From shruba at gmail.com  Fri Jun  1 06:31:08 2007
From: shruba at gmail.com (shruba at gmail.com)
Date: Fri, 1 Jun 2007 00:31:08 -0400
Subject: [Pw_forum] need help to read output
Message-ID: <822f4ec80705312131p5d09875j91279d6e49750558@mail.gmail.com>

Hi all,
           I need some help regarding reading output file (I used vc-relax
including ensemble DFT- [i am using that for geometry optimization not md
calculation] option implemented in cp code in espresso-3.2).
  Is there any keyword or option by which I can read the energy of each
iteration in order to check the convergence.
       Thanks in advance.
                                     shruba gangopadhyay
                                     Graduate Student
                                     Department of Chemistry
                                    Nanoscience Technology center
                                    University of Central Florida
                                    Orlando, Fl-32826

-- 
'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
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From giannozz at nest.sns.it  Fri Jun  1 10:59:38 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 1 Jun 2007 10:59:38 +0200
Subject: SIGSEGV with intel compiler (Was: Re [Pw_forum] example01 errors;....)
In-Reply-To: <Pine.LNX.4.44.0705301206240.31278-100000@localhost.localdomain>
References: <Pine.LNX.4.44.0705301206240.31278-100000@localhost.localdomain>
Message-ID: <1371D581-464A-4BC6-9C82-0F4CB2AB1E4E@nest.sns.it>

On May 30, 2007, at 18:26 , Axel Kohlmeyer wrote:

> this looks like you might be running out of stack space.
> since you seem to be using the intel compiler, you'll have
> to enlarge the stack space user limit. the default setting
> on many installations is too small. try setting it to the
> maximum via either: ulimit -s unlimited (if you are using a
> bourne shell, e.g. bash) or: limit stacksize unlimited
> (if you are running in a c-shell, e.g. tcsh).

I think I found (on the net, of course) the ultimate solution to this
problem. Setting 'ulimit' may not be the solution because the stack
size can be reset to some other value either by the batch system
or by the code itself (an example: the machine I am using for test,
Cineca clx, has the stack size set to unlimited by default, but the
code keep crashing for some calculations). The safe solution is to
call a C routine that resets the stack to unlimited. I don't know if it
will solve Helen's problem, but it solved Peter's problem without any
change to the code. Patch attached. Paolo

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



From lanhaiping at gmail.com  Fri Jun  1 13:51:54 2007
From: lanhaiping at gmail.com (lan haiping)
Date: Fri, 1 Jun 2007 19:51:54 +0800
Subject: [Pw_forum] need help to read output
In-Reply-To: <822f4ec80705312131p5d09875j91279d6e49750558@mail.gmail.com>
References: <822f4ec80705312131p5d09875j91279d6e49750558@mail.gmail.com>
Message-ID: <c92002fa0706010451j10b3c0b0m19a04e67fa0b819c@mail.gmail.com>

Dear Shruba,

you can try " grep "!"  pwout", then you can get energy of each iteration.

Regards,

H.P

On 6/1/07, shruba at gmail.com <shruba at gmail.com> wrote:
>
> Hi all,
>            I need some help regarding reading output file (I used vc-relax
> including ensemble DFT- [i am using that for geometry optimization not md
> calculation] option implemented in cp code in espresso-3.2).
>   Is there any keyword or option by which I can read the energy of each
> iteration in order to check the convergence.
>        Thanks in advance.
>                                      shruba gangopadhyay
>                                      Graduate Student
>                                      Department of Chemistry
>                                     Nanoscience Technology center
>                                     University of Central Florida
>                                     Orlando, Fl-32826
>
> --
> 'friendship doubles joys and reduces sorrows by half' (Francis Bacon).




-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From cyrille.barreteau at cea.fr  Fri Jun  1 15:09:02 2007
From: cyrille.barreteau at cea.fr (Cyrille Barreteau)
Date: Fri, 01 Jun 2007 15:09:02 +0200
Subject: [Pw_forum] error message...Bis
Message-ID: <46601A6E.4060002@cea.fr>

Dear all

I have just posted a message concerning an MPI error message.
I have run again the same job but with the option
wf_collect= .false. (while it was set to .false. in the
previous cas) and now the code ends properly.

cyrille



===========================Previous Message======================
Dear pwscf users and developpers

I have recently compiled the new version of pwscf (3.2) on our
new cluster (I know a good experimentalist change only
one parameter at a time!)

I managed to compile the code and the execution is going fine until the 
very end.
Just after the writing of the output data file *.save
I get some message errors on the screen: forrtl: error (78): process 
killed (SIGTERM)
and in the output file: 1 process killed (possibly by Open MPI)!

Moreover the code  does not write the usual summary about the CPU time.

Any idea would be very welcome
========================================================================

-- 
==================================================================
Cyrille Barreteau  | phone : +33 (0)1 69 08 29 51
CEA Saclay         | fax   : +33 (0)1 69 08 84 46
DSM/DRECAM/SPCSI   | email cyrille.barreteau at cea.fr
Batiment 462       |
91191 Gif sur Yvette Cedex  FRANCE
          ~~~~~~~~~~~~~~~~~~~~~~~~
http://www-drecam.cea.fr/spcsi/index.php
http://www-drecam.cea.fr/Images/Pisp/cbarreteau/cbarreteau_fr.html
http://www-drecam.cea.fr/Phocea/Membres/Cours/index.php
================================================================== 



From cyrille.barreteau at cea.fr  Fri Jun  1 14:38:08 2007
From: cyrille.barreteau at cea.fr (Cyrille Barreteau)
Date: Fri, 01 Jun 2007 14:38:08 +0200
Subject: [Pw_forum] error message
Message-ID: <46601330.5090506@cea.fr>

Dear pwscf users and developpers

I have recently compiled the new version of pwscf (3.2) on our
new cluster (I know a good experimentalist change only
one parameter at a time!)

I managed to compile the code and the execution is going fine until the 
very end.
Just after the writing of the output data file *.save
I get some message errors on the screen: forrtl: error (78): process 
killed (SIGTERM)
and in the output file: 1 process killed (possibly by Open MPI)!

Moreover the code  does not write the usual summary about the CPU time.

Any idea would be very welcome

   cyrille

==================================================================
Cyrille Barreteau  | phone : +33 (0)1 69 08 29 51
CEA Saclay         | fax   : +33 (0)1 69 08 84 46
DSM/DRECAM/SPCSI   | email cyrille.barreteau at cea.fr
Batiment 462       |
91191 Gif sur Yvette Cedex  FRANCE
           ~~~~~~~~~~~~~~~~~~~~~~~~
http://www-drecam.cea.fr/spcsi/index.php
http://www-drecam.cea.fr/Images/Pisp/cbarreteau/cbarreteau_fr.html
http://www-drecam.cea.fr/Phocea/Membres/Cours/index.php
==================================================================




From niuli1978 at yahoo.com.cn  Fri Jun  1 17:26:35 2007
From: niuli1978 at yahoo.com.cn (li niu)
Date: Fri, 1 Jun 2007 23:26:35 +0800 (CST)
Subject: [Pw_forum] the procedure of calculating the Raman tensor using the finite electric field method
In-Reply-To: <20070601043201.15352.85754.Mailman@democritos.sissa.it>
Message-ID: <600786.62363.qm@web15008.mail.cnb.yahoo.com>

Dear all.
Thanks for your advice!
I'm sure that the positions from CPMD are correctly passed to the scf code because
I have checked the input geometry using xcrysden. The atomic positions of *.xyz file from 
CPMD are the same with positions in the case of xcysden-display-unit of repetition-translational
asummetric unit.
And the microstructures,electric structures and optical properties of this semiconductor model 
have been analyed and published.  
Why are the forces and stress so big?
I should use vc-relax (pw.x code) to compute the equilibrium geometry 
before running finite electric field method to calculate Raman tensor. Is it right?
  Bests,
   
  Niu Li
Harbin Institute of Technology
China


       
---------------------------------
 ??????3.5G???20M???
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From cyrille.barreteau at cea.fr  Fri Jun  1 17:22:50 2007
From: cyrille.barreteau at cea.fr (Cyrille Barreteau)
Date: Fri, 01 Jun 2007 17:22:50 +0200
Subject: [Pw_forum] MPI error and wf_collect
Message-ID: <466039CA.8020709@cea.fr>

Dear all

This is the continuation of my previous email.
To summarize my problem:
when I run a parallel version of pw.x with wf_collect=.false.
the code runs smoothly but with wf_collect=.true. I get the
following error message "n" process killed (possibly by Open MPI)!
at the very end of the code (just after the writing of the
.save files and before the CPU time).

