From nicy04 at gmail.com  Mon Mar  1 04:09:33 2010
From: nicy04 at gmail.com (Adrian)
Date: Sun, 28 Feb 2010 21:09:33 -0600
Subject: [Pw_forum] Error in running GWW
In-Reply-To: <op.u8mjcmm0a8x26q@vanoxite.impmc.jussieu.fr>
References: <4558f4e61002221831q788c9328tfd3983e50c7588ed@mail.gmail.com>
	<6578D8B8-0801-467E-80AF-9E37419FBCA7@democritos.it>
	<4558f4e61002232038y655a7e6dq1b6d1b32988b2ae8@mail.gmail.com>
	<op.u8mjcmm0a8x26q@vanoxite.impmc.jussieu.fr>
Message-ID: <4558f4e61002281909t5a9b8387s8f8b597fd6e4ef5a@mail.gmail.com>

  Thank you so much, Lorenzo. And sorry for this late reply.
   The content of si8_ph_head.out is below:

     Program PHONON v.4.2CVS    starts on 22Feb2010 at 19:41: 1

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

     Parallel version (MPI), running on     1 processors

     Ultrasoft (Vanderbilt) Pseudopotentials

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

     Proc/  planes cols     G    planes cols    G      columns  G
     Pool       (dense grid)       (smooth grid)      (wavefct grid)
        1    30    593    11067   30    593    11067    177     1839


 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from ph_setup : error #         1
     problem with modes file
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

As you can see, the error is from ph_setup, just like what Layla said.
 Maybe I should wait for the updated package.

 Thank you again.

Best
Adrian






On Wed, Feb 24, 2010 at 3:01 AM, Lorenzo Paulatto <paulatto at sissa.it> wrote:
> On Wed, 24 Feb 2010 05:38:01 +0100, Adrian <nicy04 at gmail.com> wrote:
>> ? I noticed MPI didn't work in output files but I didn't know why.
>> ? ?Since when I tried espresso-4.1.2, MPI worked well (I can use 4
>> processors).
>> ? But for CVS version, MPI didn't work and only one processor was
>> running.
>
> Dear Adrian,
> I don't think it is an MPi problem. It is more likely that the head
> calculation (head.x) crashes for some reason while MPI is just reporting
> the crash. Please have a look at file si8_ph_head.out in the HEAD/
> subdirectory of the example. By "have a look" I mean: open the file with a
> text editor, and possibly send a copy to this mailing list.
>
> best regards
>
> --
> Lorenzo Paulatto
>
> *** Note: my affiliation has changed! please send future
> correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***
>
> post-doc @ IMPMC/UPMC - Universit? Paris 6
> phone: +33 (0)1 44 27 74 89
> www: ? http://www-int.impmc.upmc.fr/~paulatto/
>
> previously:
> phd student @ SISSA ?& ?DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> www: ? http://people.sissa.it/~paulatto/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From masoudnahali at live.com  Mon Mar  1 09:16:57 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Mon, 1 Mar 2010 08:16:57 +0000
Subject: [Pw_forum] Running Example 01 (Parallel Running on a single PC with
 3 cores, AMD, LAM-MPI)
Message-ID: <COL114-W489572245EA58ECE9E4590A13C0@phx.gbl>


Dear QE's Users

 

Sometimes the running of exapmle 01 stops !! and sometimes aborts because of MPI_INIT !! 

 

koa at linux-xd0f:~/QSPRESSO4.1.2/espresso-4.1.1-Example/examples/example01> ./run_example 

/home/koa/QSPRESSO4.1.2/espresso-4.1.1-Example/examples/example01 : starting

This example shows how to use pw.x to calculate the total energy and

the band structure of four simple systems: Si, Al, Cu, Ni.

executables directory: /home/koa/QSPRESSO4.1.2/espresso-4.1.2/bin

pseudo directory: /home/koa/QSPRESSO4.1.2/espresso-4.1.2/pseudo

temporary directory: /home/koa/tmp

checking that needed directories and files exist... done

running pw.x as: mpirun -np 3 /home/koa/QSPRESSO4.1.2/espresso-4.1.2/bin/pw.x -npool 1 -inp

running bands.x as: mpirun -np 3 /home/koa/QSPRESSO4.1.2/espresso-4.1.2/bin/bands.x -npool 1 -inp

cleaning /home/koa/tmp... done

running the scf calculation for Si...-----------------------------------------------------------------------------

The selected RPI failed to initialize during MPI_INIT. This is a

fatal error; I must abort.

This occurred on host linux-xd0f (n0).

The PID of failed process was 9075 (MPI_COMM_WORLD rank: 0)

 

or:

 

 

oa at linux-xd0f:~/QSPRESSO4.1.2/espresso-4.1.1-Example/examples/example01> ./run_example 

/home/koa/QSPRESSO4.1.2/espresso-4.1.1-Example/examples/example01 : starting

This example shows how to use pw.x to calculate the total energy and

the band structure of four simple systems: Si, Al, Cu, Ni.

executables directory: /home/koa/QSPRESSO4.1.2/espresso-4.1.2/bin

pseudo directory: /home/koa/QSPRESSO4.1.2/espresso-4.1.2/pseudo

temporary directory: /home/koa/tmp

checking that needed directories and files exist... done

running pw.x as: mpirun -np 3 /home/koa/QSPRESSO4.1.2/espresso-4.1.2/bin/pw.x -npool 1 -inp

running bands.x as: mpirun -np 3 /home/koa/QSPRESSO4.1.2/espresso-4.1.2/bin/bands.x -npool 1 -inp

cleaning /home/koa/tmp... done

running the scf calculation for Si...    ---> stops at this line

 

 

   using the -inp that is suggested by Paolo Giannozzi did not solve my problem.

I have tested my mpif77 and mpicc and I think that they works well , but I feel that the problem is related to the MPI !

but I can not find it. My QE has been compiled well by mpif77 and all binaries created well. I am not sure that LAM-MPI 

recognizes the 3 cores of a single PC or not ? I am comfused ! another amazing paradox is that once I ran this example.
 		 	   		  
_________________________________________________________________
Hotmail: Powerful Free email with security by Microsoft.
https://signup.live.com/signup.aspx?id=60969
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From nnlinh at sissa.it  Mon Mar  1 09:54:18 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Mon, 01 Mar 2010 09:54:18 +0100
Subject: [Pw_forum] Running Example 01 (Parallel Running on a single PC
 with 3 cores, AMD, LAM-MPI)
In-Reply-To: <COL114-W489572245EA58ECE9E4590A13C0@phx.gbl>
References: <COL114-W489572245EA58ECE9E4590A13C0@phx.gbl>
Message-ID: <4B8B80BA.8010602@sissa.it>

>  I have tested my mpif77 and mpicc and I think that they works well , 
but I feel that the problem is related to the MPI ! but I can not find 
it. My QE has been compiled well by mpif77 and all binaries created well.

Here, I wonder that why don't you use mpif90. In the Manual of QE, you 
can find out that the 
parallel fortran compiler should be mpif90. Therefore, I think it should 
be updated from mpif77 to mpif90.

>I am not sure that LAM-MPI recognizes the 3 cores of a single PC or not 
? I am comfused ! another amazing paradox is that once I ran this example.

QUANTUM ESPRESSO is known to work with at least two of the major MPI 
implementations (MPICH, LAM-MPI), plus with the newer MPICH2 and OpenMPI 
implementation. Therefore, if you have not been sure that the MPI 
compiler works or not, why don't you try by running some simple examples 
firstly.

Good luck,

Linh
> ------------------------------------------------------------------------
> Hotmail: Powerful Free email with security by Microsoft. Get it now. 
> <https://signup.live.com/signup.aspx?id=60969>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From baris.malcioglu at gmail.com  Mon Mar  1 09:57:18 2010
From: baris.malcioglu at gmail.com (O. Baris Malcioglu)
Date: Mon, 1 Mar 2010 09:57:18 +0100
Subject: [Pw_forum] Running Example 01 (Parallel Running on a single PC
	with 3 cores, AMD, LAM-MPI)
In-Reply-To: <COL114-W489572245EA58ECE9E4590A13C0@phx.gbl>
References: <COL114-W489572245EA58ECE9E4590A13C0@phx.gbl>
Message-ID: <ab42ba5f1003010057x437f9b49g2600ae5c244dba85@mail.gmail.com>

Dear Masoud

First of all, let me kindly mention that opening several threads for
the same problem is not very nice, these messages are sent to many
people that follow the topics thread by thread, and not everyone is
interested in this particular problem. It is also not very nice for
people searching the forum.

Now, regarding your problem: I would recommend you to read some
documentation regarding how to set up and use parallel execution
environments before setting up Q-E. It seems to me that the problem
you are experiencing is due to lack of proper communication between
the different processes. The observation you made that mpi wrappers
for compilers are working does not imply that the parallel environment
is working. Did you try a simple test program like :

#include <stdio.h>
#include "mpi.h"
int main(int argc, char **argv) {
   int rank;
   int namelen;
   MPI_Init(&argc, &argv);
   MPI_Comm_rank(MPI_COMM_WORLD, &rank);
   printf("Hello world (Rank: %d)\n", rank);
   fflush(stdout);
   MPI_Finalize();
   return 0;
}

My personal preference on the matter is to use openmpi, not lam, but
its your choice. Be careful about lamboot, and how you set the spawned
processes to communicate.

Best.
Baris



2010/3/1 Masoud Nahali <masoudnahali at live.com>:
> Dear QE's Users
>
> Sometimes the running of exapmle 01 stops !! and sometimes aborts because of
> MPI_INIT !!
>
> koa at linux-xd0f:~/QSPRESSO4.1.2/espresso-4.1.1-Example/examples/example01>
> ./run_example
> /home/koa/QSPRESSO4.1.2/espresso-4.1.1-Example/examples/example01 : starting
> This example shows how to use pw.x to calculate the total energy and
> the band structure of four simple systems: Si, Al, Cu, Ni.
> executables directory: /home/koa/QSPRESSO4.1.2/espresso-4.1.2/bin
> pseudo directory: /home/koa/QSPRESSO4.1.2/espresso-4.1.2/pseudo
> temporary directory: /home/koa/tmp
> checking that needed directories and files exist... done
> running pw.x as: mpirun -np 3
> /home/koa/QSPRESSO4.1.2/espresso-4.1.2/bin/pw.x -npool 1 -inp
> running bands.x as: mpirun -np 3
> /home/koa/QSPRESSO4.1.2/espresso-4.1.2/bin/bands.x -npool 1 -inp
> cleaning /home/koa/tmp... done
> running the scf calculation for
> Si...-----------------------------------------------------------------------------
> The selected RPI failed to initialize during MPI_INIT. This is a
> fatal error; I must abort.
> This occurred on host linux-xd0f (n0).
> The PID of failed process was 9075 (MPI_COMM_WORLD rank: 0)
>
> or:
>
>
> oa at linux-xd0f:~/QSPRESSO4.1.2/espresso-4.1.1-Example/examples/example01>
> ./run_example
> /home/koa/QSPRESSO4.1.2/espresso-4.1.1-Example/examples/example01 : starting
> This example shows how to use pw.x to calculate the total energy and
> the band structure of four simple systems: Si, Al, Cu, Ni.
> executables directory: /home/koa/QSPRESSO4.1.2/espresso-4.1.2/bin
> pseudo directory: /home/koa/QSPRESSO4.1.2/espresso-4.1.2/pseudo
> temporary directory: /home/koa/tmp
> checking that needed directories and files exist... done
> running pw.x as: mpirun -np 3
> /home/koa/QSPRESSO4.1.2/espresso-4.1.2/bin/pw.x -npool 1 -inp
> running bands.x as: mpirun -np 3
> /home/koa/QSPRESSO4.1.2/espresso-4.1.2/bin/bands.x -npool 1 -inp
> cleaning /home/koa/tmp... done
> running the scf calculation for Si...??? ---> stops at this line
>
>
> ?? using the -inp that is suggested by Paolo Giannozzi did not solve my
> problem.
> I have tested my mpif77 and mpicc and I think that they works well , but I
> feel that the problem is related to the MPI !
> but I can not find it. My QE?has been?compiled well by mpif77 and all
> binaries created well. I am not sure that LAM-MPI
> recognizes the 3 cores of a single PC or not ? I am comfused ! another
> amazing paradox is that?once I ran?this example.
>
> ________________________________
> Hotmail: Powerful Free email with security by Microsoft. Get it now.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

From janfelix.binder at epfl.ch  Mon Mar  1 10:56:33 2010
From: janfelix.binder at epfl.ch (Jan Felix Binder)
Date: Mon, 01 Mar 2010 10:56:33 +0100
Subject: [Pw_forum] Visuallization
In-Reply-To: <20100228171730.14005ixmdvff6nfe@webmail.epfl.ch>
References: <COL114-W4A51B89AAE2727682622CA13E0@phx.gbl>	<65291.213.176.122.17.1267294251.squirrel@mail.iasbs.ac.ir>
	<20100228171730.14005ixmdvff6nfe@webmail.epfl.ch>
Message-ID: <4B8B8F51.4030905@epfl.ch>

Have a look on http://gdis.sourceforge.net/

alexandra.carvalho at epfl.ch wrote:
> The xyz-formated coordinates can also be viewed with xmakemol, or jmol.
>
> Alexandra Carvalho
> EPFL
> Quoting "nazari at iasbs.ac.ir" <nazari at iasbs.ac.ir>:
>
>   
>>> Yes.
>>>       
>>   The XYZ coordinate can be transfered to GaussView input file.
>>
>>   regards
>>   Fariba Nazari
>>   IASBS
>>     
>>> Is there any other software for visullization of QE's output file except
>>> XCrysden?
>>>
>>>
>>>
>>> Many Thanks
>>>
>>> Masoud Nahali
>>>
>>> Sharif University of Technology
>>>
>>> Physical Chemistry
>>>
>>>
>>>
>>> _________________________________________________________________
>>> Hotmail: Powerful Free email with security by Microsoft.
>>> https://signup.live.com/signup.aspx?id=60969_______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>       
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>     
>
>
>
>   


From bw.hu at yahoo.com  Mon Mar  1 15:43:48 2010
From: bw.hu at yahoo.com (Bingwen Hu)
Date: Mon, 1 Mar 2010 06:43:48 -0800 (PST)
Subject: [Pw_forum] File Error of GIPAW module
Message-ID: <209034.55112.qm@web57616.mail.re1.yahoo.com>

Dear All,
  I used gipaw to calculate the NMR information and I got 
an error: 
----------------------------------------------------------------------------------------------
At line 174 of file paw_gipaw.f90 (unit = 14, file = '')
Fortran 
runtime error: File '' does not exist
----------------------------------------------------------------------------------------------
I have succeeded in running the pw.x.

The input file for GIPAW is 
shown below:
----------------------------------------------------------------------------------------------
&inputgipaw
    job = 'nmr'
    prefix = 'pwscf'
    tmp_dir = 
'/home/bingwen/espresso-4.1.2/PWgui-4.1.1/TMP/'
    iverbosity = 1
    q_gipaw = 0.01
    spline_ps = .true.
    use_nmr_macroscopic_shape = .true.
/
----------------------------------------------------------------------------------------------

Thank you in advance for your help.

Best
Bingwen



      
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From Ari.P.Seitsonen at iki.fi  Mon Mar  1 15:48:09 2010
From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen)
Date: Mon, 1 Mar 2010 15:48:09 +0100 (CET)
Subject: [Pw_forum] File Error of GIPAW module
In-Reply-To: <209034.55112.qm@web57616.mail.re1.yahoo.com>
References: <209034.55112.qm@web57616.mail.re1.yahoo.com>
Message-ID: <alpine.LNX.2.00.1003011547190.9988@pcihpc19.uzh.ch>


Dear Bingwen,

   Could you please also send the input for the self-consistent job, and 
explain to us which pseudo potentials you used?

     Greetings,

        apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
   Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
   Physikalisch-Chemisches Institut der Universitaet Zuerich
   Tel: +41 44 63 54 497  /  Mobile: +41 79 71 90 935


On Mon, 1 Mar 2010, Bingwen Hu wrote:

> Dear All,
> ? I used gipaw to calculate the NMR information and I got an error:
> ---------------------------------------------------------------------------
> -------------------
> At line 174 of file paw_gipaw.f90 (unit = 14, file = '')
> Fortran runtime error: File '' does not exist
> ---------------------------------------------------------------------------
> -------------------
> I have succeeded in running the pw.x.
> 
> The input file for GIPAW is shown below:
> ---------------------------------------------------------------------------
> -------------------
> &inputgipaw
> ??? job = 'nmr'
> ??? prefix = 'pwscf'
> ??? tmp_dir = '/home/bingwen/espresso-4.1.2/PWgui-4.1.1/TMP/'
> ??? iverbosity = 1
> ??? q_gipaw = 0.01
> ??? spline_ps = .true.
> ??? use_nmr_macroscopic_shape = .true.
> /
> ---------------------------------------------------------------------------
> -------------------
> 
> Thank you in advance for your help.
> 
> Best
> Bingwen
> 
> 
>

From lshulenburger at gmail.com  Mon Mar  1 15:52:20 2010
From: lshulenburger at gmail.com (Luke Shulenburger)
Date: Mon, 1 Mar 2010 09:52:20 -0500
Subject: [Pw_forum] reusing converged density
In-Reply-To: <DB735BE8-8341-431E-A8ED-2EA83F7A7E10@sissa.it>
References: <b74576e71002271833y1297835ex597d4d3a767b8dc1@mail.gmail.com>
	<DB735BE8-8341-431E-A8ED-2EA83F7A7E10@sissa.it>
Message-ID: <b74576e71003010652v49a24654se7904b4fc94b585e@mail.gmail.com>

Dear Stefano,

Thanks for the quick reply.  I think it probably best to stick with a
solution inside the code.  It sounds like everything is already there and my
job will more akin to plumbing than algorithm testing and validation.  I'll
take a look at it soon.  What is the proper way to submit code for review
once I get that far?

Luke
Geophysical Laboratory
Carnegie Institution of Washington
(lshulenburger at ciw.edu)


On Sun, Feb 28, 2010 at 4:17 AM, Stefano Baroni <baroni at sissa.it> wrote:

> Dear Luke:
>
> I am no longer familiar with the guts of the code, but I think this would
> require some coding. The problem is, the PW basis set (and the related FFT
> grids) slightly depends on the strain state. In variable-cell MD, this
> dependence is eliminated by using a "hard" cutoff that defines the PW basis
> set and a "smooth" one that implicitly, but continuously, eliminates some of
> the PWs according to the strain state. I can see two strategies that you may
> want to try.
>
> The first would probably require you to put your hands into PW: you simply
> have to make the "soft" cutoff option available to static scf calculations.
> I believe this should be rather easy, and I will ask some of the people who
> know the code well to assist you if you want to try.
>
> Second option. Do Fourier interpolation. Take the charge density /
> wavefunctions calculated and stored with one FFT grid and use a simple
> stand-alone program to calculate the fourier coefficients with respect to a
> different grid. Writing this simple code would not require any knowledge of
> the PW guts. If you want to give it a try, I can give you a few hints.
>
> If you decide to try either one of the above two approaches, I beileve the
> QE developers' team would be more than glald to help and to include your
> contribution in a future distribution of QE.
>
> Cheers
> Stefano B
>
> On Feb 28, 2010, at 3:33 AM, Luke Shulenburger wrote:
>
> Hello,
>
> I would like to calculate the ground state of a system with several
> different strains.  As the calculations are somewhat hard to converge, I was
> hoping that I could re-use the density and wavefunctions from one of the
> calculations as starting points of the others.  I know that the code does
> this under the hood when the geometry is changed in MD or geometry
> optimizations, but I cannot seem to get it to work for separate static scf
> calculations.   Is this feature available?
>
> Luke Shulenburger
> Geophysical Laboratory
> Carnegie Institution of Washington
> (lshulenburger at ciw.edu)
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> ---
> Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
> http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) /
> stefanobaroni (skype)
>
> La morale est une logique de l'action comme la logique est une morale de la
> pens?e - Jean Piaget
>
> Please, if possible, don't  send me MS Word or PowerPoint attachments
> Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From kazempoor at ph.iut.ac.ir  Mon Mar  1 16:17:50 2010
From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir)
Date: Mon, 1 Mar 2010 18:47:50 +0330 (IRST)
Subject: [Pw_forum] defect state
In-Reply-To: <132775804.57145.1267456364380.JavaMail.root@mta.iut.ac.ir>
Message-ID: <2066059121.57150.1267456670688.JavaMail.root@mta.iut.ac.ir>

Dear All
I investigate the oxygen vacancy in TiO2.When I plot the band structure I saw that new band falls very very closed to the CBM,but this is not clear from Dos. On the other hand for charged oxygen vacancy the defect state fall in the conduction band that is not obvious   to detect.How can I find and see which one is defect state?It is nessecary to mention that the states fall above the conduction band might have empty occupations(for example o++ in TiO2).
I would be most grateful if anyone tell me what is the true method  for observation of defect states.
thanks  a lot
Ali Kazempour
Physics Department, Isfahan University of Technology

From baroni at sissa.it  Mon Mar  1 17:20:58 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 1 Mar 2010 17:20:58 +0100
Subject: [Pw_forum] reusing converged density
In-Reply-To: <b74576e71003010652v49a24654se7904b4fc94b585e@mail.gmail.com>
References: <b74576e71002271833y1297835ex597d4d3a767b8dc1@mail.gmail.com>
	<DB735BE8-8341-431E-A8ED-2EA83F7A7E10@sissa.it>
	<b74576e71003010652v49a24654se7904b4fc94b585e@mail.gmail.com>
Message-ID: <82CB0B10-C16B-403D-865D-60756188A500@sissa.it>

Thank you, Luke. the best way to proceed would probably be to first see what some of the "core developers" think.
Stefano de Gironcoli, Paolo Giannozzi, Layla Samos, Andrea Dal Corso, any ideas?
Once the eview is ready, it should be enough to submit it to Layla (Layla Martin Samos Colomer <lmartinsamos at gmail.com>) or Paolo (Paolo Giannozzi <paolo.giannozzi at uniud.it>)
Good luck and thanks for your interest and willingness to help
Stefano B

On Mar 1, 2010, at 3:52 PM, Luke Shulenburger wrote:

> Dear Stefano,
> 
> Thanks for the quick reply.  I think it probably best to stick with a solution inside the code.  It sounds like everything is already there and my job will more akin to plumbing than algorithm testing and validation.  I'll take a look at it soon.  What is the proper way to submit code for review once I get that far?
> 
> Luke
> Geophysical Laboratory
> Carnegie Institution of Washington
> (lshulenburger at ciw.edu)
> 
> 
> On Sun, Feb 28, 2010 at 4:17 AM, Stefano Baroni <baroni at sissa.it> wrote:
> Dear Luke:
> 
> I am no longer familiar with the guts of the code, but I think this would require some coding. The problem is, the PW basis set (and the related FFT grids) slightly depends on the strain state. In variable-cell MD, this dependence is eliminated by using a "hard" cutoff that defines the PW basis set and a "smooth" one that implicitly, but continuously, eliminates some of the PWs according to the strain state. I can see two strategies that you may want to try. 
> 
> The first would probably require you to put your hands into PW: you simply have to make the "soft" cutoff option available to static scf calculations. I believe this should be rather easy, and I will ask some of the people who know the code well to assist you if you want to try.
> 
> Second option. Do Fourier interpolation. Take the charge density / wavefunctions calculated and stored with one FFT grid and use a simple stand-alone program to calculate the fourier coefficients with respect to a different grid. Writing this simple code would not require any knowledge of the PW guts. If you want to give it a try, I can give you a few hints.
> 
> If you decide to try either one of the above two approaches, I beileve the QE developers' team would be more than glald to help and to include your contribution in a future distribution of QE.
> 
> Cheers
> Stefano B
> 
> On Feb 28, 2010, at 3:33 AM, Luke Shulenburger wrote:
> 
>> Hello,
>> 
>> I would like to calculate the ground state of a system with several different strains.  As the calculations are somewhat hard to converge, I was hoping that I could re-use the density and wavefunctions from one of the calculations as starting points of the others.  I know that the code does this under the hood when the geometry is changed in MD or geometry optimizations, but I cannot seem to get it to work for separate static scf calculations.   Is this feature available?
>> 
>> Luke Shulenburger
>> Geophysical Laboratory
>> Carnegie Institution of Washington
>> (lshulenburger at ciw.edu)
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> ---
> Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
> http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)
> 
> La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget
> 
> Please, if possible, don't  send me MS Word or PowerPoint attachments
> Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html
> 
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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

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







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From bw.hu at yahoo.com  Tue Mar  2 05:08:19 2010
From: bw.hu at yahoo.com (Bingwen Hu)
Date: Mon, 1 Mar 2010 20:08:19 -0800 (PST)
Subject: [Pw_forum] File Error of GIPAW module
Message-ID: <735351.43390.qm@web57612.mail.re1.yahoo.com>

Dear Ari Paavo Seitsonen, 

?? I have attached the input file for the PWSC. All the pseudo potentials I used are downloaded in the quantum-espresso website http://www.quantum-espresso.org/pseudo.php.
? Thank you for your help in advance.

Best
Bingwen


--- On Mon, 3/1/10, Ari P Seitsonen <Ari.P.Seitsonen at iki.fi> wrote:

From: Ari P Seitsonen <Ari.P.Seitsonen at iki.fi>
Subject: Re: [Pw_forum] File Error of GIPAW module
To: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Monday, March 1, 2010, 10:48 PM


Dear Bingwen,

? Could you please also send the input for the self-consistent job, and explain to us which pseudo potentials you used?

? ? Greetings,

? ? ???apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
? Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
? Physikalisch-Chemisches Institut der Universitaet Zuerich
? Tel: +41 44 63 54 497? /? Mobile: +41 79 71 90 935


On Mon, 1 Mar 2010, Bingwen Hu wrote:

> Dear All,
> ? I used gipaw to calculate the NMR information and I got an error:
> ---------------------------------------------------------------------------
> -------------------
> At line 174 of file paw_gipaw.f90 (unit = 14, file = '')
> Fortran runtime error: File '' does not exist
> ---------------------------------------------------------------------------
> -------------------
> I have succeeded in running the pw.x.
> 
> The input file for GIPAW is shown below:
> ---------------------------------------------------------------------------
> -------------------
> &inputgipaw
> ??? job = 'nmr'
> ??? prefix = 'pwscf'
> ??? tmp_dir = '/home/bingwen/espresso-4.1.2/PWgui-4.1.1/TMP/'
> ??? iverbosity = 1
> ??? q_gipaw = 0.01
> ??? spline_ps = .true.
> ??? use_nmr_macroscopic_shape = .true.
> /
> ---------------------------------------------------------------------------
> -------------------
> 
> Thank you in advance for your help.
> 
> Best
> Bingwen
> 
> 
> ?
-----Inline Attachment Follows-----

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



      
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From gbilalbegovic at gmail.com  Tue Mar  2 12:27:57 2010
From: gbilalbegovic at gmail.com (Goranka Bilalbegovic)
Date: Tue, 2 Mar 2010 12:27:57 +0100
Subject: [Pw_forum] File Error of GIPAW module
In-Reply-To: <735351.43390.qm@web57612.mail.re1.yahoo.com>
References: <735351.43390.qm@web57612.mail.re1.yahoo.com>
Message-ID: <7332fead1003020327p504692c5ma476b7a24e95def3@mail.gmail.com>

On Tue, Mar 2, 2010 at 5:08 AM, Bingwen Hu <bw.hu at yahoo.com> wrote:
   I have attached the input file for the PWSC. All the pseudo potentials I
used are downloaded in the quantum-espresso website
http://www.quantum-espresso.org/pseudo.php.
  Thank you for your help in advance.


Dear Bingwen,

NMR calculations in Quantum Espresso are implemented within the GIPAW model.
These calculations are possible only if we use a special kind of GIPAW
pseudopotentials, and not all pseudopotentials available on the QE pp page.

Plese check the video/presentation lecture by Ari Seitsonen on:
http://www.quantum-espresso.org/wiki/index.php/QESB09 and read several
articles referenced there. Also plese search QE mailing list for "GIPAW".


Best regards,
Goranka Bilalbegovic
Department of Physics,
Faculty of Science, University of Zagreb
Croatia
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From giannozz at democritos.it  Tue Mar  2 13:24:39 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 02 Mar 2010 13:24:39 +0100
Subject: [Pw_forum] bug in data input?
In-Reply-To: <4B8638BD.4010609@unito.it>
References: <4B85676B.3000002@unito.it> <20100224180508.4d25b412@mark>
	<4B8638BD.4010609@unito.it>
Message-ID: <4B8D0387.7020701@democritos.it>

Carlo Nervi wrote:

> The input of the "A, B, C, cosAB, cosAC, cosBC" mode works
> exactly like the celldm() way. This was not clear to me

now it is explicitly stated

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

From giannozz at democritos.it  Tue Mar  2 14:56:21 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 02 Mar 2010 14:56:21 +0100
Subject: [Pw_forum] Hirshfeld charges
In-Reply-To: <c09ad1e51002220945k5c1789fbtf54cb7ec5f9f640b@mail.gmail.com>
References: <c09ad1e51002220945k5c1789fbtf54cb7ec5f9f640b@mail.gmail.com>
Message-ID: <4B8D1905.10708@democritos.it>

Leonardo Matheus wrote:

> My group is interested in calculating the Hirshfeld charges 

you may want to check whether a code calculating these quantities
already exists and whether it is possible to write an interface
from QE to such a code. There is for instance one here:
   http://mac.softpedia.com/get/Math-Scientific/Hirshfeld.shtml
Not sure what the "Guaussian fchk file" required in input
should contain, though.

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

From giannozz at democritos.it  Tue Mar  2 16:20:20 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 02 Mar 2010 16:20:20 +0100
Subject: [Pw_forum] reusing converged density
In-Reply-To: <b74576e71002271833y1297835ex597d4d3a767b8dc1@mail.gmail.com>
References: <b74576e71002271833y1297835ex597d4d3a767b8dc1@mail.gmail.com>
Message-ID: <4B8D2CB4.1000406@democritos.it>

Luke Shulenburger wrote:

> I would like to calculate the ground state of a system with several 
> different strains.  As the calculations are somewhat hard to converge,
> I was hoping that I could re-use the density and wavefunctions from
> one of the calculations as starting points of the others.

you can, but with some (serious) limitations. Basically, restarting
from the charge density of previous calculations works only if both
the cell and the cutoff for the charge density of the two calculations
are the same; restarting from previously calculated orbitals works only
if the cell, the cutoff for the orbitals, and the k-points of the two
calculations are the same. Some of these restrictions may be easy to
lift, other are not so easy

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

From dimpy.sharma at tyndall.ie  Tue Mar  2 17:36:36 2010
From: dimpy.sharma at tyndall.ie (Dimpy Sharma)
Date: Tue, 2 Mar 2010 16:36:36 -0000
Subject: [Pw_forum] spilling parameter
Message-ID: <D4A761F73683694BBD69D634FF298015533CFF@MAIL.tyndall.ie>


Hi Friends,

The term spilling parameter is not much clear to me, though I read in forum.It would be great if anyone can help me. Also  I would like to know is there any standard value for spilling paramter for Si-H system.

Thanks and regards

Dimpy (PhD)

UCC,Ireland
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From giannozz at democritos.it  Tue Mar  2 17:43:01 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 02 Mar 2010 17:43:01 +0100
Subject: [Pw_forum] spilling parameter
In-Reply-To: <D4A761F73683694BBD69D634FF298015533CFF@MAIL.tyndall.ie>
References: <D4A761F73683694BBD69D634FF298015533CFF@MAIL.tyndall.ie>
Message-ID: <4B8D4015.60609@democritos.it>

In PP/projwfc.f90:

      ! Sanchez-Portal et al., Sol. State Commun.  95, 685 (1995).
      ! The spilling parameter measures the ability of the basis provided
      ! by the pseudo-atomic wfc to represent the PW eigenstates,
      ! by measuring how much of the subspace of the Hamiltonian
      ! eigenstates falls outside the subspace spanned by the atomic basis

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

From giannozz at democritos.it  Tue Mar  2 17:45:09 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 02 Mar 2010 17:45:09 +0100
Subject: [Pw_forum] defect state
In-Reply-To: <2066059121.57150.1267456670688.JavaMail.root@mta.iut.ac.ir>
References: <2066059121.57150.1267456670688.JavaMail.root@mta.iut.ac.ir>
Message-ID: <4B8D4095.8080401@democritos.it>

kazempoor at ph.iut.ac.ir wrote:

> I would be most grateful if anyone tell me what is the true
>  method for observation of defect states

there is no "true method", and more often than not you
cannot trust the position of defect states obtained in
DFT (especially in nasty systems like TiO2).

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

From sclauzer at sissa.it  Tue Mar  2 17:51:12 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 02 Mar 2010 17:51:12 +0100
Subject: [Pw_forum] spilling parameter
In-Reply-To: <D4A761F73683694BBD69D634FF298015533CFF@MAIL.tyndall.ie>
References: <D4A761F73683694BBD69D634FF298015533CFF@MAIL.tyndall.ie>
Message-ID: <4B8D4200.3040105@sissa.it>


Dear Dimpy,

    either there are two users of this forum who share the same name and affiliation or 
you do not receive/read some of the replies from the forum.

Just one week ago I replied to the same question in another thread you've opened:

[Pw_forum] summation of total PDOS does not matches the Total DOS


Here it is:

Dimpy Sharma wrote:
 > >
 > > Hi quantum espresso users,
 > >
 > > The summation of all the projected  density of states is not matching
 > > the total density of states at higher energy.I repeated my calculationby
 > > reducing the number of bands. I got a spiiling parameter of 0.0174. My
 > > system is Si and H.Can anyone please tell me , where can I get some
 > > refrences about the spilling parameter .I used the following parameters

The best source of information is to look inside the code. For instance:

[sclauzer at hg1 espresso-4.1.2]$ grep spilling PP/*.f90
PP/projwfc.f90:  ! calculates Lowdin charges, spilling parameter, projected DOS
PP/projwfc.f90:     ! The spilling parameter measures the ability of the basis provided by
PP/projwfc.f90:     ! The spilling parameter measures the ability of the basis provided by
PP/projwfc.f90:     ! The spilling parameter measures the ability of the basis provided by

and inside the file you'll find the reference:
...
       psum = SUM(charges(:,:,:)) / nelec
       WRITE( stdout, '(5x,"Spilling Parameter: ",f8.4)') 1.0d0 - psum
       !
       ! Sanchez-Portal et al., Sol. State Commun.  95, 685 (1995).
       ! The spilling parameter measures the ability of the basis provided by
       ! the pseudo-atomic wfc to represent the PW eigenstates,
       ! by measuring how much of the subspace of the Hamiltonian
       ! eigenstates falls outside the subspace spanned by the atomic basis
       !
       DEALLOCATE (charges)
...


HTH

GS

 > >   etot_conv_thr = 1.D-4
 > >    forc_conv_thr = 1.D-3
 > >            nstep = 600
 > >           wf_collect = .true
 > >
 > >        ecutwfc = 40
 > >       ecutrho = 160.0
 > >    diagonalization ='david'
 > >         mixing_mode = 'plain'
 > >            conv_thr = 1.0d-6
 > >         mixing_beta = 0.3
 > >
 > > Thanks and regards
 > >
 > > Dimpy
 > >
 > > UCC,Ireland
 > >

Dimpy Sharma wrote:
> 
> Hi Friends,
> 
> The term spilling parameter is not much clear to me, though I read in 
> forum.It would be great if anyone can help me. Also  I would like to 
> know is there any standard value for spilling paramter for Si-H system.
> 
> Thanks and regards
> 
> Dimpy (PhD)
> 
> UCC,Ireland
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 


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

From elie.moujaes at hotmail.co.uk  Tue Mar  2 18:07:16 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Tue, 2 Mar 2010 17:07:16 +0000
Subject: [Pw_forum] from card_kpoints : error #         1
Message-ID: <SNT114-W25AA8AEE843E462B163142D33B0@phx.gbl>


Dear all,

 

I am running a program to get the band structure fro graphene and I am giving the K-POINTS in crystal type..i have got 101 points but when I run the program I get :

 

     from card_kpoints : error #         1
      error or end of file while reading crystal k points
 

The points are:

 

 

K_POINTS crystal
   101
   0.00000   0.00000   0.00000   1 
   0.01000   0.01000   0.00000   1
   0.02000   0.02000   0.00000   1
   0.03000   0.03000   0.00000   1
   0.04000   0.04000   0.00000   1
   0.05000   0.05000   0.00000   1
   0.06000   0.06000   0.00000   1
   0.07000   0.07000   0.00000   1
   0.08000   0.08000   0.00000   1
   0.09000   0.09000   0.00000   1
   0.10000   0.10000   0.00000   1
   0.11000   0.11000   0.00000   1
   0.12000   0.12000   0.00000   1
   0.13000   0.13000   0.00000   1
   0.14000   0.14000   0.00000   1
   0.15000   0.15000   0.00000   1
   0.16000   0.16000   0.00000   1
   0.17000   0.17000   0.00000   1
   0.18000   0.18000   0.00000   1
   0.19000   0.19000   0.00000   1
   0.20000   0.20000   0.00000   1
   0.21000   0.21000   0.00000   1
   0.22000   0.22000   0.00000   1
   0.23000   0.23000   0.00000   1
   0.24000   0.24000   0.00000   1
   0.25000   0.25000   0.00000   1
   0.26000   0.26000   0.00000   1
   0.27000   0.27000   0.00000   1
   0.28000   0.28000   0.00000   1
   0.29000   0.29000   0.00000   1
   0.30000   0.30000   0.00000   1
   0.31000   0.31000   0.00000   1
   0.32000   0.32000   0.00000   1
   0.33000   0.33000   0.00000   1
   0.34000   0.34000   0.00000   1
   0.35000   0.35000   0.00000   1
   0.36000   0.36000   0.00000   1
   0.37000   0.37000   0.00000   1
   0.38000   0.38000   0.00000   1
   0.39000   0.39000   0.00000   1
   0.40000   0.40000   0.00000   1
   0.41000   0.41000   0.00000   1
   0.42000   0.42000   0.00000   1
   0.43000   0.43000   0.00000   1
   0.44000   0.44000   0.00000   1
   0.45000   0.45000   0.00000   1
   0.46000   0.46000   0.00000   1
   0.47000   0.47000   0.00000   1
   0.48000   0.48000   0.00000   1
   0.49000   0.49000   0.00000   1
   0.50000   0.50000   0.00000   1
   0.50000   0.50000   0.00000   1
   0.49000   0.00000   0.00000   1
   0.48000   0.00000   0.00000   1
   0.47000   0.00000   0.00000   1
   0.46000   0.00000   0.00000   1
   0.45000   0.00000   0.00000   1
   0.44000   0.00000   0.00000   1
   0.43000   0.00000   0.00000   1
   0.42000   0.00000   0.00000   1
   0.41000   0.00000   0.00000   1
   0.40000   0.00000   0.00000   1
   0.39000   0.00000   0.00000   1
   0.38000   0.00000   0.00000   1
   0.37000   0.00000   0.00000   1
   0.36000   0.00000   0.00000   1
   0.35000   0.00000   0.00000   1
   0.34000   0.00000   0.00000   1
   0.33000   0.00000   0.00000   1
   0.32000   0.00000   0.00000   1
   0.31000   0.00000   0.00000   1
   0.30000   0.00000   0.00000   1
   0.29000   0.00000   0.00000   1
   0.28000   0.00000   0.00000   1
   0.27000   0.00000   0.00000   1
   0.26000   0.00000   0.00000   1
   0.25000   0.00000   0.00000   1
   0.24000   0.00000   0.00000   1
   0.23000   0.00000   0.00000   1
   0.22000   0.00000   0.00000   1
   0.21000   0.00000   0.00000   1
   0.20000   0.00000   0.00000   1
   0.19000   0.00000   0.00000   1
   0.18000   0.00000   0.00000   1
   0.17000   0.00000   0.00000   1
   0.16000   0.00000   0.00000   1
   0.15000   0.00000   0.00000   1
   0.14000   0.00000   0.00000   1
   0.13000   0.00000   0.00000   1
   0.12000   0.00000   0.00000   1
   0.11000   0.00000   0.00000   1
   0.10000   0.00000   0.00000   1
   0.09000   0.00000   0.00000   1
   0.08000   0.00000   0.00000   1
   0.07000   0.00000   0.00000   1
   0.06000   0.00000   0.00000   1
   0.05000   0.00000   0.00000   1
   0.04000   0.00000   0.00000   1
   0.03000   0.00000   0.00000   1
   0.02000   0.00000   0.00000   1
    0.01000   0.00000   0.00000          1

 

What could have gone wrong? Thankss

 

 


 		 	   		  
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From udayagiri3 at gmail.com  Tue Mar  2 18:35:13 2010
From: udayagiri3 at gmail.com (udayagiri sai babu)
Date: Tue, 2 Mar 2010 23:05:13 +0530
Subject: [Pw_forum] from card_kpoints : error # 1
In-Reply-To: <SNT114-W25AA8AEE843E462B163142D33B0@phx.gbl>
References: <SNT114-W25AA8AEE843E462B163142D33B0@phx.gbl>
Message-ID: <d3964cb11003020935i4d77427r6150c520d9e204ef@mail.gmail.com>

try out this K_POINTS {crystal}
instead of K_POINTS crystal

On Tue, Mar 2, 2010 at 10:37 PM, Elie Moujaes <elie.moujaes at hotmail.co.uk>wrote:

>  Dear all,
>
> I am running a program to get the band structure fro graphene and I am
> giving the K-POINTS in crystal type..i have got 101 points but when I run
> the program I get :
>
>
>      from card_kpoints : error #         1
>       error or end of file while reading crystal k points
>
> The points are:
>
>
>
> K_POINTS crystal
>
>    101
>
>    0.00000   0.00000   0.00000   1
>
>    0.01000   0.01000   0.00000   1
>
>    0.02000   0.02000   0.00000   1
>
>    0.03000   0.03000   0.00000   1
>
>    0.04000   0.04000   0.00000   1
>
>    0.05000   0.05000   0.00000   1
>
>    0.06000   0.06000   0.00000   1
>
>    0.07000   0.07000   0.00000   1
>
>    0.08000   0.08000   0.00000   1
>
>    0.09000   0.09000   0.00000   1
>
>    0.10000   0.10000   0.00000   1
>
>    0.11000   0.11000   0.00000   1
>
>    0.12000   0.12000   0.00000   1
>
>    0.13000   0.13000   0.00000   1
>
>    0.14000   0.14000   0.00000   1
>
>    0.15000   0.15000   0.00000   1
>
>    0.16000   0.16000   0.00000   1
>
>    0.17000   0.17000   0.00000   1
>
>    0.18000   0.18000   0.00000   1
>
>    0.19000   0.19000   0.00000   1
>
>    0.20000   0.20000   0.00000   1
>
>    0.21000   0.21000   0.00000   1
>
>    0.22000   0.22000   0.00000   1
>
>    0.23000   0.23000   0.00000   1
>
>    0.24000   0.24000   0.00000   1
>
>    0.25000   0.25000   0.00000   1
>
>    0.26000   0.26000   0.00000   1
>
>    0.27000   0.27000   0.00000   1
>
>    0.28000   0.28000   0.00000   1
>
>    0.29000   0.29000   0.00000   1
>
>    0.30000   0.30000   0.00000   1
>
>    0.31000   0.31000   0.00000   1
>
>    0.32000   0.32000   0.00000   1
>
>    0.33000   0.33000   0.00000   1
>
>    0.34000   0.34000   0.00000   1
>
>    0.35000   0.35000   0.00000   1
>
>    0.36000   0.36000   0.00000   1
>
>    0.37000   0.37000   0.00000   1
>
>    0.38000   0.38000   0.00000   1
>
>    0.39000   0.39000   0.00000   1
>
>    0.40000   0.40000   0.00000   1
>
>    0.41000   0.41000   0.00000   1
>
>    0.42000   0.42000   0.00000   1
>
>    0.43000   0.43000   0.00000   1
>
>    0.44000   0.44000   0.00000   1
>
>    0.45000   0.45000   0.00000   1
>
>    0.46000   0.46000   0.00000   1
>
>    0.47000   0.47000   0.00000   1
>
>    0.48000   0.48000   0.00000   1
>
>    0.49000   0.49000   0.00000   1
>
>    0.50000   0.50000   0.00000   1
>
>    0.50000   0.50000   0.00000   1
>
>    0.49000   0.00000   0.00000   1
>
>    0.48000   0.00000   0.00000   1
>
>    0.47000   0.00000   0.00000   1
>
>    0.46000   0.00000   0.00000   1
>
>    0.45000   0.00000   0.00000   1
>
>    0.44000   0.00000   0.00000   1
>
>    0.43000   0.00000   0.00000   1
>
>    0.42000   0.00000   0.00000   1
>
>    0.41000   0.00000   0.00000   1
>
>    0.40000   0.00000   0.00000   1
>
>    0.39000   0.00000   0.00000   1
>
>    0.38000   0.00000   0.00000   1
>
>    0.37000   0.00000   0.00000   1
>
>    0.36000   0.00000   0.00000   1
>
>    0.35000   0.00000   0.00000   1
>
>    0.34000   0.00000   0.00000   1
>
>    0.33000   0.00000   0.00000   1
>
>    0.32000   0.00000   0.00000   1
>
>    0.31000   0.00000   0.00000   1
>
>    0.30000   0.00000   0.00000   1
>
>    0.29000   0.00000   0.00000   1
>
>    0.28000   0.00000   0.00000   1
>
>    0.27000   0.00000   0.00000   1
>
>    0.26000   0.00000   0.00000   1
>
>    0.25000   0.00000   0.00000   1
>
>    0.24000   0.00000   0.00000   1
>
>    0.23000   0.00000   0.00000   1
>
>    0.22000   0.00000   0.00000   1
>
>    0.21000   0.00000   0.00000   1
>
>    0.20000   0.00000   0.00000   1
>
>    0.19000   0.00000   0.00000   1
>
>    0.18000   0.00000   0.00000   1
>
>    0.17000   0.00000   0.00000   1
>
>    0.16000   0.00000   0.00000   1
>
>    0.15000   0.00000   0.00000   1
>
>    0.14000   0.00000   0.00000   1
>
>    0.13000   0.00000   0.00000   1
>
>    0.12000   0.00000   0.00000   1
>
>    0.11000   0.00000   0.00000   1
>
>    0.10000   0.00000   0.00000   1
>
>    0.09000   0.00000   0.00000   1
>
>    0.08000   0.00000   0.00000   1
>
>    0.07000   0.00000   0.00000   1
>
>    0.06000   0.00000   0.00000   1
>
>    0.05000   0.00000   0.00000   1
>
>    0.04000   0.00000   0.00000   1
>
>    0.03000   0.00000   0.00000   1
>
>    0.02000   0.00000   0.00000   1
>     0.01000   0.00000   0.00000          1
>
> What could have gone wrong? Thankss
>
>
>
>
>
> ------------------------------
> Not got a Hotmail account? Sign-up now - Free<http://clk.atdmt.com/UKM/go/197222280/direct/01/>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
U.Saibabu
PhD student,
Deformation mechanisms modeling group,
Materials engineering department,
IISc Bangalore,
India.
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From elie.moujaes at hotmail.co.uk  Tue Mar  2 18:42:33 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Tue, 2 Mar 2010 17:42:33 +0000
Subject: [Pw_forum] from card_kpoints : error # 1
In-Reply-To: <d3964cb11003020935i4d77427r6150c520d9e204ef@mail.gmail.com>
References: <SNT114-W25AA8AEE843E462B163142D33B0@phx.gbl>,
	<d3964cb11003020935i4d77427r6150c520d9e204ef@mail.gmail.com>
Message-ID: <SNT114-W3081D3E9E5A8101029F363D33B0@phx.gbl>


Thanks for thr reply but is still not working..I tried

 

K_POINTS automatic

50 50 1 0 0 0

 

But the graph I get doesnt contain many points and it looks disconnected and not anywhere close to the real band structure. I am not sure if increasing the grid dimensions further would do any good.

 

 

regards
 


Date: Tue, 2 Mar 2010 23:05:13 +0530
From: udayagiri3 at gmail.com
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] from card_kpoints : error # 1

try out this K_POINTS {crystal}
instead of K_POINTS crystal


On Tue, Mar 2, 2010 at 10:37 PM, Elie Moujaes <elie.moujaes at hotmail.co.uk> wrote:


Dear all,
 
I am running a program to get the band structure fro graphene and I am giving the K-POINTS in crystal type..i have got 101 points but when I run the program I get :
 

     from card_kpoints : error #         1
      error or end of file while reading crystal k points
 
The points are:
 
 

K_POINTS crystal

   101

   0.00000   0.00000   0.00000   1 

   0.01000   0.01000   0.00000   1

   0.02000   0.02000   0.00000   1

   0.03000   0.03000   0.00000   1

   0.04000   0.04000   0.00000   1

   0.05000   0.05000   0.00000   1

   0.06000   0.06000   0.00000   1

   0.07000   0.07000   0.00000   1

   0.08000   0.08000   0.00000   1

   0.09000   0.09000   0.00000   1

   0.10000   0.10000   0.00000   1

   0.11000   0.11000   0.00000   1

   0.12000   0.12000   0.00000   1

   0.13000   0.13000   0.00000   1

   0.14000   0.14000   0.00000   1

   0.15000   0.15000   0.00000   1

   0.16000   0.16000   0.00000   1

   0.17000   0.17000   0.00000   1

   0.18000   0.18000   0.00000   1

   0.19000   0.19000   0.00000   1

   0.20000   0.20000   0.00000   1

   0.21000   0.21000   0.00000   1

   0.22000   0.22000   0.00000   1

   0.23000   0.23000   0.00000   1

   0.24000   0.24000   0.00000   1

   0.25000   0.25000   0.00000   1

   0.26000   0.26000   0.00000   1

   0.27000   0.27000   0.00000   1

   0.28000   0.28000   0.00000   1

   0.29000   0.29000   0.00000   1

   0.30000   0.30000   0.00000   1

   0.31000   0.31000   0.00000   1

   0.32000   0.32000   0.00000   1

   0.33000   0.33000   0.00000   1

   0.34000   0.34000   0.00000   1

   0.35000   0.35000   0.00000   1

   0.36000   0.36000   0.00000   1

   0.37000   0.37000   0.00000   1

   0.38000   0.38000   0.00000   1

   0.39000   0.39000   0.00000   1

   0.40000   0.40000   0.00000   1

   0.41000   0.41000   0.00000   1

   0.42000   0.42000   0.00000   1

   0.43000   0.43000   0.00000   1

   0.44000   0.44000   0.00000   1

   0.45000   0.45000   0.00000   1

   0.46000   0.46000   0.00000   1

   0.47000   0.47000   0.00000   1

   0.48000   0.48000   0.00000   1

   0.49000   0.49000   0.00000   1

   0.50000   0.50000   0.00000   1

   0.50000   0.50000   0.00000   1

   0.49000   0.00000   0.00000   1

   0.48000   0.00000   0.00000   1

   0.47000   0.00000   0.00000   1

   0.46000   0.00000   0.00000   1

   0.45000   0.00000   0.00000   1

   0.44000   0.00000   0.00000   1

   0.43000   0.00000   0.00000   1

   0.42000   0.00000   0.00000   1

   0.41000   0.00000   0.00000   1

   0.40000   0.00000   0.00000   1

   0.39000   0.00000   0.00000   1

   0.38000   0.00000   0.00000   1

   0.37000   0.00000   0.00000   1

   0.36000   0.00000   0.00000   1

   0.35000   0.00000   0.00000   1

   0.34000   0.00000   0.00000   1

   0.33000   0.00000   0.00000   1

   0.32000   0.00000   0.00000   1

   0.31000   0.00000   0.00000   1

   0.30000   0.00000   0.00000   1

   0.29000   0.00000   0.00000   1

   0.28000   0.00000   0.00000   1

   0.27000   0.00000   0.00000   1

   0.26000   0.00000   0.00000   1

   0.25000   0.00000   0.00000   1

   0.24000   0.00000   0.00000   1

   0.23000   0.00000   0.00000   1

   0.22000   0.00000   0.00000   1

   0.21000   0.00000   0.00000   1

   0.20000   0.00000   0.00000   1

   0.19000   0.00000   0.00000   1

   0.18000   0.00000   0.00000   1

   0.17000   0.00000   0.00000   1

   0.16000   0.00000   0.00000   1

   0.15000   0.00000   0.00000   1

   0.14000   0.00000   0.00000   1

   0.13000   0.00000   0.00000   1

   0.12000   0.00000   0.00000   1

   0.11000   0.00000   0.00000   1

   0.10000   0.00000   0.00000   1

   0.09000   0.00000   0.00000   1

   0.08000   0.00000   0.00000   1

   0.07000   0.00000   0.00000   1

   0.06000   0.00000   0.00000   1

   0.05000   0.00000   0.00000   1

   0.04000   0.00000   0.00000   1

   0.03000   0.00000   0.00000   1

   0.02000   0.00000   0.00000   1
    0.01000   0.00000   0.00000          1
 
What could have gone wrong? Thankss

 
 







Not got a Hotmail account? Sign-up now - Free
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum



-- 
U.Saibabu
PhD student,
Deformation mechanisms modeling group,
Materials engineering department,
IISc Bangalore,
India.

 		 	   		  
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From paulatto at sissa.it  Tue Mar  2 18:42:42 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 02 Mar 2010 18:42:42 +0100
Subject: [Pw_forum] from card_kpoints : error #         1
In-Reply-To: <SNT114-W25AA8AEE843E462B163142D33B0@phx.gbl>
References: <SNT114-W25AA8AEE843E462B163142D33B0@phx.gbl>
Message-ID: <op.u8ybhga1a8x26q@vanoxite.impmc.jussieu.fr>

On Tue, 02 Mar 2010 18:07:16 +0100, Elie Moujaes  
<elie.moujaes at hotmail.co.uk> wrote:
> I am running a program to get the band structure fro graphene and I am  
> giving the K-POINTS in crystal type..i have got 101 points but when I  
> run the program I get :

Dear Elie,
I've checked and it looks like you have indeed listed 101 kpoint. Another  
possibilities is that theer are some strange characters in the file: what  
do you see if you issue the following command?
  cat -v my_input_file

any "non-printable" character should be converted to sequences of  
printable symbols.

cheers

-- 
Lorenzo Paulatto

*** Note: my affiliation has changed! please send future
correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***

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

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

From elie.moujaes at hotmail.co.uk  Tue Mar  2 18:56:58 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Tue, 2 Mar 2010 17:56:58 +0000
Subject: [Pw_forum] from card_kpoints : error #         1
In-Reply-To: <op.u8ybhga1a8x26q@vanoxite.impmc.jussieu.fr>
References: <SNT114-W25AA8AEE843E462B163142D33B0@phx.gbl>,
	<op.u8ybhga1a8x26q@vanoxite.impmc.jussieu.fr>
Message-ID: <SNT114-W43491D11777CF60CAF7AE6D33B0@phx.gbl>


Dear Lorenzo,

 

I have issued the command and I get all the input file printed with a ^M  at the end of every lin except at the line containing the point 

 

0.01000  0.01000 0.00000   1 (the second line in the K-oints series) where I see:

 

M- M- M- 0.01000 M-   0.010000     0.000001^M

 

Is thins a sign that something is going wrong there?

 

Thanks

 

Elie


 
> To: pw_forum at pwscf.org
> Date: Tue, 2 Mar 2010 18:42:42 +0100
> From: paulatto at sissa.it
> Subject: Re: [Pw_forum] from card_kpoints : error # 1
> 
> On Tue, 02 Mar 2010 18:07:16 +0100, Elie Moujaes 
> <elie.moujaes at hotmail.co.uk> wrote:
> > I am running a program to get the band structure fro graphene and I am 
> > giving the K-POINTS in crystal type..i have got 101 points but when I 
> > run the program I get :
> 
> Dear Elie,
> I've checked and it looks like you have indeed listed 101 kpoint. Another 
> possibilities is that theer are some strange characters in the file: what 
> do you see if you issue the following command?
> cat -v my_input_file
> 
> any "non-printable" character should be converted to sequences of 
> printable symbols.
> 
> cheers
> 
> -- 
> Lorenzo Paulatto
> 
> *** Note: my affiliation has changed! please send future
> correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***
> 
> post-doc @ IMPMC/UPMC - Universit? Paris 6
> phone: +33 (0)1 44 27 74 89
> www: http://www-int.impmc.upmc.fr/~paulatto/
> 
> previously:
> phd student @ SISSA & DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> www: http://people.sissa.it/~paulatto/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
_________________________________________________________________
Send us your Hotmail stories and be featured in our newsletter
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From paulatto at sissa.it  Tue Mar  2 19:40:17 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 02 Mar 2010 19:40:17 +0100
Subject: [Pw_forum] from card_kpoints : error #         1
In-Reply-To: <SNT114-W43491D11777CF60CAF7AE6D33B0@phx.gbl>
References: <SNT114-W25AA8AEE843E462B163142D33B0@phx.gbl>
	<op.u8ybhga1a8x26q@vanoxite.impmc.jussieu.fr>
	<SNT114-W43491D11777CF60CAF7AE6D33B0@phx.gbl>
Message-ID: <op.u8yd5fj6a8x26q@vanoxite.impmc.jussieu.fr>

On Tue, 02 Mar 2010 18:56:58 +0100, Elie Moujaes  
<elie.moujaes at hotmail.co.uk> wrote:
> Is thins a sign that something is going wrong there?

It depends on the editor you have used to create the file. Normally the ^M  
are harmless (they are windows-style line termination, which most  
compilers can digest). In order to get rid of them you can eitehr used  
dos2unix (a command-line utility) or with the following command:
   cat -v input.file |sed -e 's/\^M'//g' -e 's/M-//g' > input2.file
it will create a file called input2.file which does not contain any  
"strange characters" and will also remove the "M-", which I have no idea  
what they were, but are probably the real cause of the error.

-- 
Lorenzo Paulatto

*** Note: my affiliation has changed! please send future
correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***

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

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

From Trinh.Vo at jpl.nasa.gov  Tue Mar  2 21:52:02 2010
From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Tue, 2 Mar 2010 12:52:02 -0800
Subject: [Pw_forum] Generate pseudopotential for Sb
Message-ID: <C7B2BA72.177D%Trinh.Vo@jpl.nasa.gov>

Dear PWSCF Users,

I used ld1.x to generate PP for Sb.  I have problem with the 4d wfc.  When I plot the pseudized wfc and the all-electron wfc do not coincide even though I try to change Rcut.  I am not if I made any mistake in the input.    I tried both TM and RRKJ, but I could not fix the problem. I appreciate if you could help me on this.  Below is my input:

&input
    title='Sb'
    zed=51.
    rel=2,

    rlderiv=2.2,
    eminld=-14.0,
    emaxld=8.0,
    deld=0.01d0,
    nld=4,

    config='[Kr] 4d10.0 5s2.0 5p3.0 5d-2.0'
    iswitch=3,
    dft='PBE'
 /
 &inputp
   lloc=0,
   pseudotype=2,
   file_pseudopw='Sb.rel-pbe-rrkj.UPF',
   nlcc = .true.
!  tm = .true.
!   rcore = 0.7
   author='abc?
 /
9
5P  2  1  2.00  0.00  2.70  2.70  0.50
5P  2  1  1.00  0.00  2.70  2.70  1.50
4D  3  2  4.00  0.00  0.80  0.80  1.50
4D  3  2  0.00 -0.20  0.80  0.80  1.50
4D  3  2  6.00  0.00  0.80  0.80  2.50
4D  3  2  0.00 -0.20  0.80  0.80  2.50
5D  3  2 -2.00  0.20  2.70  2.70  1.50
5D  3  2 -2.00  0.20  2.70  2.70  2.50
5S  1  0  2.00  0.00  1.90  1.90  0.50

Best,
Trinh Vo

JPL/CalTech

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From ackaur at ucdavis.edu  Tue Mar  2 21:58:12 2010
From: ackaur at ucdavis.edu (Amandeep Kaur)
Date: Tue, 2 Mar 2010 12:58:12 -0800
Subject: [Pw_forum] Use of ecfixed, qcutz,
	q2sigma in a scf calculation following 	vc-relax
Message-ID: <45e2e0d21003021258x4f3138f4j4d6fab08b034bc40@mail.gmail.com>

Hello

I did vc-relax calculation for ZrNCl and I got the optimized geometry.
Then I did a scf calculation using the relaxed coordinates and atomic
positions and I incorporated the ecfixed, qcutz and q2sigma in the scf
calculation. Then I did a phonon calculation using the same prefix as
in the scf calculation ( phonon calculation follows from a scf
calculation) and I got negative optical frequencies. Is this due to
the use of ecfixed, qcutz and q2sigma in the scf calculation because I
ran one scf calculation using the optimized geometry without using the
above parameters and did a phonon calculation following scf
calculation and there were no negative phonon frequencies.

Are these parameters (ecfixed, qcutz and q2sigma) only to be used for
vc-relax not for the scf calculation even if we want to use the
optimized geometry because the pressure from the scf calculation using
optimized geometry comes out to be small but not exactly the same as
that of vc-relax calculation.

Then the question is that should these parameters (ecfixed, qcutz and
q2sigma) be used or not for scf calculations because I got negative
optical phonon frequencies though I am using optimized geometry.

Any help will be appreciated.

Thanks


-- 
Amandeep Kaur
Graduate Student
Department of Physics
University of California,Davis

From elie.moujaes at hotmail.co.uk  Tue Mar  2 22:00:32 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Tue, 2 Mar 2010 21:00:32 +0000
Subject: [Pw_forum] from card_kpoints : error #         1
In-Reply-To: <op.u8yd5fj6a8x26q@vanoxite.impmc.jussieu.fr>
References: <SNT114-W25AA8AEE843E462B163142D33B0@phx.gbl>,
	<op.u8ybhga1a8x26q@vanoxite.impmc.jussieu.fr>,
	<SNT114-W43491D11777CF60CAF7AE6D33B0@phx.gbl>,
	<op.u8yd5fj6a8x26q@vanoxite.impmc.jussieu.fr>
Message-ID: <SNT114-W1374D099AC3796701C5965D33B0@phx.gbl>


I would just like to let you know that the problem is solved. There was something about the input. I only included two digits after the zero and changed the 1 in the last column to 0.10 and also omitted the word crystal at the end of K_POINTS and it worked out , i.e:

 

K_POINTS 
   101
   0.00 0.00 0.00  0.10
   0.01 0.01 0.00  0.10
   0.02 0.02 0.00  0.10
   0.03 0.03 0.00  0.10
   0.04 0.04 0.00  0.10
   0.05 0.05 0.00  0.10
   0.06 0.06 0.00  0.10
   0.07 0.07 0.00  0.10
   0.08 0.08 0.00  0.10
   0.09 0.09 0.00  0.10
   0.10 0.10 0.00  0.10
   0.11 0.11 0.00  0.10
   0.12 0.12 0.00  0.10
   0.13 0.13 0.00  0.10
   0.14 0.14 0.00  0.10
   0.15 0.15 0.00  0.10
   0.16 0.16 0.00  0.10
   0.17 0.17 0.00  0.10
   0.18 0.18 0.00  0.10
   0.19 0.19 0.00  0.10
   0.20 0.20 0.00  0.10
   0.21 0.21 0.00  0.10
   0.22 0.22 0.00  0.10
   0.23 0.23 0.00  0.10
   0.24 0.24 0.00  0.10
   0.25 0.25 0.00  0.10
   0.26 0.26 0.00  0.10
   0.27 0.27 0.00  0.10
   0.28 0.28 0.00  0.10
   0.29 0.29 0.00  0.10
   0.30 0.30 0.00  0.10
   0.31 0.31 0.00  0.10
   0.32 0.32 0.00  0.10
   0.33 0.33 0.00  0.10
   0.34 0.34 0.00  0.10
   0.35 0.35 0.00  0.10
   0.36 0.36 0.00  0.10
   0.37 0.37 0.00  0.10
   0.38 0.38 0.00  0.10
   0.39 0.39 0.00  0.10
   0.40 0.30 0.00  0.10
   0.41 0.41 0.00  0.10
   0.42 0.42 0.00  0.10
   0.43 0.43 0.00  0.10
   0.44 0.44 0.00  0.10
   0.45 0.45 0.00  0.10
   0.46 0.46 0.00  0.10
   0.47 0.47 0.00  0.10
   0.48 0.48 0.00  0.10
   0.49 0.49 0.00  0.10
   0.50 0.50 0.00  0.10
   0.50 0.50 0.00  0.10
   0.49 0.00 0.00  0.10
   0.48 0.00 0.00  0.10
   0.47 0.00 0.00  0.10
   0.46 0.00 0.00  0.10
   0.45 0.00 0.00  0.10
   0.44 0.00 0.00  0.10
   0.43 0.00 0.00  0.10
   0.42 0.00 0.00  0.10
   0.41 0.00 0.00  0.10
   0.40 0.00 0.00  0.10
   0.39 0.00 0.00  0.10
   0.38 0.00 0.00  0.10
   0.37 0.00 0.00  0.10
   0.36 0.00 0.00  0.10
   0.35 0.00 0.00  0.10
   0.34 0.00 0.00  0.10
   0.33 0.00 0.00  0.10
   0.32 0.00 0.00  0.10
   0.31 0.00 0.00  0.10
   0.30 0.00 0.00  0.10
   0.29 0.00 0.00  0.10
   0.28 0.00 0.00  0.10
   0.27 0.00 0.00  0.10
   0.26 0.00 0.00  0.10
   0.25 0.00 0.00  0.10
   0.24 0.00 0.00  0.10
   0.23 0.00 0.00  0.10
   0.22 0.00 0.00  0.10
   0.21 0.00 0.00  0.10
   0.20 0.00 0.00  0.10
   0.19 0.00 0.00  0.10
   0.18 0.00 0.00  0.10
   0.17 0.00 0.00  0.10
   0.16 0.00 0.00  0.10
   0.15 0.00 0.00  0.10
   0.14 0.00 0.00  0.10
   0.13 0.00 0.00  0.10
   0.12 0.00 0.00  0.10
   0.11 0.00 0.00  0.10
   0.10 0.00 0.00  0.10
   0.09 0.00 0.00  0.10
   0.08 0.00 0.00  0.10
   0.07 0.00 0.00  0.10
   0.06 0.00 0.00  0.10
   0.05 0.00 0.00  0.10
   0.04 0.00 0.00  0.10
   0.03 0.00 0.00  0.10
   0.02 0.00 0.00  0.10
   0.01 0.00 0.00  0.10 

 

Thanks for your help,

 

Elie


 
> To: pw_forum at pwscf.org
> Date: Tue, 2 Mar 2010 19:40:17 +0100
> From: paulatto at sissa.it
> Subject: Re: [Pw_forum] from card_kpoints : error # 1
> 
> On Tue, 02 Mar 2010 18:56:58 +0100, Elie Moujaes 
> <elie.moujaes at hotmail.co.uk> wrote:
> > Is thins a sign that something is going wrong there?
> 
> It depends on the editor you have used to create the file. Normally the ^M 
> are harmless (they are windows-style line termination, which most 
> compilers can digest). In order to get rid of them you can eitehr used 
> dos2unix (a command-line utility) or with the following command:
> cat -v input.file |sed -e 's/\^M'//g' -e 's/M-//g' > input2.file
> it will create a file called input2.file which does not contain any 
> "strange characters" and will also remove the "M-", which I have no idea 
> what they were, but are probably the real cause of the error.
> 
> -- 
> Lorenzo Paulatto
> 
> *** Note: my affiliation has changed! please send future
> correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***
> 
> post-doc @ IMPMC/UPMC - Universit? Paris 6
> phone: +33 (0)1 44 27 74 89
> www: http://www-int.impmc.upmc.fr/~paulatto/
> 
> previously:
> phd student @ SISSA & DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> www: http://people.sissa.it/~paulatto/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
_________________________________________________________________
Tell us your greatest, weirdest and funniest Hotmail stories
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From zdw2000 at gmail.com  Wed Mar  3 02:12:21 2010
From: zdw2000 at gmail.com (Wei Zhou)
Date: Wed, 3 Mar 2010 09:12:21 +0800
Subject: [Pw_forum] about the from scale_h : error
Message-ID: <3e36a8fc1003021712j39cb327bid162079462584697@mail.gmail.com>

dear all
 I relax the hex barium under high pressure about 500kba using the
pwscf4.1.2, and I alwalys meet a error as following
     task #         2
     from scale_h : error #         1
     Not enough space allocated for radial FFT: try restarting with a larger
cell_factor.  %%%%
in fact I have search the forum and find similar problem
http://www.democritos.it/pipermail/pw_forum/2009-September/014472.html
but I donnot know  how to deal with this problem.
any help will be appreciated




-- 
ZhouDawei
JiLin Universiyt ,ChangChun ,China
zdw2000 at gmail.com
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From bw.hu at yahoo.com  Wed Mar  3 04:26:35 2010
From: bw.hu at yahoo.com (Bingwen Hu)
Date: Tue, 2 Mar 2010 19:26:35 -0800 (PST)
Subject: [Pw_forum] File Error of GIPAW module
In-Reply-To: <7332fead1003020327p504692c5ma476b7a24e95def3@mail.gmail.com>
References: <735351.43390.qm@web57612.mail.re1.yahoo.com>
	<7332fead1003020327p504692c5ma476b7a24e95def3@mail.gmail.com>
Message-ID: <980258.85813.qm@web57614.mail.re1.yahoo.com>

Dear Gorank?
  Thank you for your help. I see where is  the problem.

Best
Bingwen





________________________________
From: Goranka Bilalbegovic <gbilalbegovic at gmail.com>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Tue, March 2, 2010 7:27:57 PM
Subject: Re: [Pw_forum] File Error of GIPAW module

On Tue, Mar 2, 2010 at 5:08 AM, Bingwen Hu <bw.hu at yahoo.com> wrote:
   I have attached the input file for the PWSC. All the pseudo potentials I used are downloaded in the quantum-espresso website http://www.quantum-espresso.org/pseudo.php.
  Thank you for your help in advance.



Dear Bingwen,

NMR calculations in Quantum Espresso are implemented within the GIPAW model. These calculations are possible only if we use a special kind of GIPAW pseudopotentials, and not all pseudopotentials available on the QE pp page.

Plese check the video/presentation lecture by Ari Seitsonen on: http://www.quantum-espresso.org/wiki/index.php/QESB09 and read several articles referenced there.  Also plese search QE mailing list for "GIPAW".


Best regards,
Goranka Bilalbegovic
Department of Physics,
Faculty of Science, University of Zagreb
Croatia



      
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From nnlinh at sissa.it  Wed Mar  3 09:08:56 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Wed, 03 Mar 2010 09:08:56 +0100
Subject: [Pw_forum] about the from scale_h : error
In-Reply-To: <3e36a8fc1003021712j39cb327bid162079462584697@mail.gmail.com>
References: <3e36a8fc1003021712j39cb327bid162079462584697@mail.gmail.com>
Message-ID: <4B8E1918.4080407@sissa.it>

Wei Zhou wrote:
> dear all
>  I relax the hex barium under high pressure about 500kba using the 
> pwscf4.1.2, and I alwalys meet a error as following 
>      task #         2
>      from scale_h : error #         1
>      Not enough space allocated for radial FFT: try restarting with a 
> larger cell_factor.  %%%%
> in fact I have search the forum and find similar problem
> http://www.democritos.it/pipermail/pw_forum/2009-September/014472.html
> but I donnot know  how to deal with this problem.
- Have you tried to do some ways as well as the previous suggestions?   

- Why don't you post up the  input file of your run?

Linh


> any help will be appreciated
>  
>  
>  
>
> -- 
> ZhouDawei
> JiLin Universiyt ,ChangChun ,China
> zdw2000 at gmail.com <mailto:zdw2000 at gmail.com>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From giannozz at democritos.it  Wed Mar  3 09:29:47 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 3 Mar 2010 09:29:47 +0100
Subject: [Pw_forum] about the from scale_h : error
In-Reply-To: <3e36a8fc1003021712j39cb327bid162079462584697@mail.gmail.com>
References: <3e36a8fc1003021712j39cb327bid162079462584697@mail.gmail.com>
Message-ID: <6D246D86-8C87-468D-9AC8-FD59A438C8B0@democritos.it>


On Mar 3, 2010, at 2:12 , Wei Zhou wrote:

> in fact I have search the forum and find similar problem
> http://www.democritos.it/pipermail/pw_forum/2009-September/014472.html
> but I donnot know  how to deal with this problem.

did you read the reply?
http://www.democritos.it/pipermail/pw_forum/2009-September/014473.html

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




From nnlinh at sissa.it  Wed Mar  3 09:28:05 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Wed, 03 Mar 2010 09:28:05 +0100
Subject: [Pw_forum] Use of ecfixed, qcutz,
 q2sigma in a scf calculation following 	vc-relax
In-Reply-To: <45e2e0d21003021258x4f3138f4j4d6fab08b034bc40@mail.gmail.com>
References: <45e2e0d21003021258x4f3138f4j4d6fab08b034bc40@mail.gmail.com>
Message-ID: <4B8E1D95.7000208@sissa.it>

Amandeep Kaur wrote:
> Hello
>
> I did vc-relax calculation for ZrNCl and I got the optimized geometry.
> Then I did a scf calculation using the relaxed coordinates and atomic
> positions and I incorporated the ecfixed, qcutz and q2sigma in the scf
> calculation. Then I did a phonon calculation using the same prefix as
> in the scf calculation ( phonon calculation follows from a scf
> calculation) and I got negative optical frequencies. 
Normally, a negative optical frequency specifies a case of unstable 
configuration.
> Is this due to
> the use of ecfixed, qcutz and q2sigma in the scf calculation because I
> ran one scf calculation using the optimized geometry without using the
> above parameters and did a phonon calculation following scf
> calculation and there were no negative phonon frequencies.
The problem possibly comes from non-synchronization of vc-relax and scf 
calculation functional, and it could result that the optimal geometry of 
vc-relax is not the optimal geometry of scf calculation.
> Are these parameters (ecfixed, qcutz and q2sigma) only to be used for
> vc-relax not for the scf calculation even if we want to use the
> optimized geometry because the pressure from the scf calculation using
> optimized geometry comes out to be small but not exactly the same as
> that of vc-relax calculation. Then the question is that should these parameters (ecfixed, qcutz and q2sigma) be used or not for scf calculations because I got negative optical phonon frequencies though I am using optimized geometry.
>
>   
I suggest that you should recalculate and synchronize functional in both 
vc-relax and scf, which is done by either keeping these parameters or 
removing them for both calculations.

Good luck

Linh
> Any help will be appreciated.
>
> Thanks
>
>
>   


From ackaur at ucdavis.edu  Wed Mar  3 09:44:57 2010
From: ackaur at ucdavis.edu (Amandeep Kaur)
Date: Wed, 3 Mar 2010 00:44:57 -0800
Subject: [Pw_forum] Use of ecfixed, qcutz,
	q2sigma in a scf calculation 	following vc-relax
In-Reply-To: <4B8E1D95.7000208@sissa.it>
References: <45e2e0d21003021258x4f3138f4j4d6fab08b034bc40@mail.gmail.com>
	<4B8E1D95.7000208@sissa.it>
Message-ID: <45e2e0d21003030044s56187c02xd6a55d424369e4bb@mail.gmail.com>

Thanks

If we remove those parameters in vc-relax calculation then it doesnt work
properly (non-zero pressure) . The scf calculation after using optimized
geometry gives almost zero pressure even if I dont use those parameters
(ecfixed, qcutz, q2sigma) but things change for phonon frequencies. I get
negative phonon frequencies (optical) by keeping those parameters inside the
scf calculation after which the phonon calculation follows.
*
*
*Aman
*

On Wed, Mar 3, 2010 at 12:28 AM, Ngoc Linh Nguyen <nnlinh at sissa.it> wrote:
> Amandeep Kaur wrote:
>> Hello
>>
>> I did vc-relax calculation for ZrNCl and I got the optimized geometry.
>> Then I did a scf calculation using the relaxed coordinates and atomic
>> positions and I incorporated the ecfixed, qcutz and q2sigma in the scf
>> calculation. Then I did a phonon calculation using the same prefix as
>> in the scf calculation ( phonon calculation follows from a scf
>> calculation) and I got negative optical frequencies.
> Normally, a negative optical frequency specifies a case of unstable
> configuration.
>> Is this due to
>> the use of ecfixed, qcutz and q2sigma in the scf calculation because I
>> ran one scf calculation using the optimized geometry without using the
>> above parameters and did a phonon calculation following scf
>> calculation and there were no negative phonon frequencies.
> The problem possibly comes from non-synchronization of vc-relax and scf
> calculation functional, and it could result that the optimal geometry of
> vc-relax is not the optimal geometry of scf calculation.
>> Are these parameters (ecfixed, qcutz and q2sigma) only to be used for
>> vc-relax not for the scf calculation even if we want to use the
>> optimized geometry because the pressure from the scf calculation using
>> optimized geometry comes out to be small but not exactly the same as
>> that of vc-relax calculation. Then the question is that should these
parameters (ecfixed, qcutz and q2sigma) be used or not for scf calculations
because I got negative optical phonon frequencies though I am using
optimized geometry.
>>
>>
> I suggest that you should recalculate and synchronize functional in both
> vc-relax and scf, which is done by either keeping these parameters or
> removing them for both calculations.
>
> Good luck
>
> Linh
>> Any help will be appreciated.
>>
>> Thanks
>>
>>
>>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Amandeep Kaur
Graduate Student
Department of Physics
University of California,Davis
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From giannozz at democritos.it  Wed Mar  3 09:51:41 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 3 Mar 2010 09:51:41 +0100
Subject: [Pw_forum] Use of ecfixed, qcutz,
	q2sigma in a scf calculation 	following vc-relax
In-Reply-To: <45e2e0d21003030044s56187c02xd6a55d424369e4bb@mail.gmail.com>
References: <45e2e0d21003021258x4f3138f4j4d6fab08b034bc40@mail.gmail.com>
	<4B8E1D95.7000208@sissa.it>
	<45e2e0d21003030044s56187c02xd6a55d424369e4bb@mail.gmail.com>
Message-ID: <7A486E71-F002-4303-8B93-89155D054BA3@democritos.it>


On Mar 3, 2010, at 9:44 , Amandeep Kaur wrote:

> I get negative phonon frequencies (optical) by keeping those  
> parameters
> inside the scf calculation after which the phonon calculation follows.

I don't think that the phonon code knows about the functional with  
modified
kinetic energy, so you shouldn't use it for phonon calculations.

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




From ackaur at ucdavis.edu  Wed Mar  3 09:57:23 2010
From: ackaur at ucdavis.edu (Amandeep Kaur)
Date: Wed, 3 Mar 2010 00:57:23 -0800
Subject: [Pw_forum] Use of ecfixed, qcutz,
	q2sigma in a scf calculation 	following vc-relax
In-Reply-To: <7A486E71-F002-4303-8B93-89155D054BA3@democritos.it>
References: <45e2e0d21003021258x4f3138f4j4d6fab08b034bc40@mail.gmail.com>
	<4B8E1D95.7000208@sissa.it>
	<45e2e0d21003030044s56187c02xd6a55d424369e4bb@mail.gmail.com>
	<7A486E71-F002-4303-8B93-89155D054BA3@democritos.it>
Message-ID: <45e2e0d21003030057q18bbb334i91de8583dc02787d@mail.gmail.com>

Thanks. That clarifies a lot of things.

Aman

On Wed, Mar 3, 2010 at 12:51 AM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Mar 3, 2010, at 9:44 , Amandeep Kaur wrote:
>
> > I get negative phonon frequencies (optical) by keeping those
> > parameters
> > inside the scf calculation after which the phonon calculation follows.
>
> I don't think that the phonon code knows about the functional with
> modified
> kinetic energy, so you shouldn't use it for phonon calculations.
>
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Amandeep Kaur
Graduate Student
Department of Physics
University of California,Davis
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From paulatto at sissa.it  Wed Mar  3 11:19:00 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 03 Mar 2010 11:19:00 +0100
Subject: [Pw_forum] Generate pseudopotential for Sb
In-Reply-To: <C7B2BA72.177D%Trinh.Vo@jpl.nasa.gov>
References: <C7B2BA72.177D%Trinh.Vo@jpl.nasa.gov>
Message-ID: <op.u8zllywba8x26q@vanoxite.impmc.jussieu.fr>

On Tue, 02 Mar 2010 21:52:02 +0100, Vo, Trinh (388C)  
<Trinh.Vo at jpl.nasa.gov> wrote:
> I used ld1.x to generate PP for Sb.  I have problem with the 4d wfc.   
> When I plot the pseudized wfc and the all-electron wfc do not coincide  
> even though I try to change Rcut.  I am not if I made any mistake in the  
> input.    I tried both TM and RRKJ, but I could not fix the problem. I  
> appreciate if you could help me on this.  Below is my input:

Dear Trinh,
of course they do not coincide: they are called "pseudo" for a reason. The  
coincide only outside the ultra-soft cutoff radius. I've checked them with  
gnuplot and this is actually the case: everything is working well.

cheers


P.S.
>   author='abc?
The closing ' above is not an apostrophe, but one of those inverted  
apostrophes that msword puts in document (it caused my ld1.x to crash).


-- 
Lorenzo Paulatto

*** Note: my affiliation has changed! please send future
correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***

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

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

From pc229 at kent.ac.uk  Wed Mar  3 12:17:03 2010
From: pc229 at kent.ac.uk (P.Canepa)
Date: Wed, 3 Mar 2010 11:17:03 +0000
Subject: [Pw_forum] "Mulliken population" and dos pojections
Message-ID: <42054E10C02CD44D81EF510077A30A0725A70FA0E1@MAPI.ad.kent.ac.uk>

Hey guys,

Just a little question, is in PWscf something like Mulliken population analysis? I was trying to get out of my dos their d character (namely  t2g and eg)!
There is any match between the order as the dos projections are printed and what will be printed within the "Mulliken population analysis or whatever", that for certain quantum espresso has already implemented?
Basically if in my projection is something like: pdosup(E)    pdosup(E)   pdosup(E)   pdosup(E)    pdosup(E) , the Mulliken routine will print out the population in the same order?

Many thanks, Piero 


-- 
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom

e-mail: pc229 at kent.ac.uk
mobile: +44 (0) 7772-9756456
-----------------------------------------------------------

From zdw2000 at gmail.com  Wed Mar  3 12:30:32 2010
From: zdw2000 at gmail.com (Wei Zhou)
Date: Wed, 3 Mar 2010 19:30:32 +0800
Subject: [Pw_forum] about the from scale_h : error
In-Reply-To: <4B8E1918.4080407@sissa.it>
References: <3e36a8fc1003021712j39cb327bid162079462584697@mail.gmail.com>
	<4B8E1918.4080407@sissa.it>
Message-ID: <3e36a8fc1003030330u7cb70fe7sf225faab87ad5392@mail.gmail.com>

2010/3/3 Ngoc Linh Nguyen <nnlinh at sissa.it>

> Wei Zhou wrote:
> > dear all
> >  I relax the hex barium under high pressure about 500kba using the
> > pwscf4.1.2, and I alwalys meet a error as following
> >      task #         2
> >      from scale_h : error #         1
> >      Not enough space allocated for radial FFT: try restarting with a
> > larger cell_factor.  %%%%
> > in fact I have search the forum and find similar problem
> > http://www.democritos.it/pipermail/pw_forum/2009-September/014472.html
> > but I donnot know  how to deal with this problem.
> - Have you tried to do some ways as well as the previous suggestions?
>
> - Why don't you post up the  input file of your run?
>
the following is the input file,

>  &control
>     calculation='vc-relax',
>     restart_mode='from_scratch',
>     dt=80,
>     prefix='ba',
>     pseudo_dir = '/home/solid/Work/PW/pseudo/',
>     outdir='/home/solid/Work/PW/temp/'
>     tstress=.t.,
>     tprnfor=.t.
>     nstep= 100
> /
>  &system
>     ibrav= 4,
>     celldm(1)=6.015350,
>     celldm(3)=1.58,
>     nat= 2,
>     ntyp=1,
>     nbnd=30
>     ecutwfc=45.0,ecutrho = 450
>     nosym = .F. ,
>     occupations = 'smearing' ,
>     degauss = 0.05D0 ,
>     smearing = 'methfessel-paxton' ,
> /
>  &electrons
>     mixing_beta = 0.7
>     conv_thr =  1.0d-9
> /
>  &IONS
>     ion_dynamics = 'bfgs' ,
> /
>  &CELL
>     cell_dynamics = 'bfgs' ,
>     press_conv_thr = 0.1 ,
>     press = 480



> /
> ATOMIC_SPECIES
> Ba  137.327 Ba.pbe-nsp-van.UPF
> ATOMIC_POSITIONS {crystal}
> Ba 0.3333333333333286 0.6666666666666714 0.2500000000000000
> Ba 0.6666666666666714 0.3333333333333286 0.7500000000000000
> K_POINTS {automatic}
> 14 14 8  0 0 0
> I add the  cell_factor =3.0,and the above error dosnot appear, however

it became



> task #         1
>      from electrons : error #         1
>      charge is wrong
>
>
> and I have increas the nbnd=30, but still the problem, what more strange is
> that the target pressure is 480 kba ,the relax pressure change like this;
> ba.optim.out_480:          total   stress  (Ry/bohr**3)
> (kbar)     P=  360.52
> ba.optim.out_480:          total   stress  (Ry/bohr**3)
> (kbar)     P=  413.28
> ba.optim.out_480:          total   stress  (Ry/bohr**3)
> (kbar)     P=  279.53
>
> the initial structure is get from the VASP soft,and is consist with the
> experiment at 500kba,
>
I wonder if the two Ba pseudo potential of pwscf web cannot  work at  high
pressre..........

>
>


> --
> ZhouDawei
> JiLin Universiyt ,ChangChun ,China
> zdw2000 at gmail.com
>
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From paulatto at sissa.it  Wed Mar  3 13:35:59 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 03 Mar 2010 13:35:59 +0100
Subject: [Pw_forum] about the from scale_h : error
In-Reply-To: <3e36a8fc1003030330u7cb70fe7sf225faab87ad5392@mail.gmail.com>
References: <3e36a8fc1003021712j39cb327bid162079462584697@mail.gmail.com>
	<4B8E1918.4080407@sissa.it>
	<3e36a8fc1003030330u7cb70fe7sf225faab87ad5392@mail.gmail.com>
Message-ID: <op.u8zrx9h8a8x26q@vanoxite.impmc.jussieu.fr>

On Wed, 03 Mar 2010 12:30:32 +0100, Wei Zhou <zdw2000 at gmail.com> wrote:
>> the initial structure is get from the VASP soft,and is consist with the
>> experiment at 500kba,

Dear Wei,
I think you may have done a unit of measure mistake while converting the  
system parameters from VASP to QE. In order to get the huge pressure you  
are requiring the cell parameter has to shrink by a factor ~ 0.57 (i.e not  
too far away from the bohr/Angstrom conversion). Furthermore, you smearing  
degauss is probably too high (remember it is expressed in Rydberg) and you  
cutoff energy is probably unnecessarily high (the pseudopotential you are  
using is well converged at much lower ecutwfc and ecutrho).

> I wonder if the two Ba pseudo potential of pwscf web cannot  work at   
> high pressre..........

It is possible: when the atoms get very close to each other you need  
harder pseudopotentials; however that's not the cause of your problem, I  
would bet on the smearing instead.

regards

-- 
Lorenzo Paulatto

*** Note: my affiliation has changed! please send future
correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***

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

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

From giuseppe.mattioli at mlib.ism.cnr.it  Wed Mar  3 14:12:04 2010
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Wed, 3 Mar 2010 14:12:04 +0100
Subject: [Pw_forum] defect state
In-Reply-To: <4B8D4095.8080401@democritos.it>
References: <2066059121.57150.1267456670688.JavaMail.root@mta.iut.ac.ir>
	<4B8D4095.8080401@democritos.it>
Message-ID: <201003031412.05001.giuseppe.mattioli@mlib.ism.cnr.it>

On the top of what Paolo said, I can only add (for the fifth or sixth time...) 
that oxygen vacancies in TiO2 are not the less studied defects in 
semiconductors... A couple of papers (amongst hundreds) could answer the 
majority of your questions...
So please span the ACS and APS repositories and flick through the results.

Giuseppe 


On Tuesday 02 March 2010 17:45:09 Paolo Giannozzi wrote:
> kazempoor at ph.iut.ac.ir wrote:
> > I would be most grateful if anyone tell me what is the true
> >  method for observation of defect states
>
> there is no "true method", and more often than not you
> cannot trust the position of defect states obtained in
> DFT (especially in nasty systems like TiO2).
>
> P.


-- 
********************************************************
- 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
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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.
********************************************************

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   CNR - ISTITUTO DI STRUTTURA DELLA MATERIA   
   v. Salaria Km 29,300 - C.P. 10                
   I 00016 - Monterotondo Stazione (RM)          
   Tel + 39 06 90672836 - Fax +39 06 90672316    
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From zdw2000 at gmail.com  Wed Mar  3 14:28:47 2010
From: zdw2000 at gmail.com (Wei Zhou)
Date: Wed, 3 Mar 2010 21:28:47 +0800
Subject: [Pw_forum] about the from scale_h : error
In-Reply-To: <op.u8zrx9h8a8x26q@vanoxite.impmc.jussieu.fr>
References: <3e36a8fc1003021712j39cb327bid162079462584697@mail.gmail.com>
	<4B8E1918.4080407@sissa.it>
	<3e36a8fc1003030330u7cb70fe7sf225faab87ad5392@mail.gmail.com>
	<op.u8zrx9h8a8x26q@vanoxite.impmc.jussieu.fr>
Message-ID: <3e36a8fc1003030528q36464b5aqeae431a1f203e41e@mail.gmail.com>

first thank your for your help......

the relaxed structure  from vasp at 500kba is
Ba
   3.12000000000000
     1.0202516248839648    0.0000000000000000    0.0000000000000000
    -0.5101258124419824    0.8835632605198342    0.0000000000000000
     0.0000000000000000    0.0000000000000000    1.6154107754936728
   2
Direct
  0.3333333300000021  0.6666659999999993  0.2500000000000000
  0.6666666599999971  0.3333330000000032  0.7500000000000000
  external pressure =        1.67 kB  Pullay stress =      500.00 kB

 pwscf input is celldm(1)=6.015350,celldm(3)=1.58,
Bohr=5.2917706   angstrom
I have changed the input file like this after accepting your suggestions
&control
    calculation='vc-relax',
    restart_mode='from_scratch',
    dt=80,
    prefix='ba',
    pseudo_dir = '/home/solid/Work/PW/pseudo/',
    outdir='/home/solid/Work/PW/temp/'
    tstress=.t.,
    tprnfor=.t.
    nstep= 100
/
 &system
    ibrav= 4,
    celldm(1)=6.0,
    celldm(3)=1.58,
    nat= 2,
    ntyp=1,
    nbnd=30
    ecutwfc=30.0,ecutrho = 300
    nosym = .f. ,
    occupations = 'smearing' ,
    degauss = 0.014D0 ,
    smearing = 'methfessel-paxton' ,
/
 &electrons
    mixing_beta = 0.7
    conv_thr =  1.0d-8
/
 &IONS
    ion_dynamics = 'bfgs' ,
/
 &CELL
    cell_dynamics = 'bfgs' ,
    press_conv_thr = 0.1 ,
    press = 500
/
ATOMIC_SPECIES
Ba  137.327 Ba.pbe-nsp-van.UPF
ATOMIC_POSITIONS {crystal}
Ba 0.3333333333333286 0.6666666666666714 0.2500000000000000
Ba 0.6666666666666714 0.3333333333333286 0.7500000000000000
K_POINTS {automatic}
14 14 8  0 0 0
then the error still is
task #         0
     from scale_h : error #         1
     Not enough space allocated for radial FFT: try restarting with a larger
cell_factor.
if I add the cell_factor =3.0 to the &CELL, then the error became

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     task #         2
     from electrons : error #         1
     charge is wrong
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

the relaxed pressure changes unexpectly as following
  grep kba *
ba.optim.out_500:          total   stress  (Ry/bohr**3)
(kbar)     P=  356.22
ba.optim.out_500:          total   stress  (Ry/bohr**3)
(kbar)     P=  420.98
ba.optim.out_500:          total   stress  (Ry/bohr**3)
(kbar)     P=  105.79
ba.optim.out_500:          total   stress  (Ry/bohr**3)
(kbar)     P=-1505.88
ba.optim.out_500:          total   stress  (Ry/bohr**3)
(kbar)     P= 9429.67
ba.optim.out_500:          total   stress  (Ry/bohr**3)
(kbar)     P=-1476.75
ba.optim.out_500:          total   stress  (Ry/bohr**3)
(kbar)     P=-1702.03
ba.optim.out_500:          total   stress  (Ry/bohr**3)
(kbar)     P=-2923.68

2010/3/3 Lorenzo Paulatto <paulatto at sissa.it>

> On Wed, 03 Mar 2010 12:30:32 +0100, Wei Zhou <zdw2000 at gmail.com> wrote:
> >> the initial structure is get from the VASP soft,and is consist with the
> >> experiment at 500kba,
>
> Dear Wei,
> I think you may have done a unit of measure mistake while converting the
> system parameters from VASP to QE. In order to get the huge pressure you
> are requiring the cell parameter has to shrink by a factor ~ 0.57 (i.e not
> too far away from the bohr/Angstrom conversion). Furthermore, you smearing
> degauss is probably too high (remember it is expressed in Rydberg) and you
> cutoff energy is probably unnecessarily high (the pseudopotential you are
> using is well converged at much lower ecutwfc and ecutrho).
>
> > I wonder if the two Ba pseudo potential of pwscf web cannot  work at
> > high pressre..........
>
> It is possible: when the atoms get very close to each other you need
> harder pseudopotentials; however that's not the cause of your problem, I
> would bet on the smearing instead.
>
> regards
>
> --
> Lorenzo Paulatto
>
> *** Note: my affiliation has changed! please send future
> correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***
>
> post-doc @ IMPMC/UPMC - Universit? Paris 6
> phone: +33 (0)1 44 27 74 89
> www:   http://www-int.impmc.upmc.fr/~paulatto/
>
> previously:
> phd student @ SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> www:   http://people.sissa.it/~paulatto/
>  _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
ZhouDawei
JiLin Universiyt ,ChangChun ,China
zdw2000 at gmail.com
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From paulatto at sissa.it  Wed Mar  3 14:55:17 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 03 Mar 2010 14:55:17 +0100
Subject: [Pw_forum] about the from scale_h : error
In-Reply-To: <3e36a8fc1003030528q36464b5aqeae431a1f203e41e@mail.gmail.com>
References: <3e36a8fc1003021712j39cb327bid162079462584697@mail.gmail.com>
	<4B8E1918.4080407@sissa.it>
	<3e36a8fc1003030330u7cb70fe7sf225faab87ad5392@mail.gmail.com>
	<op.u8zrx9h8a8x26q@vanoxite.impmc.jussieu.fr>
	<3e36a8fc1003030528q36464b5aqeae431a1f203e41e@mail.gmail.com>
Message-ID: <op.u8zvmfufa8x26q@vanoxite.impmc.jussieu.fr>

On Wed, 03 Mar 2010 14:28:47 +0100, Wei Zhou <zdw2000 at gmail.com> wrote:
> if I add the cell_factor =3.0 to the &CELL, then the error became
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      task #         2
>      from electrons : error #         1
>      charge is wrong
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

This is strange, I was able to run your input more or less without any  
problem (the bfgs algorithm had some problems toward the end of the  
minimization, but unrelated to the charge one). You may try to disable  
charge density extrapolation (check in the manual, I don't remember the  
keyword) to be safer. I think you have encountered some kind of  
library-specific bug, or similar, can you please provide the full output,  
as well as the make.sys file so that I can have a look? Finally, are you  
using pools or openmp parallelization?

regards

-- 
Lorenzo Paulatto

*** Note: my affiliation has changed! please send future
correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***

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

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

From elie.moujaes at hotmail.co.uk  Wed Mar  3 15:08:58 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Wed, 3 Mar 2010 14:08:58 +0000
Subject: [Pw_forum] cannot open ps file in Ghostscript
Message-ID: <SNT114-W22B45DC9430BA60703CBCDD33A0@phx.gbl>


Dear All,

 

I was able to produce a band structure graph with the ps format but whenever I try to open it, it doesnt and displays that message:

 

 Sview 4.9 2007-11-18
GPL Ghostscript 8.64 (2009-02-03)
Copyright (C) 2009 Artifex Software, Inc.  All rights reserved.
This software comes with NO WARRANTY: see the file PUBLIC for details.
Displaying non DSC file C:/cygwin/espresso-4.1.2/MyGraphene/mgraph.bands.ps
Loading NimbusRomNo9L-Regu font from %rom%Resource/Font/NimbusRomNo9L-Regu... 4186528 2023766 8335848 7042296 2 done.
Error: /undefined in NaN
Operand stack:
   325.239
Execution stack:
   %interp_exit   .runexec2   --nostringval--   --nostringval--   --nostringval--   2   %stopped_push   --nostringval--   --nostringval--   false   1   %stopped_push   1862   1   3   %oparray_pop   1861   1   3   %oparray_pop   1845   1   3   %oparray_pop   1739   1   3   %oparray_pop   --nostringval--   %errorexec_pop   .runexec2   --nostringval--   --nostringval--   --nostringval--   2   %stopped_push   --nostringval--
Dictionary stack:
   --dict:1156/1684(ro)(G)--   --dict:0/20(G)--   --dict:74/200(L)--   --dict:4/100(L)--
Current allocation mode is local
Last OS error: No such file or directory

--- Begin offending input ---
56   31.149  128.023   29.317  129.461
  27.484  130.859   25.652  132.212   23.820  133.512   21.988  134.755   20.155
 135.936   18.323  137.049   16.491  138.087   14.658  139.040   12.826  139.901
  10.994  140.661    9.161  141.317    7.329  141.868    5.497  142.310    3.665
 142.610    1.832  142.758    0.000  142.860
  78 banda
 160.996   79.039  151.958   82.531  142.919   88.351
   2 banda
 185.396   94.921  173.196   88.965  160.996   79.039
   2 banda
 325.239      NaN  318.882      NaN  312.526      NaN  306.169      NaN  299.813
     NaN  293.456      NaN  287.100      NaN  280.743      NaN  274.387      NaN
 268.030      NaN  261.674      NaN  255.317      NaN  248.961      NaN  242.604
     NaN  236.248      NaN  229.892      NaN  223.535      NaN  217.179      NaN
 210.822      NaN  204.466      NaN  198.109      NaN  191.753      NaN  185.396
     NaN
  22 banda
 426.795  142.782  425.737  142.705  424.679  142.532  423.621  142.335  422.563
 142.110  421.506  141.842  420.448  141.532  419.
--- End offending input ---

 

What could be the possible problem..I tried to use ghostview but it says no such command..any suggestions?

