_mode = 'plain' ,
>                    mixing_beta = 0.2 ,
>                    diagonalization = 'david' ,
>    /
> ATOMIC_SPECIES
>    B  10.811  B.pz-vbc.UPF
>    N  14.007  N.pz-vbc.UPF
> ATOMIC_POSITIONS
>     B 0.00 0.00 0.00
>     N 0.25 0.25 0.25
> K_POINTS {crystal_b}
>   5
> 0.5  0.5  0.5  400
> 0    0    0    400
> 1.0  0    0    400
> 0.75 0.75 0    400
> 0    0    0    400
> EOF
> $ECHO "  running the band-structure calculation for bn...\c"
> $PW_COMMAND<  bn.band.in>  bn.band.out
> check_failure $?
> $ECHO " done"
>
>
>
> *and WITH 8 ATOMS:
>
>   cat>  bn.band.in<<  EOF
>    &control
>       calculation='bands'
>       pseudo_dir = '$PSEUDO_DIR/',
>       outdir='$TMP_DIR/',
>       prefix='bn'
>    /
>   &system
>       ibrav= 1, celldm(1) = 6.82, nat=8, ntyp= 2,
>       ecutwfc = 40.0, nbnd = 40,
>       occupations ='smearing',
>       smearing = 'methfessel-paxton',
>       degauss= 0.02,
>    /
>
>   &electrons
>     conv_thr =  1.0d-7,
>       mixing_beta = 0.2,
>    /
>
> ATOMIC_SPECIES
>    B  10.811  B.pz-vbc.UPF
>    N  14.007  N.pz-vbc.UPF
> ATOMIC_POSITIONS
>    B      0.000     0.000     0.000
>    N      0.250     0.250     0.250
>    B      0.000     0.500     0.500
>    N      0.250     0.750     0.750
>    B      0.500     0.500     0.000
>    N      0.750     0.250     0.750
>    B      0.500     0.000     0.500
>    N      0.750     0.750     0.250
>
>   K_POINTS {crystal_b}
>   4
>   0    0    0   
>   40
>   0.5  0    0    40
>   0.5  0.5  0    40
>   0    0    0    40
>   EOF
>   $ECHO "  running the band-structure calculation for bn...\c"
>   $PW_COMMAND<  bn.band.in>  bn.band.out
>   check_failure $?
>   $ECHO " done"
>
>   Any help would be appreciated.
>   Best regards,
>   Said Asma
>
>
>
> bests
>
> Said Asma
>
>
>
> ________________________________
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From pankajsahota at gmail.com  Thu Apr 26 08:19:47 2012
From: pankajsahota at gmail.com (pankaj sahota)
Date: Thu, 26 Apr 2012 11:49:47 +0530
Subject: [Pw_forum] Error in running the scf calculation with espresso-4.2
Message-ID: <CADww=122jKCQkOLvaLSj03wMjO2chhSLnC7iYgarXCkDc62aPA@mail.gmail.com>

Hi

I am running the pw.x calculation for the examples of QE. But I am getting
the following error. Can anybody help me.

cleaning /home/sellmyer/sahota/tmp... done
  running the scf calculation for Al...forrtl: severe (174): SIGSEGV,
segmentation fault occurred
Image              PC                Routine            Line
Source
libblas.so.3       00007F8C689604E0  Unknown               Unknown  Unknown
pw.x               0000000000923363  Unknown               Unknown  Unknown
pw.x               0000000000923DEC  Unknown               Unknown  Unknown
pw.x               000000000091D502  Unknown               Unknown  Unknown
pw.x               000000000061327A  Unknown               Unknown  Unknown
pw.x               00000000005EB38F  Unknown               Unknown  Unknown
pw.x               00000000005EA8C4  Unknown               Unknown  Unknown
pw.x               00000000005492E3  Unknown               Unknown  Unknown
pw.x               00000000004827F7  Unknown               Unknown  Unknown
pw.x               000000000043A6C8  Unknown               Unknown  Unknown
pw.x               000000000043A53C  Unknown               Unknown  Unknown
libc.so.6          0000003D9D61ECDD  Unknown               Unknown  Unknown
pw.x               000000000043A439  Unknown               Unknown  Unknown
Error condition encountered during test: exit status = 174
Aborting


-- 
Pankaj Kumar
DST Project Fellow(Ph.D.)
Department of Physics
The LNM IIT Jaipur
Mob. No. +91 9736694726
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From kazempoor at ph.iut.ac.ir  Thu Apr 26 09:20:39 2012
From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir)
Date: Thu, 26 Apr 2012 11:50:39 +0430 (IRDT)
Subject: [Pw_forum] hse performance
Message-ID: <89ddb8d6-e70c-4236-a901-b845f3316e9d@mail1.iut.ac.ir>

Dear All 
I am working with the hybrid functional specially HSE which is 
implemented in espresso . As many researches show, the band gap is 
well reproduced by HSE for many semiconductors in good agreement with 
experimental gap. But as I know the overall electronic structure 
behavior like the coupling between localized and itinerant and the 
band ordering remain unclear. Can anyone introduce me suitable papers 
which compare the band structure of solids obtained by HSE and the 
results of experiments like ARPES and so one. 

With the Bests 


Ali Kazempour 
Physics Department, Isfahn University of Technology 

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From kazempoor2000 at yahoo.com  Thu Apr 26 09:35:01 2012
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Thu, 26 Apr 2012 00:35:01 -0700 (PDT)
Subject: [Pw_forum] hse performance
Message-ID: <1335425701.19653.YahooMailNeo@web114414.mail.gq1.yahoo.com>

Dear All
I am working with the hybrid functional specially HSE which is
implemented in espresso . ?As many researches show, the band gap is
well reproduced by HSE for many semiconductors in good agreement with
experimental gap. ?But as I know the overall electronic structure
behavior like the coupling between localized and itinerant and the
band ordering remain unclear. Can anyone introduce me suitable papers
which compare the band structure of ?solids obtained by HSE and the
results of experiments like ARPES and so one.

With the Bests
?
Ali Kazempour





Fritz-Haber-Institut              fax   : ++49-30-8413 4701
der Max-Planck-Gesellschaft
Faradayweg 4-6                    e-mail: kazempou at fhi-berlin.mpg.de
D-14 195 Berlin-Dahlem / German
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From giannozz at democritos.it  Thu Apr 26 10:42:31 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 26 Apr 2012 10:42:31 +0200
Subject: [Pw_forum] Error in running the scf calculation with
	espresso-4.2
In-Reply-To: <CADww=122jKCQkOLvaLSj03wMjO2chhSLnC7iYgarXCkDc62aPA@mail.gmail.com>
References: <CADww=122jKCQkOLvaLSj03wMjO2chhSLnC7iYgarXCkDc62aPA@mail.gmail.com>
Message-ID: <0EE2D534-B4C1-493A-9B02-397C0976E03A@democritos.it>


On Apr 26, 2012, at 8:19 , pankaj sahota wrote:

> I am running the pw.x calculation for the examples of QE.
> But I am getting the following error. Can anybody help me.

how can anybody help you if you provide close to zero information?
Anyway: this kind of error is almost always due to a compiler bug,
as explained many times.