Moreover I thought that everything should be put in a single file
when wf_collect=.true. But this is not at all the case. I even have
more files than with wf_collect=.false.

In case of wf_collect=.true.
I got the following files:
 *.igk_nproc *.wfc_nproc files and *.save directory which contains  
K*****(number of Kpoints)
 directories

In case of wf_collect=.false.
I do not have the *.igk_nproc *.wfc_nproc files

cyrille

-- 
==================================================================
Cyrille Barreteau  | phone : +33 (0)1 69 08 29 51
CEA Saclay         | fax   : +33 (0)1 69 08 84 46
DSM/DRECAM/SPCSI   | email cyrille.barreteau at cea.fr
Batiment 462       |
91191 Gif sur Yvette Cedex  FRANCE
          ~~~~~~~~~~~~~~~~~~~~~~~~
http://www-drecam.cea.fr/spcsi/index.php
http://www-drecam.cea.fr/Images/Pisp/cbarreteau/cbarreteau_fr.html
http://www-drecam.cea.fr/Phocea/Membres/Cours/index.php
================================================================== 



From nakhmanson at anl.gov  Fri Jun  1 18:44:58 2007
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Fri, 01 Jun 2007 11:44:58 -0500
Subject: [Pw_forum] the procedure of calculating the Raman tensor using the
 finite electric field method
In-Reply-To: <600786.62363.qm@web15008.mail.cnb.yahoo.com>
References: <600786.62363.qm@web15008.mail.cnb.yahoo.com>
Message-ID: <46604D0A.3050000@anl.gov>


li niu wrote:
> Dear all.
> Thanks for your advice!
> I'm sure that the positions from CPMD are correctly passed to the scf 
> code because
> I have checked the input geometry using xcrysden. The atomic positions 
> of *.xyz file from
> CPMD are the same with positions in the case of xcysden-display-unit of 
> repetition-translational
> asummetric unit.

 > Why are the forces and stress so big?

As you mentioned yourself, CPMD and PW use different functionals. The
minimum-energy structural configurations that these functionals find
for your model will not be the same. However, they should be reasonably
close to each other if no mistakes were made during the CPMD quench.
It is up to you to decide what is "reasonable," but IMHO the stress
on your cell is a bit large. This might suggest that the CPMD quench
has not been done carefully enough, and your PW calculation shows it.
But my previous comment was that, in general, it is quite hard to
converge to a well relaxed configuration with the "quench-from-the-melt"
procedure (this requires a long time and careful control of temperature),
and it does not matter what particular approach (CPMD, PW, TB, etc) you
are using.


> And the microstructures,electric structures and optical properties of 
> this semiconductor model
> have been analyed and published. 

And this is not a proof that the model that you are using is an
accurate one (people can publish anything they want these days).
In any case, PLZ provide a reference.

> I should use vc-relax (pw.x code) to compute the equilibrium geometry
> before running finite electric field method to calculate Raman tensor. 
> Is it right?

And how can you compute phonons if your system is not at equilibrium?
However, you have plenty of problems (as indicated in your previous
message) getting to equilibrium. It is bad (but well expected) that
your cell becomes non-cubic during stress relaxation. You should
either force it to stay cubic by manipulating the stress-tensor
components or work at some reasonable fixed volume.

Then, since you will re-relax this model from its minimum-energy
configuration found with CPMD, its structural characteristics will
change. So, before you do anything else with it, you will need to
check that you model is still structurally sound. This includes
computing RDF (should match experiment), bond/dihedral angle
distributions (the former should be narrow enough), EDOS (should
have a gap) and VDOS (should also match experiment). Atom coordination
analysis is a plus too, since a good model should be 99.9% (or
whatever it is experimentally for ta-C) 4-fold coordinated. Only after
you convince yourself that the properties of your model are in reasonable
agreement with experiment, you can proceed and compute the Raman tensor
for it, so good luck with all that.

In general, creating models for amorphous tetrahedral solids is
an *art* and the level of questions that you are asking shows that you
do not understand how this process works. There are many well-known
(both correct and incorrect) papers on that and you should read them
before you start blindly burning your CPU time. Read the WWW PRL
paper I mentioned in my previous e-mail and then read some more
recent papers that are quoting it. Then do the same with Car-Parrinello
PRL (1988).


-- 
*********************************************************
  Serge M. Nakhmanson               phone: (630) 252-5205
  Assistant Scientist                 fax: (630) 252-4798
  MSD-212, Rm. C-224
  Argonne National Laboratory
  9700 S. Cass Ave.
  Argonne, IL 60439
*********************************************************


From marzari at MIT.EDU  Sun Jun  3 17:54:17 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Sun, 03 Jun 2007 11:54:17 -0400
Subject: [Pw_forum] Roberto Car Symposium
Message-ID: <4662E429.3080400@mit.edu>


Dear Colleague,


we have the pleasure to announce that a symposium in honor
of Roberto Car and to celebrate his 60th birthday will be
held in Trieste on June 21-23 2007.

Attendance is open and free, but *it is necessary to register*
on a first-come, first-served basis (room capacity constrains
us to a maximum of 120 participants, including the speakers).

Registration requires simply sending an email to
carsymposium at mit.edu , listing name and affiliation
(note - if you are a speaker or a symposium chair, you are
already registered, and there is nothing to do).

Further informations and the symposium program are available
at http://users.ictp.it/~cm/Car_Symposium.html , together with
a list of some convenient hotels in Trieste . We regret that
we cannot provide further help with logistics.

Hoping to see you in Trieste,


Giulia Galli, Ralph Gebauer, Nicola Marzari, and Sandro Scandolo


-- 
---------------------------------------------------------------------
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 clie at aphy.iphy.ac.cn  Sun Jun  3 18:02:28 2007
From: clie at aphy.iphy.ac.cn (clie)
Date: Sun, 03 Jun 2007 16:02:28 GMT
Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #1497 - 4 msgs
In-Reply-To: <20070531140903.6687.99534.Mailman@democritos.sissa.it> 
References: <20070531140903.6687.99534.Mailman@democritos.sissa.it>
Message-ID: <20070603160228.6186.eqmail@aphy.iphy.ac.cn>


> Dear Miguel,
  thank you very much for your useful suggestions, which are very important to m
y calculation. I do  some work about EPC of hydrates just now and there are so m
any things to learn for me. If possible, we can often exchange our results and i
deas, and i would be very appreciate if you can give me more suggestions about m
y work. 