 

Regards,

 

Elie
 		 	   		  
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From zdw2000 at gmail.com  Wed Mar  3 15:15:01 2010
From: zdw2000 at gmail.com (Wei Zhou)
Date: Wed, 3 Mar 2010 22:15:01 +0800
Subject: [Pw_forum] about the from scale_h : error
In-Reply-To: <op.u8zvmfufa8x26q@vanoxite.impmc.jussieu.fr>
References: <3e36a8fc1003021712j39cb327bid162079462584697@mail.gmail.com>
	<4B8E1918.4080407@sissa.it>
	<3e36a8fc1003030330u7cb70fe7sf225faab87ad5392@mail.gmail.com>
	<op.u8zrx9h8a8x26q@vanoxite.impmc.jussieu.fr>
	<3e36a8fc1003030528q36464b5aqeae431a1f203e41e@mail.gmail.com>
	<op.u8zvmfufa8x26q@vanoxite.impmc.jussieu.fr>
Message-ID: <3e36a8fc1003030615h7e4a5253he012366618db8ae9@mail.gmail.com>

I
2010/3/3 Lorenzo Paulatto <paulatto at sissa.it>

> On Wed, 03 Mar 2010 14:28:47 +0100, Wei Zhou <zdw2000 at gmail.com> wrote:
> > if I add the cell_factor =3.0 to the &CELL, then the error became
> >
> >
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >      task #         2
> >      from electrons : error #         1
> >      charge is wrong
> >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> This is strange, I was able to run your input more or less without any
> problem (the bfgs algorithm had some problems toward the end of the
> minimization, but unrelated to the charge one). You may try to disable
> charge density extrapolation (check in the manual, I don't remember the
> keyword) to be safer. I think you have encountered some kind of
> library-specific bug, or similar, can you please provide the full output,
> as well as the make.sys file so that I can have a look? Finally, are you
> using pools or openmp parallelization?
>
> regards
>
> --OUTPUT
> WARNING: Unable to read mpd.hosts or list of hosts isn't provided. MPI job
> will be run on the current machine only.
>      Program PWSCF     v.4.1.2  starts ...
>      Today is  3Mar2010 at 22:19:18
>      Parallel version (MPI)
>      Number of processors in use:       4
>      R & G space division:  proc/pool =    4
>      For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW
>      Current dimensions of program pwscf are:
>      Max number of different atomic species (ntypx) = 10
>      Max number of k-points (npk) =  40000
>      Max angular momentum in pseudopotentials (lmaxx) =  3
>      Waiting for input...
>      Subspace diagonalization in iterative solution of the eigenvalue
> problem:
>      a parallel distributed memory algorithm will be used,
>      eigenstates matrixes will be distributed block like on
>      ortho sub-group =    2*   2 procs
>
>      Planes per process (thick) : nr3 = 50 npp =  13 ncplane = 1024
>      Planes per process (smooth): nr3s= 30 npps=   8 ncplanes=  324
>
>      Proc/  planes cols     G    planes cols    G      columns  G
>      Pool       (dense grid)       (smooth grid)      (wavefct grid)
>         1    13    162     5256    8     53     1009     19      195
>         2    13    163     5261    8     52      990     18      192
>         3    12    162     5254    7     53     1003     18      192
>         4    12    162     5254    7     53      993     18      194
>      tot     50    649    21025   30    211     3995     73      773
>
>
>      bravais-lattice index     =            4
>      lattice parameter (a_0)   =       5.6000  a.u.
>      unit-cell volume          =     238.9940 (a.u.)^3
>      number of atoms/cell      =            2
>      number of atomic types    =            1
>      number of electrons       =        20.00
>      number of Kohn-Sham states=           30
>      kinetic-energy cutoff     =      25.0000  Ry
>      charge density cutoff     =     300.0000  Ry
>      convergence threshold     =      1.0E-08
>      mixing beta               =       0.7000
>      number of iterations used =            8  plain     mixing
>      Exchange-correlation      =  SLA  PW   PBE  PBE (1434)
>      nstep                     =          100
>
>      celldm(1)=   5.600000  celldm(2)=   0.000000  celldm(3)=   1.571420
>      celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=   0.000000
>      crystal axes: (cart. coord. in units of a_0)
>                a(1) = (  1.000000  0.000000  0.000000 )
>                a(2) = ( -0.500000  0.866025  0.000000 )
>                a(3) = (  0.000000  0.000000  1.571420 )
>      reciprocal axes: (cart. coord. in units 2 pi/a_0)
>                b(1) = (  1.000000  0.577350  0.000000 )
>                b(2) = (  0.000000  1.154701  0.000000 )
>                b(3) = (  0.000000  0.000000  0.636367 )
>
>      PseudoPot. # 1 for Ba read from file Ba.pbe-nsp-van.UPF
>      Pseudo is Ultrasoft + core correction, Zval = 10.0
>      Generated by new atomic code, or converted to UPF format
>      Using radial grid of  907 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  6 coefficients,  rinner =    1.200   1.200
> 1.200
>                                                        1.200   1.200
>      atomic species   valence    mass     pseudopotential
>         Ba            10.00   137.32700     Ba( 1.00)
>      24 Sym.Ops. (with inversion)
>
>    Cartesian axes
>      site n.     atom                  positions (a_0 units)
>          1           Ba  tau(  1) = (   0.0000000   0.5773503   0.3928550
> )
>          2           Ba  tau(  2) = (   0.5000000   0.2886751   1.1785650
> )
>      number of k points=  120  gaussian broad. (Ry)=  0.0120     ngauss =
> 1
>                        cart. coord. in units 2pi/a_0
>         k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0012755
>         k(    2) = (   0.0000000   0.0000000   0.0795459), wk =   0.0025510
>         k(    3) = (   0.0000000   0.0000000   0.1590918), wk =   0.0025510
>        ................................
>         k(  116) = (   0.2857143   0.5773503   0.0000000), wk =   0.0076531
>         k(  117) = (   0.2857143   0.5773503   0.0795459), wk =   0.0153061
>         k(  118) = (   0.2857143   0.5773503   0.1590918), wk =   0.0153061
>         k(  119) = (   0.2857143   0.5773503   0.2386377), wk =   0.0153061
>         k(  120) = (   0.2857143   0.5773503  -0.3181836), wk =   0.0076531
>      G cutoff =  238.3074  (  21025 G-vectors)     FFT grid: ( 32, 32, 50)
>      G cutoff =   79.4358  (   3995 G-vectors)  smooth grid: ( 18, 18, 30)
>      Largest allocated arrays     est. size (Mb)     dimensions
>         Kohn-Sham Wavefunctions         0.06 Mb     (    135,  30)
>         NL pseudopotentials             0.07 Mb     (    135,  36)
>         Each V/rho on FFT grid          0.20 Mb     (  13312)
>         Each G-vector array             0.04 Mb     (   5256)
>         G-vector shells                 0.04 Mb     (   5256)
>      Largest temporary arrays     est. size (Mb)     dimensions
>         Auxiliary wavefunctions         0.25 Mb     (    135, 120)
>         Each subspace H/S matrix        0.22 Mb     (    120, 120)
>         Each <psi_i|beta_j> matrix      0.02 Mb     (     36,  30)
>         Arrays for rho mixing           1.62 Mb     (  13312,   8)
>      Initial potential from superposition of free atoms
>      starting charge   19.97000, renormalised to   20.00000
>      Starting wfc are   26 atomic +    4 random wfc
>      total cpu time spent up to now is      1.85 secs
>      per-process dynamical memory:     5.3 Mb
>      Self-consistent Calculation
>      iteration #  1     ecut=    25.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  1.00E-02,  avg # of iterations =  5.2
>      Threshold (ethr) on eigenvalues was too large:
>      Diagonalizing with lowered threshold
>      Davidson diagonalization with overlap
>      ethr =  7.21E-04,  avg # of iterations =  1.1
>      total cpu time spent up to now is     16.78 secs
>      total energy              =    -180.05547275 Ry
>      Harris-Foulkes estimate   =    -180.15409713 Ry
>      estimated scf accuracy    <       0.14546748 Ry
>      iteration #  2     ecut=    25.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  7.27E-04,  avg # of iterations =  2.6
>      total cpu time spent up to now is     22.28 secs
>      total energy              =    -180.08201004 Ry
>      Harris-Foulkes estimate   =    -180.08310411 Ry
>      estimated scf accuracy    <       0.00157673 Ry
>      iteration #  3     ecut=    25.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  7.88E-06,  avg # of iterations =  6.2
>      total cpu time spent up to now is     34.75 secs
>      total energy              =    -180.08234243 Ry
>      Harris-Foulkes estimate   =    -180.08239032 Ry
>      estimated scf accuracy    <       0.00008663 Ry
>      iteration #  4     ecut=    25.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  4.33E-07,  avg # of iterations =  2.2
>      total cpu time spent up to now is     39.36 secs
>      total energy              =    -180.08234940 Ry
>      Harris-Foulkes estimate   =    -180.08234952 Ry
>      estimated scf accuracy    <       0.00000068 Ry
>      iteration #  5     ecut=    25.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  3.38E-09,  avg # of iterations =  2.1
>      total cpu time spent up to now is     44.28 secs
>      total energy              =    -180.08234965 Ry
>      Harris-Foulkes estimate   =    -180.08234968 Ry
>      estimated scf accuracy    <       0.00000010 Ry
>      iteration #  6     ecut=    25.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  5.00E-10,  avg # of iterations =  2.0
>      total cpu time spent up to now is     49.06 secs
>      End of self-consistent calculation
>           k = 0.0000 0.0000 0.0000 (   525 PWs)   bands (ev):
>     -7.5077  -4.2553   4.8253  12.5286  12.5286  14.2044  14.2044  14.8220
>     21.7352  23.9498  25.7465  25.7465  26.0251  27.1761  27.5311  27.5311
>     27.5552  27.5552  27.9377  28.2291  28.2291  28.3829  31.2562  36.6993
>     36.6993  39.3932  39.3933  41.4102  41.4102  41.6156
>       .............................
>     -4.0241  -3.7851   6.4145   6.9382   7.1591   9.1534  11.1024  11.6687
>     20.8019  24.5531  24.8598  26.0962  27.5308  27.8333  28.2100  28.6546
>     30.4432  30.5194  33.3446  34.2433  34.3662  35.4987  36.0440  37.0388
>     39.6977  39.8126  40.1051  40.2970  41.0627  41.7419
>           k = 0.2857 0.5774 0.2386 (   505 PWs)   bands (ev):
>     -3.9413  -3.8102   6.1676   6.3855   7.4222   8.5510  12.1481  12.4976
>     22.0663  23.3220  23.5590  25.4455  26.5093  27.4481  28.4395  28.5762
>     29.6446  29.7275  34.8198  35.9627  36.0383  36.8640  37.3254  37.5860
>     39.2276  39.6133  39.8864  39.8885  41.1669  41.2481
>           k = 0.2857 0.5774-0.3182 (   502 PWs)   bands (ev):
>     -3.8637  -3.8637   6.1211   6.1211   7.9395   7.9395  12.7061  12.7061
>     22.8290  22.8290  23.7925  23.7925  26.8634  26.8634  28.8438  28.8438
>     29.1672  29.1672  36.0364  36.0364  37.1475  37.1475  37.9938  37.9938
>     38.8055  38.8055  39.9043  39.9043  41.2094  41.2094
>      the Fermi energy is    23.2963 ev
> !    total energy              =    -180.08234966 Ry
>      Harris-Foulkes estimate   =    -180.08234967 Ry
>      estimated scf accuracy    <          9.8E-09 Ry
>      The total energy is the sum of the following terms:
>      one-electron contribution =      31.54953500 Ry
>      hartree contribution      =       3.68728415 Ry
>      xc contribution           =     -98.07090733 Ry
>      ewald contribution        =    -117.24829605 Ry
>      smearing contrib. (-TS)   =       0.00003456 Ry
>      convergence has been achieved in   6 iterations
>      Forces acting on atoms (Ry/au):
>      atom   1 type  1   force =     0.00000000    0.00000000    0.00000000
>      atom   2 type  1   force =     0.00000000    0.00000000    0.00000000
>      Total force =     0.000000     Total SCF correction =     0.000000
>
>      entering subroutine stress ...
>           total   stress  (Ry/bohr**3)                   (kbar)     P=
> 356.42
>    0.00262856   0.00000000   0.00000000        386.67      0.00      0.00
>    0.00000000   0.00262856   0.00000000          0.00    386.67      0.00
>    0.00000000   0.00000000   0.00201147          0.00      0.00    295.90
>
>      BFGS Geometry Optimization
>      number of scf cycles    =   1
>      number of bfgs steps    =   0
>      enthalpy new            =    -179.2700254431 Ry
>      new trust radius        =       0.2000000000 bohr
>      new conv_thr            =       0.0000000100 Ry
>      new unit-cell volume =    214.73402 a.u.^3 (    31.82030 Ang^3 )
> CELL_PARAMETERS (alat)
>    0.972380845   0.000000000   0.000000000
>   -0.486190423   0.842106514   0.000000000
>    0.000000000   0.000000000   1.493252878
> ATOMIC_POSITIONS (crystal)
> Ba       0.333333333   0.666666667   0.250000000
> Ba       0.666666667   0.333333333   0.750000000
>
>      Writing output data file ba.save
>      NEW-OLD atomic charge density approx. for the potential
>      NEW k-points:
>         k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0012755
>         k(    2) = (   0.0000000   0.0000000   0.0837099), wk =   0.0025510
>         k(    3) = (   0.0000000   0.0000000   0.1674197), wk =   0.0025510
>         k(    4) = (   0.0000000   0.0000000   0.2511296), wk =   0.0025510
>         .............................
>         k(  118) = (   0.2938296   0.5937491   0.1674197), wk =   0.0153061
>         k(  119) = (   0.2938296   0.5937491   0.2511296), wk =   0.0153061
>         k(  120) = (   0.2938296   0.5937491  -0.3348395), wk =   0.0076531
>      extrapolated charge   17.74385, renormalised to   20.00000
>      total cpu time spent up to now is     51.69 secs
>      per-process dynamical memory:     4.5 Mb
>      Self-consistent Calculation
>      iteration #  1     ecut=    25.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  1.00E-06,  avg # of iterations =  8.5
>      total cpu time spent up to now is     67.75 secs
>      total energy              =    -179.97041147 Ry
>      Harris-Foulkes estimate   =    -177.83374248 Ry
>      estimated scf accuracy    <       0.03695251 Ry
>      iteration #  2     ecut=    25.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  1.85E-04,  avg # of iterations =  4.8
>      total cpu time spent up to now is     77.97 secs
>      total energy              =    -180.02045962 Ry
>      Harris-Foulkes estimate   =    -180.03224157 Ry
>      estimated scf accuracy    <       0.02356776 Ry
>      iteration #  3     ecut=    25.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  1.18E-04,  avg # of iterations =  2.2
>      total cpu time spent up to now is     82.47 secs
>      total energy              =    -180.01971209 Ry
>      Harris-Foulkes estimate   =    -180.02210285 Ry
>      estimated scf accuracy    <       0.00370170 Ry
>      iteration #  4     ecut=    25.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  1.85E-05,  avg # of iterations =  4.1
>      total cpu time spent up to now is     89.38 secs
>      total energy              =    -180.02038207 Ry
>      Harris-Foulkes estimate   =    -180.02040479 Ry
>      estimated scf accuracy    <       0.00004705 Ry
>      iteration #  5     ecut=    25.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  2.35E-07,  avg # of iterations =  2.6
>      total cpu time spent up to now is     94.79 secs
>      total energy              =    -180.02038810 Ry
>      Harris-Foulkes estimate   =    -180.02039556 Ry
>      estimated scf accuracy    <       0.00000846 Ry
>      iteration #  6     ecut=    25.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  4.23E-08,  avg # of iterations =  2.0
>      total cpu time spent up to now is     99.60 secs
>      total energy              =    -180.02039034 Ry
>      Harris-Foulkes estimate   =    -180.02039133 Ry
>      estimated scf accuracy    <       0.00000130 Ry
>      iteration #  7     ecut=    25.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  6.52E-09,  avg # of iterations =  2.0
>      total cpu time spent up to now is    104.41 secs
>      total energy              =    -180.02039065 Ry
>      Harris-Foulkes estimate   =    -180.02039066 Ry
>      estimated scf accuracy    <       0.00000002 Ry
>      iteration #  8     ecut=    25.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      ethr =  8.60E-11,  avg # of iterations =  1.7
>      total cpu time spent up to now is    108.73 secs
>      End of self-consistent calculation
>           k = 0.0000 0.0000 0.0000 (   525 PWs)   bands (ev):
>     -5.9352  -1.5838   6.3491  15.1342  15.1342  17.3993  17.3993  18.5458
>     23.8348  25.7969  27.8380  28.1470  28.1470  29.7371  29.7371  30.2050
>     30.2050  30.2872  30.2872  30.5813  31.5261  31.6805  34.0063  40.1211
>     40.1211  43.4906  43.4906  44.4380  45.4547  45.5237
>         ...........................
>           k = 0.2938 0.5937 0.1674 (   505 PWs)   bands (ev):
>     -1.6133  -1.2795   8.1641   8.8019   8.9581  11.4601  13.7618  14.4344
>     22.9370  27.5835  27.5919  28.8628  29.9563  30.2835  31.1011  31.1550
>     33.1452  33.1820  36.6391  37.9313  38.2991  38.6433  39.1904  40.9201
>     43.0673  43.0685  43.7739  43.9050  44.3872  44.5220
>           k = 0.2938 0.5937 0.2511 (   505 PWs)   bands (ev):
>     -1.4826  -1.2970   7.8249   8.0963   9.2964  10.6999  15.1033  15.5347
>     24.4117  26.0624  26.3436  28.1432  28.8718  29.9518  30.9253  30.9892
>     32.2222  32.2329  38.2110  39.9442  39.9559  40.1704  40.6617  41.2719
>     42.9339  43.1192  43.1294  43.2778  44.4365  44.4925
>           k = 0.2938 0.5937-0.3348 (   502 PWs)   bands (ev):
>     -1.3659  -1.3659   7.7590   7.7590   9.9393   9.9393  15.8344  15.8344
>     25.4841  25.4841  26.3126  26.3126  29.2729  29.2729  31.4118  31.4118
>     31.5406  31.5406  39.6484  39.6484  41.0258  41.0258  41.4271  41.4271
>     42.4194  42.4194  43.1321  43.1321  44.4583  44.4583
>      the Fermi energy is    25.6489 ev
> !    total energy              =    -180.02039065 Ry
>      Harris-Foulkes estimate   =    -180.02039065 Ry
>      estimated scf accuracy    <          1.0E-09 Ry
>      The total energy is the sum of the following terms:
>      one-electron contribution =      36.88903660 Ry
>      hartree contribution      =       2.91419118 Ry
>      xc contribution           =     -98.35334426 Ry
>      ewald contribution        =    -121.47020511 Ry
>      smearing contrib. (-TS)   =      -0.00006906 Ry
>      convergence has been achieved in   8 iterations
>      Forces acting on atoms (Ry/au):
>      atom   1 type  1   force =     0.00000000    0.00000000    0.00000000
>      atom   2 type  1   force =     0.00000000    0.00000000    0.00000000
>      Total force =     0.000000     Total SCF correction =     0.000000
>
>      entering subroutine stress ...
>           total   stress  (Ry/bohr**3)                   (kbar)     P=
> 421.03
>    0.00318745   0.00000000   0.00000000        468.89      0.00      0.00
>    0.00000000   0.00318745   0.00000000          0.00    468.89      0.00
>    0.00000000   0.00000000   0.00221141          0.00      0.00    325.31
>
>      number of scf cycles    =   2
>      number of bfgs steps    =   1
>      enthalpy old            =    -179.2700254431 Ry
>      enthalpy new            =    -179.2905244161 Ry
>      CASE: enthalpy_new < enthalpy_old
>      new trust radius        =       0.6259677229 bohr
>      new conv_thr            =       0.0000000010 Ry
>      new unit-cell volume =    156.64138 a.u.^3 (    23.21186 Ang^3 )
> CELL_PARAMETERS (alat)
>    0.917924413   0.000000000   0.000000000
>   -0.458962207   0.794945860   0.000000000
>    0.000000000   0.000000000   1.222356706
> ATOMIC_POSITIONS (crystal)
> Ba       0.333333333   0.666666667   0.250000000
> Ba       0.666666667   0.333333333   0.750000000
>
>      Writing output data file ba.save
>      first order wave-functions extrapolation
>      first order charge density extrapolation
>      NEW k-points:
>         k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0012755
>         k(    2) = (   0.0000000   0.0000000   0.1022615), wk =   0.0025510
>         k(    3) = (   0.0000000   0.0000000   0.2045230), wk =   0.0025510
>        ..............................
>         k(   97) = (   0.2334459   0.4043402   0.1022615), wk =   0.0153061
>         k(   98) = (   0.2334459   0.4043402   0.2045230), wk =   0.0153061
>         k(   99) = (   0.2334459   0.4043402   0.3067844), wk =   0.0153061
>         k(  100) = (   0.2334459   0.4043402  -0.4090459), wk =   0.0076531
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from scale_h : error #         1
>      Not enough space allocated for radial FFT: try restarting with a
> larger cell_factor.
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      stopping ...
>         k(  101) = (   0.2334459   0.4941936   0.0000000), wk =   0.0153061
>         k(  102) = (   0.2334459   0.4941936   0.1022615), wk =   0.0306122
>         k(  103) = (   0.2334459   0.4941936   0.2045230), wk =   0.0306122
>         k(  104) = (   0.2334459   0.4941936   0.3067844), wk =   0.0306122
>         k(  105) = (   0.2334459   0.4941936  -0.4090459), wk =   0.0153061
>         k(  106) = (   0.2334459   0.5840470   0.0000000), wk =   0.0153061
>         k(  107) = (   0.2334459   0.5840470   0.1022615), wk =   0.0306122
>         k(  108) = (   0.2334459   0.5840470   0.2045230), wk =   0.0306122
>         k(  109) = (   0.2334459   0.5840470   0.3067844), wk =   0.0306122
>         k(  110) = (   0.2334459   0.5840470  -0.4090459), wk =   0.0153061
>         k(  111) = (   0.3112612   0.5391203   0.0000000), wk =   0.0076531
>         k(  112) = (   0.3112612   0.5391203   0.1022615), wk =   0.0153061
>         k(  113) = (   0.3112612   0.5391203   0.2045230), wk =   0.0153061
>         k(  114) = (   0.3112612   0.5391203   0.3067844), wk =   0.0153061
>         k(  115) = (   0.3112612   0.5391203  -0.4090459), wk =   0.0076531
>         k(  116) = (   0.3112612   0.6289737   0.0000000), wk =   0.0076531
>         k(  117) = (   0.3112612   0.6289737   0.1022615), wk =   0.0153061
>         k(  118) = (   0.3112612   0.6289737   0.2045230), wk =   0.0153061
>         k(  119) = (   0.3112612   0.6289737   0.3067844), wk =   0.0153061
>         k(  120) = (   0.3112612   0.6289737  -0.4090459), wk =   0.0076531
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from scale_h : error #         1
>      Not enough space allocated for radial FFT: try restarting with a
> larger cell_factor.
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      stopping ...
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from scale_h : error #         1
>      Not enough space allocated for radial FFT: try restarting with a
> larger cell_factor.
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      stopping ...
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from scale_h : error #         1
>      Not enough space allocated for radial FFT: try restarting with a
> larger cell_factor.
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      stopping ...
> rank 3 in job 1  linux-solid_52345   caused collective abort of all ranks
>   exit status of rank 3: killed by signal 9
> rank 1 in job 1  linux-solid_52345   caused collective abort of all ranks
>   exit status of rank 1: return code 0
> rank 0 in job 1  linux-solid_52345   caused collective abort of all ranks
>   exit status of rank 0: return code 0
>
############################################


>  MAKE.SYS, I use the intel_mpi3.2.1.009,IFORT9.0, and I calculate the Ba
> structure at lower pressure ,it seem works well
>
# 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__INTEL -D__FFTW3 -D__USE_INTERNAL_FFTW -D__MPI -D__PARA
FDFLAGS        = $(DFLAGS)
# IFLAGS = how to locate directories where files to be included are
# In most cases, IFLAGS = -I../include
IFLAGS         = -I../include
# MODFLAGS = flag used by f90 compiler to locate modules
# You need to search for modules in ./, in ../iotk/src, in ../Modules
# Some applications also need modules in ../PW and ../PH
MODFLAGS       = -I./  -I../Modules  -I../iotk/src \
                 -I../PW  -I../PH  -I../EE -I../GIPAW
# 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         = mpiifort
#F90           = ifort
CC             = cc
F77            = ifort
# 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         = -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS       = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS         = -O2 -assume byterecl
# compiler flags without optimization for fortran-77
# the latter is NEEDED to properly compile dlamch.f, used by lapack
FFLAGS_NOOPT   = -O0 -assume byterecl
# Linker, linker-specific flags (if any)
# Typically LD coincides with F90 or MPIF90, LD_LIBS is empty
LD             = mpiifort
LDFLAGS        =
LD_LIBS        =
# External Libraries (if any) : blas, lapack, fft, MPI
# If you have nothing better, use the local copy : ../flib/blas.a
BLAS_LIBS      = ../flib/blas.a
# The following lapack libraries will be available in flib/ :
# ../flib/lapack.a : contains all needed routines
# ../flib/lapack_atlas.a: only routines not present in the Atlas library
# For IBM machines with essl (-D__ESSL): load essl BEFORE lapack !
# remember that LAPACK_LIBS precedes BLAS_LIBS in loading order
LAPACK_LIBS    = ../flib/lapack.a
# nothing needed here if the the internal copy of FFTW is compiled
# (needs -D__FFTW in DFLAGS)
FFT_LIBS       =  -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      =
# pgplot libraries (used by some post-processing tools)
PGPLOT_LIBS    =
# ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv
# ARFLAGS_DYNAMIC is used in iotk to produce a dynamical library,
# for Mac OS-X with PowerPC and xlf compiler. In all other cases
# ARFLAGS_DYNAMIC = $(ARFLAGS)
AR             = ar
ARFLAGS        = ruv
ARFLAGS_DYNAMIC= 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
LIBOBJS        = ../flib/ptools.a ../flib/flib.a ../clib/clib.a
../iotk/src/libiotk.a ../Multigrid/mglib.a
LIBS           = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS)
$(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS)



>  --
> ZhouDawei
> JiLin Universiyt ,ChangChun ,China
> zdw2000 at gmail.com
>
-------------- next part --------------
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From nnlinh at sissa.it  Wed Mar  3 15:41:01 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Wed, 3 Mar 2010 15:41:01 +0100 (CET)
Subject: [Pw_forum] cannot open ps file in Ghostscript
In-Reply-To: <SNT114-W22B45DC9430BA60703CBCDD33A0@phx.gbl>
References: <SNT114-W22B45DC9430BA60703CBCDD33A0@phx.gbl>
Message-ID: <50800.147.122.27.212.1267627261.squirrel@webmail.sissa.it>

> Sview 4.9 2007-11-18
> GPL Ghostscript 8.64 (2009-02-03)
> Copyright (C) 2009 Artifex Software, Inc.  All rights reserved.
> This software comes with NO WARRANTY: see the file PUBLIC for details.
> Displaying non DSC file
> C:/cygwin/espresso-4.1.2/MyGraphene/mgraph.bands.ps
> Loading NimbusRomNo9L-Regu font from
> %rom%Resource/Font/NimbusRomNo9L-Regu... 4186528 2023766 8335848 7042296 2
> done.
> Error: /undefined in NaN
> Operand stack:

It seems to be an error in the .ps file.
The error NaN (Not a Number) implements that band.x running is not
completed or is an error when it run. Check again the relevant output
files if they are available or not?


> What could be the possible problem..I tried to use ghostview but it says
> no such command..any suggestions?

"no such command" means the ghostview command has not configured yet. If
you are using Linux environment, you can install "gs" and open .ps file by
"gs"


Good luck

Linh
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------



----------------------------------------------------------------
  SISSA Webmail https://webmail.sissa.it/
  Powered by SquirrelMail http://www.squirrelmail.org/


From paulatto at sissa.it  Wed Mar  3 16:02:27 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 03 Mar 2010 16:02:27 +0100
Subject: [Pw_forum] about the from scale_h : error
In-Reply-To: <3e36a8fc1003030615h7e4a5253he012366618db8ae9@mail.gmail.com>
References: <3e36a8fc1003021712j39cb327bid162079462584697@mail.gmail.com>
	<4B8E1918.4080407@sissa.it>
	<3e36a8fc1003030330u7cb70fe7sf225faab87ad5392@mail.gmail.com>
	<op.u8zrx9h8a8x26q@vanoxite.impmc.jussieu.fr>
	<3e36a8fc1003030528q36464b5aqeae431a1f203e41e@mail.gmail.com>
	<op.u8zvmfufa8x26q@vanoxite.impmc.jussieu.fr>
	<3e36a8fc1003030615h7e4a5253he012366618db8ae9@mail.gmail.com>
Message-ID: <op.u8zyqdn7a8x26q@vanoxite.impmc.jussieu.fr>

On Wed, 03 Mar 2010 15:15:01 +0100, Wei Zhou <zdw2000 at gmail.com> wrote:
>>      from scale_h : error #         1

The output with cell_factor=3.0, please, I know what's of *this* error :-)


>
>>  MAKE.SYS, I use the intel_mpi3.2.1.009,IFORT9.0, and I calculate the Ba
>> structure at lower pressure ,it seem works well

Well, if some mathematical libraries are unstable the instability is more  
likely to pop out in extreme cases. ifort is an old and buggy compiler, if  
you have the possibility to update it I would suggest you to do so.

> BLAS_LIBS      = ../flib/blas.a
> LAPACK_LIBS    = ../flib/lapack.a

Internal blas and lapack libraries are robust but very slow if you want  
better performances, you should try to get some optimized libraries; see:  
<http://www.quantum-espresso.org/user_guide/node10.html#SECTION00033110000000000000>

-- 
Lorenzo Paulatto

*** Note: my affiliation has changed! please send future
correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***

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

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

From cristian.degliesposti at unibo.it  Wed Mar  3 16:25:12 2010
From: cristian.degliesposti at unibo.it (Cristian Degli Esposti Boschi)
Date: Wed, 3 Mar 2010 16:25:12 +0100
Subject: [Pw_forum] Problems with XSpectra code
Message-ID: <4B8E7F58.3030208@unibo.it>

Dear all,

I've installed QE 4.1.2 to try the XSpectra code.
The input file is as follows

&input_xspectra
calculation='xanes_dipole',
prefix='MbCO_scf',
outdir='/home/desposti/temp/MbCO/out/',
verbosity='high',
xiabs=1,
/
&plot
/
&pseudos
filecore='Fe.wfc'
/
&cut_occ
/
1 1 1 0 0 0


After some minutes xspectra.x stops (EXIT 2) with
the following message

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      from main program : error #        16
      Wrong xiabs!!!
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Before the message it seems that the file of the previous scf run is
correctly read (at least the crystal structure). This run is
made with a pseudpotential Fe.pbe-sp-van_ak.UPF for the absorbing
Fe atom placed in first position in the input file (so it should be
xiabs=1 right?)

I wonder if the error is related to the fact that when I generate
the core wavefunction Fe.wfc using

./upf2plotcore.sh  Fe.pbe-sp-van_ak.UPF > Fe.wfc

in the file Fe.wfc I simply get
# number of core states 0 =

The same happens to me if I try the Fe pseudo in
the QE repository called Fe.star1s-pbe-sp-mt_gipaw.UPF.
For the moment I don't want core-hole effects; it's
just to try...
So, what could it be the cause of the "xiabs" error above?


Thanks for your time. Cristian



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


From giannozz at democritos.it  Wed Mar  3 16:45:38 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 3 Mar 2010 16:45:38 +0100
Subject: [Pw_forum] "Mulliken population" and dos pojections
In-Reply-To: <42054E10C02CD44D81EF510077A30A0725A70FA0E1@MAPI.ad.kent.ac.uk>
References: <42054E10C02CD44D81EF510077A30A0725A70FA0E1@MAPI.ad.kent.ac.uk>
Message-ID: <9460D554-DD53-4EA8-AEB8-A64A517AAA55@democritos.it>


On Mar 3, 2010, at 12:17 , P.Canepa wrote:

> Just a little question, is in PWscf something like Mulliken  
> population analysis?

just a little answer: what about searching the mailing list? see e.g.
    http://www.democritos.it/pipermail/pw_forum/2008-January/008142.html
and
   http://www.democritos.it/pipermail/pw_forum/2006-November/005392.html
P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From zdw2000 at gmail.com  Wed Mar  3 17:15:29 2010
From: zdw2000 at gmail.com (Wei Zhou)
Date: Thu, 4 Mar 2010 00:15:29 +0800
Subject: [Pw_forum] about the from scale_h : error
In-Reply-To: <op.u8zyqdn7a8x26q@vanoxite.impmc.jussieu.fr>
References: <3e36a8fc1003021712j39cb327bid162079462584697@mail.gmail.com>
	<4B8E1918.4080407@sissa.it>
	<3e36a8fc1003030330u7cb70fe7sf225faab87ad5392@mail.gmail.com>
	<op.u8zrx9h8a8x26q@vanoxite.impmc.jussieu.fr>
	<3e36a8fc1003030528q36464b5aqeae431a1f203e41e@mail.gmail.com>
	<op.u8zvmfufa8x26q@vanoxite.impmc.jussieu.fr>
	<3e36a8fc1003030615h7e4a5253he012366618db8ae9@mail.gmail.com>
	<op.u8zyqdn7a8x26q@vanoxite.impmc.jussieu.fr>
Message-ID: <3e36a8fc1003030815nfa8ce85t5589d3dbc007d3f5@mail.gmail.com>

I run the job again, it appear the new
error......................................
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     task #         0
     from bfgs : error #         1
     bfgs history already reset at previous step
###########################################################################
it seems that the following OLD error come from     pot_extrapolation =
'second_order' ,
    wfc_extrapolation = 'second_order' , I erase them then it disappear
 #         2
>      from electrons : error #         1
>      charge is wrong
#########################################################################
the new input leads to   bfgs history already reset at previous step
NEWINPUT
&control
    calculation='vc-relax',
    restart_mode='from_scratch',
    dt=80,
    prefix='ba',
    pseudo_dir = '/home/solid/Work/PW/pseudo/',
    outdir='/home/solid/Work/PW/temp/'
    tstress=.t.,
    tprnfor=.t.
    nstep= 100
/
 &system
    ibrav= 4,
    celldm(1)=5.6,
    celldm(3)=1.57142,
    nat= 2,
    ntyp=1,
    nbnd=30
    ecutwfc=25.0,ecutrho = 300
    nosym = .f. ,
    occupations = 'smearing' ,
    degauss = 0.012D0 ,
    smearing = 'methfessel-paxton' ,
/
 &electrons
    mixing_beta = 0.7
    conv_thr =  1.0d-8
/
 &IONS
    ion_dynamics = 'bfgs' ,
/
 &CELL
    cell_dynamics = 'bfgs' ,
   cell_factor =3.0
    press_conv_thr = 0.1 ,
    press = 500
/
ATOMIC_SPECIES
Ba  137.327 Ba.pbe-nsp-van.UPF
ATOMIC_POSITIONS {crystal}
Ba 0.3333333333333286 0.6666666666666714 0.2500000000000000
Ba 0.6666666666666714 0.3333333333333286 0.7500000000000000
K_POINTS {automatic}
14 14 8  0 0 0
NEW OUTPUT

WARNING: Unable to read mpd.hosts or list of hosts isn't provided. MPI job
will be run on the current machine only.
     Program PWSCF     v.4.1.2  starts ...
     Today is  4Mar2010 at  0: 5:18
     Parallel version (MPI)
     Number of processors in use:       4
     R & G space division:  proc/pool =    4
     For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW
     Current dimensions of program pwscf are:
     Max number of different atomic species (ntypx) = 10
     Max number of k-points (npk) =  40000
     Max angular momentum in pseudopotentials (lmaxx) =  3
     Waiting for input...
     Subspace diagonalization in iterative solution of the eigenvalue
problem:
     a parallel distributed memory algorithm will be used,
     eigenstates matrixes will be distributed block like on
     ortho sub-group =    2*   2 procs

     Planes per process (thick) : nr3 = 50 npp =  13 ncplane = 1024
     Planes per process (smooth): nr3s= 30 npps=   8 ncplanes=  324

     Proc/  planes cols     G    planes cols    G      columns  G
     Pool       (dense grid)       (smooth grid)      (wavefct grid)
        1    13    162     5256    8     53     1009     19      195
        2    13    163     5261    8     52      990     18      192
        3    12    162     5254    7     53     1003     18      192
        4    12    162     5254    7     53      993     18      194
     tot     50    649    21025   30    211     3995     73      773


     bravais-lattice index     =            4
     lattice parameter (a_0)   =       5.6000  a.u.
     unit-cell volume          =     238.9940 (a.u.)^3
     number of atoms/cell      =            2
     number of atomic types    =            1
     number of electrons       =        20.00
     number of Kohn-Sham states=           30
     kinetic-energy cutoff     =      25.0000  Ry
     charge density cutoff     =     300.0000  Ry
     convergence threshold     =      1.0E-08
     mixing beta               =       0.7000
     number of iterations used =            8  plain     mixing
     Exchange-correlation      =  SLA  PW   PBE  PBE (1434)
     nstep                     =          100

     celldm(1)=   5.600000  celldm(2)=   0.000000  celldm(3)=   1.571420
     celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=   0.000000
     crystal axes: (cart. coord. in units of a_0)
               a(1) = (  1.000000  0.000000  0.000000 )
               a(2) = ( -0.500000  0.866025  0.000000 )
               a(3) = (  0.000000  0.000000  1.571420 )
     reciprocal axes: (cart. coord. in units 2 pi/a_0)
               b(1) = (  1.000000  0.577350  0.000000 )
               b(2) = (  0.000000  1.154701  0.000000 )
               b(3) = (  0.000000  0.000000  0.636367 )

     PseudoPot. # 1 for Ba read from file Ba.pbe-nsp-van.UPF
     Pseudo is Ultrasoft + core correction, Zval = 10.0
     Generated by new atomic code, or converted to UPF format
     Using radial grid of  907 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  6 coefficients,  rinner =    1.200   1.200   1.200
                                                       1.200   1.200
     atomic species   valence    mass     pseudopotential
        Ba            10.00   137.32700     Ba( 1.00)
     24 Sym.Ops. (with inversion)

   Cartesian axes
     site n.     atom                  positions (a_0 units)
         1           Ba  tau(  1) = (   0.0000000   0.5773503   0.3928550  )
         2           Ba  tau(  2) = (   0.5000000   0.2886751   1.1785650  )
     number of k points=  120  gaussian broad. (Ry)=  0.0120     ngauss =
1
                       cart. coord. in units 2pi/a_0
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0012755
        k(    2) = (   0.0000000   0.0000000   0.0795459), wk =   0.0025510
        k(    3) = (   0.0000000   0.0000000   0.1590918), wk =   0.0025510
        ....................
        k(  119) = (   0.2857143   0.5773503   0.2386377), wk =   0.0153061
        k(  120) = (   0.2857143   0.5773503  -0.3181836), wk =   0.0076531
     G cutoff =  238.3074  (  21025 G-vectors)     FFT grid: ( 32, 32, 50)
     G cutoff =   79.4358  (   3995 G-vectors)  smooth grid: ( 18, 18, 30)
     Largest allocated arrays     est. size (Mb)     dimensions
        Kohn-Sham Wavefunctions         0.06 Mb     (    135,  30)
        NL pseudopotentials             0.07 Mb     (    135,  36)
        Each V/rho on FFT grid          0.20 Mb     (  13312)
        Each G-vector array             0.04 Mb     (   5256)
        G-vector shells                 0.04 Mb     (   5256)
     Largest temporary arrays     est. size (Mb)     dimensions
        Auxiliary wavefunctions         0.25 Mb     (    135, 120)
        Each subspace H/S matrix        0.22 Mb     (    120, 120)
        Each <psi_i|beta_j> matrix      0.02 Mb     (     36,  30)
        Arrays for rho mixing           1.62 Mb     (  13312,   8)
     Initial potential from superposition of free atoms
     starting charge   19.97000, renormalised to   20.00000
     Starting wfc are   26 atomic +    4 random wfc
     total cpu time spent up to now is      2.04 secs
     per-process dynamical memory:     7.7 Mb
     Self-consistent Calculation
     iteration #  1     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.00E-02,  avg # of iterations =  5.2
     Threshold (ethr) on eigenvalues was too large:
     Diagonalizing with lowered threshold
     Davidson diagonalization with overlap
     ethr =  7.21E-04,  avg # of iterations =  1.1
     total cpu time spent up to now is     17.11 secs
     total energy              =    -180.05547275 Ry
     Harris-Foulkes estimate   =    -180.15409713 Ry
     estimated scf accuracy    <       0.14546748 Ry
     iteration #  2     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  7.27E-04,  avg # of iterations =  2.6
     total cpu time spent up to now is     22.42 secs
     total energy              =    -180.08201004 Ry
     Harris-Foulkes estimate   =    -180.08310411 Ry
     estimated scf accuracy    <       0.00157673 Ry
     iteration #  3     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  7.88E-06,  avg # of iterations =  6.2
     total cpu time spent up to now is     34.99 secs
     total energy              =    -180.08234243 Ry
     Harris-Foulkes estimate   =    -180.08239032 Ry
     estimated scf accuracy    <       0.00008663 Ry
     iteration #  4     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  4.33E-07,  avg # of iterations =  2.2
     total cpu time spent up to now is     39.67 secs
     total energy              =    -180.08234940 Ry
     Harris-Foulkes estimate   =    -180.08234952 Ry
     estimated scf accuracy    <       0.00000068 Ry
     iteration #  5     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  3.38E-09,  avg # of iterations =  2.1
     total cpu time spent up to now is     44.58 secs
     total energy              =    -180.08234965 Ry
     Harris-Foulkes estimate   =    -180.08234968 Ry
     estimated scf accuracy    <       0.00000010 Ry
     iteration #  6     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  5.00E-10,  avg # of iterations =  2.0
     total cpu time spent up to now is     49.37 secs
     End of self-consistent calculation
          k = 0.0000 0.0000 0.0000 (   525 PWs)   bands (ev):
    -7.5077  -4.2553   4.8253  12.5286  12.5286  14.2044  14.2044  14.8220
    21.7352  23.9498  25.7465  25.7465  26.0251  27.1761  27.5311  27.5311
    27.5552  27.5552  27.9377  28.2291  28.2291  28.3829  31.2562  36.6993
    36.6993  39.3932  39.3933  41.4102  41.4102  41.6156
..................................
          k = 0.2857 0.5774-0.3182 (   502 PWs)   bands (ev):
    -3.8637  -3.8637   6.1211   6.1211   7.9395   7.9395  12.7061  12.7061
    22.8290  22.8290  23.7925  23.7925  26.8634  26.8634  28.8438  28.8438
    29.1672  29.1672  36.0364  36.0364  37.1475  37.1475  37.9938  37.9938
    38.8055  38.8055  39.9043  39.9043  41.2094  41.2094
     the Fermi energy is    23.2963 ev
!    total energy              =    -180.08234966 Ry
     Harris-Foulkes estimate   =    -180.08234967 Ry
     estimated scf accuracy    <          9.8E-09 Ry
     The total energy is the sum of the following terms:
     one-electron contribution =      31.54953500 Ry
     hartree contribution      =       3.68728415 Ry
     xc contribution           =     -98.07090733 Ry
     ewald contribution        =    -117.24829605 Ry
     smearing contrib. (-TS)   =       0.00003456 Ry
     convergence has been achieved in   6 iterations
     Forces acting on atoms (Ry/au):
     atom   1 type  1   force =     0.00000000    0.00000000    0.00000000
     atom   2 type  1   force =     0.00000000    0.00000000    0.00000000
     Total force =     0.000000     Total SCF correction =     0.000000

     entering subroutine stress ...
          total   stress  (Ry/bohr**3)                   (kbar)     P=
356.42
   0.00262856   0.00000000   0.00000000        386.67      0.00      0.00
   0.00000000   0.00262856   0.00000000          0.00    386.67      0.00
   0.00000000   0.00000000   0.00201147          0.00      0.00    295.90

     BFGS Geometry Optimization
     number of scf cycles    =   1
     number of bfgs steps    =   0
     enthalpy new            =    -179.2700254431 Ry
     new trust radius        =       0.2000000000 bohr
     new conv_thr            =       0.0000000100 Ry
     new unit-cell volume =    214.73402 a.u.^3 (    31.82030 Ang^3 )
CELL_PARAMETERS (alat)
   0.972380845   0.000000000   0.000000000
  -0.486190423   0.842106514   0.000000000
   0.000000000   0.000000000   1.493252878
ATOMIC_POSITIONS (crystal)
Ba       0.333333333   0.666666667   0.250000000
Ba       0.666666667   0.333333333   0.750000000

     Writing output data file ba.save
     NEW-OLD atomic charge density approx. for the potential
     NEW k-points:
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0012755
       ..........................
        k(  120) = (   0.2938296   0.5937491  -0.3348395), wk =   0.0076531
     extrapolated charge   17.74385, renormalised to   20.00000
     total cpu time spent up to now is     51.94 secs
     per-process dynamical memory:     6.8 Mb
     Self-consistent Calculation
     iteration #  1     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.00E-06,  avg # of iterations =  8.5
     total cpu time spent up to now is     68.08 secs
     total energy              =    -179.97041147 Ry
     Harris-Foulkes estimate   =    -177.83374248 Ry
     estimated scf accuracy    <       0.03695251 Ry
     iteration #  2     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.85E-04,  avg # of iterations =  4.8
     total cpu time spent up to now is     78.31 secs
     total energy              =    -180.02045962 Ry
     Harris-Foulkes estimate   =    -180.03224157 Ry
     estimated scf accuracy    <       0.02356776 Ry
     iteration #  3     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.18E-04,  avg # of iterations =  2.2
     total cpu time spent up to now is     82.89 secs
     total energy              =    -180.01971209 Ry
     Harris-Foulkes estimate   =    -180.02210285 Ry
     estimated scf accuracy    <       0.00370170 Ry
     iteration #  4     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.85E-05,  avg # of iterations =  4.1
     total cpu time spent up to now is     89.82 secs
     total energy              =    -180.02038207 Ry
     Harris-Foulkes estimate   =    -180.02040479 Ry
     estimated scf accuracy    <       0.00004705 Ry
     iteration #  5     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  2.35E-07,  avg # of iterations =  2.6
     total cpu time spent up to now is     95.23 secs
     total energy              =    -180.02038810 Ry
     Harris-Foulkes estimate   =    -180.02039556 Ry
     estimated scf accuracy    <       0.00000846 Ry
     iteration #  6     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  4.23E-08,  avg # of iterations =  2.0
     total cpu time spent up to now is    100.06 secs
     total energy              =    -180.02039034 Ry
     Harris-Foulkes estimate   =    -180.02039133 Ry
     estimated scf accuracy    <       0.00000130 Ry
     iteration #  7     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  6.52E-09,  avg # of iterations =  2.0
     total cpu time spent up to now is    104.86 secs
     total energy              =    -180.02039065 Ry
     Harris-Foulkes estimate   =    -180.02039066 Ry
     estimated scf accuracy    <       0.00000002 Ry
     iteration #  8     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  8.60E-11,  avg # of iterations =  1.7
     total cpu time spent up to now is    109.07 secs
     End of self-consistent calculation
          k = 0.0000 0.0000 0.0000 (   525 PWs)   bands (ev):
    -5.9352  -1.5838   6.3491  15.1342  15.1342  17.3993  17.3993  18.5458
    23.8348  25.7969  27.8380  28.1470  28.1470  29.7371  29.7371  30.2050
    30.2050  30.2872  30.2872  30.5813  31.5261  31.6805  34.0063  40.1211
    40.1211  43.4906  43.4906  44.4380  45.4547  45.5237
.................................
          k = 0.2938 0.5937-0.3348 (   502 PWs)   bands (ev):
    -1.3659  -1.3659   7.7590   7.7590   9.9393   9.9393  15.8344  15.8344
    25.4841  25.4841  26.3126  26.3126  29.2729  29.2729  31.4118  31.4118
    31.5406  31.5406  39.6484  39.6484  41.0258  41.0258  41.4271  41.4271
    42.4194  42.4194  43.1321  43.1321  44.4583  44.4583
     the Fermi energy is    25.6489 ev
!    total energy              =    -180.02039065 Ry
     Harris-Foulkes estimate   =    -180.02039065 Ry
     estimated scf accuracy    <          1.0E-09 Ry
     The total energy is the sum of the following terms:
     one-electron contribution =      36.88903660 Ry
     hartree contribution      =       2.91419118 Ry
     xc contribution           =     -98.35334426 Ry
     ewald contribution        =    -121.47020511 Ry
     smearing contrib. (-TS)   =      -0.00006906 Ry
     convergence has been achieved in   8 iterations
     Forces acting on atoms (Ry/au):
     atom   1 type  1   force =     0.00000000    0.00000000    0.00000000
     atom   2 type  1   force =     0.00000000    0.00000000    0.00000000
     Total force =     0.000000     Total SCF correction =     0.000000

     entering subroutine stress ...
          total   stress  (Ry/bohr**3)                   (kbar)     P=
421.03
   0.00318745   0.00000000   0.00000000        468.89      0.00      0.00
   0.00000000   0.00318745   0.00000000          0.00    468.89      0.00
   0.00000000   0.00000000   0.00221141          0.00      0.00    325.31

     number of scf cycles    =   2
     number of bfgs steps    =   1
     enthalpy old            =    -179.2700254431 Ry
     enthalpy new            =    -179.2905244161 Ry
     CASE: enthalpy_new < enthalpy_old
     new trust radius        =       0.6259677229 bohr
     new conv_thr            =       0.0000000010 Ry
     new unit-cell volume =    156.64138 a.u.^3 (    23.21186 Ang^3 )
CELL_PARAMETERS (alat)
   0.917924413   0.000000000   0.000000000
  -0.458962207   0.794945860   0.000000000
   0.000000000   0.000000000   1.222356706
ATOMIC_POSITIONS (crystal)
Ba       0.333333333   0.666666667   0.250000000
Ba       0.666666667   0.333333333   0.750000000

     Writing output data file ba.save
     NEW-OLD atomic charge density approx. for the potential
     NEW k-points:
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0012755
       ...............................
        k(  120) = (   0.3112612   0.6289737  -0.4090459), wk =   0.0076531
     negative rho (up, down):  0.677E-01 0.000E+00
     extrapolated charge   12.59385, renormalised to   20.00000
     total cpu time spent up to now is    111.68 secs
     per-process dynamical memory:     6.8 Mb
     Self-consistent Calculation
     iteration #  1     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.00E-06,  avg # of iterations =  9.8
     total cpu time spent up to now is    133.65 secs
     total energy              =    -179.47443727 Ry
     Harris-Foulkes estimate   =    -172.02041237 Ry
     estimated scf accuracy    <       0.93334584 Ry
     iteration #  2     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  4.67E-03,  avg # of iterations =  2.0
     total cpu time spent up to now is    138.56 secs
     total energy              =    -179.88867067 Ry
     Harris-Foulkes estimate   =    -179.95675136 Ry
     estimated scf accuracy    <       0.11333799 Ry
     iteration #  3     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  5.67E-04,  avg # of iterations =  1.5
     total cpu time spent up to now is    142.62 secs
     total energy              =    -179.90133852 Ry
     Harris-Foulkes estimate   =    -179.90341794 Ry
     estimated scf accuracy    <       0.00351700 Ry
     iteration #  4     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.76E-05,  avg # of iterations =  3.8
     total cpu time spent up to now is    149.90 secs
     total energy              =    -179.90233358 Ry
     Harris-Foulkes estimate   =    -179.90233707 Ry
     estimated scf accuracy    <       0.00006717 Ry
     iteration #  5     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  3.36E-07,  avg # of iterations =  1.6
     total cpu time spent up to now is    154.02 secs
     total energy              =    -179.90233517 Ry
     Harris-Foulkes estimate   =    -179.90233792 Ry
     estimated scf accuracy    <       0.00000590 Ry
     iteration #  6     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  2.95E-08,  avg # of iterations =  2.0
     total cpu time spent up to now is    158.80 secs
     total energy              =    -179.90233645 Ry
     Harris-Foulkes estimate   =    -179.90233677 Ry
     estimated scf accuracy    <       0.00000045 Ry
     iteration #  7     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  2.26E-09,  avg # of iterations =  2.0
     total cpu time spent up to now is    163.46 secs
     total energy              =    -179.90233654 Ry
     Harris-Foulkes estimate   =    -179.90233655 Ry
     estimated scf accuracy    <          2.0E-09 Ry
     iteration #  8     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  9.84E-12,  avg # of iterations =  2.0
     total cpu time spent up to now is    168.35 secs
     End of self-consistent calculation
          k = 0.0000 0.0000 0.0000 (   525 PWs)   bands (ev):
....................................
          k = 0.3113 0.6290-0.4090 (   502 PWs)   bands (ev):
     6.5449   6.5449  12.9235  12.9235  16.6333  16.6333  28.0681  28.0681
    34.9379  34.9379  36.1481  36.1481  36.4713  36.4713  38.1682  38.1682
    39.5333  39.5333  51.6150  51.6150  52.1986  52.1986  53.3102  53.3102
    54.3922  54.3922  55.1422  55.1422  56.9701  56.9701
     the Fermi energy is    33.6028 ev
!    total energy              =    -179.90233655 Ry
     Harris-Foulkes estimate   =    -179.90233655 Ry
     estimated scf accuracy    <          1.8E-11 Ry
     The total energy is the sum of the following terms:
     one-electron contribution =      52.48807247 Ry
     hartree contribution      =       1.47883554 Ry
     xc contribution           =     -99.48143242 Ry
     ewald contribution        =    -134.38785054 Ry
     smearing contrib. (-TS)   =       0.00003841 Ry
     convergence has been achieved in   8 iterations
     Forces acting on atoms (Ry/au):
     atom   1 type  1   force =     0.00000000    0.00000000    0.00000000
     atom   2 type  1   force =     0.00000000    0.00000000    0.00000000
     Total force =     0.000000     Total SCF correction =     0.000000

     entering subroutine stress ...
          total   stress  (Ry/bohr**3)                   (kbar)     P=
94.16
  -0.00125433   0.00000000   0.00000000       -184.52      0.00      0.00
   0.00000000  -0.00125433   0.00000000          0.00   -184.52      0.00
   0.00000000   0.00000000   0.00442894          0.00      0.00    651.52

     number of scf cycles    =   3
     number of bfgs steps    =   2
     enthalpy old            =    -179.2905244161 Ry
     enthalpy new            =    -179.3699232118 Ry
     CASE: enthalpy_new < enthalpy_old
     new trust radius        =       0.8000000000 bohr
     new conv_thr            =       0.0000000010 Ry
     new unit-cell volume =    104.85025 a.u.^3 (    15.53720 Ang^3 )
CELL_PARAMETERS (alat)
   0.859403261   0.000000000   0.000000000
  -0.429701630   0.744265056   0.000000000
   0.000000000   0.000000000   0.933427905
ATOMIC_POSITIONS (crystal)
Ba       0.333333333   0.666666667   0.250000000
Ba       0.666666667   0.333333333   0.750000000

     Writing output data file ba.save
     NEW-OLD atomic charge density approx. for the potential
     NEW k-points:
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0012755
        k(    2) = (   0.0000000   0.0000000   0.1339150), wk =   0.0025510
    ..............................
        k(  120) = (   0.3324566   0.6718037  -0.5356600), wk =   0.0076531
     negative rho (up, down):  0.351E+00 0.000E+00
     extrapolated charge   10.13575, renormalised to   20.00000
     total cpu time spent up to now is    170.97 secs
     per-process dynamical memory:     6.8 Mb
     Self-consistent Calculation
     iteration #  1     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.00E-06,  avg # of iterations = 10.6
     negative rho (up, down):  0.130E-01 0.000E+00
     total cpu time spent up to now is    193.72 secs
     total energy              =    -179.24824037 Ry
     Harris-Foulkes estimate   =    -168.88154073 Ry
     estimated scf accuracy    <       2.18401744 Ry
     iteration #  2     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.00E-02,  avg # of iterations =  2.0
     total cpu time spent up to now is    198.42 secs
     total energy              =    -179.69005728 Ry
     Harris-Foulkes estimate   =    -179.86172588 Ry
     estimated scf accuracy    <       0.29293488 Ry
     iteration #  3     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.46E-03,  avg # of iterations =  1.8
     total cpu time spent up to now is    202.74 secs
     total energy              =    -179.74060594 Ry
     Harris-Foulkes estimate   =    -179.74228940 Ry
     estimated scf accuracy    <       0.00489558 Ry
     iteration #  4     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  2.45E-05,  avg # of iterations =  4.3
     total cpu time spent up to now is    210.28 secs
     total energy              =    -179.74103742 Ry
     Harris-Foulkes estimate   =    -179.74114368 Ry
     estimated scf accuracy    <       0.00023344 Ry
     iteration #  5     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.17E-06,  avg # of iterations =  2.1
     total cpu time spent up to now is    214.75 secs
     total energy              =    -179.74107283 Ry
     Harris-Foulkes estimate   =    -179.74107660 Ry
     estimated scf accuracy    <       0.00000767 Ry
     iteration #  6     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  3.83E-08,  avg # of iterations =  1.9
     total cpu time spent up to now is    219.39 secs
     total energy              =    -179.74107448 Ry
     Harris-Foulkes estimate   =    -179.74107457 Ry
     estimated scf accuracy    <       0.00000016 Ry
     iteration #  7     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  7.81E-10,  avg # of iterations =  2.0
     total cpu time spent up to now is    223.97 secs
     total energy              =    -179.74107452 Ry
     Harris-Foulkes estimate   =    -179.74107452 Ry
     estimated scf accuracy    <          2.0E-09 Ry
     iteration #  8     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.02E-11,  avg # of iterations =  2.0
     total cpu time spent up to now is    228.59 secs
     End of self-consistent calculation
          k = 0.0000 0.0000 0.0000 (   525 PWs)   bands (ev):
     5.5692  23.0444  29.6262  31.2173  31.2173  38.1786  38.2595  39.6413
    39.6413  44.3136  46.3391  46.3391  48.7016  48.7016  49.9016  49.9016
    55.6021  55.7915  55.7915  60.5507  63.8747  67.5483  67.9935  68.6188
    71.0641  80.9428  80.9428  84.4543  84.4543  86.7874
,,,,,,,,,,,,,
          k = 0.3325 0.6718-0.5357 (   502 PWs)   bands (ev):
    18.3684  18.3684  21.8538  21.8538  27.6028  27.6028  42.4759  42.4759
    44.0063  44.0063  46.9012  46.9012  51.8586  51.8586  53.2917  53.2917
    61.2534  61.2534  63.0859  63.0859  67.4868  67.4868  67.9459  67.9459
    71.7649  71.7649  74.7165  74.7165  78.4559  78.4559
     the Fermi energy is    44.3659 ev
!    total energy              =    -179.74107452 Ry
     Harris-Foulkes estimate   =    -179.74107452 Ry
     estimated scf accuracy    <          1.0E-10 Ry
     The total energy is the sum of the following terms:
     one-electron contribution =      73.05190263 Ry
     hartree contribution      =       1.17111934 Ry
     xc contribution           =    -101.75584475 Ry
     ewald contribution        =    -152.20821369 Ry
     smearing contrib. (-TS)   =      -0.00003804 Ry
     convergence has been achieved in   8 iterations
     Forces acting on atoms (Ry/au):
     atom   1 type  1   force =     0.00000000    0.00000000    0.00000000
     atom   2 type  1   force =     0.00000000    0.00000000    0.00000000
     Total force =     0.000000     Total SCF correction =     0.000000

     entering subroutine stress ...
          total   stress  (Ry/bohr**3)                   (kbar)
P=-1463.24
  -0.02144561   0.00000000   0.00000000      -3154.76      0.00      0.00
   0.00000000  -0.02144561   0.00000000          0.00  -3154.76      0.00
   0.00000000   0.00000000   0.01305057          0.00      0.00   1919.80

     number of scf cycles    =   4
     number of bfgs steps    =   3
     enthalpy old            =    -179.3699232118 Ry
     enthalpy new            =    -179.3846956927 Ry
     CASE: enthalpy_new < enthalpy_old
     new trust radius        =       0.8000000000 bohr
     new conv_thr            =       0.0000000010 Ry
     new unit-cell volume =     71.19555 a.u.^3 (    10.55009 Ang^3 )
CELL_PARAMETERS (alat)
   0.812946837   0.000000000   0.000000000
  -0.406473419   0.704032613   0.000000000
   0.000000000   0.000000000   0.708327035
ATOMIC_POSITIONS (crystal)
Ba       0.333333333   0.666666667   0.250000000
Ba       0.666666667   0.333333333   0.750000000

     Writing output data file ba.save
     NEW-OLD atomic charge density approx. for the potential
     NEW k-points:
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0012755
        .........................
        k(  120) = (   0.3514551   0.7101944  -0.7058886), wk =   0.0076531
     negative rho (up, down):  0.274E+00 0.000E+00
     extrapolated charge   10.56002, renormalised to   20.00000
     total cpu time spent up to now is    231.19 secs
     per-process dynamical memory:     6.8 Mb
     Self-consistent Calculation
     iteration #  1     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.00E-06,  avg # of iterations =  9.4
     negative rho (up, down):  0.272E-01 0.000E+00
     total cpu time spent up to now is    250.50 secs
     total energy              =    -178.64688266 Ry
     Harris-Foulkes estimate   =    -167.34159333 Ry
     estimated scf accuracy    <       1.44120252 Ry
     iteration #  2     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  7.21E-03,  avg # of iterations =  2.1
     negative rho (up, down):  0.251E-02 0.000E+00
     total cpu time spent up to now is    255.41 secs
     total energy              =    -179.10663630 Ry
     Harris-Foulkes estimate   =    -179.40324157 Ry
     estimated scf accuracy    <       0.53596630 Ry
     iteration #  3     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  2.68E-03,  avg # of iterations =  1.1
     total cpu time spent up to now is    259.46 secs
     total energy              =    -179.17020799 Ry
     Harris-Foulkes estimate   =    -179.18027458 Ry
     estimated scf accuracy    <       0.01870046 Ry
     iteration #  4     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  9.35E-05,  avg # of iterations =  2.6
     total cpu time spent up to now is    264.74 secs
     total energy              =    -179.17306320 Ry
     Harris-Foulkes estimate   =    -179.17425111 Ry
     estimated scf accuracy    <       0.00156877 Ry
     iteration #  5     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  7.84E-06,  avg # of iterations =  2.2
     total cpu time spent up to now is    269.98 secs
     total energy              =    -179.17349690 Ry
     Harris-Foulkes estimate   =    -179.17369743 Ry
     estimated scf accuracy    <       0.00031491 Ry
     iteration #  6     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.57E-06,  avg # of iterations =  1.2
     total cpu time spent up to now is    273.86 secs
     total energy              =    -179.17355726 Ry
     Harris-Foulkes estimate   =    -179.17355727 Ry
     estimated scf accuracy    <       0.00000006 Ry
     iteration #  7     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  2.80E-10,  avg # of iterations =  3.0
     total cpu time spent up to now is    279.89 secs
     total energy              =    -179.17355744 Ry
     Harris-Foulkes estimate   =    -179.17355745 Ry
     estimated scf accuracy    <       0.00000002 Ry
     iteration #  8     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  8.57E-11,  avg # of iterations =  1.0
     total cpu time spent up to now is    283.60 secs
     total energy              =    -179.17355744 Ry
     Harris-Foulkes estimate   =    -179.17355744 Ry
     estimated scf accuracy    <          6.2E-09 Ry
     iteration #  9     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  3.12E-11,  avg # of iterations =  1.0
     total cpu time spent up to now is    287.35 secs
     End of self-consistent calculation
          k = 0.0000 0.0000 0.0000 (   525 PWs)   bands (ev):
    15.4481  39.7850  44.0999  44.0999  46.0647  50.1706  51.4429  51.4429
    58.1753  58.1753  58.2773  64.5063  64.5063  68.6558  68.6558  74.0360
    74.0360  74.6890  75.9570  76.5327  78.1704  84.8112  89.6712  98.7488
   103.0497 103.0497 108.9915 108.9915 110.1470 114.6047
................................
          k = 0.3515 0.7102-0.7059 (   502 PWs)   bands (ev):
    33.7648  33.7648  35.4623  35.4623  42.9595  42.9595  51.9894  51.9894
    54.3233  54.3233  62.7888  62.7888  71.2510  71.2510  72.5335  72.5335
    77.6884  77.6884  80.9953  80.9953  83.6399  83.6399  87.9481  87.9481
    94.2206  94.2206 101.3399 101.3399 106.5786 106.5786
     the Fermi energy is    59.3072 ev
!    total energy              =    -179.17355744 Ry
     Harris-Foulkes estimate   =    -179.17355744 Ry
     estimated scf accuracy    <          1.2E-10 Ry
     The total energy is the sum of the following terms:
     one-electron contribution =      95.21570945 Ry
     hartree contribution      =       2.07799243 Ry
     xc contribution           =    -105.27402935 Ry
     ewald contribution        =    -171.19320324 Ry
     smearing contrib. (-TS)   =      -0.00002673 Ry
     convergence has been achieved in   9 iterations
     Forces acting on atoms (Ry/au):
     atom   1 type  1   force =     0.00000000    0.00000000    0.00000000
     atom   2 type  1   force =     0.00000000    0.00000000    0.00000000
     Total force =     0.000000     Total SCF correction =     0.000000

     entering subroutine stress ...
          total   stress  (Ry/bohr**3)                   (kbar)     P=
9145.21
   0.06562285   0.00000000   0.00000000       9653.45      0.00      0.00
   0.00000000   0.06562285   0.00000000          0.00   9653.45      0.00
   0.00000000   0.00000000   0.05525797          0.00      0.00   8128.73

     number of scf cycles    =   5
     number of bfgs steps    =   4
     enthalpy old            =    -179.3846956927 Ry
     enthalpy new            =    -178.9315686586 Ry
     CASE: enthalpy_new > enthalpy_old
     new trust radius        =       0.0384028778 bohr
     new conv_thr            =       0.0000000010 Ry
     new unit-cell volume =    103.49817 a.u.^3 (    15.33685 Ang^3 )
CELL_PARAMETERS (alat)
   0.857682746   0.000000000   0.000000000
  -0.428841373   0.742775046   0.000000000
   0.000000000   0.000000000   0.925091288
ATOMIC_POSITIONS (crystal)
Ba       0.333333333   0.666666667   0.250000000
Ba       0.666666667   0.333333333   0.750000000

     Writing output data file ba.save
     NEW-OLD atomic charge density approx. for the potential
     NEW k-points:
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0012755
       ...................................
        k(  120) = (   0.3331235   0.6731513  -0.5404872), wk =   0.0076531
     extrapolated charge   26.23280, renormalised to   20.00000
     total cpu time spent up to now is    289.95 secs
     per-process dynamical memory:     6.8 Mb
     Self-consistent Calculation
     iteration #  1     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.00E-06,  avg # of iterations =  9.7
.........................
     iteration #  8     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.73E-11,  avg # of iterations =  1.0
     total cpu time spent up to now is    342.11 secs
     End of self-consistent calculation
          k = 0.0000 0.0000 0.0000 (   525 PWs)   bands (ev):
     5.8273  23.5040  30.4240  31.5696  31.5696  38.4142  38.5967  40.0372
    40.0372  44.9606  46.7839  46.7839  49.0936  49.0936  50.5079  50.5079
    56.1462  56.2944  56.2944  61.1463  64.5519  68.2284  68.2619  69.2114
    72.4177  81.9375  81.9375  85.2932  85.2932  87.5564
........................... (ev):
    17.1914  18.3584  23.1111  24.3348  25.6382  30.4686  41.5415  42.2213
    45.1268  46.1126  46.8533  47.7179  49.5076  50.8922  51.6181  59.0630
    61.5914  62.3802  64.2027  64.6797  66.4074  68.1675  68.3861  69.6784
    71.3278  72.1637  75.5506  75.8883  77.4138  78.5614
          k = 0.3331 0.6732-0.5405 (   502 PWs)   bands (ev):
    18.8082  18.8082  22.2113  22.2113  28.0309  28.0309  42.7774  42.7774
    44.2743  44.2743  47.3200  47.3200  52.6149  52.6149  53.8894  53.8894
    61.6755  61.6755  63.8138  63.8138  67.9827  67.9827  68.5344  68.5344
    72.1968  72.1968  75.4449  75.4449  79.3829  79.3829
     the Fermi energy is    44.7773 ev
!    total energy              =    -179.73781004 Ry
     Harris-Foulkes estimate   =    -179.73781004 Ry
     estimated scf accuracy    <          7.7E-10 Ry
     The total energy is the sum of the following terms:
     one-electron contribution =      73.74379969 Ry
     hartree contribution      =       1.18401837 Ry
     xc contribution           =    -101.85015411 Ry
     ewald contribution        =    -152.81538341 Ry
     smearing contrib. (-TS)   =      -0.00009058 Ry
     convergence has been achieved in   8 iterations
     Forces acting on atoms (Ry/au):
     atom   1 type  1   force =     0.00000000    0.00000000    0.00000000
     atom   2 type  1   force =     0.00000000    0.00000000    0.00000000
     Total force =     0.000000     Total SCF correction =     0.000000

     entering subroutine stress ...
          total   stress  (Ry/bohr**3)                   (kbar)
P=-1435.79
  -0.02113062   0.00000000   0.00000000      -3108.42      0.00      0.00
   0.00000000  -0.02113062   0.00000000          0.00  -3108.42      0.00
   0.00000000   0.00000000   0.01298040          0.00      0.00   1909.48

     number of scf cycles    =   6
     number of bfgs steps    =   4
     enthalpy old            =    -179.3846956927 Ry
     enthalpy new            =    -179.3860268628 Ry
     CASE: enthalpy_new < enthalpy_old
     new trust radius        =       0.0896283779 bohr
     new conv_thr            =       0.0000000010 Ry
     new unit-cell volume =     99.43360 a.u.^3 (    14.73454 Ang^3 )
CELL_PARAMETERS (alat)
   0.852195584   0.000000000   0.000000000
  -0.426097792   0.738023025   0.000000000
   0.000000000   0.000000000   0.900243251
ATOMIC_POSITIONS (crystal)
Ba       0.333333333   0.666666667   0.250000000
Ba       0.666666667   0.333333333   0.750000000

     Writing output data file ba.save
     NEW-OLD atomic charge density approx. for the potential
     NEW k-points:
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0012755
       ..........................
        k(  119) = (   0.3352684   0.6774856   0.4165541), wk =   0.0153061
        k(  120) = (   0.3352684   0.6774856  -0.5554054), wk =   0.0076531
     extrapolated charge   19.18368, renormalised to   20.00000
     total cpu time spent up to now is    344.73 secs
     per-process dynamical memory:     6.8 Mb
     Self-consistent Calculation
     iteration #  1     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.00E-06,  avg # of iterations =  6.4
     total cpu time spent up to now is    356.64 secs
     total energy              =    -179.72530352 Ry
     Harris-Foulkes estimate   =    -178.59036770 Ry
     estimated scf accuracy    <       0.00250457 Ry
     iteration #  2     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.25E-05,  avg # of iterations =  2.4
     total cpu time spent up to now is    362.99 secs
     total energy              =    -179.72796316 Ry
     Harris-Foulkes estimate   =    -179.72886706 Ry
     estimated scf accuracy    <       0.00197369 Ry
     iteration #  3     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  9.87E-06,  avg # of iterations =  1.0
     total cpu time spent up to now is    366.76 secs
     total energy              =    -179.72795336 Ry
     Harris-Foulkes estimate   =    -179.72811597 Ry
     estimated scf accuracy    <       0.00025632 Ry
     iteration #  4     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.28E-06,  avg # of iterations =  1.6
     total cpu time spent up to now is    370.87 secs
     total energy              =    -179.72800701 Ry
     Harris-Foulkes estimate   =    -179.72800770 Ry
     estimated scf accuracy    <       0.00000140 Ry
     iteration #  5     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  6.99E-09,  avg # of iterations =  2.0
     total cpu time spent up to now is    375.56 secs
     total energy              =    -179.72800737 Ry
     Harris-Foulkes estimate   =    -179.72800740 Ry
     estimated scf accuracy    <       0.00000005 Ry
     iteration #  6     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  2.75E-10,  avg # of iterations =  1.7
     total cpu time spent up to now is    379.85 secs
     total energy              =    -179.72800738 Ry
     Harris-Foulkes estimate   =    -179.72800738 Ry
     estimated scf accuracy    <          6.4E-09 Ry
     iteration #  7     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  3.19E-11,  avg # of iterations =  1.1
     total cpu time spent up to now is    383.61 secs
     End of self-consistent calculation
          k = 0.0000 0.0000 0.0000 (   525 PWs)   bands (ev):
     6.6504  24.9563  32.7042  32.7042  32.9176  39.1516  39.6811  41.2824
    41.2824  47.0674  48.2089  48.2089  50.2876  50.2876  52.4595  52.4595
    57.8283  57.8283  57.8820  62.9031  66.6338  69.1172  70.5208  71.0836
    76.6262  84.9178  84.9178  87.8810  87.8810  89.8982
      .....................................................
          k = 0.3353 0.6775-0.5554 (   502 PWs)   bands (ev):
    20.2020  20.2020  23.3499  23.3499  29.3869  29.3869  43.7260  43.7260
    45.1056  45.1056  48.6637  48.6637  54.9654  54.9654  55.7687  55.7687
    62.8357  62.8357  66.1346  66.1346  69.5380  69.5380  70.4903  70.4903
    73.5784  73.5784  77.7822  77.7822  82.2868  82.2868
     the Fermi energy is    46.0891 ev
!    total energy              =    -179.72800738 Ry
     Harris-Foulkes estimate   =    -179.72800738 Ry
     estimated scf accuracy    <          1.4E-11 Ry
     The total energy is the sum of the following terms:
     one-electron contribution =      75.90515140 Ry
     hartree contribution      =       1.22730797 Ry
     xc contribution           =    -102.15110174 Ry
     ewald contribution        =    -154.70941157 Ry
     smearing contrib. (-TS)   =       0.00004656 Ry
     convergence has been achieved in   7 iterations
     Forces acting on atoms (Ry/au):
     atom   1 type  1   force =     0.00000000    0.00000000    0.00000000
     atom   2 type  1   force =     0.00000000    0.00000000    0.00000000
     Total force =     0.000000     Total SCF correction =     0.000000

     entering subroutine stress ...
          total   stress  (Ry/bohr**3)                   (kbar)
P=-1243.50
  -0.01950049   0.00000000   0.00000000      -2868.62      0.00      0.00
   0.00000000  -0.01950049   0.00000000          0.00  -2868.62      0.00
   0.00000000   0.00000000   0.01364151          0.00      0.00   2006.74

     number of scf cycles    =   7
     number of bfgs steps    =   5
     enthalpy old            =    -179.3860268628 Ry
     enthalpy new            =    -179.3900394018 Ry
     CASE: enthalpy_new < enthalpy_old
     new trust radius        =       0.0109747992 bohr
     new conv_thr            =       0.0000000010 Ry
     new unit-cell volume =     98.87261 a.u.^3 (    14.65141 Ang^3 )
CELL_PARAMETERS (alat)
   0.850178895   0.000000000   0.000000000
  -0.425089447   0.736276520   0.000000000
   0.000000000   0.000000000   0.899416045
ATOMIC_POSITIONS (crystal)
Ba       0.333333333   0.666666667   0.250000000
Ba       0.666666667   0.333333333   0.750000000

................................
          k = 0.3454 0.6980-0.5528 (   502 PWs)   bands (ev):
    22.4024  22.4024  25.2682  25.2682  31.1297  31.1297  45.2919  45.2919
    47.0063  47.0063  51.4668  51.4668  56.5583  56.5583  58.1957  58.1957
    66.0015  66.0015  68.5914  68.5914  72.2169  72.2169  73.4280  73.4280
    76.8283  76.8283  82.1497  82.1497  84.8128  84.8128
     the Fermi energy is    48.2425 ev
!    total energy              =    -179.87009059 Ry
     Harris-Foulkes estimate   =    -179.87009059 Ry
     estimated scf accuracy    <          3.3E-10 Ry
     The total energy is the sum of the following terms:
     one-electron contribution =      79.38355670 Ry
     hartree contribution      =       1.09698186 Ry
     xc contribution           =    -102.51125420 Ry
     ewald contribution        =    -157.83932552 Ry
     smearing contrib. (-TS)   =      -0.00004943 Ry
     convergence has been achieved in   6 iterations
     Forces acting on atoms (Ry/au):
     atom   1 type  1   force =     0.00000000    0.00000000    0.00000000
     atom   2 type  1   force =     0.00000000    0.00000000    0.00000000
     Total force =     0.000000     Total SCF correction =     0.000000

     entering subroutine stress ...
          total   stress  (Ry/bohr**3)                   (kbar)
P=-1504.97
  -0.02700114   0.00000000   0.00000000      -3972.00      0.00      0.00
   0.00000000  -0.02700114   0.00000000          0.00  -3972.00      0.00
   0.00000000   0.00000000   0.02331060          0.00      0.00   3429.11

     number of scf cycles    =  10
     number of bfgs steps    =   8
     enthalpy old            =    -179.4233882564 Ry
     enthalpy new            =    -179.5501846961 Ry
     CASE: enthalpy_new < enthalpy_old
     uphill step: resetting bfgs history
     new trust radius        =       0.3040181881 bohr
     new conv_thr            =       0.0000000010 Ry
     new unit-cell volume =     86.21408 a.u.^3 (    12.77561 Ang^3 )
CELL_PARAMETERS (alat)
   0.776108374   0.000000000   0.000000000
  -0.388054187   0.672129568   0.000000000
   0.000000000   0.000000000   0.941106458
ATOMIC_POSITIONS (crystal)
Ba       0.333333333   0.666666667   0.250000000
Ba       0.666666667   0.333333333   0.750000000

     Writing output data file ba.save
     NEW-OLD atomic charge density approx. for the potential
     NEW k-points:
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0012755
        ...........................................
        k(  117) = (   0.3681371   0.7439042   0.1328224), wk =   0.0153061
        k(  118) = (   0.3681371   0.7439042   0.2656448), wk =   0.0153061
        k(  119) = (   0.3681371   0.7439042   0.3984671), wk =   0.0153061
        k(  120) = (   0.3681371   0.7439042  -0.5312895), wk =   0.0076531
     negative rho (up, down):  0.371E-04 0.000E+00
     extrapolated charge   18.16884, renormalised to   20.00000
     total cpu time spent up to now is    494.17 secs
     per-process dynamical memory:     6.8 Mb
     Self-consistent Calculation
     iteration #  1     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.00E-06,  avg # of iterations =  7.1
     total cpu time spent up to now is    508.36 secs
     total energy              =    -180.41109586 Ry
     Harris-Foulkes estimate   =    -177.72216011 Ry
     estimated scf accuracy    <       0.01754800 Ry
     iteration #  2     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  8.77E-05,  avg # of iterations =  1.7
     total cpu time spent up to now is    512.61 secs
     total energy              =    -180.41335267 Ry
     Harris-Foulkes estimate   =    -180.41536174 Ry
     estimated scf accuracy    <       0.00337610 Ry
     iteration #  3     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.69E-05,  avg # of iterations =  1.5
     total cpu time spent up to now is    516.65 secs
     total energy              =    -180.41399060 Ry
     Harris-Foulkes estimate   =    -180.41402125 Ry
     estimated scf accuracy    <       0.00009018 Ry
     iteration #  4     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  4.51E-07,  avg # of iterations =  2.0
     total cpu time spent up to now is    521.12 secs
     total energy              =    -180.41399339 Ry
     Harris-Foulkes estimate   =    -180.41399784 Ry
     estimated scf accuracy    <       0.00000757 Ry
     iteration #  5     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  3.78E-08,  avg # of iterations =  1.4
     total cpu time spent up to now is    525.10 secs
     total energy              =    -180.41399488 Ry
     Harris-Foulkes estimate   =    -180.41399492 Ry
     estimated scf accuracy    <       0.00000007 Ry
     iteration #  6     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  3.72E-10,  avg # of iterations =  2.0
     total cpu time spent up to now is    529.88 secs
     total energy              =    -180.41399490 Ry
     Harris-Foulkes estimate   =    -180.41399490 Ry
     estimated scf accuracy    <          2.9E-09 Ry
     iteration #  7     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.43E-11,  avg # of iterations =  1.7
     total cpu time spent up to now is    534.13 secs
     End of self-consistent calculation
          k = 0.0000 0.0000 0.0000 (   525 PWs)   bands (ev):
    10.5903  27.8923  35.3558  41.0175  41.0175  41.9370  45.6343  47.7989
    49.2716  49.2716  51.5264  51.5264  59.3229  59.3229  59.9404  61.6118
    61.6118  65.5152  65.5152  68.8216  71.1947  78.5151  78.7591  78.9498
    86.3196  89.9888  89.9888  96.1866  96.1866 102.2057
..............................
          k = 0.3681 0.7439-0.5313 (   502 PWs)   bands (ev):
    26.3154  26.3154  28.7150  28.7150  33.9755  33.9755  47.7289  47.7289
    50.8330  50.8330  56.6835  56.6835  57.3178  57.3178  63.1801  63.1801
    71.2200  71.2200  73.4262  73.4262  77.5386  77.5386  79.2452  79.2452
    83.6995  83.6995  87.3000  87.3000  90.4433  90.4433
     the Fermi energy is    52.0804 ev
!    total energy              =    -180.41399490 Ry
     Harris-Foulkes estimate   =    -180.41399490 Ry
     estimated scf accuracy    <          3.5E-11 Ry
     The total energy is the sum of the following terms:
     one-electron contribution =      85.13306007 Ry
     hartree contribution      =       0.86893274 Ry
     xc contribution           =    -103.08656155 Ry
     ewald contribution        =    -163.32944264 Ry
     smearing contrib. (-TS)   =       0.00001649 Ry
     convergence has been achieved in   7 iterations
     Forces acting on atoms (Ry/au):
     atom   1 type  1   force =     0.00000000    0.00000000    0.00000000
     atom   2 type  1   force =     0.00000000    0.00000000    0.00000000
     Total force =     0.000000     Total SCF correction =     0.000000

     entering subroutine stress ...
          total   stress  (Ry/bohr**3)                   (kbar)
P=-3012.21
  -0.04937157   0.00000000   0.00000000      -7262.81      0.00      0.00
   0.00000000  -0.04937157   0.00000000          0.00  -7262.81      0.00
   0.00000000   0.00000000   0.03731345          0.00      0.00   5489.00

     number of scf cycles    =  11
     number of bfgs steps    =   9
     enthalpy old            =    -179.5501846961 Ry
     enthalpy new            =    -180.1209591443 Ry
     CASE: enthalpy_new < enthalpy_old
     uphill step: resetting bfgs history
     new trust radius        =       0.8000000000 bohr
     new conv_thr            =       0.0000000010 Ry
     new unit-cell volume =     66.74329 a.u.^3 (     9.89033 Ang^3 )
CELL_PARAMETERS (alat)
   0.649713235   0.000000000   0.000000000
  -0.324856618   0.562668167   0.000000000
   0.000000000   0.000000000   1.039607586
ATOMIC_POSITIONS (crystal)
Ba       0.333333333   0.666666667   0.250000000
Ba       0.666666667   0.333333333   0.750000000


     total cpu time spent up to now is    811.37 secs
     per-process dynamical memory:     6.8 Mb
     Self-consistent Calculation
     iteration #  1     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.00E-06,  avg # of iterations =  2.0
     Threshold (ethr) on eigenvalues was too large:
     Diagonalizing with lowered threshold
     Davidson diagonalization with overlap
     ethr =  2.96E-11,  avg # of iterations =  1.0
     total cpu time spent up to now is    820.50 secs
     total energy              =    -182.69139351 Ry
     Harris-Foulkes estimate   =    -182.69460970 Ry
     estimated scf accuracy    <          5.9E-09 Ry
     iteration #  2     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  2.95E-11,  avg # of iterations =  1.9
     total cpu time spent up to now is    824.85 secs
     End of self-consistent calculation
          k = 0.0000 0.0000 0.0000 (   525 PWs)   bands (ev):
    23.4963  39.4336  43.7097  45.9873  48.6939  51.3430  65.1151  65.1151
    67.0404  67.0404  68.4878  73.6955  73.6955  78.2896  78.2896  83.2015
    89.6283  93.6845  93.6845  93.8006  99.7041  99.7041 101.1742 106.0619
   112.6475 115.9326 115.9326 116.3172 117.0027 117.0027
          k = 0.0000 0.0000 0.1239 (   512 PWs)   bands (ev):
    23.7977  37.2687  44.8125  46.0793  50.4720  50.8940  63.0540  63.0540
    69.8561  69.9333  69.9333  71.4542  71.4542  79.7251  79.7251  80.3838
    91.6977  94.0275  94.0275  94.1655  97.8107 100.5397 100.5397 105.4469
   110.9371 113.2449 113.2449 116.4487 116.4487 118.1884
          k = 0.0000 0.0000 0.2478 (   518 PWs)   bands (ev):
    24.7111  34.0545  43.8572  48.2378  50.2151  54.5756  61.4208  61.4208
    67.8267  67.8267  73.0383  73.8788  73.8788  76.1091  81.1220  81.1220
    91.4583  93.0049  95.1313  95.1313  95.2642 102.6679 102.6679 103.9915
   109.1273 109.3394 109.3394 114.9246 114.9246 118.8463
          k = 0.0000 0.0000 0.3717 (   512 PWs)   bands (ev):
    26.2453  31.0185  43.8481  46.3102  54.0538  57.5400  61.1212  61.1212
    64.5499  64.5499  73.3925  75.7103  77.4652  77.4652  81.2478  81.2478
    86.4491  90.8075  97.0380  97.1770  97.1770 101.8808 103.4527 103.4527
   107.4355 107.4355 110.2260 112.6760 112.6760 116.3608
          k = 0.0000 0.0000-0.4956 (   494 PWs)   bands (ev):
    28.3739  28.3739  44.7219  44.7219  57.2057  57.2057  62.2095  62.2095
    62.2095  62.2095  74.3717  74.3717  80.0209  80.0209  80.0209  80.0209
    87.1787  87.1787  99.3561  99.3561 100.2141 100.2141 100.2141 100.2141
   109.9333 109.9333 109.9333 109.9333 113.1539 113.1539
          k = 0.0000 0.1331 0.0000 (   523 PWs)   bands (ev):
    23.8506  40.0094  43.5544  46.9816  49.2087  52.2230  61.4494  65.2719
    65.3076  65.6799  73.0071  75.2001  75.3097  76.7139  78.6339  82.3658
    90.8658  91.0594  91.9197  93.3569 100.2084 100.9119 102.4395 105.6537
   111.8788 113.4201 114.8129 116.3399 116.9433 120.3065
          k = 0.0000 0.1331 0.1239 (   516 PWs)   bands (ev):
    24.1506  37.6736  45.7343  46.0518  51.3182  51.4522  60.8957  62.9696
    66.5767  68.1061  72.0646  73.6487  74.3804  78.4670  79.8607  81.3074
    91.4704  91.4895  92.9815  93.7268  98.7293 101.3482 101.7604 105.0274
   109.1807 111.7694 113.8038 117.3215 117.9796 118.9554
          k = 0.0000 0.1331 0.2478 (   512 PWs)   bands (ev):
    25.0598  34.4045  44.7859  48.7129  50.5139  55.0468  60.2030  61.4987
    66.1471  67.4976  71.9588  74.3350  76.1404  77.4405  80.8166  81.3694
    91.0406  93.2180  93.2554  94.6667  94.8753 102.9279 103.9582 104.0553
   105.7103 108.1888 112.1429 115.6760 115.9359 119.7202
          k = 0.0000 0.1331 0.3717 (   509 PWs)   bands (ev):
    26.5881  31.3553  44.7710  47.1043  54.0015  57.9347  60.2433  61.3165
    62.9095  64.7154  74.1188  76.6582  77.1322  78.2525  80.6375  81.2381
    86.6882  90.7155  96.0142  96.2465  96.7344 101.1124 102.7883 103.8242
   107.1444 107.3338 111.7129 113.4496 113.4712 116.9017
     one-electron contribution =     109.52336565 Ry
     hartree contribution      =       1.49054124 Ry
     xc contribution           =    -106.63457238 Ry
     ewald contribution        =    -187.07078104 Ry
     smearing contrib. (-TS)   =       0.00005302 Ry
     convergence has been achieved in   2 iterations
     Forces acting on atoms (Ry/au):
     atom   1 type  1   force =     0.00000000    0.00000000    0.00000000
     atom   2 type  1   force =     0.00000000    0.00000000    0.00000000
     Total force =     0.000000     Total SCF correction =     0.000000

     entering subroutine stress ...
          total   stress  (Ry/bohr**3)                   (kbar)     P=
499.71
   0.00339645   0.00000000   0.00000000        499.64      0.00      0.00
   0.00000000   0.00339645   0.00000000          0.00    499.64      0.00
   0.00000000   0.00000000   0.00339797          0.00      0.00    499.86

     number of scf cycles    =  20
     number of bfgs steps    =  16
     enthalpy old            =    -182.4912648694 Ry
     enthalpy new            =    -182.4912650661 Ry
     CASE: enthalpy_new < enthalpy_old
     small trust_radius: resetting bfgs history
     new trust radius        =       0.0001000000 bohr
     new conv_thr            =       0.0000000010 Ry
     new unit-cell volume =     58.87678 a.u.^3 (     8.72464 Ang^3 )
CELL_PARAMETERS (alat)
   0.619452010   0.000000000   0.000000000
  -0.309726005   0.536461177   0.000000000
   0.000000000   0.000000000   1.008867201
ATOMIC_POSITIONS (crystal)
Ba       0.333333333   0.666666667   0.250000000
Ba       0.666666667   0.333333333   0.750000000

     Writing output data file ba.save
     NEW-OLD atomic charge density approx. for the potential
     NEW k-points:
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0012755
        k(    2) = (   0.0000000   0.0000000   0.1239013), wk =   0.0025510
      .....................................
        k(  117) = (   0.4612372   0.9320339   0.1239013), wk =   0.0153061
        k(  118) = (   0.4612372   0.9320339   0.2478027), wk =   0.0153061
        k(  119) = (   0.4612372   0.9320339   0.3717040), wk =   0.0153061
        k(  120) = (   0.4612372   0.9320339  -0.4956054), wk =   0.0076531
     extrapolated charge   19.99897, renormalised to   20.00000
     total cpu time spent up to now is    827.45 secs
     per-process dynamical memory:     6.8 Mb
     Self-consistent Calculation
     iteration #  1     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  1.00E-06,  avg # of iterations =  2.0
     Threshold (ethr) on eigenvalues was too large:
     Diagonalizing with lowered threshold
     Davidson diagonalization with overlap
     ethr =  8.89E-12,  avg # of iterations =  1.0
     total cpu time spent up to now is    836.43 secs
     total energy              =    -182.69138316 Ry
     Harris-Foulkes estimate   =    -182.68968251 Ry
     estimated scf accuracy    <          1.8E-09 Ry
     iteration #  2     ecut=    25.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     ethr =  8.87E-12,  avg # of iterations =  1.0
     total cpu time spent up to now is    840.31 secs
     End of self-consistent calculation
          k = 0.0000 0.0000 0.0000 (   525 PWs)   bands (ev):
.........................................
    40.0361  40.6009  45.7044  50.9501  51.3244  53.3623  56.0773  56.5506
    57.0623  69.6559  71.6533  74.0268  80.5679  82.3544  84.5167  88.1500
    89.2424  90.9851  92.7797  95.8605  96.7467 105.1969 107.0584 109.6477
   111.0721 112.3064 117.1311 119.1127 119.3667 121.4474
          k = 0.4612 0.9320 0.2478 (   505 PWs)   bands (ev):
    41.0802  41.8570  46.6542  49.6272  49.6791  52.8809  57.4647  57.7725
    58.9601  68.1598  68.6875  70.8414  80.1197  83.5757  84.1667  88.7632
    89.7937  90.5846  96.2445  96.4011 100.7054 104.3154 106.5183 106.8621
   110.6925 112.2676 115.4366 117.0866 118.0894 119.1179
          k = 0.4612 0.9320 0.3717 (   505 PWs)   bands (ev):
    42.6127  43.6312  46.4707  48.0678  49.6040  52.1490  58.4717  58.7590
    61.1252  65.9776  66.6406  68.0643  80.4250  83.7784  85.4584  87.1725
    89.4676  89.8571  98.2898 100.1461 103.6412 103.9378 106.3023 107.3237
   108.9653 111.7138 111.8787 114.3479 117.7829 119.0810
          k = 0.4612 0.9320-0.4956 (   502 PWs)   bands (ev):
    44.2159  44.2159  46.3159  46.3159  50.9667  50.9667  58.9664  58.9664
    63.4773  63.4773  66.5095  66.5095  82.0172  82.0172  87.1525  87.1525
    88.5421  88.5421 100.3385 100.3385 105.1346 105.1346 106.0591 106.0591
   109.5068 109.5068 114.0161 114.0161 116.7857 116.7857
     the Fermi energy is    69.2055 ev
!    total energy              =    -182.69138316 Ry
     Harris-Foulkes estimate   =    -182.69138316 Ry
     estimated scf accuracy    <          1.8E-10 Ry
     The total energy is the sum of the following terms:
     one-electron contribution =     109.52706926 Ry
     hartree contribution      =       1.49068490 Ry
     xc contribution           =    -106.63519409 Ry
     ewald contribution        =    -187.07399600 Ry
     smearing contrib. (-TS)   =       0.00005277 Ry
     convergence has been achieved in   2 iterations
     Forces acting on atoms (Ry/au):
     atom   1 type  1   force =     0.00000000    0.00000000    0.00000000
     atom   2 type  1   force =     0.00000000    0.00000000    0.00000000
     Total force =     0.000000     Total SCF correction =     0.000000

     entering subroutine stress ...
          total   stress  (Ry/bohr**3)                   (kbar)     P=
504.36
   0.00343665   0.00000000   0.00000000        505.55      0.00      0.00
   0.00000000   0.00343665   0.00000000          0.00    505.55      0.00
   0.00000000   0.00000000   0.00341231          0.00      0.00    501.97

     number of scf cycles    =  21
     number of bfgs steps    =  17
     enthalpy old            =    -182.4912650661 Ry
     enthalpy new            =    -182.4912650178 Ry
     CASE: enthalpy_new > enthalpy_old
     new trust radius        =       0.0000499654 bohr
     trust_radius < trust_radius_min
     resetting bfgs history

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from bfgs : error #         1
     bfgs history already reset at previous step
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
rank 0 in job 1  linux-solid_50241   caused collective abort of all ranks
  exit status of rank 0: killed by signal 9


2010/3/3 Lorenzo Paulatto <paulatto at sissa.it>

> On Wed, 03 Mar 2010 15:15:01 +0100, Wei Zhou <zdw2000 at gmail.com> wrote:
> >>      from scale_h : error #         1
>
> The output with cell_factor=3.0, please, I know what's of *this* error :-)
>
>
> >
> >>  MAKE.SYS, I use the intel_mpi3.2.1.009,IFORT9.0, and I calculate the Ba
> >> structure at lower pressure ,it seem works well
>
> Well, if some mathematical libraries are unstable the instability is more
> likely to pop out in extreme cases. ifort is an old and buggy compiler, if
> you have the possibility to update it I would suggest you to do so.
>
> > BLAS_LIBS      = ../flib/blas.a
> > LAPACK_LIBS    = ../flib/lapack.a
>
> Internal blas and lapack libraries are robust but very slow if you want
> better performances, you should try to get some optimized libraries; see:
> <
> http://www.quantum-espresso.org/user_guide/node10.html#SECTION00033110000000000000
> >
>
> --
> Lorenzo Paulatto
>
> *** Note: my affiliation has changed! please send future
> correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***
>
> post-doc @ IMPMC/UPMC - Universit? Paris 6
> phone: +33 (0)1 44 27 74 89
> www:   http://www-int.impmc.upmc.fr/~paulatto/
>
> previously:
> phd student @ SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> www:   http://people.sissa.it/~paulatto/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
ZhouDawei
JiLin Universiyt ,ChangChun ,China
zdw2000 at gmail.com
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From paulatto at sissa.it  Wed Mar  3 18:27:36 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 03 Mar 2010 18:27:36 +0100
Subject: [Pw_forum] about the from scale_h : error
In-Reply-To: <3e36a8fc1003030815nfa8ce85t5589d3dbc007d3f5@mail.gmail.com>
References: <3e36a8fc1003021712j39cb327bid162079462584697@mail.gmail.com>
	<4B8E1918.4080407@sissa.it>
	<3e36a8fc1003030330u7cb70fe7sf225faab87ad5392@mail.gmail.com>
	<op.u8zrx9h8a8x26q@vanoxite.impmc.jussieu.fr>
	<3e36a8fc1003030528q36464b5aqeae431a1f203e41e@mail.gmail.com>
	<op.u8zvmfufa8x26q@vanoxite.impmc.jussieu.fr>
	<3e36a8fc1003030615h7e4a5253he012366618db8ae9@mail.gmail.com>
	<op.u8zyqdn7a8x26q@vanoxite.impmc.jussieu.fr>
	<3e36a8fc1003030815nfa8ce85t5589d3dbc007d3f5@mail.gmail.com>
Message-ID: <op.u8z5gat2a8x26q@vanoxite.impmc.jussieu.fr>

On Wed, 03 Mar 2010 17:15:29 +0100, Wei Zhou <zdw2000 at gmail.com> wrote:
>      task #         0
>      from bfgs : error #         1
>      bfgs history already reset at previous step

I would say that "Pulay-stress" breaks the BFGS algorithm, what happens if  
you (manually) restart the calculation from the last valid configuration  
you've got? Also note that your atoms are so close now, that you are  
likely to get "diagonalization errors", in that case you'll need to find  
or generate harder pseudopotentials.


> it seems that the following OLD error come from     pot_extrapolation =
> 'second_order' ,
>     wfc_extrapolation = 'second_order' , I erase them then it disappear

Well, they were NOT specified in the input file you have sent to the list,  
furthermore it is specified in the documentation that those options should  
only be used for dynamics, not for BFGS.

best regards

-- 
Lorenzo Paulatto

*** Note: my affiliation has changed! please send future
correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***

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

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

From elie.moujaes at hotmail.co.uk  Wed Mar  3 21:04:04 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Wed, 3 Mar 2010 20:04:04 +0000
Subject: [Pw_forum] graphene band structure graph
Message-ID: <SNT114-W607E858450A77BB8771017D33A0@phx.gbl>


Dear all,

 

I got the band structure of graphene and I guess it is correct..I am not sure though why there are places with no points! You will find attached the input file and the ps file.

 

Regards

 

Elie
 		 	   		  
_________________________________________________________________
Do you have a story that started on Hotmail? Tell us now
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From Trinh.Vo at jpl.nasa.gov  Wed Mar  3 21:04:07 2010
From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Wed, 3 Mar 2010 12:04:07 -0800
Subject: [Pw_forum] Generate pseudopotential for Sb
In-Reply-To: <op.u8zllywba8x26q@vanoxite.impmc.jussieu.fr>
Message-ID: <C7B400B9.17B0%Trinh.Vo@jpl.nasa.gov>

Dear Lorenzo,

I did not see they coincide at r>rcut (rcut=0.8 au) for the 4d wfc.
Attached is my plot. Did you have different plot.  I use QE 4.1.2.

Thanks,

Trinh


On 3/3/10 2:19 AM, "Lorenzo Paulatto" <paulatto at sissa.it> wrote:

> On Tue, 02 Mar 2010 21:52:02 +0100, Vo, Trinh (388C)  
<Trinh.Vo at jpl.nasa.gov>
> wrote:
> I used ld1.x to generate PP for Sb.  I have problem with the 4d wfc.
> 
> When I plot the pseudized wfc and the all-electron wfc do not coincide  
>
> even though I try to change Rcut.  I am not if I made any mistake in the  
>
> input.    I tried both TM and RRKJ, but I could not fix the problem. I  
>
> appreciate if you could help me on this.  Below is my input:

Dear Trinh,
of
> course they do not coincide: they are called "pseudo" for a reason. The
> 
coincide only outside the ultra-soft cutoff radius. I've checked them with
> 
gnuplot and this is actually the case: everything is working
> well.

cheers


P.S.
>   author='abc?
The closing ' above is not an
> apostrophe, but one of those inverted  
apostrophes that msword puts in
> document (it caused my ld1.x to crash).