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 tfcao at theory.issp.ac.cn  Fri Apr 27 03:20:20 2012
From: tfcao at theory.issp.ac.cn (=?utf-8?B?Q2FvIFRG?=)
Date: Fri, 27 Apr 2012 9:20:20 +0800
Subject: [Pw_forum] =?utf-8?q?_convergence_NOT_achieved_after_100_iteratio?=
	=?utf-8?q?ns=3A_stopping?=
Message-ID: <20120427012020.708.qmail@ms.hfcas.ac.cn>

Dear QE users
   Recently, I have done some calculation of BN sheet with hydrogen atoms adsorbed on it.  The problem is that when I let hydrogen atoms adsorb on the N atoms. The calculation is hard to converge. Although, I have changed mixing_beta and the number of K points. The problem have not been solved. Dose anyone have some experience on such kind of calculations? Any suggestions will be greatly appreciated. Here is my input file.
&CONTROL
     title = 'graphene layer' ,
     calculation = 'relax' ,
     restart_mode = 'restart' ,
     outdir = './tmp' ,
     pseudo_dir = '/lustre/ISSP2/tfcao/pseudo' ,
     prefix = 'graphene' ,
     tprnfor = .TRUE. ,
     nstep = 400 ,
 /
 &SYSTEM
     ibrav = 8 ,
     a = 15.026832 , b = 13.014 , c = 15.0 ,
     nat = 74 ,
     ntyp = 3 ,
     starting_magnetization(1) = 0.5 ,
     occupations = 'smearing' ,
     nosym = .TRUE. ,
     degauss = 0.005 ,
     smearing = 'mp' ,
     nspin = 2 ,
     ecutwfc = 30.0 ,
     ecutrho = 300.0 ,
 /
 &ELECTRONS
     conv_thr = 1.0d-7 ,
     mixing_mode = 'local-TF' ,
     mixing_beta = 0.1 ,
     diagonalization = 'cg' ,
 /
 &IONS
     ion_dynamics = 'bfgs' ,
     pot_extrapolation = 'atomic' ,

/
 ATOMIC_SPECIES
  B   10.811    B.pbe-n-van.UPF
  N   14.00674  N.pbe-rrkjus.UPF
  H   1.00000   H.pbe-rrkjus.UPF
ATOMIC_POSITIONS crystal
ATOMIC_POSITIONS crystal
 N   0.0000000       0.0000000      0.50000000  0  0  0
 B   0.0000000      0.11111100      0.50000000
 N  8.33330005E-02  0.16666700      0.50000000
 B  8.33330005E-02  0.27777800      0.50000000
 N   0.0000000      0.33333299      0.50000000
 B   0.0000000      0.44444400      0.50000000
 N  8.33330005E-02  0.50000000      0.50000000
 B  8.33330005E-02  0.61111099      0.50000000
 N   0.0000000      0.66666597      0.50000000
 B   0.0000000      0.77777696      0.50000000
 N  8.33330005E-02  0.83333296      0.50000000
 B  8.33330005E-02  0.94444394      0.50000000
 N  0.16666700       0.0000000      0.50000000
 B  0.16666700      0.11111100      0.50000000
 N  0.25000000      0.16666700      0.50000000
 B  0.25000000      0.27777800      0.50000000
 N  0.16666700      0.33333299      0.50000000
 B  0.16666700      0.44444400      0.50000000
 N  0.25000000      0.50000000      0.50000000
 B  0.25000000      0.61111099      0.50000000
 N  0.16666700      0.66666597      0.50000000
 B  0.16666700      0.77777696      0.50000000
 N  0.25000000      0.83333296      0.50000000
 B  0.25000000      0.94444394      0.50000000
 N  0.33333400       0.0000000      0.50000000
 B  0.33333400      0.11111100      0.50000000
 N  0.41666698      0.16666700      0.50000000
 B  0.41666698      0.27777800      0.50000000
 N  0.33333400      0.33333299      0.50000000
 B  0.33333400      0.44444400      0.50000000
 N  0.41666698      0.50000000      0.50000000
 B  0.41666698      0.61111099      0.50000000
 N  0.33333400      0.66666597      0.50000000
 B  0.33333400      0.77777696      0.50000000
 N  0.41666698      0.83333296      0.50000000
 B  0.41666698      0.94444394      0.50000000
 N  0.50000101       0.0000000      0.50000000
 B  0.50000101      0.11111100      0.50000000
 N  0.58333403      0.16666700      0.50000000
 B  0.58333403      0.27777800      0.50000000
 N  0.50000101      0.33333299      0.50000000
 B  0.50000101      0.44444400      0.50000000
 N  0.58333403      0.50000000      0.50000000
 B  0.58333403      0.61111099      0.50000000
 N  0.50000101      0.66666597      0.50000000
 B  0.50000101      0.77777696      0.50000000
 N  0.58333403      0.83333296      0.50000000
 B  0.58333403      0.94444394      0.50000000
 N  0.66666800       0.0000000      0.50000000
 B  0.66666800      0.11111100      0.50000000
 N  0.75000101      0.16666700      0.50000000
 B  0.75000101      0.27777800      0.50000000
 N  0.66666800      0.33333299      0.50000000
 B  0.66666800      0.44444400      0.50000000
 N  0.75000101      0.50000000      0.50000000
 B  0.75000101      0.61111099      0.50000000
 N  0.66666800      0.66666597      0.50000000
 B  0.66666800      0.77777696      0.50000000
 N  0.75000101      0.83333296      0.50000000
 B  0.75000101      0.94444394      0.50000000
 N  0.83333498       0.0000000      0.50000000
 B  0.83333498      0.11111100      0.50000000
 N  0.91666800      0.16666700      0.50000000
 B  0.91666800      0.27777800      0.50000000
 N  0.83333498      0.33333299      0.50000000
 B  0.83333498      0.44444400      0.50000000
 N  0.91666800      0.50000000      0.50000000
 B  0.91666800      0.61111099      0.50000000
 N  0.83333498      0.66666597      0.50000000
 B  0.83333498      0.77777696      0.50000000
 N  0.91666800      0.83333296      0.50000000
 B  0.91666800      0.94444394      0.50000000
 H  0.50000000      0.66666600      0.56900670
 H  0.66666800      0.33333300      0.56900670
K_POINTS {automatic}
8 8 1 0 0 0
======================================================================
Teng Fei Cao
======================================================================                                                                                                                                                                                     
    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                                                                                                                                                                                                                                                                                                                                                    
   

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From shruba at gmail.com  Fri Apr 27 06:54:12 2012
From: shruba at gmail.com (Shruba Gangopadhyay)
Date: Thu, 26 Apr 2012 21:54:12 -0700
Subject: [Pw_forum] convergence NOT achieved after 100 iterations:
	stopping
In-Reply-To: <20120427012020.708.qmail@ms.hfcas.ac.cn>
References: <20120427012020.708.qmail@ms.hfcas.ac.cn>
Message-ID: <CANWKzdiSjX-S6xrOaD7iuRA00hARzEth-zFwWw0d_3o5T-_2cQ@mail.gmail.com>

Hi Teng,
           Took a quick look, did you check the convergence by increasing
degauss.
           Shruba

On Thu, Apr 26, 2012 at 6:20 PM, Cao TF <tfcao at theory.issp.ac.cn> wrote:

> **
> Dear QE users
> Recently, I have done some calculation of BN sheet with hydrogen atoms
> adsorbed on it. The problem is that when I let hydrogen atoms adsorb on the
> N atoms. The calculation is hard to converge. Although, I have changed
> mixing_beta and the number of K points. The problem have not been solved.
> Dose anyone have some experience on such kind of calculations? Any
> suggestions will be greatly appreciated. Here is my input file.
> &CONTROL
> title = 'graphene layer' ,
> calculation = 'relax' ,
> restart_mode = 'restart' ,
> outdir = './tmp' ,
> pseudo_dir = '/lustre/ISSP2/tfcao/pseudo' ,
> prefix = 'graphene' ,
> tprnfor = .TRUE. ,
> nstep = 400 ,
> /
> &SYSTEM
> ibrav = 8 ,
> a = 15.026832 , b = 13.014 , c = 15.0 ,
> nat = 74 ,
> ntyp = 3 ,
> starting_magnetization(1) = 0.5 ,
> occupations = 'smearing' ,
> nosym = .TRUE. ,
> degauss = 0.005 ,
> smearing = 'mp' ,
> nspin = 2 ,
> ecutwfc = 30.0 ,
> ecutrho = 300.0 ,
> /
> &ELECTRONS
> conv_thr = 1.0d-7 ,
> mixing_mode = 'local-TF' ,
> mixing_beta = 0.1 ,
> diagonalization = 'cg' ,
> /
> &IONS
> ion_dynamics = 'bfgs' ,
> pot_extrapolation = 'atomic' ,
>
> /
> ATOMIC_SPECIES
> B 10.811 B.pbe-n-van.UPF
> N 14.00674 N.pbe-rrkjus.UPF
> H 1.00000 H.pbe-rrkjus.UPF
> ATOMIC_POSITIONS crystal
> ATOMIC_POSITIONS crystal
> N 0.0000000 0.0000000 0.50000000 0 0 0
> B 0.0000000 0.11111100 0.50000000
> N 8.33330005E-02 0.16666700 0.50000000
> B 8.33330005E-02 0.27777800 0.50000000
> N 0.0000000 0.33333299 0.50000000
> B 0.0000000 0.44444400 0.50000000
> N 8.33330005E-02 0.50000000 0.50000000
> B 8.33330005E-02 0.61111099 0.50000000
> N 0.0000000 0.66666597 0.50000000
> B 0.0000000 0.77777696 0.50000000
> N 8.33330005E-02 0.83333296 0.50000000
> B 8.33330005E-02 0.94444394 0.50000000
> N 0.16666700 0.0000000 0.50000000
> B 0.16666700 0.11111100 0.50000000
> N 0.25000000 0.16666700 0.50000000
> B 0.25000000 0.27777800 0.50000000
> N 0.16666700 0.33333299 0.50000000
> B 0.16666700 0.44444400 0.50000000
> N 0.25000000 0.50000000 0.50000000
> B 0.25000000 0.61111099 0.50000000
> N 0.16666700 0.66666597 0.50000000
> B 0.16666700 0.77777696 0.50000000
> N 0.25000000 0.83333296 0.50000000
> B 0.25000000 0.94444394 0.50000000
> N 0.33333400 0.0000000 0.50000000
> B 0.33333400 0.11111100 0.50000000
> N 0.41666698 0.16666700 0.50000000
> B 0.41666698 0.27777800 0.50000000
> N 0.33333400 0.33333299 0.50000000
> B 0.33333400 0.44444400 0.50000000
> N 0.41666698 0.50000000 0.50000000
> B 0.41666698 0.61111099 0.50000000
> N 0.33333400 0.66666597 0.50000000
> B 0.33333400 0.77777696 0.50000000
> N 0.41666698 0.83333296 0.50000000
> B 0.41666698 0.94444394 0.50000000
> N 0.50000101 0.0000000 0.50000000
> B 0.50000101 0.11111100 0.50000000
> N 0.58333403 0.16666700 0.50000000
> B 0.58333403 0.27777800 0.50000000
> N 0.50000101 0.33333299 0.50000000
> B 0.50000101 0.44444400 0.50000000
> N 0.58333403 0.50000000 0.50000000
> B 0.58333403 0.61111099 0.50000000
> N 0.50000101 0.66666597 0.50000000
> B 0.50000101 0.77777696 0.50000000
> N 0.58333403 0.83333296 0.50000000
> B 0.58333403 0.94444394 0.50000000
> N 0.66666800 0.0000000 0.50000000
> B 0.66666800 0.11111100 0.50000000
> N 0.75000101 0.16666700 0.50000000
> B 0.75000101 0.27777800 0.50000000
> N 0.66666800 0.33333299 0.50000000
> B 0.66666800 0.44444400 0.50000000
> N 0.75000101 0.50000000 0.50000000
> B 0.75000101 0.61111099 0.50000000
> N 0.66666800 0.66666597 0.50000000
> B 0.66666800 0.77777696 0.50000000
> N 0.75000101 0.83333296 0.50000000
> B 0.75000101 0.94444394 0.50000000
> N 0.83333498 0.0000000 0.50000000
> B 0.83333498 0.11111100 0.50000000
> N 0.91666800 0.16666700 0.50000000
> B 0.91666800 0.27777800 0.50000000
> N 0.83333498 0.33333299 0.50000000
> B 0.83333498 0.44444400 0.50000000
> N 0.91666800 0.50000000 0.50000000
> B 0.91666800 0.61111099 0.50000000
> N 0.83333498 0.66666597 0.50000000
> B 0.83333498 0.77777696 0.50000000
> N 0.91666800 0.83333296 0.50000000
> B 0.91666800 0.94444394 0.50000000
> H 0.50000000 0.66666600 0.56900670
> H 0.66666800 0.33333300 0.56900670
> K_POINTS {automatic}
> 8 8 1 0 0 0
> ======================================================================
> Teng Fei Cao
> ======================================================================
> 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
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Shruba Gangopadhyay
Postdoc Term Engineer - Computational Material Science
IBM Research Division
Almaden Research Center
650 Harry Road, San Jose, CA 95120
Office: D1-242
Phone: 408-927-1458
Cell: 216-272-9471

'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
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From bfazi90 at gmail.com  Fri Apr 27 09:23:45 2012
From: bfazi90 at gmail.com (bf azi)
Date: Fri, 27 Apr 2012 11:53:45 +0430
Subject: [Pw_forum] k-point
Message-ID: <CAC+sowJjsd+4WqE8gSUxpd2Cx4rEU76-DOWDVeNaiEOFVp6x9w@mail.gmail.com>

Dear all

whether the number of k-points in final result of relax is effective?

From giannozz at democritos.it  Fri Apr 27 10:18:58 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 27 Apr 2012 10:18:58 +0200
Subject: [Pw_forum] convergence NOT achieved after 100
	iterations:	stopping
In-Reply-To: <20120427012020.708.qmail@ms.hfcas.ac.cn>
References: <20120427012020.708.qmail@ms.hfcas.ac.cn>
Message-ID: <1335514738.23132.13.camel@fe12lx.fisica.uniud.it>

On Fri, 2012-04-27 at 09:20 +0800, Cao TF wrote:

> The problem is that when I let hydrogen atoms adsorb on the N atoms,
> the calculation is hard to converge.

you should start with a smaller, more manageable calculation,
experiment a bit with parameters. It is hard to say anything
for a relatively large system without investing a sizable
amount of time and computer resources.

> nosym = .TRUE. , 

you shouldn't use this unless you have a good reason 

> degauss = 0.005 , 

it looks small to me

> nspin = 2 , 

you have 2 H atoms, so the system might be unpolarized.
Try no spin first

> starting_magnetization(1) = 0.5 , 

in any event, start with magnetization on H atoms, not on N or B

> diagonalization = 'cg' , 

you shouldn't use this unless you have a good reason 

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



From giannozz at democritos.it  Fri Apr 27 10:21:29 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 27 Apr 2012 10:21:29 +0200
Subject: [Pw_forum] query on kpoints.x
In-Reply-To: <302199868.144731.1335334233685.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <302199868.144731.1335334233685.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <1335514889.23132.17.camel@fe12lx.fisica.uniud.it>

On Wed, 2012-04-25 at 02:10 -0400, Ajit Vallabhaneni wrote:

> I want to know whether the format for k points output by kpoints.x 
> is tpiba or not ? 

I think so. This is something you can easily verify

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



From flux_ray12 at 163.com  Fri Apr 27 10:23:37 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Fri, 27 Apr 2012 16:23:37 +0800 (CST)
Subject: [Pw_forum] convergence NOT achieved after 100 iterations:
 stopping
In-Reply-To: <20120427012020.708.qmail@ms.hfcas.ac.cn>
References: <20120427012020.708.qmail@ms.hfcas.ac.cn>
Message-ID: <30a2de2a.b365.136f2e5f1cb.Coremail.flux_ray12$163.com>

How about trying to fix the movement for BN-sheet and just move H atoms. The BN-sheet may achieve a concavity during "relax" process. For the absorption of H2, the concavity will vanish and a plane-BN finally be obtained. But for single H atom, I am not sure whether one can ignore such an effect.
By the way, is it reasonable that only one H atom was absorped instead of diatom H2 molecule?