> Dear clie,
> 
> First of all, you have more severe issues than your script not working.
> Your structure isn\\'t stable (at least ph.x doesn\\'t think it is). See the
> 13!!! imaginary frequencies you get at (0 0.5 0). I haven\\'t seen the gamma
> frequencies, but if you have more thant three negative frequencies there,
> you should relax your structure. If not, double your cell in the b axis and
> relax. I\\'d also suggest increasing the cutoff, since 15 Ry seems a bit too
> small for me.
> 
> Anyway, I\\'d guess your issues are related to the K_POINTS of each scf run.
> I\\'d change it for
> 
> K_POINTS {automatic}
> 16 16 16  0 0 0
> 
> in the fine scf run. In a similar fashion, the less fine scf run should be
> 
> K_POINTS {automatic}
> 8 8 8  0 0 0
> 
> Finally, some of us would be grateful if you signed your messages with your
> real name and affiliation. Especially because I am also working on hydrides
> and would be glad to read your results once you publish them ;-)
> 
> Have a nice day,
> 
> Miguel
> 
> -- 
> ----------------------------------------
> Miguel Mart?nez Canales
> Dto. F?sica de la Materia Condensada
> UPV/EHU
> Facultad de Ciencia y Tecnolog?a
> Apdo. 644
> 48080 Bilbao (Spain)
> Fax:  +34 94 601 3500
> Tlf:  +34 94 601 5437
> ----------------------------------------
> 
>  "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
> 
>--------------------------------------------------------------
Li Zhi 
Academy  Of  Science, China
clie at aphy.iphy.ac.cn



From kondor.jess at gmail.com  Mon Jun  4 20:24:21 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Mon, 4 Jun 2007 13:24:21 -0500
Subject: [Pw_forum] big atomic forces
Message-ID: <1d9d5d9d0706041124v2454c6ddnc78e261db87cecf7@mail.gmail.com>

Hello, everybody,

 I have a question. I relaxed a surface using 8x8x1 k-point mesh and 'm-v'
smearing method with degauss=0.01 with criteria for forces 4.d-4 . Then I
performed 'scf' calculation with increased number of k-points (12x12x1) and
turn on an option 'tprnfor = .true.' in order to calculate forces. Forces
are OK (all lower than 4.d-4). But when I perform 'scf' with occupation
method 'tetrahedra'  (other parameters are the same), forces on atoms are
much higher (some of them are ~2.0d-3). Does it mean that geometry
relaxation is not been completed?

cheers,
   Jess
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From baroni at sissa.it  Mon Jun  4 21:06:48 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 4 Jun 2007 20:06:48 +0100
Subject: [Pw_forum] big atomic forces
In-Reply-To: <1d9d5d9d0706041124v2454c6ddnc78e261db87cecf7@mail.gmail.com>
References: <1d9d5d9d0706041124v2454c6ddnc78e261db87cecf7@mail.gmail.com>
Message-ID: <4F51FF2F-720B-4DFE-BC9F-DB2B364A03FA@sissa.it>

Others may have better answers than me, but ...

1) I do not know how forces are calculated with tetrahedra, but I  
think fear that the total energy calculated with tetrahedra is not  
variations, so that Helmann Feynman forces may have some problems ...

2) Not that a force of 1d-3 is that large after all ...

As said, other answers may be more illuminating than mine.

Stefano

On Jun 4, 2007, at 7:24 PM, Jess Kondor wrote:

>
> Hello, everybody,
>
>  I have a question. I relaxed a surface using 8x8x1 k-point mesh  
> and 'm-v' smearing method with degauss=0.01 with criteria for  
> forces 4.d-4 . Then I performed 'scf' calculation with increased  
> number of k-points (12x12x1) and turn on an option 'tprnfor  
> = .true.' in order to calculate forces. Forces are OK (all lower  
> than 4.d-4). But when I perform 'scf' with occupation method  
> 'tetrahedra'  (other parameters are the same), forces on atoms are  
> much higher (some of them are ~2.0d-3). Does it mean that geometry  
> relaxation is not been completed?
>
> cheers,
>    Jess
>

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

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



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From baroni at sissa.it  Mon Jun  4 21:07:59 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 4 Jun 2007 20:07:59 +0100
Subject: [Pw_forum] big atomic forces
In-Reply-To: <1d9d5d9d0706041124v2454c6ddnc78e261db87cecf7@mail.gmail.com>
References: <1d9d5d9d0706041124v2454c6ddnc78e261db87cecf7@mail.gmail.com>
Message-ID: <CA2919F4-4ED0-45EE-8091-0AA157A2D9D6@sissa.it>

PS: do not forget to attach a signature file with your affiliation  
etc., if you feel like that ...
cheers - S.

On Jun 4, 2007, at 7:24 PM, Jess Kondor wrote:

>
> Hello, everybody,
>
>  I have a question. I relaxed a surface using 8x8x1 k-point mesh  
> and 'm-v' smearing method with degauss=0.01 with criteria for  
> forces 4.d-4 . Then I performed 'scf' calculation with increased  
> number of k-points (12x12x1) and turn on an option 'tprnfor  
> = .true.' in order to calculate forces. Forces are OK (all lower  
> than 4.d-4). But when I perform 'scf' with occupation method  
> 'tetrahedra'  (other parameters are the same), forces on atoms are  
> much higher (some of them are ~2.0d-3). Does it mean that geometry  
> relaxation is not been completed?
>
> cheers,
>    Jess
>

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

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



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From baroni at sissa.it  Mon Jun  4 21:09:55 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 4 Jun 2007 20:09:55 +0100
Subject: [Pw_forum] big atomic forces
In-Reply-To: <4F51FF2F-720B-4DFE-BC9F-DB2B364A03FA@sissa.it>
References: <1d9d5d9d0706041124v2454c6ddnc78e261db87cecf7@mail.gmail.com> <4F51FF2F-720B-4DFE-BC9F-DB2B364A03FA@sissa.it>
Message-ID: <F877A707-41FF-42FE-A559-E4F2EB9DA93D@sissa.it>

PPS: sorry for the improbable English of my previous message ...
S.

On Jun 4, 2007, at 8:06 PM, Stefano Baroni wrote:

> Others may have better answers than me, but ...
>
> 1) I do not know how forces are calculated with tetrahedra, but I  
> think fear that the total energy calculated with tetrahedra is not  
> variations, so that Helmann Feynman forces may have some problems ...
>
> 2) Not that a force of 1d-3 is that large after all ...
>
> As said, other answers may be more illuminating than mine.
>
> Stefano
>
> On Jun 4, 2007, at 7:24 PM, Jess Kondor wrote:
>
>>
>> Hello, everybody,
>>
>>  I have a question. I relaxed a surface using 8x8x1 k-point mesh  
>> and 'm-v' smearing method with degauss=0.01 with criteria for  
>> forces 4.d-4 . Then I performed 'scf' calculation with increased  
>> number of k-points (12x12x1) and turn on an option 'tprnfor  
>> = .true.' in order to calculate forces. Forces are OK (all lower  
>> than 4.d-4). But when I perform 'scf' with occupation method  
>> 'tetrahedra'  (other parameters are the same), forces on atoms are  
>> much higher (some of them are ~2.0d-3). Does it mean that geometry  
>> relaxation is not been completed?
>>
>> cheers,
>>    Jess
>>
>
> ---
> Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -  
> Trieste
> [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)
>
> Please, if possible, don't  send me MS Word or PowerPoint attachments
> Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>

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

Please, if possible, don't  send me MS Word or PowerPoint attachments
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From bopengchemist at gmail.com  Tue Jun  5 05:51:29 2007
From: bopengchemist at gmail.com (Bo Peng)
Date: Tue, 5 Jun 2007 11:51:29 +0800
Subject: [Pw_forum] problem about MPI
Message-ID: <3faf0730706042051t7211bc3ex6b1da1ab54aad9d1@mail.gmail.com>

Dear all,

I have recently downloaded and installed PWscf 3.2.2. After installation,
I am trying to
run the examples. My cluster is a Linux PC cluster with MPI (mpich), use LSF
system
to manage the jobs. As the manual said (P. 20) "... if your machine does not
support
interactive use, you must run the commands specified below through the batch
queueing
system installed on that machine...."