-- 
Lorenzo Paulatto

*** Note: my
> affiliation has changed! please send future
correspondence to:
> <Lorenzo.Paulatto at impmc.upmc.fr> ***

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

previously:
phd student @ SISSA  &
> DEMOCRITOS (Trieste)
phone: +39 040 3787 511
www:
> http://people.sissa.it/~paulatto/
____________________________________________
> ___
Pw_forum mailing
> list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


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From paulatto at sissa.it  Wed Mar  3 21:22:05 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 03 Mar 2010 21:22:05 +0100
Subject: [Pw_forum] Generate pseudopotential for Sb
In-Reply-To: <C7B400B9.17B0%Trinh.Vo@jpl.nasa.gov>
References: <C7B400B9.17B0%Trinh.Vo@jpl.nasa.gov>
Message-ID: <op.u80di2m0a8x26q@paulax>

Replying to message "Re: [Pw_forum] Generate pseudopotential for Sb" from  
Vo, Trinh (388C) (03/03/10):
> I did not see they coincide at r>rcut (rcut=0.8 au) for the 4d wfc.
> Attached is my plot. Did you have different plot.  I use QE 4.1.2.

Are you sure you ploted the right couple? Maybe you are comparing the US  
wavefunction at an energy/j with the AE at another energy/j. To be sure, I  
would have to check the command you have used to generate the plot, more  
than the plot itself.

cheers


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

     *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

From baroni at sissa.it  Wed Mar  3 21:31:09 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 3 Mar 2010 21:31:09 +0100
Subject: [Pw_forum] graphene band structure graph
In-Reply-To: <SNT114-W607E858450A77BB8771017D33A0@phx.gbl>
References: <SNT114-W607E858450A77BB8771017D33A0@phx.gbl>
Message-ID: <4F681267-75FB-456B-8807-817B02DD0ED3@sissa.it>

"places with no points" ??? what do you mean?
you have seemingly calculated the energy bands on fewer symmetry directions than are displayed in the plot
do you know the meaning of each of the "points" that are displayed in the plot? have you counted them? does the count match the number of input points in your band-structure calculations?
there are a few easy checks that you can do by youselfe, I guess ...
SB

On Mar 3, 2010, at 9:04 PM, Elie Moujaes wrote:

> Dear all,
>  
> I got the band structure of graphene and I guess it is correct..I am not sure though why there are places with no points! You will find attached the input file and the ps file.
>  
> Regards
>  
> Elie
> 
> Do you want a Hotmail account? Sign-up now - Free <mgraph.bands.ps><mgraph.bands.in>_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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

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







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From Trinh.Vo at jpl.nasa.gov  Wed Mar  3 23:57:49 2010
From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Wed, 3 Mar 2010 14:57:49 -0800
Subject: [Pw_forum] Generate pseudopotential for Sb
In-Reply-To: <op.u80di2m0a8x26q@paulax>
Message-ID: <C7B4296D.17B9%Trinh.Vo@jpl.nasa.gov>

Here are the commands that I used (I don't know if I used the wrong files):

plot [0:6]   "ld1ps.wfc" u 1:3 w l lw 2
replot  "ld1ps.wfc" u 1:4 w l lw 2
replot  "ld1ps.wfc" u 1:8 w l lw 2
replot  "ld1ps.wfc" u 1:9 w l lw 2

Or 
replot  "ld1.wfc" u 1:(-$7) w l lw 2
replot  "ld1.wfc" u 1:(-$8) w l lw 2

Thank you,

Trinh


On 3/3/10 12:22 PM, "Lorenzo Paulatto" <paulatto at sissa.it> wrote:

> Replying to message "Re: [Pw_forum] Generate pseudopotential for Sb" from
> Vo, Trinh (388C) (03/03/10):
>> I did not see they coincide at r>rcut (rcut=0.8 au) for the 4d wfc.
>> Attached is my plot. Did you have different plot.  I use QE 4.1.2.
> 
> Are you sure you ploted the right couple? Maybe you are comparing the US
> wavefunction at an energy/j with the AE at another energy/j. To be sure, I
> would have to check the command you have used to generate the plot, more
> than the plot itself.
> 
> cheers
> 


From elie.moujaes at hotmail.co.uk  Thu Mar  4 00:02:33 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Wed, 3 Mar 2010 23:02:33 +0000
Subject: [Pw_forum] graphene band structure graph
In-Reply-To: <4F681267-75FB-456B-8807-817B02DD0ED3@sissa.it>
References: <SNT114-W607E858450A77BB8771017D33A0@phx.gbl>,
	<4F681267-75FB-456B-8807-817B02DD0ED3@sissa.it>
Message-ID: <SNT114-W22C2E163343E14275D4EC4D33A0@phx.gbl>


Thanks for your reply. I have actually gone to the xmgr file and deleted the extra points and used gnuplot to plot the results. However if I wanna plot things directly using "gs" (i.e reading the points from the xmgr file directly), do I have to add the points in the input file. Why does the xmgr file add more points than the ones given in input? In the bands.dat file, I have the same points as input!

 

Regards


 


From: baroni at sissa.it
Date: Wed, 3 Mar 2010 21:31:09 +0100
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] graphene band structure graph

"places with no points" ??? what do you mean?
you have seemingly calculated the energy bands on fewer symmetry directions than are displayed in the plot
do you know the meaning of each of the "points" that are displayed in the plot? have you counted them? does the count match the number of input points in your band-structure calculations?
there are a few easy checks that you can do by youselfe, I guess ...
SB





On Mar 3, 2010, at 9:04 PM, Elie Moujaes wrote:

Dear all,
 
I got the band structure of graphene and I guess it is correct..I am not sure though why there are places with no points! You will find attached the input file and the ps file.
 
Regards
 
Elie



Do you want a Hotmail account? Sign-up now - Free <mgraph.bands.ps><mgraph.bands.in>_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum








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


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


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

 		 	   		  
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From paulatto at sissa.it  Thu Mar  4 00:55:39 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 04 Mar 2010 00:55:39 +0100
Subject: [Pw_forum] Generate pseudopotential for Sb
In-Reply-To: <C7B4296D.17B9%Trinh.Vo@jpl.nasa.gov>
References: <C7B4296D.17B9%Trinh.Vo@jpl.nasa.gov>
Message-ID: <op.u80ne1pua8x26q@paulax>

Replying to message "Re: [Pw_forum] Generate pseudopotential for Sb" from  
Vo, Trinh (388C) (03/03/10):
> Here are the commands that I used (I don't know if I used the wrong  
> files):

Ok, now I understand (I had used the input keywords file_wfc??gen to save  
the wavefunctions to specific files).

I have attached a plot of the wavefunctions, the labels for the various  
functions pretty much explain everything. You have two all-electron 4D  
function: one with j=1.5 and one with j=2.5. From these you generate 2  
pseudo wavefunction, which match them perfectly (see picture).

Then you generate 2 more all-electron wavefunction (actually scattering  
states), one for each value of j, at a certain reference energy (-.20Ry):  
these two wavefunctions are not saved to file (the yare saved in  
file_wfcaegen, if you instruct ld1 to do so). From these two all-electron  
wavefunctions you generate two more pseudo waveufnction, which of course  
they do match, but you are not able to see it because they are not saved  
in the ld1.wfc file.

cheers


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

     *** save italian brains ***
  http://saveitalianbrains.wordpress.com/
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From zdw2000 at gmail.com  Thu Mar  4 02:14:57 2010
From: zdw2000 at gmail.com (Wei Zhou)
Date: Thu, 4 Mar 2010 09:14:57 +0800
Subject: [Pw_forum] about the from scale_h : error
In-Reply-To: <op.u8z5gat2a8x26q@vanoxite.impmc.jussieu.fr>
References: <3e36a8fc1003021712j39cb327bid162079462584697@mail.gmail.com>
	<4B8E1918.4080407@sissa.it>
	<3e36a8fc1003030330u7cb70fe7sf225faab87ad5392@mail.gmail.com>
	<op.u8zrx9h8a8x26q@vanoxite.impmc.jussieu.fr>
	<3e36a8fc1003030528q36464b5aqeae431a1f203e41e@mail.gmail.com>
	<op.u8zvmfufa8x26q@vanoxite.impmc.jussieu.fr>
	<3e36a8fc1003030615h7e4a5253he012366618db8ae9@mail.gmail.com>
	<op.u8zyqdn7a8x26q@vanoxite.impmc.jussieu.fr>
	<3e36a8fc1003030815nfa8ce85t5589d3dbc007d3f5@mail.gmail.com>
	<op.u8z5gat2a8x26q@vanoxite.impmc.jussieu.fr>
Message-ID: <3e36a8fc1003031714g79c719b4t8125675d496c1492@mail.gmail.com>

the restart mode does not work as well, it also appear the same error
  task #         0
     from bfgs : error #         1
     bfgs history already reset at previous step
and I use another machine run the same job ,it is the same, so I think it is
the pseudo potential problem.

thank you for Lorenzo Paulatto and Paolo Giannozzi 's help,

2010/3/4 Lorenzo Paulatto <paulatto at sissa.it>

> On Wed, 03 Mar 2010 17:15:29 +0100, Wei Zhou <zdw2000 at gmail.com> wrote:
> >      task #         0
> >      from bfgs : error #         1
> >      bfgs history already reset at previous step
>
> I would say that "Pulay-stress" breaks the BFGS algorithm, what happens if
> you (manually) restart the calculation from the last valid configuration
> you've got? Also note that your atoms are so close now, that you are
> likely to get "diagonalization errors", in that case you'll need to find
> or generate harder pseudopotentials.
>
>
> > it seems that the following OLD error come from     pot_extrapolation =
> > 'second_order' ,
> >     wfc_extrapolation = 'second_order' , I erase them then it disappear
>
> Well, they were NOT specified in the input file you have sent to the list,
> furthermore it is specified in the documentation that those options should
> only be used for dynamics, not for BFGS.
>
> best regards
>
> --
>  Lorenzo Paulatto
>
> *** Note: my affiliation has changed! please send future
> correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***
>
> post-doc @ IMPMC/UPMC - Universit? Paris 6
> phone: +33 (0)1 44 27 74 89
> www:   http://www-int.impmc.upmc.fr/~paulatto/
>
> previously:
> phd student @ SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> www:   http://people.sissa.it/~paulatto/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
ZhouDawei
JiLin Universiyt ,ChangChun ,China
zdw2000 at gmail.com
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From Trinh.Vo at jpl.nasa.gov  Thu Mar  4 06:35:33 2010
From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Wed, 3 Mar 2010 21:35:33 -0800
Subject: [Pw_forum] Generate pseudopotential for Sb
In-Reply-To: <op.u80ne1pua8x26q@paulax>
Message-ID: <C7B486A5.17DC%Trinh.Vo@jpl.nasa.gov>

Thank you very much!  I saved all the files as you said, and I could
reproduce your figure. :-).

Trinh  


On 3/3/10 3:55 PM, "Lorenzo Paulatto" <paulatto at sissa.it> wrote:

> Replying to message "Re: [Pw_forum] Generate pseudopotential for Sb" from
> Vo, Trinh (388C) (03/03/10):
>> Here are the commands that I used (I don't know if I used the wrong
>> files):
> 
> Ok, now I understand (I had used the input keywords file_wfc??gen to save
> the wavefunctions to specific files).
> 
> I have attached a plot of the wavefunctions, the labels for the various
> functions pretty much explain everything. You have two all-electron 4D
> function: one with j=1.5 and one with j=2.5. From these you generate 2
> pseudo wavefunction, which match them perfectly (see picture).
> 
> Then you generate 2 more all-electron wavefunction (actually scattering
> states), one for each value of j, at a certain reference energy (-.20Ry):
> these two wavefunctions are not saved to file (the yare saved in
> file_wfcaegen, if you instruct ld1 to do so). From these two all-electron
> wavefunctions you generate two more pseudo waveufnction, which of course
> they do match, but you are not able to see it because they are not saved
> in the ld1.wfc file.
> 
> cheers
> 


From baroni at sissa.it  Thu Mar  4 08:11:14 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 4 Mar 2010 08:11:14 +0100
Subject: [Pw_forum] graphene band structure graph
In-Reply-To: <SNT114-W22C2E163343E14275D4EC4D33A0@phx.gbl>
References: <SNT114-W607E858450A77BB8771017D33A0@phx.gbl>,
	<4F681267-75FB-456B-8807-817B02DD0ED3@sissa.it>
	<SNT114-W22C2E163343E14275D4EC4D33A0@phx.gbl>
Message-ID: <B6BC9477-5D29-4E53-98DF-56F24855BFF8@sissa.it>

I do not know. Best wishes - SB

On Mar 4, 2010, at 12:02 AM, Elie Moujaes wrote:

> Thanks for your reply. I have actually gone to the xmgr file and deleted the extra points and used gnuplot to plot the results. However if I wanna plot things directly using "gs" (i.e reading the points from the xmgr file directly), do I have to add the points in the input file. Why does the xmgr file add more points than the ones given in input? In the bands.dat file, I have the same points as input!
>  
> Regards
> 
>  
> From: baroni at sissa.it
> Date: Wed, 3 Mar 2010 21:31:09 +0100
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] graphene band structure graph
> 
> "places with no points" ??? what do you mean?
> you have seemingly calculated the energy bands on fewer symmetry directions than are displayed in the plot
> do you know the meaning of each of the "points" that are displayed in the plot? have you counted them? does the count match the number of input points in your band-structure calculations?
> there are a few easy checks that you can do by youselfe, I guess ...
> SB
> 
> On Mar 3, 2010, at 9:04 PM, Elie Moujaes wrote:
> 
> Dear all,
>  
> I got the band structure of graphene and I guess it is correct..I am not sure though why there are places with no points! You will find attached the input file and the ps file.
>  
> Regards
>  
> Elie
> 
> Do you want a Hotmail account? Sign-up now - Free <mgraph.bands.ps><mgraph.bands.in>_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> ---
> Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
> http://stefano.baroni.me  [+39] 040 3787 406  [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)
> 
> La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget
> 
> Please, if possible, don't  send me MS Word or PowerPoint attachments
> Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html
> 
> 
> 
> 
> 
> 
> 
> 
> Do you want a Hotmail account? Sign-up now - Free _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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

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







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From giovanni.cantele at na.infn.it  Thu Mar  4 10:44:46 2010
From: giovanni.cantele at na.infn.it (Giovanni Cantele)
Date: Thu, 4 Mar 2010 10:44:46 +0100
Subject: [Pw_forum] graphene band structure graph
In-Reply-To: <SNT114-W607E858450A77BB8771017D33A0@phx.gbl>
References: <SNT114-W607E858450A77BB8771017D33A0@phx.gbl>
Message-ID: <9D594BC2-4EAB-439A-B92D-03B70771E65B@na.infn.it>


On Mar 3, 2010, at 9:04 PM, Elie Moujaes wrote:

> Dear all, 
> I got the band structure of graphene and I guess it is correct..I am not sure though why there are places with no points! You will find attached the input file and the ps file.
> Regards 
> Elie

What you look on the plot exactly corresponds to what you wrote in your input:

- the first two "places with no point" correspond to the points:
0.39 0.39 0.00  0.10
0.40 0.30 0.00  0.10
0.41 0.41 0.00  0.10
it is evident the "misprint" (0.30 instead if 0.40)

- the third "place with no point" corresponds to:
0.50 0.50 0.00  0.10
0.50 0.00 0.00  0.10
where you "jump" from 1/2 1/2 0 to 1/2 0 0

What bands.x does is to convert YOUR k-point list in such a way that
x[i+1] = x[i] + | k[i+1] - k[i] |
where x is the abscissa on the band structure plot whereas k[i] is the i-th k-point vector, and |...| indicates the modulus. So if there are "unwanted" jumps in your
list, this will result in points that look "unexpectedly" far from each other.

So, there are not "places with no points". The code is at the moment quite robust in doing exactly what the user asks, I guess that there are ongoing developers' efforts
in designing it to do what the user wants!!!!!!!!   ;-)

Hope this helps,

    Giovanni

--

Dr. Giovanni Cantele
Coherentia CNR-INFM and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario di Monte S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910
Fax:   +39 081 676346
E-mail: giovanni.cantele at cnr.it
              giovanni.cantele at na.infn.it
Web: http://people.na.infn.it/~cantele
Research Group: http://www.nanomat.unina.it
Skype contact: giocan74

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From javaid at ipcms.u-strasbg.fr  Thu Mar  4 11:03:26 2010
From: javaid at ipcms.u-strasbg.fr (saqib javaid)
Date: Thu, 04 Mar 2010 11:03:26 +0100
Subject: [Pw_forum] about magnetic moment in projwfc.x
In-Reply-To: <C7B400B9.17B0%Trinh.Vo@jpl.nasa.gov>
References: <C7B400B9.17B0%Trinh.Vo@jpl.nasa.gov>
Message-ID: <4B8F856E.8000309@ipcms.u-strasbg.fr>

Dear PWSCF users,

I have a question regarding magnetic moment calculated by lowdin 
analysis. Is the
magnetic moment shown by output of projwfc.x is only spin magnetic 
moment, or total magnetic moment. I would appreciate any furthur 
clarification in this regard
with best regards
saqib javaid
univeristy of strasbourg, France

From lfhuang at theory.issp.ac.cn  Thu Mar  4 11:46:27 2010
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Thu, 04 Mar 2010 18:46:27 +0800
Subject: [Pw_forum] =?utf-8?q?graphene_band_structure_graph?=
Message-ID: <20100304104627.14300.qmail@ms.hfcas.ac.cn>

Dear  Elie
    Have you check that the k-path used in your calculation is continuous in the reciprocal space?
Best Wishes!
Yours Sincerely
L.F.Huang
------
======================================================================
L.F.Huang(???) DFT and phonon physics
======================================================================
Add: Research Laboratory for Computational Materials Sciences,
Instutue of Solid State Physics,the Chinese Academy of Sciences,
P.O.Box 1129, Hefei 230031, P.R.China
Tel: 86-551-5591464-328(office)
Fax: 86-551-5591434
Web: http://theory.issp.ac.cn (website of our theory group)
http://www.issp.ac.cn    (website of our institute)
======================================================================


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From elie.moujaes at hotmail.co.uk  Thu Mar  4 14:48:58 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Thu, 4 Mar 2010 13:48:58 +0000
Subject: [Pw_forum] graphene band structure graph
In-Reply-To: <9D594BC2-4EAB-439A-B92D-03B70771E65B@na.infn.it>
References: <SNT114-W607E858450A77BB8771017D33A0@phx.gbl>,
	<9D594BC2-4EAB-439A-B92D-03B70771E65B@na.infn.it>
Message-ID: <SNT114-W286BBE396F1F4F6194A934D3390@phx.gbl>


Thanks very much for thre clarification. It did really help and I got all results and graphs as expected.

 

Regards.
 


From: giovanni.cantele at na.infn.it
Date: Thu, 4 Mar 2010 10:44:46 +0100
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] graphene band structure graph




On Mar 3, 2010, at 9:04 PM, Elie Moujaes wrote:

Dear all, 
I got the band structure of graphene and I guess it is correct..I am not sure though why there are places with no points! You will find attached the input file and the ps file.
Regards 
Elie



What you look on the plot exactly corresponds to what you wrote in your input:


- the first two "places with no point" correspond to the points:

0.39 0.39 0.00  0.10
0.40 0.30 0.00  0.10

0.41 0.41 0.00  0.10
it is evident the "misprint" (0.30 instead if 0.40)


- the third "place with no point" corresponds to:

0.50 0.50 0.00  0.10
0.50 0.00 0.00  0.10where you "jump" from 1/2 1/2 0 to 1/2 0 0


What bands.x does is to convert YOUR k-point list in such a way that
x[i+1] = x[i] + | k[i+1] - k[i] |
where x is the abscissa on the band structure plot whereas k[i] is the i-th k-point vector, and |...| indicates the modulus. So if there are "unwanted" jumps in your
list, this will result in points that look "unexpectedly" far from each other.


So, there are not "places with no points". The code is at the moment quite robust in doing exactly what the user asks, I guess that there are ongoing developers' efforts
in designing it to do what the user wants!!!!!!!!   ;-)


Hope this helps,


    Giovanni


--


Dr. Giovanni Cantele
Coherentia CNR-INFM and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario di Monte S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910
Fax:   +39 081 676346
E-mail: giovanni.cantele at cnr.it
              giovanni.cantele at na.infn.it
Web: http://people.na.infn.it/~cantele
Research Group: http://www.nanomat.unina.it
Skype contact: giocan74
 		 	   		  
_________________________________________________________________
Got a cool Hotmail story? Tell us now
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From ttduyle at gmail.com  Thu Mar  4 17:38:07 2010
From: ttduyle at gmail.com (Duy Le)
Date: Thu, 4 Mar 2010 11:38:07 -0500
Subject: [Pw_forum] lm decomposed band structure
Message-ID: <8974d3b21003040838u19e63a1ej5d8626c24ea42363@mail.gmail.com>

Dear all,

Is there a way (already implemented) to do site-lm decomposed band
structure? I want to know characters of bands and also which atoms
contribute to those bands.

Best regards,

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

"Men don't need hand to do things"

From sclauzer at sissa.it  Thu Mar  4 18:06:32 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Thu, 04 Mar 2010 18:06:32 +0100
Subject: [Pw_forum] lm decomposed band structure
In-Reply-To: <8974d3b21003040838u19e63a1ej5d8626c24ea42363@mail.gmail.com>
References: <8974d3b21003040838u19e63a1ej5d8626c24ea42363@mail.gmail.com>
Message-ID: <4B8FE898.2050802@sissa.it>

Something like this?

PROGRAM plotproj
!
!  This small program is used to select the band eigenvalues whose
!  wavefunctions projected on atomic wavefunctions have projections larger
!  than a given threshold. It requires two input files. The first is a
!  file with the band eigenvalues, written in the output of pw.x.
!  The input file with the bands has the following format:
!  nbnd, nks     ! number of bands, number of k points
!  --- blank line
!  kvector coordinates
!  --- blank line
!  bands eigenvalues
!  ...
!  --- blank line
!  kvector coordinates
!  --- blank line
!  bands eigenvalues
!  ...
!
!  The second file is written by the projwfc.x program with the option
!  lsym=.false.
!
!  The input of this program is:
!  filename     ! name of the file with the band eigenvalues
!  filename1    ! name of the file with the projections
!  fileout      ! name of the output file where the bands are written
!  threshold    ! see below
!  ncri         ! number of criterions for selecting the bands
!  for each criterion
!  first_atomic_wfc, last_atomic_wfc   ! the band is selected if the
!                                        sum of the projections on
!                                        the atomic wavefunctions between
!                                        first_atomic_wfc and
!                                        last_atomic_wfc is larger than
!                                        threshold. The sum is done on
!                                        all criterions.
!
#include "f_defs.h"

It is the plotproj.x utility in the PP directory. I never used it actually, since at the 
time I needed this kind of thing this utility was not included in the QE distro and I made 
something similar by my own, so I cannot tell you how this works.


GS


Duy Le wrote:
> Dear all,
> 
> Is there a way (already implemented) to do site-lm decomposed band
> structure? I want to know characters of bands and also which atoms
> contribute to those bands.
> 
> Best regards,
> 
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
> 
> "Men don't need hand to do things"
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

-- 


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

From gianluca.giovannetti at gmail.com  Thu Mar  4 18:41:20 2010
From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti)
Date: Thu, 4 Mar 2010 18:41:20 +0100
Subject: [Pw_forum] l,lm decomposed density of state
Message-ID: <7234ba151003040941w5aab20f3y3fdaa823b96e72b9@mail.gmail.com>

Dear All,

i made self-consistent calculations with PW and then i have calculated with
post-processing tools the projected density of states.
For each ion in the unit cell i get a file:

fese.pdos_atm#1(Fe1)_wfc#1(s)  fese.pdos_atm#1(Fe1)_wfc#3(d)
fese.pdos_atm#1(Fe1)_wfc#5(p)
fese.pdos_atm#1(Fe1)_wfc#2(p)  fese.pdos_atm#1(Fe1)_wfc#4(s)

what are the labels wfc#1(s),wfc#2(p),wfc#3(d),wfc#4(s),wfc#5(p) standing
for?
are the d states in fese.pdos_atm#1(Fe1)_wfc#3(d)?

inside the latter file i found:

# E (eV)  ldosup(E)  ldosdw(E) pdosup(E)  pdosdw(E)  pdosup(E)  pdosdw(E)
pdosup(E)  pdosdw(E)  pdosup(E)  pdosdw(E)  pdosup(E)  pdosdw(E)
-20.000  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
-19.999  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
-19.998  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
-19.997  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
[...]

Are the colums distribued this way

energy   total up       total down   z2 up          z2 dn          xz
up          xz down     yz up          yz down     x2-y2  up     x2-y2 down
xy up         xy dn               ?

thank you.

ciao

G.
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From gianluca.giovannetti at gmail.com  Thu Mar  4 18:48:24 2010
From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti)
Date: Thu, 4 Mar 2010 18:48:24 +0100
Subject: [Pw_forum] occupancies d state from occupation matrix.
Message-ID: <7234ba151003040948h6a88c16bwcd6b5929ded0f8cb@mail.gmail.com>

Dear All,

i have performed LDA+U calculations and i want to know the occupancies of d
states.
can i get it from occupation matrix printed in the output file?
For example PW gives me:

atom  4   Tr[ns(na)]=   7.4651394
atom  4  spin  1
eigenvalues:  0.4830637 0.5075106 0.5192560 0.6802564 0.6865322
 eigenvectors
 1   0.0000000  0.0000000  1.0000000  0.0000000  0.0000000
 2   0.0000000  0.0000000  0.0000000  0.0000000  1.0000000
 3  -0.7160583  0.0000000  0.0000000  0.6980405  0.0000000
 4   0.0000000 -1.0000000  0.0000000  0.0000000  0.0000000
 5  -0.6980405  0.0000000  0.0000000 -0.7160583  0.0000000
 occupations
 0.601  0.000  0.000  0.084  0.000
 0.000  0.680  0.000  0.000  0.000
 0.000  0.000  0.483  0.000  0.000
 0.084  0.000  0.000  0.605  0.000
 0.000  0.000  0.000  0.000  0.508
atom  4  spin  2
eigenvalues:  0.8843330 0.9084008 0.9152566 0.9213736 0.9591566
 eigenvectors
 1  -0.0108812  0.0000000  0.0000000 -0.9999408  0.0000000
 2   0.0000000  0.0000000  0.0000000  0.0000000  1.0000000
 3   0.0000000  1.0000000  0.0000000  0.0000000  0.0000000
 4   0.0000000  0.0000000 -1.0000000  0.0000000  0.0000000
 5  -0.9999408  0.0000000  0.0000000  0.0108812  0.0000000
 occupations
 0.959  0.000  0.000 -0.001  0.000
 0.000  0.915  0.000  0.000  0.000
 0.000  0.000  0.921  0.000  0.000
-0.001  0.000  0.000  0.884  0.000
 0.000  0.000  0.000  0.000  0.908

can i say:

n_down_z2=0.959,
n_down_xz=0.915
n_down_yz=0.921
n_down_x2-y2=0.884
n_down_xy=0.908                 ?


thank you.

Gianluca
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From robguerra at unimore.it  Thu Mar  4 18:24:36 2010
From: robguerra at unimore.it (Roberto Guerra)
Date: Thu, 4 Mar 2010 18:24:36 +0100
Subject: [Pw_forum] "Mulliken population" and dos pojections
In-Reply-To: <9460D554-DD53-4EA8-AEB8-A64A517AAA55@democritos.it>
References: <42054E10C02CD44D81EF510077A30A0725A70FA0E1@MAPI.ad.kent.ac.uk>
	<9460D554-DD53-4EA8-AEB8-A64A517AAA55@democritos.it>
Message-ID: <f5e1aba81003040924m6e50f1d9r3f6e5bf217c0a0bf@mail.gmail.com>

I wish to search the mailing list but I could not find a page for
that. What's the way to search?

R

2010/3/3 Paolo Giannozzi <giannozz at democritos.it>:
>
> On Mar 3, 2010, at 12:17 , P.Canepa wrote:
>
>> Just a little question, is in PWscf something like Mulliken
>> population analysis?
>
> just a little answer: what about searching the mailing list? see e.g.
> ? ?http://www.democritos.it/pipermail/pw_forum/2008-January/008142.html
> and
> ? http://www.democritos.it/pipermail/pw_forum/2006-November/005392.html
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From ttduyle at gmail.com  Thu Mar  4 19:14:40 2010
From: ttduyle at gmail.com (Duy Le)
Date: Thu, 4 Mar 2010 13:14:40 -0500
Subject: [Pw_forum] lm decomposed band structure
In-Reply-To: <4B8FE898.2050802@sissa.it>
References: <8974d3b21003040838u19e63a1ej5d8626c24ea42363@mail.gmail.com> 
	<4B8FE898.2050802@sissa.it>
Message-ID: <8974d3b21003041014kc641a02s58c72ddab1c3e82b@mail.gmail.com>

Thank Gabriele, I will have a look on this utility.

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

"Men don't need hand to do things"



On Thu, Mar 4, 2010 at 12:06 PM, Gabriele Sclauzero <sclauzer at sissa.it> wrote:
> Something like this?
>
> PROGRAM plotproj
> !
> ! ?This small program is used to select the band eigenvalues whose
> ! ?wavefunctions projected on atomic wavefunctions have projections larger
> ! ?than a given threshold. It requires two input files. The first is a
> ! ?file with the band eigenvalues, written in the output of pw.x.
> ! ?The input file with the bands has the following format:
> ! ?nbnd, nks ? ? ! number of bands, number of k points
> ! ?--- blank line
> ! ?kvector coordinates
> ! ?--- blank line
> ! ?bands eigenvalues
> ! ?...
> ! ?--- blank line
> ! ?kvector coordinates
> ! ?--- blank line
> ! ?bands eigenvalues
> ! ?...
> !
> ! ?The second file is written by the projwfc.x program with the option
> ! ?lsym=.false.
> !
> ! ?The input of this program is:
> ! ?filename ? ? ! name of the file with the band eigenvalues
> ! ?filename1 ? ?! name of the file with the projections
> ! ?fileout ? ? ?! name of the output file where the bands are written
> ! ?threshold ? ?! see below
> ! ?ncri ? ? ? ? ! number of criterions for selecting the bands
> ! ?for each criterion
> ! ?first_atomic_wfc, last_atomic_wfc ? ! the band is selected if the
> ! ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?sum of the projections on
> ! ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?the atomic wavefunctions between
> ! ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?first_atomic_wfc and
> ! ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?last_atomic_wfc is larger than
> ! ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?threshold. The sum is done on
> ! ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?all criterions.
> !
> #include "f_defs.h"
>
> It is the plotproj.x utility in the PP directory. I never used it actually, since at the
> time I needed this kind of thing this utility was not included in the QE distro and I made
> something similar by my own, so I cannot tell you how this works.
>
>
> GS
>
>
> Duy Le wrote:
>> Dear all,
>>
>> Is there a way (already implemented) to do site-lm decomposed band
>> structure? I want to know characters of bands and also which atoms
>> contribute to those bands.
>>
>> Best regards,
>>
>> --------------------------------------------------
>> Duy Le
>> PhD Student
>> Department of Physics
>> University of Central Florida.
>>
>> "Men don't need hand to do things"
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
> --
>
>
> o ------------------------------------------------ o
> | Gabriele Sclauzero, PhD Student ? ? ? ? ? ? ? ? ?|
> | c/o: ? SISSA & CNR-INFM Democritos, ? ? ? ? ? ? ?|
> | ? ? ? ?via Beirut 2-4, 34014 Trieste (Italy) ? ? |
> | email: sclauzer at sissa.it ? ? ? ? ? ? ? ? ? ? ? ? |
> | phone: +39 040 3787 511 ? ? ? ? ? ? ? ? ? ? ? ? ?|
> | skype: gurlonotturno ? ? ? ? ? ? ? ? ? ? ? ? ? ? |
> o ------------------------------------------------ o
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From giannozz at democritos.it  Thu Mar  4 19:24:09 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 4 Mar 2010 19:24:09 +0100
Subject: [Pw_forum] "Mulliken population" and dos pojections
In-Reply-To: <f5e1aba81003040924m6e50f1d9r3f6e5bf217c0a0bf@mail.gmail.com>
References: <42054E10C02CD44D81EF510077A30A0725A70FA0E1@MAPI.ad.kent.ac.uk>
	<9460D554-DD53-4EA8-AEB8-A64A517AAA55@democritos.it>
	<f5e1aba81003040924m6e50f1d9r3f6e5bf217c0a0bf@mail.gmail.com>
Message-ID: <F4466C78-F6FD-4C7B-89E9-62AA4934A6AD@democritos.it>


On Mar 4, 2010, at 18:24 , Roberto Guerra wrote:

> I wish to search the mailing list but I could not find a page for
> that. What's the way to search?

search, and you will find. "You can observe a lot by watching"
(Yogi Berra, baseball player, not to be confused with Yogi Bear)

www.quantum-espresso.org => tools => "To discuss Quantum ESPRESSO
related issues among users, subscribe [link] to the pw_forum mailing  
list.
Please use the search facility [link] if you are looking for answers!"

Or, using google: "pw_forum Mulliken site:www.democritos.it"

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




From wulilixiangguo at sina.com  Thu Mar  4 21:38:29 2010
From: wulilixiangguo at sina.com (wulilixiangguo at sina.com)
Date: Fri, 05 Mar 2010 04:38:29 +0800 
Subject: [Pw_forum] Graphene--Silicon Surface(scf not converge)
Message-ID: <20100304203829.C5C6BCF5C4D@mail3-92.sinamail.sina.com.cn>

&nbsp;Hi everyone:

I am doing a scf calculation for my structure. My structure has 660 atoms(56 H,324C,280 Si). I use H terminated Si-C surface. But after 24 hours calculation(46 steps), the scf accuracy still fluctuate from about 1 to 100.

Does anyone ever know this before?How to solve it? 

Thank you very much!
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From giovanni.cantele at na.infn.it  Thu Mar  4 21:55:41 2010
From: giovanni.cantele at na.infn.it (Giovanni Cantele)
Date: Thu, 4 Mar 2010 21:55:41 +0100 (CET)
Subject: [Pw_forum] Graphene--Silicon Surface(scf not converge)
In-Reply-To: <20100304203829.C5C6BCF5C4D@mail3-92.sinamail.sina.com.cn>
References: <20100304203829.C5C6BCF5C4D@mail3-92.sinamail.sina.com.cn>
Message-ID: <49931.93.150.241.16.1267736141.squirrel@imap-ac.na.infn.it>


> Hi everyone:
> I am doing a scf calculation for my structure. My structure has 660
> atoms(56 H,324C,280 Si). I use H terminated Si-C surface. But after 24
> hours calculation(46 steps), the scf accuracy still fluctuate from about 1
> to 100.
> Does anyone ever know this before?How to solve it?
> Thank you very much!

You can try to:
1) browse the forum, the issue has been discussed many many times, there
is not a unique answer the problem might be related to several issues

2) browse the QE wiki:
http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions#Self-consistency_is_slow_or_does_not_converge_at_all

Did you check your geometry using, e.g., XCrysDen? Some times, mostly when
dealing with such a huge number of atoms, a wrong coordinate might give
atom overlap preventing the scf cycle from converging. You might also try
to tune some parameters related to the convergence of the scf cycle, like
mixing_beta.

Giovanni

-- 
Dr. Giovanni Cantele
CNR-SPIN and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario di Monte S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910 - Fax:   +39 081 676346
ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
Research Group: http://www.nanomat.unina.it
Skype contact: giocan74


From baroni at sissa.it  Thu Mar  4 23:20:45 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 4 Mar 2010 23:20:45 +0100
Subject: [Pw_forum] lm decomposed band structure
In-Reply-To: <8974d3b21003041014kc641a02s58c72ddab1c3e82b@mail.gmail.com>
References: <8974d3b21003040838u19e63a1ej5d8626c24ea42363@mail.gmail.com>
	<4B8FE898.2050802@sissa.it>
	<8974d3b21003041014kc641a02s58c72ddab1c3e82b@mail.gmail.com>
Message-ID: <05C134D8-725D-4919-991A-8A007FDFF087@sissa.it>


On Mar 4, 2010, at 7:14 PM, Duy Le wrote:

> "Men don't need hand to do things"

it depend on the thing to be done, as well as on the man trying to have it done ...

S.

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

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

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







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From ttduyle at gmail.com  Fri Mar  5 01:32:38 2010
From: ttduyle at gmail.com (Duy Le)
Date: Thu, 4 Mar 2010 19:32:38 -0500
Subject: [Pw_forum] lm decomposed band structure
In-Reply-To: <05C134D8-725D-4919-991A-8A007FDFF087@sissa.it>
References: <8974d3b21003040838u19e63a1ej5d8626c24ea42363@mail.gmail.com> 
	<4B8FE898.2050802@sissa.it>
	<8974d3b21003041014kc641a02s58c72ddab1c3e82b@mail.gmail.com> 
	<05C134D8-725D-4919-991A-8A007FDFF087@sissa.it>
Message-ID: <8974d3b21003041632neebc958pff9ebe71d7ff4c5b@mail.gmail.com>

Thank Stefano,
You are absolutely right. I will try to correct the quote after my graduation.
D.
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Thu, Mar 4, 2010 at 5:20 PM, Stefano Baroni <baroni at sissa.it> wrote:
>
> On Mar 4, 2010, at 7:14 PM, Duy Le wrote:
>
> "Men don't need hand to do things"
>
> it depend on the thing to be done, as well as on the man trying to have it
> done ...
> S.
> ---
> Stefano Baroni - SISSA??&??DEMOCRITOS National Simulation Center - Trieste
> http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni
> (skype)
> La morale est une logique de l'action comme la logique est une morale de la
> pens?e - Jean Piaget
> Please, if possible, don't??send me MS Word or PowerPoint attachments
> Why? See:??http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

From nnlinh at sissa.it  Fri Mar  5 10:16:23 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Fri, 05 Mar 2010 10:16:23 +0100
Subject: [Pw_forum] l,lm decomposed density of state
In-Reply-To: <7234ba151003040941w5aab20f3y3fdaa823b96e72b9@mail.gmail.com>
References: <7234ba151003040941w5aab20f3y3fdaa823b96e72b9@mail.gmail.com>
Message-ID: <4B90CBE7.7060102@sissa.it>

Gianluca Giovannetti wrote:
> what are the labels wfc#1(s),wfc#2(p),wfc#3(d),wfc#4(s),wfc#5(p) 
> standing for?
The labels stand for the order of the valence orbitals that is associate 
with definitions in Pseudo Potential file for each atom.
 
> are the d states in fese.pdos_atm#1(Fe1)_wfc#3(d)?
>
yes, they are
> inside the latter file i found:
>
> # E (eV)  ldosup(E)  ldosdw(E) pdosup(E)  pdosdw(E)  pdosup(E)  
> pdosdw(E)  pdosup(E)  pdosdw(E)  pdosup(E)  pdosdw(E)  pdosup(E)  
> pdosdw(E)
> -20.000  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  
> 0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  
> 0.000E+00
> -19.999  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  
> 0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  
> 0.000E+00
> -19.998  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  
> 0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  
> 0.000E+00
> -19.997  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  
> 0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  
> 0.000E+00
> [...]
>
> Are the colums distribued this way
>
> energy   total up       total down   z2 up          z2 dn          xz 
> up          xz down     yz up          yz down     x2-y2  up     x2-y2 
> down  xy up         xy dn               ?
>
You can see the format of PDOS output files in:
http://www.quantum-espresso.org/input-syntax/INPUT_PROJWFC.html#id689269

Good luck.

Linh

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


From gianluca.giovannetti at gmail.com  Fri Mar  5 10:27:24 2010
From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti)
Date: Fri, 5 Mar 2010 10:27:24 +0100
Subject: [Pw_forum] l,lm decomposed density of state
In-Reply-To: <4B90CBE7.7060102@sissa.it>
References: <7234ba151003040941w5aab20f3y3fdaa823b96e72b9@mail.gmail.com>
	<4B90CBE7.7060102@sissa.it>
Message-ID: <7234ba151003050127q7ec855a5o5ac57e36017b93a@mail.gmail.com>

Dear Linh,

thank you for your suggestions.
cheers,

G.

On Fri, Mar 5, 2010 at 10:16 AM, Ngoc Linh Nguyen <nnlinh at sissa.it> wrote:

> Gianluca Giovannetti wrote:
> > what are the labels wfc#1(s),wfc#2(p),wfc#3(d),wfc#4(s),wfc#5(p)
> > standing for?
> The labels stand for the order of the valence orbitals that is associate
> with definitions in Pseudo Potential file for each atom.
>
> > are the d states in fese.pdos_atm#1(Fe1)_wfc#3(d)?
> >
> yes, they are
> > inside the latter file i found:
> >
> > # E (eV)  ldosup(E)  ldosdw(E) pdosup(E)  pdosdw(E)  pdosup(E)
> > pdosdw(E)  pdosup(E)  pdosdw(E)  pdosup(E)  pdosdw(E)  pdosup(E)
> > pdosdw(E)
> > -20.000  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
> > 0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
> > 0.000E+00
> > -19.999  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
> > 0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
> > 0.000E+00
> > -19.998  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
> > 0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
> > 0.000E+00
> > -19.997  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
> > 0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00  0.000E+00
> > 0.000E+00
> > [...]
> >
> > Are the colums distribued this way
> >
> > energy   total up       total down   z2 up          z2 dn          xz
> > up          xz down     yz up          yz down     x2-y2  up     x2-y2
> > down  xy up         xy dn               ?
> >
> You can see the format of PDOS output files in:
> http://www.quantum-espresso.org/input-syntax/INPUT_PROJWFC.html#id689269
>
> Good luck.
>
> Linh
>
> >
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From kazempoor at ph.iut.ac.ir  Fri Mar  5 13:08:20 2010
From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir)
Date: Fri, 5 Mar 2010 15:38:20 +0330 (IRST)
Subject: [Pw_forum] n_gauss in GWW
In-Reply-To: <1717802088.71625.1267790851994.JavaMail.root@mta.iut.ac.ir>
Message-ID: <1075633290.71631.1267790900021.JavaMail.root@mta.iut.ac.ir>


Dear all
For calculation of quasi-particle band structure in 72- atom supercell, I used GWW and run with 32 node each of them containing 32 core with 800 Gigabyte memory. But the run goes on slowly and when I see the file *.head_status, it is in 20 step(after 20 hours) while the default for n_gauss is  79 I predict that I can not continue the run because I couldn't have these machines more than 24 hours for each run.
My question is : Can I reduce the value of n_gauss to (for example 20)? and which parameters increase the cost of computation?
thanks a lot

Ali Kazempour
Physics Department, Isfahn University of Technology

From quantumdft at gmail.com  Fri Mar  5 14:01:47 2010
From: quantumdft at gmail.com (vega lew)
Date: Fri, 05 Mar 2010 21:01:47 +0800
Subject: [Pw_forum] How to cite Q~E
Message-ID: <4B9100BB.4060901@gmail.com>

Dear all,

As the web page, 
http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO, 
said, I just cite the Q-E by adding a a single reference of P. 
Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni, D. 
Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso, S. 
Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann, C. 
Gougoussis, M. L. A. Kokalj, L. Martin-Samos, N. Marzari, F. Mauri, R. 
Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia, S. 
Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari and R. M. 
Wentzcovitch, /Journal of Physics: Condensed Matter/, 2009, *21*, 395502.

Do you think just a single reference is OK?

best wishes,

vega
-- 

==================================================================================
Vega Lew ( weijia liu)
Graduate students
State Key Laboratory of Materials-oriented Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
***********************************************************************************************
Email: vegalew at gmail.com
Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, 
Nanjing, Jiangsu, China
***********************************************************************************************

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From marsamos at democritos.it  Fri Mar  5 14:34:56 2010
From: marsamos at democritos.it (marsamos at democritos.it)
Date: Fri, 05 Mar 2010 14:34:56 +0100
Subject: [Pw_forum] How to cite Q~E
In-Reply-To: <4B9100BB.4060901@gmail.com>
References: <4B9100BB.4060901@gmail.com>
Message-ID: <20100305143456.qqq6gh47wwc80k0s@mail.democritos.it>

Dear vega, htis is the official reference. It is ok, just this one. Thank you.

bests

Layla

Quoting vega lew <quantumdft at gmail.com>:

> Dear all,
>
> As the web page, 
> http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO, 
> said, I just cite the Q-E by adding a a single reference of P. 
> Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni, 
> D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso, 
> S. Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann, C. 
> Gougoussis, M. L. A. Kokalj, L. Martin-Samos, N. Marzari, F. Mauri, 
> R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia, 
> S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari and 
> R. M. Wentzcovitch, /Journal of Physics: Condensed Matter/, 2009, 
> *21*, 395502.
>
> Do you think just a single reference is OK?
>
> best wishes,
>
> vega
> -- 
>
> ==================================================================================
> Vega Lew ( weijia liu)
> Graduate students
> State Key Laboratory of Materials-oriented Chemical Engineering
> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
> ***********************************************************************************************
> Email: vegalew at gmail.com
> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, 
> Nanjing, Jiangsu, China
> ***********************************************************************************************
>
>



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

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From quantumdft at gmail.com  Fri Mar  5 14:40:16 2010
From: quantumdft at gmail.com (vega lew)
Date: Fri, 05 Mar 2010 21:40:16 +0800
Subject: [Pw_forum] How to cite Q~E
In-Reply-To: <20100305143456.qqq6gh47wwc80k0s@mail.democritos.it>
References: <4B9100BB.4060901@gmail.com>
	<20100305143456.qqq6gh47wwc80k0s@mail.democritos.it>
Message-ID: <4B9109C0.2090603@gmail.com>

Well, thank you for your reply.

I'll cite the reference along with a short paragraph to thank every one 
here in the Acknowledgements section.

best,

vega

On 2010-03-05 21:34, marsamos at democritos.it wrote:
> Dear vega, htis is the official reference. It is ok, just this one. Thank you.
>
> bests
>
> Layla
>
> Quoting vega lew<quantumdft at gmail.com>:
>
>    
>> Dear all,
>>
>> As the web page,
>> http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO,
>> said, I just cite the Q-E by adding a a single reference of P.
>> Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni,
>> D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso,
>> S. Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann, C.
>> Gougoussis, M. L. A. Kokalj, L. Martin-Samos, N. Marzari, F. Mauri,
>> R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia,
>> S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari and
>> R. M. Wentzcovitch, /Journal of Physics: Condensed Matter/, 2009,
>> *21*, 395502.
>>
>> Do you think just a single reference is OK?
>>
>> best wishes,
>>
>> vega
>> -- 
>>
>> ==================================================================================
>> Vega Lew ( weijia liu)
>> Graduate students
>> State Key Laboratory of Materials-oriented Chemical Engineering
>> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
>> ***********************************************************************************************
>> Email: vegalew at gmail.com
>> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#,
>> Nanjing, Jiangsu, China
>> ***********************************************************************************************
>>
>>
>>      
>
>
>    

-- 

==================================================================================
Vega Lew ( weijia liu)
Graduate students
State Key Laboratory of Materials-oriented Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
***********************************************************************************************
Email: vegalew at gmail.com
Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, 
Nanjing, Jiangsu, China
***********************************************************************************************

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From elie.moujaes at hotmail.co.uk  Fri Mar  5 14:53:10 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Fri, 5 Mar 2010 13:53:10 +0000
Subject: [Pw_forum] crystal or tpiba_b
Message-ID: <SNT114-W26C861670ED542E971E37CD3380@phx.gbl>


Dear all,

 

I read that if we are trying to calculate the band structure, it is better to use {tpiba_b} in ATOMIC POSITIONS rather than {crystal}. Is the only difference related to the points that will be plotted at the end  because one is wrt to cartesian and the other relative to crystallographic axes?

 

 

 

Regards 
 		 	   		  
_________________________________________________________________
Tell us your greatest, weirdest and funniest Hotmail stories
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From giovanni.cantele at na.infn.it  Fri Mar  5 15:06:07 2010
From: giovanni.cantele at na.infn.it (Giovanni Cantele)
Date: Fri, 5 Mar 2010 15:06:07 +0100
Subject: [Pw_forum] crystal or tpiba_b
In-Reply-To: <SNT114-W26C861670ED542E971E37CD3380@phx.gbl>
References: <SNT114-W26C861670ED542E971E37CD3380@phx.gbl>
Message-ID: <4ADC69D1-7D88-4B56-B335-043C5A63BF55@na.infn.it>


On Mar 5, 2010, at 2:53 PM, Elie Moujaes wrote:

> Dear all,
>  
> I read that if we are trying to calculate the band structure, it is better to use {tpiba_b} in ATOMIC POSITIONS rather than {crystal}. Is the only difference related to the points that will be plotted at the end  because one is wrt to cartesian and the other relative to crystallographic axes?
>  
>  

I never used tpiba_b or crystal_b. Nevertheless, by reading the Doc/INPUT_PW.txt I understand that it is not a matter of tpiba vs crystal, but of tpiba_b/crystal_b vs tpiba/crystal. Using either tpiba or crystal, you must specify the full list of k-points you want to show in your band structure plot. On the contrary, the *_b options (tpiba_b/crystal_b) allow to specify, for each given line in the Brillouin zone, only the 1st and last point, together with the number of points along that line.

As an example, you can replace
K_POINTS {crystal}
5
0.0 0.0 0.0    1.0
0.1 0.0 0.0    1.0
0.2 0.0 0.0    1.0
0.3 0.0 0.0    1.0
0.4 0.0 0.0    1.0
0.5 0.0 0.0    1.0
with
K_POINTS {crystal_b}
2
0.0 0.0 0.0    5.0
0.5 0.0 0.0    5.0


The choice of either crystal_b or tpiba_b is instead driven by in which coordinate system (crystallographic axes or cartesian, respectively) you find easier to write the
components of the k-points you need.

Giovanni

--

Giovanni Cantele, PhD
CNR-SPIN and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910 - Fax:   +39 081 676346
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it

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From marsamos at democritos.it  Fri Mar  5 15:13:21 2010
From: marsamos at democritos.it (marsamos at democritos.it)
Date: Fri, 05 Mar 2010 15:13:21 +0100
Subject: [Pw_forum] How to cite Q~E
In-Reply-To: <4B9109C0.2090603@gmail.com>
References: <4B9100BB.4060901@gmail.com>
	<20100305143456.qqq6gh47wwc80k0s@mail.democritos.it>
	<4B9109C0.2090603@gmail.com>
Message-ID: <20100305151321.v9g2objy0wwk00w4@mail.democritos.it>

It is a very nice idea to thanks the forum! we should do it often, as 
the community lives thanks to all of you! good work!

bests

Layla


Quoting vega lew <quantumdft at gmail.com>:

> Well, thank you for your reply.
>
> I'll cite the reference along with a short paragraph to thank every 
> one here in the Acknowledgements section.
>
> best,
>
> vega
>
> On 2010-03-05 21:34, marsamos at democritos.it wrote:
>> Dear vega, htis is the official reference. It is ok, just this one. 
>> Thank you.
>>
>> bests
>>
>> Layla
>>
>> Quoting vega lew<quantumdft at gmail.com>:
>>
>>
>>> Dear all,
>>>
>>> As the web page,
>>> http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO,
>>> said, I just cite the Q-E by adding a a single reference of P.
>>> Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni,
>>> D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso,
>>> S. Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann, C.
>>> Gougoussis, M. L. A. Kokalj, L. Martin-Samos, N. Marzari, F. Mauri,
>>> R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia,
>>> S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari and
>>> R. M. Wentzcovitch, /Journal of Physics: Condensed Matter/, 2009,
>>> *21*, 395502.
>>>
>>> Do you think just a single reference is OK?
>>>
>>> best wishes,
>>>
>>> vega
>>> -- 
>>>
>>> ==================================================================================
>>> Vega Lew ( weijia liu)
>>> Graduate students
>>> State Key Laboratory of Materials-oriented Chemical Engineering
>>> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
>>> ***********************************************************************************************
>>> Email: vegalew at gmail.com
>>> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#,
>>> Nanjing, Jiangsu, China
>>> ***********************************************************************************************
>>>
>>>
>>>
>>
>>
>>
>
> -- 
>
> ==================================================================================
> Vega Lew ( weijia liu)
> Graduate students
> State Key Laboratory of Materials-oriented Chemical Engineering
> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
> ***********************************************************************************************
> Email: vegalew at gmail.com
> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, 
> Nanjing, Jiangsu, China
> ***********************************************************************************************
>
>



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

----------------------------------------------------------------
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From baroni at sissa.it  Fri Mar  5 15:52:05 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 5 Mar 2010 15:52:05 +0100
Subject: [Pw_forum] How to cite Q~E
In-Reply-To: <4B9109C0.2090603@gmail.com>
References: <4B9100BB.4060901@gmail.com>
	<20100305143456.qqq6gh47wwc80k0s@mail.democritos.it>
	<4B9109C0.2090603@gmail.com>
Message-ID: <F686C122-7E43-44D2-AE21-5F4BACB4041E@sissa.it>

Vega: thank you for raising the question. The quote you propose is OK (you may want to replace the full list of authors with "P. Giannozzi et al."). If you want you may also quote: "S. Scandolo, P. Giannozzi, C. Cavazzoni, S. de Gironcoli, A. Pasquarello, and S. Baroni,First-principles codes for computational crystallography in the Quantum-ESPRESSO package, Zeit. Krist. 220, 574 (2005). "

Best wishes - Stefano
 
On Mar 5, 2010, at 2:40 PM, vega lew wrote:

> Well, thank you for your reply.
> 
> I'll cite the reference along with a short paragraph to thank every one here in the Acknowledgements section.
> 
> best,
> 
> vega
> 
> On 2010-03-05 21:34, marsamos at democritos.it wrote:
>> 
>> Dear vega, htis is the official reference. It is ok, just this one. Thank you.
>> 
>> bests
>> 
>> Layla
>> 
>> Quoting vega lew <quantumdft at gmail.com>:
>> 
>>   
>>> Dear all,
>>> 
>>> As the web page, 
>>> http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO, 
>>> said, I just cite the Q-E by adding a a single reference of P. 
>>> Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni, 
>>> D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso, 
>>> S. Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann, C. 
>>> Gougoussis, M. L. A. Kokalj, L. Martin-Samos, N. Marzari, F. Mauri, 
>>> R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia, 
>>> S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari and 
>>> R. M. Wentzcovitch, /Journal of Physics: Condensed Matter/, 2009, 
>>> *21*, 395502.
>>> 
>>> Do you think just a single reference is OK?
>>> 
>>> best wishes,
>>> 
>>> vega
>>> -- 
>>> 
>>> ==================================================================================
>>> Vega Lew ( weijia liu)
>>> Graduate students
>>> State Key Laboratory of Materials-oriented Chemical Engineering
>>> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
>>> ***********************************************************************************************
>>> Email: vegalew at gmail.com
>>> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, 
>>> Nanjing, Jiangsu, China
>>> ***********************************************************************************************
>>> 
>>> 
>>>     
>> 
>> 
>>   
> 
> -- 
> ==================================================================================
> Vega Lew ( weijia liu)
> Graduate students
> State Key Laboratory of Materials-oriented Chemical Engineering
> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
> ***********************************************************************************************
> Email: vegalew at gmail.com
> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China
> ***********************************************************************************************
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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

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







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From baroni at sissa.it  Fri Mar  5 15:52:38 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 5 Mar 2010 15:52:38 +0100
Subject: [Pw_forum] How to cite Q~E
In-Reply-To: <20100305151321.v9g2objy0wwk00w4@mail.democritos.it>
References: <4B9100BB.4060901@gmail.com>
	<20100305143456.qqq6gh47wwc80k0s@mail.democritos.it>
	<4B9109C0.2090603@gmail.com>
	<20100305151321.v9g2objy0wwk00w4@mail.democritos.it>
Message-ID: <E6A1FEC9-3DE1-429A-9869-5BB6C6430E95@sissa.it>

I agree! Thanks for thinking of it.
Stefano

On Mar 5, 2010, at 3:13 PM, marsamos at democritos.it wrote:

> It is a very nice idea to thanks the forum! we should do it often, as 
> the community lives thanks to all of you! good work!
> 
> bests
> 
> Layla
> 
> 
> Quoting vega lew <quantumdft at gmail.com>:
> 
>> Well, thank you for your reply.
>> 
>> I'll cite the reference along with a short paragraph to thank every 
>> one here in the Acknowledgements section.
>> 
>> best,
>> 
>> vega
>> 
>> On 2010-03-05 21:34, marsamos at democritos.it wrote:
>>> Dear vega, htis is the official reference. It is ok, just this one. 
>>> Thank you.
>>> 
>>> bests
>>> 
>>> Layla
>>> 
>>> Quoting vega lew<quantumdft at gmail.com>:
>>> 
>>> 
>>>> Dear all,
>>>> 
>>>> As the web page,
>>>> http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO,
>>>> said, I just cite the Q-E by adding a a single reference of P.
>>>> Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni,
>>>> D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso,
>>>> S. Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann, C.
>>>> Gougoussis, M. L. A. Kokalj, L. Martin-Samos, N. Marzari, F. Mauri,
>>>> R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia,
>>>> S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari and
>>>> R. M. Wentzcovitch, /Journal of Physics: Condensed Matter/, 2009,
>>>> *21*, 395502.
>>>> 
>>>> Do you think just a single reference is OK?
>>>> 
>>>> best wishes,
>>>> 
>>>> vega
>>>> -- 
>>>> 
>>>> ==================================================================================
>>>> Vega Lew ( weijia liu)
>>>> Graduate students
>>>> State Key Laboratory of Materials-oriented Chemical Engineering
>>>> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
>>>> ***********************************************************************************************
>>>> Email: vegalew at gmail.com
>>>> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#,
>>>> Nanjing, Jiangsu, China
>>>> ***********************************************************************************************
>>>> 
>>>> 
>>>> 
>>> 
>>> 
>>> 
>> 
>> -- 
>> 
>> ==================================================================================
>> Vega Lew ( weijia liu)
>> Graduate students
>> State Key Laboratory of Materials-oriented Chemical Engineering
>> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
>> ***********************************************************************************************
>> Email: vegalew at gmail.com
>> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, 
>> Nanjing, Jiangsu, China
>> ***********************************************************************************************
>> 
>> 
> 
> 
> 
> -- 
> Dr. L. Martin-Samos
> tel. +39 040 3787 429
> CNR-DEMOCRITOS and
> International School for Advanced Studies (ISAS-SISSA)
> via Beirut 2-4
> 34151 Trieste Italy
> 
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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

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







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From gianluca.giovannetti at gmail.com  Fri Mar  5 15:54:04 2010
From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti)
Date: Fri, 5 Mar 2010 15:54:04 +0100
Subject: [Pw_forum] lm decomposed band structure
In-Reply-To: <4B8FE898.2050802@sissa.it>
References: <8974d3b21003040838u19e63a1ej5d8626c24ea42363@mail.gmail.com>
	<4B8FE898.2050802@sissa.it>
Message-ID: <7234ba151003050654n6b4c2fd5g927eb38e326b57d5@mail.gmail.com>

Dear Gabriele,

can i find somewhere in the web more informations on how to use plotproj.x ?
foe example what is "filename1" in PW language?

thank you.

G.

On Thu, Mar 4, 2010 at 6:06 PM, Gabriele Sclauzero <sclauzer at sissa.it>wrote:

> Something like this?
>
> PROGRAM plotproj
> !
> !  This small program is used to select the band eigenvalues whose
> !  wavefunctions projected on atomic wavefunctions have projections larger
> !  than a given threshold. It requires two input files. The first is a
> !  file with the band eigenvalues, written in the output of pw.x.
> !  The input file with the bands has the following format:
> !  nbnd, nks     ! number of bands, number of k points
> !  --- blank line
> !  kvector coordinates
> !  --- blank line
> !  bands eigenvalues
> !  ...
> !  --- blank line
> !  kvector coordinates
> !  --- blank line
> !  bands eigenvalues
> !  ...
> !
> !  The second file is written by the projwfc.x program with the option
> !  lsym=.false.
> !
> !  The input of this program is:
> !  filename     ! name of the file with the band eigenvalues
> !  filename1    ! name of the file with the projections
> !  fileout      ! name of the output file where the bands are written
> !  threshold    ! see below
> !  ncri         ! number of criterions for selecting the bands
> !  for each criterion
> !  first_atomic_wfc, last_atomic_wfc   ! the band is selected if the
> !                                        sum of the projections on
> !                                        the atomic wavefunctions between
> !                                        first_atomic_wfc and
> !                                        last_atomic_wfc is larger than
> !                                        threshold. The sum is done on
> !                                        all criterions.
> !
> #include "f_defs.h"
>
> It is the plotproj.x utility in the PP directory. I never used it actually,
> since at the
> time I needed this kind of thing this utility was not included in the QE
> distro and I made
> something similar by my own, so I cannot tell you how this works.
>
>
> GS
>
>
> Duy Le wrote:
> > Dear all,
> >
> > Is there a way (already implemented) to do site-lm decomposed band
> > structure? I want to know characters of bands and also which atoms
> > contribute to those bands.
> >
> > Best regards,
> >
> > --------------------------------------------------
> > Duy Le
> > PhD Student
> > Department of Physics
> > University of Central Florida.
> >
> > "Men don't need hand to do things"
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
> --
>
>
> o ------------------------------------------------ o
> | Gabriele Sclauzero, PhD Student                  |
> | c/o:   SISSA & CNR-INFM Democritos,              |
> |        via Beirut 2-4, 34014 Trieste (Italy)     |
> | email: sclauzer at sissa.it                         |
> | phone: +39 040 3787 511                          |
> | skype: gurlonotturno                             |
> o ------------------------------------------------ o
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From baroni at sissa.it  Fri Mar  5 15:54:37 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 5 Mar 2010 15:54:37 +0100
Subject: [Pw_forum] How to cite Q~E
In-Reply-To: <F686C122-7E43-44D2-AE21-5F4BACB4041E@sissa.it>
References: <4B9100BB.4060901@gmail.com>
	<20100305143456.qqq6gh47wwc80k0s@mail.democritos.it>
	<4B9109C0.2090603@gmail.com>
	<F686C122-7E43-44D2-AE21-5F4BACB4041E@sissa.it>
Message-ID: <7CCD7066-FA63-46A9-807F-1F0734369175@sissa.it>

and, yes ... please also quote the QE web site: http://www.quantum-espresso.org
Stefano

On Mar 5, 2010, at 3:52 PM, Stefano Baroni wrote:

> Vega: thank you for raising the question. The quote you propose is OK (you may want to replace the full list of authors with "P. Giannozzi et al."). If you want you may also quote: "S. Scandolo, P. Giannozzi, C. Cavazzoni, S. de Gironcoli, A. Pasquarello, and S. Baroni,First-principles codes for computational crystallography in the Quantum-ESPRESSO package, Zeit. Krist. 220, 574 (2005). "
> 
> Best wishes - Stefano
>  
> On Mar 5, 2010, at 2:40 PM, vega lew wrote:
> 
>> Well, thank you for your reply.
>> 
>> I'll cite the reference along with a short paragraph to thank every one here in the Acknowledgements section.
>> 
>> best,
>> 
>> vega
>> 
>> On 2010-03-05 21:34, marsamos at democritos.it wrote:
>>> 
>>> Dear vega, htis is the official reference. It is ok, just this one. Thank you.
>>> 
>>> bests
>>> 
>>> Layla
>>> 
>>> Quoting vega lew <quantumdft at gmail.com>:
>>> 
>>>   
>>>> Dear all,
>>>> 
>>>> As the web page, 
>>>> http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO, 
>>>> said, I just cite the Q-E by adding a a single reference of P. 
>>>> Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni, 
>>>> D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso, 
>>>> S. Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann, C. 
>>>> Gougoussis, M. L. A. Kokalj, L. Martin-Samos, N. Marzari, F. Mauri, 
>>>> R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia, 
>>>> S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari and 
>>>> R. M. Wentzcovitch, /Journal of Physics: Condensed Matter/, 2009, 
>>>> *21*, 395502.
>>>> 
>>>> Do you think just a single reference is OK?
>>>> 
>>>> best wishes,
>>>> 
>>>> vega
>>>> -- 
>>>> 
>>>> ==================================================================================
>>>> Vega Lew ( weijia liu)
>>>> Graduate students
>>>> State Key Laboratory of Materials-oriented Chemical Engineering
>>>> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
>>>> ***********************************************************************************************
>>>> Email: vegalew at gmail.com
>>>> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, 
>>>> Nanjing, Jiangsu, China
>>>> ***********************************************************************************************
>>>> 
>>>> 
>>>>     
>>> 
>>>   
>> 
>> -- 
>> ==================================================================================
>> Vega Lew ( weijia liu)
>> Graduate students
>> State Key Laboratory of Materials-oriented Chemical Engineering
>> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
>> ***********************************************************************************************
>> Email: vegalew at gmail.com
>> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China
>> ***********************************************************************************************
>> 
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> ---
> Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
> http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)
> 
> La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget
> 
> Please, if possible, don't  send me MS Word or PowerPoint attachments
> Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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

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







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From quantumdft at gmail.com  Fri Mar  5 16:08:10 2010
From: quantumdft at gmail.com (vega lew)
Date: Fri, 05 Mar 2010 23:08:10 +0800
Subject: [Pw_forum] How to cite Q~E
In-Reply-To: <E6A1FEC9-3DE1-429A-9869-5BB6C6430E95@sissa.it>
References: <4B9100BB.4060901@gmail.com>	<20100305143456.qqq6gh47wwc80k0s@mail.democritos.it>	<4B9109C0.2090603@gmail.com>	<20100305151321.v9g2objy0wwk00w4@mail.democritos.it>
	<E6A1FEC9-3DE1-429A-9869-5BB6C6430E95@sissa.it>
Message-ID: <4B911E5A.5000309@gmail.com>

You are welcome. I got more than I gave in the forum. So this forum 
deserve a special acknowledgments. I hope this revision of our 
manuscript could be accepted by the editors, so that we could express my 
acknowledgments to every readers.

By the way, I note Axel Kohlmeyer no longer come here for a long time. 
He put pretty much useful information for us.

best,

vega

On 2010-03-05 22:52, Stefano Baroni wrote:
> I agree! Thanks for thinking of it.
> Stefano
>
> On Mar 5, 2010, at 3:13 PM, marsamos at democritos.it 
> <mailto:marsamos at democritos.it> wrote:
>
>> It is a very nice idea to thanks the forum! we should do it often, as
>> the community lives thanks to all of you! good work!
>>
>> bests
>>
>> Layla
>>
>>
>> Quoting vega lew <quantumdft at gmail.com <mailto:quantumdft at gmail.com>>:
>>
>>> Well, thank you for your reply.
>>>
>>> I'll cite the reference along with a short paragraph to thank every
>>> one here in the Acknowledgements section.
>>>
>>> best,
>>>
>>> vega
>>>
>>> On 2010-03-05 21:34, marsamos at democritos.it 
>>> <mailto:marsamos at democritos.it> wrote:
>>>> Dear vega, htis is the official reference. It is ok, just this one.
>>>> Thank you.
>>>>
>>>> bests
>>>>
>>>> Layla
>>>>
>>>> Quoting vega lew<quantumdft at gmail.com <mailto:quantumdft at gmail.com>>:
>>>>
>>>>
>>>>> Dear all,
>>>>>
>>>>> As the web page,
>>>>> http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO,
>>>>> said, I just cite the Q-E by adding a a single reference of P.
>>>>> Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni,
>>>>> D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso,
>>>>> S. Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann, C.
>>>>> Gougoussis, M. L. A. Kokalj, L. Martin-Samos, N. Marzari, F. Mauri,
>>>>> R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia,
>>>>> S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari and
>>>>> R. M. Wentzcovitch, /Journal of Physics: Condensed Matter/, 2009,
>>>>> *21*, 395502.
>>>>>
>>>>> Do you think just a single reference is OK?
>>>>>
>>>>> best wishes,
>>>>>
>>>>> vega
>>>>> -- 
>>>>>
>>>>> ==================================================================================
>>>>> Vega Lew ( weijia liu)
>>>>> Graduate students
>>>>> State Key Laboratory of Materials-oriented Chemical Engineering
>>>>> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
>>>>> ***********************************************************************************************
>>>>> Email: vegalew at gmail.com <mailto:vegalew at gmail.com>
>>>>> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#,
>>>>> Nanjing, Jiangsu, China
>>>>> ***********************************************************************************************
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>> -- 
>>>
>>> ==================================================================================
>>> Vega Lew ( weijia liu)
>>> Graduate students
>>> State Key Laboratory of Materials-oriented Chemical Engineering
>>> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
>>> ***********************************************************************************************
>>> Email: vegalew at gmail.com <mailto:vegalew at gmail.com>
>>> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#,
>>> Nanjing, Jiangsu, China
>>> ***********************************************************************************************
>>>
>>>
>>
>>
>>
>> -- 
>> Dr. L. Martin-Samos
>> tel. +39 040 3787 429
>> CNR-DEMOCRITOS and
>> International School for Advanced Studies (ISAS-SISSA)
>> via Beirut 2-4
>> 34151 Trieste Italy
>>
>> ----------------------------------------------------------------
>> This message was sent using IMP, the Internet Messaging Program.
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
> ---
> Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste
> http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / 
> stefanobaroni (skype)
>
> La morale est une logique de l'action comme la logique est une morale 
> de la pens?e - Jean Piaget
>
> Please, if possible, don't send me MS Word or PowerPoint attachments
> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>    

-- 

================================================
Vega Lew ( weijia liu)
Graduate students
State Key Laboratory of Materials-oriented Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, China
***************************************************************
Email: vegalew at gmail.com
Office: Room A705, Technical Innovation Building,
Xinmofan Road 5#, Nanjing, China
***************************************************************

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From wulilixiangguo at sina.com  Fri Mar  5 19:13:17 2010
From: wulilixiangguo at sina.com (wulilixiangguo at sina.com)
Date: Sat, 06 Mar 2010 02:13:17 +0800 
Subject: [Pw_forum] =?gbk?b?u9i4tKO6UmU6ICBHcmFwaGVuZS0tU2lsaWNvbiBTdXJm?=
	=?gbk?q?ace=28scf_not_converge=29?=
Message-ID: <20100305181317.3E529CF61C1@mail3-92.sinamail.sina.com.cn>

Thank you!
It really help! I have solved the problem!
----- ???? -----
????Giovanni Cantele <giovanni.cantele at na.infn.it>
????PWSCF Forum <pw_forum at pwscf.org>
???Re: [Pw_forum] Graphene--Silicon Surface(scf not converge)
???2010-3-5 04:55:41



> Hi everyone:

> I am doing a scf calculation for my structure. My structure has 660

> atoms(56 H,324C,280 Si). I use H terminated Si-C surface. But after 24

> hours calculation(46 steps), the scf accuracy still fluctuate from about 1

> to 100.

> Does anyone ever know this before?How to solve it?

> Thank you very much!



You can try to:

1) browse the forum, the issue has been discussed many many times, there

is not a unique answer the problem might be related to several issues



2) browse the QE wiki:

http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions#Self-consistency_is_slow_or_does_not_converge_at_all



Did you check your geometry using, e.g., XCrysDen? Some times, mostly when

dealing with such a huge number of atoms, a wrong coordinate might give

atom overlap preventing the scf cycle from converging. You might also try

to tune some parameters related to the convergence of the scf cycle, like

mixing_beta.



Giovanni



-- 

Dr. Giovanni Cantele

CNR-SPIN and Dipartimento di Scienze Fisiche

Universita' di Napoli "Federico II"

Complesso Universitario di Monte S. Angelo - Ed. 6

Via Cintia, I-80126, Napoli, Italy

Phone: +39 081 676910 - Fax:   +39 081 676346

ResearcherID: http://www.researcherid.com/rid/A-1951-2009

Web page: http://people.na.infn.it/~cantele

Research Group: http://www.nanomat.unina.it

Skype contact: giocan74



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From elie.moujaes at hotmail.co.uk  Fri Mar  5 20:46:50 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Fri, 5 Mar 2010 19:46:50 +0000
Subject: [Pw_forum] crystal or tpiba_b
In-Reply-To: <4ADC69D1-7D88-4B56-B335-043C5A63BF55@na.infn.it>
References: <SNT114-W26C861670ED542E971E37CD3380@phx.gbl>,
	<4ADC69D1-7D88-4B56-B335-043C5A63BF55@na.infn.it>
Message-ID: <SNT114-W410FD39DA310631666A652D3380@phx.gbl>


Thanks for the reply. It was really helpful

 

Regards,

 

 


 


From: giovanni.cantele at na.infn.it
Date: Fri, 5 Mar 2010 15:06:07 +0100
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] crystal or tpiba_b




On Mar 5, 2010, at 2:53 PM, Elie Moujaes wrote:

Dear all,
 
I read that if we are trying to calculate the band structure, it is better to use {tpiba_b} in ATOMIC POSITIONS rather than {crystal}. Is the only difference related to the points that will be plotted at the end  because one is wrt to cartesian and the other relative to crystallographic axes?
 
 

I never used tpiba_b or crystal_b. Nevertheless, by reading the Doc/INPUT_PW.txt I understand that it is not a matter of tpiba vs crystal, but of tpiba_b/crystal_b vs tpiba/crystal. Using either tpiba or crystal, you must specify the full list of k-points you want to show in your band structure plot. On the contrary, the *_b options (tpiba_b/crystal_b) allow to specify, for each given line in the Brillouin zone, only the 1st and last point, together with the number of points along that line.


As an example, you can replace
K_POINTS {crystal}
5
0.0 0.0 0.0    1.00.1 0.0 0.0    1.0



0.2 0.0 0.0    1.00.3 0.0 0.0    1.0
0.4 0.0 0.0    1.0
0.5 0.0 0.0    1.0
with

K_POINTS {crystal_b}
2
0.0 0.0 0.0    5.00.5 0.0 0.0    5.0




The choice of either crystal_b or tpiba_b is instead driven by in which coordinate system (crystallographic axes or cartesian, respectively) you find easier to write the
components of the k-points you need.


Giovanni


--



Giovanni Cantele, PhD
CNR-SPIN and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910 - Fax:   +39 081 676346
Skype contact: giocan74


ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it
 		 	   		  
_________________________________________________________________
Got a cool Hotmail story? Tell us now
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From elie.moujaes at hotmail.co.uk  Fri Mar  5 20:52:52 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Fri, 5 Mar 2010 19:52:52 +0000
Subject: [Pw_forum] Graphene band structure
Message-ID: <SNT114-W10C180F635F73BDF086EADD3380@phx.gbl>


First of all, Thanks to all of you who are answerinbg my questions and being patient with me. I have drawn the band structure of graphene but for some reason there appears to be three different bands that should not exist (namely the ones starting at 4.8 , 8.8 and one of the lines at 10 on the y axis). I realized this when I compared that to other graphene band structure calculations.. I could not find anything wrong in my program that is causing the existence of those 3 structures. I was wondering if anyone can have a look at graph and program and figure out whats wrong...

 

 

Thanks

 

 
 		 	   		  
_________________________________________________________________
We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now
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From nnlinh at sissa.it  Fri Mar  5 21:35:45 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Fri, 05 Mar 2010 21:35:45 +0100
Subject: [Pw_forum] Graphene band structure
In-Reply-To: <SNT114-W10C180F635F73BDF086EADD3380@phx.gbl>
References: <SNT114-W10C180F635F73BDF086EADD3380@phx.gbl>
Message-ID: <4B916B21.2020109@sissa.it>

Elie Moujaes wrote:
> First of all, Thanks to all of you who are answerinbg my questions and 
> being patient with me. I have drawn the band structure of graphene but 
> for some reason there appears to be three different bands that should 
> not exist (namely the ones starting at 4.8 , 8.8 and one of the lines 
> at 10 on the y axis). I realized this when I compared that to other 
> graphene band structure calculations.. I could not find anything wrong 
> in my program that is causing the existence of those 3 structures. I 
> was wondering if anyone can have a look at graph and program and 
> figure out whats wrong...
>
Your system have only 8 valence electrons and you define nbnd=10, it 
means you have some bands that are unoccupied by any electrons. Maybe, 
that reason makes the higher bands  wrong.
Graphene in your model could be an insulator, so I suggest to reduce 
ndband=nele/2 = 4 or 5 and let check again if the result is available or 
not.

Good luck

Linh

>
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-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From lfhuang at theory.issp.ac.cn  Sat Mar  6 05:46:33 2010
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Sat, 06 Mar 2010 12:46:33 +0800
Subject: [Pw_forum] =?utf-8?q?Graphene_band_structure?=
Message-ID: <20100306044633.12389.qmail@ms.hfcas.ac.cn>

>three different bands that should not exist (namely the ones starting at 4.8 , 8.8 and one of the lines at 10 on the >y axis).
Why do they should  not exist? What's your computational parameters?  
Actually, these bands exist! These bands correspond to the so called "interlayer bands" in the intercalated graphite compounds (GICs) and  responsible for the superconductivity phenomenom in GICs. 
Reference: G. Csanyi et al., "The role of the interlayer state in the electronic structure of superconducting graphite intercalated compounds", Nature Physics vol. 1 page 42-45 (2005).

> I realized this when I compared that to other graphene band structure calculations. 
What's yours references for the graphene band structure? From a chinese paper in early 2009, you can verify the existence of the "interlayer bands" in the Fig. 1 therein. In addition, the reference [20] and [21] therein may be also useful for you.		 	   		  
Reference: Huang Liangfeng et al.,"Lattice dynamics of hydrogen-substituted graphene systems", Acta Physica Sinica vol. 58 page s306-312 (2009).

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


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From pholvey at gmail.com  Sun Mar  7 08:28:09 2010
From: pholvey at gmail.com (Patrick Holvey)
Date: Sun, 7 Mar 2010 02:28:09 -0500
Subject: [Pw_forum] From davcio: error #10
In-Reply-To: <4B7FEB5F.1070608@sissa.it>
References: <4011cd661002152139x43e1866jc222667bb64b742b@mail.gmail.com>
	<4011cd661002180001w211b5210ud4d234c82854b7f5@mail.gmail.com>
	<4011cd661002180828n4ab5b7abwa988bdbae3cac518@mail.gmail.com>
	<4B7D769B.70300@sissa.it>
	<4011cd661002191651m396ac30m3e06e835a8476297@mail.gmail.com>
	<4B7FEB5F.1070608@sissa.it>
Message-ID: <4011cd661003062328k535ec9b4xe8ffaa8d7238b516@mail.gmail.com>

Good evening/morning everybody!

Sorry for being incommunicado for so long (midterm exams -> done!).  So,
I've completed a script to generate all of the files for my ion/metal slab
system, but again I'm running into the davcio error.

Based on Linh's prior suggestions and explanations, I downloaded XCrysDen
and checked out my crystal sizes.  Basically, what I came up with was, given
the original set with the ion at 10.5 angstroms, the cell dimensions 1&3
were 10.5 and 4.89 respectively, that I should lock the celldm(1) in at 10.5
and decrease the celldm(3) as I bring the ion closer to the surface.  So I
measured the ion distance from the top of the cell (in the 10.5 system) and
found it to be approx. 12 angstroms, which I keep constant by decreasing the
celldm(3) by 0.09 for every ion retraction of .5 angstroms.  Thinking I had
solved my issue, I generated all of the input files and submitted them all
for running, and the majority of them promptly crashed (but for some reason
some of the 10-11 ranged systems are still running...).  I'm sure I've
missed something in Linh's initial instructions, so its distinctly possible
that I'm making a stupid error.

I've uploaded a tarball to - - nd.edu/~pholvey/PWSCF.html - - with all of
the input/output files that I've got right now.  If someone could help me
solve this issue, I feel that my calculations are close to being able to run
to completion, and I'd love to figure this out so I can start varying ion
composition.

Thank you so much for all of your help thus far.  This community is awesome!

Many Thanks,

Patrick
University of Notre Dame

On Sat, Feb 20, 2010 at 9:02 AM, Ngoc Linh Nguyen <nnlinh at sissa.it> wrote:

> Patrick Holvey wrote:
> > Thanks for all of the assistance everyone.
> >
> > Linh, I tried out your suggestions and it worked like a charm.  I was
> > wondering if you would explain to me how you arrived at those numbers
> I  suppose that you have been not familiar with Xcrysen package :D.
>
> Firstly, you should find the lattice constants of the given slab, then
> calculate the positions of atoms  belong to these parameters.
> By assuming that the values of the positions of atoms are right and
> present in your input file, I visualize the input file by Xcrysden
> package .
>    - Then, we displayed the Crystal cells  (Display -> Crystal Cells).
> Here, you can be seen that, with the celldm(1)=30, the atoms are located
> just at the conner of hole supercell.
>    - You duplicate the supercell be long to Ox or Oy (Modify -> Number
> of unit drawn), you can see that your slab is not continuous belong to
> Ox and Oy axis because the supercell sides are to lager. Thus, I should
> decrease celldm(1) to keep continuousness of the slab.  Of couse, my
> values maybe not precise completely, so you should recalculate so that
> the atom positions agree with periodicity.
> Moreover, you should also recalculate the Celldm(3) value associate with
> the new Celldm(1) one. (I suppose you've known how to get a suitable of
> Celldm(3))
> > and why they worked while the prior ones did not.
> You can see that when Celldm(1) is too large and a wrong value, the  G
> cutoff , FFT grid values are very larger, and an insufficient virtual
> memory could be happened.
> >   Further, I'm going to be moving the ion closer to the surface in
> > future calculations.  Will I have to recalculate those numbers or am I
> > ok to keep them as they are now?
> The Celldm(1) value should be fixed, because it does not relate to ion
> moving, but Celldm(3) maybe changed if you move too far from surface
> with respect to the Oz side of supercell.
>
> Linh
> > Many thanks,
> >
> > Patrick Holvey
> > University of Notre Dame
> >
> > On Thu, Feb 18, 2010 at 12:19 PM, Ngoc Linh Nguyen <nnlinh at sissa.it
> > <mailto:nnlinh at sissa.it>> wrote:
> >
> >     Patrick Holvey wrote:
> >     > Good morning everyone!  I'm new at this so I hope this posts
> >     properly.
> >     >
> >     > I'm attempting to perform an SCF calculation on an Au slab with a
> >     > single polarized ion above it.  However, every instance crashes
> with
> >     > the error from davcio: error #10.
> >     That error is induced by either error in writing or reading to/from
> >     output files or corruption of job. It seems to be 2nd case in your
> >     problem.
> >
> >     I have a look on your input file, and find out that the value of
> >     celldm(1) is too large. It not only makes that supercell does not
> >     present the slab model in the right way but also stops running of
> pw.x
> >     because of needed too much memory of RAM.
> >
> >     Let recalculate celldm(1) and celldm(3), I assume  celldm(1) = 10.50
> >     Bohr and celldm(3) = 4.979, You will have a right slab model and
> >     the run
> >     will work well.
> >
> >      Linh
> >
> >     >   I've included both the input and output files below.  This error
> >     > results from, according to what I've found in this forum results
> >     from
> >     > corrupted wavefiles?  I have all permissions necessary on this
> >     > environment and the disk is not dying, so those options are out.
> >      Any
> >     > help in the matter would be greatly appreciated.
> >
> >
> >     >
> >     > Many Thanks,
> >     >
> >     > Patrick Holvey
> >     > University of Notre Dame
> >     >
> >     > INPUT:
> >     > ----------------------------------------------------------
> >     >  &CONTROL
> >     >                  calculation = 'scf' ,
> >     >                 restart_mode = 'from_scratch' ,
> >     >                       outdir = '/dscratch/pholvey/espresso/tmp3' ,
> >     >                   pseudo_dir =
> >     > '/afs/crc.nd.edu/group/gezelter/espresso/4.1.2/peudo
> >     <http://crc.nd.edu/group/gezelter/espresso/4.1.2/peudo>
> >     > <http://crc.nd.edu/group/gezelter/espresso/4.1.2/peudo>' ,
> >     >                       prefix = 'AuSlab-li+-10.5' ,
> >     >                        nstep = 200 ,
> >     >                      tstress = .true. ,
> >     >                      tprnfor = .true. ,
> >     >                   wf_collect = .true. ,
> >     >  /
> >     >  &SYSTEM
> >     >                        ibrav = 4,
> >     >                    celldm(1) = 30.0,
> >     >                    celldm(3) = 2.979,
> >     >                          nat = 13,
> >     >                         ntyp = 2,
> >     >                      ecutwfc = 30 ,
> >     >                      ecutrho = 300 ,
> >     >                   tot_charge = 1.000000,
> >     >                  occupations = 'smearing' ,
> >     >                      degauss = 0.02 ,
> >     >                     smearing = 'methfessel-paxton' ,
> >     >                        nspin = 2 ,
> >     >    starting_magnetization(1) = 0.2,
> >     >    starting_magnetization(2) = 0.5,
> >     >    starting_magnetization(3) = 1.0,
> >     >  /
> >     >  &ELECTRONS
> >     >                     conv_thr = 1.D-6 ,
> >     >                  mixing_beta = 0.4D0 ,
> >     >              diagonalization = 'david' ,
> >     >  /
> >     >  &IONS
> >     >                 ion_dynamics = 'bfgs' ,
> >     >  /
> >     > ATOMIC_SPECIES
> >     >    Au  196.96569  Au.pbe-nd-rrkjus.UPF
> >     >    Li  6.941 Li.pbe-s-mt.UPF
> >     > ATOMIC_POSITIONS angstrom
> >     > Li       2.774511948   0.000118907   15.44640680    1   1   1
> >     > Au       2.775000000   1.602000000   0.000000000    0   0   0
> >     > Au       0.000000000   3.204000000   2.265000000    0   0   0
> >     > Au       0.000095442   0.000159091   4.946851613    0   0   0
> >     > Au       1.387000000   4.005000000   0.000000000    0   0   0
> >     > Au       1.387000000   0.801000000   2.265000000    0   0   0
> >     > Au      -1.387039610   2.402849200   4.946626283    0   0   0
> >     > Au      -1.387000000   4.005000000   0.000000000    0   0   0
> >     > Au       4.162000000   0.801000000   2.265000000    0   0   0
> >     > Au       1.387455156   2.402979759   4.946182797    0   0   0
> >     > Au       0.000000000   1.602000000   0.000000000    0   0   0
> >     > Au       2.775000000   3.204000000   2.265000000    0   0   0
> >     > Au       2.774511948   0.000118907   4.946406801    0   0   0
> >     > K_POINTS automatic
> >     >   4 4 1   1 1 1
> >     >
> >     >
> >     > OUTPUT:
> >     > -------------------------------------------------------------------
> >     >      Program PWSCF     v.4.1.2  starts ...
> >     >      Today is 15Feb2010 at 23:39:52
> >     >
> >     >      Parallel version (MPI)
> >     >
> >     >      Number of processors in use:      16
> >     >      R & G space division:  proc/pool =   16
> >     >
> >     >      For Norm-Conserving or Ultrasoft (Vanderbilt)
> >     Pseudopotentials or PAW
> >     >
> >     >      Current dimensions of program pwscf are:
> >     >      Max number of different atomic species (ntypx) = 10
> >     >      Max number of k-points (npk) =  40000
> >     >      Max angular momentum in pseudopotentials (lmaxx) =  3
> >     >      Waiting for input...
> >     > Warning: card  &IONS ignored
> >     > Warning: card                 ION_DYNAMICS = 'BFGS' , ignored
> >     > Warning: card  / ignored
> >     >
> >     >      Subspace diagonalization in iterative solution of the
> >     eigenvalue
> >     > problem:
> >     >      a parallel distributed memory algorithm will be used,
> >     >      eigenstates matrixes will be distributed block like on
> >     >      ortho sub-group =    4*   4 procs
> >     >
> >     >
> >     >      Planes per process (thick) : nr3 =500 npp =  32 ncplane =32400
> >     >      Planes per process (smooth): nr3s=320 npps=  20 ncplanes=11664
> >     >
> >     >      Proc/  planes cols     G    planes cols    G      columns  G
> >     >      Pool       (dense grid)       (smooth grid)      (wavefct
> grid)
> >     >         1    32   1162   382028   20    465    96661    123
>  13177
> >     >         2    32   1163   382035   20    465    96645    123
>  13177
> >     >         3    32   1163   382035   20    465    96625    122
>  13172
> >     >         4    32   1163   382037   20    465    96639    122
>  13172
> >     >         5    31   1162   382022   20    465    96633    122
>  13172
> >     >         6    31   1162   382022   20    465    96641    122
>  13172
> >     >         7    31   1162   382022   20    465    96633    124
>  13176
> >     >         8    31   1162   382022   20    465    96643    124
>  13176
> >     >         9    31   1162   382022   20    465    96623    124
>  13176
> >     >        10    31   1162   382022   20    466    96666    123
>  13173
> >     >        11    31   1163   382035   20    466    96688    123
>  13173
> >     >        12    31   1163   382035   20    466    96694    123
>  13175
> >     >        13    31   1163   382035   20    466    96680    123
>  13175
> >     >        14    31   1163   382035   20    466    96662    124
>  13172
> >     >        15    31   1163   382035   20    466    96688    124
>  13172
> >     >        16    31   1163   382035   20    466    96684    123
>  13175
> >     >      tot    500  18601  6112477  320   7447  1546505   1969
> 210785
> >     >
> >     >
> >     >
> >     >      bravais-lattice index     =            4
> >     >      lattice parameter (a_0)   =      30.0000  a.u.
> >     >      unit-cell volume          =   69657.0213 (a.u.)^3
> >     >      number of atoms/cell      =           13
> >     >      number of atomic types    =            2
> >     >      number of electrons       =       134.00
> >     >      number of Kohn-Sham states=           80
> >     >      kinetic-energy cutoff     =      30.0000  Ry
> >     >      charge density cutoff     =     300.0000  Ry
> >     >      convergence threshold     =      1.0E-06
> >     >      mixing beta               =       0.4000
> >     >      number of iterations used =            8  plain     mixing
> >     >      Exchange-correlation      = SLA  PW   PBE  PBE (1434)
> >     >
> >     >      celldm(1)=  30.000000  celldm(2)=   0.000000  celldm(3)=
> >     2.979000
> >     >      celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=
> >     0.000000
> >     >
> >     >      crystal axes: (cart. coord. in units of a_0)
> >     >                a(1) = (  1.000000  0.000000  0.000000 )
> >     >                a(2) = ( -0.500000  0.866025  0.000000 )
> >     >                a(3) = (  0.000000  0.000000  2.979000 )
> >     >
> >     >      reciprocal axes: (cart. coord. in units 2 pi/a_0)
> >     >                b(1) = (  1.000000  0.577350  0.000000 )
> >     >                b(2) = (  0.000000  1.154701  0.000000 )
> >     >                b(3) = (  0.000000  0.000000  0.335683 )
> >     >
> >     >
> >     >      PseudoPot. # 1 for Au read from file Au.pbe-nd-rrkjus.UPF
> >     >      Pseudo is Ultrasoft + core correction, Zval = 11.0
> >     >      Generated by new atomic code, or converted to UPF format
> >     >      Using radial grid of 1279 points,  3 beta functions with:
> >     >                 l(1) =   2
> >     >                 l(2) =   2
> >     >                 l(3) =   1
> >     >      Q(r) pseudized with 0 coefficients
> >     >
> >     >
> >     >      PseudoPot. # 2 for Li read from file Li.pbe-s-mt.UPF
> >     >      Pseudo is Norm-conserving, Zval =  3.0
> >     >      Generated by new atomic code, or converted to UPF format
> >     >      Using radial grid of  881 points,  1 beta functions with:
> >     >                 l(1) =   0
> >     >
> >     >      atomic species   valence    mass     pseudopotential
> >     >         Au            11.00   196.96569     Au( 1.00)
> >     >         Li             3.00     6.94100     Li( 1.00)
> >     >
> >     >      Starting magnetic structure
> >     >      atomic species   magnetization
> >     >         Au           0.200
> >     >         Li           0.500
> >     >
> >     >      No symmetry!
> >     >
> >     >    Cartesian axes
> >     >
> >     >      site n.     atom                  positions (a_0 units)
> >     >          1           Li  tau(  1) = (   0.1747689   0.0000075
> >     > 0.9729826  )
> >     >          2           Au  tau(  2) = (   0.1747997   0.1009114
> >     > 0.0000000  )
> >     >          3           Au  tau(  3) = (   0.0000000   0.2018228
> >     > 0.1426743  )
> >     >          4           Au  tau(  4) = (   0.0000060   0.0000100
> >     > 0.3116065  )
> >     >          5           Au  tau(  5) = (   0.0873683   0.2522784
> >     > 0.0000000  )
> >     >          6           Au  tau(  6) = (   0.0873683   0.0504557
> >     > 0.1426743  )
> >     >          7           Au  tau(  7) = (  -0.0873708   0.1513576
> >     > 0.3115923  )
> >     >          8           Au  tau(  8) = (  -0.0873683   0.2522784
> >     > 0.0000000  )
> >     >          9           Au  tau(  9) = (   0.2621680   0.0504557
> >     > 0.1426743  )
> >     >         10           Au  tau( 10) = (   0.0873970   0.1513658
> >     > 0.3115644  )
> >     >         11           Au  tau( 11) = (   0.0000000   0.1009114
> >     > 0.0000000  )
> >     >         12           Au  tau( 12) = (   0.1747997   0.2018228
> >     > 0.1426743  )
> >     >         13           Au  tau( 13) = (   0.1747689   0.0000075
> >     > 0.3115785  )
> >     >
> >     >      number of k points=   48  gaussian broad. (Ry)=  0.0200
> >     > ngauss =   1
> >     >                        cart. coord. in units 2pi/a_0
> >     >         k(    1) = (   0.1250000   0.2165064  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(    2) = (   0.1250000   0.5051815  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(    3) = (   0.1250000  -0.3608439  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(    4) = (   0.1250000  -0.0721688  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(    5) = (   0.3750000   0.6495191  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(    6) = (   0.3750000  -0.2165064  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(    7) = (  -0.1250000   0.2165064   0.1678416), wk =
> >     > 0.0416667
> >     >         k(    8) = (   0.2500000   0.0000000  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(    9) = (  -0.1250000   0.5051815   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   10) = (  -0.3750000   0.3608439  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   11) = (   0.5000000   0.1443376  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   12) = (  -0.3750000  -0.3608439   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   13) = (   0.5000000  -0.1443376   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   14) = (  -0.1250000  -0.3608439   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   15) = (   0.3750000  -0.0721688  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   16) = (  -0.2500000  -0.2886751  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   17) = (   0.3750000   0.0721688   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   18) = (  -0.2500000   0.2886751   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   19) = (  -0.1250000  -0.0721688   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   20) = (   0.0000000  -0.1443376  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   21) = (  -0.3750000   0.6495191   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   22) = (   0.7500000   0.0000000  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   23) = (  -0.3750000  -0.2165064   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   24) = (   0.0000000  -0.4330127  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   25) = (   0.1250000   0.2165064  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   26) = (   0.1250000   0.5051815  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   27) = (   0.1250000  -0.3608439  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   28) = (   0.1250000  -0.0721688  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   29) = (   0.3750000   0.6495191  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   30) = (   0.3750000  -0.2165064  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   31) = (  -0.1250000   0.2165064   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   32) = (   0.2500000   0.0000000  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   33) = (  -0.1250000   0.5051815   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   34) = (  -0.3750000   0.3608439  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   35) = (   0.5000000   0.1443376  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   36) = (  -0.3750000  -0.3608439   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   37) = (   0.5000000  -0.1443376   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   38) = (  -0.1250000  -0.3608439   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   39) = (   0.3750000  -0.0721688  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   40) = (  -0.2500000  -0.2886751  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   41) = (   0.3750000   0.0721688   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   42) = (  -0.2500000   0.2886751   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   43) = (  -0.1250000  -0.0721688   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   44) = (   0.0000000  -0.1443376  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   45) = (  -0.3750000   0.6495191   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   46) = (   0.7500000   0.0000000  -0.1678416), wk =
> >     > 0.0416667
> >     >         k(   47) = (  -0.3750000  -0.2165064   0.1678416), wk =
> >     > 0.0416667
> >     >         k(   48) = (   0.0000000  -0.4330127  -0.1678416), wk =
> >     > 0.0416667
> >     >
> >     >      G cutoff = 6839.1799  (6112477 G-vectors)     FFT grid:
> >     (180,180,500)
> >     >      G cutoff = 2735.6720  (1546505 G-vectors)  smooth grid:
> >     (108,108,320)
> >     >
> >     >      Largest allocated arrays     est. size (Mb)     dimensions
> >     >         Kohn-Sham Wavefunctions        14.81 Mb     (  12134,  80)
> >     >         NL pseudopotentials            29.07 Mb     (  12134, 157)
> >     >         Each V/rho on FFT grid         31.64 Mb     (1036800,   2)
> >     >         Each G-vector array             2.91 Mb     ( 382028)
> >     >         G-vector shells                 1.02 Mb     ( 133817)
> >     >      Largest temporary arrays     est. size (Mb)     dimensions
> >     >         Auxiliary wavefunctions        59.25 Mb     (  12134, 320)
> >     >         Each subspace H/S matrix        1.56 Mb     (    320, 320)
> >     >         Each <psi_i|beta_j> matrix      0.19 Mb     (    157,  80)
> >     >         Arrays for rho mixing         126.56 Mb     (1036800,   8)
> >     >
> >     >      Check: negative/imaginary core charge=   -0.000006    0.000000
> >     >
> >     >      Initial potential from superposition of free atoms
> >     >      Check: negative starting charge=(component1):   -0.017143
> >     >      Check: negative starting charge=(component2):   -0.005642
> >     >
> >     >      starting charge  134.96666, renormalised to  134.00000
> >     >
> >     >      negative rho (up, down):  0.170E-01 0.560E-02
> >     >      Starting wfc are  113 atomic wfcs
> >     >
> >     >      total cpu time spent up to now is    273.74 secs
> >     >
> >     >      Self-consistent Calculation
> >     >
> >     >      iteration #  1     ecut=    30.00 Ry     beta=0.40
> >     >      Davidson diagonalization with overlap
> >     >
> >     >
> >
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >     >      from davcio : error #        10
> >     >      error while writing to file
> >     >
> >
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >     >
> >     >      stopping ...
> >     >
> >
> ------------------------------------------------------------------------
> >     >
> >     > _______________________________________________
> >     > Pw_forum mailing list
> >     > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> >     > http://www.democritos.it/mailman/listinfo/pw_forum
> >     >
> >
> >     _______________________________________________
> >     Pw_forum mailing list
> >     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> >     http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> >
> > --
> > Patrick Holvey
> > pholvey at nd.edu <mailto:pholvey at nd.edu>
> > 442 Siegfried Hall
> > Notre Dame, IN 46556
> > Cell: (865)-659-9908
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Patrick Holvey
pholvey at nd.edu
442 Siegfried Hall
Notre Dame, IN 46556
Cell: (865)-659-9908
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From giannozz at democritos.it  Sun Mar  7 12:19:02 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 7 Mar 2010 12:19:02 +0100
Subject: [Pw_forum] From davcio: error #10
In-Reply-To: <4011cd661003062328k535ec9b4xe8ffaa8d7238b516@mail.gmail.com>
References: <4011cd661002152139x43e1866jc222667bb64b742b@mail.gmail.com>
	<4011cd661002180001w211b5210ud4d234c82854b7f5@mail.gmail.com>
	<4011cd661002180828n4ab5b7abwa988bdbae3cac518@mail.gmail.com>
	<4B7D769B.70300@sissa.it>
	<4011cd661002191651m396ac30m3e06e835a8476297@mail.gmail.com>
	<4B7FEB5F.1070608@sissa.it>
	<4011cd661003062328k535ec9b4xe8ffaa8d7238b516@mail.gmail.com>
Message-ID: <B52F2E4A-A9DD-43F7-960E-C7EE0A4E2D7C@democritos.it>

Patrick,

there is nothing wrong in your data (or, more exactly, nothing
obviously wrong). In any event, nothing in your data can cause
an "error in davcio", apart from a bad value of "outdir". See here:
   http://www.quantum-espresso.org/user_guide/node46.html
and here for parallel execution, in sec.3.3.1:
   http://www.quantum-espresso.org/user_guide/node17.html .