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-04-27 09:20:20,"Cao TF" <tfcao at theory.issp.ac.cn> wrote:

Dear QE users
Recently, I have done some calculation of BN sheet with hydrogen atoms adsorbed on it. The problem is that when I let hydrogen atoms adsorb on the N atoms. The calculation is hard to converge. Although, I have changed mixing_beta and the number of K points. The problem have not been solved. Dose anyone have some experience on such kind of calculations? Any suggestions will be greatly appreciated. Here is my input file.
&CONTROL
title = 'graphene layer' ,
calculation = 'relax' ,
restart_mode = 'restart' ,
outdir = './tmp' ,
pseudo_dir = '/lustre/ISSP2/tfcao/pseudo' ,
prefix = 'graphene' ,
tprnfor = .TRUE. ,
nstep = 400 ,
/
&SYSTEM
ibrav = 8 ,
a = 15.026832 , b = 13.014 , c = 15.0 ,
nat = 74 ,
ntyp = 3 ,
starting_magnetization(1) = 0.5 ,
occupations = 'smearing' ,
nosym = .TRUE. ,
degauss = 0.005 ,
smearing = 'mp' ,
nspin = 2 ,
ecutwfc = 30.0 ,
ecutrho = 300.0 ,
/
&ELECTRONS
conv_thr = 1.0d-7 ,
mixing_mode = 'local-TF' ,
mixing_beta = 0.1 ,
diagonalization = 'cg' ,
/
&IONS
ion_dynamics = 'bfgs' ,
pot_extrapolation = 'atomic' ,

/
ATOMIC_SPECIES
B 10.811 B.pbe-n-van.UPF
N 14.00674 N.pbe-rrkjus.UPF
H 1.00000 H.pbe-rrkjus.UPF
ATOMIC_POSITIONS crystal
ATOMIC_POSITIONS crystal
N 0.0000000 0.0000000 0.50000000 0 0 0
B 0.0000000 0.11111100 0.50000000
N 8.33330005E-02 0.16666700 0.50000000
B 8.33330005E-02 0.27777800 0.50000000
N 0.0000000 0.33333299 0.50000000
B 0.0000000 0.44444400 0.50000000
N 8.33330005E-02 0.50000000 0.50000000
B 8.33330005E-02 0.61111099 0.50000000
N 0.0000000 0.66666597 0.50000000
B 0.0000000 0.77777696 0.50000000
N 8.33330005E-02 0.83333296 0.50000000
B 8.33330005E-02 0.94444394 0.50000000
N 0.16666700 0.0000000 0.50000000
B 0.16666700 0.11111100 0.50000000
N 0.25000000 0.16666700 0.50000000
B 0.25000000 0.27777800 0.50000000
N 0.16666700 0.33333299 0.50000000
B 0.16666700 0.44444400 0.50000000
N 0.25000000 0.50000000 0.50000000
B 0.25000000 0.61111099 0.50000000
N 0.16666700 0.66666597 0.50000000
B 0.16666700 0.77777696 0.50000000
N 0.25000000 0.83333296 0.50000000
B 0.25000000 0.94444394 0.50000000
N 0.33333400 0.0000000 0.50000000
B 0.33333400 0.11111100 0.50000000
N 0.41666698 0.16666700 0.50000000
B 0.41666698 0.27777800 0.50000000
N 0.33333400 0.33333299 0.50000000
B 0.33333400 0.44444400 0.50000000
N 0.41666698 0.50000000 0.50000000
B 0.41666698 0.61111099 0.50000000
N 0.33333400 0.66666597 0.50000000
B 0.33333400 0.77777696 0.50000000
N 0.41666698 0.83333296 0.50000000
B 0.41666698 0.94444394 0.50000000
N 0.50000101 0.0000000 0.50000000
B 0.50000101 0.11111100 0.50000000
N 0.58333403 0.16666700 0.50000000
B 0.58333403 0.27777800 0.50000000
N 0.50000101 0.33333299 0.50000000
B 0.50000101 0.44444400 0.50000000
N 0.58333403 0.50000000 0.50000000
B 0.58333403 0.61111099 0.50000000
N 0.50000101 0.66666597 0.50000000
B 0.50000101 0.77777696 0.50000000
N 0.58333403 0.83333296 0.50000000
B 0.58333403 0.94444394 0.50000000
N 0.66666800 0.0000000 0.50000000
B 0.66666800 0.11111100 0.50000000
N 0.75000101 0.16666700 0.50000000
B 0.75000101 0.27777800 0.50000000
N 0.66666800 0.33333299 0.50000000
B 0.66666800 0.44444400 0.50000000
N 0.75000101 0.50000000 0.50000000
B 0.75000101 0.61111099 0.50000000
N 0.66666800 0.66666597 0.50000000
B 0.66666800 0.77777696 0.50000000
N 0.75000101 0.83333296 0.50000000
B 0.75000101 0.94444394 0.50000000
N 0.83333498 0.0000000 0.50000000
B 0.83333498 0.11111100 0.50000000
N 0.91666800 0.16666700 0.50000000
B 0.91666800 0.27777800 0.50000000
N 0.83333498 0.33333299 0.50000000
B 0.83333498 0.44444400 0.50000000
N 0.91666800 0.50000000 0.50000000
B 0.91666800 0.61111099 0.50000000
N 0.83333498 0.66666597 0.50000000
B 0.83333498 0.77777696 0.50000000
N 0.91666800 0.83333296 0.50000000
B 0.91666800 0.94444394 0.50000000
H 0.50000000 0.66666600 0.56900670
H 0.66666800 0.33333300 0.56900670
K_POINTS {automatic}
8 8 1 0 0 0
======================================================================
Teng Fei Cao
======================================================================
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
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From hande at newton.physics.metu.edu.tr  Fri Apr 27 10:47:26 2012
From: hande at newton.physics.metu.edu.tr (Hande Ustunel)
Date: Fri, 27 Apr 2012 11:47:26 +0300 (EEST)
Subject: [Pw_forum] convergence NOT achieved after 100 iterations ---
	related question
In-Reply-To: <1335514738.23132.13.camel@fe12lx.fisica.uniud.it>
References: <20120427012020.708.qmail@ms.hfcas.ac.cn>
	<1335514738.23132.13.camel@fe12lx.fisica.uniud.it>
Message-ID: <alpine.LFD.2.02.1204271140110.18156@newton.physics.metu.edu.tr>

Dear PWSCF community,

While we are on the subject of convergence, I would like to inquire about
something that we have consistently been observing in a very large number
of the systems we have studied (examples being metal atoms on g-Al2O3, CeO2
surfaces etc). While gaussian smearing consistently produces convergence
without problems at first shot for a smearing width of 0.01-0.02, we
frequently have problems with mv smearing (our favorite) for the same
width. Systematically exploring a giant portion of 6 or 7-dimensional
parameter space (kpoints, smearing width, vacuum length so forth)
eventually results in convergence with mv but we usually have to fiddle a
lot; with gauss instead, anything basically works. Would anyone be able to
confirm this experience or better still provide some insight on the
realtive ease of using mv vs gauss?

Thank you very much in advance.
Best regards,
Hande Toffoli


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

From nicola.marzari at epfl.ch  Fri Apr 27 11:20:30 2012
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Fri, 27 Apr 2012 11:20:30 +0200
Subject: [Pw_forum] convergence NOT achieved after 100 iterations ---
 related question
In-Reply-To: <alpine.LFD.2.02.1204271140110.18156@newton.physics.metu.edu.tr>
References: <20120427012020.708.qmail@ms.hfcas.ac.cn>
	<1335514738.23132.13.camel@fe12lx.fisica.uniud.it>
	<alpine.LFD.2.02.1204271140110.18156@newton.physics.metu.edu.tr>
Message-ID: <4F9A64DE.5000605@epfl.ch>



Hi Hande,

first question - would mp work?

In terms of "structure" of the smearing function, gaussian is
the smoothest, then mv, then mp. So if there were an intrinsic problem
with states at the fermi energy, it should be even more apparent in
mp .

As a general comment, the role of smearing is to help improve the
accuracy of k-point sampling - and so the 0.01-.02 you are using
is exactly in the right ball park.