I have used a script to submit the job:
??????????????????????????
#!/bin/bash
#BSUB -q demo
#BSUB -J ex01
#BSUB -R span[ptile=2]
#BSUB -o %J.log
#BSUB -a mpich_gm
#BSUB -c 4800:00
#BSUB -n 16

pw.x < si.scf.cg.in > si.scf.cg.out
??????????????????????????
errors?
...
<MPICH-GM> Error: Need to obtain the job magic number in GMPI_MAGIC !
/nfs/s07r2p1/beauchemist/.lsbatch/1181009945.198656.shell: line 10: 27824
Broken pipe       pw.x < si.scf.cg.in > si.scf.cg.out

Then I change the script to:
???????????????????????????
#!/bin/bash
...
#BSUB -n 16

mpirun -np 16 pw.x -npool 8 < si.scf.cg.in > si.scf.cg.out

???????????????????????????
there is no error but the .out file is empty.

When change it to?
???????????????????????????
#!/bin/bash
...
#BSUB -n 16

mpirun.lsf pw.x < si.scf.cg.in > si.scf.cg.out
???????????????????????????
error?
1 - MPI_COMM_RANK : Null communicator
[1]  Aborting program !
[1] Aborting program!
0 - MPI_COMM_RANK : Null communicator
[0]  Aborting program !
[0] Aborting program!

I do not know what is the case?Any help is appreciated!

PS: the followed is the summary of make.sys file (other variables are
empty):

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

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

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


DFLAGS         =  -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA
FDFLAGS        = $(DFLAGS)

IFLAGS         = -I../include

MODFLAGS       = -I./  -I../Modules  -I../iotk/src \
                 -I../PW  -I../PH  -I../CPV

MPIF90         = mpif90
CC             = icc
F77            = ifort

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

CFLAGS         = -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS       = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS         = -O2 -tpp6 -assume byterecl

FFLAGS_NOOPT   = -O0 -assume byterecl

BLAS_LIBS      = -L/opt/intel/mkl70/lib/32 -lmkl_ia32 -lguide -lpthread

LAPACK_LIBS    = -lmkl_lapack

MPI_LIBS       = /usr/local/mpich/smp/intel32/ssh/lib/libmpichf90.a

AR             = ar
ARFLAGS        = ruv
ARFLAGS_DYNAMIC= ruv

RANLIB         = ranlib

LIBOBJS        = ../flib/ptools.a ../flib/flib.a ../clib/clib.a
../iotk/src/libiotk.a

LIBS           = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS)
$(MASS_LIBS) $(PGPLOT_LIBS)
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From mbaris at metu.edu.tr  Tue Jun  5 07:46:53 2007
From: mbaris at metu.edu.tr (mbaris at metu.edu.tr)
Date: Tue, 05 Jun 2007 08:46:53 +0300
Subject: [Pw_forum] problem about MPI
In-Reply-To: <3faf0730706042051t7211bc3ex6b1da1ab54aad9d1@mail.gmail.com>
References: <3faf0730706042051t7211bc3ex6b1da1ab54aad9d1@mail.gmail.com>
Message-ID: <20070605084653.e30kwrlm3ylwco04@webmail2.metu.edu.tr>

Dear Bo Peng,

doing a quick google dig about the problem, I come up with
http://www.myri.com/serve/cache/236.html

that is, your secondary script for generating a dynamic port number 
used in mpi intercommunication is not working. This is most probably an 
installation issue
regarding LSF, or do you have to call such a script yourself in the 
submit batch file?

in the second case, are you sure you are using myrinet version of the 
mpi? (I suppose you are on myrinet, as the first error suggests) And 
besides that, it always is a very bad idea to try to bypass tight 
integration of grid engines, often admins try to terminate runaway jobs 
in nodes automatically. Also I am not sure you are bypassing it 
correctly in that script, are you calling mpirun two times?

I think, this problem is not related by espresso, rather it is a LSF 
issue on your site.

If you are looking for an alternative, may I suggest sun grid engine?

good day,
Osman Baris Malcioglu
METU Physics
Ankara






Alinti Bo Peng <bopengchemist at gmail.com>

> Dear all,
>
> I have recently downloaded and installed PWscf 3.2.2. After installation,
> I am trying to
> run the examples. My cluster is a Linux PC cluster with MPI (mpich), use LSF
> system
> to manage the jobs. As the manual said (P. 20) "... if your machine does not
> support
> interactive use, you must run the commands specified below through the batch
> queueing
> system installed on that machine...."
>
> I have used a script to submit the job:
> ??????????????????????????
> #!/bin/bash
> #BSUB -q demo
> #BSUB -J ex01
> #BSUB -R span[ptile=2]
> #BSUB -o %J.log
> #BSUB -a mpich_gm
> #BSUB -c 4800:00
> #BSUB -n 16
>
> pw.x < si.scf.cg.in > si.scf.cg.out
> ??????????????????????????
> errors?
> ...
> <MPICH-GM> Error: Need to obtain the job magic number in GMPI_MAGIC !
> /nfs/s07r2p1/beauchemist/.lsbatch/1181009945.198656.shell: line 10: 27824
> Broken pipe       pw.x < si.scf.cg.in > si.scf.cg.out
>
> Then I change the script to:
> ???????????????????????????
> #!/bin/bash
> ...
> #BSUB -n 16
>
> mpirun -np 16 pw.x -npool 8 < si.scf.cg.in > si.scf.cg.out
>
> ???????????????????????????
> there is no error but the .out file is empty.
>
> When change it to?
> ???????????????????????????
> #!/bin/bash
> ...
> #BSUB -n 16
>
> mpirun.lsf pw.x < si.scf.cg.in > si.scf.cg.out
> ???????????????????????????
> error?
> 1 - MPI_COMM_RANK : Null communicator
> [1]  Aborting program !
> [1] Aborting program!
> 0 - MPI_COMM_RANK : Null communicator
> [0]  Aborting program !
> [0] Aborting program!
>
> I do not know what is the case?Any help is appreciated!
>
> PS: the followed is the summary of make.sys file (other variables are
> empty):
>
> .f90.o:
>        $(MPIF90) $(F90FLAGS) -c $<
>
> .f.o:
>        $(F77) $(FFLAGS) -c $<
>
> .c.o:
>        $(CC) $(CFLAGS)  -c $<
>
>
> DFLAGS         =  -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA
> FDFLAGS        = $(DFLAGS)
>
> IFLAGS         = -I../include
>
> MODFLAGS       = -I./  -I../Modules  -I../iotk/src \
>                 -I../PW  -I../PH  -I../CPV
>
> MPIF90         = mpif90
> CC             = icc
> F77            = ifort
>
> CPP            = cpp
> CPPFLAGS       = -P -traditional $(DFLAGS) $(IFLAGS)
>
> CFLAGS         = -O3 $(DFLAGS) $(IFLAGS)
> F90FLAGS       = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS)
> FFLAGS         = -O2 -tpp6 -assume byterecl
>
> FFLAGS_NOOPT   = -O0 -assume byterecl
>
> BLAS_LIBS      = -L/opt/intel/mkl70/lib/32 -lmkl_ia32 -lguide -lpthread
>
> LAPACK_LIBS    = -lmkl_lapack
>
> MPI_LIBS       = /usr/local/mpich/smp/intel32/ssh/lib/libmpichf90.a
>
> AR             = ar
> ARFLAGS        = ruv
> ARFLAGS_DYNAMIC= ruv
>
> RANLIB         = ranlib
>
> LIBOBJS        = ../flib/ptools.a ../flib/flib.a ../clib/clib.a
> ../iotk/src/libiotk.a
>
> LIBS           = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS)
> $(MASS_LIBS) $(PGPLOT_LIBS)
>