I run one of your data file and everything seems ok. You may want to
try to find optimal values of  -npool and -ndiag to achieve maximum
speed, but this has nothing to do with your problem, which is related
uniquely to the place where you are trying to write files.

P.

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




From pholvey at gmail.com  Sun Mar  7 22:29:11 2010
From: pholvey at gmail.com (Patrick Holvey)
Date: Sun, 7 Mar 2010 16:29:11 -0500
Subject: [Pw_forum] From davcio: error #10
In-Reply-To: <B52F2E4A-A9DD-43F7-960E-C7EE0A4E2D7C@democritos.it>
References: <4011cd661002152139x43e1866jc222667bb64b742b@mail.gmail.com>
	<4011cd661002180001w211b5210ud4d234c82854b7f5@mail.gmail.com>
	<4011cd661002180828n4ab5b7abwa988bdbae3cac518@mail.gmail.com>
	<4B7D769B.70300@sissa.it>
	<4011cd661002191651m396ac30m3e06e835a8476297@mail.gmail.com>
	<4B7FEB5F.1070608@sissa.it>
	<4011cd661003062328k535ec9b4xe8ffaa8d7238b516@mail.gmail.com>
	<B52F2E4A-A9DD-43F7-960E-C7EE0A4E2D7C@democritos.it>
Message-ID: <4011cd661003071329t2fd93dd2r550af0c2bda2a44a@mail.gmail.com>

Paolo (and everyone else),

Thanks for the quick reply.  Just a few questions.  If the error in davcio
results solely from a bad outdir, why did the error resolve itself in my
original input file when I changed the celldms to correspond with Linh's
suggestions?  Further, since the runs worked on 3 of the 25 submitted input
files, doesn't that show that there is no error in writing to the
destination?  The only reason I ask is that I'm almost completely positive
that I'm not running into disk limitations (although I will check for sure
on monday), and if that's not the issue, then I need to hammer out what is
really causing this.

 Thanks again,

Patrick
University of Notre Dame

On Sun, Mar 7, 2010 at 6:19 AM, Paolo Giannozzi <giannozz at democritos.it>wrote:

> Patrick,
>
> there is nothing wrong in your data (or, more exactly, nothing
> obviously wrong). In any event, nothing in your data can cause
> an "error in davcio", apart from a bad value of "outdir". See here:
>  http://www.quantum-espresso.org/user_guide/node46.html
> and here for parallel execution, in sec.3.3.1:
>  http://www.quantum-espresso.org/user_guide/node17.html .
>
> I run one of your data file and everything seems ok. You may want to
> try to find optimal values of  -npool and -ndiag to achieve maximum
> speed, but this has nothing to do with your problem, which is related
> uniquely to the place where you are trying to write files.
>
> P.
>
>
>
>
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Patrick Holvey
pholvey at nd.edu
442 Siegfried Hall
Notre Dame, IN 46556
Cell: (865)-659-9908
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From pholvey at gmail.com  Mon Mar  8 01:12:46 2010
From: pholvey at gmail.com (Patrick Holvey)
Date: Sun, 7 Mar 2010 19:12:46 -0500
Subject: [Pw_forum] From davcio: error #10
In-Reply-To: <4011cd661003071329t2fd93dd2r550af0c2bda2a44a@mail.gmail.com>
References: <4011cd661002152139x43e1866jc222667bb64b742b@mail.gmail.com>
	<4011cd661002180001w211b5210ud4d234c82854b7f5@mail.gmail.com>
	<4011cd661002180828n4ab5b7abwa988bdbae3cac518@mail.gmail.com>
	<4B7D769B.70300@sissa.it>
	<4011cd661002191651m396ac30m3e06e835a8476297@mail.gmail.com>
	<4B7FEB5F.1070608@sissa.it>
	<4011cd661003062328k535ec9b4xe8ffaa8d7238b516@mail.gmail.com>
	<B52F2E4A-A9DD-43F7-960E-C7EE0A4E2D7C@democritos.it>
	<4011cd661003071329t2fd93dd2r550af0c2bda2a44a@mail.gmail.com>
Message-ID: <4011cd661003071612v4f5aa3d2s3f1ba0b22c8b1903@mail.gmail.com>

Alright, so it's follow-up time.

After looking over which of the 25 runs finished (4 of them did), and moving
them to a separate directory, I re-submitted the runs to the queue.  This
time, apparently 7 of them have decided to stick and do a run.  No
guarantees on them finishing, but it looks promising as the error typically
evolves for me after the wavefunction collection (wfc) call in the output.
So the question now becomes: if the input files are working properly when
they decide to stick, what could be causing them to not stick?  The outdir
is the same for every input file, so I suppose it could be just too busy
with the calls from all of the different runs.  Has anyone else had issues
with this?  Moreover, is there a limit to how many runs I should direct to a
specific outdir?  Would it be better to assign a unique outdir for each
run?  Thanks!  I appreciate all of the help.

Most Sincerely,

Patrick
University of Notre Dame

On Sun, Mar 7, 2010 at 4:29 PM, Patrick Holvey <pholvey at gmail.com> wrote:

> Paolo (and everyone else),
>
> Thanks for the quick reply.  Just a few questions.  If the error in davcio
> results solely from a bad outdir, why did the error resolve itself in my
> original input file when I changed the celldms to correspond with Linh's
> suggestions?  Further, since the runs worked on 3 of the 25 submitted input
> files, doesn't that show that there is no error in writing to the
> destination?  The only reason I ask is that I'm almost completely positive
> that I'm not running into disk limitations (although I will check for sure
> on monday), and if that's not the issue, then I need to hammer out what is
> really causing this.
>
>  Thanks again,
>
>
> Patrick
> University of Notre Dame
>
> On Sun, Mar 7, 2010 at 6:19 AM, Paolo Giannozzi <giannozz at democritos.it>wrote:
>
>> Patrick,
>>
>> there is nothing wrong in your data (or, more exactly, nothing
>> obviously wrong). In any event, nothing in your data can cause
>> an "error in davcio", apart from a bad value of "outdir". See here:
>>  http://www.quantum-espresso.org/user_guide/node46.html
>> and here for parallel execution, in sec.3.3.1:
>>  http://www.quantum-espresso.org/user_guide/node17.html .
>>
>> I run one of your data file and everything seems ok. You may want to
>> try to find optimal values of  -npool and -ndiag to achieve maximum
>> speed, but this has nothing to do with your problem, which is related
>> uniquely to the place where you are trying to write files.
>>
>> P.
>>
>>
>>
>>
>> ---
>> Paolo Giannozzi, Dept of Physics, University of Udine
>> via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> Patrick Holvey
> pholvey at nd.edu
> 442 Siegfried Hall
> Notre Dame, IN 46556
> Cell: (865)-659-9908
>



-- 
Patrick Holvey
pholvey at nd.edu
442 Siegfried Hall
Notre Dame, IN 46556
Cell: (865)-659-9908
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From ceresoli at MIT.EDU  Mon Mar  8 03:09:09 2010
From: ceresoli at MIT.EDU (Davide Ceresoli)
Date: Sun, 7 Mar 2010 21:09:09 -0500 (EST)
Subject: [Pw_forum] From davcio: error #10
In-Reply-To: <4011cd661003071612v4f5aa3d2s3f1ba0b22c8b1903@mail.gmail.com>
References: <4011cd661002152139x43e1866jc222667bb64b742b@mail.gmail.com>
	<4011cd661002180001w211b5210ud4d234c82854b7f5@mail.gmail.com>
	<4011cd661002180828n4ab5b7abwa988bdbae3cac518@mail.gmail.com>
	<4B7D769B.70300@sissa.it>
	<4011cd661002191651m396ac30m3e06e835a8476297@mail.gmail.com>
	<4B7FEB5F.1070608@sissa.it>
	<4011cd661003062328k535ec9b4xe8ffaa8d7238b516@mail.gmail.com>
	<B52F2E4A-A9DD-43F7-960E-C7EE0A4E2D7C@democritos.it>
	<4011cd661003071329t2fd93dd2r550af0c2bda2a44a@mail.gmail.com>
	<4011cd661003071612v4f5aa3d2s3f1ba0b22c8b1903@mail.gmail.com>
Message-ID: <alpine.DEB.1.10.1003072104130.24914@dr-wily.mit.edu>

On Sun, 7 Mar 2010, Patrick Holvey wrote:

> The outdir is the same for every
> input file, so I suppose it could be just too busy with the calls from all of the different
> runs.? Has anyone else had issues with this?? Moreover, is there a limit to how many runs I
> should direct to a specific outdir?? Would it be better to assign a unique outdir for each
> run?? Thanks!? I appreciate all of the help.
Dear Patrick,
     I think that a shared outdir for every job, is the mother of
all evil. If you run several jobs simultaneusly, try to assign
a different outdir.

HTH

Davide

From pholvey at gmail.com  Mon Mar  8 03:17:56 2010
From: pholvey at gmail.com (Patrick Holvey)
Date: Sun, 7 Mar 2010 21:17:56 -0500
Subject: [Pw_forum] From davcio: error #10
In-Reply-To: <alpine.DEB.1.10.1003072104130.24914@dr-wily.mit.edu>
References: <4011cd661002152139x43e1866jc222667bb64b742b@mail.gmail.com>
	<4011cd661002180828n4ab5b7abwa988bdbae3cac518@mail.gmail.com>
	<4B7D769B.70300@sissa.it>
	<4011cd661002191651m396ac30m3e06e835a8476297@mail.gmail.com>
	<4B7FEB5F.1070608@sissa.it>
	<4011cd661003062328k535ec9b4xe8ffaa8d7238b516@mail.gmail.com>
	<B52F2E4A-A9DD-43F7-960E-C7EE0A4E2D7C@democritos.it>
	<4011cd661003071329t2fd93dd2r550af0c2bda2a44a@mail.gmail.com>
	<4011cd661003071612v4f5aa3d2s3f1ba0b22c8b1903@mail.gmail.com>
	<alpine.DEB.1.10.1003072104130.24914@dr-wily.mit.edu>
Message-ID: <4011cd661003071817x6f38073bvbeea76674f1935d8@mail.gmail.com>

Dear Davide,

Awesome.  After this recent spat with my submissions and in light of your
advice, I'll only start runs with independent outdirs.  Thank you for your
advice.  I truly appreciate it.

Patrick

On Sun, Mar 7, 2010 at 9:09 PM, Davide Ceresoli <ceresoli at mit.edu> wrote:

> On Sun, 7 Mar 2010, Patrick Holvey wrote:
>
>  The outdir is the same for every
>> input file, so I suppose it could be just too busy with the calls from all
>> of the different
>> runs.  Has anyone else had issues with this?  Moreover, is there a limit
>> to how many runs I
>> should direct to a specific outdir?  Would it be better to assign a unique
>> outdir for each
>> run?  Thanks!  I appreciate all of the help.
>>
> Dear Patrick,
>    I think that a shared outdir for every job, is the mother of
> all evil. If you run several jobs simultaneusly, try to assign
> a different outdir.
>
> HTH
>
> Davide
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Patrick Holvey
pholvey at nd.edu
442 Siegfried Hall
Notre Dame, IN 46556
Cell: (865)-659-9908
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From kazempoor at ph.iut.ac.ir  Mon Mar  8 07:33:03 2010
From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir)
Date: Mon, 8 Mar 2010 10:03:03 +0330 (IRST)
Subject: [Pw_forum] GWW in wannier part
In-Reply-To: <1364904551.82844.1268029768007.JavaMail.root@mta.iut.ac.ir>
Message-ID: <1660685380.82851.1268029983003.JavaMail.root@mta.iut.ac.ir>


Dear All
 I am using GWW in espresso for 72-atom supercell to correct the state of perfect bulk supercell, but in the midway of running the pw4gww calculation for bulk supercell in wannier part it crashes and the error is :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     task #         2
     from davcio : error #        99
     error while reading from file
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     task #        11
     from davcio : error #        99
     error while reading from file
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


the input file for wannier part is :





 &inputpw4gww
    prefix='tio2-perfect'
    outdir='/p5/batch/kazempou/'
    lwannier=.true.,
    cutoff_wpr_vc = 0.1d0
    num_nbnd_first =300
    num_nbndv=288
    num_nbnds=300
    l_truncated_coulomb=.false.
    remainder=-1
    restart_gww=-1
    numw_prod=1
    n_gauss=79
    omega_gauss=20.d0
    tau_gauss=10.d0
    l_zero=.true.
    l_wing=.true.
    cprim_first=1
    cprim_last=300
    cutoff_products=0.01d0
    l_polarization_analysis=.true.
    cutoff_polarization=0.01d0
/

I would appreciate if anyone tell me what is the reason of error?
thanks a lot





Ali Kazempour
Physics Department, Isfahn University of Technology

From jcwu.suda at hotmail.com  Mon Mar  8 08:40:06 2010
From: jcwu.suda at hotmail.com (wujianchun)
Date: Mon, 8 Mar 2010 15:40:06 +0800
Subject: [Pw_forum] How to get the electrical potential of each atom
Message-ID: <SNT137-w341CA7A1ACE1701766B4CEE9350@phx.gbl>


Dear sir,

 

How to get the electrical potential of each atom for the VBM correction of defect study?

Using the postprocess PP, we can only get the total potential 1D 2D or 3D by setting the "iflag". 

 

But I want the get the electrical potential of each atom after relaxing the supercell.  Any advice will be appreciated. 

 

 

Thanks a lot.

 

regards

 

Jianchun wu

Department of physics

Soochow university,China

215006
 		 	   		  
_________________________________________________________________
?????????????????msn?????
http://ditu.live.com/?form=TL&swm=1
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From sclauzer at sissa.it  Mon Mar  8 08:55:54 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Mon, 08 Mar 2010 08:55:54 +0100
Subject: [Pw_forum] lm decomposed band structure
In-Reply-To: <7234ba151003050654n6b4c2fd5g927eb38e326b57d5@mail.gmail.com>
References: <8974d3b21003040838u19e63a1ej5d8626c24ea42363@mail.gmail.com>	<4B8FE898.2050802@sissa.it>
	<7234ba151003050654n6b4c2fd5g927eb38e326b57d5@mail.gmail.com>
Message-ID: <4B94AD8A.2030401@sissa.it>



Gianluca Giovannetti wrote:
> Dear Gabriele,
> 
> can i find somewhere in the web more informations on how to use plotproj.x ?

I don't know. I doubt so. It seems a new (maybe experimental) tool, seldom used. I don't 
know who wrote it. I think you should do some effort to read the code (which should not be 
complicated, though) and experiment a little bit.

> foe example what is "filename1" in PW language?

What do you mean exactly with "PW language"?

Anyway,

 >     !  The second file is written by the projwfc.x program with the option
 >     !  lsym=.false.

It should coincide with the filproj produced by projwfc.x I suppose.


GS


> 
> thank you.
> 
> G.
> 
> On Thu, Mar 4, 2010 at 6:06 PM, Gabriele Sclauzero <sclauzer at sissa.it 
> <mailto:sclauzer at sissa.it>> wrote:
> 
>     Something like this?
> 
>     PROGRAM plotproj
>     !
>     !  This small program is used to select the band eigenvalues whose
>     !  wavefunctions projected on atomic wavefunctions have projections
>     larger
>     !  than a given threshold. It requires two input files. The first is a
>     !  file with the band eigenvalues, written in the output of pw.x.
>     !  The input file with the bands has the following format:
>     !  nbnd, nks     ! number of bands, number of k points
>     !  --- blank line
>     !  kvector coordinates
>     !  --- blank line
>     !  bands eigenvalues
>     !  ...
>     !  --- blank line
>     !  kvector coordinates
>     !  --- blank line
>     !  bands eigenvalues
>     !  ...
>     !
>     !  The second file is written by the projwfc.x program with the option
>     !  lsym=.false.
>     !
>     !  The input of this program is:
>     !  filename     ! name of the file with the band eigenvalues
>     !  filename1    ! name of the file with the projections
>     !  fileout      ! name of the output file where the bands are written
>     !  threshold    ! see below
>     !  ncri         ! number of criterions for selecting the bands
>     !  for each criterion
>     !  first_atomic_wfc, last_atomic_wfc   ! the band is selected if the
>     !                                        sum of the projections on
>     !                                        the atomic wavefunctions
>     between
>     !                                        first_atomic_wfc and
>     !                                        last_atomic_wfc is larger than
>     !                                        threshold. The sum is done on
>     !                                        all criterions.
>     !
>     #include "f_defs.h"
> 
>     It is the plotproj.x utility in the PP directory. I never used it
>     actually, since at the
>     time I needed this kind of thing this utility was not included in
>     the QE distro and I made
>     something similar by my own, so I cannot tell you how this works.
> 
> 
>     GS
> 
> 
>     Duy Le wrote:
>      > Dear all,
>      >
>      > Is there a way (already implemented) to do site-lm decomposed band
>      > structure? I want to know characters of bands and also which atoms
>      > contribute to those bands.
>      >
>      > Best regards,
>      >
>      > --------------------------------------------------
>      > Duy Le
>      > PhD Student
>      > Department of Physics
>      > University of Central Florida.
>      >
>      > "Men don't need hand to do things"
>      > _______________________________________________
>      > Pw_forum mailing list
>      > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>      > http://www.democritos.it/mailman/listinfo/pw_forum
>      >
> 
>     --
> 
> 
>     o ------------------------------------------------ o
>     | Gabriele Sclauzero, PhD Student                  |
>     | c/o:   SISSA & CNR-INFM Democritos,              |
>     |        via Beirut 2-4, 34014 Trieste (Italy)     |
>     | email: sclauzer at sissa.it <mailto:sclauzer at sissa.it>              
>               |
>     | phone: +39 040 3787 511                          |
>     | skype: gurlonotturno                             |
>     o ------------------------------------------------ o
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 


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

From nnlinh at sissa.it  Mon Mar  8 09:21:46 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Mon, 08 Mar 2010 09:21:46 +0100
Subject: [Pw_forum] How to get the electrical potential of each atom
In-Reply-To: <SNT137-w341CA7A1ACE1701766B4CEE9350@phx.gbl>
References: <SNT137-w341CA7A1ACE1701766B4CEE9350@phx.gbl>
Message-ID: <4B94B39A.4010707@sissa.it>


>  Dear sir,
>  
> How to get the electrical potential of each atom for the VBM 
> correction of defect study?
"VBM" what is it?
It is hardly to understand the definition "electrical potential of each 
atom", do you mean "local ionic potential" ?
If yes, you can put "plot_num = 2" in input file of pp.x.

Linh.

-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From hande at newton.physics.metu.edu.tr  Mon Mar  8 09:42:14 2010
From: hande at newton.physics.metu.edu.tr (Hande Ustunel)
Date: Mon, 8 Mar 2010 10:42:14 +0200 (EET)
Subject: [Pw_forum] On the use of Quantum Espresso on GPUs
Message-ID: <Pine.LNX.4.44.1003081033340.10904-100000@newton.physics.metu.edu.tr>

Dear Quantum-Espresso community,

Following the acquisition of a couple of GPU servers by our national
computer cluster, I decided to try and see if I can compile QE on
them. Through some web searching I found some promising mention of current
progress on the porting of QE to GPUs. I was wondering if I could get from
any of you perhaps a more up-to-date idea of the current status, if it's
not too much trouble.

Thank you very much in advance.
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 jcwu.suda at hotmail.com  Mon Mar  8 10:30:31 2010
From: jcwu.suda at hotmail.com (wujianchun)
Date: Mon, 8 Mar 2010 17:30:31 +0800
Subject: [Pw_forum] How to get the electrical potential of each atom
In-Reply-To: <4B94B39A.4010707@sissa.it>
References: <SNT137-w341CA7A1ACE1701766B4CEE9350@phx.gbl>,
	<4B94B39A.4010707@sissa.it>
Message-ID: <SNT137-w50CECEF8F0F6C85B873713E9350@phx.gbl>


Dear Linh,

Thank you very much. 

 

VBM means " valence band maximum". defect study needs to align the VBM between the perfect supercell and defect supercell.

 

if I put "plot_num =2", How to put the value of iflag to get the local ionic potential of each atom? 

There is no iflag value to specify the position of 0-dimension.

 

iflag=

0 1D plot of the spherical average
1 1D plot
2 2D plot
3 3D plot
4 2D polar plot on a sphere

Many thanks

 

Regards

Jianchun  

 

 

 
> Date: Mon, 8 Mar 2010 09:21:46 +0100
> From: nnlinh at sissa.it
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] How to get the electrical potential of each atom
> 
> 
> > Dear sir,
> > 
> > How to get the electrical potential of each atom for the VBM 
> > correction of defect study?
> "VBM" what is it?
> It is hardly to understand the definition "electrical potential of each 
> atom", do you mean "local ionic potential" ?
> If yes, you can put "plot_num = 2" in input file of pp.x.
> 
> Linh.
> 
> -----------------------------------------------------
> Nguyen Ngoc Linh, PhD Student
> c/o: SISSA & CNR-INFM Democritos,
> via Beirut 2-4, 34014 Trieste (Italy)
> email: nnlinh at sissa.it
> phone: +39 04 03787 319
> skype: ngoclinh84phys
> -----------------------------------------------------
> "The physics is theoretical but the fun is real"
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
_________________________________________________________________
MSN????????????????25???????????2010?????????
http://kaba.msn.com.cn/?k=1
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From baris.malcioglu at gmail.com  Mon Mar  8 11:01:47 2010
From: baris.malcioglu at gmail.com (O. Baris Malcioglu)
Date: Mon, 8 Mar 2010 11:01:47 +0100
Subject: [Pw_forum] On the use of Quantum Espresso on GPUs
In-Reply-To: <Pine.LNX.4.44.1003081033340.10904-100000@newton.physics.metu.edu.tr>
References: <Pine.LNX.4.44.1003081033340.10904-100000@newton.physics.metu.edu.tr>
Message-ID: <ab42ba5f1003080201t3650dd3cw2cea5b1d40a89cba@mail.gmail.com>

Dear Hande,

Although not specifically related to QE you may find the following
information useful.

I have recently attended to a workshop in high performance computing,
and a series of lectures/hands-on sessions co-organized by NVIDIA.

The good news is that CUDA (the NVIDIA accelarated GPU computing
"platform" (i.e. modified compilers etc.) ) now has a LAPACK/BLAS
implementation that can be used "out of the box" (like intel MKL, no
modification to QE mandatory in principle, just download and link like
usual) but the bad news is that current blend of GPUs are not so
fantastic when performing general operations and/or when double
precision is required.

My -personal- opinion and -very limited- experience on the matter is
that I do not find the prospect particularly promising at the moment,
at least until the new GPU "fermi" and attached "general computing
platform revision of CUDA" is released. My -personal- reasoning goes
like this:

-There is a huge bottleneck when moving data through the pci-x bridge
between the card memory and the system memory, especially in
run-of-the-mill servers , and unless you do low level tricks in your
code to optimize these copies, the code runs slower not faster when
GPU is involved. Sadly, CUDA do not provide all these low level
optimizations in the wrappers they have for Fortran, and it seems not
a straightforward problem to implement C wrappers that will do this
optimization in QE.

-The NVIDIA linux drivers are not open-source and taint the kernel.
Their insist on not making their driver open-source like the others
has some nasty consequences in performance in some HPC environments.
You can browse HPC forums for details.

-The GPU is stupidly fast for some select float operations (as the
brain does not require that much precison when interpretting scenes in
a screen) but not-so-fast for precision operations involving double.
Most, if not all, of the variables in QE are double precison.

-Same thing, GPU is stupidly fast for things like multiplication and
addition, but not-so-fast for divison. Also one must use higly GPU
specific tricks like "fused multiply add" to get to the posterity
results they are showing around.

-Since the 3rd party companies do nasty things like overclocking etc.
to the GPU cards they supply, in the same sense that the precision is
not mandatory for visual applications, the platform is highly volatile
for scientific applications. Personally I wouldn't trust the outcome
of a run unless proven otherwise for a specific machine (should be
tested very well).


I will start modfying my code if I have access to a Fermi GPU just to
give it a try, but otherwise I prefer to spend my time on more
pressing topics.

Best,
Baris


2010/3/8 Hande Ustunel <hande at newton.physics.metu.edu.tr>:
> Dear Quantum-Espresso community,
>
> Following the acquisition of a couple of GPU servers by our national
> computer cluster, I decided to try and see if I can compile QE on
> them. Through some web searching I found some promising mention of current
> progress on the porting of QE to GPUs. I was wondering if I could get from
> any of you perhaps a more up-to-date idea of the current status, if it's
> not too much trouble.
>
> Thank you very much in advance.
> 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
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From nnlinh at sissa.it  Mon Mar  8 11:31:56 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Mon, 08 Mar 2010 11:31:56 +0100
Subject: [Pw_forum] How to get the electrical potential of each atom
In-Reply-To: <SNT137-w50CECEF8F0F6C85B873713E9350@phx.gbl>
References: <SNT137-w341CA7A1ACE1701766B4CEE9350@phx.gbl>,
	<4B94B39A.4010707@sissa.it>
	<SNT137-w50CECEF8F0F6C85B873713E9350@phx.gbl>
Message-ID: <4B94D21C.4010100@sissa.it>

wujianchun wrote:
> Dear Linh,
> Thank you very much.
>
> VBM means " valence band maximum". defect study needs to align the VBM 
> between the perfect supercell and defect supercell.
Interesting, thank for explain. Maybe when you draw the local ionic 
potential belong to Oz, you can see a change of the potential curve at 
the defect plane.
> if I put "plot_num =2", How to put the value of /iflag to get the 
> /local ionic potential/ /of each atom/? /
> /There is no iflag value to specify the position of 0-dimension./
> //
You put iflag=3, output_format=3
Then you need run average.x to average from 3D to 1D presentations. The 
input file for average.x run can be referred in PP/average.f90 file.
Anyway, you can refer similarly the input files and the calculation of 
Work-function example, but plot_num =2

Good luck,
Linh



> iflag=
> 0 1D plot of the spherical average
> 1 1D plot
> 2 2D plot
> 3 3D plot
> 4 2D polar plot on a sphere
>
> Many thanks
>
> Regards
> Jianchun
>
>
>
> > Date: Mon, 8 Mar 2010 09:21:46 +0100
> > From: nnlinh at sissa.it
> > To: pw_forum at pwscf.org
> > Subject: Re: [Pw_forum] How to get the electrical potential of each atom
> >
> >
> > > Dear sir,
> > >
> > > How to get the electrical potential of each atom for the VBM
> > > correction of defect study?
> > "VBM" what is it?
> > It is hardly to understand the definition "electrical potential of each
> > atom", do you mean "local ionic potential" ?
> > If yes, you can put "plot_num = 2" in input file of pp.x.
> >
> > Linh.
> >
> > -----------------------------------------------------
> > Nguyen Ngoc Linh, PhD Student
> > c/o: SISSA & CNR-INFM Democritos,
> > via Beirut 2-4, 34014 Trieste (Italy)
> > email: nnlinh at sissa.it
> > phone: +39 04 03787 319
> > skype: ngoclinh84phys
> > -----------------------------------------------------
> > "The physics is theoretical but the fun is real"
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
> ------------------------------------------------------------------------
> ????? Windows Live Messenger ???????! ????! 
> <http://www.windowslive.cn/messenger/>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From marsamos at democritos.it  Mon Mar  8 12:24:02 2010
From: marsamos at democritos.it (marsamos at democritos.it)
Date: Mon, 08 Mar 2010 12:24:02 +0100
Subject: [Pw_forum] defect state
In-Reply-To: <2066059121.57150.1267456670688.JavaMail.root@mta.iut.ac.ir>
References: <2066059121.57150.1267456670688.JavaMail.root@mta.iut.ac.ir>
Message-ID: <20100308122402.f9cpxv9r4g8ssskg@mail.democritos.it>

Dear Ali, take a look to


Martin-Samos, L; Roma, G; Rinke, P, et al.
Source: PHYSICAL REVIEW LETTERS   Volume: 104   Issue: 7   Article 
Number: 075502   Published: 2010

and the related references

bests

Layla


Quoting kazempoor at ph.iut.ac.ir:

> Dear All
> I investigate the oxygen vacancy in TiO2.When I plot the band 
> structure I saw that new band falls very very closed to the CBM,but 
> this is not clear from Dos. On the other hand for charged oxygen 
> vacancy the defect state fall in the conduction band that is not 
> obvious   to detect.How can I find and see which one is defect 
> state?It is nessecary to mention that the states fall above the 
> conduction band might have empty occupations(for example o++ in TiO2).
> I would be most grateful if anyone tell me what is the true method  
> for observation of defect states.
> thanks  a lot
> Ali Kazempour
> Physics Department, Isfahan University of Technology
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



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

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From dimpy.sharma at tyndall.ie  Mon Mar  8 13:13:22 2010
From: dimpy.sharma at tyndall.ie (Dimpy Sharma)
Date: Mon, 8 Mar 2010 12:13:22 -0000
Subject: [Pw_forum] simulations at 100 nodes
Message-ID: <D4A761F73683694BBD69D634FF298015533D06@MAIL.tyndall.ie>


Hi everyone,
I have to run my nscf calculation at 100 nodes for just 5 k points, I have tired running at 80 nodes.but in that case it crashes without any error message.I cannot increase my k points more than 5.And I want to plot the band structure so,I need atleast 25 kpoints. Can anyone give me some advice ?

Thanks a million !

Dimpy (PhD)

UCC,Ireland
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From elie.moujaes at hotmail.co.uk  Mon Mar  8 13:56:09 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Mon, 8 Mar 2010 12:56:09 +0000
Subject: [Pw_forum] Graphene band structure
In-Reply-To: <20100306044633.12389.qmail@ms.hfcas.ac.cn>
References: <20100306044633.12389.qmail@ms.hfcas.ac.cn>
Message-ID: <SNT114-W176907FBD4E12C5CA79DB7D3350@phx.gbl>


Thanks again for your reply. I will have a look at these papers. But my case is simply monolayer graphene and there is no intercalation..Can these bands still exist?

 

 

Reagrds

 

 


 


To: pw_forum at pwscf.org
From: lfhuang at theory.issp.ac.cn
Date: Sat, 6 Mar 2010 12:46:33 +0800
Subject: Re: [Pw_forum] Graphene band structure




>three different bands that should not exist (namely the ones starting at 4.8 , 8.8 and one of the lines at 10 on the >y axis). 
Why do they should not exist? What's your computational parameters? 
Actually, these bands exist! These bands correspond to the so called "interlayer bands" in the intercalated graphite compounds (GICs) and responsible for the superconductivity phenomenom in GICs. 
Reference: G. Csanyi et al., "The role of the interlayer state in the electronic structure of superconducting graphite intercalated compounds", Nature Physics vol. 1 page 42-45 (2005). 

> I realized this when I compared that to other graphene band structure calculations. 
What's yours references for the graphene band structure? From a chinese paper in early 2009, you can verify the existence of the "interlayer bands" in the Fig. 1 therein. In addition, the reference [20] and [21] therein may be also useful for you. 
Reference: Huang Liangfeng et al.,"Lattice dynamics of hydrogen-substituted graphene systems", Acta Physica Sinica vol. 58 page s306-312 (2009). 

Best Wishes! 
Yours Sincerely 
L.F.Huang 
------ 
====================================================================== 
L.F.Huang(???) DFT and phonon physics 
====================================================================== 
Add: Research Laboratory for Computational Materials Sciences, 
Instutue of Solid State Physics,the Chinese Academy of Sciences, 
P.O.Box 1129, Hefei 230031, P.R.China 
Tel: 86-551-5591464-328(office) 
Fax: 86-551-5591434 
Web: http://theory.issp.ac.cn</A> (website of our theory group) 
http://www.issp.ac.cn</A> (website of our institute) 
====================================================================== 
 		 	   		  
_________________________________________________________________
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From mohnish.iitk at gmail.com  Mon Mar  8 13:56:12 2010
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Mon, 8 Mar 2010 18:26:12 +0530
Subject: [Pw_forum] calculation which will result in the change of the
	supercell symmetry
Message-ID: <c40d64601003080456x42f706a3mff25025f95008526@mail.gmail.com>

Dear PWSCF users,

  I am doing relaxed calculation for gold nanofilm. I am trying to get the
result of an experimental paper computationally. The calculation is for
(001) surface. The reference is
 " Phys. Rev. Lett. 82, 751?754 , Thickness Induced Structural Phase
Transition of Gold Nanofilm"But I am not getting any surface transition from
(001) to (111) . Can anybody please suggest how to do calculation which will
result in the change of the supercell symmetry. I couldnt attach the paper
because it is showing that "mail size is too large cant send the message"

Sincere thanks in advance.
MOHNISH PANDEY

My input file is

&control
    calculation = 'relax'
    prefix='gold'
    outdir='/home/rajpala/Desktop/gold_3layers'
    pseudo_dir="/home/rajpala/Desktop/gold_3layers"
 /
 &system
    ibrav= 6, a = 4.23203772,c=20,nat= 6, ntyp= 1,
    ecutwfc =
35,ecutrho=280,occupations='smearing',degauss=0.015,smearing='gaussian'
 /
 &electrons
   diagonalization='david'
   mixing_mode = 'local-TF'
   mixing_beta = 0.7
   conv_thr = 1.0d-6
 /
&IONS
  ion_dynamics='bfgs'
  trust_radius_min=1.D-6
 /
ATOMIC_SPECIES
 Au 196.9665 Au.blyp-van_ak.UPF
ATOMIC_POSITIONS (crystal)
 Au 0.0 0.0 0.0
 Au 0.5 0.5 0.0
 Au 0.5 0.0 0.105800943
 Au 0.0 0.5 0.105800943
 Au 0.0 0.0 0.211601886
 Au 0.5 0.5 0.211601886
K_POINTS (automatic)
 8 8 1 1 1 1


-- 
Mohnish Pandey
Y6927262,4th Year dual degree student,
Department of Chemical Engineering,
IIT KANPUR
09235721300
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From kazempoor at ph.iut.ac.ir  Mon Mar  8 14:03:07 2010
From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir)
Date: Mon, 8 Mar 2010 16:33:07 +0330 (IRST)
Subject: [Pw_forum] raman conversion of tensor to intensity(spectra)
Message-ID: <1738029595.85406.1268053387071.JavaMail.root@mta.iut.ac.ir>

Dear all
In example 15 ,How can I see the  raman intensity instead of their raman tensor?
I used this example with modified input file and run fist pw.x and then phcg.x and at last dynmat.x to see the raman spectra(intensity), but the code stop in the midway and I think the error is in the input file . my input file is listed in the following:
scf.in:

&control
    calculation='scf'
    restart_mode='from_scratch',
    tstress = .true.
    tprnfor = .true.
    prefix='alas',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
 /
 &system    
    nosym = .false.,
    ibrav=  2, celldm(1) =10.575, nat=  2, ntyp= 2,
    ecutwfc = 10.0
 /
 &electrons
    conv_thr =  1.0d-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Al  26.98  Al.vbc.UPF
 As  74.92  As.gon.UPF
ATOMIC_POSITIONS
 Al 0.00 0.00 0.00
 As 0.25 0.25 0.25
K_POINTS {automatic}
 2 2 2  0 0 0

phcg.in :
phonons of AlAs at Gamma
 &inputph
  tr2_ph=1.0d-12,
  prefix='alas',
  epsil=.true.,
  trans=.true.,
  lraman=.true.,
  amass(1)=69.72,
  amass(2)=26.98,
  outdir='$TMP_DIR/',
  fildyn='alas.dynG',
 /
0.0 0.0 0.0
  and dynmat.in:

 &input fildyn='alas.dynG',    /


I would appreciate if anyone tell me about the mistake that I have done in inut file.
thanks a lot

Ali Kazempour
Physics Department, Isfahn University of Technology

From nnlinh at sissa.it  Mon Mar  8 14:23:05 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Mon, 08 Mar 2010 14:23:05 +0100
Subject: [Pw_forum] calculation which will result in the change of the
 supercell symmetry
In-Reply-To: <c40d64601003080456x42f706a3mff25025f95008526@mail.gmail.com>
References: <c40d64601003080456x42f706a3mff25025f95008526@mail.gmail.com>
Message-ID: <4B94FA39.6070209@sissa.it>

mohnish pandey wrote:
> Dear PWSCF users,
> I am doing relaxed calculation for gold nanofilm. I am trying to get 
> the result of an experimental paper computationally. The calculation 
> is for (001) surface. The reference is
>
>
>     " Phys. Rev. Lett. 82, 751?754 , Thickness Induced Structural
>     Phase Transition of Gold Nanofilm"
>
> But I am not getting any surface transition from (001) to (111) .
You can not, for sure, obtain a phase transition from the surface (001) 
to (111) just by relaxing (001) surface. Because the relax calculation 
results the optimal geometry at certain conditions.

However, you can do something in similar to experiment by considering 
the different structural phases that corresponding to different 
thickness gold nanofilms, in your case. With these structural phases, 
you can relax models to obtain the optimal geometry under certain 
conditions, and then you can have a full picture of phase diagram at 
different conditions.

General ideals can be referred in some papers relating to pressure 
induced phase transition of Prof. Scandolo, ICTP.

http://users.ictp.it/~scandolo/publications.htm

Good luck

Linh

-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From jcwu.suda at hotmail.com  Mon Mar  8 15:05:34 2010
From: jcwu.suda at hotmail.com (wujianchun)
Date: Mon, 8 Mar 2010 22:05:34 +0800
Subject: [Pw_forum] How to get the electrical potential of each atom
In-Reply-To: <4B94D21C.4010100@sissa.it>
References: <SNT137-w341CA7A1ACE1701766B4CEE9350@phx.gbl>, ,
	<4B94B39A.4010707@sissa.it>,
	<SNT137-w50CECEF8F0F6C85B873713E9350@phx.gbl>,
	<4B94D21C.4010100@sissa.it>
Message-ID: <SNT137-w33AEB92A8A107848C5FACBE9350@phx.gbl>



 Dear Linh,

Thank you very much.

I'll try it!

regards

Jianchun

 
> Date: Mon, 8 Mar 2010 11:31:56 +0100
> From: nnlinh at sissa.it
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] How to get the electrical potential of each atom
> 
> wujianchun wrote:
> > Dear Linh,
> > Thank you very much.
> >
> > VBM means " valence band maximum". defect study needs to align the VBM 
> > between the perfect supercell and defect supercell.
> Interesting, thank for explain. Maybe when you draw the local ionic 
> potential belong to Oz, you can see a change of the potential curve at 
> the defect plane.
> > if I put "plot_num =2", How to put the value of /iflag to get the 
> > /local ionic potential/ /of each atom/? /
> > /There is no iflag value to specify the position of 0-dimension./
> > //
> You put iflag=3, output_format=3
> Then you need run average.x to average from 3D to 1D presentations. The 
> input file for average.x run can be referred in PP/average.f90 file.
> Anyway, you can refer similarly the input files and the calculation of 
> Work-function example, but plot_num =2
> 
> Good luck,
> Linh
> 
> 
> 
> > iflag=
> > 0 1D plot of the spherical average
> > 1 1D plot
> > 2 2D plot
> > 3 3D plot
> > 4 2D polar plot on a sphere
> >
> > Many thanks
> >
> > Regards
> > Jianchun
> >
> >
> >
> > > Date: Mon, 8 Mar 2010 09:21:46 +0100
> > > From: nnlinh at sissa.it
> > > To: pw_forum at pwscf.org
> > > Subject: Re: [Pw_forum] How to get the electrical potential of each atom
> > >
> > >
> > > > Dear sir,
> > > >
> > > > How to get the electrical potential of each atom for the VBM
> > > > correction of defect study?
> > > "VBM" what is it?
> > > It is hardly to understand the definition "electrical potential of each
> > > atom", do you mean "local ionic potential" ?
> > > If yes, you can put "plot_num = 2" in input file of pp.x.
> > >
> > > Linh.
> > >
> > > -----------------------------------------------------
> > > Nguyen Ngoc Linh, PhD Student
> > > c/o: SISSA & CNR-INFM Democritos,
> > > via Beirut 2-4, 34014 Trieste (Italy)
> > > email: nnlinh at sissa.it
> > > phone: +39 04 03787 319
> > > skype: ngoclinh84phys
> > > -----------------------------------------------------
> > > "The physics is theoretical but the fun is real"
> > >
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> > ------------------------------------------------------------------------
> > ????? Windows Live Messenger ???????! ????! 
> > <http://www.windowslive.cn/messenger/>
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> > 
> 
> 
> -- 
> -----------------------------------------------------
> Nguyen Ngoc Linh, PhD Student
> c/o: SISSA & CNR-INFM Democritos,
> via Beirut 2-4, 34014 Trieste (Italy)
> email: nnlinh at sissa.it
> phone: +39 04 03787 319
> skype: ngoclinh84phys
> -----------------------------------------------------
> "The physics is theoretical but the fun is real"
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
_________________________________________________________________
?????????Windows Live?????????
http://windowslivesky.spaces.live.com/blog/cns!5892B6048E2498BD!889.entry
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From stewart at cnf.cornell.edu  Mon Mar  8 15:29:42 2010
From: stewart at cnf.cornell.edu (Derek Stewart)
Date: Mon, 08 Mar 2010 09:29:42 -0500
Subject: [Pw_forum] Graphene band structure
In-Reply-To: <SNT114-W176907FBD4E12C5CA79DB7D3350@phx.gbl>
References: <20100306044633.12389.qmail@ms.hfcas.ac.cn>
	<SNT114-W176907FBD4E12C5CA79DB7D3350@phx.gbl>
Message-ID: <4B9509D6.1060302@cnf.cornell.edu>

Dear Elie,

Even with a single layer of graphene, you can get an high energy
"interlayer" band. This has been seen recently in near-edge x-ray
absorption experiments on graphene. See the following paper for details:

"Near-Edge X-Ray Absorption Fine-Structure Investigation of Graphene",
D. Pacile et al., Phys. Rev. Lett, 101, 066806 (2008)
http://dx.doi.org/10.1103/PhysRevLett.101.066806

Best regards,

Derek

################################
Derek Stewart, Ph. D.
Senior Research Associate
** New Webpage **
http://sites.google.com/site/dft4nano/
250 Duffield Hall
Cornell Nanoscale Facility (CNF)
Ithaca, NY 14853
stewart (at) cnf.cornell.edu
(607) 255-2856




Elie Moujaes wrote:
> Thanks again for your reply. I will have a look at these papers. But
> my case is simply monolayer graphene and there is no
> intercalation..Can these bands still exist?
>
>
> Reagrds
>
>
>
>
> ------------------------------------------------------------------------
> To: pw_forum at pwscf.org
> From: lfhuang at theory.issp.ac.cn
> Date: Sat, 6 Mar 2010 12:46:33 +0800
> Subject: Re: [Pw_forum] Graphene band structure
>
> >three different bands that should not exist (namely the ones starting
> at 4.8 , 8.8 and one of the lines at 10 on the >y axis).
> Why do they should not exist? What's your computational parameters?
> Actually, these bands exist! These bands correspond to the so called
> "interlayer bands" in the intercalated graphite compounds (GICs) and
> responsible for the superconductivity phenomenom in GICs.
> Reference: G. Csanyi et al., "The role of the interlayer state in the
> electronic structure of superconducting graphite intercalated
> compounds", Nature Physics vol. 1 page 42-45 (2005).
>
> > I realized this when I compared that to other graphene band
> structure calculations.
> What's yours references for the graphene band structure? From a
> chinese paper in early 2009, you can verify the existence of the
> "interlayer bands" in the Fig. 1 therein. In addition, the reference
> [20] and [21] therein may be also useful for you.
> Reference: Huang Liangfeng et al.,"Lattice dynamics of
> hydrogen-substituted graphene systems", Acta Physica Sinica vol. 58
> page s306-312 (2009).
>
> Best Wishes!
> Yours Sincerely
> L.F.Huang
> ------
> ======================================================================
> L.F.Huang(???) DFT and phonon physics
> ======================================================================
> Add: Research Laboratory for Computational Materials Sciences,
> Instutue of Solid State Physics,the Chinese Academy of Sciences,
> P.O.Box 1129, Hefei 230031, P.R.China
> Tel: 86-551-5591464-328(office)
> Fax: 86-551-5591434
> Web: http://theory.issp.ac.cn</A <http://theory.issp.ac.cn/>> (website
> of our theory group)
> <http://theory.issp.ac.cn/>http://www.issp.ac.cn</A
> <http://www.issp.ac.cn/>> (website of our institute)
> ======================================================================
> <http://www.issp.ac.cn/>
>
> ------------------------------------------------------------------------
> Not got a Hotmail account? Sign-up now - Free
> <http://clk.atdmt.com/UKM/go/197222280/direct/01/>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   



From elie.moujaes at hotmail.co.uk  Mon Mar  8 15:31:28 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Mon, 8 Mar 2010 14:31:28 +0000
Subject: [Pw_forum] DOS for graphene using plot_num=3
Message-ID: <SNT114-W297776CE3A0A09EB80D243D3350@phx.gbl>


I am trying to plot the DOS of graphene versus E-EF but I could not find what the required inout is in the DOC file INPUT_PP in espresso and also if I used plot_num=3, it will give same results as plot_num=0 (for the charge). Is there a special inpout for plot_num=3 and if yes where can I find it?

 

 

Regards

 

 
 		 	   		  
_________________________________________________________________
Got a cool Hotmail story? Tell us now
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From elie.moujaes at hotmail.co.uk  Mon Mar  8 15:48:23 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Mon, 8 Mar 2010 14:48:23 +0000
Subject: [Pw_forum] Graphene band structure
In-Reply-To: <4B9509D6.1060302@cnf.cornell.edu>
References: <20100306044633.12389.qmail@ms.hfcas.ac.cn>,
	<SNT114-W176907FBD4E12C5CA79DB7D3350@phx.gbl>,
	<4B9509D6.1060302@cnf.cornell.edu>
Message-ID: <SNT114-W299E1E27429C6FF33411A7D3350@phx.gbl>


Thanks very much for the information. I will be checking the paper.

 

Regards
 
> Date: Mon, 8 Mar 2010 09:29:42 -0500
> From: stewart at cnf.cornell.edu
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Graphene band structure
> 
> Dear Elie,
> 
> Even with a single layer of graphene, you can get an high energy
> "interlayer" band. This has been seen recently in near-edge x-ray
> absorption experiments on graphene. See the following paper for details:
> 
> "Near-Edge X-Ray Absorption Fine-Structure Investigation of Graphene",
> D. Pacile et al., Phys. Rev. Lett, 101, 066806 (2008)
> http://dx.doi.org/10.1103/PhysRevLett.101.066806
> 
> Best regards,
> 
> Derek
> 
> ################################
> Derek Stewart, Ph. D.
> Senior Research Associate
> ** New Webpage **
> http://sites.google.com/site/dft4nano/
> 250 Duffield Hall
> Cornell Nanoscale Facility (CNF)
> Ithaca, NY 14853
> stewart (at) cnf.cornell.edu
> (607) 255-2856
> 
> 
> 
> 
> Elie Moujaes wrote:
> > Thanks again for your reply. I will have a look at these papers. But
> > my case is simply monolayer graphene and there is no
> > intercalation..Can these bands still exist?
> >
> >
> > Reagrds
> >
> >
> >
> >
> > ------------------------------------------------------------------------
> > To: pw_forum at pwscf.org
> > From: lfhuang at theory.issp.ac.cn
> > Date: Sat, 6 Mar 2010 12:46:33 +0800
> > Subject: Re: [Pw_forum] Graphene band structure
> >
> > >three different bands that should not exist (namely the ones starting
> > at 4.8 , 8.8 and one of the lines at 10 on the >y axis).
> > Why do they should not exist? What's your computational parameters?
> > Actually, these bands exist! These bands correspond to the so called
> > "interlayer bands" in the intercalated graphite compounds (GICs) and
> > responsible for the superconductivity phenomenom in GICs.
> > Reference: G. Csanyi et al., "The role of the interlayer state in the
> > electronic structure of superconducting graphite intercalated
> > compounds", Nature Physics vol. 1 page 42-45 (2005).
> >
> > > I realized this when I compared that to other graphene band
> > structure calculations.
> > What's yours references for the graphene band structure? From a
> > chinese paper in early 2009, you can verify the existence of the
> > "interlayer bands" in the Fig. 1 therein. In addition, the reference
> > [20] and [21] therein may be also useful for you.
> > Reference: Huang Liangfeng et al.,"Lattice dynamics of
> > hydrogen-substituted graphene systems", Acta Physica Sinica vol. 58
> > page s306-312 (2009).
> >
> > Best Wishes!
> > Yours Sincerely
> > L.F.Huang
> > ------
> > ======================================================================
> > L.F.Huang(???) DFT and phonon physics
> > ======================================================================
> > Add: Research Laboratory for Computational Materials Sciences,
> > Instutue of Solid State Physics,the Chinese Academy of Sciences,
> > P.O.Box 1129, Hefei 230031, P.R.China
> > Tel: 86-551-5591464-328(office)
> > Fax: 86-551-5591434
> > Web: http://theory.issp.ac.cn</A <http://theory.issp.ac.cn/>> (website
> > of our theory group)
> > <http://theory.issp.ac.cn/>http://www.issp.ac.cn</A
> > <http://www.issp.ac.cn/>> (website of our institute)
> > ======================================================================
> > <http://www.issp.ac.cn/>
> >
> > ------------------------------------------------------------------------
> > Not got a Hotmail account? Sign-up now - Free
> > <http://clk.atdmt.com/UKM/go/197222280/direct/01/>
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> > 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
_________________________________________________________________
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From nnlinh at sissa.it  Mon Mar  8 16:15:31 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Mon, 08 Mar 2010 16:15:31 +0100
Subject: [Pw_forum] DOS for graphene using plot_num=3
In-Reply-To: <SNT114-W297776CE3A0A09EB80D243D3350@phx.gbl>
References: <SNT114-W297776CE3A0A09EB80D243D3350@phx.gbl>
Message-ID: <4B951493.1050208@sissa.it>

Elie Moujaes wrote:
> I am trying to plot the DOS of graphene versus E-EF but I could not 
> find what the required inout is in the DOC file INPUT_PP in espresso 
> and also if I used plot_num=3, it will give same results as plot_num=0 
> (for the charge). Is there a special inpout for plot_num=3 and if yes 
> where can I find it?
If you want to present DOS (density of states), you have to use dos.x 
instead of pp.x

The input file descriptions are presented in:
http://www.quantum-espresso.org/input-syntax/INPUT_DOS.html

Good luck

Linh

P/s  Next times, I think it is better if you enclose your informations 
in email such as: Affiliation, your full name ...ect :D
 
>  
>  
> Regards
>  
>  
>
> ------------------------------------------------------------------------
> Got a cool Hotmail story? Tell us now 
> <http://clk.atdmt.com/UKM/go/195013117/direct/01/>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From nnlinh at sissa.it  Mon Mar  8 16:24:29 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Mon, 08 Mar 2010 16:24:29 +0100
Subject: [Pw_forum] simulations at 100 nodes
In-Reply-To: <D4A761F73683694BBD69D634FF298015533D06@MAIL.tyndall.ie>
References: <D4A761F73683694BBD69D634FF298015533D06@MAIL.tyndall.ie>
Message-ID: <4B9516AD.2050404@sissa.it>

Dimpy Sharma wrote:
>
> Hi everyone,
> I have to run my nscf calculation at 100 nodes for just 5 k points, I 
> have tired running at 80 nodes.but in that case it crashes without any 
> error message.I cannot increase my k points more than 5.And I want to 
> plot the band structure so,I need atleast 25 kpoints. Can anyone give 
> me some advice ?
>
Hardly to image the problem that you got. Maybe it's resulted by your 
calculating system or maybe the input parameters result an inefficient 
memory.

It's better to enclose the input file to be easier for everyone to consider.

Best regards,

Linh


>
> Thanks a million !
>
> Dimpy (PhD)
>
> UCC,Ireland
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From ttduyle at gmail.com  Mon Mar  8 19:16:56 2010
From: ttduyle at gmail.com (Duy Le)
Date: Mon, 8 Mar 2010 13:16:56 -0500
Subject: [Pw_forum] simulations at 100 nodes
In-Reply-To: <4B9516AD.2050404@sissa.it>
References: <D4A761F73683694BBD69D634FF298015533D06@MAIL.tyndall.ie> 
	<4B9516AD.2050404@sissa.it>
Message-ID: <8974d3b21003081016lcbd70fkd4e715eaa43b57d6@mail.gmail.com>

You need more memory for large number of k-points.
The easiest solution: Do 5 different band structure calculations for 5
different sets of k-points.
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Mon, Mar 8, 2010 at 10:24 AM, Ngoc Linh Nguyen <nnlinh at sissa.it> wrote:
> Dimpy Sharma wrote:
>>
>> Hi everyone,
>> I have to run my nscf calculation at 100 nodes for just 5 k points, I
>> have tired running at 80 nodes.but in that case it crashes without any
>> error message.I cannot increase my k points more than 5.And I want to
>> plot the band structure so,I need atleast 25 kpoints. Can anyone give
>> me some advice ?
>>
> Hardly to image the problem that you got. Maybe it's resulted by your
> calculating system or maybe the input parameters result an inefficient
> memory.
>
> It's better to enclose the input file to be easier for everyone to consider.
>
> Best regards,
>
> Linh
>
>
>>
>> Thanks a million !
>>
>> Dimpy (PhD)
>>
>> UCC,Ireland
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
> --
> -----------------------------------------------------
> ?Nguyen Ngoc Linh, PhD Student
> ?c/o: ? SISSA & CNR-INFM Democritos,
> ? ? ? ?via Beirut 2-4, 34014 Trieste (Italy)
> ?email: nnlinh at sissa.it
> ?phone: +39 04 03787 319
> ?skype: ngoclinh84phys
> -----------------------------------------------------
> "The physics is theoretical but the fun is real"
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From elie.moujaes at hotmail.co.uk  Mon Mar  8 20:12:18 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Mon, 8 Mar 2010 19:12:18 +0000
Subject: [Pw_forum] (no subject)
Message-ID: <SNT114-W1516C7555B3FCDC962FFBDD3350@phx.gbl>


I am tryingto plot a DOS graph using gnuplot by trying to shift the Fermi energy as well which is on the x axis so in fact I wnat to draw DOS vs E-EF..I tried a command but it was not working..I am not sure if I typed it correctly. i used

Efermi=-0.9877

set yzeroaxis

plot "graph.title" u ($1+Efermi):2 wl lw 2

 

but the title of the graph included (1$+Efermi) as well which is should not be the case! I guess another $ must be included somewhere.

 

Thanks

 

Elie Moujaes

University of Nottingham

University Park

NG7 2RD

UK
 		 	   		  
_________________________________________________________________
Send us your Hotmail stories and be featured in our newsletter
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From elie.moujaes at hotmail.co.uk  Mon Mar  8 20:12:43 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Mon, 8 Mar 2010 19:12:43 +0000
Subject: [Pw_forum] Shifting x axis using gnuplot
Message-ID: <SNT114-W440E818D9137A2BC44264CD3350@phx.gbl>


I am tryingto plot a DOS graph using gnuplot by trying to shift the Fermi energy as well which is on the x axis so in fact I wnat to draw DOS vs E-EF..I tried a command but it was not working..I am not sure if I typed it correctly. i used

Efermi=-0.9877

set yzeroaxis

plot "graph.title" u ($1+Efermi):2 wl lw 2

 

but the title of the graph included (1$+Efermi) as well which is should not be the case! I guess another $ must be included somewhere.

 

Thanks

 

Elie Moujaes

University of Nottingham

University Park

NG7 2RD

UK
 		 	   		  
_________________________________________________________________
Send us your Hotmail stories and be featured in our newsletter
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From paulatto at sissa.it  Mon Mar  8 20:49:11 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Mon, 08 Mar 2010 20:49:11 +0100
Subject: [Pw_forum] Shifting x axis using gnuplot
In-Reply-To: <SNT114-W440E818D9137A2BC44264CD3350@phx.gbl>
References: <SNT114-W440E818D9137A2BC44264CD3350@phx.gbl>
Message-ID: <op.u89lb9pka8x26q@paulax>

Replying to message "[Pw_forum] Shifting x axis using gnuplot" from Elie  
Moujaes (08/03/10):
> but the title of the graph included (1$+Efermi) as well which is should  
> not be the case! I guess another $ must be included somewhere.

Dear Elie,
with gnuplot you can freely change the title of a plot according to your  
needs. Please refer to the gnuplot documentation:  
<http://www.gnuplot.info/docs/gnuplot.html>, the gnuplot internal  
documentation system (e.g. type "help") and the never over-praised gnuplot  
tips: <http://t16web.lanl.gov/Kawano/gnuplot/index-e.html>.

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

     *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

From amezagahv at gmail.com  Mon Mar  8 22:59:10 2010
From: amezagahv at gmail.com (Alexis Amezaga)
Date: Mon, 8 Mar 2010 18:59:10 -0300
Subject: [Pw_forum] How to generate a new PP with fractional charge?
Message-ID: <b905bdf91003081359k169859ddhbd91da9ed019135b@mail.gmail.com>

Dear users,

Someone can suggest me how can I generate a PseudoPotential with fractional
charge?

Greetings,

Alexis Am?zaga
GNM, Physics Department
University of Chile
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From paulatto at sissa.it  Tue Mar  9 00:30:40 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 09 Mar 2010 00:30:40 +0100
Subject: [Pw_forum] How to generate a new PP with fractional charge?
In-Reply-To: <b905bdf91003081359k169859ddhbd91da9ed019135b@mail.gmail.com>
References: <b905bdf91003081359k169859ddhbd91da9ed019135b@mail.gmail.com>
Message-ID: <op.u89vlevfa8x26q@paulax>

Replying to message "[Pw_forum] How to generate a new PP with fractional  
charge?" from Alexis Amezaga (08/03/10):
> Someone can suggest me how can I generate a PseudoPotential with  
> fractional
> charge?

In the input file for ld1.x you can specify fractional occupations for the  
orbitals (you have to do it for the all-electron configuration, the pseudo  
configuration will follow).

regards


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

     *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

From lfhuang at theory.issp.ac.cn  Tue Mar  9 02:24:09 2010
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Tue, 09 Mar 2010 9:24:09 +0800
Subject: [Pw_forum] =?utf-8?q?Graphene_band_structure?=
Message-ID: <20100309012409.32323.qmail@ms.hfcas.ac.cn>

>  But my case is simply monolayer graphene and there is no intercalation..Can these bands still exist?
Yes. 

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


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From rui_zhi_zhang at yahoo.com  Tue Mar  9 08:41:44 2010
From: rui_zhi_zhang at yahoo.com (ruizhi zhang)
Date: Mon, 8 Mar 2010 23:41:44 -0800 (PST)
Subject: [Pw_forum] How to output the symmetry operation matrix?
Message-ID: <686474.21881.qm@web38902.mail.mud.yahoo.com>

Dear all,
?
I want to output the symmetry operation matrix from PW,?could any one give some hint?
?
I want to obtain ALL k-points in the whole Brillouin zone from the k-points in the irreducable Brillouin zone, as given in *.scf.out file. So the symmetry operation matrix are needed. In the *.out file, only the number of sysmmetry operation is?given. Could any one?tell me in which file the matrix can be output??
?
I read the source file of allsysm.f90 and some others, but haven't find any useful information.
?
Thanks in advance!
?
Ruizhi?

--------------
Ruizhi Zhang, PhD
Graduate School of Engeering, Nagoya University, Nagoya, Japan
School of Physics, Shandong University, Jinan, P.R.C.


      
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From sclauzer at sissa.it  Tue Mar  9 09:06:25 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 09 Mar 2010 09:06:25 +0100
Subject: [Pw_forum] How to output the symmetry operation matrix?
In-Reply-To: <686474.21881.qm@web38902.mail.mud.yahoo.com>
References: <686474.21881.qm@web38902.mail.mud.yahoo.com>
Message-ID: <4B960181.6070802@sissa.it>

ruizhi zhang wrote:
> Dear all,
>  
> I want to output the symmetry operation matrix from PW, could any one 
> give some hint?

verbosity='high'

>  
> I want to obtain ALL k-points in the whole Brillouin zone from the 
> k-points in the irreducable Brillouin zone, as given in *.scf.out file. 
> So the symmetry operation matrix are needed. In the *.out file, only the 
> number of sysmmetry operation is given. Could any one tell me in which 
> file the matrix can be output? 

the matrices will be printed on the standard output after the number of symmetry operations

>  
> I read the source file of allsysm.f90 and some others, but haven't find 
> any useful information.
>  
> Thanks in advance!

You're welcome,


GS

>  
> Ruizhi 
> 
> --------------
> Ruizhi Zhang, PhD
> Graduate School of Engeering, Nagoya University, Nagoya, Japan
> School of Physics, Shandong University, Jinan, P.R.C.
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 


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

From pholvey at gmail.com  Tue Mar  9 09:30:04 2010
From: pholvey at gmail.com (Patrick Holvey)
Date: Tue, 9 Mar 2010 03:30:04 -0500
Subject: [Pw_forum] From davcio: error #10
In-Reply-To: <4011cd661003071817x6f38073bvbeea76674f1935d8@mail.gmail.com>
References: <4011cd661002152139x43e1866jc222667bb64b742b@mail.gmail.com>
	<4B7D769B.70300@sissa.it>
	<4011cd661002191651m396ac30m3e06e835a8476297@mail.gmail.com>
	<4B7FEB5F.1070608@sissa.it>
	<4011cd661003062328k535ec9b4xe8ffaa8d7238b516@mail.gmail.com>
	<B52F2E4A-A9DD-43F7-960E-C7EE0A4E2D7C@democritos.it>
	<4011cd661003071329t2fd93dd2r550af0c2bda2a44a@mail.gmail.com>
	<4011cd661003071612v4f5aa3d2s3f1ba0b22c8b1903@mail.gmail.com>
	<alpine.DEB.1.10.1003072104130.24914@dr-wily.mit.edu>
	<4011cd661003071817x6f38073bvbeea76674f1935d8@mail.gmail.com>
Message-ID: <4011cd661003090030s76fc0457u21503f68e6dc0e2f@mail.gmail.com>

Good evening everyone!

Alright, so after implementing the changes in regards to the separate outdir
for each run, I'm having better success running the jobs, usually having
approx. 50% of the runs go to completion.  However, that means that 50% of
them fail and I have to resubmit them to the queue.  I have not yet seen if
they'll run to completion as they're still on the queue, but if I've
addressed the ourdir business, can anyone think of any other reason why my
jobs would be failing in this manner?

Thanks!

Patrick
University of Notre Dame

On Sun, Mar 7, 2010 at 9:17 PM, Patrick Holvey <pholvey at gmail.com> wrote:

> Dear Davide,
>
> Awesome.  After this recent spat with my submissions and in light of your
> advice, I'll only start runs with independent outdirs.  Thank you for your
> advice.  I truly appreciate it.
>
> Patrick
>
> On Sun, Mar 7, 2010 at 9:09 PM, Davide Ceresoli <ceresoli at mit.edu> wrote:
>
>> On Sun, 7 Mar 2010, Patrick Holvey wrote:
>>
>>  The outdir is the same for every
>>> input file, so I suppose it could be just too busy with the calls from
>>> all of the different
>>> runs.  Has anyone else had issues with this?  Moreover, is there a limit
>>> to how many runs I
>>> should direct to a specific outdir?  Would it be better to assign a
>>> unique outdir for each
>>> run?  Thanks!  I appreciate all of the help.
>>>
>> Dear Patrick,
>>    I think that a shared outdir for every job, is the mother of
>> all evil. If you run several jobs simultaneusly, try to assign
>> a different outdir.
>>
>> HTH
>>
>> Davide
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> Patrick Holvey
> pholvey at nd.edu
> 442 Siegfried Hall
> Notre Dame, IN 46556
> Cell: (865)-659-9908
>



-- 
Patrick Holvey
pholvey at nd.edu
442 Siegfried Hall
Notre Dame, IN 46556
Cell: (865)-659-9908
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From giannozz at democritos.it  Tue Mar  9 11:31:28 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 09 Mar 2010 11:31:28 +0100
Subject: [Pw_forum] simulations at 100 nodes
In-Reply-To: <8974d3b21003081016lcbd70fkd4e715eaa43b57d6@mail.gmail.com>
References: <D4A761F73683694BBD69D634FF298015533D06@MAIL.tyndall.ie>
	<4B9516AD.2050404@sissa.it>
	<8974d3b21003081016lcbd70fkd4e715eaa43b57d6@mail.gmail.com>
Message-ID: <4B962380.30002@democritos.it>

Duy Le wrote:

> You need more memory for large number of k-points.

not exactly. If you store wavefunctions in memory (disk_io='low')
you need an array (number of k-points)*(size of wavefunctions).
Otherwise, the number of k-points affects only marginally the
amount of needed memory

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



From giannozz at democritos.it  Tue Mar  9 11:48:00 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 09 Mar 2010 11:48:00 +0100
Subject: [Pw_forum] How to output the symmetry operation matrix?
In-Reply-To: <686474.21881.qm@web38902.mail.mud.yahoo.com>
References: <686474.21881.qm@web38902.mail.mud.yahoo.com>
Message-ID: <4B962760.6060606@democritos.it>

ruizhi zhang wrote:

> I want to obtain ALL k-points in the whole Brillouin zone from the 
> k-points in the irreducable Brillouin zone, as given in *.scf.out file

if you just need all k-vectors in the Brillouin Zone, you can use
auxiliary code kpoints.x; or just break the symmetry by e.g.
displacing one atom

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

From giannozz at democritos.it  Tue Mar  9 11:53:41 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 09 Mar 2010 11:53:41 +0100
Subject: [Pw_forum] From davcio: error #10
In-Reply-To: <4011cd661003090030s76fc0457u21503f68e6dc0e2f@mail.gmail.com>
References: <4011cd661002152139x43e1866jc222667bb64b742b@mail.gmail.com>	<4B7D769B.70300@sissa.it>	<4011cd661002191651m396ac30m3e06e835a8476297@mail.gmail.com>	<4B7FEB5F.1070608@sissa.it>	<4011cd661003062328k535ec9b4xe8ffaa8d7238b516@mail.gmail.com>	<B52F2E4A-A9DD-43F7-960E-C7EE0A4E2D7C@democritos.it>	<4011cd661003071329t2fd93dd2r550af0c2bda2a44a@mail.gmail.com>	<4011cd661003071612v4f5aa3d2s3f1ba0b22c8b1903@mail.gmail.com>	<alpine.DEB.1.10.1003072104130.24914@dr-wily.mit.edu>	<4011cd661003071817x6f38073bvbeea76674f1935d8@mail.gmail.com>
	<4011cd661003090030s76fc0457u21503f68e6dc0e2f@mail.gmail.com>
Message-ID: <4B9628B5.8060509@democritos.it>

Patrick Holvey wrote:

> However, that means that 50% of them fail [..]  can anyone think 
> of any other reason why my jobs would be failing in this manner?

which manner? with the same error in "davcio"? then the same
reasons apply

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

From yukihiro_okuno at fujifilm.co.jp  Tue Mar  9 13:22:16 2010
From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp)
Date: Tue, 9 Mar 2010 21:22:16 +0900
Subject: [Pw_forum] Error in running GWW  wrong data-file.xml file
Message-ID: <OFFDB438AB.3E31D4C9-ON492576E1.00390126-492576E1.0043F2D5@mta.fujifilm.co.jp>


Dear PWSCF users and Dr Adrian.

I also met the same error in example02 in GWW
and it comes in the head.x,  and I saw the program
of GWW a little.

In the head.f90,

call ph_writefile('init',0)

and in ph_writefile ( and function called from ph_writefile,,, )

write XML file in *.phsave/data-file.xml

which is wrong for later reading ,,

In the program, later need  the data-file.xml

call ph_readfile('data_u',ierr)  and then inside the ph_readfile,

call read_u(dirname,ierr)

and in this function ,  the program read "data-file.xml."1" file

(where "1" will be the wave number index of phonon or others, I think )

and furthermore, the information in data-file.xml

is not enough for read_u (like TENSOR.INFO,,,,,,, ).


The resent CVS GWW codes still contains the error in
GWW_examples/example02.

Are there any correct sample input file for GW calculation  for GWW program
?

Sincerely,

Yukihiro Okuno.



From uccaati at ucl.ac.uk  Tue Mar  9 14:10:17 2010
From: uccaati at ucl.ac.uk (Antonio Tilocca)
Date: Tue, 9 Mar 2010 13:10:17 +0000 (GMT)
Subject: [Pw_forum]  matvecd.f
Message-ID: <Pine.GSO.4.58.1003091259080.14146@socrates-a.ucl.ac.uk>


I am compiling QE v4.1.2 on a Cray XT4 (HECToR) using the PGI 9.0.4 compilers.

The compilation of matvecd.f fails as:

pgf77 -fast -r8 -c matvecd.f
/tmp/pgf77y2MhiirvmC4b.s: Assembler messages:
/tmp/pgf77y2MhiirvmC4b.s:43737: Error: suffix or operands invalid for `movhpd'
make[1]: *** [matvecd.o] Error 2

but it succeeds with no errors if the -fast flag is removed:
pgf77 -r8 -c matvecd.f

I just wanted to report this small glitch.

Antonio Tilocca
UCL Chemistry


From giannozz at democritos.it  Tue Mar  9 14:15:24 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 09 Mar 2010 14:15:24 +0100
Subject: [Pw_forum] matvecd.f
In-Reply-To: <Pine.GSO.4.58.1003091259080.14146@socrates-a.ucl.ac.uk>
References: <Pine.GSO.4.58.1003091259080.14146@socrates-a.ucl.ac.uk>
Message-ID: <4B9649EC.2050001@democritos.it>

Antonio Tilocca wrote:

> /tmp/pgf77y2MhiirvmC4b.s: Assembler messages:
> /tmp/pgf77y2MhiirvmC4b.s:43737: Error: suffix or operands invalid for `movhpd'

100% guaranteed compiler bug. Try to compile without "-fast".

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

From giannozz at democritos.it  Tue Mar  9 14:17:36 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 09 Mar 2010 14:17:36 +0100
Subject: [Pw_forum] matvecd.f
In-Reply-To: <Pine.GSO.4.58.1003091259080.14146@socrates-a.ucl.ac.uk>
References: <Pine.GSO.4.58.1003091259080.14146@socrates-a.ucl.ac.uk>
Message-ID: <4B964A70.3050901@democritos.it>

Antonio Tilocca wrote:

> but it succeeds with no errors if the -fast flag is removed:

oops, sorry, I answered before reading all your mail....thank
you

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

From dalcorso at sissa.it  Tue Mar  9 14:29:43 2010
From: dalcorso at sissa.it (Dal Corso Andrea)
Date: Tue, 09 Mar 2010 14:29:43 +0100
Subject: [Pw_forum] Error in running GWW  wrong data-file.xml file
In-Reply-To: <OFFDB438AB.3E31D4C9-ON492576E1.00390126-492576E1.0043F2D5@mta.fujifilm.co.jp>
References: <OFFDB438AB.3E31D4C9-ON492576E1.00390126-492576E1.0043F2D5@mta.fujifilm.co.jp>
Message-ID: <1268141383.3256.3.camel@dhcp-5-36.sissa.it>

Thank you for reporting this and for your detailed explanations. 
It is due to a recent change in the phonon code that is not compatible
with GWW. It should now be fixed in the CVS version.

Andrea


On Tue, 2010-03-09 at 21:22 +0900, yukihiro_okuno at fujifilm.co.jp wrote:
> Dear PWSCF users and Dr Adrian.
> 
> I also met the same error in example02 in GWW
> and it comes in the head.x,  and I saw the program
> of GWW a little.
> 
> In the head.f90,
> 
> call ph_writefile('init',0)
> 
> and in ph_writefile ( and function called from ph_writefile,,, )
> 
> write XML file in *.phsave/data-file.xml
> 
> which is wrong for later reading ,,
> 
> In the program, later need  the data-file.xml
> 
> call ph_readfile('data_u',ierr)  and then inside the ph_readfile,
> 
> call read_u(dirname,ierr)
> 
> and in this function ,  the program read "data-file.xml."1" file
> 
> (where "1" will be the wave number index of phonon or others, I think )
> 
> and furthermore, the information in data-file.xml
> 
> is not enough for read_u (like TENSOR.INFO,,,,,,, ).
> 
> 
> The resent CVS GWW codes still contains the error in
> GWW_examples/example02.
> 
> Are there any correct sample input file for GW calculation  for GWW program
> ?
> 
> Sincerely,
> 
> Yukihiro Okuno.
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
34151 Trieste (Italy)               e-mail: dalcorso at sissa.it



From kazempoor2000 at yahoo.com  Tue Mar  9 14:54:45 2010
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Tue, 9 Mar 2010 05:54:45 -0800 (PST)
Subject: [Pw_forum] example15
Message-ID: <339643.42237.qm@web113617.mail.gq1.yahoo.com>


Dear All
?
?To see Raman intensity I used example 15 that gives Raman tensor . Then I run dynmat.x to get? Raman intensity. Is it true? But the plot of raman intensity is not continous. Should I use any fit to get the continous plot or should I use supercell calculation?
?
What can I do to get pretty diagram?Could anyone give me any example?
thanks a lot
Ali Kazempour, Isfahan University of technology



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 zdw2000 at gmail.com  Tue Mar  9 15:11:33 2010
From: zdw2000 at gmail.com (Wei Zhou)
Date: Tue, 9 Mar 2010 22:11:33 +0800
Subject: [Pw_forum] the code for pwscf to castep
Message-ID: <3e36a8fc1003090611l6bd31774qbff3bb7344593765@mail.gmail.com>

hello users

-- http://www2.tcm.phy.cam.ac.uk/onetep/Main/Utilities
there are a code which can translate the castep pseudo potential to pwscf ,
however I found the effect does not good, for the same pseudo the castep and
pwscf can not give the same lattic parameters, the author also said the ussp
of castep to pwscf does not test accurately, so if somebody have interests
about it ,he can inverstigate the source code and change it to more
accurate.

ZhouDawei
JiLin Universiyt ,ChangChun ,China
zdw2000 at gmail.com
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From eyvaz_isaev at yahoo.com  Tue Mar  9 17:49:02 2010
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 9 Mar 2010 08:49:02 -0800 (PST)
Subject: [Pw_forum] Phonon plotting utility
Message-ID: <81278.79606.qm@web65708.mail.ac4.yahoo.com>

Dear developers,
Dear Quantum ESPRESSO users,

Hereby I submit a utility to plot phonon dispersion relations.
Hopefully it is user-friendly.
What you need (almost) are IFC and atomic masses. 

Bests,
Eyvaz

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


      
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From amezagahv at gmail.com  Tue Mar  9 20:36:40 2010
From: amezagahv at gmail.com (Alexis Amezaga)
Date: Tue, 9 Mar 2010 16:36:40 -0300
Subject: [Pw_forum] Pw_forum Digest, Vol 33, Issue 32
In-Reply-To: <mailman.903.1268120524.15525.pw_forum@pwscf.org>
References: <mailman.903.1268120524.15525.pw_forum@pwscf.org>
Message-ID: <b905bdf91003091136s96b6159r85be2a97dc6cd9b1@mail.gmail.com>

Hi Lorenzo, thanks for reply. Sorry I didn't was very especific in my
request before, I need generate a PP with fractional charge in the core, is
it possible with esspreso or the only way is by combining two PP, using
virtual.x?


> >Someone can suggest me how can I generate a PseudoPotential with
> fractional
> >charge?
>

In the input file for ld1.x you can specify fractional occupations for the
> orbitals (you have to do it for the all-electron configuration, the pseudo
> configuration will follow).
>
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From elie.moujaes at hotmail.co.uk  Tue Mar  9 20:50:00 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Tue, 9 Mar 2010 19:50:00 +0000
Subject: [Pw_forum] calculating the cell parameters in crystals
Message-ID: <SNT114-W651CA2149834CB8BC8CAA2D3340@phx.gbl>


Is there a way (maybe a free software or program) to get celldim (i) (i=1,...6) before giving it as an input in the calculations?

 

Regards

 

Elie Moujaes

University of Nottingham

NG7 2RD

UK

 
 		 	   		  
_________________________________________________________________
Send us your Hotmail stories and be featured in our newsletter
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From elie.moujaes at hotmail.co.uk  Tue Mar  9 21:26:29 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Tue, 9 Mar 2010 20:26:29 +0000
Subject: [Pw_forum] DOS of graphene
Message-ID: <SNT114-W40AF61030478F6620CE09AD3340@phx.gbl>


Dear all,

 

I have plotted the density of states of graphene but when I looked at the graph, DOS was not zero at the fermi level (I got it to be -0.988 eV). my Programm seems pretty fine and i have checked it several times but with in vain..You will find attached the ps version and the input for the dos.x command...

 

 

Regards

 

Elie Moujaes

University of Nottingham

NG7 2RD

UK
 		 	   		  
_________________________________________________________________
Tell us your greatest, weirdest and funniest Hotmail stories
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From giovanni.cantele at na.infn.it  Tue Mar  9 21:52:59 2010
From: giovanni.cantele at na.infn.it (Giovanni Cantele)
Date: Tue, 9 Mar 2010 21:52:59 +0100 (CET)
Subject: [Pw_forum] DOS of graphene
In-Reply-To: <SNT114-W40AF61030478F6620CE09AD3340@phx.gbl>
References: <SNT114-W40AF61030478F6620CE09AD3340@phx.gbl>
Message-ID: <49491.93.147.187.115.1268167979.squirrel@imap-ac.na.infn.it>

> Dear all,
> I have plotted the density of states of graphene but when I looked at the
> graph, DOS was not zero at the fermi level (I got it to be -0.988 eV). my
> Programm seems pretty fine and i have checked it several times but with in
> vain..You will find attached the ps version and the input for the dos.x
> command...
> Regards
> Elie Moujaes
> University of Nottingham
> NG7 2RD
> UK

The problem that the Fermi level is not at the energy you expect might not
be related to a mistake. The zero energy is not well defined in a
plane-wave calculation (try to browse the forum, there should be more than
one topic about that!). One should compute the DOS, then calculate the
Fermi energy (as the energy at which the integrated DOS matches the number
of the electrons), then for the sake of clarity you can shift you DOS (or
band structure) plot so as the Fermi energy is at 0.

However, this might not be the problem in you calculation.
I'm not very sure that your calculation is right, because the shape of
your DOS plot does not look like the one of graphene. So the first problem
to solve is to understand on the top of which scf / nscf calculation you
have built your DOS plot. Unless I missed something, there are not
sufficient elements to understand what happened.

Giovanni

-- 
Giovanni Cantele, PhD
CNR-SPIN and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910 - Fax:   +39 081 676346
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
          http://www.nanomat.unina.it


From giovanni.cantele at na.infn.it  Tue Mar  9 22:11:34 2010
From: giovanni.cantele at na.infn.it (Giovanni Cantele)
Date: Tue, 9 Mar 2010 22:11:34 +0100 (CET)
Subject: [Pw_forum] calculating the cell parameters in crystals
In-Reply-To: <SNT114-W651CA2149834CB8BC8CAA2D3340@phx.gbl>
References: <SNT114-W651CA2149834CB8BC8CAA2D3340@phx.gbl>
Message-ID: <49769.93.147.187.115.1268169094.squirrel@imap-ac.na.infn.it>


> Is there a way (maybe a free software or program) to get celldim (i)
> (i=1,...6) before giving it as an input in the calculations?
> Regards
> Elie Moujaes
> University of Nottingham
> NG7 2RD
> UK

I don't know. But if you know your Bravais lattice parameters (a,b,c and
the three angles) it should be not that difficult to get the celldm's
using the definitions you find in Doc/INPUT_PW.txt
However, also consider that, unless you are using very old versions of QE,
you DO NOT need to use the celldm(1:6) array. It is a possibility, but
another one is to specify directly, a, b, c, cosAB, cosAC and cosBC (have
a look at the same file).

Giovanni

-- 
Giovanni Cantele, PhD
CNR-SPIN and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910 - Fax:   +39 081 676346
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                    http://www.nanomat.unina.it


From giannozz at democritos.it  Tue Mar  9 22:55:24 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 9 Mar 2010 22:55:24 +0100
Subject: [Pw_forum] Pw_forum Digest, Vol 33, Issue 32
In-Reply-To: <b905bdf91003091136s96b6159r85be2a97dc6cd9b1@mail.gmail.com>
References: <mailman.903.1268120524.15525.pw_forum@pwscf.org>
	<b905bdf91003091136s96b6159r85be2a97dc6cd9b1@mail.gmail.com>
Message-ID: <436ABADC-5645-4639-B41C-E3A2CF1D0AC2@democritos.it>


On Mar 9, 2010, at 20:36 , Alexis Amezaga wrote:

> I need generate a PP with fractional charge in the core, is it  
> possible with espresso

it is: just specify a fractional charge in the core states

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




From modaresi.mohsen at gmail.com  Wed Mar 10 02:18:11 2010
From: modaresi.mohsen at gmail.com (mohsen modaresi)
Date: Wed, 10 Mar 2010 04:18:11 +0300
Subject: [Pw_forum] About supercell App.
Message-ID: <a6ebdd4d1003091718w6d86cb43t79174fa6d781c761@mail.gmail.com>

Hi every body
I read all discussion about 'super cell' generation, But i can't understand.
In 2009 there is a discussion about supercell generation and any body
refferd to PHON code, But i could'nt install PHON.
Is there any why to determine the parameters?
for example could you explain this part of a SCF calculation for Pt-H2-Pt
chain.
      ibrav=8,
      celldm(1)=18.0,------>This
      celldm(2)=1.0,--------->This
      celldm(3)=2.21412992, ----->  This
      ...
ATOMIC_POSITIONS {angstrom}
Pt    0.000    0.000   0.000----->and this
Pt    0.000    0.000   2.410----->and this
Pt    0.000    0.000   4.820----->and this
Pt    0.000    0.000   7.230----->and this
H     0.000    0.000   8.900----->and this
H     0.000    0.000   9.780----->and this
Pt    0.000    0.000  11.450----->and this
Pt    0.000    0.000  13.860----->and this
Pt    0.000    0.000  16.270----->and this
Pt    0.000    0.000  18.680----->and this
suppose we want to change (Pt--->Cu) how can i get new parameters?
Thanks so much for your answers
Mohsen Modarsei
M.Sc student of solid state physics\
Ferdowsi University of Mashhad
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From mohnish.iitk at gmail.com  Wed Mar 10 06:14:22 2010
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Wed, 10 Mar 2010 10:44:22 +0530
Subject: [Pw_forum] calculating the cell parameters in crystals
In-Reply-To: <SNT114-W651CA2149834CB8BC8CAA2D3340@phx.gbl>
References: <SNT114-W651CA2149834CB8BC8CAA2D3340@phx.gbl>
Message-ID: <c40d64601003092114s6bb1d6dcnfd5f91e241c1642e@mail.gmail.com>

Dear Elie,
               I you have to give the celldm's initially. You can get the
experimental value from literatures and use that as initial value. Then you
can do "vc-relax" calculation to get equilibrium values of cell parameters
computationally. Of course it will be different from experimental value. GGA
calculation overestimates the value while LDA calculation underestimates the
lattice parameter.
Regards,
MOHNISH

On Wed, Mar 10, 2010 at 1:20 AM, Elie Moujaes <elie.moujaes at hotmail.co.uk>wrote:

>  Is there a way (maybe a free software or program) to get celldim (i)
> (i=1,...6) before giving it as an input in the calculations?
>
>
> Regards
>
> Elie Moujaes
> University of Nottingham
> NG7 2RD
> UK
>
>
> ------------------------------
> Do you have a story that started on Hotmail? Tell us now<http://clk.atdmt.com/UKM/go/195013117/direct/01/>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Mohnish Pandey
Y6927262,4th Year dual degree student,
Department of Chemical Engineering,
IIT KANPUR
09235721300
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From alexandra.carvalho at epfl.ch  Wed Mar 10 07:07:32 2010
From: alexandra.carvalho at epfl.ch (alexandra.carvalho at epfl.ch)
Date: Wed, 10 Mar 2010 07:07:32 +0100
Subject: [Pw_forum] DOS of graphene
In-Reply-To: <49491.93.147.187.115.1268167979.squirrel@imap-ac.na.infn.it>
References: <SNT114-W40AF61030478F6620CE09AD3340@phx.gbl>
	<49491.93.147.187.115.1268167979.squirrel@imap-ac.na.infn.it>
Message-ID: <20100310070732.1699634hqunlxu04@webmail.epfl.ch>

Dear Elie,

The Fermi level in graphene converges very slowly with the k-point  
sampling. Did you check the result with a very large number of k-points?

Alexandra

-----------------------------------------------------------
Alexandra Carvalho,
Ceramics Laboratory
Swiss Federal Institute of Technology of Lausanne (EPFL)


Quoting Giovanni Cantele <giovanni.cantele at na.infn.it>:

>> Dear all,
>> I have plotted the density of states of graphene but when I looked at the
>> graph, DOS was not zero at the fermi level (I got it to be -0.988 eV). my
>> Programm seems pretty fine and i have checked it several times but with in
>> vain..You will find attached the ps version and the input for the dos.x
>> command...
>> Regards
>> Elie Moujaes
>> University of Nottingham
>> NG7 2RD
>> UK
>
> The problem that the Fermi level is not at the energy you expect might not
> be related to a mistake. The zero energy is not well defined in a
> plane-wave calculation (try to browse the forum, there should be more than
> one topic about that!). One should compute the DOS, then calculate the
> Fermi energy (as the energy at which the integrated DOS matches the number
> of the electrons), then for the sake of clarity you can shift you DOS (or
> band structure) plot so as the Fermi energy is at 0.
>
> However, this might not be the problem in you calculation.
> I'm not very sure that your calculation is right, because the shape of
> your DOS plot does not look like the one of graphene. So the first problem
> to solve is to understand on the top of which scf / nscf calculation you
> have built your DOS plot. Unless I missed something, there are not
> sufficient elements to understand what happened.
>
> Giovanni
>
> --
> Giovanni Cantele, PhD
> CNR-SPIN and Dipartimento di Scienze Fisiche
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> Phone: +39 081 676910 - Fax:   +39 081 676346
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>           http://www.nanomat.unina.it
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 

Alexandra Carvalho,
Ceramics Laboratory
Swiss Federal Institute of Technology of Lausanne (EPFL)


From baris.malcioglu at gmail.com  Wed Mar 10 08:52:11 2010
From: baris.malcioglu at gmail.com (O. Baris Malcioglu)
Date: Wed, 10 Mar 2010 08:52:11 +0100
Subject: [Pw_forum] calculating the cell parameters in crystals
In-Reply-To: <c40d64601003092114s6bb1d6dcnfd5f91e241c1642e@mail.gmail.com>
References: <SNT114-W651CA2149834CB8BC8CAA2D3340@phx.gbl>
	<c40d64601003092114s6bb1d6dcnfd5f91e241c1642e@mail.gmail.com>
Message-ID: <ab42ba5f1003092352o7f907a9oc4e1fed8f0c13347@mail.gmail.com>

Dear Elie,

In case you are interested in isolated systems, not crystals, and if you are
trying to visually choose a cell that has the minimum volume with adequate
vacuum, apart from XCRYSDEN + playing with pwscf input solution you can also
use the free (but not open source) editor  DSVIEWER by Accelrys.

http://accelrys.com/products/discovery-studio/visualization-download.php

I use it to draw initial structures, to play with the periodic cell, and
align coordinates with respect to the cell. The program does not have any
means to export PWSCF input. I export the structure in XYZ format, which is
a text file that can be directly used in PWSCF in "angstrom" coordinate mode
when first two lines are removed, and I edit the cell dimensions using the
values I depicted by hand.

By the way, I would be glad if someone can point me an open source
alternative which has extensive editing/monitoring capabilites for isolated
systems like this one, and stable at the same time.

Best,
Baris



2010/3/10 mohnish pandey <mohnish.iitk at gmail.com>

> Dear Elie,
>                I you have to give the celldm's initially. You can get the
> experimental value from literatures and use that as initial value. Then you
> can do "vc-relax" calculation to get equilibrium values of cell parameters
> computationally. Of course it will be different from experimental value. GGA
> calculation overestimates the value while LDA calculation underestimates the
> lattice parameter.
> Regards,
> MOHNISH
>
> On Wed, Mar 10, 2010 at 1:20 AM, Elie Moujaes <elie.moujaes at hotmail.co.uk>wrote:
>
>>  Is there a way (maybe a free software or program) to get celldim (i)
>> (i=1,...6) before giving it as an input in the calculations?
>>
>>
>> Regards
>>
>> Elie Moujaes
>> University of Nottingham
>> NG7 2RD
>> UK
>>
>>
>> ------------------------------
>> Do you have a story that started on Hotmail? Tell us now<http://clk.atdmt.com/UKM/go/195013117/direct/01/>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> Mohnish Pandey
> Y6927262,4th Year dual degree student,
> Department of Chemical Engineering,
> IIT KANPUR
> 09235721300
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From nnlinh at sissa.it  Wed Mar 10 09:24:44 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Wed, 10 Mar 2010 09:24:44 +0100
Subject: [Pw_forum] About supercell App.
In-Reply-To: <a6ebdd4d1003091718w6d86cb43t79174fa6d781c761@mail.gmail.com>
References: <a6ebdd4d1003091718w6d86cb43t79174fa6d781c761@mail.gmail.com>
Message-ID: <4B97574C.8000801@sissa.it>

mohsen modaresi wrote:
> Hi every body
> I read all discussion about 'super cell' generation, But i can't 
> understand.
> In 2009 there is a discussion about supercell generation and any body 
> refferd to PHON code, But i could'nt install PHON.
PHON is used when you want to consider the more complicated structure, 
but it's not the only way.
> Is there any why to determine the parameters? 
You mean "Is there any ways to determine the parameters?" ?
of course, Yes. Let refer the previous question "calculation the cell 
parameters in crystals" in forum.

> for example could you explain this part of a SCF calculation for 
> Pt-H2-Pt chain.
>       ibrav=8,
>       celldm(1)=18.0,------>This
>       celldm(2)=1.0,--------->This
>       celldm(3)=2.21412992, ----->  This
>       ...
> ATOMIC_POSITIONS {angstrom}
> Pt    0.000    0.000   0.000----->and this
> Pt    0.000    0.000   2.410----->and this
> Pt    0.000    0.000   4.820----->and this
> Pt    0.000    0.000   7.230----->and this
> H     0.000    0.000   8.900----->and this
> H     0.000    0.000   9.780----->and this
> Pt    0.000    0.000  11.450----->and this
> Pt    0.000    0.000  13.860----->and this
> Pt    0.000    0.000  16.270----->and this
> Pt    0.000    0.000  18.680----->and this
> suppose we want to change (Pt--->Cu) how can i get new parameters?
With a simple orthorhombic lattice, you need the value of lattice 
constant of Cu, and estimate the celldm(1), celldm(2), and celldm(3) of 
unit cell from that value.

Let do similarly to Pt but for Cu values

Good luck

Linh

> Thanks so much for your answers
> Mohsen Modarsei
> M.Sc student of solid state physics\
> Ferdowsi University of Mashhad 
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From moronaphtaly84 at gmail.com  Wed Mar 10 09:44:52 2010
From: moronaphtaly84 at gmail.com (naphtaly moro)
Date: Wed, 10 Mar 2010 11:44:52 +0300
Subject: [Pw_forum] QE & Xcrysden
Message-ID: <fe3b32711003100044t31b012aen17eacad01974f4ee@mail.gmail.com>

Dear Q.E. & Xcrysden
I am working on the various phase transitions of GaAs. I am trying to
contact these structures. I ahve managed to construct the ZB and RS
structures with success. I am using Xcrysden with Quantum Espresso.
When i try to view the CsCl-GaAs structure,  I only see the Ga atoms
and with no As atoms in the matrix. Can someone show me please where I
am going wrong
 my input file is this
 &control
   prefix='GaAs',
   pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo'
   outdir = './tmp',
 /
 &system
   ibrav=  3, celldm(1) =10.2, nat=  2, ntyp= 2,
   ecutwfc = 12.0,
 /
 &electrons
 /
ATOMIC_SPECIES
 Ga  69.723  Ga.pbe-nsp-van.UPF
 As  74.9216 As.pbe-n-van.UPF
ATOMIC_POSITIONS
 Ga 0.00 0.00 0.00
 As 0.50 0.50 0.50
K_POINTS {automatic}
 4 4 4 0 0 0

Thanks


-- 
Cecil Naphtaly Moro

From nnlinh at sissa.it  Wed Mar 10 10:07:19 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Wed, 10 Mar 2010 10:07:19 +0100
Subject: [Pw_forum] QE & Xcrysden
In-Reply-To: <fe3b32711003100044t31b012aen17eacad01974f4ee@mail.gmail.com>
References: <fe3b32711003100044t31b012aen17eacad01974f4ee@mail.gmail.com>
Message-ID: <4B976147.6060104@sissa.it>

naphtaly moro wrote:
> Dear Q.E. & Xcrysden
> I am working on the various phase transitions of GaAs. I am trying to
> contact these structures. I ahve managed to construct the ZB and RS
> structures with success. I am using Xcrysden with Quantum Espresso.
> When i try to view the CsCl-GaAs structure,  I only see the Ga atoms
> and with no As atoms in the matrix. Can someone show me please where I
> am going wrong
>  my input file is this
>  &control
>    prefix='GaAs',
>    pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo'
>    outdir = './tmp',
>  /
>  &system
>    ibrav=  3, celldm(1) =10.2, nat=  2, ntyp= 2,
>    ecutwfc = 12.0,
>  /
>  &electrons
>  /
> ATOMIC_SPECIES
>  Ga  69.723  Ga.pbe-nsp-van.UPF
>  As  74.9216 As.pbe-n-van.UPF
> ATOMIC_POSITIONS
>  Ga 0.00 0.00 0.00
>  As 0.50 0.50 0.50
> K_POINTS {automatic}
>  4 4 4 0 0 0
>
>   
You are having a wrong input structure. Namely, you chose ibrav= 3 which 
means BCC lattice, so in a periodic lattice the As atoms will be 
overlapped by Ga atoms.

How to fix the problem. You should again pick up another ibrav value and 
calculate the Gs and As positions.
As far as I know, GaAs lattice have a similarity to diamond lattice, so 
I suggest ibrav=2, and

Ga 0.00 0.00 0.00
As 0.25 0.25 0.25

Good luck

Linh


> Thanks
>
>
>   


-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From giovanni.cantele at na.infn.it  Wed Mar 10 10:12:03 2010
From: giovanni.cantele at na.infn.it (Giovanni Cantele)
Date: Wed, 10 Mar 2010 10:12:03 +0100
Subject: [Pw_forum] QE & Xcrysden
In-Reply-To: <fe3b32711003100044t31b012aen17eacad01974f4ee@mail.gmail.com>
References: <fe3b32711003100044t31b012aen17eacad01974f4ee@mail.gmail.com>
Message-ID: <A01EC0FD-0226-4351-A0A6-040071AACB82@na.infn.it>


On Mar 10, 2010, at 9:44 AM, naphtaly moro wrote:

> Dear Q.E. & Xcrysden
> I am working on the various phase transitions of GaAs. I am trying to
> contact these structures. I ahve managed to construct the ZB and RS
> structures with success. I am using Xcrysden with Quantum Espresso.
> When i try to view the CsCl-GaAs structure,  I only see the Ga atoms
> and with no As atoms in the matrix. Can someone show me please where I
> am going wrong
> my input file is this
> &control
>   prefix='GaAs',
>   pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo'
>   outdir = './tmp',
> /
> &system
>   ibrav=  3, celldm(1) =10.2, nat=  2, ntyp= 2,
>   ecutwfc = 12.0,
> /
> &electrons
> /
> ATOMIC_SPECIES
> Ga  69.723  Ga.pbe-nsp-van.UPF
> As  74.9216 As.pbe-n-van.UPF
> ATOMIC_POSITIONS
> Ga 0.00 0.00 0.00
> As 0.50 0.50 0.50
> K_POINTS {automatic}
> 4 4 4 0 0 0
> 
> Thanks
> 
> 
> -- 
> Cecil Naphtaly Moro


The reason is that you specify ibrav = 3 that, according to what explained in Doc/INPUT_PW.txt is a bcc lattice.
At the same time you give the ATOMIC_POSITIONS in units of the alat (namely, a in bohr units).
Therefore, the As atom is placed at (a/2, a/2, a/2) which is, by chance (!), also a site of the bcc lattice.
In other words, what XCrysDen sees is a Ga atom in a/2,a/2,a/2 but ALSO an As atom at the same place and decides
to delete the latter.
Maybe you want to specify the fcc lattice (ibrav=2) and the As atom at a/4,a/4,a/4.

Giovanni


PS not very sure that ecutwfc = 12.0 whould give you converged results. Also, because you choosed
ultrasoft pseudopotentials, you might want also check the ecutrho parameter (by default = 4 * ecutwfc,
but larger values are needed when using US pseudo).

--

Giovanni Cantele, PhD
CNR-SPIN and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910 - Fax:   +39 081 676346
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it


From sebastijan.peljhan at ijs.si  Wed Mar 10 10:22:31 2010
From: sebastijan.peljhan at ijs.si (Sebastijan Peljhan)
Date: Wed, 10 Mar 2010 10:22:31 +0100
Subject: [Pw_forum] QE & Xcrysden
In-Reply-To: <fe3b32711003100044t31b012aen17eacad01974f4ee@mail.gmail.com>
References: <fe3b32711003100044t31b012aen17eacad01974f4ee@mail.gmail.com>
Message-ID: <1268212951.2427.22.camel@surf>

Dear Cecil, 

On Wed, 2010-03-10 at 11:44 +0300, naphtaly moro wrote:
> Dear Q.E. & Xcrysden
> I am working on the various phase transitions of GaAs. I am trying to
> contact these structures. I ahve managed to construct the ZB and RS
> structures with success. I am using Xcrysden with Quantum Espresso.
> When i try to view the CsCl-GaAs structure,  I only see the Ga atoms
> and with no As atoms in the matrix. Can someone show me please where I
> am going wrong
>  my input file is this
>  &control
>    prefix='GaAs',
>    pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo'
>    outdir = './tmp',
>  /
>  &system

ibrav = 3 represents bcc cubic cell, hence the Ga and As atoms in your
structure overlap. Xcrysden actually warns you, that some of the atoms
overlap and they will be deleted. 

According to QE example06 you should try with ibrav = 2 (fcc) and As
atom at (0.25 0.25 0.25) position.  