A side effect (a positive one) for smearing is to help convergence
in iterative algorithms (as in PWSCF) - for that side effect,
0.01-0.02 is actually small, and so the more "structure" of
mv or mp could hamper the iterative convergence. So you could try
converging first with a larger smearing (.04 to .08), and then restart
with the "right" one. I'd be somewhat surprised to see much difference
between gaussian/mp/mp for say 0.07 Ry ~ 1 eV of smearing. Of
course, such a large smearing shoudl be used only to help
get convergence, and then reduced.

				nicola



On 27/04/2012 10:47, Hande Ustunel wrote:
> Dear PWSCF community,
>
> While we are on the subject of convergence, I would like to inquire about
> something that we have consistently been observing in a very large number
> of the systems we have studied (examples being metal atoms on g-Al2O3, CeO2
> surfaces etc). While gaussian smearing consistently produces convergence
> without problems at first shot for a smearing width of 0.01-0.02, we
> frequently have problems with mv smearing (our favorite) for the same
> width. Systematically exploring a giant portion of 6 or 7-dimensional
> parameter space (kpoints, smearing width, vacuum length so forth)
> eventually results in convergence with mv but we usually have to fiddle a
> lot; with gauss instead, anything basically works. Would anyone be able to
> confirm this experience or better still provide some insight on the
> realtive ease of using mv vs gauss?
>
> Thank you very much in advance.
> Best regards,
> Hande Toffoli
>
>
> --
> Hande Toffoli
> Department of Physics
> Office 439
> Middle East Technical University
> Ankara 06531, Turkey
> Tel : +90 312 210 3264
> http://www.physics.metu.edu.tr/~hande
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 

----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL

From hande at newton.physics.metu.edu.tr  Fri Apr 27 11:38:11 2012
From: hande at newton.physics.metu.edu.tr (Hande Ustunel)
Date: Fri, 27 Apr 2012 12:38:11 +0300 (EEST)
Subject: [Pw_forum] convergence NOT achieved after 100 iterations ---
 related question
In-Reply-To: <4F9A64DE.5000605@epfl.ch>
References: <20120427012020.708.qmail@ms.hfcas.ac.cn>
	<1335514738.23132.13.camel@fe12lx.fisica.uniud.it>
	<alpine.LFD.2.02.1204271140110.18156@newton.physics.metu.edu.tr>
	<4F9A64DE.5000605@epfl.ch>
Message-ID: <alpine.LFD.2.02.1204271229190.18156@newton.physics.metu.edu.tr>

Dear Nicola,

Many thanks for the prompt reply.

> first question - would mp work?

This we haven't tried. Since mv and mp give very similar numerical results
for a given smearing width I guess I thought I should try something a bit
different, i.e. gauss.

> In terms of "structure" of the smearing function, gaussian is
> the smoothest, then mv, then mp. So if there were an intrinsic problem
> with states at the fermi energy, it should be even more apparent in
> mp .

I see. I'll surely take a look at mp then.

> As a general comment, the role of smearing is to help improve the
> accuracy of k-point sampling - and so the 0.01-.02 you are using
> is exactly in the right ball park.

Sure. Actually using a larger kpoint set sometimes helps but it gets a bit
tricky because if you've run a number of calculations with a smaller kpoint
set (say for a publication), then you want to stick to that. So sometimes
we actually try with a larger set and then once (if) we see convergence
revert back to the one we want. This only works about half the time
though. Our g-Al2O3 + precious metal atom calculations were particularly
notorious so we got to try this close to about 20-30 times.

> A side effect (a positive one) for smearing is to help convergence
> in iterative algorithms (as in PWSCF) - for that side effect,
> 0.01-0.02 is actually small, and so the more "structure" of
> mv or mp could hamper the iterative convergence. So you could try
> converging first with a larger smearing (.04 to .08), and then restart
> with the "right" one. I'd be somewhat surprised to see much difference
> between gaussian/mp/mp for say 0.07 Ry ~ 1 eV of smearing. Of
> course, such a large smearing shoudl be used only to help
> get convergence, and then reduced.

Oh, wow. We haven't done that since I'm a bit scared of large smearings but
this is a great suggestion. We do make use of a similar trick though,
namely going back and forth between an initial gauss shot followed by mv
but I'm afraid this works even less than half the time. But I will
definitely give this a shot and report back the result.

Many thanks once again.
Best wishes,
Hande

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

From d.tiana at bath.ac.uk  Fri Apr 27 16:04:46 2012
From: d.tiana at bath.ac.uk (Davide Tiana)
Date: Fri, 27 Apr 2012 15:04:46 +0100
Subject: [Pw_forum] pw bands calculation crash
Message-ID: <20120427150446.Horde.LZtqbVLxr25Pmqd_jvt2UJA@webmail.bath.ac.uk>

Dear all,
After optimised a molecule I tried to calculate the band structure but  
pw crashes and I can't figure out why.

The optimisation step should be fine(here it converge immediately  
since I rerun my previous calculation):

     BFGS Geometry Optimization

      bfgs converged in   1 scf cycles and   0 bfgs steps
      (criteria: energy < 0.10E-03, force < 0.10E-02)

      Final energy   =    -646.2249695321 Ry
Begin final coordinates

ATOMIC_POSITIONS (crystal)
C        0.953315090   0.000413805   0.235484404
..
..
H        1.009939685   0.169442779   0.056058275
H        1.044496546   0.158711398  -0.056214459
End final coordinates



      Writing output data file mol_a.save

..
..
..
    This run was terminated on:  13: 4:41  27Apr2012

=------------------------------------------------------------------------------=
    JOB DONE.
=------------------------------------------------------------------------------=
"

but when I run pw.x to calculate bands it crashes

"
      Atomic positions and unit cell read from directory:
      ./mol_a.save/


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

Application 1981542 exit codes: 139
Application 1981542 exit signals: Killed
Application 1981542 resources: utime ~2s, stime ~2s
"
My input should not contain any errors. I used it for other systems  
similar to this one and it works. just in case:
"
&control
     calculation='bands',
     title='mol_a',
     wf_collect=.true.,
     outdir='./',
     prefix='mol_a'
     etot_conv_thr=1.0d-4,
     forc_conv_thr=1.0d-3,
  /
  &system
    ibrav=14,
    celldm(1)=28.4693677,
    celldm(2)=1.058648879,
    celldm(3)=0.600431923,
    celldm(4)=0,
    celldm(5)=0,
    celldm(6)=0,
    nat=23,
    ntyp=6,
    nbnd=70
    tot_charge=0.0,
    ecutwfc=45.0,
    ecutrho=450.0,
    nosym=.false.,
    nosym_evc=.false.,
    london=.true.,
    london_s6=0.75,
    london_rcut=200,
  /
  &electrons
    electron_maxstep=80,
    conv_thr=1.0d-6,
    mixing_mode='plain',
    mixing_beta=0.7,
    mixing_ndim=8,
    mixing_fixed_ns=0,
    diagonalization='david',
  /
  ATOMIC_SPECIES
    H  1.007   H.pw91-van_ak.UPF
  ...
    Zn 65.409  Zn.pw91-n-van.UPF
  ATOMIC_POSITIONS {crystal}
    C   0.952835      0.500000      0.826917
....
Zn   0.0000        0.500000      0.191590
K_POINTS {crystal}
11
0 0  0 1
0 0 .1 2
0 0 .2 3
0 0 .3 4
0 0 .4 5
0 0 .5 6
0 0 .6 7
0 0 .7 8
0 0 .8 9
0 0 .9 10
0 0  1 11
"


Any suggestion?
thanks a lot
Davide


From rostami7.m at gmail.com  Fri Apr 27 16:39:14 2012
From: rostami7.m at gmail.com (m rostami)
Date: Fri, 27 Apr 2012 19:09:14 +0430
Subject: [Pw_forum]  convergence not achieved .related problem
Message-ID: <CAJRxHUe5f3aPPjFhw0Z-Y5PkKVxtap4E8Y+qHC-1iHCZ+dDU+g@mail.gmail.com>

Dear users
I have been trying to relax a graphene structure with a vacancy but
many erros stoped optimization and convergence not achieved.like

1. Efermy cannot braket :
2. to0 many bands not coveraged

for solving the errors I have chenged these parametrs

 increasing ecutoff to 60 and ecuthro to 720 .increasing edeguss to
0.07 and changing diagnolization from cg to david  . I have tested
smearing for m-v and mp .increasing nbands from   70 to 120  too .but
optimization didnt achived .I appreciate if any one helpe me .

my input file is :
&control
    calculation='relax',
    prefix='graphene'
    pseudo_dir = '/media/espresso-4.2/pseudo/',
    outdir='./tmp/',
    etot_conv_thr=1.0D-3 ,
    forc_conv_thr=1.0D-2 ,

 /
 &system
    ibrav=  4, celldm(1) =13.9506, celldm(3)=1.667,nat=35, ntyp= 1,nbnd=120
   ecutwfc =80.0,ecutrho = 900,
    occupations='smearing',smearing='m-v',degauss=0.07,
 /
 &electrons
  diagonalization='cg',
  conv_thr=1.D-8 ,
  mixing_beta=0.1,
 /
 &ions
 upscale=20,
 /
ATOMIC_SPECIES
C  1.00  C.blyp-mt.UPF
ATOMIC_POSITIONS {angstrom}
    C    0.0071683270    0.0041386380    1.6740000000
 .........
......
K_POINTS  AUTOMATIC
8 8 1 0 0 0


.............................
I am not sure about these questions to0 :.