From ding at sissa.it  Tue Jun  5 10:02:26 2007
From: ding at sissa.it (Xunlei Ding)
Date: Tue, 05 Jun 2007 10:02:26 +0200
Subject: [Pw_forum] big atomic forces
In-Reply-To: <1d9d5d9d0706041124v2454c6ddnc78e261db87cecf7@mail.gmail.com>
References: <1d9d5d9d0706041124v2454c6ddnc78e261db87cecf7@mail.gmail.com>
Message-ID: <46651892.604@sissa.it>

Dear Jess,
Is your system metals or /semiconductors and insulators ?/
Tetrahedron is good for scf calculation, but not for relaxation of 
metals, because of the forces from this method are not good for metals.

I found below on web. Hope it is useful.
For the calculation of the / total energy/ in bulk materials we 
recommend the tetrahedron method with Bl?chl corrections. This method 
also gives a good account for the electronic density of states (DOS). 
The only drawback is that the methods is not variational with respect to 
the partial occupancies. Therefore the calculated forces are wrong by 5 
to 10 % in metals.

Best regards,
Ding

Jess Kondor wrote:

>
> Hello, everybody,
>
>  I have a question. I relaxed a surface using 8x8x1 k-point mesh and 
> 'm-v' smearing method with degauss=0.01 with criteria for forces 4.d-4 
> . Then I performed 'scf' calculation with increased number of k-points 
> (12x12x1) and turn on an option 'tprnfor = .true.' in order to 
> calculate forces. Forces are OK (all lower than 4.d-4). But when I 
> perform 'scf' with occupation method 'tetrahedra'  (other parameters 
> are the same), forces on atoms are much higher (some of them are 
> ~2.0d-3). Does it mean that geometry relaxation is not been completed?
>
> cheers,
>    Jess
>


From baroni at sissa.it  Tue Jun  5 11:27:43 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Tue, 5 Jun 2007 10:27:43 +0100
Subject: [Pw_forum] problem about MPI
In-Reply-To: <3faf0730706042051t7211bc3ex6b1da1ab54aad9d1@mail.gmail.com>
References: <3faf0730706042051t7211bc3ex6b1da1ab54aad9d1@mail.gmail.com>
Message-ID: <5AA5A21A-9B32-40EA-9FB1-16D1110ACD73@sissa.it>

Dear Bo Peng,

welcome to our community. I am pleased that your post has been  
answered very quickly and I am sure so will you. We would greatly  
appreciate your signing in full (with name and affiliation) your  
correspondence with us. Is this possible?

Thanks - Stefano Baroni


On Jun 5, 2007, at 4:51 AM, Bo Peng wrote:

> Dear all,
>
> I have recently downloaded and installed PWscf 3.2.2. After  
> installation, I am trying to
> run the examples. My cluster is a Linux PC cluster with MPI  
> (mpich), use LSF system
> to manage the jobs. As the manual said (P. 20) "... if your machine  
> does not support
> interactive use, you must run the commands specified below through  
> the batch queueing
> system installed on that machine...."
>
> I have used a script to submit the job:
> ??????????????????????????
> #!/bin/bash
> #BSUB -q demo
> #BSUB -J ex01
> #BSUB -R span[ptile=2]
> #BSUB -o %J.log
> #BSUB -a mpich_gm
> #BSUB -c 4800:00
> #BSUB -n 16
>
> pw.x <  si.scf.cg.in > si.scf.cg.out
> ??????????????????????????
> errors?
> ...
> <MPICH-GM> Error: Need to obtain the job magic number in GMPI_MAGIC !
> /nfs/s07r2p1/beauchemist/.lsbatch/1181009945.198656.shell: line 10:  
> 27824
> Broken pipe       pw.x < si.scf.cg.in > si.scf.cg.out
>
> Then I change the script to:
> ???????????????????????????
> #!/bin/bash
> ...
> #BSUB -n 16
>
> mpirun -np 16 pw.x -npool 8 < si.scf.cg.in > si.scf.cg.out
>
> ???????????????????????????
> there is no error but the .out file is empty.
>
> When change it to?
> ???????????????????????????
> #!/bin/bash
> ...
> #BSUB -n 16
>
> mpirun.lsf pw.x < si.scf.cg.in > si.scf.cg.out
> ???????????????????????????
> error?
> 1 - MPI_COMM_RANK : Null communicator
> [1]  Aborting program !
> [1] Aborting program!
> 0 - MPI_COMM_RANK : Null communicator
> [0]  Aborting program !
> [0] Aborting program!
>
> I do not know what is the case?Any help is appreciated!
>
> PS: the followed is the summary of make.sys file (other variables  
> are empty):
> .f90.o:
>         $(MPIF90) $(F90FLAGS) -c $<
>
> .f.o:
>         $(F77) $(FFLAGS) -c $<
>
> .c.o:
>         $(CC) $(CFLAGS)  -c $<
>
>
> DFLAGS         =  -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI - 
> D__PARA
> FDFLAGS        = $(DFLAGS)
>
> IFLAGS         = -I../include
>
> MODFLAGS       = -I./  -I../Modules  -I../iotk/src \
>                  -I../PW  -I../PH  -I../CPV
>
> MPIF90         = mpif90
> CC             = icc
> F77            = ifort
>
> CPP            = cpp
> CPPFLAGS       = -P -traditional $(DFLAGS) $(IFLAGS)
>
> CFLAGS         = -O3 $(DFLAGS) $(IFLAGS)
> F90FLAGS       = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $ 
> (MODFLAGS)
> FFLAGS         = -O2 -tpp6 -assume byterecl
>
> FFLAGS_NOOPT   = -O0 -assume byterecl
>
> BLAS_LIBS      = -L/opt/intel/mkl70/lib/32 -lmkl_ia32 -lguide - 
> lpthread
>
> LAPACK_LIBS    = -lmkl_lapack
>
> MPI_LIBS       = /usr/local/mpich/smp/intel32/ssh/lib/libmpichf90.a
>
> AR             = ar
> ARFLAGS        = ruv
> ARFLAGS_DYNAMIC= ruv
>
> RANLIB         = ranlib
>
> LIBOBJS        = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../ 
> iotk/src/libiotk.a
>
> LIBS           = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $ 
> (MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS)
>
>
>
>

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

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 bopengchemist at gmail.com  Tue Jun  5 12:27:10 2007
From: bopengchemist at gmail.com (Bo Peng)
Date: Tue, 5 Jun 2007 18:27:10 +0800
Subject: [Pw_forum] Re: problem about MPI
Message-ID: <3faf0730706050327n608f7764l372b67f099c3bce8@mail.gmail.com>

Dear colleage,

sorry for my carelessness.

M>Dear Bo Peng,

M>doing a quick google dig about the problem, I come up with
M>http://www.myri.com/serve/cache/236.html
Thank you for your linking.

M>that is, your secondary script for generating a dynamic port number
M>used in mpi intercommunication is not working. This is most probably an
M>installation issue
M>regarding LSF, or do you have to call such a script yourself in the
M>submit batch file?
yes, the cluster do not support the interactive submit.

M>in the second case, are you sure you are using myrinet version of the
M>mpi?
yes.