Cheers,

Sebastijan


>    ibrav=  3, celldm(1) =10.2, nat=  2, ntyp= 2,
>    ecutwfc = 12.0,
>  /
>  &electrons
>  /
> ATOMIC_SPECIES
>  Ga  69.723  Ga.pbe-nsp-van.UPF
>  As  74.9216 As.pbe-n-van.UPF
> ATOMIC_POSITIONS
>  Ga 0.00 0.00 0.00
>  As 0.50 0.50 0.50
> K_POINTS {automatic}
>  4 4 4 0 0 0
> 
> Thanks
> 
> 

-- 
Sebastijan Peljhan
Department of Physical and Organic Chemistry
"Jozef Stefan" Institute
Jamova 39
1000 Ljubljana
Slovenia

tel.:+386 1 4773 523
fax.:+386 1 4773 822
email: sebastijan.peljhan at IJS.SI


From masoudnahali at live.com  Wed Mar 10 10:29:15 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Wed, 10 Mar 2010 09:29:15 +0000
Subject: [Pw_forum] calculating the cell parameters in crystals
In-Reply-To: <mailman.934.1268207581.15525.pw_forum@pwscf.org>
References: <mailman.934.1268207581.15525.pw_forum@pwscf.org>
Message-ID: <COL114-W57423189F36CD2A9DAB553A1330@phx.gbl>


Dear Elie

Try the VESTA software ! I am not that this can solve your problem; anyhow is a good graphical software for solids.

Best Wishes
Masoud Nahali
Sharif University of Technology

 		 	   		  
_________________________________________________________________
Hotmail: Trusted email with Microsoft?s powerful SPAM protection.
https://signup.live.com/signup.aspx?id=60969
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From mohnish.iitk at gmail.com  Wed Mar 10 10:35:26 2010
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Wed, 10 Mar 2010 15:05:26 +0530
Subject: [Pw_forum] SURFACE RECONSTRUCTION USING RELAX CALCULATION
Message-ID: <c40d64601003100135sc393a66h1f2a5ada30fac6cc@mail.gmail.com>

Dear users,
                   I want to get the results for surface reconstructions
computationally, but the problem is as we have specify the "ibrav" i.e
symmetry of the system the relax calculation only optimizes the structure
within the given symmetry. Can anybody suggest a way to model
reconstructions .
Thanks in advance,
MOHNISH

-- 
Mohnish Pandey
Y6927262,4th Year dual degree student,
Department of Chemical Engineering,
IIT KANPUR
09235721300
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From usagi at alumni.rice.edu  Wed Mar 10 10:41:29 2010
From: usagi at alumni.rice.edu (Bryan M. Wong)
Date: Wed, 10 Mar 2010 01:41:29 -0800
Subject: [Pw_forum] vc-relax with starting_magnetization
Message-ID: <9c9214d71003100141v51ffb64bm3705f2aaf80a98d0@mail.gmail.com>

Hi,

     Does anyone know how to do a "vc-relax" with the
"starting_magnetization" option turned on?

     I can always do a regular "relax" with the starting_magnetization
guess, and the structure will relax constrained to my fixed unit cell
dimensions. However, when I do a vc-relax with starting_magnetization set to
any value, the 2nd step in the cell relaxation always reverts to the
spin-unpolarized case (and the optimization will continue with the
spin-unpolarized case).

Bryan
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From nnlinh at sissa.it  Wed Mar 10 10:59:32 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Wed, 10 Mar 2010 10:59:32 +0100
Subject: [Pw_forum] SURFACE RECONSTRUCTION USING RELAX CALCULATION
In-Reply-To: <c40d64601003100135sc393a66h1f2a5ada30fac6cc@mail.gmail.com>
References: <c40d64601003100135sc393a66h1f2a5ada30fac6cc@mail.gmail.com>
Message-ID: <4B976D84.8070607@sissa.it>

mohnish pandey wrote:
>                    I want to get the results for surface 
> reconstructions computationally, but the problem is as we have specify 
> the "ibrav" i.e symmetry of the system the relax calculation only 
> optimizes the structure within the given symmetry.
Not exactly, the relax calculation plays a role to find out an optimal 
configuration from an initial configuration.
If you want to consider the surface reconstruction of given material, 
you should build a supercell in that the defect or adatom can be existed.

And how to form a supercell. Let see the previous archives of PW_forum

Good luck

Linh




-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From giovanni.cantele at na.infn.it  Wed Mar 10 11:10:20 2010
From: giovanni.cantele at na.infn.it (Giovanni Cantele)
Date: Wed, 10 Mar 2010 11:10:20 +0100
Subject: [Pw_forum] SURFACE RECONSTRUCTION USING RELAX CALCULATION
In-Reply-To: <c40d64601003100135sc393a66h1f2a5ada30fac6cc@mail.gmail.com>
References: <c40d64601003100135sc393a66h1f2a5ada30fac6cc@mail.gmail.com>
Message-ID: <C1F70D93-3106-46A2-8DD4-A048B2C7052F@na.infn.it>


On Mar 10, 2010, at 10:35 AM, mohnish pandey wrote:

> Dear users,
>                    I want to get the results for surface reconstructions computationally, but the problem is as we have specify the "ibrav" i.e symmetry of the system the relax calculation only optimizes the structure within the given symmetry. Can anybody suggest a way to model reconstructions .
> Thanks in advance,
> MOHNISH
> 
> -- 
> Mohnish Pandey
> Y6927262,4th Year dual degree student,
> Department of Chemical Engineering,
> IIT KANPUR
> 09235721300
> 

Well, I think that a "very general" answer is difficult to give (maybe someone more expert could try). What one usually does in studying surfaces, is try to identify,
step by step, possible reconstructions and look at the lower energy ones.

In practice, for a given surface direction (e.g. the silicon 100 surface) you first identify the "minimal" unit cell (size and symmetry) in the plane parallel to the surface. Then, you must decide
the number of atomic planes that you want to include in your calculation (this will fix the lattice constant in the direction orthogonal to the surface). This
will represent a so-called 1x1 model, meaning that your "surface unit cell" is made by just one unit cell. Possible reconstruction (which means atomic rearrangement of the atoms with respect to the ideal positions) will be, of course, the same in all surface unit cells.

More complicated reconstructions might arise because:

i) there can be a surface atomic displacement different in neighbor unit cells (for example, in the case of the cited Si surface two Si atoms in different 1x1 cells approach to each other to form a dimer, this gives you a 2x1 reconstruction; then two neighbor dimers can show different tilt with respect to the surface plane, this gives a 2x2 reconstruction, etc.); to include
this effect in your calculation you replicate your surface unit cell (building a "supercell") in one or both directions parallel to the surface, so as to build 1x2, 2x1, 2x2, 1x4, etc. models. Of course one should
be driven by either already known results, experimental evidences, etc. or by physically/chemically meaningful guesses. In this case one should also be careful to break possible symmetries that would prevent from reaching the energy minimum. Again, in the case of the Si(100) surface, if you just replicate the 1x1 unit cell along one surface direction, to build the 2x1 model, the code will just give you
a structure identical to the 1x1 model, with an energy 2 times larger; so, what you do is to move (even by a small amount) the atoms you expect will move, namely, the two Si atoms which dimerize. Alternatively, you can randomize the position of some/all atoms, just to break the symmetry.

ii) there can be a reconstruction where there are more/less atoms than you would expect in the "ideal" surface, a typical example is the case of O vacancies in oxide surfaces.

Because the plane-wave calculation, as you probably already know, is by construction periodic in all directions, you must be sure to include, along the direction orthogonal to the surface a
"vacuum space" (that means to increase the corresponding lattice parameter) to prevent two consecutive slabs from interacting. Convergence must be checked against the vacuum space.
Also, if you want to retrieve the "bulk surface" properties, the thickness of your slab should be larger enough (this is controlled by the number of atomic planes included in the unit cell) to prevent
opposite sides of a given slab from interacting with each other.

Another issue is that the "optimal" surface unit cell might show a completely different "symmetry" than the bulk one. For example, in the case of Au/Pt/etc. (111) surfaces, the bulk crystal is a cubic
fcc lattice, whereas the minimal surface unit cell can be represented using an hexagonal lattice.

Hope this helps,

    Giovanni


--

Giovanni Cantele, PhD
CNR-SPIN and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910 - Fax:   +39 081 676346
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it


From jdai3 at mail.ustc.edu.cn  Wed Mar 10 12:31:32 2010
From: jdai3 at mail.ustc.edu.cn (Jun Dai)
Date: Wed, 10 Mar 2010 19:31:32 +0800 (CST)
Subject: [Pw_forum] About the deformation potential approximation and
 elctron-phonon coupling
In-Reply-To: <81278.79606.qm@web65708.mail.ac4.yahoo.com>
References: <81278.79606.qm@web65708.mail.ac4.yahoo.com>
Message-ID: <26967577.575651268220692878.JavaMail.coremail@mailweb>

Dear QE users,

Recently, I heard about that the deformation potential approximation as implemented in QE may not work
to deal with the electron-phonon coupling at high frequencies, but I don't quite understand the physics
lie in, since QE seems to work fine in phonon mediated superconductors such as boron-doped diamond. I am 
wondering if QE do fail to deal with the el-ph coupling at high frequencies? if so, what is this high 
frequencies stand for(in what range?), or in what cases we can use the el-ph method implemented in QE? 
I would also appreciate those who can provide some backgroud methodology in this area. Thanks in advance.

Best regards?

Jun DAI
 

--
=================================================
 Jun DAI
 Ph.D Candidate
 Hefei National Laboratory for Physical Sciences at the Microscale
 University of Science & Technology of China
 Hefei, Anhui 230026, P.R.China
 Tel.: +86-551-3606428
=================================================



From giuseppe.mattioli at mlib.ism.cnr.it  Wed Mar 10 12:42:49 2010
From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it)
Date: Wed, 10 Mar 2010 12:42:49 +0100
Subject: [Pw_forum] SURFACE RECONSTRUCTION USING RELAX CALCULATION
In-Reply-To: <C1F70D93-3106-46A2-8DD4-A048B2C7052F@na.infn.it>
References: <c40d64601003100135sc393a66h1f2a5ada30fac6cc@mail.gmail.com>
	<C1F70D93-3106-46A2-8DD4-A048B2C7052F@na.infn.it>
Message-ID: <20100310124249.guup0pldwkwgcocw@webmail.sic.rm.cnr.it>

On the top of what Giovanni said (which is already very interesting) I  
would add that, in my experience, it is very, VERY difficult to study  
all but very simple surface reconstructions without a (minimal)  
experimental support. In other words, if you do not know, for example,  
whether the surface matches the periodicity of the bulk lattice by  
means of (at least) LEED patterns or (and this is better) LEED and STM  
patterns, you can try an 1x1 model and stop there... So, I suggest you  
to look for some experimental papers, before you start your  
theoretical investigation.

Yours

Giuseppe

ISM-CNR

Quoting Giovanni Cantele <giovanni.cantele at na.infn.it>:

>
> On Mar 10, 2010, at 10:35 AM, mohnish pandey wrote:
>
>> Dear users,
>>                    I want to get the results for surface   
>> reconstructions computationally, but the problem is as we have   
>> specify the "ibrav" i.e symmetry of the system the relax   
>> calculation only optimizes the structure within the given symmetry.  
>>  Can anybody suggest a way to model reconstructions .
>> Thanks in advance,
>> MOHNISH
>>
>> --
>> Mohnish Pandey
>> Y6927262,4th Year dual degree student,
>> Department of Chemical Engineering,
>> IIT KANPUR
>> 09235721300
>>
>
> Well, I think that a "very general" answer is difficult to give   
> (maybe someone more expert could try). What one usually does in   
> studying surfaces, is try to identify,
> step by step, possible reconstructions and look at the lower energy ones.
>
> In practice, for a given surface direction (e.g. the silicon 100   
> surface) you first identify the "minimal" unit cell (size and   
> symmetry) in the plane parallel to the surface. Then, you must decide
> the number of atomic planes that you want to include in your   
> calculation (this will fix the lattice constant in the direction   
> orthogonal to the surface). This
> will represent a so-called 1x1 model, meaning that your "surface   
> unit cell" is made by just one unit cell. Possible reconstruction   
> (which means atomic rearrangement of the atoms with respect to the   
> ideal positions) will be, of course, the same in all surface unit   
> cells.
>
> More complicated reconstructions might arise because:
>
> i) there can be a surface atomic displacement different in neighbor   
> unit cells (for example, in the case of the cited Si surface two Si   
> atoms in different 1x1 cells approach to each other to form a dimer,  
>  this gives you a 2x1 reconstruction; then two neighbor dimers can   
> show different tilt with respect to the surface plane, this gives a   
> 2x2 reconstruction, etc.); to include
> this effect in your calculation you replicate your surface unit cell  
>  (building a "supercell") in one or both directions parallel to the   
> surface, so as to build 1x2, 2x1, 2x2, 1x4, etc. models. Of course   
> one should
> be driven by either already known results, experimental evidences,   
> etc. or by physically/chemically meaningful guesses. In this case   
> one should also be careful to break possible symmetries that would   
> prevent from reaching the energy minimum. Again, in the case of the   
> Si(100) surface, if you just replicate the 1x1 unit cell along one   
> surface direction, to build the 2x1 model, the code will just give you
> a structure identical to the 1x1 model, with an energy 2 times   
> larger; so, what you do is to move (even by a small amount) the   
> atoms you expect will move, namely, the two Si atoms which dimerize.  
>  Alternatively, you can randomize the position of some/all atoms,   
> just to break the symmetry.
>
> ii) there can be a reconstruction where there are more/less atoms   
> than you would expect in the "ideal" surface, a typical example is   
> the case of O vacancies in oxide surfaces.
>
> Because the plane-wave calculation, as you probably already know, is  
>  by construction periodic in all directions, you must be sure to   
> include, along the direction orthogonal to the surface a
> "vacuum space" (that means to increase the corresponding lattice   
> parameter) to prevent two consecutive slabs from interacting.   
> Convergence must be checked against the vacuum space.
> Also, if you want to retrieve the "bulk surface" properties, the   
> thickness of your slab should be larger enough (this is controlled   
> by the number of atomic planes included in the unit cell) to prevent
> opposite sides of a given slab from interacting with each other.
>
> Another issue is that the "optimal" surface unit cell might show a   
> completely different "symmetry" than the bulk one. For example, in   
> the case of Au/Pt/etc. (111) surfaces, the bulk crystal is a cubic
> fcc lattice, whereas the minimal surface unit cell can be   
> represented using an hexagonal lattice.
>
> Hope this helps,
>
>     Giovanni
>
>
> --
>
> Giovanni Cantele, PhD
> CNR-SPIN and Dipartimento di Scienze Fisiche
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> Phone: +39 081 676910 - Fax:   +39 081 676346
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>                      http://www.nanomat.unina.it
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>





From masoudnahali at live.com  Wed Mar 10 13:03:05 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Wed, 10 Mar 2010 12:03:05 +0000
Subject: [Pw_forum] 'Relax' variable
Message-ID: <COL114-W503E1DC1F95DC8FFA68FE2A1330@phx.gbl>


Dear QE users

Is there any variable alongside the 'relax' for these usages ?! :  

                            1. fixing or changing the cell symmetry through the calculation.
                            2. fixing or optimizing the cell size through the calculation.
                            3. optimizing all positions without considering any restrictions.

Many Thanks
Masoud Nahali
Sharif University of Technology
 		 	   		  
_________________________________________________________________
Hotmail: Trusted email with Microsoft?s powerful SPAM protection.
https://signup.live.com/signup.aspx?id=60969
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From elie.moujaes at hotmail.co.uk  Wed Mar 10 13:39:51 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Wed, 10 Mar 2010 12:39:51 +0000
Subject: [Pw_forum] DOS of graphene
In-Reply-To: <20100310070732.1699634hqunlxu04@webmail.epfl.ch>
References: <SNT114-W40AF61030478F6620CE09AD3340@phx.gbl>,
	<49491.93.147.187.115.1268167979.squirrel@imap-ac.na.infn.it>,
	<20100310070732.1699634hqunlxu04@webmail.epfl.ch>
Message-ID: <SNT114-W20D9186FD4C0ADF013DBC1D3330@phx.gbl>


Dear Alexandra,

 

my sampling included 210 points. I will be checking the program again and see what went wrong. Than you

 

Elie

 

Elie Moujaes 
 University of Nottingham
 NG7 2RD

 UK



 
> Date: Wed, 10 Mar 2010 07:07:32 +0100
> From: alexandra.carvalho at epfl.ch
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] DOS of graphene
> 
> Dear Elie,
> 
> The Fermi level in graphene converges very slowly with the k-point 
> sampling. Did you check the result with a very large number of k-points?
> 
> Alexandra
> 
> -----------------------------------------------------------
> Alexandra Carvalho,
> Ceramics Laboratory
> Swiss Federal Institute of Technology of Lausanne (EPFL)
> 
> 
> Quoting Giovanni Cantele <giovanni.cantele at na.infn.it>:
> 
> >> Dear all,
> >> I have plotted the density of states of graphene but when I looked at the
> >> graph, DOS was not zero at the fermi level (I got it to be -0.988 eV). my
> >> Programm seems pretty fine and i have checked it several times but with in
> >> vain..You will find attached the ps version and the input for the dos.x
> >> command...
> >> Regards
> >> Elie Moujaes
> >> University of Nottingham
> >> NG7 2RD
> >> UK
> >
> > The problem that the Fermi level is not at the energy you expect might not
> > be related to a mistake. The zero energy is not well defined in a
> > plane-wave calculation (try to browse the forum, there should be more than
> > one topic about that!). One should compute the DOS, then calculate the
> > Fermi energy (as the energy at which the integrated DOS matches the number
> > of the electrons), then for the sake of clarity you can shift you DOS (or
> > band structure) plot so as the Fermi energy is at 0.
> >
> > However, this might not be the problem in you calculation.
> > I'm not very sure that your calculation is right, because the shape of
> > your DOS plot does not look like the one of graphene. So the first problem
> > to solve is to understand on the top of which scf / nscf calculation you
> > have built your DOS plot. Unless I missed something, there are not
> > sufficient elements to understand what happened.
> >
> > Giovanni
> >
> > --
> > Giovanni Cantele, PhD
> > CNR-SPIN and Dipartimento di Scienze Fisiche
> > Universita' di Napoli "Federico II"
> > Complesso Universitario M. S. Angelo - Ed. 6
> > Via Cintia, I-80126, Napoli, Italy
> > Phone: +39 081 676910 - Fax: +39 081 676346
> > Skype contact: giocan74
> >
> > ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> > Web page: http://people.na.infn.it/~cantele
> > http://www.nanomat.unina.it
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> 
> 
> 
> -- 
> 
> Alexandra Carvalho,
> Ceramics Laboratory
> Swiss Federal Institute of Technology of Lausanne (EPFL)
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
_________________________________________________________________
Tell us your greatest, weirdest and funniest Hotmail stories
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From paulatto at sissa.it  Wed Mar 10 14:02:42 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 10 Mar 2010 14:02:42 +0100
Subject: [Pw_forum] 'Relax' variable
In-Reply-To: <COL114-W503E1DC1F95DC8FFA68FE2A1330@phx.gbl>
References: <COL114-W503E1DC1F95DC8FFA68FE2A1330@phx.gbl>
Message-ID: <op.u9cruslsa8x26q@vanoxite.impmc.jussieu.fr>

On Wed, 10 Mar 2010 13:03:05 +0100, Masoud Nahali <masoudnahali at live.com>  
wrote:
> 1. fixing or changing the cell symmetry  through the calculation.

Stress and force components that would break the symmetry are always  
zero... by symmetry

> 2. fixing or optimizing the cell size through the calculation.

Just use relax instead of vc-relax, if you mean the *volume* of the cell,  
than there is a keyword for that but unluckily it does not work very well  
with bfgs...

> 3. optimizing all positions without considering any restrictions.

This is the default, however you can fix the position of one or more atoms  
along any cartesian direction if you wish.

best regards

-- 
Lorenzo Paulatto

*** Note: my affiliation has changed! please send future
correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***

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

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

From gianluca.giovannetti at gmail.com  Wed Mar 10 16:09:02 2010
From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti)
Date: Wed, 10 Mar 2010 16:09:02 +0100
Subject: [Pw_forum] pseudopotential for Fe and Se
Message-ID: <7234ba151003100709v336abb52of77812d1e6006cc7@mail.gmail.com>

Dear All,

i`m new to the PW code.
i did some calculations using
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From gianluca.giovannetti at gmail.com  Wed Mar 10 16:11:14 2010
From: gianluca.giovannetti at gmail.com (Gianluca Giovannetti)
Date: Wed, 10 Mar 2010 16:11:14 +0100
Subject: [Pw_forum] pseudopotential for Fe and Se
In-Reply-To: <7234ba151003100709v336abb52of77812d1e6006cc7@mail.gmail.com>
References: <7234ba151003100709v336abb52of77812d1e6006cc7@mail.gmail.com>
Message-ID: <7234ba151003100711r30ebe55g6248c92efa05bdfc@mail.gmail.com>

>
> Dear All,
>
> i`m new to the PW code. it is only couples of weeks i`m using it.
>
    i did some calculations using  pseudopotentials:  Fe.pbe-sp-van.UPF ,
Se.pbe-van.UPF.
    results are very similar to ones i can get with another dft code.
    are these pseudopotentials consistent in PW?

    thank you.

    Gianluca




On Wed, Mar 10, 2010 at 4:09 PM, Gianluca Giovannetti <
gianluca.giovannetti at gmail.com> wrote:

> Dear All,
>
> i`m new to the PW code.
> i did some calculations using
>
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From mohnish.iitk at gmail.com  Wed Mar 10 16:32:09 2010
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Wed, 10 Mar 2010 21:02:09 +0530
Subject: [Pw_forum] SURFACE RECONSTRUCTION USING RELAX CALCULATION
In-Reply-To: <C1F70D93-3106-46A2-8DD4-A048B2C7052F@na.infn.it>
References: <c40d64601003100135sc393a66h1f2a5ada30fac6cc@mail.gmail.com>
	<C1F70D93-3106-46A2-8DD4-A048B2C7052F@na.infn.it>
Message-ID: <c40d64601003100732u38623c2fs9353d789303d2086@mail.gmail.com>

Dear Giovanni!
                       Thank you so much for you reply. As you suggested for
experimental evidence of the reconstruction I have got the reference below
which is experimental. This paper involves the structural change in gold
nanofilm for certain thickness in which (001) surface changes to (111)
surface.
                I  am unable to attach the paper because its size is large.
I hope your suggestion will definitely help.
Thank you very much to all of you
Sincerely,
MOHNISH
 " Phys. Rev. Lett. 82, 751?754 , Thickness Induced Structural Phase
Transition of Gold Nanofilm"


On Wed, Mar 10, 2010 at 3:40 PM, Giovanni Cantele <
giovanni.cantele at na.infn.it> wrote:

>
> On Mar 10, 2010, at 10:35 AM, mohnish pandey wrote:
>
> > Dear users,
> >                    I want to get the results for surface reconstructions
> computationally, but the problem is as we have specify the "ibrav" i.e
> symmetry of the system the relax calculation only optimizes the structure
> within the given symmetry. Can anybody suggest a way to model
> reconstructions .
> > Thanks in advance,
> > MOHNISH
> >
> > --
> > Mohnish Pandey
> > Y6927262,4th Year dual degree student,
> > Department of Chemical Engineering,
> > IIT KANPUR
> > 09235721300
> >
>
> Well, I think that a "very general" answer is difficult to give (maybe
> someone more expert could try). What one usually does in studying surfaces,
> is try to identify,
> step by step, possible reconstructions and look at the lower energy ones.
>
> In practice, for a given surface direction (e.g. the silicon 100 surface)
> you first identify the "minimal" unit cell (size and symmetry) in the plane
> parallel to the surface. Then, you must decide
> the number of atomic planes that you want to include in your calculation
> (this will fix the lattice constant in the direction orthogonal to the
> surface). This
> will represent a so-called 1x1 model, meaning that your "surface unit cell"
> is made by just one unit cell. Possible reconstruction (which means atomic
> rearrangement of the atoms with respect to the ideal positions) will be, of
> course, the same in all surface unit cells.
>
> More complicated reconstructions might arise because:
>
> i) there can be a surface atomic displacement different in neighbor unit
> cells (for example, in the case of the cited Si surface two Si atoms in
> different 1x1 cells approach to each other to form a dimer, this gives you a
> 2x1 reconstruction; then two neighbor dimers can show different tilt with
> respect to the surface plane, this gives a 2x2 reconstruction, etc.); to
> include
> this effect in your calculation you replicate your surface unit cell
> (building a "supercell") in one or both directions parallel to the surface,
> so as to build 1x2, 2x1, 2x2, 1x4, etc. models. Of course one should
> be driven by either already known results, experimental evidences, etc. or
> by physically/chemically meaningful guesses. In this case one should also be
> careful to break possible symmetries that would prevent from reaching the
> energy minimum. Again, in the case of the Si(100) surface, if you just
> replicate the 1x1 unit cell along one surface direction, to build the 2x1
> model, the code will just give you
> a structure identical to the 1x1 model, with an energy 2 times larger; so,
> what you do is to move (even by a small amount) the atoms you expect will
> move, namely, the two Si atoms which dimerize. Alternatively, you can
> randomize the position of some/all atoms, just to break the symmetry.
>
> ii) there can be a reconstruction where there are more/less atoms than you
> would expect in the "ideal" surface, a typical example is the case of O
> vacancies in oxide surfaces.
>
> Because the plane-wave calculation, as you probably already know, is by
> construction periodic in all directions, you must be sure to include, along
> the direction orthogonal to the surface a
> "vacuum space" (that means to increase the corresponding lattice parameter)
> to prevent two consecutive slabs from interacting. Convergence must be
> checked against the vacuum space.
> Also, if you want to retrieve the "bulk surface" properties, the thickness
> of your slab should be larger enough (this is controlled by the number of
> atomic planes included in the unit cell) to prevent
> opposite sides of a given slab from interacting with each other.
>
> Another issue is that the "optimal" surface unit cell might show a
> completely different "symmetry" than the bulk one. For example, in the case
> of Au/Pt/etc. (111) surfaces, the bulk crystal is a cubic
> fcc lattice, whereas the minimal surface unit cell can be represented using
> an hexagonal lattice.
>
> Hope this helps,
>
>    Giovanni
>
>
> --
>
> Giovanni Cantele, PhD
> CNR-SPIN and Dipartimento di Scienze Fisiche
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> Phone: +39 081 676910 - Fax:   +39 081 676346
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele<http://people.na.infn.it/%7Ecantele>
>                     http://www.nanomat.unina.it
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Mohnish Pandey
Y6927262,4th Year dual degree student,
Department of Chemical Engineering,
IIT KANPUR
09235721300
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From dmheggo at student.matnat.uio.no  Wed Mar 10 17:19:46 2010
From: dmheggo at student.matnat.uio.no (Dan Michael Olsen =?iso-8859-1?Q?Hegg=F8?=)
Date: Wed, 10 Mar 2010 17:19:46 +0100
Subject: [Pw_forum] Wrong oxygen mass in example 13
Message-ID: <5402fae9bf72dc5584f7602ae5b53f64.squirrel@webmail.uio.no>

Hi,

While playing around with the many wonderful examples provided, I
discovered that the oxygen mass is given as 55.847 in example 13, which is
in fact the mass of iron. While this doesn't affect the result, it should
probably be corrected :)

This leads me to a (perhaps stupid) question: In what type of calculations
is the ionic mass used? MD and phonon calculations?

Thanks!

-- 
Dan Michael Hegg?, Master Student
University of Oslo





From giannozz at democritos.it  Wed Mar 10 17:49:07 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 10 Mar 2010 17:49:07 +0100
Subject: [Pw_forum] Wrong oxygen mass in example 13
In-Reply-To: <5402fae9bf72dc5584f7602ae5b53f64.squirrel@webmail.uio.no>
References: <5402fae9bf72dc5584f7602ae5b53f64.squirrel@webmail.uio.no>
Message-ID: <B14EC77E-4857-41F8-80B2-DAD9EDCA2143@democritos.it>


On Mar 10, 2010, at 17:19 , Dan Michael Olsen Hegg? wrote:

> I discovered that the oxygen mass is given as 55.847 in example 13,
> which is in fact the mass of iron. While this doesn't affect the  
> result, it
> should probably be corrected :)

done, thank you

> This leads me to a (perhaps stupid) question: In what type of  
> calculations
> is the ionic mass used? MD and phonon calculations?

correct (not sure about phonons, though: the phonon code also reads
masses in input data)

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




From moronaphtaly84 at gmail.com  Wed Mar 10 18:07:47 2010
From: moronaphtaly84 at gmail.com (naphtaly moro)
Date: Wed, 10 Mar 2010 20:07:47 +0300
Subject: [Pw_forum] QE & Xcrysden
Message-ID: <fe3b32711003100907y3fc83344i48ddaae131eef24f@mail.gmail.com>

Dear Re: Ngoc Linh Nguyen, Giovanni Cantele & Sebastijan Peljhan

I am working on the various phases of GaAs. at normal conditions, GaAs
assumes a Zincblende structures fcc ibrav=2, as pressure increases it
assumes Rocksalt structure and then assumes a CsCl structure which is
bcc ibrav=3 that is why my input as i posted it. Can you advice me
further?
Regards


On 3/10/10, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org> wrote:
> Send Pw_forum mailing list submissions to
> 	pw_forum at pwscf.org
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> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
>    1. Re: About supercell App. (Ngoc Linh Nguyen)
>    2. QE & Xcrysden (naphtaly moro)
>    3. Re: QE & Xcrysden (Ngoc Linh Nguyen)
>    4. Re: QE & Xcrysden (Giovanni Cantele)
>    5. Re: QE & Xcrysden (Sebastijan Peljhan)
>    6. Re: calculating the cell parameters in crystals (Masoud Nahali)
>    7. SURFACE RECONSTRUCTION USING RELAX CALCULATION (mohnish pandey)
>    8. vc-relax with starting_magnetization (Bryan M. Wong)
>    9. Re: SURFACE RECONSTRUCTION USING RELAX CALCULATION
>       (Ngoc Linh Nguyen)
>   10. Re: SURFACE RECONSTRUCTION USING RELAX CALCULATION
>       (Giovanni Cantele)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 10 Mar 2010 09:24:44 +0100
> From: Ngoc Linh Nguyen <nnlinh at sissa.it>
> Subject: Re: [Pw_forum] About supercell App.
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4B97574C.8000801 at sissa.it>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> mohsen modaresi wrote:
>> Hi every body
>> I read all discussion about 'super cell' generation, But i can't
>> understand.
>> In 2009 there is a discussion about supercell generation and any body
>> refferd to PHON code, But i could'nt install PHON.
> PHON is used when you want to consider the more complicated structure,
> but it's not the only way.
>> Is there any why to determine the parameters?
> You mean "Is there any ways to determine the parameters?" ?
> of course, Yes. Let refer the previous question "calculation the cell
> parameters in crystals" in forum.
>
>> for example could you explain this part of a SCF calculation for
>> Pt-H2-Pt chain.
>>       ibrav=8,
>>       celldm(1)=18.0,------>This
>>       celldm(2)=1.0,--------->This
>>       celldm(3)=2.21412992, ----->  This
>>       ...
>> ATOMIC_POSITIONS {angstrom}
>> Pt    0.000    0.000   0.000----->and this
>> Pt    0.000    0.000   2.410----->and this
>> Pt    0.000    0.000   4.820----->and this
>> Pt    0.000    0.000   7.230----->and this
>> H     0.000    0.000   8.900----->and this
>> H     0.000    0.000   9.780----->and this
>> Pt    0.000    0.000  11.450----->and this
>> Pt    0.000    0.000  13.860----->and this
>> Pt    0.000    0.000  16.270----->and this
>> Pt    0.000    0.000  18.680----->and this
>> suppose we want to change (Pt--->Cu) how can i get new parameters?
> With a simple orthorhombic lattice, you need the value of lattice
> constant of Cu, and estimate the celldm(1), celldm(2), and celldm(3) of
> unit cell from that value.
>
> Let do similarly to Pt but for Cu values
>
> Good luck
>
> Linh
>
>> Thanks so much for your answers
>> Mohsen Modarsei
>> M.Sc student of solid state physics\
>> Ferdowsi University of Mashhad
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
> --
> -----------------------------------------------------
>  Nguyen Ngoc Linh, PhD Student
>  c/o:   SISSA & CNR-INFM Democritos,
>         via Beirut 2-4, 34014 Trieste (Italy)
>  email: nnlinh at sissa.it
>  phone: +39 04 03787 319
>  skype: ngoclinh84phys
> -----------------------------------------------------
> "The physics is theoretical but the fun is real"
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 10 Mar 2010 11:44:52 +0300
> From: naphtaly moro <moronaphtaly84 at gmail.com>
> Subject: [Pw_forum] QE & Xcrysden
> To: pw_forum at pwscf.org
> Message-ID:
> 	<fe3b32711003100044t31b012aen17eacad01974f4ee at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Q.E. & Xcrysden
> I am working on the various phase transitions of GaAs. I am trying to
> contact these structures. I ahve managed to construct the ZB and RS
> structures with success. I am using Xcrysden with Quantum Espresso.
> When i try to view the CsCl-GaAs structure,  I only see the Ga atoms
> and with no As atoms in the matrix. Can someone show me please where I
> am going wrong
>  my input file is this
>  &control
>    prefix='GaAs',
>    pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo'
>    outdir = './tmp',
>  /
>  &system
>    ibrav=  3, celldm(1) =10.2, nat=  2, ntyp= 2,
>    ecutwfc = 12.0,
>  /
>  &electrons
>  /
> ATOMIC_SPECIES
>  Ga  69.723  Ga.pbe-nsp-van.UPF
>  As  74.9216 As.pbe-n-van.UPF
> ATOMIC_POSITIONS
>  Ga 0.00 0.00 0.00
>  As 0.50 0.50 0.50
> K_POINTS {automatic}
>  4 4 4 0 0 0
>
> Thanks
>
>
> --
> Cecil Naphtaly Moro
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 10 Mar 2010 10:07:19 +0100
> From: Ngoc Linh Nguyen <nnlinh at sissa.it>
> Subject: Re: [Pw_forum] QE & Xcrysden
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4B976147.6060104 at sissa.it>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> naphtaly moro wrote:
>> Dear Q.E. & Xcrysden
>> I am working on the various phase transitions of GaAs. I am trying to
>> contact these structures. I ahve managed to construct the ZB and RS
>> structures with success. I am using Xcrysden with Quantum Espresso.
>> When i try to view the CsCl-GaAs structure,  I only see the Ga atoms
>> and with no As atoms in the matrix. Can someone show me please where I
>> am going wrong
>>  my input file is this
>>  &control
>>    prefix='GaAs',
>>    pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo'
>>    outdir = './tmp',
>>  /
>>  &system
>>    ibrav=  3, celldm(1) =10.2, nat=  2, ntyp= 2,
>>    ecutwfc = 12.0,
>>  /
>>  &electrons
>>  /
>> ATOMIC_SPECIES
>>  Ga  69.723  Ga.pbe-nsp-van.UPF
>>  As  74.9216 As.pbe-n-van.UPF
>> ATOMIC_POSITIONS
>>  Ga 0.00 0.00 0.00
>>  As 0.50 0.50 0.50
>> K_POINTS {automatic}
>>  4 4 4 0 0 0
>>
>>
> You are having a wrong input structure. Namely, you chose ibrav= 3 which
> means BCC lattice, so in a periodic lattice the As atoms will be
> overlapped by Ga atoms.
>
> How to fix the problem. You should again pick up another ibrav value and
> calculate the Gs and As positions.
> As far as I know, GaAs lattice have a similarity to diamond lattice, so
> I suggest ibrav=2, and
>
> Ga 0.00 0.00 0.00
> As 0.25 0.25 0.25
>
> Good luck
>
> Linh
>
>
>> Thanks
>>
>>
>>
>
>
> --
> -----------------------------------------------------
>  Nguyen Ngoc Linh, PhD Student
>  c/o:   SISSA & CNR-INFM Democritos,
>         via Beirut 2-4, 34014 Trieste (Italy)
>  email: nnlinh at sissa.it
>  phone: +39 04 03787 319
>  skype: ngoclinh84phys
> -----------------------------------------------------
> "The physics is theoretical but the fun is real"
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 10 Mar 2010 10:12:03 +0100
> From: Giovanni Cantele <giovanni.cantele at na.infn.it>
> Subject: Re: [Pw_forum] QE & Xcrysden
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <A01EC0FD-0226-4351-A0A6-040071AACB82 at na.infn.it>
> Content-Type: text/plain; charset=us-ascii
>
>
> On Mar 10, 2010, at 9:44 AM, naphtaly moro wrote:
>
>> Dear Q.E. & Xcrysden
>> I am working on the various phase transitions of GaAs. I am trying to
>> contact these structures. I ahve managed to construct the ZB and RS
>> structures with success. I am using Xcrysden with Quantum Espresso.
>> When i try to view the CsCl-GaAs structure,  I only see the Ga atoms
>> and with no As atoms in the matrix. Can someone show me please where I
>> am going wrong
>> my input file is this
>> &control
>>   prefix='GaAs',
>>   pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo'
>>   outdir = './tmp',
>> /
>> &system
>>   ibrav=  3, celldm(1) =10.2, nat=  2, ntyp= 2,
>>   ecutwfc = 12.0,
>> /
>> &electrons
>> /
>> ATOMIC_SPECIES
>> Ga  69.723  Ga.pbe-nsp-van.UPF
>> As  74.9216 As.pbe-n-van.UPF
>> ATOMIC_POSITIONS
>> Ga 0.00 0.00 0.00
>> As 0.50 0.50 0.50
>> K_POINTS {automatic}
>> 4 4 4 0 0 0
>>
>> Thanks
>>
>>
>> --
>> Cecil Naphtaly Moro
>
>
> The reason is that you specify ibrav = 3 that, according to what explained
> in Doc/INPUT_PW.txt is a bcc lattice.
> At the same time you give the ATOMIC_POSITIONS in units of the alat (namely,
> a in bohr units).
> Therefore, the As atom is placed at (a/2, a/2, a/2) which is, by chance (!),
> also a site of the bcc lattice.
> In other words, what XCrysDen sees is a Ga atom in a/2,a/2,a/2 but ALSO an
> As atom at the same place and decides
> to delete the latter.
> Maybe you want to specify the fcc lattice (ibrav=2) and the As atom at
> a/4,a/4,a/4.
>
> Giovanni
>
>
> PS not very sure that ecutwfc = 12.0 whould give you converged results.
> Also, because you choosed
> ultrasoft pseudopotentials, you might want also check the ecutrho parameter
> (by default = 4 * ecutwfc,
> but larger values are needed when using US pseudo).
>
> --
>
> Giovanni Cantele, PhD
> CNR-SPIN and Dipartimento di Scienze Fisiche
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> Phone: +39 081 676910 - Fax:   +39 081 676346
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>                      http://www.nanomat.unina.it
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 10 Mar 2010 10:22:31 +0100
> From: Sebastijan Peljhan <sebastijan.peljhan at ijs.si>
> Subject: Re: [Pw_forum] QE & Xcrysden
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <1268212951.2427.22.camel at surf>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Cecil,
>
> On Wed, 2010-03-10 at 11:44 +0300, naphtaly moro wrote:
>> Dear Q.E. & Xcrysden
>> I am working on the various phase transitions of GaAs. I am trying to
>> contact these structures. I ahve managed to construct the ZB and RS
>> structures with success. I am using Xcrysden with Quantum Espresso.
>> When i try to view the CsCl-GaAs structure,  I only see the Ga atoms
>> and with no As atoms in the matrix. Can someone show me please where I
>> am going wrong
>>  my input file is this
>>  &control
>>    prefix='GaAs',
>>    pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo'
>>    outdir = './tmp',
>>  /
>>  &system
>
> ibrav = 3 represents bcc cubic cell, hence the Ga and As atoms in your
> structure overlap. Xcrysden actually warns you, that some of the atoms
> overlap and they will be deleted.
>
> According to QE example06 you should try with ibrav = 2 (fcc) and As
> atom at (0.25 0.25 0.25) position.
>
>
> Cheers,
>
> Sebastijan
>
>
>>    ibrav=  3, celldm(1) =10.2, nat=  2, ntyp= 2,
>>    ecutwfc = 12.0,
>>  /
>>  &electrons
>>  /
>> ATOMIC_SPECIES
>>  Ga  69.723  Ga.pbe-nsp-van.UPF
>>  As  74.9216 As.pbe-n-van.UPF
>> ATOMIC_POSITIONS
>>  Ga 0.00 0.00 0.00
>>  As 0.50 0.50 0.50
>> K_POINTS {automatic}
>>  4 4 4 0 0 0
>>
>> Thanks
>>
>>
>
> --
> Sebastijan Peljhan
> Department of Physical and Organic Chemistry
> "Jozef Stefan" Institute
> Jamova 39
> 1000 Ljubljana
> Slovenia
>
> tel.:+386 1 4773 523
> fax.:+386 1 4773 822
> email: sebastijan.peljhan at IJS.SI
>
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 10 Mar 2010 09:29:15 +0000
> From: Masoud Nahali <masoudnahali at live.com>
> Subject: Re: [Pw_forum] calculating the cell parameters in crystals
> To: Quantum Espresso <pw_forum at pwscf.org>
> Message-ID: <COL114-W57423189F36CD2A9DAB553A1330 at phx.gbl>
> Content-Type: text/plain; charset="windows-1256"
>
>
> Dear Elie
>
> Try the VESTA software ! I am not that this can solve your problem; anyhow
> is a good graphical software for solids.
>
> Best Wishes
> Masoud Nahali
> Sharif University of Technology
>
>  		 	   		
> _________________________________________________________________
> Hotmail: Trusted email with Microsoft?s powerful SPAM protection.
> https://signup.live.com/signup.aspx?id=60969
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> ------------------------------
>
> Message: 7
> Date: Wed, 10 Mar 2010 15:05:26 +0530
> From: mohnish pandey <mohnish.iitk at gmail.com>
> Subject: [Pw_forum] SURFACE RECONSTRUCTION USING RELAX CALCULATION
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> 	<c40d64601003100135sc393a66h1f2a5ada30fac6cc at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear users,
>                    I want to get the results for surface reconstructions
> computationally, but the problem is as we have specify the "ibrav" i.e
> symmetry of the system the relax calculation only optimizes the structure
> within the given symmetry. Can anybody suggest a way to model
> reconstructions .
> Thanks in advance,
> MOHNISH
>
> --
> Mohnish Pandey
> Y6927262,4th Year dual degree student,
> Department of Chemical Engineering,
> IIT KANPUR
> 09235721300
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>
> ------------------------------
>
> Message: 8
> Date: Wed, 10 Mar 2010 01:41:29 -0800
> From: "Bryan M. Wong" <usagi at alumni.rice.edu>
> Subject: [Pw_forum] vc-relax with starting_magnetization
> To: pw_forum at pwscf.org
> Message-ID:
> 	<9c9214d71003100141v51ffb64bm3705f2aaf80a98d0 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
>      Does anyone know how to do a "vc-relax" with the
> "starting_magnetization" option turned on?
>
>      I can always do a regular "relax" with the starting_magnetization
> guess, and the structure will relax constrained to my fixed unit cell
> dimensions. However, when I do a vc-relax with starting_magnetization set to
> any value, the 2nd step in the cell relaxation always reverts to the
> spin-unpolarized case (and the optimization will continue with the
> spin-unpolarized case).
>
> Bryan
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 9
> Date: Wed, 10 Mar 2010 10:59:32 +0100
> From: Ngoc Linh Nguyen <nnlinh at sissa.it>
> Subject: Re: [Pw_forum] SURFACE RECONSTRUCTION USING RELAX CALCULATION
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4B976D84.8070607 at sissa.it>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> mohnish pandey wrote:
>>                    I want to get the results for surface
>> reconstructions computationally, but the problem is as we have specify
>> the "ibrav" i.e symmetry of the system the relax calculation only
>> optimizes the structure within the given symmetry.
> Not exactly, the relax calculation plays a role to find out an optimal
> configuration from an initial configuration.
> If you want to consider the surface reconstruction of given material,
> you should build a supercell in that the defect or adatom can be existed.
>
> And how to form a supercell. Let see the previous archives of PW_forum
>
> Good luck
>
> Linh
>
>
>
>
> --
> -----------------------------------------------------
>  Nguyen Ngoc Linh, PhD Student
>  c/o:   SISSA & CNR-INFM Democritos,
>         via Beirut 2-4, 34014 Trieste (Italy)
>  email: nnlinh at sissa.it
>  phone: +39 04 03787 319
>  skype: ngoclinh84phys
> -----------------------------------------------------
> "The physics is theoretical but the fun is real"
>
>
>
>
> ------------------------------
>
> Message: 10
> Date: Wed, 10 Mar 2010 11:10:20 +0100
> From: Giovanni Cantele <giovanni.cantele at na.infn.it>
> Subject: Re: [Pw_forum] SURFACE RECONSTRUCTION USING RELAX CALCULATION
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <C1F70D93-3106-46A2-8DD4-A048B2C7052F at na.infn.it>
> Content-Type: text/plain; charset=us-ascii
>
>
> On Mar 10, 2010, at 10:35 AM, mohnish pandey wrote:
>
>> Dear users,
>>                    I want to get the results for surface reconstructions
>> computationally, but the problem is as we have specify the "ibrav" i.e
>> symmetry of the system the relax calculation only optimizes the structure
>> within the given symmetry. Can anybody suggest a way to model
>> reconstructions .
>> Thanks in advance,
>> MOHNISH
>>
>> --
>> Mohnish Pandey
>> Y6927262,4th Year dual degree student,
>> Department of Chemical Engineering,
>> IIT KANPUR
>> 09235721300
>>
>
> Well, I think that a "very general" answer is difficult to give (maybe
> someone more expert could try). What one usually does in studying surfaces,
> is try to identify,
> step by step, possible reconstructions and look at the lower energy ones.
>
> In practice, for a given surface direction (e.g. the silicon 100 surface)
> you first identify the "minimal" unit cell (size and symmetry) in the plane
> parallel to the surface. Then, you must decide
> the number of atomic planes that you want to include in your calculation
> (this will fix the lattice constant in the direction orthogonal to the
> surface). This
> will represent a so-called 1x1 model, meaning that your "surface unit cell"
> is made by just one unit cell. Possible reconstruction (which means atomic
> rearrangement of the atoms with respect to the ideal positions) will be, of
> course, the same in all surface unit cells.
>
> More complicated reconstructions might arise because:
>
> i) there can be a surface atomic displacement different in neighbor unit
> cells (for example, in the case of the cited Si surface two Si atoms in
> different 1x1 cells approach to each other to form a dimer, this gives you a
> 2x1 reconstruction; then two neighbor dimers can show different tilt with
> respect to the surface plane, this gives a 2x2 reconstruction, etc.); to
> include
> this effect in your calculation you replicate your surface unit cell
> (building a "supercell") in one or both directions parallel to the surface,
> so as to build 1x2, 2x1, 2x2, 1x4, etc. models. Of course one should
> be driven by either already known results, experimental evidences, etc. or
> by physically/chemically meaningful guesses. In this case one should also be
> careful to break possible symmetries that would prevent from reaching the
> energy minimum. Again, in the case of the Si(100) surface, if you just
> replicate the 1x1 unit cell along one surface direction, to build the 2x1
> model, the code will just give you
> a structure identical to the 1x1 model, with an energy 2 times larger; so,
> what you do is to move (even by a small amount) the atoms you expect will
> move, namely, the two Si atoms which dimerize. Alternatively, you can
> randomize the position of some/all atoms, just to break the symmetry.
>
> ii) there can be a reconstruction where there are more/less atoms than you
> would expect in the "ideal" surface, a typical example is the case of O
> vacancies in oxide surfaces.
>
> Because the plane-wave calculation, as you probably already know, is by
> construction periodic in all directions, you must be sure to include, along
> the direction orthogonal to the surface a
> "vacuum space" (that means to increase the corresponding lattice parameter)
> to prevent two consecutive slabs from interacting. Convergence must be
> checked against the vacuum space.
> Also, if you want to retrieve the "bulk surface" properties, the thickness
> of your slab should be larger enough (this is controlled by the number of
> atomic planes included in the unit cell) to prevent
> opposite sides of a given slab from interacting with each other.
>
> Another issue is that the "optimal" surface unit cell might show a
> completely different "symmetry" than the bulk one. For example, in the case
> of Au/Pt/etc. (111) surfaces, the bulk crystal is a cubic
> fcc lattice, whereas the minimal surface unit cell can be represented using
> an hexagonal lattice.
>
> Hope this helps,
>
>     Giovanni
>
>
> --
>
> Giovanni Cantele, PhD
> CNR-SPIN and Dipartimento di Scienze Fisiche
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> Phone: +39 081 676910 - Fax:   +39 081 676346
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>                      http://www.nanomat.unina.it
>
>
>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 33, Issue 37
> ****************************************
>


-- 
Cecil Naphtaly Moro

From dalcorso at sissa.it  Wed Mar 10 18:11:09 2010
From: dalcorso at sissa.it (Dal Corso Andrea)
Date: Wed, 10 Mar 2010 18:11:09 +0100
Subject: [Pw_forum] Wrong oxygen mass in example 13
In-Reply-To: <B14EC77E-4857-41F8-80B2-DAD9EDCA2143@democritos.it>
References: <5402fae9bf72dc5584f7602ae5b53f64.squirrel@webmail.uio.no>
	<B14EC77E-4857-41F8-80B2-DAD9EDCA2143@democritos.it>
Message-ID: <1268241069.3267.7.camel@dhcp-5-36.sissa.it>

On Wed, 2010-03-10 at 17:49 +0100, Paolo Giannozzi wrote:
> On Mar 10, 2010, at 17:19 , Dan Michael Olsen Hegg? wrote:
> 
> > I discovered that the oxygen mass is given as 55.847 in example 13,
> > which is in fact the mass of iron. While this doesn't affect the  
> > result, it
> > should probably be corrected :)
> 
> done, thank you
> 
> > This leads me to a (perhaps stupid) question: In what type of  
> > calculations
> > is the ionic mass used? MD and phonon calculations?
> 
> correct (not sure about phonons, though: the phonon code also reads
> masses in input data)
> 

In the phonon code the masses are as follows:
masses in input of ph.x are always used. 
If no mass is given to ph.x and the mass in pw.x is not zero this 
mass is used. If both the mass in the input of pw.x and of ph.x are zero
(or not given) the phonon uses its internally coded masses that are
decided using the name of the element.  

HTH

Andrea


> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
34151 Trieste (Italy)               e-mail: dalcorso at sissa.it



From giovanni.cantele at na.infn.it  Wed Mar 10 18:15:29 2010
From: giovanni.cantele at na.infn.it (Giovanni Cantele)
Date: Wed, 10 Mar 2010 18:15:29 +0100
Subject: [Pw_forum] QE & Xcrysden
In-Reply-To: <fe3b32711003100907y3fc83344i48ddaae131eef24f@mail.gmail.com>
References: <fe3b32711003100907y3fc83344i48ddaae131eef24f@mail.gmail.com>
Message-ID: <733ED863-5BA1-4D6D-AC0B-B65F9D48574C@na.infn.it>



On Mar 10, 2010, at 6:07 PM, naphtaly moro wrote:

> Dear Re: Ngoc Linh Nguyen, Giovanni Cantele & Sebastijan Peljhan
> 
> I am working on the various phases of GaAs. at normal conditions, GaAs
> assumes a Zincblende structures fcc ibrav=2, as pressure increases it
> assumes Rocksalt structure and then assumes a CsCl structure which is
> bcc ibrav=3 that is why my input as i posted it. Can you advice me
> further?
> Regards

This is possible, but as I explained, your positions are wrong. Indeed, the atom in 000
will be periodically replicated according to the bcc lattice sites. That means that you have
a Ga atom in 0.5 0.5 0.5 too.
If you specify the As position as 0.5 0.5 0.5 that will be overlapped to the Ga atom end no 
code will know what to do.

Therefore, you should understand after the fcc -> bcc transition what changes to the basis
occur, namely the "new" atomic positions in the bcc lattice unit cell.

Giovanni



> 
> 
>> 
>> 
>> 
>> 
>> ------------------------------
>> 
>> Message: 2
>> Date: Wed, 10 Mar 2010 11:44:52 +0300
>> From: naphtaly moro <moronaphtaly84 at gmail.com>
>> Subject: [Pw_forum] QE & Xcrysden
>> To: pw_forum at pwscf.org
>> Message-ID:
>> 	<fe3b32711003100044t31b012aen17eacad01974f4ee at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>> 
>> Dear Q.E. & Xcrysden
>> I am working on the various phase transitions of GaAs. I am trying to
>> contact these structures. I ahve managed to construct the ZB and RS
>> structures with success. I am using Xcrysden with Quantum Espresso.
>> When i try to view the CsCl-GaAs structure,  I only see the Ga atoms
>> and with no As atoms in the matrix. Can someone show me please where I
>> am going wrong
>> my input file is this
>> &control
>>   prefix='GaAs',
>>   pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo'
>>   outdir = './tmp',
>> /
>> &system
>>   ibrav=  3, celldm(1) =10.2, nat=  2, ntyp= 2,
>>   ecutwfc = 12.0,
>> /
>> &electrons
>> /
>> ATOMIC_SPECIES
>> Ga  69.723  Ga.pbe-nsp-van.UPF
>> As  74.9216 As.pbe-n-van.UPF
>> ATOMIC_POSITIONS
>> Ga 0.00 0.00 0.00
>> As 0.50 0.50 0.50
>> K_POINTS {automatic}
>> 4 4 4 0 0 0
>> 
>> Thanks
>> 
>> 
>> --
>> Cecil Naphtaly Moro
>> 
>> 
>> ------------------------------
>> 
>> Message: 3
>> Date: Wed, 10 Mar 2010 10:07:19 +0100
>> From: Ngoc Linh Nguyen <nnlinh at sissa.it>
>> Subject: Re: [Pw_forum] QE & Xcrysden
>> To: PWSCF Forum <pw_forum at pwscf.org>
>> Message-ID: <4B976147.6060104 at sissa.it>
>> Content-Type: text/plain; charset=us-ascii; format=flowed
>> 
>> naphtaly moro wrote:
>>> Dear Q.E. & Xcrysden
>>> I am working on the various phase transitions of GaAs. I am trying to
>>> contact these structures. I ahve managed to construct the ZB and RS
>>> structures with success. I am using Xcrysden with Quantum Espresso.
>>> When i try to view the CsCl-GaAs structure,  I only see the Ga atoms
>>> and with no As atoms in the matrix. Can someone show me please where I
>>> am going wrong
>>> my input file is this
>>> &control
>>>   prefix='GaAs',
>>>   pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo'
>>>   outdir = './tmp',
>>> /
>>> &system
>>>   ibrav=  3, celldm(1) =10.2, nat=  2, ntyp= 2,
>>>   ecutwfc = 12.0,
>>> /
>>> &electrons
>>> /
>>> ATOMIC_SPECIES
>>> Ga  69.723  Ga.pbe-nsp-van.UPF
>>> As  74.9216 As.pbe-n-van.UPF
>>> ATOMIC_POSITIONS
>>> Ga 0.00 0.00 0.00
>>> As 0.50 0.50 0.50
>>> K_POINTS {automatic}
>>> 4 4 4 0 0 0
>>> 
>>> 
>> You are having a wrong input structure. Namely, you chose ibrav= 3 which
>> means BCC lattice, so in a periodic lattice the As atoms will be
>> overlapped by Ga atoms.
>> 
>> How to fix the problem. You should again pick up another ibrav value and
>> calculate the Gs and As positions.
>> As far as I know, GaAs lattice have a similarity to diamond lattice, so
>> I suggest ibrav=2, and
>> 
>> Ga 0.00 0.00 0.00
>> As 0.25 0.25 0.25
>> 
>> Good luck
>> 
>> Linh
>> 
>> 
>>> Thanks
>>> 
>>> 
>>> 
>> 
>> 
>> --
>> -----------------------------------------------------
>> Nguyen Ngoc Linh, PhD Student
>> c/o:   SISSA & CNR-INFM Democritos,
>>        via Beirut 2-4, 34014 Trieste (Italy)
>> email: nnlinh at sissa.it
>> phone: +39 04 03787 319
>> skype: ngoclinh84phys
>> -----------------------------------------------------
>> "The physics is theoretical but the fun is real"
>> 
>> 
>> 
>> 
>> ------------------------------
>> 
>> Message: 4
>> Date: Wed, 10 Mar 2010 10:12:03 +0100
>> From: Giovanni Cantele <giovanni.cantele at na.infn.it>
>> Subject: Re: [Pw_forum] QE & Xcrysden
>> To: PWSCF Forum <pw_forum at pwscf.org>
>> Message-ID: <A01EC0FD-0226-4351-A0A6-040071AACB82 at na.infn.it>
>> Content-Type: text/plain; charset=us-ascii
>> 
>> 
>> On Mar 10, 2010, at 9:44 AM, naphtaly moro wrote:
>> 
>>> Dear Q.E. & Xcrysden
>>> I am working on the various phase transitions of GaAs. I am trying to
>>> contact these structures. I ahve managed to construct the ZB and RS
>>> structures with success. I am using Xcrysden with Quantum Espresso.
>>> When i try to view the CsCl-GaAs structure,  I only see the Ga atoms
>>> and with no As atoms in the matrix. Can someone show me please where I
>>> am going wrong
>>> my input file is this
>>> &control
>>>  prefix='GaAs',
>>>  pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo'
>>>  outdir = './tmp',
>>> /
>>> &system
>>>  ibrav=  3, celldm(1) =10.2, nat=  2, ntyp= 2,
>>>  ecutwfc = 12.0,
>>> /
>>> &electrons
>>> /
>>> ATOMIC_SPECIES
>>> Ga  69.723  Ga.pbe-nsp-van.UPF
>>> As  74.9216 As.pbe-n-van.UPF
>>> ATOMIC_POSITIONS
>>> Ga 0.00 0.00 0.00
>>> As 0.50 0.50 0.50
>>> K_POINTS {automatic}
>>> 4 4 4 0 0 0
>>> 
>>> Thanks
>>> 
>>> 
>>> --
>>> Cecil Naphtaly Moro
>> 
>> 
>> The reason is that you specify ibrav = 3 that, according to what explained
>> in Doc/INPUT_PW.txt is a bcc lattice.
>> At the same time you give the ATOMIC_POSITIONS in units of the alat (namely,
>> a in bohr units).
>> Therefore, the As atom is placed at (a/2, a/2, a/2) which is, by chance (!),
>> also a site of the bcc lattice.
>> In other words, what XCrysDen sees is a Ga atom in a/2,a/2,a/2 but ALSO an
>> As atom at the same place and decides
>> to delete the latter.
>> Maybe you want to specify the fcc lattice (ibrav=2) and the As atom at
>> a/4,a/4,a/4.
>> 
>> Giovanni
>> 
>> 
>> PS not very sure that ecutwfc = 12.0 whould give you converged results.
>> Also, because you choosed
>> ultrasoft pseudopotentials, you might want also check the ecutrho parameter
>> (by default = 4 * ecutwfc,
>> but larger values are needed when using US pseudo).
>> 
>> --
>> 
>> Giovanni Cantele, PhD
>> CNR-SPIN and Dipartimento di Scienze Fisiche
>> Universita' di Napoli "Federico II"
>> Complesso Universitario M. S. Angelo - Ed. 6
>> Via Cintia, I-80126, Napoli, Italy
>> Phone: +39 081 676910 - Fax:   +39 081 676346
>> Skype contact: giocan74
>> 
>> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
>> Web page: http://people.na.infn.it/~cantele
>>                     http://www.nanomat.unina.it
>> 
>> 
>> 
>> ------------------------------
>> 
>> Message: 5
>> Date: Wed, 10 Mar 2010 10:22:31 +0100
>> From: Sebastijan Peljhan <sebastijan.peljhan at ijs.si>
>> Subject: Re: [Pw_forum] QE & Xcrysden
>> To: PWSCF Forum <pw_forum at pwscf.org>
>> Message-ID: <1268212951.2427.22.camel at surf>
>> Content-Type: text/plain; charset="UTF-8"
>> 
>> Dear Cecil,
>> 
>> On Wed, 2010-03-10 at 11:44 +0300, naphtaly moro wrote:
>>> Dear Q.E. & Xcrysden
>>> I am working on the various phase transitions of GaAs. I am trying to
>>> contact these structures. I ahve managed to construct the ZB and RS
>>> structures with success. I am using Xcrysden with Quantum Espresso.
>>> When i try to view the CsCl-GaAs structure,  I only see the Ga atoms
>>> and with no As atoms in the matrix. Can someone show me please where I
>>> am going wrong
>>> my input file is this
>>> &control
>>>   prefix='GaAs',
>>>   pseudo_dir='/home/physics/Desktop/espresso-4.0.5/pseudo'
>>>   outdir = './tmp',
>>> /
>>> &system
>> 
>> ibrav = 3 represents bcc cubic cell, hence the Ga and As atoms in your
>> structure overlap. Xcrysden actually warns you, that some of the atoms
>> overlap and they will be deleted.
>> 
>> According to QE example06 you should try with ibrav = 2 (fcc) and As
>> atom at (0.25 0.25 0.25) position.
>> 
>> 
>> Cheers,
>> 
>> Sebastijan
>> 
>> 
>>>   ibrav=  3, celldm(1) =10.2, nat=  2, ntyp= 2,
>>>   ecutwfc = 12.0,
>>> /
>>> &electrons
>>> /
>>> ATOMIC_SPECIES
>>> Ga  69.723  Ga.pbe-nsp-van.UPF
>>> As  74.9216 As.pbe-n-van.UPF
>>> ATOMIC_POSITIONS
>>> Ga 0.00 0.00 0.00
>>> As 0.50 0.50 0.50
>>> K_POINTS {automatic}
>>> 4 4 4 0 0 0
>>> 
>>> Thanks
>>> 
>>> 
>> 




--

Giovanni Cantele, PhD
CNR-SPIN and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910 - Fax:   +39 081 676346
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it

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From nnlinh at sissa.it  Wed Mar 10 18:13:57 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Wed, 10 Mar 2010 18:13:57 +0100
Subject: [Pw_forum] QE & Xcrysden
In-Reply-To: <fe3b32711003100907y3fc83344i48ddaae131eef24f@mail.gmail.com>
References: <fe3b32711003100907y3fc83344i48ddaae131eef24f@mail.gmail.com>
Message-ID: <4B97D355.9040600@sissa.it>

naphtaly moro wrote:
> Dear Re: Ngoc Linh Nguyen, Giovanni Cantele & Sebastijan Peljhan
>
> I am working on the various phases of GaAs. at normal conditions, GaAs
> assumes a Zincblende structures fcc ibrav=2, as pressure increases it
> assumes Rocksalt structure and then assumes a CsCl structure which is
> bcc ibrav=3 that is why my input as i posted it. Can you advice me
> further?
>   
I see, let put ibrav = 1 simple cubic, the primitive vector will be (0.5 
0.5 0.5).

You will see a right CsCls structure for GaAs.

Linh

> Regards
>   
p/s You should reply the answer or question belong to thread, don't 
reply all the questions of a day. Many thanks.



-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From paulatto at sissa.it  Wed Mar 10 18:15:17 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 10 Mar 2010 18:15:17 +0100
Subject: [Pw_forum] QE & Xcrysden
In-Reply-To: <fe3b32711003100907y3fc83344i48ddaae131eef24f@mail.gmail.com>
References: <fe3b32711003100907y3fc83344i48ddaae131eef24f@mail.gmail.com>
Message-ID: <op.u9c3jrhaa8x26q@vanoxite.impmc.jussieu.fr>

On Wed, 10 Mar 2010 18:07:47 +0100, naphtaly moro  
<moronaphtaly84 at gmail.com> wrote:
> I am working on the various phases of GaAs. at normal conditions, GaAs
> assumes a Zincblende structures fcc ibrav=2, as pressure increases it
> assumes Rocksalt structure and then assumes a CsCl structure which is
> bcc ibrav=3 that is why my input as i posted it. Can you advice me
> further?


Dear Naphtaly,
according to what I see here:  
<http://cst-www.nrl.navy.mil/lattice/struk/b2.html> the CsCl structure is  
not BCC but simple-cubic. More specifically, the positions of Cs and Cl  
ions form together a BCC lattice; nevertheless, as Cl is not equal to Cs,  
you have to use a SC unit cell to describe the system.

regards

-- 
Lorenzo Paulatto

*** Note: my affiliation has changed! please send future
correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***

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

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

From bipulrr at gmail.com  Wed Mar 10 18:28:44 2010
From: bipulrr at gmail.com (Bipul Rakshit)
Date: Wed, 10 Mar 2010 22:58:44 +0530
Subject: [Pw_forum] Drawing 2D plane using XCRYSDEN
Message-ID: <3a749911003100928j5a20e964y96c707b9c4c52f52@mail.gmail.com>

Dear PWSCF users,
I have a zince blende crystal ZnS. Now i want to see how the 110 plane
(or any plane) in that crystal structure.
So can anybody tell me how to ( with which command) to see a plane
with the help of pwscf input file and xcrysden?

To view the structure i am using

xcrysden --pwi ZnS.scf.in



-- 
Bipul Rakshit
Research Fellow,
S N Bose Centre for Basic Sciences,
Salt Lake,
Kolkata 700 098
India

From elie.moujaes at hotmail.co.uk  Wed Mar 10 19:10:47 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Wed, 10 Mar 2010 18:10:47 +0000
Subject: [Pw_forum] density of states of graphene
Message-ID: <SNT114-W51AEED215BB8B502ACF4A0D3330@phx.gbl>


Dear all, I have got results for the density of states of graphene using both scf and nscf techniques and both gave different results. The SCF calculation was with the C.pz-rrkjus.UPF and with a k points grid of 30x30x1. The NSCF calculation was with C.pz-vbc.UPF nad with 700 points (crystal_b)..I think the nscf converges more towards a zero DOS at some point. I am attaching both results and I would be greatful if someone can let me know if any of them looks like the DOS of graphene and why that difference.

 

Regards.

 

Elie Moujaes

University of Nottingham

Physics department

NG7 2RD

nOTTINGHAM,

UK
 		 	   		  
_________________________________________________________________
Do you have a story that started on Hotmail? Tell us now
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From jibiaoli at gmail.com  Wed Mar 10 19:30:31 2010
From: jibiaoli at gmail.com (Jibiao Li)
Date: Wed, 10 Mar 2010 19:30:31 +0100
Subject: [Pw_forum] Drawing 2D plane using XCRYSDEN
In-Reply-To: <3a749911003100928j5a20e964y96c707b9c4c52f52@mail.gmail.com>
References: <3a749911003100928j5a20e964y96c707b9c4c52f52@mail.gmail.com>
Message-ID: <b8b82da21003101030v7850460dq9ce0ba8f72958cc8@mail.gmail.com>

pls specify two vectors in pp.input file for the plane of your interest
e.g. vector E1 and E2 represent the plane
e1(1)=1, e1(2)=1, e1(3)=0
e2(1)=0, e2(2)=0, e2(3)=0


On Wed, Mar 10, 2010 at 6:28 PM, Bipul Rakshit <bipulrr at gmail.com> wrote:

> Dear PWSCF users,
> I have a zince blende crystal ZnS. Now i want to see how the 110 plane
> (or any plane) in that crystal structure.
> So can anybody tell me how to ( with which command) to see a plane
> with the help of pwscf input file and xcrysden?
>
> To view the structure i am using
>
> xcrysden --pwi ZnS.scf.in
>
>
>
> --
> Bipul Rakshit
> Research Fellow,
> S N Bose Centre for Basic Sciences,
> Salt Lake,
> Kolkata 700 098
> India
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Jibiao Li

AlbaNova University Center
Department of Physics
Stockholm University
Tel. :  08-55378720 (office)
Email: jibiaoli at gmail.com
         jibiao.li at hotmail.com
         jibiao at fysik.su.se
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From elie.moujaes at hotmail.co.uk  Wed Mar 10 20:16:32 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Wed, 10 Mar 2010 19:16:32 +0000
Subject: [Pw_forum] density of states of graphene
In-Reply-To: <4B97EE3B.6080404@cnf.cornell.edu>
References: <SNT114-W51AEED215BB8B502ACF4A0D3330@phx.gbl>,
	<4B97EE3B.6080404@cnf.cornell.edu>
Message-ID: <SNT114-W30607C34DD840533985D35D3330@phx.gbl>


Thanks very much for your help. I thought something was still not quite right.  will send you the files and meanwhile might run the scf one using a 96x96x1 grid.

 

Regards

 

Elie Moujaes

University of Nottingham

Nottingham

NG7 2RD

UK
 
> Date: Wed, 10 Mar 2010 14:08:43 -0500
> From: stewart at cnf.cornell.edu
> To: elie.moujaes at hotmail.co.uk
> Subject: Re: [Pw_forum] density of states of graphene
> 
> Hi Elie,
> 
> Based on the DOS you sent, I think there are still some problems with 
> your scf input file. I may have missed it in the earlier 
> correspondence, but if you send it my way, I'll take a look at it and 
> see if I have any suggestions.
> 
> I looked at the DOS for graphene about a year ago when I was working on 
> graphene oxide. I found that you need a very high k-point grid in the 
> 2d plane to get an accurate DOS. For example for the scf part, I used 
> 66x66x1 and for the DOS calculation, I believe I used 96x96x1.
> 
> Best regards,
> 
> Derek
> 
> ################################
> Derek Stewart, Ph. D.
> Senior Research Associate
> ** New Webpage **
> http://sites.google.com/site/dft4nano/
> 250 Duffield Hall
> Cornell Nanoscale Facility (CNF)
> Ithaca, NY 14853
> stewart (at) cnf.cornell.edu
> (607) 255-2856
> 
> 
> 
> 
> Elie Moujaes wrote:
> > Dear all, I have got results for the density of states of graphene 
> > using both scf and nscf techniques and both gave different results. 
> > The SCF calculation was with the C.pz-rrkjus.UPF and with a k points 
> > grid of 30x30x1. The NSCF calculation was with C.pz-vbc.UPF nad with 
> > 700 points (crystal_b)..I think the nscf converges more towards a zero 
> > DOS at some point. I am attaching both results and I would be greatful 
> > if someone can let me know if any of them looks like the DOS of 
> > graphene and why that difference.
> > 
> > Regards.
> > 
> > Elie Moujaes
> > University of Nottingham
> > Physics department
> > NG7 2RD
> > nOTTINGHAM,
> > UK
> >
> > ------------------------------------------------------------------------
> > Do you want a Hotmail account? Sign-up now - Free 
> > <http://clk.atdmt.com/UKM/go/197222280/direct/01/>
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> > 
> 
> 
 		 	   		  
_________________________________________________________________
Do you have a story that started on Hotmail? Tell us now
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From yfang1 at tulane.edu  Wed Mar 10 20:43:15 2010
From: yfang1 at tulane.edu (Fang, Yuan)
Date: Wed, 10 Mar 2010 13:43:15 -0600
Subject: [Pw_forum] xc functional
References: <9c9214d71003100141v51ffb64bm3705f2aaf80a98d0@mail.gmail.com>
Message-ID: <D8E427248814A143AF7763DFA469B5F925CFEF@EX04.ad.tulane.edu>

Hey;
    Anyone know how to control the xc functional used in the scf calculation?I cant find the variable in the input to adjust this.And where are the file  in the source code that describe different functionals,we want to change pbe to pbesol if possible.
           Thank you!
                             Y Fang
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From ferretti at mit.edu  Wed Mar 10 21:01:12 2010
From: ferretti at mit.edu (Andrea Ferretti)
Date: Wed, 10 Mar 2010 20:01:12 +0000 (GMT)
Subject: [Pw_forum] xc functional
In-Reply-To: <D8E427248814A143AF7763DFA469B5F925CFEF@EX04.ad.tulane.edu>
References: <9c9214d71003100141v51ffb64bm3705f2aaf80a98d0@mail.gmail.com>
	<D8E427248814A143AF7763DFA469B5F925CFEF@EX04.ad.tulane.edu>
Message-ID: <alpine.LNX.2.00.1003101959450.31211@grey.materials.ox.ac.uk>



Hi Y Fang,

you have to add
input_dft = "PBEsol"
to the SYSTEM namelist.

the source code controlling this part is in
Modules/functionals.f90
Modules/input_parameters.f90

hope it helps
andrea

> Hey;
>    Anyone know how to control the xc functional used in the
>    scf calculation?I cant find the variable in the input to adjust
>    this. And where are the file  in the source code that describe
>    different functionals,we want to change pbe to pbesol if possible.
>           Thank you!
>                             Y Fang
>

-- 
Andrea Ferretti
Oxford University, Department of Materials
Parks Road, Oxford OX1 3PH, UK
Tel: +44 (0)1865 612796;  Skype: andrea_ferretti
URL: http://quasiamore.mit.edu

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

From giovanni.cantele at na.infn.it  Wed Mar 10 22:18:16 2010
From: giovanni.cantele at na.infn.it (Giovanni Cantele)
Date: Wed, 10 Mar 2010 22:18:16 +0100 (CET)
Subject: [Pw_forum] density of states of graphene
In-Reply-To: <SNT114-W51AEED215BB8B502ACF4A0D3330@phx.gbl>
References: <SNT114-W51AEED215BB8B502ACF4A0D3330@phx.gbl>
Message-ID: <49536.93.150.241.25.1268255896.squirrel@imap-ac.na.infn.it>

> Dear all, I have got results for the density of states of graphene using
> both scf and nscf techniques and both gave different results. The SCF
> calculation was with the C.pz-rrkjus.UPF and with a k points grid of
> 30x30x1. The NSCF calculation was with C.pz-vbc.UPF nad with 700 points
> (crystal_b)..I think the nscf converges more towards a zero DOS at some
> point. I am attaching both results and I would be greatful if someone can
> let me know if any of them looks like the DOS of graphene and why that
> difference.
> Regards.
> Elie Moujaes
> University of Nottingham
> Physics department
> NG7 2RD
> nOTTINGHAM,
> UK

Dear Elie,
I think there is something wrong with the procedure you are following. It
has no meaning (generally speaking) to have a DOS built using an "scf
technique" and a DOS built using an "nscf technique".

First try to understand what is the difference between scf and nscf: they
are not alternative techniques to get the same answer, but just two
different things.
An "scf" calculation consists in starting from an initial wave function
guess, building the initial Hamiltonian, diagonalizing it, getting the new
wave functions, then the new Hamiltonian. The process is iterated until
convergence is achieved. The final result is the ground state charge
density (GSCD), which is stored in some format within your outdir.

The "nscf" calculation means that you ALREADY have the GSCD, so you do not
need to iterate as described above, to obtain the self-consistent
Hamiltonian / GSCD. In this sense you say non-self-consistent-field=nscf.
Using this procedure you can get, for example, the eigenvalues along
special lines in the Brilluoin zone (BZ), namely, the band structure.
Else, you can calculate (by specifying the nbnd variable) the "unoccupied"
eigenvalues, that are not needed of course to build the GSCD.

Let's come now to the DOS calculation: what do you need for it? You need a
very fine sampling of the BZ, much denser than the one needed to
self-consistently calculate the GSCD. Because it would be very expensive
to do the scf calculation with such dense grids (the scf converges with
respect to the BZ sampling much faster than the DOS), one usually makes
FIRST the scf calculation with a reasonable k-point grid, THEN the nscf
calculation where you specify a much denser grid.

For example, a safe choice in the case of graphene would be:
- scf
K_POINTS { automatic }
16  16  1    0  0  0

-nscf
K_POINTS { automatic }
64  64  1    0  0  0
(128  128 1    0  0  0 might be checcked as well!)

That means that by sampling the graphene BZ with a uniform 16x16x1 grid
should be enough to get a converged GSCD, but if you want to calculate the
DOS you need a sampling with a 64x64x1 or 128x128x1 grid.


From yukihiro_okuno at fujifilm.co.jp  Thu Mar 11 02:37:16 2010
From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp)
Date: Thu, 11 Mar 2010 10:37:16 +0900
Subject: [Pw_forum] Error in running GWW  wrong data-file.xml file
Message-ID: <OFAEAF8A34.C910E740-ON492576E3.000827EC-492576E3.0008E80C@mta.fujifilm.co.jp>


Dear Prof. Andrea and PWSCF users.

Thank you your reply in mailing lists and  your plan to correct phonon
codes which
works with GWW.

By the way,  are there any version of Quantum Expresso which works GWW?
I want to try to use GWW.

Sincerely.


>Thank you for reporting this and for your detailed explanations.
>It is due to a recent change in the phonon code that is not compatible
>with GWW. It should now be fixed in the CVS version.

>Andrea


>On Tue, 2010-03-09 at 21:22 +0900, yukihiro_okuno at fujifilm.co.jp wrote:
>> Dear PWSCF users and Dr Adrian.
>>
>> I also met the same error in example02 in GWW
>> and it comes in the head.x,  and I saw the program
>> of GWW a little.
>>
>>> In the head.f90,
>>
>> call ph_writefile('init',0)
>> and in ph_writefile ( and function called from ph_writefile,,, )
>>
>> write XML file in *.phsave/data-file.xml
>>
>> which is wrong for later reading ,,
>>
>> In the program, later need  the data-file.xml
>> call ph_readfile('data_u',ierr)  and then inside the ph_readfile,
>>
>> call read_u(dirname,ierr)
>>
>> and in this function ,  the program read "data-file.xml."1" file
>>
>> (where "1" will be the wave number index of phonon or others, I think )
>>
>> and furthermore, the information in data-file.xml
>>
>> is not enough for read_u (like TENSOR.INFO,,,,,,, ).
>>
>>
>> The resent CVS GWW codes still contains the error in
>> GWW_examples/example02.
>>
>> Are there any correct sample input file for GW calculation  for GWW
program
>> ?
>>
>> Sincerely,
>>
>> Yukihiro Okuno.


From ttduyle at gmail.com  Thu Mar 11 03:07:13 2010
From: ttduyle at gmail.com (Duy Le)
Date: Wed, 10 Mar 2010 21:07:13 -0500
Subject: [Pw_forum] SURFACE RECONSTRUCTION USING RELAX CALCULATION
In-Reply-To: <4B976D84.8070607@sissa.it>
References: <c40d64601003100135sc393a66h1f2a5ada30fac6cc@mail.gmail.com> 
	<4B976D84.8070607@sissa.it>
Message-ID: <8974d3b21003101807r10629100y45855b85e4b65f8a@mail.gmail.com>

How about ibrav=0?
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Wed, Mar 10, 2010 at 4:59 AM, Ngoc Linh Nguyen <nnlinh at sissa.it> wrote:
> mohnish pandey wrote:
>> ? ? ? ? ? ? ? ? ? ?I want to get the results for surface
>> reconstructions computationally, but the problem is as we have specify
>> the "ibrav" i.e symmetry of the system the relax calculation only
>> optimizes the structure within the given symmetry.
> Not exactly, the relax calculation plays a role to find out an optimal
> configuration from an initial configuration.
> If you want to consider the surface reconstruction of given material,
> you should build a supercell in that the defect or adatom can be existed.
>
> And how to form a supercell. Let see the previous archives of PW_forum
>
> Good luck
>
> Linh
>
>
>
>
> --
> -----------------------------------------------------
> ?Nguyen Ngoc Linh, PhD Student
> ?c/o: ? SISSA & CNR-INFM Democritos,
> ? ? ? ?via Beirut 2-4, 34014 Trieste (Italy)
> ?email: nnlinh at sissa.it
> ?phone: +39 04 03787 319
> ?skype: ngoclinh84phys
> -----------------------------------------------------
> "The physics is theoretical but the fun is real"
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From giannozz at democritos.it  Thu Mar 11 08:32:02 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 11 Mar 2010 08:32:02 +0100
Subject: [Pw_forum] Error in running GWW  wrong data-file.xml file
In-Reply-To: <OFAEAF8A34.C910E740-ON492576E3.000827EC-492576E3.0008E80C@mta.fujifilm.co.jp>
References: <OFAEAF8A34.C910E740-ON492576E3.000827EC-492576E3.0008E80C@mta.fujifilm.co.jp>
Message-ID: <AA4CCBC0-FABE-446F-832B-AF410FA7A7C0@democritos.it>


On Mar 11, 2010, at 2:37 , yukihiro_okuno at fujifilm.co.jp wrote:

> By the way,  are there any version of Quantum Expresso which works  
> GWW?

the current cvs version works (or at least, it doesn't crash)

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




From giannozz at democritos.it  Thu Mar 11 08:46:11 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 11 Mar 2010 08:46:11 +0100
Subject: [Pw_forum] pseudopotential for Fe and Se
In-Reply-To: <7234ba151003100711r30ebe55g6248c92efa05bdfc@mail.gmail.com>
References: <7234ba151003100709v336abb52of77812d1e6006cc7@mail.gmail.com>
	<7234ba151003100711r30ebe55g6248c92efa05bdfc@mail.gmail.com>
Message-ID: <8102F807-CBCB-49D7-993A-7447C668C48C@democritos.it>


On Mar 10, 2010, at 16:11 , Gianluca Giovannetti wrote:

>     i did some calculations using  pseudopotentials:  Fe.pbe-sp- 
> van.UPF , Se.pbe-van.UPF.
>     results are very similar to ones i can get with another dft code.
>     are these pseudopotentials consistent in PW?

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




From nnlinh at sissa.it  Thu Mar 11 10:07:08 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Thu, 11 Mar 2010 10:07:08 +0100
Subject: [Pw_forum] SURFACE RECONSTRUCTION USING RELAX CALCULATION
In-Reply-To: <8974d3b21003101807r10629100y45855b85e4b65f8a@mail.gmail.com>
References: <c40d64601003100135sc393a66h1f2a5ada30fac6cc@mail.gmail.com>
	<4B976D84.8070607@sissa.it>
	<8974d3b21003101807r10629100y45855b85e4b65f8a@mail.gmail.com>
Message-ID: <4B98B2BC.5050805@sissa.it>

It's also ok with the  cell-parameters of only either cubic or hexagonal.

So I prefer using supercell then putting ibrav=0
 
Linh


Duy Le wrote:
> How about ibrav=0?
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
>
> On Wed, Mar 10, 2010 at 4:59 AM, Ngoc Linh Nguyen <nnlinh at sissa.it> wrote:
>   
>> mohnish pandey wrote:
>>     
>>>                    I want to get the results for surface
>>> reconstructions computationally, but the problem is as we have specify
>>> the "ibrav" i.e symmetry of the system the relax calculation only
>>> optimizes the structure within the given symmetry.
>>>       
>> Not exactly, the relax calculation plays a role to find out an optimal
>> configuration from an initial configuration.
>> If you want to consider the surface reconstruction of given material,
>> you should build a supercell in that the defect or adatom can be existed.
>>
>> And how to form a supercell. Let see the previous archives of PW_forum
>>
>> Good luck
>>
>> Linh
>>
>>
>>
>>
>> --
>> -----------------------------------------------------
>>  Nguyen Ngoc Linh, PhD Student
>>  c/o:   SISSA & CNR-INFM Democritos,
>>        via Beirut 2-4, 34014 Trieste (Italy)
>>  email: nnlinh at sissa.it
>>  phone: +39 04 03787 319
>>  skype: ngoclinh84phys
>> -----------------------------------------------------
>> "The physics is theoretical but the fun is real"
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>     
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From elie.moujaes at hotmail.co.uk  Thu Mar 11 15:26:49 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Thu, 11 Mar 2010 14:26:49 +0000
Subject: [Pw_forum] DOS of graphene
Message-ID: <SNT114-W138A4B6097802A487BA1BCD3320@phx.gbl>


I  have done the calculations using a K_PONTS automatic
                                                 20 20 1  0 0 0 
for the scf calculation and a K_POINTS automatic
                                       64 64 1  0 0 0
and I got almost the right DOS but only for -ve values of energy. Nothing was produced for the +ve part. Is it because I need to include more points? like trying the 128 128 1  0 0 0 grid? N.B: I did specify that Emin=-7 and Emax=7 in the inout pp file..
 
 
Regards
 
ELie Mouhaes
University of Nottingham
NG7 2RD
Nottingham
UK
 		 	   		  
_________________________________________________________________
Send us your Hotmail stories and be featured in our newsletter
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From ttduyle at gmail.com  Thu Mar 11 15:30:04 2010
From: ttduyle at gmail.com (Duy Le)
Date: Thu, 11 Mar 2010 09:30:04 -0500
Subject: [Pw_forum] SURFACE RECONSTRUCTION USING RELAX CALCULATION
In-Reply-To: <4B98B2BC.5050805@sissa.it>
References: <c40d64601003100135sc393a66h1f2a5ada30fac6cc@mail.gmail.com>
	<4B976D84.8070607@sissa.it>
	<8974d3b21003101807r10629100y45855b85e4b65f8a@mail.gmail.com>
	<4B98B2BC.5050805@sissa.it>
Message-ID: <8974d3b21003110630o36ce0ba3x965aec2167cf0c3f@mail.gmail.com>

One can't choose between supercell and ibrav=0. Ibrav defines the
bravais index. Hence it defines the crystalline geometry, symmetry
group. Supercell is a method for studying the periodic boundary
condition in solid-state physics.

What ever the ibrav is, one need to define a supercell (direct or indirect way).

For study the surface reconstruction, one may use ibrav=0 in order to
avoid pre-chosen bravais index. It's just a guess. I haven't done so.

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

"Men don't need hand to do things"



On Thu, Mar 11, 2010 at 4:07 AM, Ngoc Linh Nguyen <nnlinh at sissa.it> wrote:
> It's also ok with the ?cell-parameters of only either cubic or hexagonal.
>
> So I prefer using supercell then putting ibrav=0
>
> Linh
>
>
> Duy Le wrote:
>> How about ibrav=0?
>> --------------------------------------------------
>> Duy Le
>> PhD Student
>> Department of Physics
>> University of Central Florida.
>>
>> "Men don't need hand to do things"
>>
>>
>>
>> On Wed, Mar 10, 2010 at 4:59 AM, Ngoc Linh Nguyen <nnlinh at sissa.it> wrote:
>>
>>> mohnish pandey wrote:
>>>
>>>> ? ? ? ? ? ? ? ? ? ?I want to get the results for surface
>>>> reconstructions computationally, but the problem is as we have specify
>>>> the "ibrav" i.e symmetry of the system the relax calculation only
>>>> optimizes the structure within the given symmetry.
>>>>
>>> Not exactly, the relax calculation plays a role to find out an optimal
>>> configuration from an initial configuration.
>>> If you want to consider the surface reconstruction of given material,
>>> you should build a supercell in that the defect or adatom can be existed.
>>>
>>> And how to form a supercell. Let see the previous archives of PW_forum
>>>
>>> Good luck
>>>
>>> Linh
>>>
>>>
>>>
>>>
>>> --
>>> -----------------------------------------------------
>>> ?Nguyen Ngoc Linh, PhD Student
>>> ?c/o: ? SISSA & CNR-INFM Democritos,
>>> ? ? ? ?via Beirut 2-4, 34014 Trieste (Italy)
>>> ?email: nnlinh at sissa.it
>>> ?phone: +39 04 03787 319
>>> ?skype: ngoclinh84phys
>>> -----------------------------------------------------
>>> "The physics is theoretical but the fun is real"
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
> --
> -----------------------------------------------------
> ?Nguyen Ngoc Linh, PhD Student
> ?c/o: ? SISSA & CNR-INFM Democritos,
> ? ? ? ?via Beirut 2-4, 34014 Trieste (Italy)
> ?email: nnlinh at sissa.it
> ?phone: +39 04 03787 319
> ?skype: ngoclinh84phys
> -----------------------------------------------------
> "The physics is theoretical but the fun is real"
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From ttduyle at gmail.com  Thu Mar 11 15:52:27 2010
From: ttduyle at gmail.com (Duy Le)
Date: Thu, 11 Mar 2010 09:52:27 -0500
Subject: [Pw_forum] DOS of graphene
In-Reply-To: <SNT114-W138A4B6097802A487BA1BCD3320@phx.gbl>
References: <SNT114-W138A4B6097802A487BA1BCD3320@phx.gbl>
Message-ID: <8974d3b21003110652x3c470776q1a28f0f8d8c7fc3a@mail.gmail.com>

Did you open the scf output file and look for the fermi level written in it?

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

"Men don't need hand to do things"



On Thu, Mar 11, 2010 at 9:26 AM, Elie Moujaes
<elie.moujaes at hotmail.co.uk> wrote:
> I ?have done the calculations using a K_PONTS automatic
> ???????????????????????????????????????????????? 20 20 1? 0 0 0
> for the scf calculation and a K_POINTS automatic
> ?????????????????????????????????????? 64 64 1? 0 0 0
> and I got almost the right DOS but only for -ve values of energy. Nothing
> was produced for the +ve part. Is it because I need to include more points?
> like trying the 128 128?1? 0 0 0 grid? N.B:?I did specify that?Emin=-7 and
> Emax=7 in the inout pp file..
>
>
> Regards
>
> ELie Mouhaes
> University of Nottingham
> NG7 2RD
> Nottingham
> UK
>
> ________________________________
> Do you have a story that started on Hotmail? Tell us now
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

From ttduyle at gmail.com  Thu Mar 11 15:52:42 2010
From: ttduyle at gmail.com (Duy Le)
Date: Thu, 11 Mar 2010 09:52:42 -0500
Subject: [Pw_forum] DOS of graphene
In-Reply-To: <SNT114-W138A4B6097802A487BA1BCD3320@phx.gbl>
References: <SNT114-W138A4B6097802A487BA1BCD3320@phx.gbl>
Message-ID: <8974d3b21003110652m4e81d1cdt896e0af5dfbbbc57@mail.gmail.com>

Did you Open the scf output file and look for the fermi level written in it.
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Thu, Mar 11, 2010 at 9:26 AM, Elie Moujaes
<elie.moujaes at hotmail.co.uk> wrote:
> I ?have done the calculations using a K_PONTS automatic
> ???????????????????????????????????????????????? 20 20 1? 0 0 0
> for the scf calculation and a K_POINTS automatic
> ?????????????????????????????????????? 64 64 1? 0 0 0
> and I got almost the right DOS but only for -ve values of energy. Nothing
> was produced for the +ve part. Is it because I need to include more points?
> like trying the 128 128?1? 0 0 0 grid? N.B:?I did specify that?Emin=-7 and
> Emax=7 in the inout pp file..
>
>
> Regards
>
> ELie Mouhaes
> University of Nottingham
> NG7 2RD
> Nottingham
> UK
>
> ________________________________
> Do you have a story that started on Hotmail? Tell us now
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

From elie.moujaes at hotmail.co.uk  Thu Mar 11 16:06:59 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Thu, 11 Mar 2010 15:06:59 +0000
Subject: [Pw_forum] Crystal for XCrySDen
Message-ID: <SNT114-W28B210167B60C0E0159596D3320@phx.gbl>


I have a tiny question on XCrySDen. I need the crystal package to view crsytal sctructrues on XCrySDen but I think one has to subscribe and pay for that as far as I know. Is it downloadble somewhere?

 

 

Regards

 

Elie Moujaes

University of Nottingham

NG7 2RD

Notiingham

UK
 		 	   		  
_________________________________________________________________
Do you have a story that started on Hotmail? Tell us now
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From giannozz at democritos.it  Thu Mar 11 16:13:31 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 11 Mar 2010 16:13:31 +0100
Subject: [Pw_forum] Crystal for XCrySDen
In-Reply-To: <SNT114-W28B210167B60C0E0159596D3320@phx.gbl>
References: <SNT114-W28B210167B60C0E0159596D3320@phx.gbl>
Message-ID: <4B99089B.3070301@democritos.it>

Elie Moujaes wrote:

>   I need the crystal package to view crsytal structures on XCrySDen

you don't

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

From sandabotis at gmail.com  Thu Mar 11 16:15:02 2010
From: sandabotis at gmail.com (Sanda Botis)
Date: Thu, 11 Mar 2010 10:15:02 -0500
Subject: [Pw_forum] Crystal for XCrySDen
In-Reply-To: <SNT114-W28B210167B60C0E0159596D3320@phx.gbl>
References: <SNT114-W28B210167B60C0E0159596D3320@phx.gbl>
Message-ID: <98e923e51003110715q7f84e31ay29771f1d23fdfe42@mail.gmail.com>

You don't need Crystal if you want just to view crystal structures on
XCrySDen. You can create in XCrySDen the structures that you want to view.I
believe that there are a few tutorials on XCrysDen webpage on how to do
this.

And if you really need Crystal for calculations on crystal structures, then
yes you need to pay for the package.

Cheers,
Sanda

On Thu, Mar 11, 2010 at 10:06 AM, Elie Moujaes
<elie.moujaes at hotmail.co.uk>wrote:

>  I have a tiny question on XCrySDen. I need the crystal package to view
> crsytal sctructrues on XCrySDen but I think one has to subscribe and pay for
> that as far as I know. Is it downloadble somewhere?
>
>
> Regards
>
> Elie Moujaes
> University of Nottingham
> NG7 2RD
> Notiingham
> UK
>
> ------------------------------
> Do you want a Hotmail account? Sign-up now - Free<http://clk.atdmt.com/UKM/go/197222280/direct/01/>
>
> _______________________________________________
> 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 Mar 11 17:07:42 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 11 Mar 2010 17:07:42 +0100
Subject: [Pw_forum] vc-relax with starting_magnetization
In-Reply-To: <9c9214d71003100141v51ffb64bm3705f2aaf80a98d0@mail.gmail.com>
References: <9c9214d71003100141v51ffb64bm3705f2aaf80a98d0@mail.gmail.com>
Message-ID: <4B99154E.3050600@democritos.it>

Bryan M. Wong wrote:

> when I do a vc-relax with starting_magnetization set to any 
> value, the 2nd step in the cell relaxation always reverts 
> to the spin-unpolarized case

what was the magnetization at the end of the first step?
if it was zero, this is the expected behavior. This is why,
by the way, a final step with nonzero starting polarization
is performed at the end of a structural optimization if the
spin polarization is zero.

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

From carlo.nervi at unito.it  Thu Mar 11 19:39:16 2010
From: carlo.nervi at unito.it (Carlo Nervi)
Date: Thu, 11 Mar 2010 19:39:16 +0100
Subject: [Pw_forum] pw.x diagonalization (DSYGV*) failed
Message-ID: <4B9938D4.1030906@unito.it>

Dear all,

I generated paw PP-US using ld1.x of QE412, following some examples 
given by Lorenzo Paulatto in the paw directory.

A simple scf calculation run with the mpirun command exits with:
    from  pdpotrf  : error #        82
    problems computing cholesky decomposition

After reading the forum I followed the suggestion given by Paolo 
Giannozzi and used "pw.x -ndiag 1" and the error is now:

    from rdiaghg : error #       503
    diagonalization (DSYGV*) failed

Anyone could give me a hint where I'm wrong?
Wrong Pseudopotentials?

I tried also to use the example given in
espresso-4.1.2/atomic_doc/paw_library/input/S.in
however, ld1.x exit with error
      from new_paw_hamiltonian : error #         1
      negative rho

Thank you,
	Carlo

-- 
------------------------------------------------------
Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8
Fax: +39 011 6707855   -   Dipartimento di Chimica IFM
via P. Giuria 7, 10125 Torino, Italy
http://lem.ch.unito.it/

From paulatto at sissa.it  Thu Mar 11 21:24:23 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 11 Mar 2010 21:24:23 +0100
Subject: [Pw_forum] pw.x diagonalization (DSYGV*) failed
In-Reply-To: <4B9938D4.1030906@unito.it>
References: <4B9938D4.1030906@unito.it>
Message-ID: <op.u9e6ywy9a8x26q@paulax>

Replying to message "[Pw_forum] pw.x diagonalization (DSYGV*) failed" from  
Carlo Nervi (11/03/10):
> Anyone could give me a hint where I'm wrong?
> Wrong Pseudopotentials?

Probably, I would bet you have ghost states.

> I tried also to use the example given in
> espresso-4.1.2/atomic_doc/paw_library/input/S.in
> however, ld1.x exit with error
>       from new_paw_hamiltonian : error #         1
>       negative rho

Remove the input parameter rmatch_augfun and it will work (already fixed  
in CVS).

cheers

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

     *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

From elie.moujaes at hotmail.co.uk  Thu Mar 11 21:30:58 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Thu, 11 Mar 2010 20:30:58 +0000
Subject: [Pw_forum] .WIN file structure
Message-ID: <SNT114-W1082E3D849F2CF1620D548D3320@phx.gbl>


Dear all,
 
I am trying to get the band structure of graphene using a tight binding model. I need the form of the .WIN file so that I can input the parameters and execute wannier 90.x command.
 
Regards
 
Elie Moujaes
University of Nottingham
NG7 2RD
Nottingham 
UK
 		 	   		  
_________________________________________________________________
Send us your Hotmail stories and be featured in our newsletter
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From rgonzalezh at unal.edu.co  Fri Mar 12 06:46:20 2010
From: rgonzalezh at unal.edu.co (Rafael Julian Gonzalez Hernandez)
Date: Fri, 12 Mar 2010 00:46:20 -0500
Subject: [Pw_forum] plotproj
Message-ID: <fd1df88d18f6.4b998edc@unal.edu.co>

Hi,  

Could some one give me a example input for the plotproj.x program.

Thanks,

Rafael Gonzalez

====================================================
Rafael Julian Gonzalez    Tel:+57(1)3165000
Department of Physics
Universidad Nacional de Colombia   
email: rgonzalezh at unal.edu.co
==================================================== 

From sclauzer at sissa.it  Fri Mar 12 08:52:16 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Fri, 12 Mar 2010 08:52:16 +0100
Subject: [Pw_forum] .WIN file structure
In-Reply-To: <SNT114-W1082E3D849F2CF1620D548D3320@phx.gbl>
References: <SNT114-W1082E3D849F2CF1620D548D3320@phx.gbl>
Message-ID: <4B99F2B0.9020300@sissa.it>

Here you have some material to study how to use W90

W90/doc/
examples/WAN90_example/
http://media.quantum-espresso.org/santa_barbara_2009_07/index.php#20090731

HTH

GS


Elie Moujaes wrote:
> Dear all,
>  
> I am trying to get the band structure of graphene using a tight binding 
> model. I need the form of the .WIN file so that I can input the 
> parameters and execute wannier 90.x command.
>  
> Regards
>  
> Elie Moujaes
> University of Nottingham
> NG7 2RD
> Nottingham
> UK
> 
> ------------------------------------------------------------------------
> Do you have a story that started on Hotmail? Tell us now 
> <http://clk.atdmt.com/UKM/go/195013117/direct/01/>
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 


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

From carlo.nervi at unito.it  Fri Mar 12 10:50:43 2010
From: carlo.nervi at unito.it (Carlo Nervi)
Date: Fri, 12 Mar 2010 10:50:43 +0100
Subject: [Pw_forum] pw.x diagonalization (DSYGV*) failed
In-Reply-To: <op.u9e6ywy9a8x26q@paulax>
References: <4B9938D4.1030906@unito.it> <op.u9e6ywy9a8x26q@paulax>
Message-ID: <4B9A0E73.5010105@unito.it>

Dear Lorenzo,
thank you for the suggestions.
Finally I decided to use your PP (I'm using C, H, N, O and S).
The generation of paw PP now apparently goes smoothly.
However, a simple scf calculation on my system (52 atoms in the cell) 
cannot reach self-consistency: the energy continue to oscillate even 
after 200 scf cycles... (I tried with a couple of ecutoff, i.e. 40).

Sorry to ask again... do you have any hints?
Should I roll back to non-paw PP (I was using rrkjus)?
Should I update to the latest CVS?