1.in example 3 the atomic weight for different atoms is set to 1 in
relax process.is this correct? as I did for carbon (ATOMIC_SPECIES
C  1.00  C.blyp-mt.UPF)
I am not sure about k-point .is 8 8 1 0 0 0  enough for this structure
with 10 A` vaccum .

how many nbands I should for coverage ?

wich diagnbolization is better david or cg ?

mixing_beta should be around 0.1-0.3?


thanks alot

Melika Rostami
Master Student of Sharif University

From giannozz at democritos.it  Fri Apr 27 17:05:47 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 27 Apr 2012 17:05:47 +0200
Subject: [Pw_forum] pw bands calculation crash
In-Reply-To: <20120427150446.Horde.LZtqbVLxr25Pmqd_jvt2UJA@webmail.bath.ac.uk>
References: <20120427150446.Horde.LZtqbVLxr25Pmqd_jvt2UJA@webmail.bath.ac.uk>
Message-ID: <1335539147.29838.6.camel@fe12lx.fisica.uniud.it>

On Fri, 2012-04-27 at 15:04 +0100, Davide Tiana wrote:

> Application 1981542 exit codes: 139
> Application 1981542 exit signals: Killed

it looks like an out-of-bounds memory error

> Any suggestion?

0) the usual suggestions apply: 
  http://www.quantum-espresso.org/?page_id=26#2.0
1) locate where the code crashes, either with a debugger or
the dumb way, with print statements.

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



From x_y_meng at mail.neu.edu.cn  Sat Apr 28 01:10:57 2012
From: x_y_meng at mail.neu.edu.cn (=?GBK?b?w8/P6dOx?=)
Date: Sat, 28 Apr 2012 07:10:57 +0800 (CST) 
Subject: [Pw_forum] question report
Message-ID: <20120427231057.ABB2E7FB6@mail.neu.edu.cn>

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From ptao10b at imr.ac.cn  Sat Apr 28 03:12:53 2012
From: ptao10b at imr.ac.cn (Peng Tao)
Date: Sat, 28 Apr 2012 09:12:53 +0800 (CST)
Subject: [Pw_forum] Error band structure
In-Reply-To: <1335370074.23583.YahooMailNeo@web29007.mail.ird.yahoo.com>
References: <1335370074.23583.YahooMailNeo@web29007.mail.ird.yahoo.com>
	<mailman.2211.1334762790.9401.pw_forum@pwscf.org>
	<1334828257.36755.YahooMailNeo@web29009.mail.ird.yahoo.com>
Message-ID: <1b58360.10309.136f681f25f.Coremail.ptao10b@imr.ac.cn>

Dear Said,
It is not an error. When you enlarge the primitive cell, the  brillouin zone gets smaller. Moreover, some high symmetric points might be overlapped with Gamma, for the symmetry is changed (ibrav changes). This effect is called  brillouin zone folding.

Plato Tao

-----Original Messages-----
From: "Said Asma" <saidasma1987 at yahoo.fr>
Sent Time: Thursday, April 26, 2012
To: "giannozz at democritos.it" <giannozz at democritos.it>, "pw_forum at pwscf.org" <pw_forum at pwscf.org>
Cc:
Subject: [Pw_forum] Error band structure






 Dear Giannozzi ,

I did the band structure of  BN (zinc blende) with two atoms and I found a indirect gap  (like literature) Gamma-X. But when I did it with 8 atoms I found direct gap Gamma -Gamma.
Normally if we change (nat = 2, ibrav = 2) to (nat = 8, ibrav = 1),we find the same nature of gap (the unit cell has changedtosimplecubic).
If such we have the composition B0.25Ga0.75N how we can determine the nature of gap?

 Why such a problem occurs?

 My input files is as following:

  *With TWO ATOMS:

 cat > bn.band.in << EOF
  &control
    calculation='bands'
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/',
    prefix='bn'
  /
  &system
    ibrav=  2, celldm(1) = 6.76, nat=  2, ntyp= 2,
    ecutwfc = 60.0,
    occupations ='smearing',
    smearing = 'methfessel-paxton',
    degauss= 0.03,
  /
  &electrons
                  conv_thr = 1.0d-7 ,
                  mixing_mode = 'plain' ,
                  mixing_beta = 0.2 ,
                  diagonalization = 'david' ,
  /
ATOMIC_SPECIES
  B  10.811  B.pz-vbc.UPF
  N  14.007  N.pz-vbc.UPF
ATOMIC_POSITIONS
  B 0.00 0.00 0.00
  N 0.25 0.25 0.25
K_POINTS {crystal_b}
 5
0.5  0.5  0.5  400
0    0    0    400
1.0  0    0    400
0.75 0.75 0    400
0    0    0    400
EOF
$ECHO "  running the band-structure calculation for bn...\c"
$PW_COMMAND < bn.band.in > bn.band.out
check_failure $?
$ECHO " done"



*and WITH 8 ATOMS:

 cat > bn.band.in << EOF
  &control
    calculation='bands'
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/',
    prefix='bn'
  /
 &system
    ibrav= 1, celldm(1) = 6.82, nat=8, ntyp= 2,
    ecutwfc = 40.0, nbnd = 40,
    occupations ='smearing',
    smearing = 'methfessel-paxton',
    degauss= 0.02,
  /
  &electrons
  conv_thr =  1.0d-7,
    mixing_beta = 0.2,
  /

ATOMIC_SPECIES
  B  10.811  B.pz-vbc.UPF
  N  14.007  N.pz-vbc.UPF
ATOMIC_POSITIONS
  B      0.000    0.000    0.000
  N      0.250    0.250    0.250
  B      0.000    0.500    0.500
  N      0.250    0.750    0.750
  B      0.500    0.500    0.000
  N      0.750    0.250    0.750
  B      0.500    0.000    0.500
  N      0.750    0.750    0.250

 K_POINTS {crystal_b}
 4
 0    0    0    40
 0.5  0    0    40
 0.5  0.5  0    40
 0    0    0    40
 EOF
 $ECHO "  running the band-structure calculation for bn...\c"
 $PW_COMMAND < bn.band.in > bn.band.out
 check_failure $?
 $ECHO " done"

 Any help would be appreciated.
 Best regards,
 Said Asma



bests

Said Asma



________________________________







--
-------------------------------------------------------------------
PH.D. candidate Peng Tao 
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751
-------------------------------------------------------------------



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From bfazi90 at gmail.com  Sun Apr 29 21:41:47 2012
From: bfazi90 at gmail.com (bf azi)
Date: Mon, 30 Apr 2012 00:11:47 +0430
Subject: [Pw_forum] absorption
Message-ID: <CAC+sowL1gFgTXUo=TJ79Akg3zHHL8=uu6FZ83pkG5Pg7Ukxu-w@mail.gmail.com>

Dear all

Which Bravais-lattice better for absorption hydrogen on BNNT
"Hexagonal and Trigonal P" or "Tetragonal P (st)" ?

From bdslipun at gmail.com  Mon Apr 30 08:10:50 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Mon, 30 Apr 2012 11:40:50 +0530
Subject: [Pw_forum] optical properties
Message-ID: <CAJVAAvCCFf3MzCJ+jWeKvZFm58o_PNnZ9yP7=zPUe5XWo+Xfag@mail.gmail.com>

can any one help me to find the optical properies by espresso code
is there any example in espresso
but i know  ev.x command can do this but i donot what should be the input
file for this


any suggetions are highly appricieted














 b sahoo
mumbai
reserch scholar
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From eariel99 at gmail.com  Mon Apr 30 12:00:32 2012
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Mon, 30 Apr 2012 12:00:32 +0200
Subject: [Pw_forum] optical properties (bhabya sahoo)
Message-ID: <CAM5Vcw9ZpNZ8dqYwTquxDBnH7Eni=SpE1-ZkCR=1Gse34hUkxg@mail.gmail.com>

Dear Bhabya

Optical properties in RPA
make pp
use bin/epsilon.x
read Doc/eps_man.pdf
no example, but it is straightforward reading the manual.