M>(I suppose you are on myrinet, as the first error suggests) And
M>besides that, it always is a very bad idea to try to bypass tight
M>integration of grid engines, often admins try to terminate runaway jobs
M>in nodes automatically. Also I am not sure you are bypassing it
M>correctly in that script, are you calling mpirun two times?
In the sencondary file, it is really bad to do so as you said, so
I created the
third file to submit my jobs. The errors related to the third file,
"1 - MPI_COMM_RANK : Null communicator
 [1]  Aborting program !
 [1] Aborting program!
 0 - MPI_COMM_RANK : Null communicator
 [0]  Aborting program !
 [0] Aborting program!"
may be the real case.

M>I think, this problem is not related by espresso, rather it is a LSF
M>issue on your site.
I agree with you.

M>If you are looking for an alternative, may I suggest sun grid engine?
Thank you for your suggenstion.

M>good day,
M>Osman Baris Malcioglu
M>METU Physics
M>Ankara

Regards,

Bo Peng

BTW: It is my pleasure to join the community. :)

+++++++++++++++++++++++++++++++++++++++++++++++++
Bo Peng, Ph.D Candidate, Department of Chemistry, Nankai University,
TianJin, P.R.China
phone: (86)022-23506808
email: bopengchemist at gmail.com
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From giannozz at nest.sns.it  Tue Jun  5 13:25:40 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 5 Jun 2007 13:25:40 +0200
Subject: [Pw_forum] About phonon frequency in .dynG out-put file
In-Reply-To: <974823.40097.qm@web50603.mail.re2.yahoo.com>
References: <974823.40097.qm@web50603.mail.re2.yahoo.com>
Message-ID: <E43B086D-1089-4133-8254-578CD44D2CAF@nest.sns.it>

On May 31, 2007, at 19:55 , vu ongphuong wrote:

> My question is the  omega's  in the .dynG out-put file is the  
> eigenvalues of dynamical matrix i.e the square of phonon  
> frequencies or phonon frequencies themselves?

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




From giannozz at nest.sns.it  Tue Jun  5 14:38:02 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 5 Jun 2007 14:38:02 +0200
Subject: [Pw_forum] MPI error and wf_collect
In-Reply-To: <466039CA.8020709@cea.fr>
References: <466039CA.8020709@cea.fr>
Message-ID: <0A3846E2-00E7-463A-AD14-9A432FB94434@nest.sns.it>

On Jun 1, 2007, at 17:22 , Cyrille Barreteau wrote:

> Moreover I thought that everything should be put in a single file
> when wf_collect=.true.

wf_collect=.true. collects Kohn-Sham orbitals for each k-point
into a single file, but there is a file per k-point (stored into the
K*****/ directories). Everything you need is in the .save/ directory.

> In case of wf_collect=.true. I got the following files:
> *.igk_nproc *.wfc_nproc files
> and *.save directory which contains  K*****(number of Kpoints)  
> directories

_nproc = _1, _2, _3, ..., or _nproc = _nproc ? I cannot find any place
in the code where such files are written.

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




From cyrille.barreteau at cea.fr  Tue Jun  5 15:38:14 2007
From: cyrille.barreteau at cea.fr (Cyrille Barreteau)
Date: Tue, 05 Jun 2007 15:38:14 +0200
Subject: [Pw_forum] MPI error and wf_collect
In-Reply-To: <0A3846E2-00E7-463A-AD14-9A432FB94434@nest.sns.it>
References: <466039CA.8020709@cea.fr> <0A3846E2-00E7-463A-AD14-9A432FB94434@nest.sns.it>
Message-ID: <46656746.7060104@cea.fr>

Paolo,

I have attached to my email a file containing the list of the different
files contained in the "outdir" directory (which in my case is tmp)

You will see that *.igk_nproc *.wfc_nproc (nproc=1,2,3...64) files
do exist... together with a lot of others..
These files do not exist in the case of wf_collect=.false.

Let me also add that this test calculation contains 128 k points
and was run on 16 nodes and 64 processors.

  cyrille

-- 
==================================================================
Cyrille Barreteau  | phone : +33 (0)1 69 08 29 51
CEA Saclay         | fax   : +33 (0)1 69 08 84 46
DSM/DRECAM/SPCSI   | email cyrille.barreteau at cea.fr
Batiment 462       |
91191 Gif sur Yvette Cedex  FRANCE
          ~~~~~~~~~~~~~~~~~~~~~~~~
http://www-drecam.cea.fr/spcsi/index.php
http://www-drecam.cea.fr/Images/Pisp/cbarreteau/cbarreteau_fr.html
http://www-drecam.cea.fr/Phocea/Membres/Cours/index.php
================================================================== 



Paolo Giannozzi wrote:

>
> On Jun 1, 2007, at 17:22 , Cyrille Barreteau wrote:
>
>> Moreover I thought that everything should be put in a single file
>> when wf_collect=.true.
>
>
> wf_collect=.true. collects Kohn-Sham orbitals for each k-point
> into a single file, but there is a file per k-point (stored into the
> K*****/ directories). Everything you need is in the .save/ directory.
>
>> In case of wf_collect=.true. I got the following files:
>> *.igk_nproc *.wfc_nproc files
>> and *.save directory which contains  K*****(number of Kpoints)  
>> directories
>
>
> _nproc = _1, _2, _3, ..., or _nproc = _nproc ? I cannot find any place
> in the code where such files are written.
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



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From kondor.jess at gmail.com  Tue Jun  5 15:53:46 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Tue, 5 Jun 2007 08:53:46 -0500
Subject: [Pw_forum] big atomic forces
In-Reply-To: <46651892.604@sissa.it>
References: <1d9d5d9d0706041124v2454c6ddnc78e261db87cecf7@mail.gmail.com>
	 <46651892.604@sissa.it>
Message-ID: <1d9d5d9d0706050653p2fd00b63k18baaf5bac99dc40@mail.gmail.com>

 Hi Ding,

  According the DOS it is a small-gap semiconductor. By the way, I used
tetrahedron method only for 'scf' calculation using relaxed geometry
obtained with 'm-v' smearing method.

I found below on web. Hope it is useful.
> For the calculation of the / total energy/ in bulk materials we
> recommend the tetrahedron method with Bl?chl corrections. This method
> also gives a good account for the electronic density of states (DOS).
> The only drawback is that the methods is not variational with respect to
> the partial occupancies. Therefore the calculated forces are wrong by 5
> to 10 % in metals.
>
>
Yes, I am aware of that. That's why I didn't use 'tetrahedra' for geometry
relaxation.


cheers,

=====================================
 Jess Kondor

 PICYT, Av. Venustiano Carranza 2425-A,
  San Luis Potos? 78210, M?xico
=====================================
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From giannozz at nest.sns.it  Tue Jun  5 16:56:53 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 5 Jun 2007 16:56:53 +0200
Subject: [Pw_forum] MPI error and wf_collect
In-Reply-To: <46656746.7060104@cea.fr>
References: <466039CA.8020709@cea.fr> <0A3846E2-00E7-463A-AD14-9A432FB94434@nest.sns.it> <46656746.7060104@cea.fr>
Message-ID: <96A86723-579D-4582-A4EB-8DAC97838EEE@nest.sns.it>

On Jun 5, 2007, at 15:38 , Cyrille Barreteau wrote:

> You will see that *.igk_nproc *.wfc_nproc (nproc=1,2,3...64) files
> do exist... together with a lot of others..
> These files do not exist in the case of wf_collect=.false.

sure they do. The *igkN files are removed at the end of the
calculation, irrespective of wf_collect. The *wfcN files are
removed if wf_collect=.true. after the wave function is collected
to a single (per k-point) file ; they are left where they are (i.e. in
the directory containing the *.save/ directory) otherwise.
Of course, assuming that the code does not crash before
the end of execution.