Thanks,
	Carlo

Lorenzo Paulatto ha scritto:
> Replying to message "[Pw_forum] pw.x diagonalization (DSYGV*) failed" from  
> Carlo Nervi (11/03/10):
>> Anyone could give me a hint where I'm wrong?
>> Wrong Pseudopotentials?
> 
> Probably, I would bet you have ghost states.
> 
>> I tried also to use the example given in
>> espresso-4.1.2/atomic_doc/paw_library/input/S.in
>> however, ld1.x exit with error
>>       from new_paw_hamiltonian : error #         1
>>       negative rho
> 
> Remove the input parameter rmatch_augfun and it will work (already fixed  
> in CVS).
> 
> cheers
> 


-- 
------------------------------------------------------
Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8
Fax: +39 011 6707855   -   Dipartimento di Chimica IFM
via P. Giuria 7, 10125 Torino, Italy
http://lem.ch.unito.it/

From paulatto at sissa.it  Fri Mar 12 10:59:32 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Fri, 12 Mar 2010 10:59:32 +0100
Subject: [Pw_forum] pw.x diagonalization (DSYGV*) failed
In-Reply-To: <4B9A0E73.5010105@unito.it>
References: <4B9938D4.1030906@unito.it> <op.u9e6ywy9a8x26q@paulax>
	<4B9A0E73.5010105@unito.it>
Message-ID: <op.u9f8piasa8x26q@vanoxite.impmc.jussieu.fr>

On Fri, 12 Mar 2010 10:50:43 +0100, Carlo Nervi <carlo.nervi at unito.it>  
wrote:
> However, a simple scf calculation on my system (52 atoms in the cell)
> cannot reach self-consistency: the energy continue to oscillate even
> after 200 scf cycles... (I tried with a couple of ecutoff, i.e. 40).

In the latest CVS there is a fix (by ADC) that can improve convergency of  
PAW calculations. Yet there may be many other sources of poor convergence,  
like degenerate ground state or poor choice of smearing or bad geometry.

cheers

-- 
Lorenzo Paulatto

*** Note: my affiliation has changed! please send future
correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***

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

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

From nnlinh at sissa.it  Fri Mar 12 11:07:30 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Fri, 12 Mar 2010 11:07:30 +0100 (CET)
Subject: [Pw_forum] plotproj
In-Reply-To: <fd1df88d18f6.4b998edc@unal.edu.co>
References: <fd1df88d18f6.4b998edc@unal.edu.co>
Message-ID: <56077.147.122.5.207.1268388450.squirrel@webmail.sissa.it>

> Hi,
>
> Could some one give me a example input for the plotproj.x program.

You can see the details of input file in:
http://www.quantum-espresso.org/input-syntax/INPUT_PP.html


Here is an example of my input file run by pp.x for plot_num =11

&inputPP
   prefix='pureCu_111',
   outdir='$TMP_DIR2',
   plot_num=11
   filplot = 'wf_Cu'
/
&plot
   iflag=3,
   output_format=3
   nx =50, ny=50, nz=50
/


Good luck,

Linh


-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"


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From nnlinh at sissa.it  Fri Mar 12 11:16:46 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Fri, 12 Mar 2010 11:16:46 +0100 (CET)
Subject: [Pw_forum] plotproj
In-Reply-To: <56077.147.122.5.207.1268388450.squirrel@webmail.sissa.it>
References: <fd1df88d18f6.4b998edc@unal.edu.co>
	<56077.147.122.5.207.1268388450.squirrel@webmail.sissa.it>
Message-ID: <43003.147.122.5.207.1268389006.squirrel@webmail.sissa.it>

I'm sorry I have a mistake in last reply.

The detail of iput file of  plotproj.x  should be:

!  The input of this program is:
!  filename     ! name of the file with the band eigenvalues
!  filename1    ! name of the file with the projections
!  fileout      ! name of the output file where the bands are written
!  threshold    ! see below
!  ncri         ! number of criterions for selecting the bands
!  for each criterion
!  first_atomic_wfc, last_atomic_wfc   ! the band is selected if the
!                                        sum of the projections on
!                                        the atomic wavefunctions between
!                                        first_atomic_wfc and
!                                        last_atomic_wfc is larger than
!                                        threshold. The sum is done on
!                                        all criterions.
!

you can read in: PP/plotproj.f90

Best regards,

Linh



>> Hi,
>>
>> Could some one give me a example input for the plotproj.x program.
>
> You can see the details of input file in:
> http://www.quantum-espresso.org/input-syntax/INPUT_PP.html
>
>
> Here is an example of my input file run by pp.x for plot_num =11
>
> &inputPP
>    prefix='pureCu_111',
>    outdir='$TMP_DIR2',
>    plot_num=11
>    filplot = 'wf_Cu'
> /
> &plot
>    iflag=3,
>    output_format=3
>    nx =50, ny=50, nz=50
> /
>
>
> Good luck,
>
> Linh
>
>
> -----------------------------------------------------
>  Nguyen Ngoc Linh, PhD Student
>  c/o:   SISSA & CNR-INFM Democritos,
>         via Beirut 2-4, 34014 Trieste (Italy)
>  email: nnlinh at sissa.it
>  phone: +39 04 03787 319
>  skype: ngoclinh84phys
> -----------------------------------------------------
> "The physics is theoretical but the fun is real"
>
>
> ----------------------------------------------------------------
>   SISSA Webmail https://webmail.sissa.it/
>   Powered by SquirrelMail http://www.squirrelmail.org/
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"


----------------------------------------------------------------
  SISSA Webmail https://webmail.sissa.it/
  Powered by SquirrelMail http://www.squirrelmail.org/


From elie.moujaes at hotmail.co.uk  Fri Mar 12 13:46:28 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Fri, 12 Mar 2010 12:46:28 +0000
Subject: [Pw_forum] .WIN file structure
In-Reply-To: <4B99F2B0.9020300@sissa.it>
References: <SNT114-W1082E3D849F2CF1620D548D3320@phx.gbl>,
	<4B99F2B0.9020300@sissa.it>
Message-ID: <SNT114-W16492BCF2DAF6514FA2129D3310@phx.gbl>


Thanks very much for the site.

 

Regards

 

Elie
 
> Date: Fri, 12 Mar 2010 08:52:16 +0100
> From: sclauzer at sissa.it
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] .WIN file structure
> 
> Here you have some material to study how to use W90
> 
> W90/doc/
> examples/WAN90_example/
> http://media.quantum-espresso.org/santa_barbara_2009_07/index.php#20090731
> 
> HTH
> 
> GS
> 
> 
> Elie Moujaes wrote:
> > Dear all,
> > 
> > I am trying to get the band structure of graphene using a tight binding 
> > model. I need the form of the .WIN file so that I can input the 
> > parameters and execute wannier 90.x command.
> > 
> > Regards
> > 
> > Elie Moujaes
> > University of Nottingham
> > NG7 2RD
> > Nottingham
> > UK
> > 
> > ------------------------------------------------------------------------
> > Do you have a story that started on Hotmail? Tell us now 
> > <http://clk.atdmt.com/UKM/go/195013117/direct/01/>
> > 
> > 
> > ------------------------------------------------------------------------
> > 
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> 
> -- 
> 
> 
> o ------------------------------------------------ o
> | Gabriele Sclauzero, PhD Student |
> | c/o: SISSA & CNR-INFM Democritos, |
> | via Beirut 2-4, 34014 Trieste (Italy) |
> | email: sclauzer at sissa.it |
> | phone: +39 040 3787 511 |
> | skype: gurlonotturno |
> o ------------------------------------------------ o
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
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From elie.moujaes at hotmail.co.uk  Fri Mar 12 13:54:01 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Fri, 12 Mar 2010 12:54:01 +0000
Subject: [Pw_forum] error while configuring W90 on pwscf
Message-ID: <SNT114-W62A512A8C3131B73FB3262D3310@phx.gbl>


 

Dear All

 

I am trying to configure w90 on PWSCF and when I execute the command 

 

make w90, I get the following error:

 

Entering dirrectory ;espresso-4.1.2/W90/src

ifort -02-c constants .F90

make[2]: ifort: command not found

make[2]: *** [cosntants.o] error 127

make[2]: leaving directory espresso-4.1.2/W90/src

make[1]: *** [wannier] error 2

make[1]: leaving directory espresso-4.1.2/W90

make[1]: *** [w90] error 2

 

Also I realised I do not have the wannier90.x file in bin in the espresso-4.1.2 package...Can anyone tell me what can be done now?

 

 

Thanks

 

Regards

   

Elie Moujaes
University of Nottingham
NG7 2RD
Nottingham 
UK


 

 

 

 

 

 

 

 

 

 
 		 	   		  
_________________________________________________________________
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From nnlinh at sissa.it  Fri Mar 12 14:15:31 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Fri, 12 Mar 2010 14:15:31 +0100
Subject: [Pw_forum] error while configuring W90 on pwscf
In-Reply-To: <SNT114-W62A512A8C3131B73FB3262D3310@phx.gbl>
References: <SNT114-W62A512A8C3131B73FB3262D3310@phx.gbl>
Message-ID: <4B9A3E73.6030707@sissa.it>

Elie Moujaes wrote:
>  
> Dear All
>  
> I am trying to configure w90 on PWSCF and when I execute the command
>  
> make w90, I get the following error:
>  
> Entering dirrectory ;espresso-4.1.2/W90/src
> ifort -02-c constants .F90
> make[2]: ifort: command not found
> make[2]: *** [cosntants.o] error 127
> make[2]: leaving directory espresso-4.1.2/W90/src
> make[1]: *** [wannier] error 2
> make[1]: leaving directory espresso-4.1.2/W90
> make[1]: *** [w90] error 2
Error comes from that the ifort compiler is not found, it's not an error 
of QE but your computer system.
Solutions:
- You re-check the ifort compiler if it is available on your computer or 
not? Then "make w90" again.
- Maybe, you can use other compilers such as gfortran or g95 if you 
don't have ifort compiler. Then "make w90".
- If you want run parallel, you need mpif90 compiler.

Good luck,

Linh
>  


> Also I realised I do not have the wannier90.x file in bin in the 
> espresso-4.1.2 package...Can anyone tell me what can be done now?
>  
>  
> Thanks
>  
> Regards
>   
> Elie Moujaes
> University of Nottingham
> NG7 2RD
> Nottingham
> UK
>
>  
>  
>  
>  
>  
>  
>  
>  
>  
>  
>
> ------------------------------------------------------------------------
> Not got a Hotmail account? Sign-up now - Free 
> <http://clk.atdmt.com/UKM/go/197222280/direct/01/>
> ------------------------------------------------------------------------
>
> _______________________________________________
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From elie.moujaes at hotmail.co.uk  Fri Mar 12 20:30:46 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Fri, 12 Mar 2010 19:30:46 +0000
Subject: [Pw_forum] W90 error: too many projections defined/k_points
Message-ID: <SNT114-W50A9337B445F95854E9D48D3310@phx.gbl>


Dear all,

 

I am executing the Wannier90.x command foir graphene and I am getting the following error:

 

 

Wannier90: Execution started on 12Mar2010 at 16:13:07 
 Exiting.......
 param_get_projection: too many projections defined

 
Is that related to the projection functions used to construct the initial guess for the unitary transformations? 
 
 
 
I also tried to see if I can set k_points to be automatic abut i could not find it in the wannier90 mannual. I will attach the WIN file as well if anyone decided to look at it
 
Thanks
 
 
  		 	   		  
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From paulatto at sissa.it  Sat Mar 13 16:43:42 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Sat, 13 Mar 2010 16:43:42 +0100
Subject: [Pw_forum] W90 error: too many projections defined/k_points
In-Reply-To: <SNT114-W50A9337B445F95854E9D48D3310@phx.gbl>
References: <SNT114-W50A9337B445F95854E9D48D3310@phx.gbl>
Message-ID: <op.u9ija3wya8x26q@paulax>

Replying to message "[Pw_forum] W90 error: too many projections  
defined/k_points" from Elie Moujaes (12/03/10):

> param_get_projection: too many projections defined

Dear Elie,
provided that I've never used Wannier90, here's a link where the "issue"  
is briefly discussed and a solution proposed:  
<http://www.democritos.it/pipermail/wannier/2007-May/000066.html>

regards


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

     *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

From elie.moujaes at hotmail.co.uk  Sat Mar 13 22:43:11 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Sat, 13 Mar 2010 21:43:11 +0000
Subject: [Pw_forum] W90 error: too many projections defined/k_points
In-Reply-To: <op.u9ija3wya8x26q@paulax>
References: <SNT114-W50A9337B445F95854E9D48D3310@phx.gbl>,
	<op.u9ija3wya8x26q@paulax>
Message-ID: <SNT114-W44C73D7E427E4AC5A99480D3300@phx.gbl>


Dear professor Paulatto,

 

Thank you for your help and your time in answering. I will check and I am sure the problem will be solved. Thanks very much again

 

Elie Moujaes

University of Nottingham

NG7 2RD

Nottingham
 
> To: pw_forum at pwscf.org
> Date: Sat, 13 Mar 2010 16:43:42 +0100
> From: paulatto at sissa.it
> Subject: Re: [Pw_forum] W90 error: too many projections defined/k_points
> 
> Replying to message "[Pw_forum] W90 error: too many projections 
> defined/k_points" from Elie Moujaes (12/03/10):
> 
> > param_get_projection: too many projections defined
> 
> Dear Elie,
> provided that I've never used Wannier90, here's a link where the "issue" 
> is briefly discussed and a solution proposed: 
> <http://www.democritos.it/pipermail/wannier/2007-May/000066.html>
> 
> regards
> 
> 
> -- 
> Lorenzo Paulatto
> SISSA & DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www: http://people.sissa.it/~paulatto/
> 
> *** save italian brains ***
> http://saveitalianbrains.wordpress.com/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
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From science35 at gmail.com  Sun Mar 14 14:24:06 2010
From: science35 at gmail.com (patriot pershing)
Date: Sun, 14 Mar 2010 14:24:06 +0100
Subject: [Pw_forum] about charged defects in supercell calculations
Message-ID: <9fdec6371003140624xfdadcd5ke43bb76f6e1c5917@mail.gmail.com>

Dear all:
we know that it is possible to study charged supercell ( supercell +
charged defect or impurities) using espresso (pw) by fixing the cell
(supercell) total charge, but i would ask if it is possible using pw
to fixing the supercell charge or the defect charge in a given
position, for example i would test the ZnS supercell which contain
oxygen as impurity and i would test the positive charge (o+) or the
(o-) by fixing the position of charge in the Oxygen atomic position .

From modaresi.mohsen at gmail.com  Sun Mar 14 18:02:17 2010
From: modaresi.mohsen at gmail.com (mohsen modaresi)
Date: Sun, 14 Mar 2010 20:32:17 +0330
Subject: [Pw_forum] DOS of graphene
In-Reply-To: <8974d3b21003110652m4e81d1cdt896e0af5dfbbbc57@mail.gmail.com>
References: <SNT114-W138A4B6097802A487BA1BCD3320@phx.gbl>
	<8974d3b21003110652m4e81d1cdt896e0af5dfbbbc57@mail.gmail.com>
Message-ID: <a6ebdd4d1003141002v1f6dca6cq4a3c124788360ed8@mail.gmail.com>

Hi
Install "WANT", you can find a test about graphene.
Good luck
Mohsen Modaresi

On 3/11/10, Duy Le <ttduyle at gmail.com> wrote:
> Did you Open the scf output file and look for the fermi level written in it.
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
>
> On Thu, Mar 11, 2010 at 9:26 AM, Elie Moujaes
> <elie.moujaes at hotmail.co.uk> wrote:
>> I ?have done the calculations using a K_PONTS automatic
>> ???????????????????????????????????????????????? 20 20 1? 0 0 0
>> for the scf calculation and a K_POINTS automatic
>> ?????????????????????????????????????? 64 64 1? 0 0 0
>> and I got almost the right DOS but only for -ve values of energy. Nothing
>> was produced for the +ve part. Is it because I need to include more
>> points?
>> like trying the 128 128?1? 0 0 0 grid? N.B:?I did specify that?Emin=-7 and
>> Emax=7 in the inout pp file..
>>
>>
>> Regards
>>
>> ELie Mouhaes
>> University of Nottingham
>> NG7 2RD
>> Nottingham
>> UK
>>
>> ________________________________
>> Do you have a story that started on Hotmail? Tell us now
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From yaldachem at gmail.com  Sun Mar 14 19:20:03 2010
From: yaldachem at gmail.com (yaldaa kh)
Date: Sun, 14 Mar 2010 21:50:03 +0330
Subject: [Pw_forum] error reference
Message-ID: <47431d9f1003141120j6da27398r14ce5633062dd924@mail.gmail.com>

dear all
where can I find explanation about encountered errors while running
the code?( for example error# 11)
thanks alot
Yaldaa
Chem. student
Iran

From baroni at sissa.it  Sun Mar 14 21:19:52 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Sun, 14 Mar 2010 21:19:52 +0100
Subject: [Pw_forum] error reference
In-Reply-To: <47431d9f1003141120j6da27398r14ce5633062dd924@mail.gmail.com>
References: <47431d9f1003141120j6da27398r14ce5633062dd924@mail.gmail.com>
Message-ID: <0C401E43-321B-4FBC-A0C6-61AAB559D911@sissa.it>

in all cases, browsing the source code itself
in a few frequently encountered occurrences, browising the QE doc and faq, as well as the archive of this mailing list may help
SB

On Mar 14, 2010, at 7:20 PM, yaldaa kh wrote:

> dear all
> where can I find explanation about encountered errors while running
> the code?( for example error# 11)
> thanks alot
> Yaldaa
> Chem. student
> Iran
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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

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







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From degironc at sissa.it  Mon Mar 15 09:35:17 2010
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Mon, 15 Mar 2010 09:35:17 +0100
Subject: [Pw_forum] error reference
In-Reply-To: <47431d9f1003141120j6da27398r14ce5633062dd924@mail.gmail.com>
References: <47431d9f1003141120j6da27398r14ce5633062dd924@mail.gmail.com>
Message-ID: <4B9DF145.80508@sissa.it>

Dear Yaldaa,

   usually more than the error NUMBER  it is useful to look at the error 
"MESSAGE" and at the name of the ROUTINE where the error occurred. The 
error message explains (*hopefully* in a  clear way) the reason why the 
code stops,  and the error number is typically the value of the variable 
that  generated the error condition ... as such it is not useful to 
identify the error but rather to trace back some possible wrong input 
value or the like.
Inspection of the routine source and a search for the error message 
string should help in locating the point where the error was detected 
and looking at the code nearby should help understanding the reason of 
the error and the meaning of the  code number...

  hope this help,
    stefano


yaldaa kh wrote:
> dear all
> where can I find explanation about encountered errors while running
> the code?( for example error# 11)
> thanks alot
> Yaldaa
> Chem. student
> Iran
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From lfhuang at theory.issp.ac.cn  Mon Mar 15 09:31:50 2010
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Mon, 15 Mar 2010 16:31:50 +0800
Subject: [Pw_forum]
	=?utf-8?q?about_charged_defects_in_supercell_calculati?=
	=?utf-8?q?ons?=
Message-ID: <20100315083150.31591.qmail@ms.hfcas.ac.cn>

Dear P. Pershing:
    The words below may be not related with your specific case, which I know little.
    In my opinion, the realistic charged system sometimes could not be simply simulated just by doping the supercell, because the effect of the background should be paid attention to. That depends on your knowledge on your material. :)
 
    Maybe the context on the charge doping technique in the book:
Richard M. Martin, "Electronic Structure: Basic Theory and Practical Methods"
could inform you of the ability of this method.

Best Wishes!
Yours Sincerely
L.F.Huang

> Date: Sun, 14 Mar 2010 14:24:06 +0100
> From: patriot pershing 
> Subject: [Pw_forum] about charged defects in supercell calculations
> To: pw_forum at pwscf.org
> Message-ID:
> 	
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Dear all:
> we know that it is possible to study charged supercell ( supercell +
> charged defect or impurities) using espresso (pw) by fixing the cell
> (supercell) total charge, but i would ask if it is possible using pw
> to fixing the supercell charge or the defect charge in a given
> position, for example i would test the ZnS supercell which contain
> oxygen as impurity and i would test the positive charge (o+) or the
> (o-) by fixing the position of charge in the Oxygen atomic position .
> 
> 

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


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From carlo.nervi at unito.it  Mon Mar 15 14:30:21 2010
From: carlo.nervi at unito.it (Carlo Nervi)
Date: Mon, 15 Mar 2010 14:30:21 +0100
Subject: [Pw_forum] AMD Open64 Compiler Suite
Message-ID: <4B9E366D.1070009@unito.it>

Dear PWSCF users,
anyone tried to compile PWSCF using the AMD Open64 Compiler Suite (the 
last versione -afaik- is v4.2.3), possibly with the AMD Core Math 
Library (ACML)?
I know that ACML should work, but how about Open64?
After reading that Intel Compilers deliberately does not take in account 
of all math speedup present in non-intel CPUs, I'm considering which 
optimized compiler I should use on my old non-Intel based linux...

Thanks,
	Carlo
-- 
------------------------------------------------------
Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8
Fax: +39 011 6707855   -   Dipartimento di Chimica IFM
via P. Giuria 7, 10125 Torino, Italy
http://lem.ch.unito.it/

From giuseppe.mattioli at mlib.ism.cnr.it  Mon Mar 15 14:34:09 2010
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Mon, 15 Mar 2010 14:34:09 +0100
Subject: [Pw_forum] core wavefunction in xspectra calculations
Message-ID: <201003151434.10231.giuseppe.mattioli@mlib.ism.cnr.it>


Dear all
I'm trying to perform some xspectra calculations. The QE/Doc/INPUT_XSPECTRA 
guide says:

>The code needs the 1s radial core wavefunction (for the 1s state in the 
>absence of a core-hole) in input. This is necessary to calculate the XAS 
>matrix element.

Where can I get such wfc? Do I need to perform an all-electron calculation 
with lda1.x?

Thanks

Giuseppe

-- 
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libres et ?gaux en droits. Les distinctions sociales
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imprescriptibles de l'homme. Ces droits sont la libert?,
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From elie.moujaes at hotmail.co.uk  Mon Mar 15 15:06:14 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Mon, 15 Mar 2010 14:06:14 +0000
Subject: [Pw_forum] w90: existing...non symmetric k points neighbours
Message-ID: <SNT114-W23CFD550316E16F385757DD32E0@phx.gbl>


Dear All, I am trying to run the wannier90.x command for graphene and I keep on having the following error:
 

Exiting.......
 Non-symmetric k-point neighbours! 
I have changed the grid points but in vain. Please anyone can tell me how can i avoid this error. Here is the list of k-points I am using:
 
 
 

mp_grid : 4 4 4
 
 
begin kpoints
  0.00000000  0.00000000  0.00000000 
  0.01000000  0.01000000  0.00000000 
  0.02000000  0.02000000  0.00000000
  0.03000000  0.03000000  0.00000000 
  0.05000000  0.05000000  0.00000000
  0.06000000  0.06000000  0.06000000 
  0.07000000  0.07000000  0.00000000 
  0.08000000  0.08000000  0.00000000 
  0.09000000  0.09000000  0.08000000
  0.10000000  0.10000000  0.10000000
  0.11000000  0.11000000  0.00000000
  0.12000000  0.12000000  0.12000000 
  0.13000000  0.13000000  0.00000000 
  0.15000000  0.15000000  0.00000000
  0.16000000  0.16000000  0.16000000 
  0.17000000  0.17000000  0.00000000
  0.18000000  0.18000000  0.00000000 
  0.19000000  0.19000000  0.00000000 
  0.20000000  0.20000000  0.20000000
  0.21000000  0.21000000  0.00000000
  0.22000000  0.22000000  0.00000000 
  0.23000000  0.23000000  0.00000000 
  0.25000000  0.25000000  0.00000000 
  0.27000000  0.27000000  0.00000000 
  0.29000000  0.29000000  0.00000000 
  0.31000000  0.31000000  0.00000000 
  0.33000000  0.33000000  0.00000000 
  0.00000000  0.01000000  0.00000000 
  0.00000000  0.03000000  0.00000000 
  0.00000000  0.05000000  0.00000000 
  0.00000000  0.07000000  0.00000000
  0.00000000  0.09000000  0.00000000 
  0.00000000  0.11000000  0.00000000
  0.00000000  0.12000000  0.00000000
  0.00000000  0.13000000  0.00000000 
  0.00000000  0.15000000  0.00000000
  0.00000000  0.17000000  0.00000000
  0.00000000  0.18000000  0.00000000 
  0.00000000  0.19000000  0.00000000
  0.00000000  0.21000000  0.00000000 
  0.00000000  0.22000000  0.00000000
  0.00000000  0.23000000  0.00000000 
  0.00000000  0.25000000  0.00000000 
  0.00000000  0.27000000  0.00000000
  0.00000000  0.29000000  0.00000000 
  0.00000000  0.31000000  0.00000000 
  0.00000000  0.33000000  0.00000000 
  0.00000000  0.34000000  0.00000000
  0.00000000  0.35000000  0.00000000 
  0.00000000  0.36000000  0.00000000
  0.00000000  0.37000000  0.00000000 
  0.00000000  0.38000000  0.00000000   
  0.00000000  0.39000000  0.00000000
  0.00000000  0.40000000  0.00000000
  0.00000000  0.41000000  0.00000000 
  0.00000000  0.42000000  0.00000000
  0.00000000  0.43000000  0.00000000
  0.00000000  0.44000000  0.00000000
  0.00000000  0.45000000  0.00000000 
  0.00000000  0.46000000  0.00000000 
  0.00000000  0.47000000  0.00000000
  0.00000000  0.48000000  0.00000000
  0.00000000  0.49000000  0.00000000 
  0.00000000  0.50000000  0.00000000
end kpoints
 

 
thanks
 
Elie Moujaes
University of Nottingham
NG7 2RD
Nottingham
UK


 		 	   		  
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From sclauzer at sissa.it  Mon Mar 15 15:18:14 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Mon, 15 Mar 2010 15:18:14 +0100
Subject: [Pw_forum] w90: existing...non symmetric k points neighbours
In-Reply-To: <SNT114-W23CFD550316E16F385757DD32E0@phx.gbl>
References: <SNT114-W23CFD550316E16F385757DD32E0@phx.gbl>
Message-ID: <4B9E41A6.10300@sissa.it>



Elie Moujaes wrote:
> Dear All, I am trying to run the wannier90.x command for graphene and I 
> keep on having the following error:
>  
> 
> Exiting.......
>  Non-symmetric k-point neighbours!
> 
>  
> I have changed the grid points but in vain. Please anyone can tell me 
> how can i avoid this error. Here is the list of k-points I am using:
>  
>  
>  
> 
> mp_grid : 4 4 4
> 
>  
> 
>  
> 
> begin kpoints
> 
>   0.00000000  0.00000000  0.00000000
> 
>   0.01000000  0.01000000  0.00000000
> 
>   0.02000000  0.02000000  0.00000000

[...]
> 
>   0.21000000  0.21000000  0.00000000
> 
>   0.22000000  0.22000000  0.00000000
> 
>   0.23000000  0.23000000  0.00000000
> 
>   0.25000000  0.25000000  0.00000000
> 
>   0.27000000  0.27000000  0.00000000
> 
>   0.29000000  0.29000000  0.00000000
> 
>   0.31000000  0.31000000  0.00000000
> 
>   0.33000000  0.33000000  0.00000000

Why do you skip some k-points here?

0.24 0.24 0.00
0.26 0.26 0.00
...
and many others.

Perhaps you have to specify a more regular grid.


GS

-- 


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

From marzari at MIT.EDU  Mon Mar 15 15:59:48 2010
From: marzari at MIT.EDU (Nicola Marzari)
Date: Mon, 15 Mar 2010 14:59:48 +0000
Subject: [Pw_forum] w90: existing...non symmetric k points neighbours
In-Reply-To: <4B9E41A6.10300@sissa.it>
References: <SNT114-W23CFD550316E16F385757DD32E0@phx.gbl>
	<4B9E41A6.10300@sissa.it>
Message-ID: <4B9E4B64.8020300@mit.edu>


> Elie Moujaes wrote:
>   
>> Dear All, I am trying to run the wannier90.x command for graphene and I 
>> keep on having the following error:
>>  
>>
>> Exiting.......
>>  Non-symmetric k-point neighbours!
>>
>>  
>> I have changed the grid points but in vain. Please anyone can tell me 
>> how can i avoid this error. Here is the list of k-points I am using:
>>  
>>  


Jonathan Yates has kindly answered to this in the wannier forum - 
please  post
here only after not having received any replies there. And example 10 in the
distribution is graphite. Basically you need a homogenous grid in 2d, so 
that
the keypoints are equispaced in a tringaular lattice. In the 
perpendicular direction,
you do not need k-point sampling, since there is no band dispersion in 
that direction
for an isolated system.


                   nicola


-- 
---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu 


From Trinh.Vo at jpl.nasa.gov  Mon Mar 15 20:25:33 2010
From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Mon, 15 Mar 2010 12:25:33 -0700
Subject: [Pw_forum] Fortran compiler
Message-ID: <C7C3D7BD.1A16%Trinh.Vo@jpl.nasa.gov>

Dear PWSCF uses,

I am planning to install some Fortran compiler and MPI for running QE on my cluster.  I don?t have Intel compiler (previously I only used Intel Compiler on another cluster), and I don?t know which free compiler and MPI are most suited for QE.  Could you give me advise on which compiler and MPI that I should install for use with QE.

Thank you very much in advance,

Trinh Vo

JPL/CalTech
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From nnlinh at sissa.it  Mon Mar 15 22:46:58 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Mon, 15 Mar 2010 22:46:58 +0100 (CET)
Subject: [Pw_forum] Fortran compiler
In-Reply-To: <C7C3D7BD.1A16%Trinh.Vo@jpl.nasa.gov>
References: <C7C3D7BD.1A16%Trinh.Vo@jpl.nasa.gov>
Message-ID: <56479.93.149.238.216.1268689618.squirrel@webmail.sissa.it>

MPI Open Mpi is a good option. You can see and download in:

    http://www.open-mpi.org/

It needs gfortran compiler which is complied on your system.

Good luck,

Linh


> Dear PWSCF uses,
>
> I am planning to install some Fortran compiler and MPI for running QE on
> my cluster.  I don?t have Intel compiler (previously I only used Intel
> Compiler on another cluster), and I don?t know which free compiler and MPI
> are most suited for QE.  Could you give me advise on which compiler and
> MPI that I should install for use with QE.
>
> Thank you very much in advance,
>
> Trinh Vo
>
> JPL/CalTech
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"


----------------------------------------------------------------
  SISSA Webmail https://webmail.sissa.it/
  Powered by SquirrelMail http://www.squirrelmail.org/


From Trinh.Vo at jpl.nasa.gov  Mon Mar 15 23:30:46 2010
From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Mon, 15 Mar 2010 15:30:46 -0700
Subject: [Pw_forum] Fortran compiler
In-Reply-To: <56479.93.149.238.216.1268689618.squirrel@webmail.sissa.it>
Message-ID: <C7C40326.1A2B%Trinh.Vo@jpl.nasa.gov>

Thank you, Linh.

Trinh


On 3/15/10 2:46 PM, "Ngoc Linh Nguyen" <nnlinh at sissa.it> wrote:

> MPI Open Mpi is a good option. You can see and download in:
> 
>     http://www.open-mpi.org/
> 
> It needs gfortran compiler which is complied on your system.
> 
> Good luck,
> 
> Linh
> 
> 
>> Dear PWSCF uses,
>> 
>> I am planning to install some Fortran compiler and MPI for running QE on
>> my cluster.  I don?t have Intel compiler (previously I only used Intel
>> Compiler on another cluster), and I don?t know which free compiler and MPI
>> are most suited for QE.  Could you give me advise on which compiler and
>> MPI that I should install for use with QE.
>> 
>> Thank you very much in advance,
>> 
>> Trinh Vo
>> 
>> JPL/CalTech
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>> 
> 
> 
> -----------------------------------------------------
>  Nguyen Ngoc Linh, PhD Student
>  c/o:   SISSA & CNR-INFM Democritos,
>         via Beirut 2-4, 34014 Trieste (Italy)
>  email: nnlinh at sissa.it
>  phone: +39 04 03787 319
>  skype: ngoclinh84phys
> -----------------------------------------------------
> "The physics is theoretical but the fun is real"
> 
> 
> ----------------------------------------------------------------
>   SISSA Webmail https://webmail.sissa.it/
>   Powered by SquirrelMail http://www.squirrelmail.org/
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From lily_physics at yahoo.com.sg  Tue Mar 16 09:29:26 2010
From: lily_physics at yahoo.com.sg (Lily Anh)
Date: Tue, 16 Mar 2010 16:29:26 +0800 (SGT)
Subject: [Pw_forum] where is the "search" link in this forum
Message-ID: <649021.57562.qm@web76109.mail.sg1.yahoo.com>

Dear all,

Could anyone please tell me the "search" link? I could view all the archives. However, I could not search for my specific purpose.

Thank you very much!

Lily
Nanyang Technological Univerisity
Singapore



      
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From giannozz at democritos.it  Tue Mar 16 09:32:12 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 16 Mar 2010 09:32:12 +0100
Subject: [Pw_forum] where is the "search" link in this forum
In-Reply-To: <649021.57562.qm@web76109.mail.sg1.yahoo.com>
References: <649021.57562.qm@web76109.mail.sg1.yahoo.com>
Message-ID: <4B9F420C.1070903@democritos.it>

Lily Anh wrote:

> Could anyone please tell me the "search" link? 

In http://www.quantum-espresso.org/tools.php
Also, using google: site:www.democritos.it

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

From lily_physics at yahoo.com.sg  Tue Mar 16 09:39:11 2010
From: lily_physics at yahoo.com.sg (Lily Anh)
Date: Tue, 16 Mar 2010 16:39:11 +0800 (SGT)
Subject: [Pw_forum] where is the "search" link in this forum
Message-ID: <153169.33901.qm@web76105.mail.sg1.yahoo.com>

Dear Paolo,

Maybe I did not make myself clear on this problem. I could view all the archives in this forum.(http://www.democritos.it/pipermail/pw_forum/)

What I want to know is the link to "search" by topic relevance as the old PWSCF website provided. So I could easy to find the relevant questions posted before and also save time and energy to avoid ask same questions again and again.

Lily



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From giannozz at democritos.it  Tue Mar 16 09:48:35 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 16 Mar 2010 09:48:35 +0100
Subject: [Pw_forum] Fortran compiler
In-Reply-To: <C7C3D7BD.1A16%Trinh.Vo@jpl.nasa.gov>
References: <C7C3D7BD.1A16%Trinh.Vo@jpl.nasa.gov>
Message-ID: <4B9F45E3.4070901@democritos.it>

Vo, Trinh (388C) wrote:

> I don?t know which free compiler and  MPI are most suited for QE.

what is written in the user guide still applies: gfortran works,
sort of, but it is buggy. g95 works nicely but it produces slow
executables. All non-buggy, properly installed MPI libraries
work.

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

From giannozz at democritos.it  Tue Mar 16 09:55:20 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 16 Mar 2010 09:55:20 +0100
Subject: [Pw_forum] about charged defects in supercell calculations
In-Reply-To: <9fdec6371003140624xfdadcd5ke43bb76f6e1c5917@mail.gmail.com>
References: <9fdec6371003140624xfdadcd5ke43bb76f6e1c5917@mail.gmail.com>
Message-ID: <4B9F4778.4060504@democritos.it>

patriot pershing wrote:

> i would ask if it is possible using pw to fixing the supercell
> charge or the defect charge in a given position

no. The charge will go where it will like to go

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

From giannozz at democritos.it  Tue Mar 16 10:00:08 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 16 Mar 2010 10:00:08 +0100
Subject: [Pw_forum] where is the "search" link in this forum
In-Reply-To: <153169.33901.qm@web76105.mail.sg1.yahoo.com>
References: <153169.33901.qm@web76105.mail.sg1.yahoo.com>
Message-ID: <4B9F4898.90005@democritos.it>

Lily Anh wrote:

> What I want to know is the link to "search" by topic relevance as the 
> old PWSCF website provided.

...and can't you locate the link you are referring to in a 10-line
page?

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

From nnlinh at sissa.it  Tue Mar 16 10:14:55 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Tue, 16 Mar 2010 10:14:55 +0100
Subject: [Pw_forum] where is the "search" link in this forum
In-Reply-To: <153169.33901.qm@web76105.mail.sg1.yahoo.com>
References: <153169.33901.qm@web76105.mail.sg1.yahoo.com>
Message-ID: <4B9F4C0F.6090300@sissa.it>

In http://www.quantum-espresso.org/tools.php,
you can find in "search facility 
<http://www.democritos.it/cgi-bin/htsearch?config=&restrict=&exclude=&method=and&format=builtin-long&sort=score&words=pw_forum> 
" a link to link to PW_forum searching, as below:
 http://www.democritos.it/cgi-bin/htsearch?config=&restrict=&exclude=&method=and&format=builtin-long&sort=score&words=pw_forum

good luck,

Linh

-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From paulatto at sissa.it  Tue Mar 16 10:18:20 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 16 Mar 2010 10:18:20 +0100
Subject: [Pw_forum] Fortran compiler
In-Reply-To: <C7C3D7BD.1A16%Trinh.Vo@jpl.nasa.gov>
References: <C7C3D7BD.1A16%Trinh.Vo@jpl.nasa.gov>
Message-ID: <op.u9nlgtm1a8x26q@paulax>

Replying to message "[Pw_forum] Fortran compiler" from Vo, Trinh (388C)  
(15/03/10):
> I am planning to install some Fortran compiler and MPI for running QE on  
> my cluster.  I don?t have Intel compiler (previously I only used Intel  
> Compiler on another cluster), and I don?t know which free compiler and  
> MPI are most suited for QE.  Could you give me advise on which compiler  
> and MPI that I should install for use with QE.


Also the Sun compiler is free <developers.sun.com/sunstudio/>, and comes  
with a set of algebra libraries that can be
used in place of the slow built-in libraries. It also supports openmp,  
which g95 does not. On the other hand, it is a pain to compile mpi with  
it. Furthermore the most recent version has a terrible bug that totally  
miscompiles the iotk input/output library (you'll have to compile it with  
reduced optimization).

In case you are planning to give it a try I would suggest you contact me  
so I can tell you the 2 or 3 hacks that are necessary.

best regards

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

     *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

From paulatto at sissa.it  Tue Mar 16 10:25:13 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 16 Mar 2010 10:25:13 +0100
Subject: [Pw_forum] where is the "search" link in this forum
In-Reply-To: <649021.57562.qm@web76109.mail.sg1.yahoo.com>
References: <649021.57562.qm@web76109.mail.sg1.yahoo.com>
Message-ID: <op.u9nlsbbba8x26q@paulax>

Replying to message "[Pw_forum] where is the "search" link in this forum"  
 from Lily Anh (16/03/10):
> Could anyone please tell me the "search" link? I could view all the  
> archives. However, I could not search for my specific purpose.

I'm not very happy with the built-in search of the mailing list software,  
as it tends to not give all the results I expect: normally I use google  
instead. You can use this personalized query to search in the pw_forum:
<http://www.google.com/cse/home?cx=000217952118062629757:xew9tb5yarq>
or the shortened version: <http://tr.im/pw_forum>.

best regards

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

     *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

From kajalmh18 at gmail.com  Tue Mar 16 13:02:35 2010
From: kajalmh18 at gmail.com (kajal jindal)
Date: Tue, 16 Mar 2010 17:32:35 +0530
Subject: [Pw_forum] file not converging
Message-ID: <d9147321003160502v71f2795fvb428b2349064ac58@mail.gmail.com>

I am working on a 3*3*3 supercell of ZnO...and I am doping Co into it... but
when I am doing the scf calculations, the file does not converge..... The
scf Accuracy keeps on oscillating and finally displays the message "100
iterations completed, file does not converge".... I have read forum
regarding this problem.. and have accordingly increased the  value of
degauss to 0.05...ecutwfc to 30 Ry....ecutrho to 400 Ry....
I have kept mixing_ beta=0.1... amd mixing_mode = local-TF.....
My structure has 969 electrons and accordingly I have kept the value of
nbnd=600...
So can anybody plz suggest me where am I making a mistake????????What should
I do in order to make my file converge...

Thanks in advance...
sincerely,
Miss Kajal
(UTA)(University of Delhi)
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From masoudnahali at live.com  Tue Mar 16 13:29:20 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Tue, 16 Mar 2010 12:29:20 +0000
Subject: [Pw_forum] AMD Open64 Compiler Suite
In-Reply-To: <mailman.1076.1268661978.15525.pw_forum@pwscf.org>
References: <mailman.1076.1268661978.15525.pw_forum@pwscf.org>
Message-ID: <COL114-W154B9B7FF2C685265AE6EA12D0@phx.gbl>




> anyone tried to compile PWSCF using the AMD Open64 Compiler Suite (the 
> last versione -afaik- is v4.2.3), possibly with the AMD Core Math 
> Library (ACML)?
> I know that ACML should work, but how about Open64?
> After reading that Intel Compilers deliberately does not take in account 
> of all math speedup present in non-intel CPUs, I'm considering which 
> optimized compiler I should use on my old non-Intel based linux...
> 
> Thanks,
> 	Carlo


Dear Carlo 

I have compiled QE using GNU compilers (gfortran, gcc, and g++) on my AMD(3 Cores CPU) . the operating system is SUSE 11.2 (64 bit). Both ACML and MathKernel libraries have been installed on my system before. with these configurations QE works but I am not sure about the efficiency of the work. I had tried intel compilers (ifort, icc, and icpc) before ! but I think that you will have less error in compiling when use the gnu compilers here.

Best Wishes
Masoud Nahali
Sharif University of Technology


 		 	   		  
_________________________________________________________________
Hotmail: Powerful Free email with security by Microsoft.
https://signup.live.com/signup.aspx?id=60969
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From nnlinh at sissa.it  Tue Mar 16 13:52:47 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Tue, 16 Mar 2010 13:52:47 +0100
Subject: [Pw_forum] file not converging
In-Reply-To: <d9147321003160502v71f2795fvb428b2349064ac58@mail.gmail.com>
References: <d9147321003160502v71f2795fvb428b2349064ac58@mail.gmail.com>
Message-ID: <4B9F7F1F.2090805@sissa.it>

kajal jindal wrote:
> I am working on a 3*3*3 supercell of ZnO...and I am doping Co into 
> it... but when I am doing the scf calculations, the file does not 
> converge..... The scf Accuracy keeps on oscillating and finally 
> displays the message "100 iterations completed, file does not 
> converge".... I have read forum regarding this problem.. and have 
> accordingly increased the  value of degauss to 0.05...ecutwfc to 30 
> Ry....ecutrho to 400 Ry....
> I have kept mixing_ beta=0.1... amd mixing_mode = local-TF....My 
> structure has 969 electrons and accordingly I have kept the value of 
> nbnd=600... 
The problem of non-convergence could be resulted by the atoms' 
configuration, so in opinion,  
   - you should check again Co doping into ZnO substrate if it has any 
problem such as overlap position or too close between atoms. Normally, 
with that problem you should enclose the input file when you make a 
question, it could help members clear to find out the reason. 
 Moreover, you can increase degauss to lager values such as 0.07 ; 0.1; 
0.3 and check if the calculation is converged or not.

Good luck

Linh



-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From miguel.martinez at ehu.es  Tue Mar 16 18:15:06 2010
From: miguel.martinez at ehu.es (Miguel Martinez Canales)
Date: Tue, 16 Mar 2010 18:15:06 +0100
Subject: [Pw_forum] Fortran compiler
In-Reply-To: <4B9F45E3.4070901@democritos.it>
References: <C7C3D7BD.1A16%Trinh.Vo@jpl.nasa.gov>
	<4B9F45E3.4070901@democritos.it>
Message-ID: <20100316181506.11344erdezjr1p4w@www.ehu.es>

Dear Paolo,

As I still haven't got an Intel license for my nw workstation and I'm  
actually planning on using OpenMPI with gfortran for a while, I was  
wondering what kind of bugs I should expect when coupling gfortran  
with quantum-Espresso. I suppose it's not as bad as using the Portland  
Group Compiler, though.

Paolo Giannozzi <giannozz at democritos.it> escribi?:

> Vo, Trinh (388C) wrote:
>
>> I don?t know which free compiler and  MPI are most suited for QE.
>
> what is written in the user guide still applies: gfortran works,
> sort of, but it is buggy. g95 works nicely but it produces slow
> executables. All non-buggy, properly installed MPI libraries
> work.
>
> P.
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>



-- 
----------------------------------------
Miguel Martinez Canales
   Condensed Matter Physics Dpt.
   UPV/EHU
   Faculty of Science and Technology
   Apdo. 644
   48080 Bilbao (Spain)
   Fax: +34 94 601 3500
   Tlf: +34 94 601 5326
----------------------------------------

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

George Bernard Shaw


From giannozz at democritos.it  Tue Mar 16 19:12:32 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 16 Mar 2010 19:12:32 +0100
Subject: [Pw_forum] AMD Open64 Compiler Suite
In-Reply-To: <4B9E366D.1070009@unito.it>
References: <4B9E366D.1070009@unito.it>
Message-ID: <4B9FCA10.60505@democritos.it>

Carlo Nervi wrote:

> anyone tried to compile PWSCF using the AMD Open64 Compiler Suite 

just tried: it works, sort of (it fails a few tests). If
you find the best options, we can add it to "configure"

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy
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From merlin.meheut at lmtg.obs-mip.fr  Tue Mar 16 19:24:32 2010
From: merlin.meheut at lmtg.obs-mip.fr (Merlin Meheut)
Date: Tue, 16 Mar 2010 19:24:32 +0100
Subject: [Pw_forum] Problem with raman calculations
Message-ID: <4B9FCCE0.8020003@lmtg.obs-mip.fr>


Dear PWSCF users,

I have successfully computed Raman spectra with version 4.0.4 of quantum 
espresso (with lraman=.true.), with PBE functional.
With version 4.1.2, I have the following error message:


 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from phq_setup : error #         1
     third order derivatives not implemented with GGA
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Have Raman calculation procedures changed between the two versions?

Thanks in advance...
sincerely,

Merlin
(University of Toulouse, France)

--  

Merlin M?heut
Maitre de conf?rences 
LMTG- Universit? Paul Sabatier Toulouse 3
14 avenue Edoaurd Belin
31400 Toulouse
tel: (+33)5 61 33 26 21
Fax: (+33) 5 61 33 25 60
Mobile: (+33) 6 34 67 57 02



From marsamos at democritos.it  Tue Mar 16 19:29:09 2010
From: marsamos at democritos.it (marsamos at democritos.it)
Date: Tue, 16 Mar 2010 19:29:09 +0100
Subject: [Pw_forum] GIPAW
Message-ID: <20100316192909.e2myuammkg4w4o0c@mail.democritos.it>

For those who are interested in GIPAW, the past tutorial (held in 
zurich at the CECAM, 2009), is available at 
http://www.gipaw.net/work.html.

Thanks Jonathan Yates!

bests

Layla

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

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


From carlo.nervi at unito.it  Tue Mar 16 20:31:16 2010
From: carlo.nervi at unito.it (Carlo Nervi)
Date: Tue, 16 Mar 2010 20:31:16 +0100 (CET)
Subject: [Pw_forum] AMD Open64 Compiler Suite
In-Reply-To: <4B9FCA10.60505@democritos.it>
References: <4B9E366D.1070009@unito.it> <4B9FCA10.60505@democritos.it>
Message-ID: <51300.130.192.119.45.1268767876.squirrel@mail.unito.it>

Thanks Paolo,
On  a old dual socket opteron 248 I tried to compile PW
using the default gfortran.
Apparently it works. You mentioned that gfortran is buggy.
Which version is buggy?
I tried with 4.1.2
There are also newer versions (on another machine I have
the 4.3.4), but I did no try yet...

Concerning the AMD Open64 I was wondering if it is worth
to try.
Perhaps it would make sense only in the case of new AMD
CPUs of some
"power", not my "old dual socket Opteron 248" (I'd like to
try the new 12 core Magny-Cours...)

However, first or later I hope I'll be able to find some
spare time to try to install open64 and try....

Cheers,
   Carlo

> Carlo Nervi wrote:
>
>> anyone tried to compile PWSCF using the AMD Open64
>> Compiler Suite
>
> just tried: it works, sort of (it fails a few tests). If
> you find the best options, we can add it to "configure"
>
> P.
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


From carlo.nervi at unito.it  Tue Mar 16 20:32:56 2010
From: carlo.nervi at unito.it (Carlo Nervi)
Date: Tue, 16 Mar 2010 20:32:56 +0100 (CET)
Subject: [Pw_forum] GIPAW
In-Reply-To: <20100316192909.e2myuammkg4w4o0c@mail.democritos.it>
References: <20100316192909.e2myuammkg4w4o0c@mail.democritos.it>
Message-ID: <44178.130.192.119.45.1268767976.squirrel@mail.unito.it>

Yep, thanks Layla and Jonathan!
  Carlo

--
------------------------------------------------------
Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8
Fax: +39 011 6707855 - Dipartimento di Chimica IFM
via P. Giuria 7, 10125 Torino, Italy
http://lem.ch.unito.it/

>
>
> ------------------ Messaggio originale -------------------
> Oggetto: [Pw_forum] GIPAW
> Da:      marsamos at democritos.it
> Data:    Mar, 16 Marzo 2010, 7:29 pm
> A:       pw_forum at pwscf.org
> ----------------------------------------------------------
>
> For those who are interested in GIPAW, the past tutorial
> (held in
> zurich at the CECAM, 2009), is available at
> http://www.gipaw.net/work.html.
>
> Thanks Jonathan Yates!
>
> bests
>
> Layla
>
> --
> Dr. L. Martin-Samos
> tel. +39 040 3787 429
> CNR-DEMOCRITOS and
> International School for Advanced Studies (ISAS-SISSA)
> via Beirut 2-4
> 34151 Trieste Italy
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging
> Program.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


From giannozz at democritos.it  Tue Mar 16 21:26:15 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 16 Mar 2010 21:26:15 +0100
Subject: [Pw_forum] AMD Open64 Compiler Suite
In-Reply-To: <51300.130.192.119.45.1268767876.squirrel@mail.unito.it>
References: <4B9E366D.1070009@unito.it> <4B9FCA10.60505@democritos.it>
	<51300.130.192.119.45.1268767876.squirrel@mail.unito.it>
Message-ID: <352096B4-A4F5-4B9C-8080-30A16F79C7FD@democritos.it>

On Mar 16, 2010, at 20:31 , Carlo Nervi wrote:

> You mentioned that gfortran is buggy. Which version is buggy?

it depends. Recent versions typically produce a working executable
for pw.x , but not yet a working phonon executable. All I know about
the various compilers is written in the user guide (and continuously
updated in the cvs version)

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




From giannozz at democritos.it  Tue Mar 16 22:02:43 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 16 Mar 2010 22:02:43 +0100
Subject: [Pw_forum] Problem with raman calculations
In-Reply-To: <4B9FCCE0.8020003@lmtg.obs-mip.fr>
References: <4B9FCCE0.8020003@lmtg.obs-mip.fr>
Message-ID: <060A7B78-E086-4791-9823-3489EF28C9A0@democritos.it>


On Mar 16, 2010, at 19:24 , Merlin Meheut wrote:

> I have successfully computed Raman spectra with version 4.0.4 of  
> quantum
> espresso (with lraman=.true.), with PBE functional.
> With version 4.1.2, I have the following error message:
>
>      from phq_setup : error #         1
>      third order derivatives not implemented with GGA
>
> Have Raman calculation procedures changed between the two versions?

http://www.democritos.it/pipermail/pw_forum/2008-September/010123.html

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




From payam.norouzzadeh at gmail.com  Tue Mar 16 23:24:55 2010
From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh)
Date: Wed, 17 Mar 2010 01:54:55 +0330
Subject: [Pw_forum] from set_irr : error # 2
Message-ID: <5a8b78941003161524g121e5b24p28f97e876161fc46@mail.gmail.com>

Hello
I got the following error while performing phonon calculation on Ge46
clathrate:
     task #        88
     from set_irr : error #         2
     npert > max_irr_dim

I am using the newest version of espresso 4.1.2.
Could anynone let me know how I can resolve this problem?
Thanks in advance.

Best regards,Payam Norouzzadeh
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From eyvaz_isaev at yahoo.com  Wed Mar 17 00:01:05 2010
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 16 Mar 2010 16:01:05 -0700 (PDT)
Subject: [Pw_forum] from set_irr : error # 2
In-Reply-To: <5a8b78941003161524g121e5b24p28f97e876161fc46@mail.gmail.com>
Message-ID: <415196.84898.qm@web65703.mail.ac4.yahoo.com>

Dear Payam,

> On Wed, 3/17/10, Payam Norouzzadeh <payam.norouzzadeh at gmail.com> wrote:
>      task #        88
>      from set_irr : error #         2
>      npert > max_irr_dim 

This question has been discussed several times in the forum. You could find the answer if searched the forum archive.

Nevertheless, simply change max_irr_dim = 4 to some reasonable value (6 or 8, say) in phcom.f90 in PH directory. And recompile phonon code.
This will fix the problem.

Bests,
Eyvaz.

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

 


      


From baris.malcioglu at gmail.com  Wed Mar 17 09:46:26 2010
From: baris.malcioglu at gmail.com (O. Baris Malcioglu)
Date: Wed, 17 Mar 2010 09:46:26 +0100
Subject: [Pw_forum] AMD Open64 Compiler Suite
In-Reply-To: <352096B4-A4F5-4B9C-8080-30A16F79C7FD@democritos.it>
References: <4B9E366D.1070009@unito.it> <4B9FCA10.60505@democritos.it> 
	<51300.130.192.119.45.1268767876.squirrel@mail.unito.it>
	<352096B4-A4F5-4B9C-8080-30A16F79C7FD@democritos.it>
Message-ID: <ab42ba5f1003170146q4eef9e10od445253a68e4a9c3@mail.gmail.com>

MKL and Intel compilers were as good as AMD supplied ones on AMD machines
upto some version (10.x possibly I don't remember exactly). After that
version, AMD performance started to degrade.

Also, I would like to add if I may, obtaining a working executable does not
necessarily mean that the executable will output what you expect.

Actually, the "optimization methods" compilers employ make a significant
difference. In my experience the IBM compilers are the most problematic,
since I get large numerical drifts, (on the level 1e-8 per operation,
although I am using double precision) and the code I am working on is
especially vulnerable to those. I vaguely remember having to change how I
write some loops due to how loop unrolling is handled in gfortran.

In any case, please test your outcome. In case you get unphysical results,
please mention it here in the forum so that we can have a look. At least
people will know.

Best,
Baris

2010/3/16 Paolo Giannozzi <giannozz at democritos.it>

> On Mar 16, 2010, at 20:31 , Carlo Nervi wrote:
>
> > You mentioned that gfortran is buggy. Which version is buggy?
>
> it depends. Recent versions typically produce a working executable
> for pw.x , but not yet a working phonon executable. All I know about
> the various compilers is written in the user guide (and continuously
> updated in the cvs version)
>
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From sks.jnc at gmail.com  Wed Mar 17 11:52:50 2010
From: sks.jnc at gmail.com (S. K. S.)
Date: Wed, 17 Mar 2010 16:22:50 +0530
Subject: [Pw_forum] flow-chart in PWSCF
Message-ID: <d5eefb3d1003170352s6dd97f66j36e6475b21960e10@mail.gmail.com>

    Dear All,

    http://cms.mpi.univie.ac.at/vasp/vasp/node199.html

   This link has a flow chart describing
    the algorithms used in VASP.
    Is there such a flow-chart in PWSCF also?
    If not, then I would like to know whether PWSCF
    follows the same flow-chart or not?
    I mean, PWSCF check energy convergence or
    density scf convergence or both?
    It would be really nice if  somebody send me a full
    flow chart  which has been used in PWSCF.

   With my best regards,
   Saha S. K.
   JNCASR
   R&D Assistant
   Bangalore
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From aryjunior at gmail.com  Wed Mar 17 12:30:59 2010
From: aryjunior at gmail.com (Ary Junior)
Date: Wed, 17 Mar 2010 08:30:59 -0300
Subject: [Pw_forum] GIPAW
In-Reply-To: <20100316192909.e2myuammkg4w4o0c@mail.democritos.it>
References: <20100316192909.e2myuammkg4w4o0c@mail.democritos.it>
Message-ID: <4c9c61c21003170430h1eebe614t1ed62fcf042adc9f@mail.gmail.com>

Hi, I can't extract two files from that tutorial:
gipaw_day2.tgz<http://www.tcm.phy.cam.ac.uk/%7Ejry20/gipaw/gipaw_day2.tgz>and
gipaw_day3.tgz <http://www.tcm.phy.cam.ac.uk/%7Ejry20/gipaw/gipaw_day3.tgz>.
The other files were extracted normally.

Thank you very much!

--
Ary Junior
Universidade Federal de Juiz de Fora
Juiz de Fora - Minas Gerais - Brasil

On Tue, Mar 16, 2010 at 3:29 PM, <marsamos at democritos.it> wrote:

> For those who are interested in GIPAW, the past tutorial (held in
> zurich at the CECAM, 2009), is available at
> http://www.gipaw.net/work.html.
>
> Thanks Jonathan Yates!
>
> bests
>
> Layla
>
> --
> Dr. L. Martin-Samos
> tel. +39 040 3787 429
> CNR-DEMOCRITOS and
> International School for Advanced Studies (ISAS-SISSA)
> via Beirut 2-4
> 34151 Trieste Italy
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
http://lattes.cnpq.br/8221674673413336
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From science35 at gmail.com  Wed Mar 17 14:28:22 2010
From: science35 at gmail.com (patriot pershing)
Date: Wed, 17 Mar 2010 14:28:22 +0100
Subject: [Pw_forum] about Ueff in LDA+U calculation
Message-ID: <9fdec6371003170628u5c3e861kea584946a21f85c4@mail.gmail.com>

dear please:
i would do LDA+U calculation on ZnS and ZnO material using Quantum
Espresso code and i would use Ueff in my calculations which is defined
as U - J by changing these 2 parameters but when i have traied to do
this using espresso code i don't arrived to do this because only the U
value as well as alpha parameter can be modified for this reason i
would if any one can help me in this point. secondly, i would ask what
i need to do GGA+U calculations? ( i think in espresso is just do
LDA+U calculation + USPP with GGA exchange-correlation function)
best regards

From degironc at sissa.it  Wed Mar 17 14:33:23 2010
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 17 Mar 2010 14:33:23 +0100
Subject: [Pw_forum] about Ueff in LDA+U calculation
In-Reply-To: <9fdec6371003170628u5c3e861kea584946a21f85c4@mail.gmail.com>
References: <9fdec6371003170628u5c3e861kea584946a21f85c4@mail.gmail.com>
Message-ID: <4BA0DA23.5080003@sissa.it>

dear patriot
please provide your identity and  affilaition
best regards,
Stefano de Gironcoli - SISSA nd DEMOCRITOS

patriot pershing wrote:
> dear please:
> i would do LDA+U calculation on ZnS and ZnO material using Quantum
> Espresso code and i would use Ueff in my calculations which is defined
> as U - J by changing these 2 parameters but when i have traied to do
> this using espresso code i don't arrived to do this because only the U
> value as well as alpha parameter can be modified for this reason i
> would if any one can help me in this point. secondly, i would ask what
> i need to do GGA+U calculations? ( i think in espresso is just do
> LDA+U calculation + USPP with GGA exchange-correlation function)
> best regards
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From science35 at gmail.com  Wed Mar 17 15:01:16 2010
From: science35 at gmail.com (patriot pershing)
Date: Wed, 17 Mar 2010 15:01:16 +0100
Subject: [Pw_forum] about Ueff in LDA+U calculation
In-Reply-To: <4BA0DA23.5080003@sissa.it>
References: <9fdec6371003170628u5c3e861kea584946a21f85c4@mail.gmail.com>
	<4BA0DA23.5080003@sissa.it>
Message-ID: <9fdec6371003170701g40e3c38dn73c6851ef57ce3bb@mail.gmail.com>

M Lahmer
Laboratory of physics and chemistry of semiconductors
university of constantine

2010/3/17, Stefano de Gironcoli <degironc at sissa.it>:
> dear patriot
> please provide your identity and  affilaition
> best regards,
> Stefano de Gironcoli - SISSA nd DEMOCRITOS
>
> patriot pershing wrote:
>> dear please:
>> i would do LDA+U calculation on ZnS and ZnO material using Quantum
>> Espresso code and i would use Ueff in my calculations which is defined
>> as U - J by changing these 2 parameters but when i have traied to do
>> this using espresso code i don't arrived to do this because only the U
>> value as well as alpha parameter can be modified for this reason i
>> would if any one can help me in this point. secondly, i would ask what
>> i need to do GGA+U calculations? ( i think in espresso is just do
>> LDA+U calculation + USPP with GGA exchange-correlation function)
>> best regards
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From giannozz at democritos.it  Wed Mar 17 15:09:56 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 17 Mar 2010 15:09:56 +0100
Subject: [Pw_forum] flow-chart in PWSCF
In-Reply-To: <d5eefb3d1003170352s6dd97f66j36e6475b21960e10@mail.gmail.com>
References: <d5eefb3d1003170352s6dd97f66j36e6475b21960e10@mail.gmail.com>
Message-ID: <4BA0E2B4.7020401@democritos.it>

S. K. S. wrote:

>     Is there such a flow-chart in PWSCF also?

not that I know

>     If not, then I would like to know whether PWSCF
>     follows the same flow-chart or not?

all self-consistent codes follow more or less the same flow chart

>     I mean, PWSCF check energy convergence or
>     density scf convergence or both?

the latter. More detials in the QE paper

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

From degironc at sissa.it  Wed Mar 17 15:34:16 2010
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 17 Mar 2010 15:34:16 +0100
Subject: [Pw_forum] about Ueff in LDA+U calculation
In-Reply-To: <9fdec6371003170701g40e3c38dn73c6851ef57ce3bb@mail.gmail.com>
References: <9fdec6371003170628u5c3e861kea584946a21f85c4@mail.gmail.com>	<4BA0DA23.5080003@sissa.it>
	<9fdec6371003170701g40e3c38dn73c6851ef57ce3bb@mail.gmail.com>
Message-ID: <4BA0E868.60906@sissa.it>

Dear M Lahmer

 the DFT+U implementation in PWscf is the one described in Phys Rev B 
71, 035105 (2005) by M. Cococcioni and S de Gironcoli.
The U parameter defined in PWscf is directly the U_eff = U-J you are 
referring to and the alpha parameters are used to perturb the system 
away from its LDA minimum, or other reference systems that might be more 
convenient [see PRL 97, 103001 (2006) by Kulik, Cococcioni, Scherlis  
and Marzari], to calculate the U parameter from first principles 
following the recipe given in that paper.

hope this helps,
best regards,
 stefano de Gironcoli - SISSA and DEMOCRITOS

patriot pershing wrote:
> M Lahmer
> Laboratory of physics and chemistry of semiconductors
> university of constantine
>
> 2010/3/17, Stefano de Gironcoli <degironc at sissa.it>:
>   
>> dear patriot
>> please provide your identity and  affilaition
>> best regards,
>> Stefano de Gironcoli - SISSA nd DEMOCRITOS
>>
>> patriot pershing wrote:
>>     
>>> dear please:
>>> i would do LDA+U calculation on ZnS and ZnO material using Quantum
>>> Espresso code and i would use Ueff in my calculations which is defined
>>> as U - J by changing these 2 parameters but when i have traied to do
>>> this using espresso code i don't arrived to do this because only the U
>>> value as well as alpha parameter can be modified for this reason i
>>> would if any one can help me in this point. secondly, i would ask what
>>> i need to do GGA+U calculations? ( i think in espresso is just do
>>> LDA+U calculation + USPP with GGA exchange-correlation function)
>>> best regards
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>       
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>     
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From daijiayu at nudt.edu.cn  Wed Mar 17 15:19:34 2010
From: daijiayu at nudt.edu.cn (Jiayu Dai)
Date: Wed, 17 Mar 2010 22:19:34 +0800
Subject: [Pw_forum] Baldereschi and MP point.
Message-ID: <468835574.29889@nudt.edu.cn>

Dear users, 

I have a question about the sample points in the Brillouin zone. We usaually use
the MP point in our calculations, and it works well and fast in cubic crystal.
However, for disordered materials or liquids, we usually use Gamma point only,
such as point in CPMD. My question is how do we know the Gamma point is better
than the Baldereschi mean value point, or on the contrary??Which one gives faster
convergence?

Thanks a lot.

Jiayu




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

From degironc at sissa.it  Wed Mar 17 16:19:58 2010
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 17 Mar 2010 16:19:58 +0100
Subject: [Pw_forum] Baldereschi and MP point.
In-Reply-To: <468835574.29889@nudt.edu.cn>
References: <468835574.29889@nudt.edu.cn>
Message-ID: <4BA0F31E.8090602@sissa.it>

Dear Jiayu Dai

the Baldereschi point and MP points are efficient choice because they 
exploit the SYMMETRY properties of the system in order to sample the BZ 
on a hopefully small set of points.
In liquid and disordered materials there is no symmetry and therefore 
there is no symmetry-related k-point reduction and any regular grid of 
points should be equally efficient.
On the other hand for large systems the BZ shrinks and the refolded 
bands in the mini-BZ are almost flat which means that any single point 
in the BZ should do the work.
In this situation Gamma is convenient because  wfc (in absence of 
spin-orbit) can be chosen as real in real space which implies that wfc 
Fourier components of G and -G are related  by complex conjugation and 
you can use half the memory storage and cut by two the number of operations.

best,
  stefano

Jiayu Dai wrote:
> Dear users, 
>
> I have a question about the sample points in the Brillouin zone. We usaually use
> the MP point in our calculations, and it works well and fast in cubic crystal.
> However, for disordered materials or liquids, we usually use Gamma point only,
> such as point in CPMD. My question is how do we know the Gamma point is better
> than the Baldereschi mean value point, or on the contrary??Which one gives faster
> convergence?
>
> Thanks a lot.
>
> Jiayu
>
>
>
>
> ------------------------------
> -------------------------------------------
> Jiayu Dai
> Department of Physics
> National University of Defense Technology, 
> Changsha, 410073, P R China
> -----------------------------------------
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From marzari at MIT.EDU  Wed Mar 17 16:19:31 2010
From: marzari at MIT.EDU (Nicola Marzari)
Date: Wed, 17 Mar 2010 15:19:31 +0000
Subject: [Pw_forum] Baldereschi and MP point.
In-Reply-To: <468835574.29889@nudt.edu.cn>
References: <468835574.29889@nudt.edu.cn>
Message-ID: <4BA0F303.8070900@mit.edu>

Jiayu Dai wrote:
> Dear users, 
>
> I have a question about the sample points in the Brillouin zone. We usaually use
> the MP point in our calculations, and it works well and fast in cubic crystal.
> However, for disordered materials or liquids, we usually use Gamma point only,
> such as point in CPMD. My question is how do we know the Gamma point is better
> than the Baldereschi mean value point, or on the contrary??Which one gives faster
> convergence?
>
> Thanks a lot.
>
> Jiayu


My personal bias is that the Baldereschi point always works better, and that
in an orthormombic cell using 1/4 1/4 1/4 (relative coordinates) is 
almost as
good as using the full 2x2x2 monkhorst pack mesh, shifted, and, for a metal,
much much better than gamma.

Note that

1) if you use only 1/4 1/4 1/4 the forces will not be exactly symmetric 
even for a
symmetric system

2) if you do not use nosym=.true. pwscf will in any case increase the 
k-points to recover
symmetry

3) the wavefunction at 1/4 1/4 1/4 are complex, while at gamma can be 
chosen to be real,
making the code twise as fast (I think) and the memory half. That's why 
e.g. the cp code
uses gamma, even if it is actually the worst choice possible from the 
point of view of the sampling.


nicola


-- 
---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu 


From Trinh.Vo at jpl.nasa.gov  Wed Mar 17 16:35:20 2010
From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Wed, 17 Mar 2010 08:35:20 -0700
Subject: [Pw_forum] Fortran compiler
In-Reply-To: <4B9F45E3.4070901@democritos.it>
Message-ID: <C7C644C8.1AC9%Trinh.Vo@jpl.nasa.gov>

Thanks very much Paolo, Lorenzo, and other users who have provided useful
information on gfortran.  I am actually compiling QE with the current
version of gfortran, and I have to think again whether I should continue to
use it.  :-).

Trinh


On 3/16/10 1:48 AM, "Paolo Giannozzi" <giannozz at democritos.it> wrote:

> Vo, Trinh (388C) wrote:
> 
>> I don?t know which free compiler and  MPI are most suited for QE.
> 
> what is written in the user guide still applies: gfortran works,
> sort of, but it is buggy. g95 works nicely but it produces slow
> executables. All non-buggy, properly installed MPI libraries
> work.
> 
> P.


From junkermeier at bloch.nrl.navy.mil  Wed Mar 17 16:45:37 2010
From: junkermeier at bloch.nrl.navy.mil (Chad Junkermeier)
Date: Wed, 17 Mar 2010 11:45:37 -0400
Subject: [Pw_forum] lattice constant from unit cell vs. from supercell
Message-ID: <629F20AD-563D-4EF8-9FEE-16B5641338D2@bloch.nrl.navy.mil>

Hi,
   I am trying to perform a set of SCF calculations on graphene with F  
atoms attached.  If I do this using the unit cell, everything seems to  
work correctly, and the equilibrium lattice constant for the system  
seems to be correct.  If, in stead, I use a 2x2 supercell I find that  
the equilibrium lattice constant is not the same (or even close) to  
the unit cell result.
   The only differences between the two sets of calculations are the  
number of atoms and the value used for alat, and the number of kpoints.

The supercell case has the following output (no analog of which is  
found in the unit cell case):

     Found symmetry operation: I + (  0.0000 -0.5000  0.0000)
      This is a supercell, fractional translation are disabled


Can anyone please tell me where I am going wrong in the supercell case?

Thank you.


Chad Junkermeier, Ph.D.
NRC Post-Doctoral Fellow
Naval Research Laboratory
4555 Overlook Ave, S.W.
Washington DC 20375
Office: (202) 404-4635
Fax: (202) 767-1165
Email:  junkermeier(at)bloch.nrl.navy.mil


Note that the value for celldm(3) in both of these files was computed:  
celldm(3) = 46.5/alat

The commands for the unit cell case (alat = 4.80):

&CONTROL
calculation = "relax",
pseudo_dir  = "/app/espresso/pseudo",
outdir      = "/workspace/junky/lattice_top/tmp",
/
&SYSTEM
ibrav       = 4,
celldm(1)   = 4.800,
celldm(3)   = 9.68750000000000000000,
nat         = 3,
ntyp        = 2,
ecutwfc     = 300.0,
occupations = "smearing",
smearing    = "methfessel-paxton",
degauss     = 0.050,
/
&ELECTRONS
conv_thr    = 0.000001,
mixing_beta = 0.30,
/
&IONS
bfgs_ndim         = 3,
pot_extrapolation = "second_order",
wfc_extrapolation = "second_order",
/
ATOMIC_SPECIES
C  6.0 C.pbe-van_ak.UPF
F  9.0 F.pbe-n-van.UPF
ATOMIC_POSITIONS crystal
C   0.0000000    0.0000000    0.0000
C   1.00/3.00  2.00/3.00    0.0000
F   0.0000000    0.0000000    0.050000
K_POINTS automatic
8 8 1  0 0  0





The commands for the supercell case (alat = 4.65, celldm(1)=2*alat):

&CONTROL
calculation = "relax",
pseudo_dir  = "/app/espresso/pseudo",
outdir      = "/workspace/junky/twotwoF01/tmp",
/
&SYSTEM
ibrav       = 4,
celldm(1)   = 9.300,
celldm(3)   = 10.00000000000000000000,
nat         = 10,
ntyp        = 2,
ecutwfc     = 300.0,
occupations = "smearing",
smearing    = "methfessel-paxton",
degauss     = 0.05,
/
&ELECTRONS
conv_thr    = 0.000001,
mixing_beta = 0.3,
/
&IONS
bfgs_ndim         = 3,
pot_extrapolation = "second_order",
wfc_extrapolation = "second_order",
/
ATOMIC_SPECIES
C  6.0 C.pbe-van_ak.UPF
F  9.0 F.pbe-n-van.UPF
ATOMIC_POSITIONS crystal
C       0.0     0.0     0.0
C       0.1666666666666667      0.3333333333333333      0.0
C       0.0     0.5     0.0
C       0.1666666666666667      0.8333333333333333      0.0
C       0.5     0.0     0.0
C       0.6666666666666667      0.3333333333333333      0.0
C       0.5     0.5     0.0
C       0.6666666666666667      0.8333333333333333      0.0
F       0.0     0.0     0.05
F       0.1666666666666667      0.3333333333333333      0.05
K_POINTS automatic
4 4 1  0 0  0










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From daijiayu at nudt.edu.cn  Wed Mar 17 16:43:45 2010
From: daijiayu at nudt.edu.cn (Jiayu Dai)
Date: Wed, 17 Mar 2010 23:43:45 +0800
Subject: [Pw_forum] Baldereschi and MP point.
Message-ID: <468840625.31566@nudt.edu.cn>

Thanks Stefano and Nicola. Your anwsers are so professional and very helpful. As
your comments, i guess Gamma point used in the large disordered materials and
liquids can improve the calculational efficiency twice as fast. And for symmetric
crystal, Baldereschi point works better. Am i right? And i did not find the
Baldereschi point in PWscf, so it is not implemented here?

Thanks.

In your mail:
>From: Stefano de Gironcoli <degironc at sissa.it>
>Reply-To: 
>To: Jiayu Dai <daijiayu at nudt.edu.cn>, PWSCF Forum <pw_forum at pwscf.org>
>Subject: Re: [Pw_forum] Baldereschi and MP point.
>Date:Wed, 17 Mar 2010 16:19:58 +0100
>
>Dear Jiayu Dai
>
>the Baldereschi point and MP points are efficient choice because they 
>exploit the SYMMETRY properties of the system in order to sample the BZ 
>on a hopefully small set of points.
>In liquid and disordered materials there is no symmetry and therefore 
>there is no symmetry-related k-point reduction and any regular grid of 
>points should be equally efficient.
>On the other hand for large systems the BZ shrinks and the refolded 
>bands in the mini-BZ are almost flat which means that any single point 
>in the BZ should do the work.
>In this situation Gamma is convenient because  wfc (in absence of 
>spin-orbit) can be chosen as real in real space which implies that wfc 
>Fourier components of G and -G are related  by complex conjugation and 
>you can use half the memory storage and cut by two the number of operations.
>
>best,
>  stefano
>
>Jiayu Dai wrote:
>> Dear users, 
>>
>> I have a question about the sample points in the Brillouin zone. We usaually
use
>> the MP point in our calculations, and it works well and fast in cubic crystal.
>> However, for disordered materials or liquids, we usually use Gamma point only,
>> such as point in CPMD. My question is how do we know the Gamma point is better
>> than the Baldereschi mean value point, or on the contrary??Which one gives
faster
>> convergence?
>>
>> Thanks a lot.
>>
>> Jiayu
>>
>>
>>
>>
>> ------------------------------
>> -------------------------------------------
>> Jiayu Dai
>> Department of Physics
>> National University of Defense Technology, 
>> Changsha, 410073, P R China
>> -----------------------------------------
>>   
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>   
>
>
> 




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

From degironc at sissa.it  Wed Mar 17 17:44:57 2010
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 17 Mar 2010 17:44:57 +0100
Subject: [Pw_forum] Baldereschi and MP point.
In-Reply-To: <468840625.31566@nudt.edu.cn>
References: <468840625.31566@nudt.edu.cn>
Message-ID: <4BA10709.5080305@sissa.it>

Baldereschi's point or any set of points can be provided using  input 
formats "tpiba" or "cystal" that reads the number of k-points in the 
list and then a line for each point with coordinate (in unit of 2PI/a 
{tpiba} or as fraction of the reciprocal lattice vectors {crystal}) and 
its weight.

stefano

Jiayu Dai wrote:
> Thanks Stefano and Nicola. Your anwsers are so professional and very helpful. As
> your comments, i guess Gamma point used in the large disordered materials and
> liquids can improve the calculational efficiency twice as fast. And for symmetric
> crystal, Baldereschi point works better. Am i right? And i did not find the
> Baldereschi point in PWscf, so it is not implemented here?
>
> Thanks.
>
> In your mail:
>   
>> From: Stefano de Gironcoli <degironc at sissa.it>
>> Reply-To: 
>> To: Jiayu Dai <daijiayu at nudt.edu.cn>, PWSCF Forum <pw_forum at pwscf.org>
>> Subject: Re: [Pw_forum] Baldereschi and MP point.
>> Date:Wed, 17 Mar 2010 16:19:58 +0100
>>
>> Dear Jiayu Dai
>>
>> the Baldereschi point and MP points are efficient choice because they 
>> exploit the SYMMETRY properties of the system in order to sample the BZ 
>> on a hopefully small set of points.
>> In liquid and disordered materials there is no symmetry and therefore 
>> there is no symmetry-related k-point reduction and any regular grid of 
>> points should be equally efficient.
>> On the other hand for large systems the BZ shrinks and the refolded 
>> bands in the mini-BZ are almost flat which means that any single point 
>> in the BZ should do the work.
>> In this situation Gamma is convenient because  wfc (in absence of 
>> spin-orbit) can be chosen as real in real space which implies that wfc 
>> Fourier components of G and -G are related  by complex conjugation and 
>> you can use half the memory storage and cut by two the number of operations.
>>
>> best,
>>  stefano
>>
>> Jiayu Dai wrote:
>>     
>>> Dear users, 
>>>
>>> I have a question about the sample points in the Brillouin zone. We usaually
>>>       
> use
>   
>>> the MP point in our calculations, and it works well and fast in cubic crystal.
>>> However, for disordered materials or liquids, we usually use Gamma point only,
>>> such as point in CPMD. My question is how do we know the Gamma point is better
>>> than the Baldereschi mean value point, or on the contrary??Which one gives
>>>       
> faster
>   
>>> convergence?
>>>
>>> Thanks a lot.
>>>
>>> Jiayu
>>>
>>>
>>>
>>>
>>> ------------------------------
>>> -------------------------------------------
>>> Jiayu Dai
>>> Department of Physics
>>> National University of Defense Technology, 
>>> Changsha, 410073, P R China
>>> -----------------------------------------
>>>   
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>   
>>>       
>>
>>     
>
>
>
>
> ------------------------------
> -------------------------------------------
> Jiayu Dai
> Department of Physics
> National University of Defense Technology, 
> Changsha, 410073, P R China
> -----------------------------------------
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From giannozz at democritos.it  Wed Mar 17 17:52:33 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 17 Mar 2010 17:52:33 +0100
Subject: [Pw_forum] lattice constant from unit cell vs. from supercell
In-Reply-To: <629F20AD-563D-4EF8-9FEE-16B5641338D2@bloch.nrl.navy.mil>
References: <629F20AD-563D-4EF8-9FEE-16B5641338D2@bloch.nrl.navy.mil>
Message-ID: <4BA108D1.7010403@democritos.it>

Chad Junkermeier wrote:

> If I do this using the unit cell, everything seems to 
> work correctly, and the equilibrium lattice constant for the system 
> seems to be correct.  If, instead, I use a 2x2 supercell I find that 
> the equilibrium lattice constant is not the same (or even close) to the 
> unit cell result.

your data are for fixed-cell structural optimization: what do you mean
by "the equilibrium lattice constant is not the same"? You choose the
lattice constant

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

From ttduyle at gmail.com  Wed Mar 17 18:25:42 2010
From: ttduyle at gmail.com (Duy Le)
Date: Wed, 17 Mar 2010 13:25:42 -0400
Subject: [Pw_forum] lattice constant from unit cell vs. from supercell
In-Reply-To: <4BA108D1.7010403@democritos.it>
References: <629F20AD-563D-4EF8-9FEE-16B5641338D2@bloch.nrl.navy.mil>
	<4BA108D1.7010403@democritos.it>
Message-ID: <8974d3b21003171025t32ae7296qff97c9176f2fd599@mail.gmail.com>

Not really sure if I understand your question. However, there seems to
be an incorrectness.
Simple logic:
1F, 2 C in a "1x1" supercell
4F, 8 C in a "2x2" supercell
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Wed, Mar 17, 2010 at 12:52 PM, Paolo Giannozzi
<giannozz at democritos.it> wrote:
> Chad Junkermeier wrote:
>
>> If I do this using the unit cell, everything seems to
>> work correctly, and the equilibrium lattice constant for the system
>> seems to be correct. ?If, instead, I use a 2x2 supercell I find that
>> the equilibrium lattice constant is not the same (or even close) to the
>> unit cell result.
>
> your data are for fixed-cell structural optimization: what do you mean
> by "the equilibrium lattice constant is not the same"? You choose the
> lattice constant
>
> P.
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From elbuesta at icqmail.com  Wed Mar 17 18:21:01 2010
From: elbuesta at icqmail.com (elbuesta at icqmail.com)
Date: Wed, 17 Mar 2010 13:21:01 -0400
Subject: [Pw_forum] lattice constant from unit cell vs. from supercell
In-Reply-To: <8CC940C6A44036E-E7C-1F45@webmail-m063.sysops.aol.com>
References: <8CC940C6A44036E-E7C-1F45@webmail-m063.sysops.aol.com>
Message-ID: <8CC940D598AE358-E7C-216A@webmail-m063.sysops.aol.com>

Hi Dr. Junkermeier,
 
 If you check with xcrysden, you will see that the first input does not reproduce a graphene layer because the carbon atoms are overlapped. I believe the first input should be something like:
 
 &CONTROL
 calculation = "relax",
 pseudo_dir? = "/app/espresso/pseudo",
 outdir????? = "/workspace/junky/lattice_top/tmp",
 /
 &SYSTEM
 ibrav?????? = 4,
 celldm(1)?? = 4.80,
 celldm(3)?? = 9.6875,
 nat???????? = 3,
 ntyp??????? = 2,
 ecutwfc???? = 300.0,
 occupations = "smearing",
 smearing??? = "methfessel-paxton",
 degauss???? = 0.050,
 /
 &ELECTRONS
 conv_thr??? = 0.000001,
 mixing_beta = 0.30,
 /
 &IONS
 bfgs_ndim???????? = 3,
 pot_extrapolation = "second_order",
 wfc_extrapolation = "second_order",
 /
 ATOMIC_SPECIES
 C? 6.0 C.pbe-van_ak.UPF
 F? 9.0 F.pbe-n-van.UPF
 ATOMIC_POSITIONS crystal
 C?? 0.0000000??? 0.0000000??? 0.000000
 C?? 0.3333333??? 0.6666666??? 0.000000
 F?? 0.0000000??? 0.0000000??? 0.050000
 K_POINTS automatic
 8 8 1? 0 0? 0
 
   
 
  But even using this input, the position of the F atoms is not the same compared to the second input. I don't know how many F atoms you want on top of the carbon, so I suggest you to use Xcrysden and than decide how do you exactly want your structure.
 I hope it helps. All best.
 
 Fabio Negreiros Ribeiro
 Departamento de F?sica da Universidade Federal de Minas Gerais - Brasil
 
 
 -----Original Message-----
 From: Chad Junkermeier &lt;junkermeier at bloch.nrl.navy.mil&gt;
 To: pw_forum at pwscf.org
 Sent: Wed, Mar 17, 2010 4:45 pm
 Subject: [Pw_forum] lattice constant from unit cell vs. from supercell
 
              Hi, ??I am trying to perform a set of SCF calculations on graphene with F atoms attached. ?If I do this using the unit cell, everything seems to work correctly, and the equilibrium lattice constant for the system seems to be correct. ?If, in stead, I use a 2x2 supercell I find that the equilibrium lattice constant is not the same (or even close) to the unit cell result.
  ??The only differences between the two sets of calculations are the number of atoms and the value used for alat, and the number of kpoints.
  
 
  The supercell case has the following output (no analog of which is found in the unit cell case):
                         
 
   ?? ?Found symmetry operation: I + ( ?0.0000 -0.5000 ?0.0000)
  ?? ? This is a supercell, fractional translation are disabled
  
 
 
  
 
   Can anyone please tell me where I am going wrong in the supercell case?
  
 
  Thank you.
  
 
 
  
 
   Chad Junkermeier, Ph.D.
  NRC Post-Doctoral Fellow
  Naval Research Laboratory
  4555 Overlook Ave, S.W.
  Washington DC 20375
  Office: (202) 404-4635
  Fax: (202) 767-1165
  Email:??junkermeier(at)bloch.nrl.navy.mil??
  
 
  
 
  Note that the value for celldm(3) in both of these files was computed: celldm(3) = 46.5/alat
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
  The commands for the unit cell case (alat = 4.80):?
  
 
    &CONTROL
  calculation = "relax",
  pseudo_dir ?= "/app/espresso/pseudo",
  outdir ? ? ?= "/workspace/junky/lattice_top/tmp",
  /
  &SYSTEM
  ibrav ? ? ? = 4,
  celldm(1) ? = 4.800,
  celldm(3) ? = 9.68750000000000000000,
  nat ? ? ? ? = 3,
  ntyp ? ? ? ?= 2,
  ecutwfc ? ? = 300.0,
  occupations = "smearing",
  smearing ? ?= "methfessel-paxton",
  degauss ? ? = 0.050,
  /
  &ELECTRONS
  conv_thr ? ?= 0.000001,
  mixing_beta = 0.30,
  /
  &IONS
  bfgs_ndim ? ? ? ? = 3,
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
  /
  ATOMIC_SPECIES
  C ?6.0 C.pbe-van_ak.UPF
  F ?9.0 F.pbe-n-van.UPF
  ATOMIC_POSITIONS crystal
  C ? 0.0000000 ? ?0.0000000 ? ?0.0000
  C ? 1.00/3.00 ?2.00/3.00 ? ?0.0000
  F ? 0.0000000 ? ?0.0000000 ? ?0.050000
  K_POINTS automatic
  8 8 1 ?0 0 ?0
  
 
 
  
 
  
 
  
 
  
 
  The commands for the supercell case?(alat = 4.65, celldm(1)=2*alat):
  
 
    &CONTROL
  calculation = "relax",
  pseudo_dir ?= "/app/espresso/pseudo",
  outdir ? ? ?= "/workspace/junky/twotwoF01/tmp",
  /
  &SYSTEM
  ibrav ? ? ? = 4,
  celldm(1) ? = 9.300,
  celldm(3) ? = 10.00000000000000000000,
  nat ? ? ? ? = 10,
  ntyp ? ? ? ?= 2,
  ecutwfc ? ? = 300.0,
  occupations = "smearing",
  smearing ? ?= "methfessel-paxton",
  degauss ? ? = 0.05,
  /
  &ELECTRONS
  conv_thr ? ?= 0.000001,
  mixing_beta = 0.3,
  /
  &IONS
  bfgs_ndim ? ? ? ? = 3,
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
  /
  ATOMIC_SPECIES
  C ?6.0 C.pbe-van_ak.UPF
  F ?9.0 F.pbe-n-van.UPF
  ATOMIC_POSITIONS crystal
  C ? ? ? 0.0 ? ? 0.0 ? ? 0.0
  C ? ? ? 0.1666666666666667 ? ? ?0.3333333333333333 ? ? ?0.0
  C ? ? ? 0.0 ? ? 0.5 ? ? 0.0
  C ? ? ? 0.1666666666666667 ? ? ?0.8333333333333333 ? ? ?0.0
  C ? ? ? 0.5 ? ? 0.0 ? ? 0.0
  C ? ? ? 0.6666666666666667 ? ? ?0.3333333333333333 ? ? ?0.0
  C ? ? ? 0.5 ? ? 0.5 ? ? 0.0
  C ? ? ? 0.6666666666666667 ? ? ?0.8333333333333333 ? ? ?0.0
  F ? ? ? 0.0 ? ? 0.0 ? ? 0.05
  F ? ? ? 0.1666666666666667 ? ? ?0.3333333333333333 ? ? ?0.05
  K_POINTS automatic
  4 4 1 ?0 0 ?0
   
 
 
 
 
 
 
 
 
 










 

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From junkermeier at bloch.nrl.navy.mil  Wed Mar 17 18:32:20 2010
From: junkermeier at bloch.nrl.navy.mil (Chad Junkermeier)
Date: Wed, 17 Mar 2010 13:32:20 -0400
Subject: [Pw_forum] lattice constant from unit cell vs. from supercell
In-Reply-To: <4BA108D1.7010403@democritos.it>
References: <629F20AD-563D-4EF8-9FEE-16B5641338D2@bloch.nrl.navy.mil>
	<4BA108D1.7010403@democritos.it>
Message-ID: <83411FC3-1186-46F4-A811-897DA26BD423@bloch.nrl.navy.mil>

Yes, from what I wrote in my last post I can see the confusion.

In my last post I sent two representative files.  In actuality, I  
performed a series of calculations, each with a different alat value,  
on the unit cell.  The calculation that had the lowest "Final energy"  
was the was the one that I say has the equilibrium lattice constant  
for the unit cell.  I give here a listing of some of the results:

alat = 4.7
      Final energy   =     -71.3700391584 Ry
alat = 4.750
      Final energy   =     -71.3737078425 Ry
alat = 4.800                                                       
<---- Equilibrium value
      Final energy   =     -71.3753602156 Ry
alat = 4.850
      Final energy   =     -71.3751659760 Ry
alat = 4.900
      Final energy   =     -71.3732897789 Ry
alat = 4.950
      Final energy   =     -71.3698878408 Ry


I also performed a series of calculations, each with a different alat  
value, on the 2x2 supercell.  Of those calculations, the one with the  
lowest "Final energy" is the one that has the equilibrium lattice  
constant for the supercell case.  Here are some of the results for  
this case:

glat = 4.55
      Final energy   =    -285.4093082597 Ry
glat = 4.6
      Final energy   =    -285.4217551819 Ry
glat = 4.625
      Final energy   =    -285.4242025245 Ry
glat = 4.65                                                      <----  
Equilibrium value
      Final energy   =    -285.4242932895 Ry
glat = 4.675
      Final energy   =    -285.4221256935 Ry
glat = 4.700
      Final energy   =    -285.4177075378 Ry
glat = 4.725
      Final energy   =    -285.4115070010 Ry



Since the supercell case is essentially the same system as the unit  
cell case, the equilibrium value for alat should be the same in both  
cases.  I am finding that they are not.  Further, the final positions  
of the unit cell case has atom positions near where we think they  
should be, but in the 2x2 unit cell the final atom positions are not.



Chad Junkermeier, Ph.D.
NRC Post-Doctoral Fellow
Naval Research Laboratory
4555 Overlook Ave, S.W.
Washington DC 20375
Office: (202) 404-4635
Fax: (202) 767-1165







On Mar 17, 2010, at 12:52 PM, Paolo Giannozzi wrote:

> Chad Junkermeier wrote:
>
>> If I do this using the unit cell, everything seems to
>> work correctly, and the equilibrium lattice constant for the system
>> seems to be correct.  If, instead, I use a 2x2 supercell I find that
>> the equilibrium lattice constant is not the same (or even close) to  
>> the
>> unit cell result.
>
> your data are for fixed-cell structural optimization: what do you mean
> by "the equilibrium lattice constant is not the same"? You choose the
> lattice constant
>
> P.
> -- 
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From junkermeier at bloch.nrl.navy.mil  Wed Mar 17 18:40:03 2010
From: junkermeier at bloch.nrl.navy.mil (Chad Junkermeier)
Date: Wed, 17 Mar 2010 13:40:03 -0400
Subject: [Pw_forum] lattice constant from unit cell vs. from supercell
In-Reply-To: <8974d3b21003171025t32ae7296qff97c9176f2fd599@mail.gmail.com>
References: <629F20AD-563D-4EF8-9FEE-16B5641338D2@bloch.nrl.navy.mil>
	<4BA108D1.7010403@democritos.it>
	<8974d3b21003171025t32ae7296qff97c9176f2fd599@mail.gmail.com>
Message-ID: <ED97F9B2-5A61-4F5E-A3A4-3D67888F464A@bloch.nrl.navy.mil>

I copied the wrong file into the original email.  In the 2x2 unit cell  
case the atoms started out in the following positions.

ATOMIC_POSITIONS crystal
C       0.0     0.0     0.0
C       0.1666666666666667      0.3333333333333333      0.0
C       0.0     0.5     0.0
C       0.1666666666666667      0.8333333333333333      0.0
C       0.5     0.0     0.0
C       0.6666666666666667      0.3333333333333333      0.0
C       0.5     0.5     0.0
C       0.6666666666666667      0.8333333333333333      0.0
F       0.0     0.0     0.05
F       0.0     0.5     0.05
F       0.5     0.0     0.05
F       0.5     0.5     0.05





On Mar 17, 2010, at 1:25 PM, Duy Le wrote:

> Not really sure if I understand your question. However, there seems to
> be an incorrectness.
> Simple logic:
> 1F, 2 C in a "1x1" supercell
> 4F, 8 C in a "2x2" supercell
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
>

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From degironc at sissa.it  Wed Mar 17 18:50:49 2010
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 17 Mar 2010 18:50:49 +0100
Subject: [Pw_forum] lattice constant from unit cell vs. from supercell
In-Reply-To: <83411FC3-1186-46F4-A811-897DA26BD423@bloch.nrl.navy.mil>
References: <629F20AD-563D-4EF8-9FEE-16B5641338D2@bloch.nrl.navy.mil>	<4BA108D1.7010403@democritos.it>
	<83411FC3-1186-46F4-A811-897DA26BD423@bloch.nrl.navy.mil>
Message-ID: <4BA11679.4070902@sissa.it>

dear Chad Junkermeier,
if two calculations are equivalent the code gives the same result.

your calculation at alat = 4.7 has
Final energy = -71.3700391584 Ry in the 1x1 cell and
Final energy = -285.4177075378 Ry = -71.35442688 Ry x 4  in  the 2x2 cell.
This difference is significant,  the two systems are not the same....

Check your positions, your k-point sampling, your cutoff etc ...
hope this helps,
 stefano

Chad Junkermeier wrote:
> Yes, from what I wrote in my last post I can see the confusion.
>
> In my last post I sent two representative files.  In actuality, I  
> performed a series of calculations, each with a different alat value,  
> on the unit cell.  The calculation that had the lowest "Final energy"  
> was the was the one that I say has the equilibrium lattice constant  
> for the unit cell.  I give here a listing of some of the results:
>
> alat = 4.7
>       Final energy   =     -71.3700391584 Ry
> alat = 4.750
>       Final energy   =     -71.3737078425 Ry
> alat = 4.800                                                       
> <---- Equilibrium value
>       Final energy   =     -71.3753602156 Ry
> alat = 4.850
>       Final energy   =     -71.3751659760 Ry
> alat = 4.900
>       Final energy   =     -71.3732897789 Ry
> alat = 4.950
>       Final energy   =     -71.3698878408 Ry
>
>
> I also performed a series of calculations, each with a different alat  
> value, on the 2x2 supercell.  Of those calculations, the one with the  
> lowest "Final energy" is the one that has the equilibrium lattice  
> constant for the supercell case.  Here are some of the results for  
> this case:
>
> glat = 4.55
>       Final energy   =    -285.4093082597 Ry
> glat = 4.6
>       Final energy   =    -285.4217551819 Ry
> glat = 4.625
>       Final energy   =    -285.4242025245 Ry
> glat = 4.65                                                      <----  
> Equilibrium value
>       Final energy   =    -285.4242932895 Ry
> glat = 4.675
>       Final energy   =    -285.4221256935 Ry
> glat = 4.700
>       Final energy   =    -285.4177075378 Ry
> glat = 4.725
>       Final energy   =    -285.4115070010 Ry
>
>
>
> Since the supercell case is essentially the same system as the unit  
> cell case, the equilibrium value for alat should be the same in both  
> cases.  I am finding that they are not.  Further, the final positions  
> of the unit cell case has atom positions near where we think they  
> should be, but in the 2x2 unit cell the final atom positions are not.
>
>
>
> Chad Junkermeier, Ph.D.
> NRC Post-Doctoral Fellow
> Naval Research Laboratory
> 4555 Overlook Ave, S.W.
> Washington DC 20375
> Office: (202) 404-4635
> Fax: (202) 767-1165
>
>
>
>
>
>
>
> On Mar 17, 2010, at 12:52 PM, Paolo Giannozzi wrote:
>
>   
>> Chad Junkermeier wrote:
>>
>>     
>>> If I do this using the unit cell, everything seems to
>>> work correctly, and the equilibrium lattice constant for the system
>>> seems to be correct.  If, instead, I use a 2x2 supercell I find that
>>> the equilibrium lattice constant is not the same (or even close) to  
>>> the
>>> unit cell result.
>>>       
>> your data are for fixed-cell structural optimization: what do you mean
>> by "the equilibrium lattice constant is not the same"? You choose the
>> lattice constant
>>
>> P.
>> -- 
>> Paolo Giannozzi, Democritos and University of Udine, Italy
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>     
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From saishi at inbox.ru  Wed Mar 17 19:43:02 2010
From: saishi at inbox.ru (=?koi8-r?Q?=F3=C5=D2=C7=C5=CA_=EE=C9=CB=CF=CC=C1=C5=D7?=)
Date: Wed, 17 Mar 2010 21:43:02 +0300
Subject: [Pw_forum] (no subject)
Message-ID: <E1NryCs-0004cK-00.saishi-inbox-ru@f282.mail.ru>

Hello.
I am trying to perform ph calculation after optimization of crystal structure. First I make SCF-calculation, then vc-relax. But when I run ph.x, I get error#20:error while reading input file. 
Explaine me please where I am going wrong.

Thank you.

From giannozz at democritos.it  Wed Mar 17 20:54:04 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 17 Mar 2010 20:54:04 +0100
Subject: [Pw_forum] Fortran compiler
In-Reply-To: <C7C644C8.1AC9%Trinh.Vo@jpl.nasa.gov>
References: <C7C644C8.1AC9%Trinh.Vo@jpl.nasa.gov>
Message-ID: <896650C5-FEAD-4471-8324-6E3320A5441D@democritos.it>


On Mar 17, 2010, at 16:35 , Vo, Trinh (388C) wrote:

> I am actually compiling QE with the current version of gfortran,
> and I have to think again whether I should continue to use it.  :-).

you should, unless you have evidence of the opposite, or unless
you are using exotic features, or the phonon code. The basic
functionalities seem to work.