Optical properties by TDDFPT (absolutely better than RPA for isolated
systems, buy still in progress for periodical systems)
make tddfpt
read documentation at TDDFPT/Doc/
and see examples in
TDDFPT/Examples/

For more advanced methods to calculate optical properties you can use other
codes like YAMBO, that use the output of PWSCF and produce optical
properties un several approximations. http://www.yambo-code.org/
YAMBO can de downloaded and compiled within QE, but it is a bit tricky to
compile ( by my own experience two weeks ago).

Good luck
Eduardo


> ---------- Mensaje reenviado ----------
> From: bhabya sahoo <bdslipun at gmail.com>
> To: PWSCF Forum <pw_forum at pwscf.org>
> Cc:
> Date: Mon, 30 Apr 2012 11:40:50 +0530
> Subject: [Pw_forum] optical properties
> can any one help me to find the optical properies by espresso code
> is there any example in espresso
> but i know  ev.x command can do this but i donot what should be the input
> file for this
>
>
> any suggetions are highly appricieted
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>  b sahoo
> mumbai
> reserch scholar
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 


Eduardo Menendez Proupin
Departamento de Qu?mica Fisica Aplicada
Facultad de Ciencias
Universidad Aut?noma de Madrid
28049 Madrid, Spain
Phone: +34 91 497 6706

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

"...man never knows for who he suffers and waits. He suffers and waits and
works for peoples he will never meet, and who at the same time will suffer
and wait and work for others who will also not be happy, as man always
desires a happiness that is beyond the lot that he is given. But the
greatness of man is precisely in wanting to improve what he is. In
assigning himself Tasks. In the Kingdom of Heaven there is no greatness to
conquer, for everything there is an established hierarchy, the unknown is
unobscured, existence is without end, sacrifice, rest, and delight are
impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful
within his misery, capable of loving in the middle of calamity, man can
only find his greatness, his full self-realization, in the Kingdom of this
World." - Alejo Carpentier
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From reishme04 at gmail.com  Mon Apr 30 12:23:25 2012
From: reishme04 at gmail.com (matt reish)
Date: Mon, 30 Apr 2012 23:08:25 +1245
Subject: [Pw_forum] Input help
Message-ID: <CAPb1f4uoBb6V95Ja0CydggQtSw2ZCr5EP6LDM2_oPcXm8wZU4Q@mail.gmail.com>

*Hi Guys,

I am new to Quantum Espresso and am having trouble getting an input to
submit. My input file is as follows:*

 &CONTROL
                       title = benzacidscftest ,
                 calculation = 'scf' ,
                restart_mode = 'from_scratch' ,
                      outdir = '/home/mreish/tmp/' ,
                  pseudo_dir = '/usr/share/espresso/pseudo/' ,
                      prefix = 'batest' ,
                     disk_io = 'default' ,
 /
 &SYSTEM
                       ibrav = 12,
                         nat = 60,
                        ntyp = 3,
                     ecutwfc = 5 ,
                     ecutrho = 40 ,
 /
 &ELECTRONS
                    conv_thr = 1.0d-8 ,
                 mixing_beta = 0.7 ,
 /
ATOMIC_SPECIES
    C   12.01000  C.pz-vbc.UPF
    O   16.00000  O.pz-van_ak.UPF
    H    1.00000  H.pz-vbc.UPF
ATOMIC_POSITIONS alat
    O      0.221300000    0.237200000    0.013200000
    C      0.100100000    0.271300000    0.057600000
    C      0.181600000    0.474000000    0.103700000
    C      0.384900000    0.626500000    0.097000000
    C      0.459600000    0.818200000    0.140600000
    C      0.331700000    0.853400000    0.190200000
    C      0.129900000    0.702400000    0.196500000
    C      0.053300000    0.513300000    0.153400000
    H      0.473000000    0.599000000    0.061000000
    H      0.606000000    0.924000000    0.136000000
    H      0.382000000    0.991000000    0.221000000
    H      0.041000000    0.730000000    0.232000000
    O      0.909200000    0.141000000    0.064700000
    H      0.909000000    0.405000000    0.158000000
    H      0.864000000    0.013000000    0.038000000
    O      0.090800000    0.641000000    0.435300000
    H      0.091000000    0.905000000    0.342000000
    H      0.136000000    0.513000000    0.462000000
    C      0.615100000    0.126500000    0.403000000
    C      0.540400000    0.318200000    0.359400000
    C      0.668300000    0.353400000    0.309800000
    C      0.870100000    0.202400000    0.303500000
    C      0.946700000    0.013300000    0.346600000
    H      0.527000000    0.099000000    0.439000000
    H      0.394000000    0.424000000    0.364000000
    H      0.618000000    0.491000000    0.279000000
    H      0.959000000    0.230000000    0.268000000
    O      0.778700000    0.737200000    0.486800000
    C      0.899900000    0.771300000    0.442400000
    C      0.818400000    0.974000000    0.396300000
    O      0.090800000    0.859000000    0.935300000
    H      0.091000000    0.595000000    0.842000000
    H      0.136000000    0.987000000    0.962000000
    O      0.778700000    0.762800000    0.986800000
    C      0.899900000    0.728700000    0.942400000
    C      0.818400000    0.526000000    0.896300000
    C      0.615100000    0.373500000    0.903000000
    C      0.540400000    0.181800000    0.859400000
    C      0.668300000    0.146600000    0.809800000
    C      0.870100000    0.297600000    0.803500000
    C      0.946700000    0.486700000    0.846600000
    H      0.527000000    0.401000000    0.939000000
    H      0.394000000    0.076000000    0.864000000
    H      0.618000000    0.009000000    0.779000000
    H      0.959000000    0.270000000    0.768000000
    O      0.221300000    0.262800000    0.513200000
    C      0.100100000    0.228700000    0.557600000
    C      0.181600000    0.026000000    0.603700000
    C      0.384900000    0.873500000    0.597000000
    C      0.459600000    0.681800000    0.640600000
    C      0.331700000    0.646600000    0.690200000
    C      0.129900000    0.797600000    0.696500000
    C      0.053300000    0.986700000    0.653400000
    H      0.473000000    0.901000000    0.561000000
    H      0.606000000    0.576000000    0.636000000
    H      0.382000000    0.509000000    0.721000000
    H      0.041000000    0.770000000    0.732000000
    O      0.909200000    0.359000000    0.564700000
    H      0.909000000    0.095000000    0.658000000
    H      0.864000000    0.487000000    0.538000000
K_POINTS automatic
  1 1 1   1 1 1

*This job cannot be run by QE and give me the following output:*

 Program PWSCF v.4.3.2      starts on 30Apr2012 at 22:10:50

     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     1 processors

     Current dimensions of program PWSCF are:
     Max number of different atomic species (ntypx) = 10
     Max number of k-points (npk) =  40000
     Max angular momentum in pseudopotentials (lmaxx) =  3
     Waiting for input...
     Reading input from stdin

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from  read_namelists  : error #      5010
      reading namelist control
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

*Sorry for the obvious lack of knowledge with the program but I am having
trouble figuring out what the error message " *error #      5010*" means
and any help would be greatly appreciated. (also apologies if this message
is outside of the forum rules but the link explaining the forum rules seems
not to be working)*

Cheers,

Matthew Reish
University of Otago Chemistry Department
Dunedin, New Zealand
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From giannozz at democritos.it  Mon Apr 30 12:35:09 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 30 Apr 2012 12:35:09 +0200
Subject: [Pw_forum] Input help
In-Reply-To: <CAPb1f4uoBb6V95Ja0CydggQtSw2ZCr5EP6LDM2_oPcXm8wZU4Q@mail.gmail.com>
References: <CAPb1f4uoBb6V95Ja0CydggQtSw2ZCr5EP6LDM2_oPcXm8wZU4Q@mail.gmail.com>
Message-ID: <B896BD33-138B-447F-9D25-A9708D9F30E3@democritos.it>


On Apr 30, 2012, at 12:23 , matt reish wrote:

>                        title = benzacidscftest

title = 'benzacidscftest'