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




From cyrille.barreteau at cea.fr  Tue Jun  5 18:51:54 2007
From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille)
Date: Tue, 5 Jun 2007 18:51:54 +0200
Subject: [Pw_forum] MPI error and wf_collect
References: <466039CA.8020709@cea.fr> <0A3846E2-00E7-463A-AD14-9A432FB94434@nest.sns.it> <46656746.7060104@cea.fr> <96A86723-579D-4582-A4EB-8DAC97838EEE@nest.sns.it>
Message-ID: <18E4AC9C2FAC504E994A6759DE5ABE8D20F132@DIODON.extra.cea.fr>


I guess it means that pw.x is crashing for an
unknown reason before the
files are removed! It is not really a problem 
if all the important files are saved! but that
I have to ckeck.

   cyrille

-------- Message d'origine--------
De: pw_forum-admin at pwscf.org de la part de Paolo Giannozzi
Date: mar. 05/06/2007 16:56
?: pw_forum at pwscf.org
Objet : Re: [Pw_forum] MPI error and wf_collect
 

On Jun 5, 2007, at 15:38 , Cyrille Barreteau wrote:

> You will see that *.igk_nproc *.wfc_nproc (nproc=1,2,3...64) files
> do exist... together with a lot of others..
> These files do not exist in the case of wf_collect=.false.

sure they do. The *igkN files are removed at the end of the
calculation, irrespective of wf_collect. The *wfcN files are
removed if wf_collect=.true. after the wave function is collected
to a single (per k-point) file ; they are left where they are (i.e. in
the directory containing the *.save/ directory) otherwise.
Of course, assuming that the code does not crash before
the end of execution.

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


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

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From kondor.jess at gmail.com  Tue Jun  5 22:43:42 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Tue, 5 Jun 2007 15:43:42 -0500
Subject: [Pw_forum] Fermi energy in 'scf' and 'nscf'
Message-ID: <1d9d5d9d0706051343i5bc72fbdn40d2e578acfa5c66@mail.gmail.com>

Dear users,

 I performed 'scf' and 'nscf' calculations with 'm-v' smearing method. In
the end of both calculations, the Fermi energy is the same. But if these
calculations are performed using 'tetrahedra', Fermi levels are different (
5.05 eV from 'scf' and 3.86 eV from 'nscf'). Is it normal?

cheers,


----
=====================================
Jess Kondor

PICYT, Av. Venustiano Carranza 2425-A,
San Luis Potos? 78210, M?xico
=====================================
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From rui_zhi_zhang at yahoo.com  Wed Jun  6 05:41:34 2007
From: rui_zhi_zhang at yahoo.com (ruizhi zhang)
Date: Tue, 5 Jun 2007 20:41:34 -0700 (PDT)
Subject: [Pw_forum] Reference about Total Energy Method used in PWscf
Message-ID: <440089.11095.qm@web39803.mail.mud.yahoo.com>

Dear all
   
  I try to understand how the total energy was calculated in PWscf. Can anyone give some reference that was used to implement total energy calculation?
   
  I found many research papers about total energy method, but I donot know which method is used by PWscf
   
  Thanks a lot 
  Ruizhi Zhang
   
    


--------------
Ruizhi Zhang, PhD
School of Physics and Microelectronics
Shandong University, Jinan, P.R.C.
       
---------------------------------
Moody friends. Drama queens. Your life? Nope! - their life, your story.
 Play Sims Stories at Yahoo! Games. 
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From lanhaiping at gmail.com  Wed Jun  6 08:22:24 2007
From: lanhaiping at gmail.com (lan haiping)
Date: Wed, 6 Jun 2007 14:22:24 +0800
Subject: [Pw_forum] Reference about Total Energy Method used in PWscf
In-Reply-To: <440089.11095.qm@web39803.mail.mud.yahoo.com>
References: <440089.11095.qm@web39803.mail.mud.yahoo.com>
Message-ID: <c92002fa0706052322g370b2399i7ab0e1659b7ff92d@mail.gmail.com>

Dear RZ,

 You can refer to
Rev. Mod. Phys. 64, 1045 - 1097 (1992) ,
iterative minimization techniques for ab initio total-energy calculations:
molecular dynamics and conjugate gradients .

This paper discussed most theory and technique detail about total energy
calculation, especially about PW method.

Regards,

H.P






On 6/6/07, ruizhi zhang <rui_zhi_zhang at yahoo.com> wrote:
>
> Dear all
>
> I try to understand how the total energy was calculated in PWscf. Can
> anyone give some reference that was used to implement total energy
> calculation?
>
> I found many research papers about total energy method, but I donot know
> which method is used by PWscf
>
> Thanks a lot
> Ruizhi Zhang
>
>
>
>
> --------------
> Ruizhi Zhang, PhD
> School of Physics and Microelectronics
> Shandong University, Jinan, P.R.C.
>
> ------------------------------
> Moody friends. Drama queens. Your life? Nope! - their life, your story.
> Play Sims Stories at Yahoo! Games.
> <http://us.rd.yahoo.com/evt=48224/*http://sims.yahoo.com/>
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From giannozz at nest.sns.it  Wed Jun  6 09:26:34 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 6 Jun 2007 09:26:34 +0200
Subject: [Pw_forum] Reference about Total Energy Method used in PWscf
In-Reply-To: <440089.11095.qm@web39803.mail.mud.yahoo.com>
References: <440089.11095.qm@web39803.mail.mud.yahoo.com>
Message-ID: <5EF662D3-9517-4EEC-B9A2-BFB37296D4C7@nest.sns.it>

On Jun 6, 2007, at 5:41 , ruizhi zhang wrote:

> I try to understand how the total energy was calculated in PWscf.  
> Can anyone give some reference that was used to implement total  
> energy calculation?

a (short) list of references can be found here:
http://www.quantum-espresso.org/wiki/index.php/Bibliography

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




From giannozz at nest.sns.it  Wed Jun  6 09:30:39 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 6 Jun 2007 09:30:39 +0200
Subject: [Pw_forum] Fermi energy in 'scf' and 'nscf'
In-Reply-To: <1d9d5d9d0706051343i5bc72fbdn40d2e578acfa5c66@mail.gmail.com>
References: <1d9d5d9d0706051343i5bc72fbdn40d2e578acfa5c66@mail.gmail.com>
Message-ID: <3837402B-A3D6-4993-8C63-6097CB648AB1@nest.sns.it>

On Jun 5, 2007, at 22:43 , Jess Kondor wrote:

>  I performed 'scf' and 'nscf' calculations with 'm-v' smearing  
> method. In the end of both calculations, the Fermi energy is the  
> same. But if these calculations are performed using 'tetrahedra',  
> Fermi levels are different ( 5.05 eV from 'scf' and 3.86 eV from  
> 'nscf'). Is it normal?

are the grid for scf and nscf the same? are you getting the same
Kohn-Sham eigenvalues?