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




From carlo.nervi at unito.it  Wed Mar 17 20:54:41 2010
From: carlo.nervi at unito.it (Carlo Nervi)
Date: Wed, 17 Mar 2010 20:54:41 +0100 (CET)
Subject: [Pw_forum] (no subject)
In-Reply-To: <E1NryCs-0004cK-00.saishi-inbox-ru@f282.mail.ru>
References: <E1NryCs-0004cK-00.saishi-inbox-ru@f282.mail.ru>
Message-ID: <46543.130.192.119.45.1268855681.squirrel@mail.unito.it>

Dear Sergey,
it is difficult to understand your question, which is too
general, and it is impossible to help you if you don't
provide any further informations, at least about your
input files... since the error message is about the input
file
Please, also, provide your affiliation.
 Carlo

--
------------------------------------------------------
Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8
Fax: +39 011 6707855 - Dipartimento di Chimica IFM
via P. Giuria 7, 10125 Torino, Italy
http://lem.ch.unito.it/

>
>
> ------------------ Messaggio originale -------------------
> Oggetto: [Pw_forum] (no subject)
> Da:      ?????? ???????? <saishi at inbox.ru>
> Data:    Mer, 17 Marzo 2010, 7:43 pm
> A:       Pw_forum at pwscf.org
> ----------------------------------------------------------
>
> Hello.
> I am trying to perform ph calculation after optimization
> of crystal structure. First I make SCF-calculation, then
> vc-relax. But when I run ph.x, I get error#20:error while
> reading input file.
> Explaine me please where I am going wrong.
>
> Thank you.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


From kazempoor2000 at yahoo.com  Thu Mar 18 11:21:37 2010
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Thu, 18 Mar 2010 03:21:37 -0700 (PDT)
Subject: [Pw_forum] source of error
Message-ID: <624492.96092.qm@web113619.mail.gq1.yahoo.com>


Dear all
Using GWW interface in wannier part(CVS version)?I run PW4GWW on its input file m but in the midway I see this error.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
???? task #???????? 9
???? from davcio : error #??????? 99
???? error while reading from file
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Where can i find the?reason of such error(in which f90 program)?
?
?
thanks a lot
?
?
?
Ali Kazempour



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


      
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From kazempoor2000 at yahoo.com  Thu Mar 18 11:22:25 2010
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Thu, 18 Mar 2010 03:22:25 -0700 (PDT)
Subject: [Pw_forum] source of error
Message-ID: <411058.83640.qm@web113616.mail.gq1.yahoo.com>


Dear all
Using GWW interface in wannier part(CVS version)?I run PW4GWW on its input file m but in the midway I see this error.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
???? task #???????? 9
???? from davcio : error #??????? 99
???? error while reading from file
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Where can i find the?reason of such error(in which f90 program)?
?
?
thanks a lot
?
?
?
Ali Kazempour



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


      
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From nnlinh at sissa.it  Thu Mar 18 11:47:50 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Thu, 18 Mar 2010 11:47:50 +0100 (CET)
Subject: [Pw_forum] source of error
In-Reply-To: <411058.83640.qm@web113616.mail.gq1.yahoo.com>
References: <411058.83640.qm@web113616.mail.gq1.yahoo.com>
Message-ID: <49196.147.122.27.212.1268909270.squirrel@webmail.sissa.it>




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


-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"


----------------------------------------------------------------
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From nnlinh at sissa.it  Thu Mar 18 11:49:23 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Thu, 18 Mar 2010 11:49:23 +0100 (CET)
Subject: [Pw_forum] source of error
In-Reply-To: <411058.83640.qm@web113616.mail.gq1.yahoo.com>
References: <411058.83640.qm@web113616.mail.gq1.yahoo.com>
Message-ID: <49202.147.122.27.212.1268909363.squirrel@webmail.sissa.it>

The davcio error can be explained in frequency questions.

but if you want to see , it is in PW/davcio.f90


Linh


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


-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"


----------------------------------------------------------------
  SISSA Webmail https://webmail.sissa.it/
  Powered by SquirrelMail http://www.squirrelmail.org/


From nnlinh at sissa.it  Thu Mar 18 11:51:45 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Thu, 18 Mar 2010 11:51:45 +0100
Subject: [Pw_forum] source of error
In-Reply-To: <49202.147.122.27.212.1268909363.squirrel@webmail.sissa.it>
References: <411058.83640.qm@web113616.mail.gq1.yahoo.com>
	<49202.147.122.27.212.1268909363.squirrel@webmail.sissa.it>
Message-ID: <4BA205C1.3080107@sissa.it>

I would like to add the link of "frequently asked questions":
http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions

Linh

Ngoc Linh Nguyen wrote:
> The davcio error can be explained in frequency questions.
>
> but if you want to see , it is in PW/davcio.f90
>
>
> Linh
>
>
>   
>> Dear all
>> Using GWW interface in wannier part(CVS version) I run PW4GWW on its input
>> file m but in the midway I see this error.
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>      task #         9
>>      from davcio : error #        99
>>      error while reading from file
>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>> Where can i find the reason of such error(in which f90 program)?
>>  
>>  
>> thanks a lot
>>  
>>  
>>  
>> Ali Kazempour
>>
>>
>>
>> Fritz-Haber-Institut fax : ++49-30-8413 4701
>> der Max-Planck-Gesellschaft
>> Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de
>> D-14 195 Berlin-Dahlem / German
>>
>>
>>       _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>     
>
>
> -----------------------------------------------------
>  Nguyen Ngoc Linh, PhD Student
>  c/o:   SISSA & CNR-INFM Democritos,
>         via Beirut 2-4, 34014 Trieste (Italy)
>  email: nnlinh at sissa.it
>  phone: +39 04 03787 319
>  skype: ngoclinh84phys
> -----------------------------------------------------
> "The physics is theoretical but the fun is real"
>
>
> ----------------------------------------------------------------
>   SISSA Webmail https://webmail.sissa.it/
>   Powered by SquirrelMail http://www.squirrelmail.org/
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From marsamos at democritos.it  Thu Mar 18 12:08:02 2010
From: marsamos at democritos.it (marsamos at democritos.it)
Date: Thu, 18 Mar 2010 12:08:02 +0100
Subject: [Pw_forum] GIPAW
In-Reply-To: <4c9c61c21003170430h1eebe614t1ed62fcf042adc9f@mail.gmail.com>
References: <20100316192909.e2myuammkg4w4o0c@mail.democritos.it>
	<4c9c61c21003170430h1eebe614t1ed62fcf042adc9f@mail.gmail.com>
Message-ID: <20100318120802.hf1op6t1c0cw84go@mail.democritos.it>

Dear Ary you can download it also from

http://qe-forge.org/docman/?group_id=37

bests

Layla

Quoting Ary Junior <aryjunior at gmail.com>:

> Hi, I can't extract two files from that tutorial:
> gipaw_day2.tgz<http://www.tcm.phy.cam.ac.uk/%7Ejry20/gipaw/gipaw_day2.tgz>and
> gipaw_day3.tgz <http://www.tcm.phy.cam.ac.uk/%7Ejry20/gipaw/gipaw_day3.tgz>.
> The other files were extracted normally.
>
> Thank you very much!
>
> --
> Ary Junior
> Universidade Federal de Juiz de Fora
> Juiz de Fora - Minas Gerais - Brasil
>
> On Tue, Mar 16, 2010 at 3:29 PM, <marsamos at democritos.it> wrote:
>
>> For those who are interested in GIPAW, the past tutorial (held in
>> zurich at the CECAM, 2009), is available at
>> http://www.gipaw.net/work.html.
>>
>> Thanks Jonathan Yates!
>>
>> bests
>>
>> Layla
>>
>> --
>> Dr. L. Martin-Samos
>> tel. +39 040 3787 429
>> CNR-DEMOCRITOS and
>> International School for Advanced Studies (ISAS-SISSA)
>> via Beirut 2-4
>> 34151 Trieste Italy
>>
>> ----------------------------------------------------------------
>> This message was sent using IMP, the Internet Messaging Program.
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
> --
> http://lattes.cnpq.br/8221674673413336
>



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

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


From kazempoor2000 at yahoo.com  Thu Mar 18 13:08:41 2010
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Thu, 18 Mar 2010 05:08:41 -0700 (PDT)
Subject: [Pw_forum] source of error
In-Reply-To: <49202.147.122.27.212.1268909363.squirrel@webmail.sissa.it>
Message-ID: <249197.33803.qm@web113616.mail.gq1.yahoo.com>

Dear Linh
Could you explain what can I do to remove this error related to frequency?
Do you have any experience with GWW?
Can I send My script to you to check which part is wrong?
I appreciate if you? help and guide ?me .
thanks? a lot

Ali Kazempour



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

--- On Thu, 3/18/10, Ngoc Linh Nguyen <nnlinh at sissa.it> wrote:


From: Ngoc Linh Nguyen <nnlinh at sissa.it>
Subject: Re: [Pw_forum] source of error
To: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Thursday, March 18, 2010, 3:49 AM


The davcio error can be explained in frequency questions.

but if you want to see , it is in PW/davcio.f90


Linh


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


-----------------------------------------------------
Nguyen Ngoc Linh, PhD Student
c/o:???SISSA & CNR-INFM Democritos,
? ? ? ? via Beirut 2-4, 34014 Trieste (Italy)
email: nnlinh at sissa.it
phone: +39 04 03787 319
skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"


----------------------------------------------------------------
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? Powered by SquirrelMail http://www.squirrelmail.org/

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Pw_forum mailing list
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From eyvaz_isaev at yahoo.com  Thu Mar 18 14:59:36 2010
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 18 Mar 2010 06:59:36 -0700 (PDT)
Subject: [Pw_forum] source of error
Message-ID: <231463.84919.qm@web65712.mail.ac4.yahoo.com>

Dear Ali,

--- On Thu, 3/18/10, ali kazempour <kazempoor2000 at yahoo.com> wrote:
?
>Could you explain what can I do to remove this error related to >frequency?
 
The message you got is not connected to any frequency, but it is one of frequently asked questions.
 
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> ???? task #???????? 9
> ???? from davcio : error #??????? 99
> ???? error while reading from file
>? %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Most likely you have a corrupted file (may be due to network connection, lack of free disk space, etc.). Please see also User Gide, page 78 (v.4.1.2), or Troubleshooting section.

Bests,
Eyvaz. 

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

Prof. Eyvaz Isaev, 

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


      


From udayagiri3 at gmail.com  Thu Mar 18 16:28:11 2010
From: udayagiri3 at gmail.com (udayagiri sai babu)
Date: Thu, 18 Mar 2010 20:58:11 +0530
Subject: [Pw_forum] vc-relax
Message-ID: <d3964cb11003180828r6acd2b52g1716f846ed51ba68@mail.gmail.com>

Dear all I wanted to run some vc-relax calculations. To start with I took
pbtio3 system and tried to relax it. for the following input file it
predicted the c/a ratio as 1.23. The output structure (both coordinates and
lattice parameters) is grossly in error. In the forum i have seen people
reporting c/a ratio which is in good agreement with the experimental value.
Later I realized for different input configurations it is predicting
different c/a ratios. At one time for pbtio3 I got cubic structure after
relaxing!!!. As i understood it is stuck up in local minimum. Since i know
the structure is tetragonal i could figure out the error but for an unknown
system how can i relax the system with confidence.
(if there is some literature that i can read up on this please refere me the
same i will read)

entering subroutine stress ...

          total   stress  (Ry/bohr**3)                   (kbar)     P=
0.38
   0.00000259   0.00000000   0.00000000          0.38      0.00      0.00
   0.00000000   0.00000259   0.00000000          0.00      0.38      0.00
   0.00000000   0.00000000   0.00000248          0.00      0.00      0.36


     bfgs converged in  34 scf cycles and  27 bfgs steps

     End of BFGS Geometry Optimization

     Final enthalpy =    -333.0490579145 Ry

CELL_PARAMETERS (alat)
   0.983673643   0.000000000   0.000000000
   0.000000000   0.983673643   0.000000000
   0.000000000   0.000000000   1.208160764

ATOMIC_POSITIONS (crystal)
Ti       0.500000000   0.500000000   0.562608151
O        0.500000000   0.500000000  -0.068487782
O        0.500000000   0.000000000   0.453495153
O        0.000000000   0.500000000   0.453495153
Pb       0.000000000   0.000000000   0.118889324


&control
calculation = 'vc-relax',
restart_mode='from_scratch',
outdir='/home/sai/pbtio3/'
prefix='pbtio3'
pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo'
tstress=.true.,
/
&system
ibrav=0
nat=5,
ntyp=3,
ecutwfc=55,
ecutrho=550,
nbnd=22,
occupations='fixed',
degauss=0.00
/
&electrons
conv_thr=1.D-6,
mixing_beta= 0.3
/
&ions
/
&cell
cell_dynamics='bfgs'
/
ATOMIC_SPECIES
Pb  207.21  Pb.pbe-d-van.UPF
Ti 47.87  Ti.pbe-sp-van_ak.UPF
O  16  O.pbe-rrkjus.UPF
ATOMIC_POSITIONS {crystal}
Ti 0.5 0.5 0.52
O 0.5 0.5 0
O 0.5 0 0.5
O 0 0.5 0.5
Pb 0 0 0
K_POINTS {automatic}
8 8 7 0 0 0
CELL_PARAMETERS
7.374 0 0
0 7.374 0
0 0 7.669

-- 
U.Saibabu
PhD student,
Deformation mechanisms modeling group,
Materials engineering department,
IISc Bangalore,
India.
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From yfang1 at tulane.edu  Thu Mar 18 19:43:43 2010
From: yfang1 at tulane.edu (Fang, Yuan)
Date: Thu, 18 Mar 2010 13:43:43 -0500
Subject: [Pw_forum] functional
References: <d5eefb3d1003170352s6dd97f66j36e6475b21960e10@mail.gmail.com>
Message-ID: <D8E427248814A143AF7763DFA469B5F925CFF0@EX04.ad.tulane.edu>

Hello;
  How can we change different functional used in the self-consistent calculation for atom ,like from LDA to GGA? Is there any variable to control this or just by changing the pseudopotentials?
    Thank you!
                                                     Y Fang
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From elie.moujaes at hotmail.co.uk  Thu Mar 18 20:13:42 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Thu, 18 Mar 2010 19:13:42 +0000
Subject: [Pw_forum] Tight Binding (TB) model up to n nearest neighbours
Message-ID: <SNT114-W61D85375F2B51F8BE27D35D32B0@phx.gbl>


Dear all,
 
I calculated the band structure of graphene using a TB model using the Wannier90 package. Results are pretty good. But I am interested in calculating the band structure using a semi empirical TB model where one can input the number of nearest neighbours like 3 nearest neighbours, 6 nearest neighbours , 3 next next nearest neighbours,.....for graphene. Is there a package to do that in QE or does it need to be implemented. Would md (molecular dynamics) perform that?
 
Regards
 
 
Elie Moujaes
University of Nottingham
NG7 2RD
Nottingham
UK
 		 	   		  
_________________________________________________________________
Do you have a story that started on Hotmail? Tell us now
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From baroni at sissa.it  Thu Mar 18 21:02:07 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 18 Mar 2010 21:02:07 +0100
Subject: [Pw_forum] Tight Binding (TB) model up to n nearest neighbours
In-Reply-To: <SNT114-W61D85375F2B51F8BE27D35D32B0@phx.gbl>
References: <SNT114-W61D85375F2B51F8BE27D35D32B0@phx.gbl>
Message-ID: <1578495E-DEA7-461D-941A-97399FA17EDE@sissa.it>

molecular dynamics? SB

On Mar 18, 2010, at 8:13 PM, Elie Moujaes wrote:

> Dear all,
>  
> I calculated the band structure of graphene using a TB model using the Wannier90 package. Results are pretty good. But I am interested in calculating the band structure using a semi empirical TB model where one can input the number of nearest neighbours like 3 nearest neighbours, 6 nearest neighbours , 3 next next nearest neighbours,.....for graphene. Is there a package to do that in QE or does it need to be implemented. Would md (molecular dynamics) perform that?
>  
> Regards
>  
>  
> Elie Moujaes
> University of Nottingham
> NG7 2RD
> Nottingham
> UK
> 
> Do you want a Hotmail account? Sign-up now - Free _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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

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







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From giannozz at democritos.it  Thu Mar 18 21:52:45 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 18 Mar 2010 21:52:45 +0100
Subject: [Pw_forum] functional
In-Reply-To: <D8E427248814A143AF7763DFA469B5F925CFF0@EX04.ad.tulane.edu>
References: <d5eefb3d1003170352s6dd97f66j36e6475b21960e10@mail.gmail.com>
	<D8E427248814A143AF7763DFA469B5F925CFF0@EX04.ad.tulane.edu>
Message-ID: <6C4AAB3F-0CF6-42C0-8830-E943F9100FC0@democritos.it>


On Mar 18, 2010, at 19:43 , Fang, Yuan wrote:

> How can we change different functional used in the self-consistent  
> calculation
> for atom, like from LDA to GGA? Is there any variable to control this

yes, "input_dft"

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




From prasenjit.jnc at gmail.com  Fri Mar 19 10:21:15 2010
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Fri, 19 Mar 2010 10:21:15 +0100
Subject: [Pw_forum] pseudopotential for K
Message-ID: <627e0ffa1003190221k72a71fbdu1d2eed1508ff0baa@mail.gmail.com>

Hi everybody,

Does any one have a working ultrasoft pseudopotential for K with PBE
exchange correlation functional?

If so I will be grateful if he/she can send it to me.

With regards,
Prasenjit.

-- 
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
              +39 3807528672 (M)
URL: http://portal.ictp.it/cmsp/members/postdoctoral-fellows/prasenjit-ghosh/prasenjit_ghosh

From nnlinh at sissa.it  Fri Mar 19 16:11:51 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Fri, 19 Mar 2010 16:11:51 +0100 (CET)
Subject: [Pw_forum] vc-relax
In-Reply-To: <d3964cb11003180828r6acd2b52g1716f846ed51ba68@mail.gmail.com>
References: <d3964cb11003180828r6acd2b52g1716f846ed51ba68@mail.gmail.com>
Message-ID: <10450.62.2.168.58.1269011511.squirrel@webmail.sissa.it>


> Dear all I wanted to run some vc-relax calculations. To start with I took
> pbtio3 system and tried to relax it. for the following input file it
> predicted the c/a ratio as 1.23. The output structure (both coordinates
> and
> lattice parameters) is grossly in error. In the forum i have seen people
> reporting c/a ratio which is in good agreement with the experimental
> value.

Normally, we should start with a value that's close experiment one.

> Later I realized for different input configurations it is predicting
> different c/a ratios. At one time for pbtio3 I got cubic structure after
> relaxing!!!. As i understood it is stuck up in local minimum. Since i know
> the structure is tetragonal i could figure out the error but for an
> unknown
> system how can i relax the system with confidence.

That depends on how much your understand about the configurations that you
wanna consider. For example, under pressure structure will be induced a
structural phase transition, so you need a knowledge about the kinds of
structure, which are tetrahedral or hexagonal, at different finite
pressures.


> (if there is some literature that i can read up on this please refere me
> the
> same i will read)
Renata M. Wentzconvitch et. al. , Physical Review Letter 70, 3947 (1993).
 or you can search on google.com by keyword: "Molecular dynamics variable
cell shape "  to see more related literatures.


Good luck,

Linh


-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"


----------------------------------------------------------------
  SISSA Webmail https://webmail.sissa.it/
  Powered by SquirrelMail http://www.squirrelmail.org/


From prasenjit.jnc at gmail.com  Fri Mar 19 16:54:57 2010
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Fri, 19 Mar 2010 16:54:57 +0100
Subject: [Pw_forum] pseudopotential for K
Message-ID: <627e0ffa1003190854i557b15b3je37de53f7bc9226a@mail.gmail.com>

Hi everybody,

Does any one have a working ultrasoft pseudopotential for K with PBE
exchange correlation functional?

If so I will be grateful if he/she can send it to me.

With regards,
Prasenjit.


-- 
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
              +39 3807528672 (M)
URL: http://portal.ictp.it/cmsp/members/postdoctoral-fellows/prasenjit-ghosh/prasenjit_ghosh

From jhouska at kfy.zcu.cz  Sat Mar 20 09:44:17 2010
From: jhouska at kfy.zcu.cz (Jiri Houska)
Date: Sat, 20 Mar 2010 09:44:17 +0100
Subject: [Pw_forum] Orthogonalization
Message-ID: <20100320094417.3sj8wdsxj44wcg4w@webmail.zcu.cz>

Hello,
I understand that when running a projwfc.x calculation, the orbitals  
are orthogonalized first. However, I realized that I do not understand  
HOW the orthogonalization is performed. Please can anyone write the  
basic principle(s) of that, or alternatively a link where is it  
explained? Thanks!
Jiri Houska
University of West Bohemia


From degironc at sissa.it  Sat Mar 20 12:46:30 2010
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Sat, 20 Mar 2010 12:46:30 +0100
Subject: [Pw_forum] Orthogonalization
In-Reply-To: <20100320094417.3sj8wdsxj44wcg4w@webmail.zcu.cz>
References: <20100320094417.3sj8wdsxj44wcg4w@webmail.zcu.cz>
Message-ID: <4BA4B596.2010908@sissa.it>

google is your friend. search for  Loewdin (or L\"{o}wdin) 
orthogonalization.
stefano

Jiri Houska wrote:
> Hello,
> I understand that when running a projwfc.x calculation, the orbitals  
> are orthogonalized first. However, I realized that I do not understand  
> HOW the orthogonalization is performed. Please can anyone write the  
> basic principle(s) of that, or alternatively a link where is it  
> explained? Thanks!
> Jiri Houska
> University of West Bohemia
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From ilyeshamdi at yahoo.fr  Sat Mar 20 14:00:25 2010
From: ilyeshamdi at yahoo.fr (ilyes hamdi)
Date: Sat, 20 Mar 2010 13:00:25 +0000 (GMT)
Subject: [Pw_forum] Antiferromagnetic coupling between vacancies in a III-V
	ZB semiconductor
In-Reply-To: <Pine.LNX.4.44.1003081033340.10904-100000@newton.physics.metu.edu.tr>
References: <Pine.LNX.4.44.1003081033340.10904-100000@newton.physics.metu.edu.tr>
Message-ID: <437567.6499.qm@web24306.mail.ird.yahoo.com>

Dear QE users,

I try to  calculate the exchange coupling constants J in the Heisenberg model, for a  128 atom Zinc Blend supercell of BN containing two vacancies of Boron.
To do this one should determine the energy of the ferromagnetic (FM) and the antiferromagnetic (AFM) states.
The FM state is simple to simulate since the spins of the 4 N atom surrounding one  vacancy are parallel. However for the AFM state, an ambiguity arises since one have many spin configurations, for exemple: 1) The 4 N atoms surrounding the first  vacancy may have spin up and the other 4 N atoms surrounding the second vacancy have spin down.  2) For the first vacancy, 2 N atoms may have spin up and the other 2 N atoms spin down. For the second vacancy, we use the translation symmetry to get the same  spin configuration as the first vacancy.

For  these AFM states, we obtain a different energy. My question is how to choose the correct AFM state? 
For me, I think the first is the correct one, because one must think as one have  two primitive unit cells containing each one  vacancy. To  get
an AFM coupling, the first N atoms (surrounding the first vacancy) may have spin up and second N spin down.

PS: To simulate the AFM state, I have chosen 4 type of atoms B , N, N1 (surrounding the first vacancy) and N2 (surrounding the second vacancy) with:
starting_magnetization(1) = 0.0
starting_magnetization(2) = 0.0
starting_magnetization(3) =  0.5
starting_magnetization(4) = -0.5


-- 
Dr. Ilyes Hamdi Ass. Prof
Department of electronics and automatics
Institute of Applied sciences and technology
Tunisia
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum



      

From Trinh.Vo at jpl.nasa.gov  Sat Mar 20 20:28:05 2010
From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Sat, 20 Mar 2010 12:28:05 -0700
Subject: [Pw_forum] Pseudopotential for Lathanides
Message-ID: <C7CA6FD5.1BD1%Trinh.Vo@jpl.nasa.gov>

Dear PWSCF Users,

When I searched QE forum, I saw in the past there had been a discussion about pseudopotential of Lanthnides (see the link below):

 http://www.democritos.it/pipermail/pw_forum/2009-May/012897.html

After that I did not see any further information.  If these PPs have been posted,or if any of you have further information about this, I appreciate if you could give it to me.

Thank you very much,

Trinh Vo

JPL/CalTech
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From prasenjit.jnc at gmail.com  Sun Mar 21 11:04:13 2010
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Sun, 21 Mar 2010 11:04:13 +0100
Subject: [Pw_forum] pseudopotential for K
Message-ID: <627e0ffa1003210304t58212cb6o5c4f4eb4d6424d22@mail.gmail.com>

Hi everybody,

Does any one have a working ultrasoft pseudopotential for K with PBE
exchange correlation functional?

If so I will be grateful if he/she can send it to me.

With regards,
Prasenjit.

-- 
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
              +39 3807528672 (M)
URL: http://portal.ictp.it/cmsp/members/postdoctoral-fellows/prasenjit-ghosh/prasenjit_ghosh

From kazempoor at ph.iut.ac.ir  Sun Mar 21 15:33:09 2010
From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir)
Date: Sun, 21 Mar 2010 18:03:09 +0330 (IRST)
Subject: [Pw_forum] GWW-WANNIER part
Message-ID: <210207866.13366.1269181989965.JavaMail.root@mta.iut.ac.ir>


Dear ALL
For running pw4gww on wannier input file I see the running is crashed in mideway.

the input file is in the following:
 &inputpw4gww
    prefix='tio2-perfect'
    outdir='/p5/batch/kazempou/tmp'
    lwannier=.true.,
    cutoff_wpr_vc=0.02d0
    cutoff_products=0.01d0
    cutoff_polarization=0.01d0
    num_nbnd_first =310
    num_nbndv=288
    num_nbnds=300
    l_truncated_coulomb=.false.
    remainder=-1
    restart_gww=0
    numw_prod=1
    n_gauss=79
    omega_gauss=20.d0
    tau_gauss=10.d0
    l_zero=.true.
    l_wing=.true.
    cprim_first=1
    cprim_last=300
    l_polarization_analysis=.true.
 /
and in the end of output file I faced with this error:

 ------------------------------
 call go_wannier
 Transform to real wfcs
 MATRIX BIG1
 NRS 70 70 64
 NRXS 70 70 65
 Calculate grid
 MATRIX BIG2
 MATRIX IIW 1
 MATRIX JJW 1
 MATRIX JJW 2

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from davcio : error #        99
     error while reading from file
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

What is the reason ?
I read several time in the fourom that the davcio error is originate from some problem like : (disk is full ,or ....) but i checked several time my tmp directories and also the my voulum of the disk ,but everything is ok. I can not understand what  can I do 

Thanks a lot 



Ali Kazempour
Physics Department, Isfahn University of Technology

From nnlinh at sissa.it  Mon Mar 22 10:09:22 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Mon, 22 Mar 2010 10:09:22 +0100
Subject: [Pw_forum] GWW-WANNIER part
In-Reply-To: <210207866.13366.1269181989965.JavaMail.root@mta.iut.ac.ir>
References: <210207866.13366.1269181989965.JavaMail.root@mta.iut.ac.ir>
Message-ID: <4BA733C2.4000707@sissa.it>


>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from davcio : error #        99
>      error while reading from file
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> What is the reason ?
> I read several time in the fourom that the davcio error is originate from some problem like : (disk is full ,or ....) but i checked several time my tmp directories and also the my voulum of the disk, but everything is ok. I can not understand what  can I do 
>   
The davcio problem normally relates to reading from output files.
In your calculation, if you see in PW/matrix_wannier_gamma.f90, it is 
corrupted when reading the wavefunctions (wfc) of previous run (scf or 
nscf), and the wcf maybe get problem.
Therefore, I think it is better to rerun the scf and nscf before 
rechecking if GW work or not.

Good luck,
Linh



> Thanks a lot 
>
>
>
> Ali Kazempour
> Physics Department, Isfahn University of Technology
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   



-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From daijiayu at nudt.edu.cn  Tue Mar 23 04:28:07 2010
From: daijiayu at nudt.edu.cn (Jiayu Dai)
Date: Tue, 23 Mar 2010 11:28:07 +0800
Subject: [Pw_forum] volume in output file.
Message-ID: <469314887.06340@nudt.edu.cn>

Dear all users,

When i performed the vc-relax calculation, i found the "unit-cell volume" in the
output file is not the volume of the supercell i used. I also found it is the same
in the SCF calculation. For example, in SCF calculation, my input lattice ibrav =2
(.ie., fcc), celldm(1)=10.6920, then the output parameters are:

lattice parameter (a_0)   =      10.6920  a.u.  -------a
unit-cell volume          =     305.5743        -------omega

You can see omega is not the cubic of a. Then, how the volume "omega" in the code
is calculated here? Is it included in the cell_base.f90 file?

Thanks a lot.

Jiayu




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

From sunshoutian168 at yahoo.com.cn  Tue Mar 23 05:07:03 2010
From: sunshoutian168 at yahoo.com.cn (shoutian sun)
Date: Tue, 23 Mar 2010 12:07:03 +0800 (CST)
Subject: [Pw_forum] Re. pseudopotential for K
Message-ID: <574636.30473.qm@web15301.mail.cnb.yahoo.com>

Hi PRASENJIT GHOSH,

You can generate your own pp with the code of uspp736.
This code can be download freely from the fallowing site:
http://www.physics.rutgers.edu/~dhv/uspp/

The pp generation input files for K is not so good, however
you can modifiy and test them. Most of uspp are generate by
this code which can be easily found in QE pp library.

You can generate the uspp form for pwscf.

Best regard


sun
Chemistry
CUHK HONG KONG


      
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From mfshun1013 at gmail.com  Tue Mar 23 05:51:37 2010
From: mfshun1013 at gmail.com (Fanshun-Meng)
Date: Tue, 23 Mar 2010 12:51:37 +0800
Subject: [Pw_forum] so large magnitude in phonon calculation
Message-ID: <2813cdb91003222151j755b77c3pad9dd9e9e00ad1cb@mail.gmail.com>

Dear ESPRESSO Users:

these days, when i used pw.x and ph.x to find the phonon frequencies of a
molecular at gamma point, met a serious problem:
 if I  use "occupied = smearing" in SCF calculation, a part of the ph.x
output file as follows:
\#    Pert. #  1: Fermi energy shift (Ry) =     0.1232E+13     0.1115E+11

  if I  use "occupied = tetrahedra" in SCF calculation,  a part of the ph.x
output file as follows:
#    Pert. #  1: Fermi energy shift (Ry) =     0.4332E+44     0.1115E+47

no matter which occupied methods were used, why the Fermi energy shift is so
large(E11 or E45)?
 or  I make a mistake?
thank you!

my SCF input file:

 &CONTROL
                 calculation = 'scf' ,
                      outdir = './result/' ,
                      wfcdir = './result/' ,
                  pseudo_dir = './espresso-4.1.2/pseudo/' ,
                      prefix = 'ag2h2s' ,
                       nstep = 300 ,
 /
 &SYSTEM
                       ibrav = 0,
                   celldm(1) = 28.343722662,
                         nat = 5,
                        ntyp = 3,
                     ecutwfc = 40 ,
                     ecutrho = 320 ,
                 occupations = 'tetrahedra' ,
                     degauss = 0.03 ,
                    smearing = 'fermi-dirac' ,
 /
 &ELECTRONS
 /
CELL_PARAMETERS cubic
     1.000000000    0.000000000    0.000000000
     0.000000000    1.000000000    0.000000000
     0.000000000    0.000000000    1.000000000
ATOMIC_SPECIES
   Ag  107.86800  Ag.pbe-d-rrkjus.UPF
    S   32.07000  S.pbe-van_bm.UPF
    H    1.00800  H.pbe-van_bm.UPF
ATOMIC_POSITIONS angstrom
   Ag      6.783586392    7.506654156    7.504688044
   Ag      9.369904699    7.525335176    7.518919416
    S      4.245485150    7.495289160    7.482481411
    H      4.063583478    7.391786920    8.822219040
    H      4.080059280    8.840841587    7.518732089
K_POINTS automatic
  1 1 1   0 0 0
my phonons PH.X input file:

phono of h2s at Gamma
 &INPUTPH
                      outdir = ./result/' ,
                      prefix = 'ag2h2s' ,
                      fildyn = 'ag2h2s.dynG' ,
                       ldisp = .false.,
                       trans = .true.,
                     tr2_ph = 1.0E-14 ,
 /
0.0 0.0 0.0

-- 
Fanshun-Meng
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From mighfar at jncasr.ac.in  Tue Mar 23 06:06:55 2010
From: mighfar at jncasr.ac.in (Mighfar Imam)
Date: Tue, 23 Mar 2010 10:36:55 +0530 (IST)
Subject: [Pw_forum] volume in output file.
In-Reply-To: <469314887.06340@nudt.edu.cn>
References: <469314887.06340@nudt.edu.cn>
Message-ID: <77820ba56e41e2db0c3c7544dc231f7d.squirrel@mercury.jncasr.ac.in>

Dear Jiayu,
The lattice vectors of a fcc crystal are taken
as a_1=a/2(i+j) etc. So the volume |a_1.(a_2 x
a_3)|
will turn out to be 1/4(a^3) rather than a^3.

-Mighfar Imam
JNCASR,
B'lore, India.

> Dear all users,
>
> When i performed the vc-relax calculation, i
> found the "unit-cell volume" in the
> output file is not the volume of the supercell i
> used. I also found it is the same
> in the SCF calculation. For example, in SCF
> calculation, my input lattice ibrav =2
> (.ie., fcc), celldm(1)=10.6920, then the output
> parameters are:
>
> lattice parameter (a_0)   =      10.6920  a.u.
> -------a
> unit-cell volume          =     305.5743
> -------omega
>
> You can see omega is not the cubic of a. Then,
> how the volume "omega" in the code
> is calculated here? Is it included in the
> cell_base.f90 file?
>
> Thanks a lot.
>
> Jiayu
>
>
>
>
> ------------------------------
> -------------------------------------------
> Jiayu Dai
> Department of Physics
> National University of Defense Technology,
> Changsha, 410073, P R China
> -----------------------------------------
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



From degironc at sissa.it  Tue Mar 23 08:40:31 2010
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Tue, 23 Mar 2010 08:40:31 +0100
Subject: [Pw_forum] volume in output file.
In-Reply-To: <469314887.06340@nudt.edu.cn>
References: <469314887.06340@nudt.edu.cn>
Message-ID: <4BA8706F.9070402@sissa.it>

Jiayu Dai wrote:
> Dear all users,
>
> When i performed the vc-relax calculation, i found the "unit-cell volume" in the
> output file is not the volume of the supercell i used. I also found it is the same
> in the SCF calculation. For example, in SCF calculation, my input lattice ibrav =2
> (.ie., fcc), celldm(1)=10.6920, then the output parameters are:
>
> lattice parameter (a_0)   =      10.6920  a.u.  -------a
> unit-cell volume          =     305.5743        -------omega
>
> You can see omega is not the cubic of a. Then, how the volume "omega" in the code
> is calculated here? Is it included in the cell_base.f90 file?
>   
omega is the volume of the unit cell which in FCC is not alat^3 but 1/4 
of alat^3

stefano

> Thanks a lot.
>
> Jiayu
>
>
>
>
> ------------------------------
> -------------------------------------------
> Jiayu Dai
> Department of Physics
> National University of Defense Technology, 
> Changsha, 410073, P R China
> -----------------------------------------
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From degironc at sissa.it  Tue Mar 23 08:44:23 2010
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Tue, 23 Mar 2010 08:44:23 +0100
Subject: [Pw_forum] so large magnitude in phonon calculation
In-Reply-To: <2813cdb91003222151j755b77c3pad9dd9e9e00ad1cb@mail.gmail.com>
References: <2813cdb91003222151j755b77c3pad9dd9e9e00ad1cb@mail.gmail.com>
Message-ID: <4BA87157.3050805@sissa.it>

is your molecule metallic ? what does this mean ? what is the density of 
state at the Fermi energy ?
stefano


Fanshun-Meng wrote:
> Dear ESPRESSO Users:
>
> these days, when i used pw.x and ph.x to find the phonon frequencies of a
> molecular at gamma point, met a serious problem:
>  if I  use "occupied = smearing" in SCF calculation, a part of the ph.x
> output file as follows:
> \#    Pert. #  1: Fermi energy shift (Ry) =     0.1232E+13     0.1115E+11
>
>   if I  use "occupied = tetrahedra" in SCF calculation,  a part of the ph.x
> output file as follows:
> #    Pert. #  1: Fermi energy shift (Ry) =     0.4332E+44     0.1115E+47
>
> no matter which occupied methods were used, why the Fermi energy shift is so
> large(E11 or E45)?
>  or  I make a mistake?
> thank you!
>
> my SCF input file:
>
>  &CONTROL
>                  calculation = 'scf' ,
>                       outdir = './result/' ,
>                       wfcdir = './result/' ,
>                   pseudo_dir = './espresso-4.1.2/pseudo/' ,
>                       prefix = 'ag2h2s' ,
>                        nstep = 300 ,
>  /
>  &SYSTEM
>                        ibrav = 0,
>                    celldm(1) = 28.343722662,
>                          nat = 5,
>                         ntyp = 3,
>                      ecutwfc = 40 ,
>                      ecutrho = 320 ,
>                  occupations = 'tetrahedra' ,
>                      degauss = 0.03 ,
>                     smearing = 'fermi-dirac' ,
>  /
>  &ELECTRONS
>  /
> CELL_PARAMETERS cubic
>      1.000000000    0.000000000    0.000000000
>      0.000000000    1.000000000    0.000000000
>      0.000000000    0.000000000    1.000000000
> ATOMIC_SPECIES
>    Ag  107.86800  Ag.pbe-d-rrkjus.UPF
>     S   32.07000  S.pbe-van_bm.UPF
>     H    1.00800  H.pbe-van_bm.UPF
> ATOMIC_POSITIONS angstrom
>    Ag      6.783586392    7.506654156    7.504688044
>    Ag      9.369904699    7.525335176    7.518919416
>     S      4.245485150    7.495289160    7.482481411
>     H      4.063583478    7.391786920    8.822219040
>     H      4.080059280    8.840841587    7.518732089
> K_POINTS automatic
>   1 1 1   0 0 0
> my phonons PH.X input file:
>
> phono of h2s at Gamma
>  &INPUTPH
>                       outdir = ./result/' ,
>                       prefix = 'ag2h2s' ,
>                       fildyn = 'ag2h2s.dynG' ,
>                        ldisp = .false.,
>                        trans = .true.,
>                      tr2_ph = 1.0E-14 ,
>  /
> 0.0 0.0 0.0
>
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From giannozz at democritos.it  Tue Mar 23 08:49:50 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 23 Mar 2010 08:49:50 +0100
Subject: [Pw_forum] so large magnitude in phonon calculation
In-Reply-To: <2813cdb91003222151j755b77c3pad9dd9e9e00ad1cb@mail.gmail.com>
References: <2813cdb91003222151j755b77c3pad9dd9e9e00ad1cb@mail.gmail.com>
Message-ID: <A81EB420-C417-4727-9E28-6B3F1C646119@democritos.it>


On Mar 23, 2010, at 5:51 , Fanshun-Meng wrote:

>   if I  use "occupied = tetrahedra" in SCF calculation

you shouldn't use 'tetrahedra' for forces and phonon calculations

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




From prasenjit.jnc at gmail.com  Tue Mar 23 09:35:22 2010
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Tue, 23 Mar 2010 09:35:22 +0100
Subject: [Pw_forum] Re. pseudopotential for K
In-Reply-To: <574636.30473.qm@web15301.mail.cnb.yahoo.com>
References: <574636.30473.qm@web15301.mail.cnb.yahoo.com>
Message-ID: <627e0ffa1003230135n2bcafff0ndc4c30bffa01d5de@mail.gmail.com>

2010/3/23 shoutian sun <sunshoutian168 at yahoo.com.cn>:
> Hi PRASENJIT GHOSH,
>
> You can generate your own pp with the code of uspp736.
> This code can be download freely from the fallowing site:
> http://www.physics.rutgers.edu/~dhv/uspp/
>
> The pp generation input files for K is not so good, however
> you can modifiy and test them. Most of uspp are generate by
> this code which can be easily found in QE pp library.
>
> You can generate the uspp form for pwscf.
>

Dear sun,

thanks for your message......

I managed to generate the pp....and it seems to work fine for my system.

Prasenjit

-- 
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
              +39 3807528672 (M)
URL: http://portal.ictp.it/cmsp/members/postdoctoral-fellows/prasenjit-ghosh/prasenjit_ghosh

From miguel.martinez at ehu.es  Tue Mar 23 09:44:04 2010
From: miguel.martinez at ehu.es (Miguel =?UTF-8?B?TWFydMOtbmV6?=)
Date: Tue, 23 Mar 2010 08:44:04 +0000
Subject: [Pw_forum] Re. pseudopotential for K
In-Reply-To: <627e0ffa1003230135n2bcafff0ndc4c30bffa01d5de@mail.gmail.com>
References: <574636.30473.qm@web15301.mail.cnb.yahoo.com>
	<627e0ffa1003230135n2bcafff0ndc4c30bffa01d5de@mail.gmail.com>
Message-ID: <20100323084404.08501a8a@mark>

Actually, the system you are interested in is fundamental when
determining how to generate the pseudopotential. Maybe, and just maybe,
it could be enough for you to consider a 4s1 pseudo with nlcc. However,
especially if you're interested in high pressure, you may have to
include semicore electrons, with the additional performance penalty
that implies. 

So next time you ask for a PP to be given to you, perhaps you should
mention what kind of PP you want.

Regards,

Miguel 

On Tue, 23 Mar 2010 09:35:22 +0100 Prasenjit Ghosh
<prasenjit.jnc at gmail.com> wrote:
> 2010/3/23 shoutian sun <sunshoutian168 at yahoo.com.cn>:
> > Hi PRASENJIT GHOSH,
> >
> > You can generate your own pp with the code of uspp736.
> > This code can be download freely from the fallowing site:
> > http://www.physics.rutgers.edu/~dhv/uspp/
> >
> > The pp generation input files for K is not so good, however
> > you can modifiy and test them. Most of uspp are generate by
> > this code which can be easily found in QE pp library.
> >
> > You can generate the uspp form for pwscf.
> >
> 
> Dear sun,
> 
> thanks for your message......
> 
> I managed to generate the pp....and it seems to work fine for my
> system.
> 
> Prasenjit
> 


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

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

 George Bernard Shaw 


From daijiayu at nudt.edu.cn  Tue Mar 23 10:00:19 2010
From: daijiayu at nudt.edu.cn (Jiayu Dai)
Date: Tue, 23 Mar 2010 17:00:19 +0800
Subject: [Pw_forum] volume in output file.
Message-ID: <469334819.15900@nudt.edu.cn>


>>   
>omega is the volume of the unit cell which in FCC is not alat^3 but 1/4 
>of alat^3
>

OK, thank you, Stefano and Mighfar Imam. I think it is the volume of ??unit cell",
not "cell" as your anwser. We also can understand it as the volume of one
effective atom in the cell. Therefore, for bcc, it should be 1/2 of alat^3, is
right?

Jiayu




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

From junkermeier at bloch.nrl.navy.mil  Tue Mar 23 16:37:17 2010
From: junkermeier at bloch.nrl.navy.mil (Chad Junkermeier)
Date: Tue, 23 Mar 2010 11:37:17 -0400
Subject: [Pw_forum] too many bands are not converged
Message-ID: <16C0C963-46FE-4B09-9A83-9A423BBBB4A8@bloch.nrl.navy.mil>

Hello Pw_forum,
   I was working on a model system using a 2x2 supercell, everything  
worked fine.  I switched a 4x4 system and I repeatedly get the  
following error:
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
%%%%%%%%%
      from c_bands : error #         1
      too many bands are not converged
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
%%%%%%%%%

The only changes I made to the input file were nat, ATOMIC_POSITIONS,  
and K_POINTS.  The changes to nat and ATOMIC_POSITIONS, are obvious  
due to the increase in cell size.  In moving to the larger supercell I  
went from

K_POINTS automatic
4 4 1  0 0  0

to

K_POINTS automatic
2 2 1  0 0  0

What is the general cause of the error?  Is there a change to the  
input that normally solves this problem?

Chad Junkermeier, Ph.D.
NRC Post-Doctoral Fellow
Naval Research Laboratory
4555 Overlook Ave, S.W.
Washington DC 20375










From junkermeier at bloch.nrl.navy.mil  Tue Mar 23 16:43:28 2010
From: junkermeier at bloch.nrl.navy.mil (Chad Junkermeier)
Date: Tue, 23 Mar 2010 11:43:28 -0400
Subject: [Pw_forum] too many bands are not converged
In-Reply-To: <16C0C963-46FE-4B09-9A83-9A423BBBB4A8@bloch.nrl.navy.mil>
References: <16C0C963-46FE-4B09-9A83-9A423BBBB4A8@bloch.nrl.navy.mil>
Message-ID: <33AFEA9A-B578-4400-9F0A-61F69D60D4DB@bloch.nrl.navy.mil>

I also made the appropriate changes to the lattice constants.



Chad Junkermeier, Ph.D.
NRC Post-Doctoral Fellow
Naval Research Laboratory
4555 Overlook Ave, S.W.
Washington DC 20375







On Mar 23, 2010, at 11:37 AM, Chad Junkermeier wrote:

> Hello Pw_forum,
>  I was working on a model system using a 2x2 supercell, everything  
> worked fine.  I switched a 4x4 system and I repeatedly get the  
> following error:
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
> %%%%%%%%%
>     from c_bands : error #         1
>     too many bands are not converged
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
> %%%%%%%%%
>
> The only changes I made to the input file were nat,  
> ATOMIC_POSITIONS, and K_POINTS.  The changes to nat and  
> ATOMIC_POSITIONS, are obvious due to the increase in cell size.  In  
> moving to the larger supercell I went from
>
> K_POINTS automatic
> 4 4 1  0 0  0
>
> to
>
> K_POINTS automatic
> 2 2 1  0 0  0
>
> What is the general cause of the error?  Is there a change to the  
> input that normally solves this problem?
>
> Chad Junkermeier, Ph.D.
> NRC Post-Doctoral Fellow
> Naval Research Laboratory
> 4555 Overlook Ave, S.W.
> Washington DC 20375
>
>
>
>
>
>
>
>
>


From nnlinh at sissa.it  Tue Mar 23 16:51:11 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Tue, 23 Mar 2010 16:51:11 +0100
Subject: [Pw_forum] too many bands are not converged
In-Reply-To: <33AFEA9A-B578-4400-9F0A-61F69D60D4DB@bloch.nrl.navy.mil>
References: <16C0C963-46FE-4B09-9A83-9A423BBBB4A8@bloch.nrl.navy.mil>
	<33AFEA9A-B578-4400-9F0A-61F69D60D4DB@bloch.nrl.navy.mil>
Message-ID: <4BA8E36F.2090701@sissa.it>

Chad Junkermeier wrote:
> I also made the appropriate changes to the lattice constants.
>
>   
>> Hello Pw_forum,
>>  I was working on a model system using a 2x2 supercell, everything  
>> worked fine.  I switched a 4x4 system and I repeatedly get the  
>> following error:
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
>> %%%%%%%%%
>>     from c_bands : error #         1
>>     too many bands are not converged
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
>> %%%%%%%%%
>>
>>     
This is very frequently asked question.
Normal ways to fix are: - reduce mixing_beta or change the scheme of 
diagonalization
- visualize to model to check if there are any too close or overlap 
atoms' positions.


Good luck,

Linh


-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From giuseppe.mattioli at mlib.ism.cnr.it  Tue Mar 23 17:36:32 2010
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Tue, 23 Mar 2010 17:36:32 +0100
Subject: [Pw_forum] LDA+U calculations in CP.x
Message-ID: <201003231736.33568.giuseppe.mattioli@mlib.ism.cnr.it>


Dear all
Does anybody know if the Hubbard_U(i) values that can be inserted in a CP 
input file have to be expressed in eV (as in PW) or in Ry? Neither the CP 
input manual, nor the cplib.f90 file, which contains the LDA+U routines used 
by CP, nor the CP output helped me to answer the question...

It seems that PW transforms the Hubbard_U(i) value provided by input (in eV) 

lda_plus_u=.true.,
Hubbard_U(1)=7.07,
Hubbard_U(2)=5.9,

in an internal Hubbard_U(i) value (in Ry) 

     LDA+U calculation, Hubbard_lmax = 2 
     atomic species  L   Hubbard U  Hubbard alpha  
        Co           2    0.519635    0.000000
        O            1    0.433642    0.000000

Does CP perform a similar conversion?

Thanks in advance

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 00016 - Monterotondo Stazione (RM)          
   Tel + 39 06 90672836 - Fax +39 06 90672316    
   E-mail: <giuseppe.mattioli at ism.cnr.it>
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From hlsit77 at gmail.com  Tue Mar 23 19:47:23 2010
From: hlsit77 at gmail.com (Patrick Sit)
Date: Wed, 24 Mar 2010 02:47:23 +0800
Subject: [Pw_forum] LDA+U calculations in CP.x
In-Reply-To: <201003231736.33568.giuseppe.mattioli@mlib.ism.cnr.it>
References: <201003231736.33568.giuseppe.mattioli@mlib.ism.cnr.it>
Message-ID: <60f6c72b1003231147r25850de4q47f216f653cf31b6@mail.gmail.com>

Dear Giuseppe,

The U value you define in cp input file is in eV. there is a line to
convert eV to au in the ldaU_init subroutine.

Best,

Patrick

On Wed, Mar 24, 2010 at 12:36 AM, Giuseppe Mattioli
<giuseppe.mattioli at mlib.ism.cnr.it> wrote:
>
> Dear all
> Does anybody know if the Hubbard_U(i) values that can be inserted in a CP
> input file have to be expressed in eV (as in PW) or in Ry? Neither the CP
> input manual, nor the cplib.f90 file, which contains the LDA+U routines used
> by CP, nor the CP output helped me to answer the question...
>
> It seems that PW transforms the Hubbard_U(i) value provided by input (in eV)
>
> lda_plus_u=.true.,
> Hubbard_U(1)=7.07,
> Hubbard_U(2)=5.9,
>
> in an internal Hubbard_U(i) value (in Ry)
>
> LDA+U calculation, Hubbard_lmax = 2
> atomic species L Hubbard U Hubbard alpha
> Co 2 0.519635 0.000000
> O 1 0.433642 0.000000
>
> Does CP perform a similar conversion?
>
> Thanks in advance
>
> 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 00016 - 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
>
>

From seung43210 at yahoo.com  Tue Mar 23 20:41:18 2010
From: seung43210 at yahoo.com (seunghwan lee)
Date: Tue, 23 Mar 2010 12:41:18 -0700 (PDT)
Subject: [Pw_forum] spin-polarized band structure
Message-ID: <587495.8731.qm@web50506.mail.re2.yahoo.com>

Hi All,

I am trying to calculate the band structure of a metallic system,
but I am not sure how I can get a separate band structure for each
spin component. With nspin=2, I get all other quantities (like DOS
and PDOS) for each component, but not the band structure.
Is it possible to do this with QuantumEspresso?

Thanks for your help.

Seunghwan Lee
University of North Carolina


      

From giovanni.cantele at na.infn.it  Tue Mar 23 21:10:08 2010
From: giovanni.cantele at na.infn.it (Giovanni Cantele)
Date: Tue, 23 Mar 2010 21:10:08 +0100 (CET)
Subject: [Pw_forum] spin-polarized band structure
In-Reply-To: <587495.8731.qm@web50506.mail.re2.yahoo.com>
References: <587495.8731.qm@web50506.mail.re2.yahoo.com>
Message-ID: <54736.93.150.96.207.1269375008.squirrel@imap-ac.na.infn.it>


> Hi All,
> I am trying to calculate the band structure of a metallic system,
> but I am not sure how I can get a separate band structure for each
> spin component. With nspin=2, I get all other quantities (like DOS
> and PDOS) for each component, but not the band structure.
> Is it possible to do this with QuantumEspresso?
>
> Thanks for your help.
>
> Seunghwan Lee
> University of North Carolina

It is possible. As you might see in the outputs of pw.x, eigenvalues for
both spin components are printed. If you usually use bands.x, just add to
its input the variable spin_component (possible values: 1, 2). You must
execute bands.x twice, of course fiving two different names to filband.
More details in Doc/INPUT_BANDS.*

Giovanni

-- 
Giovanni Cantele, PhD
CNR-SPIN and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910 - Fax:   +39 081 676346
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
          http://www.nanomat.unina.it


From yfang1 at tulane.edu  Tue Mar 23 22:25:26 2010
From: yfang1 at tulane.edu (Fang, Yuan)
Date: Tue, 23 Mar 2010 16:25:26 -0500
Subject: [Pw_forum] phonon dos of Fe
References: <2813cdb91003222151j755b77c3pad9dd9e9e00ad1cb@mail.gmail.com>
	<A81EB420-C417-4727-9E28-6B3F1C646119@democritos.it>
Message-ID: <D8E427248814A143AF7763DFA469B5F925CFF1@EX04.ad.tulane.edu>

Hey;
   Nowadays,I am calculating the phonon DOS of some elements.But I got some really strange result of Fe-bcc structure.I got some states with minus frequency. Attached is mu input file and output frequency file. Can someone help me find where the problem is.Thank you very much.
                               Y Fang

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From kacsssj at gmail.com  Wed Mar 24 00:08:15 2010
From: kacsssj at gmail.com (Keitel Cervantes Salguero)
Date: Tue, 23 Mar 2010 18:08:15 -0500
Subject: [Pw_forum] PP generation for specific exchange and correlation
Message-ID: <u2q5f526cf51003231608wf7685126vabf8cea442df2fe@mail.gmail.com>

Dear people,

I need to do a calculation with
the OPBE functional (OPTX exchange
and PBE correlation) and PW basis set.

Through the internet I have found that most
of the PPs have only one functional type (the same X and C)
for generation.
Is it correct if I generate my pseudopotential
with the OPTX and PBE type ?
If that is correct, which program do you recommend me ?

Many thanks in advanced.

Best Regards


-- 
Atte.
Keitel Cervantes Salguero
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From rcjhawk at gmail.com  Wed Mar 24 03:56:24 2010
From: rcjhawk at gmail.com (Michael Mehl)
Date: Tue, 23 Mar 2010 22:56:24 -0400
Subject: [Pw_forum] phonon dos of Fe
In-Reply-To: <D8E427248814A143AF7763DFA469B5F925CFF1@EX04.ad.tulane.edu>
References: <2813cdb91003222151j755b77c3pad9dd9e9e00ad1cb@mail.gmail.com>	<A81EB420-C417-4727-9E28-6B3F1C646119@democritos.it>
	<D8E427248814A143AF7763DFA469B5F925CFF1@EX04.ad.tulane.edu>
Message-ID: <4BA97F58.20802@gmail.com>

 From which I infer that you are not doing a spin-polarized calculation 
for iron -- the lowest energy structure for non-polarized iron is hcp, 
with fcc right above it, and bcc significantly above that.  For 
non-polarized bcc Fe, C11 - C12 < 0, which implies imaginary phonon 
frequencies at least near Gamma.

Turn on spin polarization and try it again.

Fang, Yuan wrote:

> Hey;
>    Nowadays,I am calculating the phonon DOS of some elements.But I got some really strange result of Fe-bcc structure.I got some states with minus frequency. Attached is mu input file and output frequency file. Can someone help me find where the problem is.Thank you very much.
>                                Y Fang
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 
Michael J. Mehl
Naval Research Laboratory
Washington DC


From baroni at sissa.it  Wed Mar 24 04:14:01 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 24 Mar 2010 04:14:01 +0100
Subject: [Pw_forum] volume in output file.
In-Reply-To: <469334819.15900@nudt.edu.cn>
References: <469334819.15900@nudt.edu.cn>
Message-ID: <60814EF4-415E-49A0-9A25-F1FBDFC0C30A@sissa.it>


On Mar 23, 2010, at 10:00 AM, Jiayu Dai wrote:

> 
>>> 
>> omega is the volume of the unit cell which in FCC is not alat^3 but 1/4 
>> of alat^3
>> 
> 
> OK, thank you, Stefano and Mighfar Imam. I think it is the volume of ??unit cell",
> not "cell" as your anwser. We also can understand it as the volume of one
> effective atom in the cell. Therefore, for bcc, it should be 1/2 of alat^3, is
> right?

It is the volume of the unit cell of the selected Bravais lattice (a^3/4 for FCC, a^3/2 for BCC, a^3 for SC)

SB

> 
> Jiayu
> 
> 
> 
> 
> ------------------------------
> -------------------------------------------
> Jiayu Dai
> Department of Physics
> National University of Defense Technology, 
> Changsha, 410073, P R China
> -----------------------------------------
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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

Please, if possible, don't  send me MS Word or PowerPoint attachments
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From xomiakk at gmail.com  Wed Mar 24 11:40:52 2010
From: xomiakk at gmail.com (Olga Sedelnikova)
Date: Wed, 24 Mar 2010 16:40:52 +0600
Subject: [Pw_forum] DOS at Ef
Message-ID: <ff62e3f1003240340y4405033as4fe4f160e1cf6af3@mail.gmail.com>

Dear Users,

I need to calculate the value of DOS at Ef. But I could not find it in the
out files of pw.x (neither for scf -  nor for nscf - calculations) or in the
out files of PP codes (dos.x and projwfc.x.).
How can I find this value?


Best regards,

Olga Sedelnikova
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From giovanni.cantele at na.infn.it  Wed Mar 24 12:08:48 2010
From: giovanni.cantele at na.infn.it (Giovanni Cantele)
Date: Wed, 24 Mar 2010 12:08:48 +0100
Subject: [Pw_forum] DOS at Ef
In-Reply-To: <ff62e3f1003240340y4405033as4fe4f160e1cf6af3@mail.gmail.com>
References: <ff62e3f1003240340y4405033as4fe4f160e1cf6af3@mail.gmail.com>
Message-ID: <16276991-3B8E-44BB-A1CD-9FE8A18DC107@na.infn.it>


On Mar 24, 2010, at 11:40 AM, Olga Sedelnikova wrote:

> Dear Users,
> 
> I need to calculate the value of DOS at Ef. But I could not find it in the out files of pw.x (neither for scf -  nor for nscf - calculations) or in the out files of PP codes (dos.x and projwfc.x.).
> How can I find this value?


I don't remember if Ef is printed in the output of pw.x. However, you can just use the definition:

the Fermi level is the energy level at which the integrated density of states equals the number of electrons. If you use a plot program, e.g. xmgrace,
you can plot the DOS as a function of energy, then calculate the integrated dos (IDOS):

IDOS(E) = \int_{-infty}^E   [ dE' DOS(E') ] 

and from the resulting curve calculate Ef as the energy at which IDOS(Ef) = number of electrons

giovanni



--

Giovanni Cantele, PhD
CNR-SPIN and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910 - Fax:   +39 081 676346
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it


From nnlinh at sissa.it  Wed Mar 24 12:16:43 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Wed, 24 Mar 2010 12:16:43 +0100
Subject: [Pw_forum] DOS at Ef
In-Reply-To: <ff62e3f1003240340y4405033as4fe4f160e1cf6af3@mail.gmail.com>
References: <ff62e3f1003240340y4405033as4fe4f160e1cf6af3@mail.gmail.com>
Message-ID: <4BA9F49B.60405@sissa.it>

Olga Sedelnikova wrote:
> Dear Users,
>
> I need to calculate the value of DOS at Ef. But I could not find it in 
> the out files of pw.x
Are you sure? In pw.x calculated output file (both scf and relax), you 
can see the Fermi energy value by typing grep -e "Fermi energy" 
output_file_name.out
> (neither for scf -  nor for nscf - calculations) or in the out files 
> of PP codes (dos.x and projwfc.x.).
> How can I find this value?
Using dos.x, you can obtain the Ef value by using its definition basing 
on number occupied electrons, but, in my opinion, this way is not such 
accurate.

Good luck,

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


-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From giovanni.cantele at na.infn.it  Wed Mar 24 12:21:45 2010
From: giovanni.cantele at na.infn.it (Giovanni Cantele)
Date: Wed, 24 Mar 2010 12:21:45 +0100
Subject: [Pw_forum] DOS at Ef
In-Reply-To: <4BA9F49B.60405@sissa.it>
References: <ff62e3f1003240340y4405033as4fe4f160e1cf6af3@mail.gmail.com>
	<4BA9F49B.60405@sissa.it>
Message-ID: <D1DC911E-78C3-4284-9BA4-41067AE5F694@na.infn.it>

> 
>> (neither for scf -  nor for nscf - calculations) or in the out files 
>> of PP codes (dos.x and projwfc.x.).
>> How can I find this value?
> Using dos.x, you can obtain the Ef value by using its definition basing 
> on number occupied electrons, but, in my opinion, this way is not such 
> accurate.



Can someone comment on that?
I would say that, based on the fact that dos.x is run
after an nscf calculation where a very dense grid in k space is used, this should be
more accurate than other approaches.

giovanni


--

Giovanni Cantele, PhD
CNR-SPIN and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910 - Fax:   +39 081 676346
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it


From miguel.martinez at ehu.es  Wed Mar 24 12:25:01 2010
From: miguel.martinez at ehu.es (Miguel Martinez Canales)
Date: Wed, 24 Mar 2010 12:25:01 +0100
Subject: [Pw_forum] Fortran compiler
In-Reply-To: <896650C5-FEAD-4471-8324-6E3320A5441D@democritos.it>
References: <C7C644C8.1AC9%Trinh.Vo@jpl.nasa.gov>
	<896650C5-FEAD-4471-8324-6E3320A5441D@democritos.it>
Message-ID: <20100324122501.19112igszmanu8ow@www.ehu.es>

Dear all,

Following Paolo's warning, I've performed some tests with a not so  
surprising result: Paolo was right. For some reason, the ubuntu 9.10  
builds of gfortran 4.3 and 4.4.1 give astonishingly different results  
for example07. Well, the pw.x output is the same as in the reference,  
but the lambda values... at least they are of the same order of  
magnitude. Mind you, for once this is not an ubuntu bug, as it also  
happens in self-compiled gfortran 4.4.3 (Red Hat 5.4 in this case).  
However, the differences in lambda don't seem important in the case of  
gfortran 4.1.2 (the default in Red Hat) or 4.2.4 (the oldest version  
available in ubuntu 9.10).

I'm going to check other examples to see whether there are very  
different phonon frequencies elsewhere, but I don't expect anything  
good at all.

Regards,

Miguel

Paolo Giannozzi <giannozz at democritos.it> escribi?:

>
> On Mar 17, 2010, at 16:35 , Vo, Trinh (388C) wrote:
>
>> I am actually compiling QE with the current version of gfortran,
>> and I have to think again whether I should continue to use it.  :-).
>
> you should, unless you have evidence of the opposite, or unless
> you are using exotic features, or the phonon code. The basic
> functionalities seem to work.
>
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



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

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

George Bernard Shaw


From dimpy.sharma at tyndall.ie  Wed Mar 24 12:46:54 2010
From: dimpy.sharma at tyndall.ie (Dimpy Sharma)
Date: Wed, 24 Mar 2010 11:46:54 -0000
Subject: [Pw_forum] nscf calculations
Message-ID: <D4A761F73683694BBD69D634FF298015533D3B@MAIL.tyndall.ie>

Hi there,

I have submitted my input file for nscf calcuation with 22 kpoints ( for the first brilloiun zone from kpoint from k=0 to 0.47) however in the output file of nscf , it calcuates the eigenvalues at k points 0,0.148,0.2960..3.1076 .Thus while plotting the band diagram my kvectir range becomes upto 3.1076. May I know why it happen? and to calculate the eigenvalues only on the given kpoints in th input file?

Thanks

Dimpy

Dimpy Sharma(Msc Nanotechnology
              PhD)
UCC
Ireland
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From giovanni.cantele at na.infn.it  Wed Mar 24 13:02:54 2010
From: giovanni.cantele at na.infn.it (Giovanni Cantele)
Date: Wed, 24 Mar 2010 13:02:54 +0100
Subject: [Pw_forum] nscf calculations
In-Reply-To: <D4A761F73683694BBD69D634FF298015533D3B@MAIL.tyndall.ie>
References: <D4A761F73683694BBD69D634FF298015533D3B@MAIL.tyndall.ie>
Message-ID: <A3B7D8A1-BEE9-45C4-AC2C-2FC3908EEBA3@na.infn.it>


On Mar 24, 2010, at 12:46 PM, Dimpy Sharma wrote:

> Hi there,
> 
> I have submitted my input file for nscf calcuation with 22 kpoints ( for the first brilloiun zone from kpoint from k=0 to 0.47) however in the output file of nscf , it calcuates the eigenvalues at k points 0,0.148,0.2960..3.1076 .Thus while plotting the band diagram my kvectir range becomes upto 3.1076. May I know why it happen? and to calculate the eigenvalues only on the given kpoints in th input file?
> 
> Thanks
> 
> Dimpy
> 
> Dimpy Sharma(Msc Nanotechnology
>               PhD)
> UCC
> Ireland
> 


possible issues:

i) if the number of k-points in the output is greater than the number of k-points you specify in the input, then the issue can be related
to symmetries. Unless you explicitly specify nosym = .true. (in nscf) the code always "complete" the k-point list in such a way it gets
compatible with the symmetry operations

ii) you are just "reading" your k-points in different units than you expect. Indeed, when the codes prints out the eigenvalues at each
k-point, the coordinates of the latter are tpiba, namely, 2 * pi / a (where a is the lattice constant along the first direct lattice axis).
Therefore, if you give, in the input
K_POINTS {crystal}
0.0    0.0    0.5    1.0
then if the system is not cubic ad c is the lattice parameter along the third direct lattice axis, the coordinates found in the output
will be 0.5 *a / c
I think that the band structure calculation requires not to keep the original "crystal units", because if you want to compute the band structure
along a given path in the Brilluoin zone, you want to keep the relative dimension of different segments (e.g. L-Gamma, Gamma-X) and for
that you cannot use a different unit along different directions (as it would occur in crystal coordinates in non-cubic systems).

giovanni

--

Giovanni Cantele, PhD
CNR-SPIN and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910 - Fax:   +39 081 676346
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
                     http://www.nanomat.unina.it

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From sclauzer at sissa.it  Wed Mar 24 13:31:24 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Wed, 24 Mar 2010 13:31:24 +0100
Subject: [Pw_forum] DOS at Ef
In-Reply-To: <D1DC911E-78C3-4284-9BA4-41067AE5F694@na.infn.it>
References: <ff62e3f1003240340y4405033as4fe4f160e1cf6af3@mail.gmail.com>	<4BA9F49B.60405@sissa.it>
	<D1DC911E-78C3-4284-9BA4-41067AE5F694@na.infn.it>
Message-ID: <4BAA061C.6060602@sissa.it>

Dear all,

Giovanni Cantele wrote:
>>> (neither for scf -  nor for nscf - calculations) or in the out files 
>>> of PP codes (dos.x and projwfc.x.).

the Fermi energy is printed only at the end of calculations for metals. In the case of 
insulators it is not defined. You can take any energy in the gap as reference value for 
the DOS plot.

>>> How can I find this value?
>> Using dos.x, you can obtain the Ef value by using its definition basing 
>> on number occupied electrons, but, in my opinion, this way is not such 
>> accurate.

For metals the Fermi level determined in this way is as accurate as in the previous scf or 
nscf calculation as long as you use the same kind and width of smearing.
Anyway, if you simply want to visualize the DOS you should use gaussians in order to avoid 
negative densities in the plot.

When dealing with insulators there's no Fermi level, but you can determined to a desired 
accuracy the top of the valence band, or, if you want, the energy of the HOMO.
To my knowledge the best way is to use the tetrahedron method (specify 
occupations='tetrahedra' in the nscf run): you don't need to specify any smearing and you 
can control the accuracy by comparing the DOS obtained with increasingly large k-points 
grids (in the nscf calculation).


HTH

GS

>  > 
> Can someone comment on that?
> I would say that, based on the fact that dos.x is run
> after an nscf calculation where a very dense grid in k space is used, this should be
> more accurate than other approaches.
> 
> giovanni
> 
> 
> --
> 
> Giovanni Cantele, PhD
> CNR-SPIN and Dipartimento di Scienze Fisiche
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> Phone: +39 081 676910 - Fax:   +39 081 676346
> Skype contact: giocan74
> 
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>                      http://www.nanomat.unina.it
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

-- 


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

From paulatto at sissa.it  Wed Mar 24 14:40:37 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 24 Mar 2010 14:40:37 +0100
Subject: [Pw_forum] DOS at Ef
In-Reply-To: <4BAA061C.6060602@sissa.it>
References: <ff62e3f1003240340y4405033as4fe4f160e1cf6af3@mail.gmail.com>
	<4BA9F49B.60405@sissa.it>
	<D1DC911E-78C3-4284-9BA4-41067AE5F694@na.infn.it>
	<4BAA061C.6060602@sissa.it>
Message-ID: <op.u92qxzika8x26q@vanoxite.impmc.jussieu.fr>

On Wed, 24 Mar 2010 13:31:24 +0100, Gabriele Sclauzero <sclauzer at sissa.it>  
wrote:
> the Fermi energy is printed only at the end of calculations for metals.  
> In the case of insulators it is not defined. You can take any energy in  
> the gap as reference value for
> the DOS plot.

I would add a small note on this: if for an insulator, or an isolated  
system, you specify a number of bands larger than the strict minimum  
(nelec/2) than you will get in output the LUMO and HOMO level. If you  
instead use the minimum number of bands than you can still get the HOMO,  
but you have to get it yourself from the bands printout, which can be a  
bit annoying but does not require any specific skill. Nevertheless, those  
number are good for isolated systems, not for insulator. The reason is  
that for an insulator you will probably use reciprocal-space grid with a  
small number of kpoints, hence the real HOMO and the real LUMO may as well  
be in point which is not in the grid. In order to have more accurate  
values you can do an NSCF calculation with a few more bands and many more  
kpoints.

regards


-- 
Lorenzo Paulatto

*** Note: my affiliation has changed! please send future
correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***

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

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

From payam.norouzzadeh at gmail.com  Wed Mar 24 16:43:14 2010
From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh)
Date: Wed, 24 Mar 2010 10:43:14 -0500
Subject: [Pw_forum] procedure for stopping jobs by prefix.EXIT file
Message-ID: <5a8b78941003240843i6379dc1br6beea8a0c0d12b98@mail.gmail.com>

Hello everybody

I don't know how to use prefix.EXIT file to stop jobs. May someone tell me
what is the procedure?

Best regards,Payam Norouzzadeh
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From sclauzer at sissa.it  Wed Mar 24 17:29:56 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Wed, 24 Mar 2010 17:29:56 +0100
Subject: [Pw_forum] procedure for stopping jobs by prefix.EXIT file
In-Reply-To: <5a8b78941003240843i6379dc1br6beea8a0c0d12b98@mail.gmail.com>
References: <5a8b78941003240843i6379dc1br6beea8a0c0d12b98@mail.gmail.com>
Message-ID: <4BAA3E04.7030609@sissa.it>

Hello Payam,

Payam Norouzzadeh wrote:
> Hello everybody
> 
> I don't know how to use prefix.EXIT file to stop jobs. May someone tell 
> me what is the procedure?

Very easy: just create a file with that name (substitute to prefix the actual prefix, i.e. 
the string that you put after prefix= in the input file) in the directory from where you 
launched the pw.x program.

For instance, if prefix='xyz', then you can use:

touch xyz.EXIT




GS



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

-- 


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

From lfhuang at theory.issp.ac.cn  Wed Mar 24 17:18:29 2010
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Thu, 25 Mar 2010 0:18:29 +0800
Subject: [Pw_forum] =?utf-8?q?one_question_on_=7Cpsi=7C=5E2?=
Message-ID: <20100324161829.11370.qmail@ms.hfcas.ac.cn>

Dear PWSCF developers:
     I have a question on |psi|^2 when using projwfc.x and reading projwfc.f90:
 Does |psi|^2 just denote the "Lowdin charge/net atomic charges" for specific band at specific k point? And the "bonding charges" are not included, are'nt they? 
I guess so, because there is: 
proj(nwfc,ibnd,ik)=ABS(proj0(nwfc,ibnd))**2
in projwfc.f90, am I right?
Maybe the questions on the calculations of Lowdin charge and PDOS have been proposed so many times, but my question is somewhat specific and any reply can help my understanding of the code. 
I would like to highly appreciate any helpful comment!

PS: I cannot open the "TOOLs/search facility" on the homepage of PWSCF in China, because if I click it, the page will jump to "Google". Is this normal? It is not like this before. Is the "search facility" related with Google?
In addition, Google company has retreated out of the Inland of China to Hongkong recently, and does this will affect our usage of "search facility"? 

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


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From baroni at sissa.it  Wed Mar 24 21:26:08 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 24 Mar 2010 21:26:08 +0100
Subject: [Pw_forum] one question on |psi|^2
In-Reply-To: <20100324161829.11370.qmail@ms.hfcas.ac.cn>
References: <20100324161829.11370.qmail@ms.hfcas.ac.cn>
Message-ID: <6798825F-C333-4B80-8828-E2FD8D6C476A@sissa.it>


On Mar 24, 2010, at 5:18 PM, lfhuang wrote:
> 
> PS: I cannot open the "TOOLs/search facility" on the homepage of PWSCF in China, because if I click it, the page will jump to "Google". Is this normal? It is not like this before. Is the "search facility" related with Google? 
> In addition, Google company has retreated out of the Inland of China to Hongkong recently, and does this will affect our usage of "search facility"? 

yeap! I am afraid this is the case. This is a small demonstration of how censorship can affect domains that are very far away and seemingly unrelated to its main targets. Actually, freedom of thought, speech, and press lies at the very basis of scientific knowledge: seemingly unrelated, actually tightly interwoven.

This being said, we will do what we can to cope with this situation.
Layla, Alberto: any idea? Can we provide an option to use some internal search engine for those not able / willing to use google?

Best wishes - Stefano

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

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

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







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From giannozz at democritos.it  Wed Mar 24 21:37:21 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 24 Mar 2010 21:37:21 +0100
Subject: [Pw_forum] one question on |psi|^2
In-Reply-To: <6798825F-C333-4B80-8828-E2FD8D6C476A@sissa.it>
References: <20100324161829.11370.qmail@ms.hfcas.ac.cn>
	<6798825F-C333-4B80-8828-E2FD8D6C476A@sissa.it>
Message-ID: <31EBB0A3-E357-4E57-A9A1-6DFCEBA22970@democritos.it>


On Mar 24, 2010, at 21:26 , Stefano Baroni wrote:

> This being said, we will do what we can to cope with this situation.
> Layla, Alberto: any idea? Can we provide an option to use some
> internal search engine for those not able / willing to use google?

the one that was used before:
http://www.democritos.it/cgi-bin/htsearch? 
config=&restrict=&exclude=&method=and&format=builtin- 
long&sort=score&words=pw_forum

(found on the cached copy, using google ...)

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




From Michael.Mehl at nrl.navy.mil  Wed Mar 24 21:45:07 2010
From: Michael.Mehl at nrl.navy.mil (Mike Mehl)
Date: Wed, 24 Mar 2010 16:45:07 -0400
Subject: [Pw_forum] pw.x generates duplicate k-points in scf mode
Message-ID: <4BAA79D3.1090402@nrl.navy.mil>

Apologies if this goes through twice, the first time I used the wrong 
email address and I don't know if the moderator will pass the message on 
or not:

Attached, if I did things correctly, are two input files.  Both of them
are used to do an scf calculation for a frozen phonon determination of
frequencies at the X point of the B11 structure of AgZr.  As such, the
primitive vectors of the unit cell look orthorhombic, but the symmetry
of the structure is monoclinic:  P2_1/c (#14).  For this particular
orientation the 4 symmetry operations are +\- (x,y,z) and +/- (x+1/2,
-y+1/2, -z).  I mention all of that because I suspect it's relevant to
the problem.

Once I've properly adjusted the FFT mesh pw.x finds 4 symmetry
operations, including the fractional ones and the inversion, consistent
with the P2_1/c space group.

The attached file X_gen.in generates the k-point mesh using:

K_POINTS (automatic)
   8 4 4 0 0 0

This results in 50 points.  I have a k-point generating routine lifted
from our old LAPW program which also computes k-points from the lattice
vectors and the space group operations.  Both programs give identical
(within a symmetry operation) k-points, so I'm sure this is correct.

For many of my calculations I want to keep the identical k-point list,
in a standard order.  So:

The attached file X_raw50.in inputs the k-points via:

K_POINTS (crystal)
50
    0.0000  0.0000  0.0000  0.01562500
    0.0000  0.0000  0.2500  0.03125000
    0.0000  0.0000 -0.5000  0.01562500
[47 lines omitted]

where the 50 k-points are the lattice coordinates of the points
generated by X_gen.in.

Here's where the problem occurs:  running pw.x on with X_raw50.in as
input generates 60 k-points.  The first 50 are identical to those
generated by the first run, except that 10 of them have different
weights.  The last 10 k-points are duplicates of points of the 10 points
which changed weights in the first part of the list.  Not points related
by symmetry, but the exact k-points.

For example, if we look at point 5 in the run generated by the first
input file, we find:

k(    5) = (   0.0000000   0.0189061   0.0198824), wk =   0.0312500

The same point in the output generated by the second input file gives:

k(    5) = (   0.0000000   0.0189061   0.0198824), wk =   0.0156250

not to worry, the rest of the weight shows up later:

k(   56) = (   0.0000000   0.0189061   0.0198824), wk =   0.0156250

Furthermore, if I take the 60 k-points of this output and use those as
input to pw.x I get 80 k-points generated.  If I use those 80 points, I
get 120 points generated.  Presumably this continues forever, the same
10 k-points and duplicates being reduplicated with every iteration.

Of course all of these runs generate the same total energy at every
iteration, and converge in the same number of iterations.

The mailing list hints that this kind of thing may happen in **nscf**
runs, where the solution is to run with nosym=.true.  I'm leery of doing
this in an scf run, since I don't know how it affects the final charge
density, and my test calculation showed a slight difference in total
energies.

One of my long-term goals for using QE is to generate, more or less
automatically, a large number of runs for frozen phonon calculations
over a variety of supercells, using k-points generated externally.  I'll
be happy to discuss the whys and wherefores off-list.  But I don't want
to take the 20% performance hit (more with larger meshes) that comes
with this k-point duplication.

So, should I run with nosym=.true.?

Alternatively, I assume that this is happening because of something in
the k-point generation routine.  Perhaps there is a tolerance factor in
comparing k-points that is set too tightly.  Is there a variable which
would allow me to adjust this tolerance?  (In kpoint_grid.f90 the
tolerance is set to 1.0d-5, which is too big to cause problems.  But
that routine doesn't seem to deal with externally generated k-points.)

-- 
Michael J. Mehl
Head, Center for Computational Materials Science
Naval Research Laboratory Code 6390
Washington DC
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From giannozz at democritos.it  Wed Mar 24 22:47:28 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 24 Mar 2010 22:47:28 +0100
Subject: [Pw_forum] pw.x generates duplicate k-points in scf mode
In-Reply-To: <4BAA79D3.1090402@nrl.navy.mil>
References: <4BAA79D3.1090402@nrl.navy.mil>
Message-ID: <0D2C71D8-62CB-4437-914D-28E999246EF3@democritos.it>


On Mar 24, 2010, at 21:45 , Mike Mehl wrote:

> I don't know if the moderator will pass the message on or not

not: messages "held for moderator approval" are automatically discarded
after one day. Unfortunately there is no (known) way to instruct the  
mailing
list software to tell the truth: "your message will be lost, please  
resubmit it
from an authorized e-mail"

> Alternatively, I assume that this is happening because of something in
> the k-point generation routine.

I don't think this is the case. The code espects k-points in the  
input list
to be in the irreducible BZ of the lattice, with all lattice symmetries.
Changing this behavior (which I don't like either) requires some (simple
but delicate) coding

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




From pbsorokin at gmail.com  Wed Mar 24 23:39:41 2010
From: pbsorokin at gmail.com (Pavel B Sorokin)
Date: Wed, 24 Mar 2010 17:39:41 -0500
Subject: [Pw_forum] Sound velocity calculation
Message-ID: <1664350715.20100324173941@gmail.com>

Dear all!

I would like to calculate the sound velocity for graphene. It seems
rather simple but I have encountered a problem which I still can't
solve.
I have calculated the phonon band structure which seems reasonable
and have got the frequencies near gamma point (in cm-1).
Now I should just derivate omega (in s-1 = cm-1*3*10^10) by k and obtain velocity. But the
what units of k should I use?
The k units using in PWSCF is 2*pi/a0 where a0=4.66625 Bohr = 2.13
Ang and it seems correct.

The reciprocal lattice vectors are following:

 b(1) = (  1.0000  0.5774  0.0000 )
 b(2) = (  0.0000  1.1547  0.0000 )
 b(3) = (  0.0000  0.0000  0.1900 )

But when I try to evaluate the velocity I obtain the answer nearly in
six time less then reported early: 2200 m/s and 3400 m/s vs. 12200
m/s and 19500 m/s.
I do some stupid mistake, but where? Does anybody has the experience
in such calculations?

Thank you!!

-- 
Sincerely yours,
Pavel B Sorokin                         mailto:PBSorokin at gmail.com
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From elie.moujaes at hotmail.co.uk  Thu Mar 25 02:20:04 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Thu, 25 Mar 2010 01:20:04 +0000
Subject: [Pw_forum] band structure of bi layer graphene
Message-ID: <SNT114-W165046928917A350FF0C33D3240@phx.gbl>


Dear all,

 

I am trying to obtain the band structure of graphene. to do that, I supposed that celldim(1) =4.608737, celldm(3)=4.53666 so that c is 4.53666 *a....The carbon atoms are chosen such that:

 

 

ATOMIC_POSITIONS crystal
 C 0.000000  0.000000  0.000000  1 1 1
 C 0.000000  0.000000  0.200000  1 1 1
 C 0.333333  -0.33333  0.000000  1 1 1
 C -0.333333  0.33333   0.200000  1 1 1 
 

 

we have 4 carbon atoms in bilayer graphene and the primitive cell has a z direction of 0.2*c= 1/5 so that the primitive cell is 3D. Since QE is a 3D program, I thought that setting c= 4.5366 will produce an image of the primitive cell that is 4.53666*4.608737 Bohrs away from the original one so that no interaction happens( in the acse of which I will be modelling something similar to graphite). I got the results whioch are satisfactory but still need some  amendments...I just want to know if this line of thought is correct and if someone can have a look at the graph because it is not entirely correct. Maybe I need to increase the number of points.. I am open to suggestions if any...You will find ps file attached....

 

 

Regards

 

ELie moujaes

University of Nottingham

NG7 2RD

UK 
 		 	   		  
_________________________________________________________________
Send us your Hotmail stories and be featured in our newsletter
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From lfhuang at theory.issp.ac.cn  Thu Mar 25 03:57:59 2010
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Thu, 25 Mar 2010 10:57:59 +0800
Subject: [Pw_forum] =?utf-8?q?one_question_on_=7Cpsi=7C=5E2?=
Message-ID: <20100325025759.769.qmail@ms.hfcas.ac.cn>

Dear prof. S. Baroni and P. Giannozzi:
    Thank you very much for your help on the "search facility"! I can use it now with the URL provided by prof. P. Giannozzi.
 
    And could any one have more comment on my another question on |psi|^2? Is it the Lowdin charge for a specific band at a specific k point? Thanks!

Best Wishes!
Yours Sincerely 
L.F.Huang

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


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From lfhuang at theory.issp.ac.cn  Thu Mar 25 04:04:00 2010
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Thu, 25 Mar 2010 11:04:00 +0800
Subject: [Pw_forum] =?utf-8?q?Sound_velocity_calculation?=
Message-ID: <20100325030400.2340.qmail@ms.hfcas.ac.cn>

Dear P. B. Sorokin: 
> But when I try to evaluate the velocity I obtain the answer nearly in
> six time less then reported early: 2200 m/s and 3400 m/s vs. 12200
> m/s and 19500 m/s.
> I do some stupid mistake, but where? Does anybody has the experience
> in such calculations?
Where does your reference for the sound velocity come from? And there are 3 acoustic bands for graphene, one of which is the bending mode with a parabolic dispersion near gamma point. Have you pay attention to this band?
 
Best Wishes!
Yours Sincerely
L.F.Huang

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


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From giannozz at democritos.it  Thu Mar 25 09:30:41 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 25 Mar 2010 09:30:41 +0100
Subject: [Pw_forum] one question on |psi|^2
In-Reply-To: <20100324161829.11370.qmail@ms.hfcas.ac.cn>
References: <20100324161829.11370.qmail@ms.hfcas.ac.cn>
Message-ID: <AE152626-3270-46B8-9E8C-FCFDA76AC7A0@democritos.it>


On Mar 24, 2010, at 17:18 , lfhuang wrote:

> Maybe the questions on the calculations of Lowdin charge and PDOS
> have been proposed so many times, but my question is somewhat specific

>

I find it obscure, not specific
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From yukihiro_okuno at fujifilm.co.jp  Thu Mar 25 11:30:56 2010
From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp)
Date: Thu, 25 Mar 2010 19:30:56 +0900
Subject: [Pw_forum] Error of GWW in running head.x
Message-ID: <OF3363C4AB.6907DD77-ON492576F1.0031FC9A-492576F1.0039C42E@mta.fujifilm.co.jp>


Dear PWSCF users and developers.

I began to use GWW code, and run the simple examples.
But, I  met  the error in running head.x
for GWW calculation.

I run the example02 without shell script "run_example".
(si8 periodic system)

I run scf calculation first, then run the head.x in
order to get si.head, si.e_head.

But the calculation stop with the error message,

from seqopn : error #    1
wrong unit.

I checked  the souce code to see the origin of the error.

The calculation of head parts of dielectric constants has finished
with  all values of frequency, ngauss +1 = 80.

But after the calculation of E_HEAD, at the timing of the close files,

call close_phq( .TRUE. )  (in head.f90 at line 413)

and in close_phq,

call seqopn(iurec,'recover','UNFORMATTED',exst)

but, the "prefix.,recover" file was not generated in the calculation of
head.x

and furthermore the wrong "iurec" is given.


My procedure of the calculate SCF and head are,

pw.x < si8_scf.in


head.x < si8_ph_head.in


and the input files are follows,

The scf parts

&control
    calculation='scf'
    restart_mode='from_scratch',
    pseudo_dir = '/espresso/pseudo/',
    prefix='si'
    outdir='./'
/
 &system
    ibrav= 8, celldm(1)= 10.26,celldm(2)= 1, celldm(3)=1,
    nat=  8, ntyp= 1,
    ecutwfc = 18.0, nosym=.false.
 /
 &electrons
    diagonalization='david',
    conv_thr =  1.0d-10,
    mixing_beta = 0.5,
    startingwfc='random',
 /
ATOMIC_SPECIES
 Si  1. Si.pz-rrkj.UPF
ATOMIC_POSITIONS (crystal)
Si 0.00000 0.00000 0.00000
Si 0.50000 0.50000 0.00000
Si 0.00000 0.50000 0.50000
Si 0.50000 0.00000 0.50000
Si 0.25000 0.25000 0.25000
Si 0.75000 0.75000 0.25000
Si 0.75000 0.25000 0.75000
Si 0.25000 0.75000 0.75000
K_POINTS (automatic)
4 4 4 1 1 1

and HEAD parts

phonons of Si at Gamma
 &inputph
  tr2_ph=1.d-4,
  prefix='si',
  outdir='./',
  epsil=.false.,
  amass(1)=28.08,
  fildyn='si.dynG',
  recover=.false.
  trans=.false.
  l_head=.true.
  omega_gauss=20.
  n_gauss=79
  grid_type=2
  niter_ph=1
 /
0.0 0.0 0.0

Sincerely,

Yukihiro Okuno.


From lfhuang at theory.issp.ac.cn  Thu Mar 25 11:09:36 2010
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Thu, 25 Mar 2010 18:09:36 +0800
Subject: [Pw_forum] =?utf-8?q?one_question_on_=7Cpsi=7C=5E2?=
Message-ID: <20100325100936.6366.qmail@ms.hfcas.ac.cn>

Dear prof. P. Giannozzi:
    Thank you for your attention!
    Maybe I have mistaken the meaning of the word "specific". I will rewritten my question (or my confusion) below:
|psi|^2 usually denotes the modulus of the wavefucntion, but from the code projwfc.f90, there is 
......
 proj(nwfc,ibnd,ik)=ABS(proj0(nwfc,ibnd))**2
......
DO nwfc = 1, natomwfc
              psum = psum + proj (nwfc, ibnd, ik)
           END DO
           WRITE( stdout, '(4x,"|psi|^2 = ",f5.3)') psum
......

does this mean that |psi|^2 just denote the sum over the moduluses of the weighted atomic orbitals, and the overlaps between atomic orbitals are not accounted? So |psi|^2 is not the modulus of the KS orbital, am I right? 

Thanks for your time and attention!
Best Wishes!

Yours Sincerely
L.F.Huang

> From: Paolo Giannozzi 
> Subject: Re: [Pw_forum] one question on |psi|^2
> To: PWSCF Forum 
> Message-ID: 
> Content-Type: text/plain; charset=US-ASCII; format=flowed
> 
> 
> On Mar 24, 2010, at 17:18 , lfhuang wrote:
> 
> > Maybe the questions on the calculations of Lowdin charge and PDOS
> > have been proposed so many times, but my question is somewhat specific
> 
> >
> 
> I find it obscure, not specific
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222


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


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From giannozz at democritos.it  Thu Mar 25 15:09:01 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 25 Mar 2010 15:09:01 +0100
Subject: [Pw_forum] one question on |psi|^2
In-Reply-To: <20100325100936.6366.qmail@ms.hfcas.ac.cn>
References: <20100325100936.6366.qmail@ms.hfcas.ac.cn>
Message-ID: <C7A9281D-9BAD-49A3-A7F2-A5B89BCFCD55@democritos.it>


On Mar 25, 2010, at 11:09 , lfhuang wrote:

>
> |psi|^2 usually denotes the modulus of the wavefucntion, but from  
> the code projwfc.f90, there is
> ......
> proj(nwfc,ibnd,ik)=ABS(proj0(nwfc,ibnd))**2
> ......
> DO nwfc = 1, natomwfc
> psum = psum + proj (nwfc, ibnd, ik)
> END DO
> WRITE( stdout, '(4x,"|psi|^2 = ",f5.3)') psum
> ......
>
> does this mean that |psi|^2 just denote the sum over the moduluses  
> of the weighted atomic orbitals, and the overlaps between atomic  
> orbitals are not accounted? So |psi|^2 is not the modulus of the KS  
> orbital, am I right?

what are you referring to? to |psi^2| as printed in the line above?
or to |psi^2| in general? the latter is 1 by construction; the former
is < 1. What is printed is just a check, for your  convenience. It
tells you how well the projection over atomic states reproduces
the Kohn-Sham orbitals

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




From daijiayu at nudt.edu.cn  Thu Mar 25 16:16:17 2010
From: daijiayu at nudt.edu.cn (Jiayu Dai)
Date: Thu, 25 Mar 2010 23:16:17 +0800
Subject: [Pw_forum] internal energy
Message-ID: <EHWTUSXJODNLUEUAOYQQENWWDBCM.daijiayu@nudt.edu.cn>

Dear all,

I found in the previous discussion that the energy in PWscf using Fermi-Dirac smearing is the free energy. Is it the total free energy including electrons and ions contribution? Furthermore, how to get the internal energy here? The kinetic energy is easy to calculate, but how about the potential energy?

Thanks a lot.

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

From pbsorokin at gmail.com  Thu Mar 25 16:49:45 2010
From: pbsorokin at gmail.com (Pavel B Sorokin)
Date: Thu, 25 Mar 2010 10:49:45 -0500
Subject: [Pw_forum] Sound velocity calculation
In-Reply-To: <20100325030400.2340.qmail@ms.hfcas.ac.cn>
References: <20100325030400.2340.qmail@ms.hfcas.ac.cn>
Message-ID: <13410584258.20100325104945@gmail.com>

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From baroni at sissa.it  Thu Mar 25 19:02:08 2010
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 25 Mar 2010 19:02:08 +0100
Subject: [Pw_forum] internal energy
In-Reply-To: <EHWTUSXJODNLUEUAOYQQENWWDBCM.daijiayu@nudt.edu.cn>
References: <EHWTUSXJODNLUEUAOYQQENWWDBCM.daijiayu@nudt.edu.cn>
Message-ID: <8BCE29F1-1D88-482F-AFF3-DE96C6F21B52@sissa.it>


On Mar 25, 2010, at 4:16 PM, Jiayu Dai wrote:

> Dear all,
> 
> I found in the previous discussion that the energy in PWscf using Fermi-Dirac smearing is the free energy.

It is *NOT* any free energy of any physical system. It can be interpreted as the free energy of a system of electrons in the field of clamped nuclei, at the *fictitious* temperature corresponding to the smearing you use. The reason why this concept is useful is that the free energy is variational, while the internal energy is not. That's why Hellman-Feynman forces are derivatives of the free energy, but not of the internal energy.

> Is it the total free energy including electrons and ions contribution?

As said, electrons only.

> Furthermore, how to get the internal energy here? The kinetic energy is easy to calculate, but how about the potential energy?

You do not need any internal energy. what you may actually want to estimate is the T->0 extrapolation of both the free and internal energies (which coincide in the T->0 limit). I think that some estimate of this are available in the pw output, but others may know more than me about this.

Stefano B

> 
> Thanks a lot.
> 
> Jiayu
> ----------------
> -------------------------------------------
> Jiayu Dai
> Department of Physics
> National University of Defense Technology, 
> Changsha, 410073, P R China
> -----------------------------------------
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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

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







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From elie.moujaes at hotmail.co.uk  Thu Mar 25 19:39:12 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Thu, 25 Mar 2010 18:39:12 +0000
Subject: [Pw_forum] graph of band structure of bi layer graphene
Message-ID: <SNT114-W576B1B38547A98C1CCD199D3240@phx.gbl>


Dear PWSCF users and developers,

 

I am trying trying to find the band structure of bi layer graphene using pw package. Everything goes fine until i execute?

 

/espresso-4.1.2/bin/bands.x<bigraphene.bands.in>bigraphene.bands.out then the output looks like:

 

 

 

Program POST-PROC v.4.1.2  starts ...
     Today is 25Mar2010 at 15:13:13 
     file C.pz-rrkjus.UPF: wavefunction(s)  2S renormalized

     negative rho (up, down):  0.214E-04 0.000E+00

what does the negative rho means and why the up rho is not exactly zero? When the graph is plotted using plotband.x I get a fairly decent graph but at the left corner I get some vertical thick lines (appearing on the negative side whereas the graph looks ok). I need to know what is this rho related to and how to make it exactly zero. is it by choosing a convenient degauss value?
 
 
Thanks
 
 
 
Elie Moujaes
University of Nottingham
NG7 2RD
Nottingham 		 	   		  
_________________________________________________________________
Tell us your greatest, weirdest and funniest Hotmail stories
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From elbuesta at icqmail.com  Thu Mar 25 21:40:16 2010
From: elbuesta at icqmail.com (elbuesta at icqmail.com)
Date: Thu, 25 Mar 2010 16:40:16 -0400
Subject: [Pw_forum]  Occupation matrix in LDA+U
In-Reply-To: <8BCE29F1-1D88-482F-AFF3-DE96C6F21B52@sissa.it>
References: <8BCE29F1-1D88-482F-AFF3-DE96C6F21B52@sissa.it>
Message-ID: <8CC9A728236A701-175C-14E@webmail-m012.sysops.aol.com>

Dear all,

We have a fews questions/doubts concerning the ns occupation matrix for LDA+U calculations (starting_ns_eigenvalue(m,ispin,I)). Following the idea presented in example 25 of quantum espresso, we are trying to fix the initial occupation of the "d" orbital of Ni in a monolayer of NiO in an anti-ferromagnetic state. The questions we have are:

1) Are each of the diagonal elements of the occupation matrix associated with the d orbitals? Something like, 
(1,1) -&gt; dz2, (2,2) -&gt; dzx, (3,3) -&gt; dzy, (4,4) -&gt; d(x2-y2) and? (5,5) -&gt; dxy?? ?
2) If there is this correspondence, is it possible to specify an initial occupation of each of the orbitals after the initial guess is evaluated in the first iteration? For example, in the attached input, how could we specify that only the dz2, dxz and dyz orbitals are initially completely occupied with 2 electrons? In other words, how can we change the "spin down occupation matrix" of the Ni atom from 
0.6 0.0 0.0 0.0 0.0???? ?? ? ? 1.0 0.0 0.0 0.0 0.0
0.0 0.6 0.0 0.0 0.0???? ?? ? ? 0.0 1.0 0.0 0.0 0.0
0.0 0.0 0.6 0.0 0.0???? -&gt;??? 0.0 0.0 1.0 0.0 0.0
0.0 0.0 0.0 0.6 0.0???? ?? ??? 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.6???? ?? ??? 0.0 0.0 0.0 0.0 0.0
??

Thanks very much for your time,
With best regards,

Luca Sementa, F?bio Negreiros
Postdoc students,
IPCF - CNR - Pisa, Italy
 

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From giannozz at democritos.it  Thu Mar 25 22:03:31 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 25 Mar 2010 22:03:31 +0100
Subject: [Pw_forum] graph of band structure of bi layer graphene
In-Reply-To: <SNT114-W576B1B38547A98C1CCD199D3240@phx.gbl>
References: <SNT114-W576B1B38547A98C1CCD199D3240@phx.gbl>
Message-ID: <426F7881-324F-4130-BF44-0F5C332DF53F@democritos.it>


On Mar 25, 2010, at 19:39 , Elie Moujaes wrote:

> what does the negative rho means


http://www.quantum-espresso.org/user_guide/node61.html

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




From matteo at umn.edu  Thu Mar 25 22:01:09 2010
From: matteo at umn.edu (Matteo Cococcioni)
Date: Thu, 25 Mar 2010 16:01:09 -0500
Subject: [Pw_forum] Occupation matrix in LDA+U
In-Reply-To: <8CC9A728236A701-175C-14E@webmail-m012.sysops.aol.com>
References: <8BCE29F1-1D88-482F-AFF3-DE96C6F21B52@sissa.it>
	<8CC9A728236A701-175C-14E@webmail-m012.sysops.aol.com>
Message-ID: <4BABCF15.2050702@umn.edu>


Dear Luca and Fabio

here are my answers.

1) the diagonal elements of the occupation matrix are the projection on 
the atomic orbitals in the order
you wrote. Of course also non diagonal elements are associated with d 
orbitals. they are not projection strictly
speaking but you can see them as generalized overlap terms between d 
atomic orbitals in the subspace of occupied Kohn-Sham states.

2) yes. from Doc/INPUT_PW:

   +--------------------------------------------------------------------
   Variable:       starting_ns_eigenvalue(m,ispin,I)

   Type:           REAL
   Default:        -1.d0 that means NOT SET
   Description:    In the first iteration of an LDA+U run it overwrites
                   the m-th eigenvalue of the ns occupation matrix for the
                   ispin component of atomic species I. Leave unchanged
                   eigenvalues that are not set. This is useful to suggest
                   the desired orbital occupations when the default choice
                   takes another path.
   +--------------------------------------------------------------------

keep in mind that you are adjusting the eigenvalue of the matrix. So you 
better give a look at the occupation matrix
and its spectrum after the first iteration of a non constraint run.

hope this helps,

Matteo



elbuesta at icqmail.com wrote:
> Dear all,
>
> We have a fews questions/doubts concerning the ns occupation matrix 
> for LDA+U calculations (starting_ns_eigenvalue(m,ispin,I)). Following 
> the idea presented in example 25 of quantum espresso, we are trying to 
> fix the initial occupation of the "d" orbital of Ni in a monolayer of 
> NiO in an anti-ferromagnetic state. The questions we have are:
>
> 1) Are each of the diagonal elements of the occupation matrix 
> associated with the d orbitals? Something like,
> (1,1) -> dz2, (2,2) -> dzx, (3,3) -> dzy, (4,4) -> d(x2-y2) and  (5,5) 
> -> dxy   ?
> 2) If there is this correspondence, is it possible to specify an 
> initial occupation of each of the orbitals after the initial guess is 
> evaluated in the first iteration? For example, in the attached input, 
> how could we specify that only the dz2, dxz and dyz orbitals are 
> initially completely occupied with 2 electrons? In other words, how 
> can we change the "spin down occupation matrix" of the Ni atom from
> 0.6 0.0 0.0 0.0 0.0            1.0 0.0 0.0 0.0 0.0
> 0.0 0.6 0.0 0.0 0.0            0.0 1.0 0.0 0.0 0.0
> 0.0 0.0 0.6 0.0 0.0     ->    0.0 0.0 1.0 0.0 0.0
> 0.0 0.0 0.0 0.6 0.0            0.0 0.0 0.0 0.0 0.0
> 0.0 0.0 0.0 0.0 0.6            0.0 0.0 0.0 0.0 0.0
> ??
>
> Thanks very much for your time,
> With best regards,
>
> Luca Sementa, F?bio Negreiros
> Postdoc students,
> IPCF - CNR - Pisa, Italy
>
> =
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From yfang1 at tulane.edu  Thu Mar 25 22:09:09 2010
From: yfang1 at tulane.edu (Fang, Yuan)
Date: Thu, 25 Mar 2010 16:09:09 -0500
Subject: [Pw_forum] phonon dos of Fe
References: <2813cdb91003222151j755b77c3pad9dd9e9e00ad1cb@mail.gmail.com>	<A81EB420-C417-4727-9E28-6B3F1C646119@democritos.it>
	<D8E427248814A143AF7763DFA469B5F925CFF1@EX04.ad.tulane.edu>
	<4BA97F58.20802@gmail.com>
Message-ID: <D8E427248814A143AF7763DFA469B5F925CFF2@EX04.ad.tulane.edu>

  Hi,I tried the spin-polarized calculation by setting nspin to be 2 or 4 or noncolin=.TRUE. ,but still got the imaginary result. Is there anything else can handle this?
    Thank you.