> I am having trouble figuring out what the error message " error  
> #      5010" means

it means nothing

> but the link explaining the forum rules seems not to be working

which link doesn't work? the forum rules are in
http://www.quantum-espresso.org/ under "Contacts",
"posting guidelines". The web site has been changed a few
days ago so some links reported in the current documentation
or in the forum may no longer work (documentation will be
updated in the next few days)

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 1009ukumar at gmail.com  Mon Apr 30 14:52:39 2012
From: 1009ukumar at gmail.com (Sonu Kumar)
Date: Mon, 30 Apr 2012 18:22:39 +0530
Subject: [Pw_forum] download MD Slides from QE website?
Message-ID: <CAHePdfAAsgogx_JY8j41MuX0Fzn9HfWbKTtkVMra01MqLB6vPg@mail.gmail.com>

Dear all,

I am unable to get the following slides from QE website.
Can anyone provide these to me?

http://www.quantum-espresso.org/wiki/images/f/fd/Galli_072809.pdf

http://www.quantum-espresso.org/wiki/images/6/69/Gygi_ICMR2009.pdf

regards,
sonu
==========================================
Sonu Kumar
Phd Student,Physics Department
Indian Institute of Technology ,Delhi-110016, India
web:-http://www.iitd.ac.in/
==========================================
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From giannozz at democritos.it  Mon Apr 30 15:08:55 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 30 Apr 2012 15:08:55 +0200
Subject: [Pw_forum] download MD Slides from QE website?
In-Reply-To: <CAHePdfAAsgogx_JY8j41MuX0Fzn9HfWbKTtkVMra01MqLB6vPg@mail.gmail.com>
References: <CAHePdfAAsgogx_JY8j41MuX0Fzn9HfWbKTtkVMra01MqLB6vPg@mail.gmail.com>
Message-ID: <B4DC8FC7-0254-4448-8CC9-6A83EE485F4E@democritos.it>


On Apr 30, 2012, at 14:52 , Sonu Kumar wrote:

> I am unable to get the following slides from QE website [...]
> http://www.quantum-espresso.org/wiki/images/f/fd/Galli_072809.pdf
> http://www.quantum-espresso.org/wiki/images/6/69/Gygi_ICMR2009.pdf

for the time being, please replace "www.quantum-espresso.org"
with "testwp.qe-forge.it". Some files have yet to be moved to their
new location


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 sbinnie at sissa.it  Mon Apr 30 15:44:50 2012
From: sbinnie at sissa.it (Simon Binnie)
Date: Mon, 30 Apr 2012 15:44:50 +0200
Subject: [Pw_forum] Input help
In-Reply-To: <B896BD33-138B-447F-9D25-A9708D9F30E3@democritos.it>
References: <CAPb1f4uoBb6V95Ja0CydggQtSw2ZCr5EP6LDM2_oPcXm8wZU4Q@mail.gmail.com>
	<B896BD33-138B-447F-9D25-A9708D9F30E3@democritos.it>
Message-ID: <op.wdky40w0b4z88i@mugon.cm.sissa.it>

On Mon, 30 Apr 2012 12:35:09 +0200, Paolo Giannozzi  
<giannozz at democritos.it> wrote:
>
> which link doesn't work? the forum rules are in
> http://www.quantum-espresso.org/ under "Contacts",
> "posting guidelines". The web site has been changed a few
> days ago so some links reported in the current documentation
> or in the forum may no longer work (documentation will be
> updated in the next few days)
>

I think he might mean that the links to the QE site served by google  
aren't currently working (i.e. google "quantum espresso parallelization"  
and the top three results give you a 404). I assume that this will just  
resolve it self in a few days when google (and other search engines)  
update their links.

Simon


-- 
Simon Binnie | Post Doc, Condensed Matter Sector
Scuola Internazionale di Studi Avanzati (SISSA)
Via Bonomea 256 | 34100 Trieste | sbinnie at sissa.it

From vas at fc.up.pt  Mon Apr 30 16:26:27 2012
From: vas at fc.up.pt (Vasumathi Velachi)
Date: Mon, 30 Apr 2012 15:26:27 +0100
Subject: [Pw_forum] Input preparation
Message-ID: <22192306509cbd3edb1c29293297048c@fc.up.pt>


Dear All
I am very new to using Quantum Espresso. I have pdb file for my system 
(CNT-dendrimer). I would like to calculate the charge transfer between 
them.
Is there any way to convert pdb file to input file to run in Quantum 
Espresso or one has to write manually?
Thanking you in advance.
-- 
Vasumathi Velachi



From 1009ukumar at gmail.com  Mon Apr 30 18:31:03 2012
From: 1009ukumar at gmail.com (Sonu Kumar)
Date: Mon, 30 Apr 2012 22:01:03 +0530
Subject: [Pw_forum] download MD Slides from QE website?
In-Reply-To: <B4DC8FC7-0254-4448-8CC9-6A83EE485F4E@democritos.it>
References: <CAHePdfAAsgogx_JY8j41MuX0Fzn9HfWbKTtkVMra01MqLB6vPg@mail.gmail.com>
	<B4DC8FC7-0254-4448-8CC9-6A83EE485F4E@democritos.it>
Message-ID: <CAHePdfCRDrKE3Q3pN1sx5=19TJUTrdFowwAPDnvbUz4B9ugi2Q@mail.gmail.com>

Thank you very much Prof. Paolo Giannozzi.

regards,
sonu
==========================================
Sonu Kumar
Phd Student,Physics Department
Indian Institute of Technology ,Delhi-110016, India
web:-http://www.iitd.ac.in/
==========================================



On Mon, Apr 30, 2012 at 6:38 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Apr 30, 2012, at 14:52 , Sonu Kumar wrote:
>
>  I am unable to get the following slides from QE website [...]
>> http://www.quantum-espresso.**org/wiki/images/f/fd/Galli_**072809.pdf<http://www.quantum-espresso.org/wiki/images/f/fd/Galli_072809.pdf>
>> http://www.quantum-espresso.**org/wiki/images/6/69/Gygi_**ICMR2009.pdf<http://www.quantum-espresso.org/wiki/images/6/69/Gygi_ICMR2009.pdf>
>>
>
> for the time being, please replace "www.quantum-espresso.org"
> with "testwp.qe-forge.it". Some files have yet to be moved to their
> new location
>
>
> 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 makhyoun2 at yahoo.com  Mon Apr 30 21:04:21 2012
From: makhyoun2 at yahoo.com (mohamed makhyoun)
Date: Mon, 30 Apr 2012 12:04:21 -0700 (PDT)
Subject: [Pw_forum] problems in generating pseudopotentials
Message-ID: <1335812661.48455.YahooMailClassic@web126005.mail.ne1.yahoo.com>

Dear All:

The generation of pseudopotentials from the ld1.x code is not a trivial job I needed to generate the potential in the hse functional as well as other functionals I have many difficulties but at last I get the pbe potential for copper with the characteristics listed below (the second potential) . There are some differences between the one I produced and the one obtainable from the QE web site.
Now I am not content with my produced potential and appreciate any opinion in this respect.


Cu.pbe-n-van.UPF
?
?nl pn? l?? occ?????????????? Rcut??????????? Rcut US???????????? E pseu
3D? 3? 2? 9.50???? 10.00000000000????? 2.00000000000???? -0.60492460120
4S? 4? 0? 1.00???? 10.00000000000????? 2.10000000000???? -0.43710222811
4P? 4? 1? 0.50???? 10.00000000000????? 2.20000000000???? -0.10740671642

Cu.pbe-rrkjus.UPF

? Valence configuration: 
??? nl pn? l?? occ?????? Rcut??? Rcut US?????? E pseu
??? 3D? 3? 2 10.00????? 1.800????? 2.400??? -0.370268
??? 4S? 1? 0? 1.00????? 3.634????? 3.861??? -0.338779
??? 4P? 2? 1? 0.00????? 2.500????? 2.500??? -0.051219
??? Generation configuration:
??? 4P? 2? 1 -1.00????? 2.500????? 2.500???? 0.200000
??? 3D? 3? 2 10.00????? 1.800????? 2.400??? -0.370267
??? 4S? 1? 0? 1.00????? 2.300????? 2.300??? -0.338778

Best regard
Mohamed Makhyoun
Faculty of Science
Alexandria Egypt

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