-----Original Message-----
From: pw_forum-bounces at pwscf.org on behalf of Michael Mehl
Sent: Tue 3/23/2010 9:56 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] phonon dos of Fe
 

 From which I infer that you are not doing a spin-polarized calculation 
for iron -- the lowest energy structure for non-polarized iron is hcp, 
with fcc right above it, and bcc significantly above that.  For 
non-polarized bcc Fe, C11 - C12 < 0, which implies imaginary phonon 
frequencies at least near Gamma.

Turn on spin polarization and try it again.

Fang, Yuan wrote:

> Hey;
>    Nowadays,I am calculating the phonon DOS of some elements.But I got some really strange result of Fe-bcc structure.I got some states with minus frequency. Attached is mu input file and output frequency file. Can someone help me find where the problem is.Thank you very much.
>                                Y Fang
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 
Michael J. Mehl
Naval Research Laboratory
Washington DC

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

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From elie.moujaes at hotmail.co.uk  Thu Mar 25 23:48:03 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Thu, 25 Mar 2010 22:48:03 +0000
Subject: [Pw_forum] graph of band structure of bi layer graphene
In-Reply-To: <426F7881-324F-4130-BF44-0F5C332DF53F@democritos.it>
References: <SNT114-W576B1B38547A98C1CCD199D3240@phx.gbl>,
	<426F7881-324F-4130-BF44-0F5C332DF53F@democritos.it>
Message-ID: <SNT114-W3A0C8BF6F8CD6EF71D0D3D3240@phx.gbl>


Thank you.

 

Elie

 

 

Regards


 
> From: giannozz at democritos.it
> Date: Thu, 25 Mar 2010 22:03:31 +0100
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] graph of band structure of bi layer graphene
> 
> 
> On Mar 25, 2010, at 19:39 , Elie Moujaes wrote:
> 
> > what does the negative rho means
> 
> 
> http://www.quantum-espresso.org/user_guide/node61.html
> 
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
_________________________________________________________________
Tell us your greatest, weirdest and funniest Hotmail stories
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From lfhuang at theory.issp.ac.cn  Fri Mar 26 01:13:30 2010
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Fri, 26 Mar 2010 8:13:30 +0800
Subject: [Pw_forum] =?utf-8?q?one_question_on_=7Cpsi=7C=5E2?=
Message-ID: <20100326001330.21814.qmail@ms.hfcas.ac.cn>

Dear prof. P. Giannozzi:
    Thank you very much for your kind attention and patience!
    From your description, I am clear about the meaning of "that" |psi|^2 (<1) written in the output sentences in projwfc.f90 as I have mentioned. 
Thanks!
Best Wishes!
Yours Sincerely
L. F. Huang

> From: Paolo Giannozzi  
> what are you referring to? to |psi^2| as printed in the line above?
> or to |psi^2| in general? the latter is 1 by construction; the former
> is  tells you how well the projection over atomic states reproduces
> the Kohn-Sham orbitals
> 
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 



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


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From daijiayu at nudt.edu.cn  Fri Mar 26 08:52:51 2010
From: daijiayu at nudt.edu.cn (Jiayu Dai)
Date: Fri, 26 Mar 2010 15:52:51 +0800
Subject: [Pw_forum] internal energy
Message-ID: <IMBZIJQBIDNUMSRIUYLUWUZFKINE.daijiayu@nudt.edu.cn>


 
It is *NOT* any free energy of any physical system. It can be interpreted as the free energy of a system of electrons in the field of clamped nuclei, at the *fictitious* temperature corresponding to the smearing you use. The reason why this concept is useful is that the free energy is variational, while the internal energy is not. That's why Hellman-Feynman forces are derivatives of the free energy, but not of the internal energy.

Thanks Stefano. So, if we want to get the real physical free energy, we should do something else. As far as i know, it is difficult to estimate the free energy. There are several methods calculating it, one of which is from the phonon density of states. But i did not sure this method can be used at high temperature, because the anhormanic effect is important here.


Furthermore, how to get the internal energy here? The kinetic energy is easy to calculate, but how about the potential energy?



You do not need any internal energy. what you may actually want to estimate is the T->0 extrapolation of both the free and internal energies (which coincide in the T->0 limit). I think that some estimate of this are available in the pw output, but others may know more than me about this.

Yes, what you said is what i want. Maybe from the scf calculation, we can get something useful, cause scf gives out more information about energies. So, could some experts can said a little about this problem?

Thank all.

Jiayu


----------------
-------------------------------------------
Jiayu Dai
Department of Physics
National University of Defense Technology, 
Changsha, 410073, P R China
-----------------------------------------
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From baris.malcioglu at gmail.com  Fri Mar 26 10:12:56 2010
From: baris.malcioglu at gmail.com (O. Baris Malcioglu)
Date: Fri, 26 Mar 2010 10:12:56 +0100
Subject: [Pw_forum] internal energy
In-Reply-To: <IMBZIJQBIDNUMSRIUYLUWUZFKINE.daijiayu@nudt.edu.cn>
References: <IMBZIJQBIDNUMSRIUYLUWUZFKINE.daijiayu@nudt.edu.cn>
Message-ID: <ab42ba5f1003260212n1b6a5b4bi570140f6f6b0f99b@mail.gmail.com>

> So, if we want to get the real physical free energy, we should do something else.

Dear Jiayu Dai,

Recently I have attended to an inspiring talk by Michiel Sprik on how
to model a correct water-TiO2 interface in select cases, which, I
think, the methodology  may contain more or less answers related to
your question. At least it certainly contains some well made remarks
on what can be calculated using DFT based methods, and how it can be
related to absolute values employed in chemistry.

The afterwork lead to some papers that I am now working on:
Phys. Chem. Chem. Phys., 2008, 10, 5238-5249
J. Phys. Chem. C, 2008, 112 (26), pp 9872?9879

I hope you find them useful,

O. Baris Malcioglu

2010/3/26 Jiayu Dai <daijiayu at nudt.edu.cn>
>
>
>
> It is *NOT* any free energy of any physical system. It can be interpreted as the free energy of a system of electrons in the field of clamped nuclei, at the *fictitious* temperature corresponding to the smearing you use. The reason why this concept is useful is that the free energy is variational, while the internal energy is not. That's why Hellman-Feynman forces are derivatives of the free energy, but not of the internal energy.
> Thanks Stefano. So, if we want to get the real physical free energy, we should do something else. As far as i know, it is difficult to estimate the free energy. There are several methods calculating it, one of which is from the phonon density of states. But i did not sure this method can be used at high temperature, because the anhormanic effect is important here.
>
>
>
> Furthermore, how to get the internal energy here? The kinetic energy is easy to calculate, but how about the potential energy?
>
> You do not need any internal energy. what you may actually want to estimate is the T->0 extrapolation of both the free and internal energies (which coincide in the T->0 limit). I think that some estimate of this are available in the pw output, but others may know more than me about this.
> Yes, what you said is what i want. Maybe from the scf calculation, we can get something useful, cause scf gives out more information about energies. So, could some experts can said a little about this problem?
>
> Thank all.
>
> Jiayu
>
> ----------------
> -------------------------------------------
> Jiayu?Dai
> Department?of?Physics
> National?University?of?Defense?Technology,
> Changsha,?410073,?P?R?China
> -----------------------------------------
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From daijiayu at nudt.edu.cn  Fri Mar 26 10:25:37 2010
From: daijiayu at nudt.edu.cn (Jiayu Dai)
Date: Fri, 26 Mar 2010 17:25:37 +0800
Subject: [Pw_forum] internal energy
Message-ID: <YOADMFUGPHYDTKOLRIWDJTJPGBML.daijiayu@nudt.edu.cn>

Thanks, Dear Malcioglu. I downloaded the papers you referred. In fact, i think there should be some simple ways to estimate the internal energy. But it seems to be a little difficult.

Thanks.

Jiayu

>

> So, if we want to get the real physical free energy, we should do something else.

Dear Jiayu Dai,

Recently I have attended to an inspiring talk by Michiel Sprik on how
to model a correct water-TiO2 interface in select cases, which, I
think, the methodology  may contain more or less answers related to
your question. At least it certainly contains some well made remarks
on what can be calculated using DFT based methods, and how it can be
related to absolute values employed in chemistry.

The afterwork lead to some papers that I am now working on:
Phys. Chem. Chem. Phys., 2008, 10, 5238-5249
J. Phys. Chem. C, 2008, 112 (26), pp 9872?C9879

I hope you find them useful,

O. Baris Malcioglu

2010/3/26 Jiayu Dai

>
>
>
> It is *NOT* any free energy of any physical system. It can be interpreted as the free energy of a system of electrons in the field of clamped nuclei, at the *fictitious* temperature corresponding to the smearing you use. The reason why this concept is useful is that the free energy is variational, while the internal energy is not. That's why Hellman-Feynman forces are derivatives of the free energy, but not of the internal energy.
> Thanks Stefano. So, if we want to get the real physical free energy, we should do something else. As far as i know, it is difficult to estimate the free energy. There are several methods calculating it, one of which is from the phonon density of states. But i did not sure this method can be used at high temperature, because the anhormanic effect is important here.
>
>
>
> Furthermore, how to get the internal energy here? The kinetic energy is easy to calculate, but how about the potential energy?
>
> You do not need any internal energy. what you may actually want to estimate is the T->0 extrapolation of both the free and internal energies (which coincide in the T->0 limit). I think that some estimate of this are available in the pw output, but others may know more than me about this.
> Yes, what you said is what i want. Maybe from the scf calculation, we can get something useful, cause scf gives out more information about energies. So, could some experts can said a little about this problem?
>
> Thank all.
>
> Jiayu
>
> ----------------
> -------------------------------------------
> JiayuDai
> DepartmentofPhysics
> NationalUniversityofDefenseTechnology,
> Changsha,410073,PRChina
> -----------------------------------------
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

 
----------------
-------------------------------------------
Jiayu Dai
Department of Physics
National University of Defense Technology, 
Changsha, 410073, P R China
-----------------------------------------
From carlo.nervi at unito.it  Fri Mar 26 12:07:15 2010
From: carlo.nervi at unito.it (Carlo Nervi)
Date: Fri, 26 Mar 2010 12:07:15 +0100
Subject: [Pw_forum] B3LYP: two conflicting matching values
Message-ID: <4BAC9563.5090501@unito.it>

Dear PWSCF users and developers,
I recently tried to use the -DEXX option compiling PWSCF (17 March 2010 
version), because I'd like to test b3lyp functional.
Since I did not found much b3lyp PPs, I'm trying to play a little around 
with ld1.x and generate them.
However, if I use dft='b3lyp', the ld1.x exit with the following message:

      from set_dft_value : error #         1
      two conflicting matching values

If I choose another dft (for example hse) there is no error message.
Reading the source code I understood that it could be some overlapping 
with the blyp functional calling the set_dft_value subroutine, but I 
cannot go any further in my thoughts....

Anyone could give a suggestion?

Thanks,
	Carlo

P.S.: the same happens using the atomic_doc/paw_library/input/C.in by 
Lorenzo Paulatto if you modift dft='PBE' into dft='b3lyp'.

-- 
------------------------------------------------------
Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8
Fax: +39 011 6707855   -   Dipartimento di Chimica IFM
via P. Giuria 7, 10125 Torino, Italy
http://lem.ch.unito.it/

From paulatto at sissa.it  Fri Mar 26 12:08:30 2010
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Fri, 26 Mar 2010 12:08:30 +0100
Subject: [Pw_forum] B3LYP: two conflicting matching values
In-Reply-To: <4BAC9563.5090501@unito.it>
References: <4BAC9563.5090501@unito.it>
Message-ID: <op.u9588gq4a8x26q@vanoxite.impmc.jussieu.fr>

On Fri, 26 Mar 2010 12:07:15 +0100, Carlo Nervi <carlo.nervi at unito.it>  
wrote:
> P.S.: the same happens using the atomic_doc/paw_library/input/C.in by
> Lorenzo Paulatto if you modift dft='PBE' into dft='b3lyp'.

PAW does not support BLYP nor exact exchange (yet?) so don't waste your  
time on that.

Unluckily, I have no clue about your primary question.

regards

-- 
Lorenzo Paulatto

*** Note: my affiliation has changed! please send future
correspondence to: <Lorenzo.Paulatto at impmc.upmc.fr> ***

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

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

From carlo.nervi at unito.it  Fri Mar 26 12:36:15 2010
From: carlo.nervi at unito.it (Carlo Nervi)
Date: Fri, 26 Mar 2010 12:36:15 +0100
Subject: [Pw_forum] B3LYP: two conflicting matching values
In-Reply-To: <op.u9588gq4a8x26q@vanoxite.impmc.jussieu.fr>
References: <4BAC9563.5090501@unito.it>
	<op.u9588gq4a8x26q@vanoxite.impmc.jussieu.fr>
Message-ID: <4BAC9C2F.4060107@unito.it>

Thanks Lorenzo,
indeed I'm trying to generate b3lyp using the norm conserving PP.
I was not very clear in my email...
Unfortunately the error message appears in all ceses, including the NC 
PP generation..
In any cases thanks,
	Carlo

Lorenzo Paulatto ha scritto:
> On Fri, 26 Mar 2010 12:07:15 +0100, Carlo Nervi <carlo.nervi at unito.it>  
> wrote:
>> P.S.: the same happens using the atomic_doc/paw_library/input/C.in by
>> Lorenzo Paulatto if you modift dft='PBE' into dft='b3lyp'.
> 
> PAW does not support BLYP nor exact exchange (yet?) so don't waste your  
> time on that.
> 
> Unluckily, I have no clue about your primary question.
> 
> regards
> 


-- 
------------------------------------------------------
Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8
Fax: +39 011 6707855   -   Dipartimento di Chimica IFM
via P. Giuria 7, 10125 Torino, Italy
http://lem.ch.unito.it/

From elbuesta at icqmail.com  Fri Mar 26 12:39:08 2010
From: elbuesta at icqmail.com (elbuesta at icqmail.com)
Date: Fri, 26 Mar 2010 07:39:08 -0400
Subject: [Pw_forum] Occupation matrix in LDA+U
In-Reply-To: <4BABCF15.2050702@umn.edu>
References: <4BABCF15.2050702@umn.edu>
Message-ID: <8CC9AF014EFD7BA-EA8-102D4@webmail-m053.sysops.aol.com>

 Dear Dr. Cococcioni,

Thanks very much for your explanation and your tips. They were very valuable.

All best!

 



-----Original Message-----
From: Matteo Cococcioni &lt;matteo at umn.edu&gt;
To: PWSCF Forum &lt;pw_forum at pwscf.org&gt;
Sent: Thu, Mar 25, 2010 10:01 pm
Subject: Re: [Pw_forum] Occupation matrix in LDA+U

 
 
 
 
Dear Luca and Fabio 
 
here are my answers. 
 
1) the diagonal elements of the occupation matrix are the projection on  
the atomic orbitals in the order 
you wrote. Of course also non diagonal elements are associated with d  
orbitals. they are not projection strictly 
speaking but you can see them as generalized overlap terms between d  
atomic orbitals in the subspace of occupied Kohn-Sham states. 
 
2) yes. from Doc/INPUT_PW: 
 
   +-------------------------------------------------------------------- 
   Variable:       starting_ns_eigenvalue(m,ispin,I) 
 
   Type:           REAL 
   Default:        -1.d0 that means NOT SET 
   Description:    In the first iteration of an LDA+U run it overwrites 
                   the m-th eigenvalue of the ns occupation matrix for the 
                   ispin component of atomic species I. Leave unchanged 
                   eigenvalues that are not set. This is useful to suggest 
                   the desired orbital occupations when the default choice 
                   takes another path. 
   +-------------------------------------------------------------------- 
 
keep in mind that you are adjusting the eigenvalue of the matrix. So you  
better give a look at the occupation matrix 
and its spectrum after the first iteration of a non constraint run. 
 
hope this helps, 
 
Matteo 
 
 
 
elbuesta at icqmail.com wrote: 
&gt; Dear all, 
&gt; 
&gt; We have a fews questions/doubts concerning the ns occupation matrix  
&gt; for LDA+U calculations (starting_ns_eigenvalue(m,ispin,I)). Following  
&gt; the idea presented in example 25 of quantum espresso, we are trying to  
&gt; fix the initial occupation of the "d" orbital of Ni in a monolayer of  
&gt; NiO in an anti-ferromagnetic state. The questions we have are: 
&gt; 
&gt; 1) Are each of the diagonal elements of the occupation matrix  
&gt; associated with the d orbitals? Something like, 
&gt; (1,1) -&gt; dz2, (2,2) -&gt; dzx, (3,3) -&gt; dzy, (4,4) -&gt; d(x2-y2) and  (5,5)  
&gt; -&gt; dxy   ? 
&gt; 2) If there is this correspondence, is it possible to specify an  
&gt; initial occupation of each of the orbitals after the initial guess is  
&gt; evaluated in the first iteration? For example, in the attached input,  
&gt; how could we specify that only the dz2, dxz and dyz orbitals are  
&gt; initially completely occupied with 2 electrons? In other words, how  
&gt; can we change the "spin down occupation matrix" of the Ni atom from 
&gt; 0.6 0.0 0.0 0.0 0.0            1.0 0.0 0.0 0.0 0.0 
&gt; 0.0 0.6 0.0 0.0 0.0            0.0 1.0 0.0 0.0 0.0 
&gt; 0.0 0.0 0.6 0.0 0.0     -&gt;    0.0 0.0 1.0 0.0 0.0 
&gt; 0.0 0.0 0.0 0.6 0.0            0.0 0.0 0.0 0.0 0.0 
&gt; 0.0 0.0 0.0 0.0 0.6            0.0 0.0 0.0 0.0 0.0 
&gt; ?? 
&gt; 
&gt; Thanks very much for your time, 
&gt; With best regards, 
&gt; 
&gt; Luca Sementa, F?bio Negreiros 
&gt; Postdoc students, 
&gt; IPCF - CNR - Pisa, Italy 
&gt; 
&gt; = 
&gt; ------------------------------------------------------------------------ 
&gt; 
&gt; _______________________________________________ 
&gt; Pw_forum mailing list 
&gt; Pw_forum at pwscf.org 
&gt; http://www.democritos.it/mailman/listinfo/pw_forum 
 
_______________________________________________ 
Pw_forum mailing list 
Pw_forum at pwscf.org 
http://www.democritos.it/mailman/listinfo/pw_forum 
 

 

=
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From carlo.nervi at unito.it  Fri Mar 26 13:42:15 2010
From: carlo.nervi at unito.it (Carlo Nervi)
Date: Fri, 26 Mar 2010 13:42:15 +0100
Subject: [Pw_forum] B3LYP: two conflicting matching values
In-Reply-To: <op.u9588gq4a8x26q@vanoxite.impmc.jussieu.fr>
References: <4BAC9563.5090501@unito.it>
	<op.u9588gq4a8x26q@vanoxite.impmc.jussieu.fr>
Message-ID: <4BACABA7.9050002@unito.it>

I apologize to everybody...
it seems that it was a my mistake. I used again ld1.x and the errors 
does not pop up any more.... Very probably i was mixing different ld1.x 
compiled versions...
Sorry,
	Carlo

Lorenzo Paulatto ha scritto:
> On Fri, 26 Mar 2010 12:07:15 +0100, Carlo Nervi <carlo.nervi at unito.it>  
> wrote:
>> P.S.: the same happens using the atomic_doc/paw_library/input/C.in by
>> Lorenzo Paulatto if you modift dft='PBE' into dft='b3lyp'.
> 
> PAW does not support BLYP nor exact exchange (yet?) so don't waste your  
> time on that.
> 
> Unluckily, I have no clue about your primary question.
> 
> regards
> 


-- 
------------------------------------------------------
Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8
Fax: +39 011 6707855   -   Dipartimento di Chimica IFM
via P. Giuria 7, 10125 Torino, Italy
http://lem.ch.unito.it/

From sks.jnc at gmail.com  Fri Mar 26 14:07:44 2010
From: sks.jnc at gmail.com (S. K. S.)
Date: Fri, 26 Mar 2010 18:37:44 +0530
Subject: [Pw_forum] flow-chart in PWSCF
In-Reply-To: <4BA0E2B4.7020401@democritos.it>
References: <d5eefb3d1003170352s6dd97f66j36e6475b21960e10@mail.gmail.com>
	<4BA0E2B4.7020401@democritos.it>
Message-ID: <d5eefb3d1003260607u6b7c982eg4cf535b98d100f51@mail.gmail.com>

  Dear All,

  At first, let me take this opportunity to thank Prof. Paolo for his
helpful reply.
A part of his reply is given here:

>>     I mean, PWSCF check energy convergence or
>>     density scf convergence or both?

> the latter. More detials in the QE paper.

  Now just to be fully sure, I would like to ask, does  PWSCF follow
the attached flow-chart (Please see the attached file) where
density-convergence is being checked????
On the other hand, in the earlier link:
 http://cms.mpi.univie.ac.at/vasp/vasp/node199.html
energy-convergence had been checked.
 I believe, both the flowcharts  are more or less same within
a technical difference. Am I right?

 Looking forward to your further comments.

 Thanking you and with my best regards,
  Saha SK
   R&D Assistant
  JNCASR
  Bangalore
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From dalcorso at sissa.it  Fri Mar 26 14:15:06 2010
From: dalcorso at sissa.it (Dal Corso Andrea)
Date: Fri, 26 Mar 2010 14:15:06 +0100
Subject: [Pw_forum] B3LYP: two conflicting matching values
In-Reply-To: <4BACABA7.9050002@unito.it>
References: <4BAC9563.5090501@unito.it>
	<op.u9588gq4a8x26q@vanoxite.impmc.jussieu.fr>
	<4BACABA7.9050002@unito.it>
Message-ID: <1269609306.3254.3.camel@dhcp-5-36.sissa.it>

On Fri, 2010-03-26 at 13:42 +0100, Carlo Nervi wrote:
> I apologize to everybody...
> it seems that it was a my mistake. I used again ld1.x and the errors 
> does not pop up any more.... Very probably i was mixing different ld1.x 
> compiled versions...
> Sorry,
> 	Carlo

Presently ld1.x does not support hybrid functionals. As far as I know, 
so far nobody has implemented it. 

Andrea



> 
> Lorenzo Paulatto ha scritto:
> > On Fri, 26 Mar 2010 12:07:15 +0100, Carlo Nervi <carlo.nervi at unito.it>  
> > wrote:
> >> P.S.: the same happens using the atomic_doc/paw_library/input/C.in by
> >> Lorenzo Paulatto if you modift dft='PBE' into dft='b3lyp'.
> > 
> > PAW does not support BLYP nor exact exchange (yet?) so don't waste your  
> > time on that.
> > 
> > Unluckily, I have no clue about your primary question.
> > 
> > regards
> > 
> 
> 
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
34151 Trieste (Italy)               e-mail: dalcorso at sissa.it



From nnlinh at sissa.it  Fri Mar 26 15:11:13 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Fri, 26 Mar 2010 15:11:13 +0100
Subject: [Pw_forum] flow-chart in PWSCF
In-Reply-To: <d5eefb3d1003260607u6b7c982eg4cf535b98d100f51@mail.gmail.com>
References: <d5eefb3d1003170352s6dd97f66j36e6475b21960e10@mail.gmail.com>	<4BA0E2B4.7020401@democritos.it>
	<d5eefb3d1003260607u6b7c982eg4cf535b98d100f51@mail.gmail.com>
Message-ID: <4BACC081.8030504@sissa.it>

S. K. S. wrote:
>
>   Now just to be fully sure, I would like to ask, does  PWSCF follow
> the attached flow-chart (Please see the attached file) where
> density-convergence is being checked????
>   
I think after step of "mixing charge density" where to create a new 
density, a density convergence will be checked.
And a  faster Harris-Foulkes estimation will also be calculated, which 
based on new density and previous density, to justify the convergence 
belong to energy.

> On the other hand, in the earlier link:
>  http://cms.mpi.univie.ac.at/vasp/vasp/node199.html
> energy-convergence had been checked.
>   
In general, the scf processes are similar, but in QE a density 
convergence check is applied to accelerate convergence in scf 
caculation, i.e. see in PRB 38,  12807 (1988).
 
Linh
>  
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From carlo.nervi at unito.it  Fri Mar 26 15:52:15 2010
From: carlo.nervi at unito.it (Carlo Nervi)
Date: Fri, 26 Mar 2010 15:52:15 +0100
Subject: [Pw_forum] B3LYP: two conflicting matching values
In-Reply-To: <1269609306.3254.3.camel@dhcp-5-36.sissa.it>
References: <4BAC9563.5090501@unito.it>	<op.u9588gq4a8x26q@vanoxite.impmc.jussieu.fr>	<4BACABA7.9050002@unito.it>
	<1269609306.3254.3.camel@dhcp-5-36.sissa.it>
Message-ID: <4BACCA1F.7030505@unito.it>

Dal Corso Andrea ha scritto:
> On Fri, 2010-03-26 at 13:42 +0100, Carlo Nervi wrote:
>> I apologize to everybody...
>> it seems that it was a my mistake. I used again ld1.x and the errors 
>> does not pop up any more.... Very probably i was mixing different ld1.x 
>> compiled versions...
>> Sorry,
>> 	Carlo
> 
> Presently ld1.x does not support hybrid functionals. As far as I know, 
> so far nobody has implemented it. 
> 
> Andrea
> 
???
This is confusing to me...

I managed to generate a NC b3lyp PP, and apparently it works in PWSCF 
(compiled with -DEXX). Apparently a simple scf test worked out...
Of course, I had still no time to check whether this b3lyp PP is 
reliable or not... but this should be (I think) another question...

Am I wrong?
	Carlo

-- 
------------------------------------------------------
Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8
Fax: +39 011 6707855   -   Dipartimento di Chimica IFM
via P. Giuria 7, 10125 Torino, Italy
http://lem.ch.unito.it/

From dalcorso at sissa.it  Fri Mar 26 15:59:59 2010
From: dalcorso at sissa.it (Dal Corso Andrea)
Date: Fri, 26 Mar 2010 15:59:59 +0100
Subject: [Pw_forum] B3LYP: two conflicting matching values
In-Reply-To: <4BACCA1F.7030505@unito.it>
References: <4BAC9563.5090501@unito.it>
	<op.u9588gq4a8x26q@vanoxite.impmc.jussieu.fr>	<4BACABA7.9050002@unito.it>
	<1269609306.3254.3.camel@dhcp-5-36.sissa.it>
	<4BACCA1F.7030505@unito.it>
Message-ID: <1269615599.3254.36.camel@dhcp-5-36.sissa.it>

On Fri, 2010-03-26 at 15:52 +0100, Carlo Nervi wrote:
> Dal Corso Andrea ha scritto:
> > On Fri, 2010-03-26 at 13:42 +0100, Carlo Nervi wrote:
> >> I apologize to everybody...
> >> it seems that it was a my mistake. I used again ld1.x and the errors 
> >> does not pop up any more.... Very probably i was mixing different ld1.x 
> >> compiled versions...
> >> Sorry,
> >> 	Carlo
> > 
> > Presently ld1.x does not support hybrid functionals. As far as I know, 
> > so far nobody has implemented it. 
> > 
> > Andrea
> > 
> ???
> This is confusing to me...
> 
> I managed to generate a NC b3lyp PP, and apparently it works in PWSCF 
> (compiled with -DEXX). Apparently a simple scf test worked out...
> Of course, I had still no time to check whether this b3lyp PP is 
> reliable or not... but this should be (I think) another question...
> 
> Am I wrong?
> 	Carlo

Probably ld1.x should stop in this case writing some message, but B3LYP
is a new feature and not all codes have been updated. 

Andrea


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



From kacsssj at gmail.com  Fri Mar 26 20:13:14 2010
From: kacsssj at gmail.com (Keitel Cervantes Salguero)
Date: Fri, 26 Mar 2010 20:13:14 +0100
Subject: [Pw_forum] PP generation for specific exchange and correlation
Message-ID: <5f526cf51003261213x26bf3ec9yef45f9f5941ee5ea@mail.gmail.com>

Dear people,

I want to generate a PP with the OPTX for exchange and PBE for correlation.
Would you, please, recommend me a program ?
And also if there is a suitable scheme (hamman, TM .. ) for the PP generation of
a transition metal, considering that I want to use core correction.

Any suggestion is always welcome.
Many thanks in advanced.

Best Regards



-- 
Atte.
Keitel Cervantes Salguero
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From ihsanas at yahoo.com  Sun Mar 28 13:51:42 2010
From: ihsanas at yahoo.com (Ihsan Erikat)
Date: Sun, 28 Mar 2010 04:51:42 -0700 (PDT)
Subject: [Pw_forum] value of adir
Message-ID: <234069.25132.qm@web52307.mail.re2.yahoo.com>

Dear all

I want to do a dipole correction for a system? of adsorbed over a
slab of 5 atomic layers.and about 8 layers of? avaccum.? How
can I choose the righet value for edir (1, 2, 3) , eamp, eophey.



best regards

Ihsan Erikat

Jordan University




      
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From nnlinh at sissa.it  Sun Mar 28 18:46:03 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Sun, 28 Mar 2010 18:46:03 +0200
Subject: [Pw_forum] value of adir
In-Reply-To: <234069.25132.qm@web52307.mail.re2.yahoo.com>
References: <234069.25132.qm@web52307.mail.re2.yahoo.com>
Message-ID: <4BAF87CB.9020908@sissa.it>

Ihsan Erikat wrote:
> Dear all
> I want to do a dipole correction for a system  of adsorbed over a slab 
> of 5 atomic layers.and about 8 layers of  avaccum. 
>
Meanings of the input parameters for dipole correction can be seen in

> How can I choose the righet value for edir (1, 2, 3) , eamp, eophey.
>
- In your case, the vacuum space belong to z axis,  edir = 3.

- In order to have an accuracy of the "eamp" values, you should 
calculate the "V_bare + V_H potential" by pp.x and estimate "eamp" by 
the highness of slope of the V_bare + V_H potential in vacuum place of 
the unit cell, that is effected by dipole interactions (if dipole 
doesn't present the slope should equal 0), but it is normally very small 
to estimate, so you can let it equals to default value.

- About "eophey" ??? I don't know what you mean? Maybe you want know 
about  "eopreg", it is the zone in vacuum place of unit cell in which a 
slope of the "V_bare+ V_H potential" presents.

Good luck,

Linh
> best regards
> Ihsan Erikat
> Jordan University
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From glaweh at physik.fu-berlin.de  Sun Mar 28 21:05:35 2010
From: glaweh at physik.fu-berlin.de (Henning Glawe)
Date: Sun, 28 Mar 2010 21:05:35 +0200
Subject: [Pw_forum] Fortran compiler
In-Reply-To: <20100324122501.19112igszmanu8ow@www.ehu.es>
References: <C7C644C8.1AC9%Trinh.Vo@jpl.nasa.gov>
	<896650C5-FEAD-4471-8324-6E3320A5441D@democritos.it>
	<20100324122501.19112igszmanu8ow@www.ehu.es>
Message-ID: <20100328190535.GA4146@ford.simpsons.bogus>

On Wed, Mar 24, 2010 at 12:25:01PM +0100, Miguel Martinez Canales wrote:
> Dear all,
> 
> Following Paolo's warning, I've performed some tests with a not so  
> surprising result: Paolo was right. For some reason, the ubuntu 9.10  
> builds of gfortran 4.3 and 4.4.1 give astonishingly different results  
> for example07. Well, the pw.x output is the same as in the reference,  
> but the lambda values... at least they are of the same order of  
> magnitude. Mind you, for once this is not an ubuntu bug, as it also  
> happens in self-compiled gfortran 4.4.3 (Red Hat 5.4 in this case).  
> However, the differences in lambda don't seem important in the case of  
> gfortran 4.1.2 (the default in Red Hat) or 4.2.4 (the oldest version  
> available in ubuntu 9.10).
> 
> I'm going to check other examples to see whether there are very  
> different phonon frequencies elsewhere, but I don't expect anything  
> good at all.

I am in contact with one of the gfortran developers, and reported the problem
with ph.x to him; he now spent quite some time tracing the problem down, and
apparently there is a patch on-queue:
http://gcc.gnu.org/bugzilla/show_bug.cgi?id=43551#c10

-- 
c u
henning

From tkaloni at gmail.com  Mon Mar 29 14:27:50 2010
From: tkaloni at gmail.com (Thaneshwor Kaloni)
Date: Mon, 29 Mar 2010 17:57:50 +0530
Subject: [Pw_forum] hi
Message-ID: <aecd86391003290527k5db0da88xc10b6aa4d4cfc002@mail.gmail.com>

Dear all
I am running programme  to  calculate the band structure of graphene,
but I am not getting it.
Please  , help!
sincerely









###################################
******************************************
Thaneshwor Prashad Kaloni
TWAS-BOSE FELLOW /JRF
S N Bose national Centre for Basic Sciences
Kolkata 700098,
INDIA
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From nnlinh at sissa.it  Mon Mar 29 14:30:58 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Mon, 29 Mar 2010 14:30:58 +0200
Subject: [Pw_forum] hi
In-Reply-To: <aecd86391003290527k5db0da88xc10b6aa4d4cfc002@mail.gmail.com>
References: <aecd86391003290527k5db0da88xc10b6aa4d4cfc002@mail.gmail.com>
Message-ID: <4BB09D82.1000101@sissa.it>

Thaneshwor Kaloni wrote:
> Dear all
> I am running programme  to  calculate the band structure of graphene,
> but I am not getting it.
Hardly to image what is your problems. Can you specify more about your 
problem, such as: what did you do? or what is error you got?

There are some questions about Graphene band structures published in 
PW_forum previously.

Linh

> Please  , help!
> sincerely
>
>
>
>
>
>
>
>
>
> ###################################
> ******************************************
> Thaneshwor Prashad Kaloni
> TWAS-BOSE FELLOW /JRF
> S N Bose national Centre for Basic Sciences
> Kolkata 700098,
> INDIA
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From sheena.shah at materials.ox.ac.uk  Mon Mar 29 19:43:21 2010
From: sheena.shah at materials.ox.ac.uk (Sheena Shah)
Date: Mon, 29 Mar 2010 18:43:21 +0100
Subject: [Pw_forum] Phonon calculations - separating modes
Message-ID: <C08332C9F3ACC344A118400525375BC723437FBC3A@EXMBX06.ad.oak.ox.ac.uk>

Dear all

I am trying to run a phonon calculation (ph.x) by splitting up the modes into different calculations using start_irr and last_irr.  I am having troubles in the recombination process to create a phonon dispersion.  The frequencies are correct but I am unable to use the potential file (dv1) for  doing electron phonon coupling calculations.  Can someone please help me with this?

Many thanks

Sheena Shah
University of Oxford
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From Trinh.Vo at jpl.nasa.gov  Mon Mar 29 20:12:46 2010
From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Mon, 29 Mar 2010 11:12:46 -0700
Subject: [Pw_forum] Phonon calculations - separating modes
In-Reply-To: <C08332C9F3ACC344A118400525375BC723437FBC3A@EXMBX06.ad.oak.ox.ac.uk>
Message-ID: <C7D63BAE.1DD4%Trinh.Vo@jpl.nasa.gov>

Thanks chi Lanh.  I sent the check (for charity) yesterday.  Whenever you receive it, could you let me know.  I just would like to make sure the check is not lost.

Thanks a lot,

Trinh

P.S.  Yesterday, Si~ emailed.  He said that PTTA told hime to meditate more hours (at least 3h per night).  It is more urgent now.  I guess sth is about to happen.  That is why PTTA urges him to meditate.  He said that a few more years he and anh Loc will go to ?Vung Kinh Te moi?.  I guess he meant VN.


On 3/29/10 10:43 AM, "Sheena Shah" <sheena.shah at materials.ox.ac.uk> wrote:

Dear all

I am trying to run a phonon calculation (ph.x) by splitting up the modes into different calculations using start_irr and last_irr.  I am having troubles in the recombination process to create a phonon dispersion.  The frequencies are correct but I am unable to use the potential file (dv1) for  doing electron phonon coupling calculations. Can someone please help me with this?

Many thanks

Sheena Shah
University of Oxford

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From Trinh.Vo at jpl.nasa.gov  Mon Mar 29 20:18:35 2010
From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Mon, 29 Mar 2010 11:18:35 -0700
Subject: [Pw_forum] Sorry for mis-sending an email
Message-ID: <C7D63D0B.1DD6%Trinh.Vo@jpl.nasa.gov>

Dear PWSCF Users,

I apologize for the previous email.  I sent to a friend, but clicked to the wrong place.

Trinh
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From sheena.shah at materials.ox.ac.uk  Mon Mar 29 21:19:41 2010
From: sheena.shah at materials.ox.ac.uk (Sheena Shah)
Date: Mon, 29 Mar 2010 20:19:41 +0100
Subject: [Pw_forum] Phonon calculations - separating modes
In-Reply-To: <A069E197366113458C4E58F1B32326181D517E1025@EXMBX06.ad.oak.ox.ac.uk>
References: <A069E197366113458C4E58F1B32326181D517E1025@EXMBX06.ad.oak.ox.ac.uk>
Message-ID: <C08332C9F3ACC344A118400525375BC723437FBC3E@EXMBX06.ad.oak.ox.ac.uk>

Dear all,



Further to my previous email, here are some more details:



I have been running tests for phonon calculations by splitting up the modes for each q-point using start_irr and last_irr input parameters (an example of the input file used for the Gamma-point is given below).  I was able to obtain the correct frequencies at each q-point by collecting all data-file.xml.#iq.#irr files in one directory and running ph.x one last time.



As a final step I was planning to run an electron-phonon calculation. The problem I encountered was that at the end of a phonon calculation performed as described above I do not have a correct deformation potential file (a different *.dv1 file is obtained depending on the start_irr and last_irr parameters). I noticed that for the calculation where last_irr is equal to the last irreducible representation the *.dv1 file has the same size as the one from a calculation performed over all representations at once. However, the electron-phonon parameters obtained using these two files are very different. Is there a way I could recover the correct deformation potential at the end of an irreducible-split phonon calculation?



&inputph

  tr2_ph=1.0d-14,

  prefix='c',

  fildvscf='dv',

  amass(1)=12.011,

  outdir='./',

  fildyn='c.dyn',

  trans=.true.,

  lnscf=.true.,

  strart_irr=1,

  last_irr=3

 /

 0.000000000 0.000000000 0.000000000



Thank you for your help.



Sheena Shah

sheena.shah at materials.ox.ac.uk<mailto:Sheena.shah at materials.ox.ac.uk>

University of Oxford

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From elie.moujaes at hotmail.co.uk  Mon Mar 29 21:32:45 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Mon, 29 Mar 2010 20:32:45 +0100
Subject: [Pw_forum] Input to calculate band structure of bi layer graphene
Message-ID: <SNT114-W2918172B18B24DDA4CCAFD3200@phx.gbl>


Dear all,

 

I am trying to get the band structure of bi layer graphene but I am not quite sure about the input..I am using experimental values for a and c..Of course a= 2.46 A and c=6.7079 A. Also for bilayer graphene we have 4 atoms per unit cell..what is confusing me is the distance between the layers within one bilyaer primitive cell. I read that the distance between one layer and the other within the bi layer primitive cell is 0.5 c= 3.35 A. this means that the interaction between the upper layer of one bilayer primitive cell and the lower layer of the next one is also 0.5c because the whole distance is c.

 

 

My question is shouldnt the distance within the same primitive cell be less than that between one end of a bilayer primitive cell and the other end of the next one because as far as I know (not sure if I have this as a misconception), Qunatum Espresso produces images of the main primitive cell and in my case the next image must be further away so that no interaction would happen between all layers which would then be a model for graphite. My input for atomic positions and a and c are as follows:

 

 

  celldm(1) =4.608737, celldm(3)=2.725459
   
  /
ATOMIC_SPECIES
 C  12.00000  C.pz-rrkjus.UPF
ATOMIC_POSITIONS crystal
 C 0.000000  0.000000  0.000000  
 C 0.000000  0.000000  0.500000  
 C 0.333333  -0.33333  0.000000  
 C -0.333333  0.33333  0.500000  

 

 

Hope someone can give me advise or suggestions on this matter.. Thank you

 

 

Elie Moujaes

University of Nottingham

NG7 2RD

UK
 		 	   		  
_________________________________________________________________
Send us your Hotmail stories and be featured in our newsletter
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From pbsorokin at gmail.com  Mon Mar 29 21:48:00 2010
From: pbsorokin at gmail.com (Pavel B Sorokin)
Date: Mon, 29 Mar 2010 14:48:00 -0500
Subject: [Pw_forum] Input to calculate band structure of bi layer
	graphene
In-Reply-To: <SNT114-W2918172B18B24DDA4CCAFD3200@phx.gbl>
References: <SNT114-W2918172B18B24DDA4CCAFD3200@phx.gbl>
Message-ID: <452252731.20100329144800@gmail.com>

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From mohnish.iitk at gmail.com  Tue Mar 30 06:47:31 2010
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Tue, 30 Mar 2010 10:17:31 +0530
Subject: [Pw_forum] phonon calculation for silicon
Message-ID: <c40d64601003292147h63f2c48cw78456ba566d5d750@mail.gmail.com>

Dear QE users,
                        I am trying to do the example 2(phonon dispersion
relation) but I am getting some error. I am pasting my input and output file
below. Please tell me where I am going wrong.
Thanks a lot in advance.
MOHNISH

*INPUT FOR SCF CALCULATION*

&control
    calculation='scf',
    restart_mode='restart',
    prefix='si'
    pseudo_dir = '/home/rajpala/Desktop/phonon',
    outdir='/home/rajpala/Desktop/phonon'
 /
 &system
    ibrav = 2, celldm(1) =10.20, nat=  2, ntyp= 1,
    ecutwfc = 30.0
 /
 &electrons
    mixing_beta = 0.7
    conv_thr =  1.0d-8
 /
ATOMIC_SPECIES
 Si  28.086  SiPBE-rrkj.UPF
ATOMIC_POSITIONS
 Si 0.00 0.00 0.00
 Si 0.25 0.25 0.25
K_POINTS (automatic)
  6 6 6 0 0 0

*INPUT FOR PH.X *

&INPUTPH
  amass(1)=28.086
  outdir='/home/rajpala/Desktop/phonon'
  prefix='si'
  tr2_ph=1.0d-14
  fildyn='si.dynG
  epsil=.true.
 /
0.0 0.0 0.0

*OUTPUT*

Program PHONON    v.4.1.1  starts ...
     Today is 29Mar2010 at 11:24:23

     Parallel version (MPI)

     Number of processors in use:       1

     Ultrasoft (Vanderbilt) Pseudopotentials

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from phq_readin : error #         1
     reading inputph namelist
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
p0_16851:  p4_error: : 0

-- 
Mohnish Pandey
Y6927262,4th Year dual degree student,
Department of Chemical Engineering,
IIT KANPUR
09235721300
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From ackaur at ucdavis.edu  Tue Mar 30 06:57:28 2010
From: ackaur at ucdavis.edu (Amandeep Kaur)
Date: Mon, 29 Mar 2010 21:57:28 -0700
Subject: [Pw_forum] phonon calculation for silicon
In-Reply-To: <c40d64601003292147h63f2c48cw78456ba566d5d750@mail.gmail.com>
References: <c40d64601003292147h63f2c48cw78456ba566d5d750@mail.gmail.com>
Message-ID: <45e2e0d21003292157g588de7f3rcdd31e995beb62b1@mail.gmail.com>

You need to give the title (a line header ) at the beginning of phonon input
file.

On Mon, Mar 29, 2010 at 9:47 PM, mohnish pandey <mohnish.iitk at gmail.com>wrote:

> Dear QE users,
>                         I am trying to do the example 2(phonon dispersion
> relation) but I am getting some error. I am pasting my input and output file
> below. Please tell me where I am going wrong.
> Thanks a lot in advance.
> MOHNISH
>
> *INPUT FOR SCF CALCULATION*
>
> &control
>     calculation='scf',
>     restart_mode='restart',
>     prefix='si'
>     pseudo_dir = '/home/rajpala/Desktop/phonon',
>     outdir='/home/rajpala/Desktop/phonon'
>  /
>  &system
>     ibrav = 2, celldm(1) =10.20, nat=  2, ntyp= 1,
>     ecutwfc = 30.0
>  /
>  &electrons
>     mixing_beta = 0.7
>     conv_thr =  1.0d-8
>  /
> ATOMIC_SPECIES
>  Si  28.086  SiPBE-rrkj.UPF
> ATOMIC_POSITIONS
>  Si 0.00 0.00 0.00
>  Si 0.25 0.25 0.25
> K_POINTS (automatic)
>   6 6 6 0 0 0
>
> *INPUT FOR PH.X *
>
> &INPUTPH
>   amass(1)=28.086
>   outdir='/home/rajpala/Desktop/phonon'
>   prefix='si'
>   tr2_ph=1.0d-14
>   fildyn='si.dynG
>   epsil=.true.
>  /
> 0.0 0.0 0.0
>
> *OUTPUT*
>
> Program PHONON    v.4.1.1  starts ...
>      Today is 29Mar2010 at 11:24:23
>
>      Parallel version (MPI)
>
>      Number of processors in use:       1
>
>      Ultrasoft (Vanderbilt) Pseudopotentials
>
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from phq_readin : error #         1
>      reading inputph namelist
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>      stopping ...
> p0_16851:  p4_error: : 0
>
> --
> Mohnish Pandey
> Y6927262,4th Year dual degree student,
> Department of Chemical Engineering,
> IIT KANPUR
> 09235721300
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Amandeep Kaur
Graduate Student
Department of Physics
University of California,Davis
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From mohnish.iitk at gmail.com  Tue Mar 30 07:07:30 2010
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Tue, 30 Mar 2010 10:37:30 +0530
Subject: [Pw_forum] phonon calculation for silicon
In-Reply-To: <45e2e0d21003292157g588de7f3rcdd31e995beb62b1@mail.gmail.com>
References: <c40d64601003292147h63f2c48cw78456ba566d5d750@mail.gmail.com>
	<45e2e0d21003292157g588de7f3rcdd31e995beb62b1@mail.gmail.com>
Message-ID: <c40d64601003292207y26c652e0i55851019ab967cc4@mail.gmail.com>

Thanks Dear Amandeep...It woked..
MOHNISH

On Tue, Mar 30, 2010 at 10:27 AM, Amandeep Kaur <ackaur at ucdavis.edu> wrote:

> You need to give the title (a line header ) at the beginning of phonon
> input file.
>
> On Mon, Mar 29, 2010 at 9:47 PM, mohnish pandey <mohnish.iitk at gmail.com>wrote:
>
>> Dear QE users,
>>                         I am trying to do the example 2(phonon dispersion
>> relation) but I am getting some error. I am pasting my input and output file
>> below. Please tell me where I am going wrong.
>> Thanks a lot in advance.
>> MOHNISH
>>
>> *INPUT FOR SCF CALCULATION*
>>
>> &control
>>     calculation='scf',
>>     restart_mode='restart',
>>     prefix='si'
>>     pseudo_dir = '/home/rajpala/Desktop/phonon',
>>     outdir='/home/rajpala/Desktop/phonon'
>>  /
>>  &system
>>     ibrav = 2, celldm(1) =10.20, nat=  2, ntyp= 1,
>>     ecutwfc = 30.0
>>  /
>>  &electrons
>>     mixing_beta = 0.7
>>     conv_thr =  1.0d-8
>>  /
>> ATOMIC_SPECIES
>>  Si  28.086  SiPBE-rrkj.UPF
>> ATOMIC_POSITIONS
>>  Si 0.00 0.00 0.00
>>  Si 0.25 0.25 0.25
>> K_POINTS (automatic)
>>   6 6 6 0 0 0
>>
>> *INPUT FOR PH.X *
>>
>> &INPUTPH
>>   amass(1)=28.086
>>   outdir='/home/rajpala/Desktop/phonon'
>>   prefix='si'
>>   tr2_ph=1.0d-14
>>   fildyn='si.dynG
>>   epsil=.true.
>>  /
>> 0.0 0.0 0.0
>>
>> *OUTPUT*
>>
>> Program PHONON    v.4.1.1  starts ...
>>      Today is 29Mar2010 at 11:24:23
>>
>>      Parallel version (MPI)
>>
>>      Number of processors in use:       1
>>
>>      Ultrasoft (Vanderbilt) Pseudopotentials
>>
>>
>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>      from phq_readin : error #         1
>>      reading inputph namelist
>>
>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>>      stopping ...
>> p0_16851:  p4_error: : 0
>>
>> --
>> Mohnish Pandey
>> Y6927262,4th Year dual degree student,
>> Department of Chemical Engineering,
>> IIT KANPUR
>> 09235721300
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> Amandeep Kaur
> Graduate Student
> Department of Physics
> University of California,Davis
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Mohnish Pandey
Y6927262,4th Year dual degree student,
Department of Chemical Engineering,
IIT KANPUR
09235721300
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From mueni_sylvia at yahoo.com  Tue Mar 30 17:01:31 2010
From: mueni_sylvia at yahoo.com (sylvia mueni)
Date: Tue, 30 Mar 2010 08:01:31 -0700 (PDT)
Subject: [Pw_forum] (no subject)
Message-ID: <743658.31414.qm@web44715.mail.sp1.yahoo.com>

hi im working on the latice constants of BaF2. I have a problem in determining the atomic positions of the hexagonal phase.
please help
 
thanks,
sylvia


      
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From asubedi at gmail.com  Wed Mar 31 01:27:06 2010
From: asubedi at gmail.com (asubedi)
Date: Tue, 30 Mar 2010 19:27:06 -0400
Subject: [Pw_forum] projector for local channel in ultrasoft pseudopotential
Message-ID: <532cb13c1003301627q75dc8729i3c9df4c697d5599d@mail.gmail.com>

Dear all,

I am a complete newbie trying to create an ultrasoft pseudopotential
for bismuth. I would like to use l=1 for the local part and I also
want projectors for it.  So I have (excluding other valence electrons)

6P  2  1  2.00  0.00  3.10  3.20  0.5
6P  2  1  0.00 -0.50  3.10  3.20  0.5
6P  2  1  1.00  0.00  3.10  3.20  1.5
6P  2  1  0.00 -0.50  3.10  3.20  1.5

However, the code gives an error:

     from ld1_readin : error #         1
     only one local channel

Am I right in concluding that ld1.x cannot make ultasoft
pseudopotential for the local channel? I checked the formula for
decomposition of pseudopotential to local plus nonlocal part. For the
nonlocal part, summation is over l=0 to lmax and does not exclude
l_local.

Thanks,
Alaska
UTK and ORNL

From tkaloni at gmail.com  Wed Mar 31 10:15:36 2010
From: tkaloni at gmail.com (Thaneshwor Kaloni)
Date: Wed, 31 Mar 2010 13:45:36 +0530
Subject: [Pw_forum] hi
Message-ID: <y2xaecd86391003310115kdc151722pf58bea78bf046486@mail.gmail.com>

Dear all,
I am unable to get the seedname.eig file when ever running it, this is
showing some error as follows.
Anybody may help me!!!

     Program POST-PROC v.4.1.2  starts ...
     Today is 31Mar2010 at 11:32:28

     Parallel version (MPI)

     Number of processors in use:       1

  Reading nscf_save data

     Planes per process (thick) : nr3 = 54 npp =  54 ncplane =  400

     Proc/  planes cols     G    planes cols    G      columns  G
     Pool       (dense grid)       (smooth grid)      (wavefct grid)
        1    54    241     8115   54    241     8115    109     2325


  Spin CASE ( default = unpolarized )

  Wannier mode is: standalone

  -----------------
  *** Reading nnkp
  -----------------

  Checking info from wannier.nnkp file

  Something wrong!
  rlatt(i,j) =  0.406567584527892       at(i,j)=   1.00000000000000

-- 
###################################
******************************************
Thaneshwor Prashad Kaloni
TWAS-BOSE FELLOW /JRF
S N Bose national Centre for Basic Sciences
Kolkata 700098,
INDIA
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From maaaxim at yahoo.com  Wed Mar 31 10:37:51 2010
From: maaaxim at yahoo.com (Maxim Ivanov)
Date: Wed, 31 Mar 2010 01:37:51 -0700 (PDT)
Subject: [Pw_forum] problems with Ta2O5 compound
Message-ID: <50361.49168.qm@web56405.mail.re3.yahoo.com>

Hello all,
Has anyone work with Ta2O5 ? I have some problems with that compound. I am working with delta modification [1]. First of all energy gap is too small. It is about 1.5 eV, however for amorfous Ta2O5 experiments say it is about 4 eV. It is too big underestimation of Eg.?Moreover I have not find defect level in 14, 42, 168 atoms supercells with oxygen vacancy in the center of the cell.I have made LDA+U calculations. I found that Hubbard U is about 2 eV for supercell with 42 atoms, however no changes happened. Eg has slightly increased but no defect level appeared.Ta has 3 d electrons and is described by ultrasoft pseudopotential. I took it from pwscf.org. It might be problem in the potential. What do you think about all of these?
[1]?A. Fukumoto and K. Miwa,
Phys. Rev. B 55, 11?155 (1997)


      
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From nicomwas at yahoo.com  Wed Mar 31 12:19:58 2010
From: nicomwas at yahoo.com (Nicholas Muthaka)
Date: Wed, 31 Mar 2010 03:19:58 -0700 (PDT)
Subject: [Pw_forum] magnesium diboride
Message-ID: <875430.54644.qm@web112314.mail.gq1.yahoo.com>

hi.am working on properties of magnesium diboride and wish to run the equation of state but have problems on how to insert the c lattice constant in the script since the one i have come across seems to be the one for cubics systems. please help.



      
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From nicomwas at yahoo.com  Wed Mar 31 12:25:31 2010
From: nicomwas at yahoo.com (Nicholas Muthaka)
Date: Wed, 31 Mar 2010 03:25:31 -0700 (PDT)
Subject: [Pw_forum] Fw: magnesium diboride
Message-ID: <348967.56615.qm@web112314.mail.gq1.yahoo.com>





----- Forwarded Message ----
From: Nicholas Muthaka <nicomwas at yahoo.com>
To: pw_forum at pwscf.org
Sent: Wed, March 31, 2010 1:19:58 PM
Subject: magnesium diboride


 &control
    prefix='MgB2',
    pseudo_dir='./'
    outdir = './',
 /
 &system
    ibrav=  4,celldm(1) =5.83, celldm(3) =1.14, nat=  3, ntyp= 2,
    ecutwfc = 80.0,ecutrho=800,nspin=2,starting_magnetization(1)= 0.7,starting_magnetization(2)= 0.7,
    occupations='smearing', smearing='marzari-vanderbilt', degauss=0.010000
 /
 &electrons
 diagonalization='david'
 mixing_mode='plain'
 mixing_beta=0.7
 conv_thr=1.0d-8
 electron_maxstep=200
/
ATOMIC_SPECIES
 Mg  24.30   Mg.pz-bhs.UPF
 B   10.81   B.pz-bhs.UPF
ATOMIC_POSITIONS (crystal)
 Mg 0.00 0.00 0.00
 B  0.33 0.67 0.50
 B  0.67 0.33 0.50
K_POINTS {automatic}
 10 10 10 1 1 1


      
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From marsamos at democritos.it  Wed Mar 31 15:47:14 2010
From: marsamos at democritos.it (marsamos at democritos.it)
Date: Wed, 31 Mar 2010 15:47:14 +0200
Subject: [Pw_forum] PLUMED plug-in for quantum ESPRESSO available
Message-ID: <20100331154714.vsrlvozuskcokgco@mail.democritos.it>

Dear users

the PLUMED plug-in for quantum ESPRESSO version 4.1.x is now available 
at http://qe-forge.org/frs/?group_id=10 (the download page at 
www.quantum-espresso.org will be updated soon). PLUMED 
(http://merlino.mi.infn.it/~plumed/PLUMED/) allows to perform 
metadynamics calculations with quantum ESPRESSO (and many other codes). 
It replaces and supersedes the current implementation of metadynamics.

In the same page you will find patches for minor bugs (as a diff file) 
for quantum ESPRESSO 4.1.2 . For details on the installation of patches 
see the user guide 
(http://www.quantum-espresso.org/user_guide/node8.html).

Bests

Paolo and Layla

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

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


From elie.moujaes at hotmail.co.uk  Wed Mar 31 17:06:38 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Wed, 31 Mar 2010 16:06:38 +0100
Subject: [Pw_forum] phonon dispersion for graphene
Message-ID: <SNT114-W37F089203F978CE29089ECD31E0@phx.gbl>


Sear PWSCF users,

 

I am calculating the phonon dispersion for graphene. I did the scf calculations then when I am running the ph.x command, I always get the error:

 

 

     Program PHONON    v.4.1.2  starts ...
     Today is 31Mar2010 at 12: 1:50 

     Ultrasoft (Vanderbilt) Pseudopotentials

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from phq_readin : error #         1
     reading inputph namelist
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
 
 
which means that something is wrong in the input. But I could not fins any mistake in the input file...Can anyone please check it for me? My input is:
 
 
 
&inputph
  tr2_ph=1.0d-14,
  prefix='ph mono graphene',
  ldisp=.true.,
  nq1=28, nq2=28, nq3=1,
  amass(1)=12.00000,
  outdir='/tmp/results_MOUJAES/',
  fildyn='phmgraphene.dyn'
/
 
Thanks
 
Elie Moujaes
University of Nottingham
NG7 2RD
UK
 
  		 	   		  
_________________________________________________________________
Got a cool Hotmail story? Tell us now
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From nnlinh at sissa.it  Wed Mar 31 17:16:57 2010
From: nnlinh at sissa.it (Ngoc Linh Nguyen)
Date: Wed, 31 Mar 2010 17:16:57 +0200
Subject: [Pw_forum] phonon dispersion for graphene
In-Reply-To: <SNT114-W37F089203F978CE29089ECD31E0@phx.gbl>
References: <SNT114-W37F089203F978CE29089ECD31E0@phx.gbl>
Message-ID: <4BB36769.4060507@sissa.it>

Your input file lacks the points where you want to calculate phonon 
dispersion (Gamma, X, ...)
So, you should see in example02 for reference of phonon input file

Good luck
Linh

Elie Moujaes wrote:
> Sear PWSCF users,
>  
> I am calculating the phonon dispersion for graphene. I did the scf 
> calculations then when I am running the ph.x command, I always get the 
> error:
>  
>  
>
>      Program PHONON    v.4.1.2  starts ...
>      Today is 31Mar2010 at 12: 1:50
>
>      Ultrasoft (Vanderbilt) Pseudopotentials
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from phq_readin : error #         1
>      reading inputph namelist
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>      stopping ...
>  
>
>  
>
> which means that something is wrong in the input. But I could not fins 
> any mistake in the input file...Can anyone please check it for me? My 
> input is:
>
>  
>
>  
>
>  
>
> &inputph
>
>   tr2_ph=1.0d-14,
>
>   prefix='ph mono graphene',
>
>   ldisp=.true.,
>
>   nq1=28, nq2=28, nq3=1,
>
>   amass(1)=12.00000,
>
>   outdir='/tmp/results_MOUJAES/',
>
>   fildyn='phmgraphene.dyn'
>
> /
>
>  
>
> Thanks
>
>  
>
> Elie Moujaes
>
> University of Nottingham
>
> NG7 2RD
>
> UK
>
>  
>
>  
>
>
> ------------------------------------------------------------------------
> Got a cool Hotmail story? Tell us now 
> <http://clk.atdmt.com/UKM/go/195013117/direct/01/>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
-----------------------------------------------------
 Nguyen Ngoc Linh, PhD Student
 c/o:   SISSA & CNR-INFM Democritos,
        via Beirut 2-4, 34014 Trieste (Italy)
 email: nnlinh at sissa.it
 phone: +39 04 03787 319
 skype: ngoclinh84phys
-----------------------------------------------------
"The physics is theoretical but the fun is real"



From kumar.198 at buckeyemail.osu.edu  Wed Mar 31 17:49:02 2010
From: kumar.198 at buckeyemail.osu.edu (Ashutosh Kumar)
Date: Wed, 31 Mar 2010 15:49:02 +0000
Subject: [Pw_forum] Symmetry problem in Ge and phonon calculation problem in
	InP
Message-ID: <6D7E0C0F56302745BD0EC910BF4FF30813FB0201@BL2PRD0103MB037.prod.exchangelabs.com>

Dear pwscf users

I've been trying to do phonon calculations, for elemental and compound semiconductors(Si, Ge, InP and SiC). Si and Ge both have exactly the same structure and space group, so symmetry operations are also same. Below is the self consistent input file, i'm using. In case of Si and Ge, the scf.out file works with all the 48 symmetry operations but in case of Ge it rejects all the inversion symmetry opertors. Also, for further calculations i'm using exactly the procedure given in example07 directory.

Also, for InP, I used the same procedure, but i'm missing the splitting of phonon spectra at higher frequency, as reported in publications. After going through the forums, I got to know that I should use zasr=.true. and epsil=.true. for calculations in InP, since it is a polar semiconductor. I tried this and the phonon calculation job keeps on crashing. I don't understand what should I do to solve this problem?


 &control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='ge',
    pseudo_dir = '/nfs/18/osu5465/espresso/espresso-3.2/pseudo/',
    outdir='/nfs/18/osu5465/espresso/tmp/'
 /
 &system
    ibrav= 2, celldm(1) =10.691, nat=2 , ntyp= 1,
    ecutwfc =25.0,
    occupations='smearing', smearing='methfessel-paxton', degauss=0.05,
 /
 &electrons
    conv_thr =  1.0d-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Ge  72.61   Ge.pz-bhs.UPF
ATOMIC_POSITIONS {crystal}
Ge     0.250000  0.250000    0.25000000
Ge     0.000000  0.000000    0.00000000
K_POINTS {automatic}
 8 8 8 0 0 0

--
Ashutosh Kumar
Grad Student
The Ohio State University
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From sclauzer at sissa.it  Wed Mar 31 17:59:08 2010
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Wed, 31 Mar 2010 17:59:08 +0200
Subject: [Pw_forum] (no subject)
In-Reply-To: <743658.31414.qm@web44715.mail.sp1.yahoo.com>
References: <743658.31414.qm@web44715.mail.sp1.yahoo.com>
Message-ID: <4BB3714C.9080109@sissa.it>

sylvia mueni wrote:
> hi im working on the latice constants of BaF2. I have a problem in determining the
> atomic positions of the hexagonal phase. please help

Which kind of problem?

GS

P.S. please specify your affiliation. Thanks!

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

-- 


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

From sh.shapt at gmail.com  Wed Mar 31 18:12:56 2010
From: sh.shapt at gmail.com (Shaptrishi Sharma)
Date: Wed, 31 Mar 2010 17:12:56 +0100
Subject: [Pw_forum] about xcrysden
Message-ID: <j2ta8a0c4081003310912ja99b91b5vd10b645460b11338@mail.gmail.com>

Hi there,

I am not much familar with xcrysden. I wanted to make a supercell in
xcrysden with a certain cell_parametrs (in put file of scf calculation in
quantum espresso), but on going to option 'Modify' and then try to draw the
number of units to 3 along y and z axis. It shows me that certain number of
atoms are being deleted. I have checked the cell_parameter by changing the
cell_parameter , but not much help. Kindly help !
Thanks

Shaptarishi

Msc (Physics)
Pune
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From elie.moujaes at hotmail.co.uk  Wed Mar 31 19:40:10 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Wed, 31 Mar 2010 18:40:10 +0100
Subject: [Pw_forum] phonon dispersion for graphene
In-Reply-To: <4BB36769.4060507@sissa.it>
References: <SNT114-W37F089203F978CE29089ECD31E0@phx.gbl>,
	<4BB36769.4060507@sissa.it>
Message-ID: <SNT114-W5535D5628F735BE0382F62D31E0@phx.gbl>


Thanks very much for your reply. What if I want to plot the graph of frequency versus the wavevector K specifying the Gamma, K and M points..Can one do this in one go or does he have to calculate the frequencies for each of the points separately and then connect them.

 

N.B: I was trying to use ldisp=true and provide an nq1 x nq2 x nq3 grid and I got the previous error. Any examples dealing with this?

 

 

Thanks

 

Elie Mouaes

University of Nottingham

NG7 2RD

UK
 
> Date: Wed, 31 Mar 2010 17:16:57 +0200
> From: nnlinh at sissa.it
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] phonon dispersion for graphene
> 
> Your input file lacks the points where you want to calculate phonon 
> dispersion (Gamma, X, ...)
> So, you should see in example02 for reference of phonon input file
> 
> Good luck
> Linh
> 
> Elie Moujaes wrote:
> > Sear PWSCF users,
> > 
> > I am calculating the phonon dispersion for graphene. I did the scf 
> > calculations then when I am running the ph.x command, I always get the 
> > error:
> > 
> > 
> >
> > Program PHONON v.4.1.2 starts ...
> > Today is 31Mar2010 at 12: 1:50
> >
> > Ultrasoft (Vanderbilt) Pseudopotentials
> >
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > from phq_readin : error # 1
> > reading inputph namelist
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> > stopping ...
> > 
> >
> > 
> >
> > which means that something is wrong in the input. But I could not fins 
> > any mistake in the input file...Can anyone please check it for me? My 
> > input is:
> >
> > 
> >
> > 
> >
> > 
> >
> > &inputph
> >
> > tr2_ph=1.0d-14,
> >
> > prefix='ph mono graphene',
> >
> > ldisp=.true.,
> >
> > nq1=28, nq2=28, nq3=1,
> >
> > amass(1)=12.00000,
> >
> > outdir='/tmp/results_MOUJAES/',
> >
> > fildyn='phmgraphene.dyn'
> >
> > /
> >
> > 
> >
> > Thanks
> >
> > 
> >
> > Elie Moujaes
> >
> > University of Nottingham
> >
> > NG7 2RD
> >
> > UK
> >
> > 
> >
> > 
> >
> >
> > ------------------------------------------------------------------------
> > Got a cool Hotmail story? Tell us now 
> > <http://clk.atdmt.com/UKM/go/195013117/direct/01/>
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> > 
> 
> 
> -- 
> -----------------------------------------------------
> Nguyen Ngoc Linh, PhD Student
> c/o: SISSA & CNR-INFM Democritos,
> via Beirut 2-4, 34014 Trieste (Italy)
> email: nnlinh at sissa.it
> phone: +39 04 03787 319
> skype: ngoclinh84phys
> -----------------------------------------------------
> "The physics is theoretical but the fun is real"
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
_________________________________________________________________
Tell us your greatest, weirdest and funniest Hotmail stories
http://clk.atdmt.com/UKM/go/195013117/direct/01/
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From giannozz at democritos.it  Wed Mar 31 19:52:37 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 31 Mar 2010 19:52:37 +0200
Subject: [Pw_forum] phonon dispersion for graphene
In-Reply-To: <SNT114-W5535D5628F735BE0382F62D31E0@phx.gbl>
References: <SNT114-W37F089203F978CE29089ECD31E0@phx.gbl>,
	<4BB36769.4060507@sissa.it>
	<SNT114-W5535D5628F735BE0382F62D31E0@phx.gbl>
Message-ID: <A8AC1F4B-8966-45DE-BC4E-8991A5DCF8E9@democritos.it>


On Mar 31, 2010, at 19:40 , Elie Moujaes wrote:

>  N.B: I was trying to use ldisp=true and provide an nq1 x nq2 x nq3  
> grid and I got the previous error. Any examples dealing with this?

examples/example06

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




From giannozz at democritos.it  Wed Mar 31 20:04:05 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 31 Mar 2010 20:04:05 +0200
Subject: [Pw_forum] Symmetry problem in Ge and phonon calculation
	problem in InP
In-Reply-To: <6D7E0C0F56302745BD0EC910BF4FF30813FB0201@BL2PRD0103MB037.prod.exchangelabs.com>
References: <6D7E0C0F56302745BD0EC910BF4FF30813FB0201@BL2PRD0103MB037.prod.exchangelabs.com>
Message-ID: <EC8CE1AB-745D-499C-B4FE-F2EDF5F72DF2@democritos.it>


On Mar 31, 2010, at 17:49 , Ashutosh Kumar wrote:

> In case of Si and Ge, the scf.out file works with all the 48  
> symmetry operations
> but in case of Ge it rejects all the inversion symmetry opertors.

congratulations! this is the 1000000th time somebody reports this.  
You win the
right to write parallel symmetrization in G-space for the phonon  
code. Once you
have done this, Ge will no longer reject any symmetry operation.

By the way, is Ge in the first row different from Ge in the second?

> I tried this and the phonon calculation job keeps on crashing

crashing how? If it crashes for a good reason, the reason is printed  
on output.
If it crashes for no apparent reason: consider that many compilers  
miscompile
the phonon code.

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




From giannozz at democritos.it  Wed Mar 31 20:21:41 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 31 Mar 2010 20:21:41 +0200
Subject: [Pw_forum] problems with Ta2O5 compound
In-Reply-To: <50361.49168.qm@web56405.mail.re3.yahoo.com>
References: <50361.49168.qm@web56405.mail.re3.yahoo.com>
Message-ID: <F56577F0-9448-47C8-885C-C68662D0F7D9@democritos.it>

On Mar 31, 2010, at 10:37 , Maxim Ivanov wrote:
> First of all energy gap is too small
>
this is a well known problem of DFT
> Moreover I have not find defect level in 14, 42, 168 atoms  
> supercells with oxygen vacancy in the center of the cell.
>
oxides are notoriously nasty stuff, in which sometimes you don't get  
things right
> Ta has 3 d electrons and is described by ultrasoft pseudopotential.  
> I took it from pwscf.org. It might be problem in the potential.
>
why should the problem be in the pseudopotential? any evidence, or  
any other
calculations to compare with?

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




From giannozz at democritos.it  Wed Mar 31 20:28:15 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 31 Mar 2010 20:28:15 +0200
Subject: [Pw_forum] hi
In-Reply-To: <y2xaecd86391003310115kdc151722pf58bea78bf046486@mail.gmail.com>
References: <y2xaecd86391003310115kdc151722pf58bea78bf046486@mail.gmail.com>
Message-ID: <4F276755-9D2E-4B92-B564-40DCABDA6616@democritos.it>


On Mar 31, 2010, at 10:15 , Thaneshwor Kaloni wrote:

> I am unable to get the seedname.eig file

I guess you may get more help from the Wannier mailing list:
http://www.wannier.org/forum.html

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




From elie.moujaes at hotmail.co.uk  Wed Mar 31 21:26:41 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Wed, 31 Mar 2010 20:26:41 +0100
Subject: [Pw_forum] phonon dispersion for graphene
In-Reply-To: <A8AC1F4B-8966-45DE-BC4E-8991A5DCF8E9@democritos.it>
References: <SNT114-W37F089203F978CE29089ECD31E0@phx.gbl>, ,
	<4BB36769.4060507@sissa.it>,
	<SNT114-W5535D5628F735BE0382F62D31E0@phx.gbl>,
	<A8AC1F4B-8966-45DE-BC4E-8991A5DCF8E9@democritos.it>
Message-ID: <SNT114-W373294495608665005FBA3D31E0@phx.gbl>


Dear All,

 

I worked through example 06 but i am still getting the error which again is:

 

 

Program PHONON    v.4.1.2  starts ...
     Today is 31Mar2010 at 16:15:30 

     Ultrasoft (Vanderbilt) Pseudopotentials

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from phq_readin : error #         1
     reading inputph namelist
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
 

In Example 06 they do not provide X, gamma,...positions. This is the case when one wants to calculate the dispersion at one particular point where providing the nq1 x nq2 xnq3 is no more necessary..I do not know what is going wrong..Here is the input again:

 

 

inputph
  tr2_ph=1.0d-14,
  prefix='ph mono graphene',
  ldisp=.true.
  nq1=7, nq2=7, nq3=7
  amass(1)=12.00000,
  outdir='/tmp/results_MOUJAES/',
  fildyn='phmgraphene.dyn'
/

 

 
thanks
 
elie moujaes
University of Nottingham
NG7 2RD
 

 


> From: giannozz at democritos.it
> Date: Wed, 31 Mar 2010 19:52:37 +0200
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] phonon dispersion for graphene
> 
> 
> On Mar 31, 2010, at 19:40 , Elie Moujaes wrote:
> 
> > N.B: I was trying to use ldisp=true and provide an nq1 x nq2 x nq3 
> > grid and I got the previous error. Any examples dealing with this?
> 
> examples/example06
> 
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
_________________________________________________________________
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From giannozz at democritos.it  Wed Mar 31 21:30:58 2010
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 31 Mar 2010 21:30:58 +0200
Subject: [Pw_forum] phonon dispersion for graphene
In-Reply-To: <SNT114-W373294495608665005FBA3D31E0@phx.gbl>
References: <SNT114-W37F089203F978CE29089ECD31E0@phx.gbl>, ,
	<4BB36769.4060507@sissa.it>,
	<SNT114-W5535D5628F735BE0382F62D31E0@phx.gbl>,
	<A8AC1F4B-8966-45DE-BC4E-8991A5DCF8E9@democritos.it>
	<SNT114-W373294495608665005FBA3D31E0@phx.gbl>
Message-ID: <C87A891F-A0D4-44A5-8024-447B88C3934F@democritos.it>


On Mar 31, 2010, at 21:26 , Elie Moujaes wrote:

>      reading inputph namelist

if the code says that your namelist is wrong: it is wrong.

> inputph

Missing: a title line; a & before inputph
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From kumar.198 at buckeyemail.osu.edu  Wed Mar 31 22:41:13 2010
From: kumar.198 at buckeyemail.osu.edu (Ashutosh Kumar)
Date: Wed, 31 Mar 2010 20:41:13 +0000
Subject: [Pw_forum] Symmetry problem in Ge and phonon calculation
	problem in InP
Message-ID: <6D7E0C0F56302745BD0EC910BF4FF30813FB0247@BL2PRD0103MB037.prod.exchangelabs.com>

Sorry, I forgot to write the error I was getting. With InP, it says
              task #         0
              from phq_readin : error #         1
              no elec. field with metals

with q=0. I tried the example02 for Si and C, and it worked fine, but in InP, it keeps on saying above. 

Extremely sorry for writing again the symmetry problem in Ge. I searched the forum about germanium and read many of those results, but could not find anything, so I wrote the problem here.


Ashutosh Kumar
Grad Student
The Ohio State University

________________________________________
From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] on behalf of pw_forum-request at pwscf.org [pw_forum-request at pwscf.org]
Sent: Wednesday, March 31, 2010 2:28 PM
To: pw_forum at pwscf.org
Subject: Pw_forum Digest, Vol 33, Issue 83

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Today's Topics:

   1. Symmetry problem in Ge and phonon calculation problem in  InP
      (Ashutosh Kumar)
   2. Re: (no subject) (Gabriele Sclauzero)
   3. about xcrysden (Shaptrishi Sharma)
   4. Re: phonon dispersion for graphene (Elie Moujaes)
   5. Re: phonon dispersion for graphene (Paolo Giannozzi)
   6. Re: Symmetry problem in Ge and phonon calculation problem in
      InP (Paolo Giannozzi)
   7. Re: problems with Ta2O5 compound (Paolo Giannozzi)
   8. Re: hi (Paolo Giannozzi)


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

Message: 1
Date: Wed, 31 Mar 2010 15:49:02 +0000
From: Ashutosh Kumar <kumar.198 at buckeyemail.osu.edu>
Subject: [Pw_forum] Symmetry problem in Ge and phonon calculation
        problem in      InP
To: "pw_forum at pwscf.org" <pw_forum at pwscf.org>
Message-ID:
        <6D7E0C0F56302745BD0EC910BF4FF30813FB0201 at BL2PRD0103MB037.prod.exchangelabs.com>

Content-Type: text/plain; charset="iso-8859-1"

Dear pwscf users

I've been trying to do phonon calculations, for elemental and compound semiconductors(Si, Ge, InP and SiC). Si and Ge both have exactly the same structure and space group, so symmetry operations are also same. Below is the self consistent input file, i'm using. In case of Si and Ge, the scf.out file works with all the 48 symmetry operations but in case of Ge it rejects all the inversion symmetry opertors. Also, for further calculations i'm using exactly the procedure given in example07 directory.

Also, for InP, I used the same procedure, but i'm missing the splitting of phonon spectra at higher frequency, as reported in publications. After going through the forums, I got to know that I should use zasr=.true. and epsil=.true. for calculations in InP, since it is a polar semiconductor. I tried this and the phonon calculation job keeps on crashing. I don't understand what should I do to solve this problem?


 &control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='ge',
    pseudo_dir = '/nfs/18/osu5465/espresso/espresso-3.2/pseudo/',
    outdir='/nfs/18/osu5465/espresso/tmp/'
 /
 &system
    ibrav= 2, celldm(1) =10.691, nat=2 , ntyp= 1,
    ecutwfc =25.0,
    occupations='smearing', smearing='methfessel-paxton', degauss=0.05,
 /
 &electrons
    conv_thr =  1.0d-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Ge  72.61   Ge.pz-bhs.UPF
ATOMIC_POSITIONS {crystal}
Ge     0.250000  0.250000    0.25000000
Ge     0.000000  0.000000    0.00000000
K_POINTS {automatic}
 8 8 8 0 0 0

--
Ashutosh Kumar
Grad Student
The Ohio State University
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------------------------------

Message: 2
Date: Wed, 31 Mar 2010 17:59:08 +0200
From: Gabriele Sclauzero <sclauzer at sissa.it>
Subject: Re: [Pw_forum] (no subject)
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <4BB3714C.9080109 at sissa.it>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

sylvia mueni wrote:
> hi im working on the latice constants of BaF2. I have a problem in determining the
> atomic positions of the hexagonal phase. please help

Which kind of problem?

GS

P.S. please specify your affiliation. Thanks!

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

--


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


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

Message: 3
Date: Wed, 31 Mar 2010 17:12:56 +0100
From: Shaptrishi Sharma <sh.shapt at gmail.com>
Subject: [Pw_forum] about xcrysden
To: pw_forum at pwscf.org
Message-ID:
        <j2ta8a0c4081003310912ja99b91b5vd10b645460b11338 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi there,

I am not much familar with xcrysden. I wanted to make a supercell in
xcrysden with a certain cell_parametrs (in put file of scf calculation in
quantum espresso), but on going to option 'Modify' and then try to draw the
number of units to 3 along y and z axis. It shows me that certain number of
atoms are being deleted. I have checked the cell_parameter by changing the
cell_parameter , but not much help. Kindly help !
Thanks

Shaptarishi

Msc (Physics)
Pune
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Message: 4
Date: Wed, 31 Mar 2010 18:40:10 +0100
From: Elie Moujaes <elie.moujaes at hotmail.co.uk>
Subject: Re: [Pw_forum] phonon dispersion for graphene
To: <pw_forum at pwscf.org>
Message-ID: <SNT114-W5535D5628F735BE0382F62D31E0 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"


Thanks very much for your reply. What if I want to plot the graph of frequency versus the wavevector K specifying the Gamma, K and M points..Can one do this in one go or does he have to calculate the frequencies for each of the points separately and then connect them.



N.B: I was trying to use ldisp=true and provide an nq1 x nq2 x nq3 grid and I got the previous error. Any examples dealing with this?





Thanks



Elie Mouaes

University of Nottingham

NG7 2RD

UK

> Date: Wed, 31 Mar 2010 17:16:57 +0200
> From: nnlinh at sissa.it
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] phonon dispersion for graphene
>
> Your input file lacks the points where you want to calculate phonon
> dispersion (Gamma, X, ...)
> So, you should see in example02 for reference of phonon input file
>
> Good luck
> Linh
>
> Elie Moujaes wrote:
> > Sear PWSCF users,
> >
> > I am calculating the phonon dispersion for graphene. I did the scf
> > calculations then when I am running the ph.x command, I always get the
> > error:
> >
> >
> >
> > Program PHONON v.4.1.2 starts ...
> > Today is 31Mar2010 at 12: 1:50
> >
> > Ultrasoft (Vanderbilt) Pseudopotentials
> >
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > from phq_readin : error # 1
> > reading inputph namelist
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> > stopping ...
> >
> >
> >
> >
> > which means that something is wrong in the input. But I could not fins
> > any mistake in the input file...Can anyone please check it for me? My
> > input is:
> >
> >
> >
> >
> >
> >
> >
> > &inputph
> >
> > tr2_ph=1.0d-14,
> >
> > prefix='ph mono graphene',
> >
> > ldisp=.true.,
> >
> > nq1=28, nq2=28, nq3=1,
> >
> > amass(1)=12.00000,
> >
> > outdir='/tmp/results_MOUJAES/',
> >
> > fildyn='phmgraphene.dyn'
> >
> > /
> >
> >
> >
> > Thanks
> >
> >
> >
> > Elie Moujaes
> >
> > University of Nottingham
> >
> > NG7 2RD
> >
> > UK
> >
> >
> >
> >
> >
> >
> > ------------------------------------------------------------------------
> > Got a cool Hotmail story? Tell us now
> > <http://clk.atdmt.com/UKM/go/195013117/direct/01/>
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
> --
> -----------------------------------------------------
> Nguyen Ngoc Linh, PhD Student
> c/o: SISSA & CNR-INFM Democritos,
> via Beirut 2-4, 34014 Trieste (Italy)
> email: nnlinh at sissa.it
> phone: +39 04 03787 319
> skype: ngoclinh84phys
> -----------------------------------------------------
> "The physics is theoretical but the fun is real"
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

Message: 5
Date: Wed, 31 Mar 2010 19:52:37 +0200
From: Paolo Giannozzi <giannozz at democritos.it>
Subject: Re: [Pw_forum] phonon dispersion for graphene
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <A8AC1F4B-8966-45DE-BC4E-8991A5DCF8E9 at democritos.it>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed


On Mar 31, 2010, at 19:40 , Elie Moujaes wrote:

>  N.B: I was trying to use ldisp=true and provide an nq1 x nq2 x nq3
> grid and I got the previous error. Any examples dealing with this?

examples/example06

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





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

Message: 6
Date: Wed, 31 Mar 2010 20:04:05 +0200
From: Paolo Giannozzi <giannozz at democritos.it>
Subject: Re: [Pw_forum] Symmetry problem in Ge and phonon calculation
        problem in InP
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <EC8CE1AB-745D-499C-B4FE-F2EDF5F72DF2 at democritos.it>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed


On Mar 31, 2010, at 17:49 , Ashutosh Kumar wrote:

> In case of Si and Ge, the scf.out file works with all the 48
> symmetry operations
> but in case of Ge it rejects all the inversion symmetry opertors.

congratulations! this is the 1000000th time somebody reports this.
You win the
right to write parallel symmetrization in G-space for the phonon
code. Once you
have done this, Ge will no longer reject any symmetry operation.

By the way, is Ge in the first row different from Ge in the second?

> I tried this and the phonon calculation job keeps on crashing

crashing how? If it crashes for a good reason, the reason is printed
on output.
If it crashes for no apparent reason: consider that many compilers
miscompile
the phonon code.

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





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

Message: 7
Date: Wed, 31 Mar 2010 20:21:41 +0200
From: Paolo Giannozzi <giannozz at democritos.it>
Subject: Re: [Pw_forum] problems with Ta2O5 compound
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <F56577F0-9448-47C8-885C-C68662D0F7D9 at democritos.it>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

On Mar 31, 2010, at 10:37 , Maxim Ivanov wrote:
> First of all energy gap is too small
>
this is a well known problem of DFT
> Moreover I have not find defect level in 14, 42, 168 atoms
> supercells with oxygen vacancy in the center of the cell.
>
oxides are notoriously nasty stuff, in which sometimes you don't get
things right
> Ta has 3 d electrons and is described by ultrasoft pseudopotential.
> I took it from pwscf.org. It might be problem in the potential.
>
why should the problem be in the pseudopotential? any evidence, or
any other
calculations to compare with?

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





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

Message: 8
Date: Wed, 31 Mar 2010 20:28:15 +0200
From: Paolo Giannozzi <giannozz at democritos.it>
Subject: Re: [Pw_forum] hi
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <4F276755-9D2E-4B92-B564-40DCABDA6616 at democritos.it>
Content-Type: text/plain; charset=US-ASCII; format=flowed


On Mar 31, 2010, at 10:15 , Thaneshwor Kaloni wrote:

> I am unable to get the seedname.eig file

I guess you may get more help from the Wannier mailing list:
http://www.wannier.org/forum.html

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





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

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


End of Pw_forum Digest, Vol 33, Issue 83
****************************************

From elie.moujaes at hotmail.co.uk  Wed Mar 31 22:46:06 2010
From: elie.moujaes at hotmail.co.uk (Elie Moujaes)
Date: Wed, 31 Mar 2010 21:46:06 +0100
Subject: [Pw_forum] phonon dispersion for graphene
In-Reply-To: <C87A891F-A0D4-44A5-8024-447B88C3934F@democritos.it>
References: <SNT114-W37F089203F978CE29089ECD31E0@phx.gbl>,
	, , <4BB36769.4060507@sissa.it>, ,
	<SNT114-W5535D5628F735BE0382F62D31E0@phx.gbl>, ,
	<A8AC1F4B-8966-45DE-BC4E-8991A5DCF8E9@democritos.it>,
	<SNT114-W373294495608665005FBA3D31E0@phx.gbl>,
	<C87A891F-A0D4-44A5-8024-447B88C3934F@democritos.it>
Message-ID: <SNT114-W171C271A63D75AB10FBBA9D31E0@phx.gbl>


Dear Prof. Gianozzi and all,

 

Actually the "&" was there but I missed it when i copied the file. The missing title was the problem. This is sorted but when I started running the ph.x I got another error:

 

 

 

Atomic displacements:
     There are   6 irreducible representations

     Representation     1      1 modes -A To be done

     Representation     2      1 modes -A To be done

     Representation     3      1 modes -A To be done

     Representation     4      1 modes -A To be done

     Representation     5      1 modes - To be done

     Representation     6      1 modes - To be done

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from davcio : error #        20
     error while reading from file

 

 

Well, I found that some people on the forum have got such an error but with  I/O error than "reading from file". The error probably means that something was wrong while reading the previous file...I ran a scf calculation (pw.x) followed by the ph.x. I would appreciate it if you can suggest how to fic this problem..I repeated the calculations several times  but in vain..

 

Regards

 

 


 
> From: giannozz at democritos.it
> Date: Wed, 31 Mar 2010 21:30:58 +0200
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] phonon dispersion for graphene
> 
> 
> On Mar 31, 2010, at 21:26 , Elie Moujaes wrote:
> 
> > reading inputph namelist
> 
> if the code says that your namelist is wrong: it is wrong.
> 
> > inputph
> 
> Missing: a title line; a & before inputph
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
 		 	   		  
_________________________________________________________________
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From degironc at sissa.it  Wed Mar 31 23:30:11 2010
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 31 Mar 2010 23:30:11 +0200
Subject: [Pw_forum] Symmetry problem in Ge and phonon
 calculation	problem in InP
In-Reply-To: <6D7E0C0F56302745BD0EC910BF4FF30813FB0247@BL2PRD0103MB037.prod.exchangelabs.com>
References: <6D7E0C0F56302745BD0EC910BF4FF30813FB0247@BL2PRD0103MB037.prod.exchangelabs.com>
Message-ID: <4BB3BEE3.8060909@sissa.it>

dear Ashutosh Kumar,
the LO-TO splitting comes from macroscopic electric fields that build up 
in the cell of polar materials.
however you are using occupations='smearing' which is appropriate for 
metals where no electric field can be calculated.
remove the occupation='smearing' bit so that the code knows you are 
woking with an insulator.

stefano

Ashutosh Kumar wrote:
> Sorry, I forgot to write the error I was getting. With InP, it says
>               task #         0
>               from phq_readin : error #         1
>               no elec. field with metals
>
> with q=0. I tried the example02 for Si and C, and it worked fine, but in InP, it keeps on saying above. 
>
> Extremely sorry for writing again the symmetry problem in Ge. I searched the forum about germanium and read many of those results, but could not find anything, so I wrote the problem here.
>
>
> Ashutosh Kumar
> Grad Student
> The Ohio State University
>
> ________________________________________
> From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] on behalf of pw_forum-request at pwscf.org [pw_forum-request at pwscf.org]
> Sent: Wednesday, March 31, 2010 2:28 PM
> To: pw_forum at pwscf.org
> Subject: Pw_forum Digest, Vol 33, Issue 83
>
> 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. Symmetry problem in Ge and phonon calculation problem in  InP
>       (Ashutosh Kumar)
>    2. Re: (no subject) (Gabriele Sclauzero)
>    3. about xcrysden (Shaptrishi Sharma)
>    4. Re: phonon dispersion for graphene (Elie Moujaes)
>    5. Re: phonon dispersion for graphene (Paolo Giannozzi)
>    6. Re: Symmetry problem in Ge and phonon calculation problem in
>       InP (Paolo Giannozzi)
>    7. Re: problems with Ta2O5 compound (Paolo Giannozzi)
>    8. Re: hi (Paolo Giannozzi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 31 Mar 2010 15:49:02 +0000
> From: Ashutosh Kumar <kumar.198 at buckeyemail.osu.edu>
> Subject: [Pw_forum] Symmetry problem in Ge and phonon calculation
>         problem in      InP
> To: "pw_forum at pwscf.org" <pw_forum at pwscf.org>
> Message-ID:
>         <6D7E0C0F56302745BD0EC910BF4FF30813FB0201 at BL2PRD0103MB037.prod.exchangelabs.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear pwscf users
>
> I've been trying to do phonon calculations, for elemental and compound semiconductors(Si, Ge, InP and SiC). Si and Ge both have exactly the same structure and space group, so symmetry operations are also same. Below is the self consistent input file, i'm using. In case of Si and Ge, the scf.out file works with all the 48 symmetry operations but in case of Ge it rejects all the inversion symmetry opertors. Also, for further calculations i'm using exactly the procedure given in example07 directory.
>
> Also, for InP, I used the same procedure, but i'm missing the splitting of phonon spectra at higher frequency, as reported in publications. After going through the forums, I got to know that I should use zasr=.true. and epsil=.true. for calculations in InP, since it is a polar semiconductor. I tried this and the phonon calculation job keeps on crashing. I don't understand what should I do to solve this problem?
>
>
>  &control
>     calculation='scf'
>     restart_mode='from_scratch',
>     prefix='ge',
>     pseudo_dir = '/nfs/18/osu5465/espresso/espresso-3.2/pseudo/',
>     outdir='/nfs/18/osu5465/espresso/tmp/'
>  /
>  &system
>     ibrav= 2, celldm(1) =10.691, nat=2 , ntyp= 1,
>     ecutwfc =25.0,
>     occupations='smearing', smearing='methfessel-paxton', degauss=0.05,
>  /
>  &electrons
>     conv_thr =  1.0d-8
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Ge  72.61   Ge.pz-bhs.UPF
> ATOMIC_POSITIONS {crystal}
> Ge     0.250000  0.250000    0.25000000
> Ge     0.000000  0.000000    0.00000000
> K_POINTS {automatic}
>  8 8 8 0 0 0
>
> --
> Ashutosh Kumar
> Grad Student
> The Ohio State University
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> ------------------------------
>
> Message: 2
> Date: Wed, 31 Mar 2010 17:59:08 +0200
> From: Gabriele Sclauzero <sclauzer at sissa.it>
> Subject: Re: [Pw_forum] (no subject)
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4BB3714C.9080109 at sissa.it>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> sylvia mueni wrote:
>   
>> hi im working on the latice constants of BaF2. I have a problem in determining the
>> atomic positions of the hexagonal phase. please help
>>     
>
> Which kind of problem?
>
> GS
>
> P.S. please specify your affiliation. Thanks!
>
>   
>> thanks, sylvia
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________ Pw_forum mailing list
>> Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum
>>     
>
> --
>
>
> o ------------------------------------------------ o
> | Gabriele Sclauzero, PhD Student                  |
> | c/o:   SISSA & CNR-INFM Democritos,              |
> |        via Beirut 2-4, 34014 Trieste (Italy)     |
> | email: sclauzer at sissa.it                         |
> | phone: +39 040 3787 511                          |
> | skype: gurlonotturno                             |
> o ------------------------------------------------ o
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 31 Mar 2010 17:12:56 +0100
> From: Shaptrishi Sharma <sh.shapt at gmail.com>
> Subject: [Pw_forum] about xcrysden
> To: pw_forum at pwscf.org
> Message-ID:
>         <j2ta8a0c4081003310912ja99b91b5vd10b645460b11338 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi there,
>
> I am not much familar with xcrysden. I wanted to make a supercell in
> xcrysden with a certain cell_parametrs (in put file of scf calculation in
> quantum espresso), but on going to option 'Modify' and then try to draw the
> number of units to 3 along y and z axis. It shows me that certain number of
> atoms are being deleted. I have checked the cell_parameter by changing the
> cell_parameter , but not much help. Kindly help !
> Thanks
>
> Shaptarishi
>
> Msc (Physics)
> Pune
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 4
> Date: Wed, 31 Mar 2010 18:40:10 +0100
> From: Elie Moujaes <elie.moujaes at hotmail.co.uk>
> Subject: Re: [Pw_forum] phonon dispersion for graphene
> To: <pw_forum at pwscf.org>
> Message-ID: <SNT114-W5535D5628F735BE0382F62D31E0 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Thanks very much for your reply. What if I want to plot the graph of frequency versus the wavevector K specifying the Gamma, K and M points..Can one do this in one go or does he have to calculate the frequencies for each of the points separately and then connect them.
>
>
>
> N.B: I was trying to use ldisp=true and provide an nq1 x nq2 x nq3 grid and I got the previous error. Any examples dealing with this?
>
>
>
>
>
> Thanks
>
>
>
> Elie Mouaes
>
> University of Nottingham
>
> NG7 2RD
>
> UK
>
>   
>> Date: Wed, 31 Mar 2010 17:16:57 +0200
>> From: nnlinh at sissa.it
>> To: pw_forum at pwscf.org
>> Subject: Re: [Pw_forum] phonon dispersion for graphene
>>
>> Your input file lacks the points where you want to calculate phonon
>> dispersion (Gamma, X, ...)
>> So, you should see in example02 for reference of phonon input file
>>
>> Good luck
>> Linh
>>
>> Elie Moujaes wrote:
>>     
>>> Sear PWSCF users,
>>>
>>> I am calculating the phonon dispersion for graphene. I did the scf
>>> calculations then when I am running the ph.x command, I always get the
>>> error:
>>>
>>>
>>>
>>> Program PHONON v.4.1.2 starts ...
>>> Today is 31Mar2010 at 12: 1:50
>>>
>>> Ultrasoft (Vanderbilt) Pseudopotentials
>>>
>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>> from phq_readin : error # 1
>>> reading inputph namelist
>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>
>>> stopping ...
>>>
>>>
>>>
>>>
>>> which means that something is wrong in the input. But I could not fins
>>> any mistake in the input file...Can anyone please check it for me? My
>>> input is:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> &inputph
>>>
>>> tr2_ph=1.0d-14,
>>>
>>> prefix='ph mono graphene',
>>>
>>> ldisp=.true.,
>>>
>>> nq1=28, nq2=28, nq3=1,
>>>
>>> amass(1)=12.00000,
>>>
>>> outdir='/tmp/results_MOUJAES/',
>>>
>>> fildyn='phmgraphene.dyn'
>>>
>>> /
>>>
>>>
>>>
>>> Thanks
>>>
>>>
>>>
>>> Elie Moujaes
>>>
>>> University of Nottingham
>>>
>>> NG7 2RD
>>>
>>> UK
>>>
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>> Got a cool Hotmail story? Tell us now
>>> <http://clk.atdmt.com/UKM/go/195013117/direct/01/>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>       
>> --
>> -----------------------------------------------------
>> Nguyen Ngoc Linh, PhD Student
>> c/o: SISSA & CNR-INFM Democritos,
>> via Beirut 2-4, 34014 Trieste (Italy)
>> email: nnlinh at sissa.it
>> phone: +39 04 03787 319
>> skype: ngoclinh84phys
>> -----------------------------------------------------
>> "The physics is theoretical but the fun is real"
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>     
>
> _________________________________________________________________
> Tell us your greatest, weirdest and funniest Hotmail stories
> http://clk.atdmt.com/UKM/go/195013117/direct/01/
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> ------------------------------
>
> Message: 5
> Date: Wed, 31 Mar 2010 19:52:37 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] phonon dispersion for graphene
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <A8AC1F4B-8966-45DE-BC4E-8991A5DCF8E9 at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
>
> On Mar 31, 2010, at 19:40 , Elie Moujaes wrote:
>
>   
>>  N.B: I was trying to use ldisp=true and provide an nq1 x nq2 x nq3
>> grid and I got the previous error. Any examples dealing with this?
>>     
>
> examples/example06
>
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 31 Mar 2010 20:04:05 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] Symmetry problem in Ge and phonon calculation
>         problem in InP
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <EC8CE1AB-745D-499C-B4FE-F2EDF5F72DF2 at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
>
> On Mar 31, 2010, at 17:49 , Ashutosh Kumar wrote:
>
>   
>> In case of Si and Ge, the scf.out file works with all the 48
>> symmetry operations
>> but in case of Ge it rejects all the inversion symmetry opertors.
>>     
>
> congratulations! this is the 1000000th time somebody reports this.
> You win the
> right to write parallel symmetrization in G-space for the phonon
> code. Once you
> have done this, Ge will no longer reject any symmetry operation.
>
> By the way, is Ge in the first row different from Ge in the second?
>
>   
>> I tried this and the phonon calculation job keeps on crashing
>>     
>
> crashing how? If it crashes for a good reason, the reason is printed
> on output.
> If it crashes for no apparent reason: consider that many compilers
> miscompile
> the phonon code.
>
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 31 Mar 2010 20:21:41 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] problems with Ta2O5 compound
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <F56577F0-9448-47C8-885C-C68662D0F7D9 at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> On Mar 31, 2010, at 10:37 , Maxim Ivanov wrote:
>   
>> First of all energy gap is too small
>>
>>     
> this is a well known problem of DFT
>   
>> Moreover I have not find defect level in 14, 42, 168 atoms
>> supercells with oxygen vacancy in the center of the cell.
>>
>>     
> oxides are notoriously nasty stuff, in which sometimes you don't get
> things right
>   
>> Ta has 3 d electrons and is described by ultrasoft pseudopotential.
>> I took it from pwscf.org. It might be problem in the potential.
>>
>>     
> why should the problem be in the pseudopotential? any evidence, or
> any other
> calculations to compare with?
>
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Wed, 31 Mar 2010 20:28:15 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] hi
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4F276755-9D2E-4B92-B564-40DCABDA6616 at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
>
> On Mar 31, 2010, at 10:15 , Thaneshwor Kaloni wrote:
>
>   
>> I am unable to get the seedname.eig file
>>     
>
> I guess you may get more help from the Wannier mailing list:
> http://www.wannier.org/forum.html
>
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
>
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