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




From giannozz at nest.sns.it  Wed Jun  6 09:38:22 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 6 Jun 2007 09:38:22 +0200
Subject: [Pw_forum] error message
In-Reply-To: <46601330.5090506@cea.fr>
References: <46601330.5090506@cea.fr>
Message-ID: <F87F14D3-AF61-452D-81E5-8D1145706A83@nest.sns.it>

On Jun 1, 2007, at 14:38 , Cyrille Barreteau wrote:

> I have recently compiled the new version of pwscf (3.2) on our
> new cluster (I know a good experimentalist change only
> one parameter at a time!)

so let's try to be good experimentalists:
- is the problem present for specific data only, or is it always present
   whenever the option wf_collect=.true. is used?
- is it specific to the number of processors/pools used or not?
- if the problem is present for specific data only:
   - does it work on other machines/compilers/mpi libraries?
   - does it work for other versions of the code, or for the cvs  
version?
Paolo
---
Paolo Giannozzi, Democritos and University of Udine, Italy




From cyrille.barreteau at cea.fr  Wed Jun  6 10:08:25 2007
From: cyrille.barreteau at cea.fr (Cyrille Barreteau)
Date: Wed, 06 Jun 2007 10:08:25 +0200
Subject: [Pw_forum] error message
In-Reply-To: <F87F14D3-AF61-452D-81E5-8D1145706A83@nest.sns.it>
References: <46601330.5090506@cea.fr> <F87F14D3-AF61-452D-81E5-8D1145706A83@nest.sns.it>
Message-ID: <46666B79.3090607@cea.fr>

I have just done some tests on example01 input data si.scf.cg.in (10 
kpoints)
My conclusion is that it happens when wf_collect=.true. and
when npool is greater than 1

For example

nproc=10 npool=1 runs OK
but all other cases npool=2,5,10 crash

I have not tried yet the cvs version...
  cyrille

>
> On Jun 1, 2007, at 14:38 , Cyrille Barreteau wrote:
>
>> I have recently compiled the new version of pwscf (3.2) on our
>> new cluster (I know a good experimentalist change only
>> one parameter at a time!)
>
>
> so let's try to be good experimentalists:
> - is the problem present for specific data only, or is it always present
>   whenever the option wf_collect=.true. is used?
> - is it specific to the number of processors/pools used or not?
> - if the problem is present for specific data only:
>   - does it work on other machines/compilers/mpi libraries?
>   - does it work for other versions of the code, or for the cvs  version?
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



-- 
==================================================================
Cyrille Barreteau  | phone : +33 (0)1 69 08 29 51
CEA Saclay         | fax   : +33 (0)1 69 08 84 46
DSM/DRECAM/SPCSI   | email cyrille.barreteau at cea.fr
Batiment 462       |
91191 Gif sur Yvette Cedex  FRANCE
          ~~~~~~~~~~~~~~~~~~~~~~~~
http://www-drecam.cea.fr/spcsi/index.php
http://www-drecam.cea.fr/Images/Pisp/cbarreteau/cbarreteau_fr.html
http://www-drecam.cea.fr/Phocea/Membres/Cours/index.php
================================================================== 



From giannozz at nest.sns.it  Thu Jun  7 12:04:26 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 7 Jun 2007 12:04:26 +0200
Subject: [Pw_forum] error message
In-Reply-To: <46666B79.3090607@cea.fr>
References: <46601330.5090506@cea.fr> <F87F14D3-AF61-452D-81E5-8D1145706A83@nest.sns.it> <46666B79.3090607@cea.fr>
Message-ID: <BB28D461-10D0-4D73-9973-FDD80C6113BA@nest.sns.it>

On Jun 6, 2007, at 10:08 , Cyrille Barreteau wrote:

> I have just done some tests on example01 input data si.scf.cg.in
> (10 kpoints)
> My conclusion is that it happens when wf_collect=.true. and
> when npool is greater than 1

I cannot reproduce such an error on two different parallel
machines

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




From cyrille.barreteau at cea.fr  Thu Jun  7 12:17:41 2007
From: cyrille.barreteau at cea.fr (Cyrille Barreteau)
Date: Thu, 07 Jun 2007 12:17:41 +0200
Subject: [Pw_forum] error message
In-Reply-To: <BB28D461-10D0-4D73-9973-FDD80C6113BA@nest.sns.it>
References: <46601330.5090506@cea.fr> <F87F14D3-AF61-452D-81E5-8D1145706A83@nest.sns.it> <46666B79.3090607@cea.fr> <BB28D461-10D0-4D73-9973-FDD80C6113BA@nest.sns.it>
Message-ID: <4667DB45.2040506@cea.fr>

I have tried to run the same example on another cluster
(with another mpi: mpich, while it was openmpi on the new cluster)
and the problem disappears! I have then tried to compile with a similar 
mpi on
the new cluster but I have a lot of other problems coming out!!!

Moreover I have tested 2 other versions (cvs and 3.1.1) and I get
the same error!

I am still trying to solve the problem but I am running out of new
ideas:-)



  cyrille


>
> On Jun 6, 2007, at 10:08 , Cyrille Barreteau wrote:
>
>> I have just done some tests on example01 input data si.scf.cg.in
>> (10 kpoints)
>> My conclusion is that it happens when wf_collect=.true. and
>> when npool is greater than 1
>
>
> I cannot reproduce such an error on two different parallel
> machines
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



-- 
==================================================================
Cyrille Barreteau  | phone : +33 (0)1 69 08 29 51
CEA Saclay         | fax   : +33 (0)1 69 08 84 46
DSM/DRECAM/SPCSI   | email cyrille.barreteau at cea.fr
Batiment 462       |
91191 Gif sur Yvette Cedex  FRANCE
          ~~~~~~~~~~~~~~~~~~~~~~~~
http://www-drecam.cea.fr/spcsi/index.php
http://www-drecam.cea.fr/Images/Pisp/cbarreteau/cbarreteau_fr.html
http://www-drecam.cea.fr/Phocea/Membres/Cours/index.php
================================================================== 



From kondor.jess at gmail.com  Thu Jun  7 18:40:41 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Thu, 7 Jun 2007 11:40:41 -0500
Subject: [Pw_forum] Fermi energy in 'scf' and 'nscf'
In-Reply-To: <3837402B-A3D6-4993-8C63-6097CB648AB1@nest.sns.it>
References: <1d9d5d9d0706051343i5bc72fbdn40d2e578acfa5c66@mail.gmail.com>
	 <3837402B-A3D6-4993-8C63-6097CB648AB1@nest.sns.it>
Message-ID: <1d9d5d9d0706070940i4783b411n29dae27b14c6ad66@mail.gmail.com>

Paolo,

Yes, FFT grid is the same for scf and nscf, only k-point mesh is different
(13x13x1  -scf vs. 23x23x1 -nscf). But, I repeated again scf calculation and
funny enough Fermi level is 3.86 eV (not 5.05 eV as before). I will repeat
nscf again to see what is going on.

cheers,
 J.

On 6/6/07, Paolo Giannozzi <giannozz at nest.sns.it> wrote:
>
>
> On Jun 5, 2007, at 22:43 , Jess Kondor wrote:
>
> >  I performed 'scf' and 'nscf' calculations with 'm-v' smearing
> > method. In the end of both calculations, the Fermi energy is the
> > same. But if these calculations are performed using 'tetrahedra',
> > Fermi levels are different ( 5.05 eV from 'scf' and 3.86 eV from
> > 'nscf'). Is it normal?
>
> are the grid for scf and nscf the same? are you getting the same
> Kohn-Sham eigenvalues?
>
> 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
>



-- 
=====================================
 Jess Kondor

PICYT, Av. Venustiano Carranza 2425-A,
San Luis Potos? 78210, M?xico
=====================================
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From nedward at MIT.EDU  Thu Jun  7 19:34:58 2007
From: nedward at MIT.EDU (Nicholas E. Singh-Miller)
Date: Thu, 7 Jun 2007 13:34:58 -0400 (EDT)
Subject: [Pw_forum] Fermi energy in 'scf' and 'nscf'
In-Reply-To: <1d9d5d9d0706070940i4783b411n29dae27b14c6ad66@mail.gmail.com>
References: <1d9d5d9d0706051343i5bc72fbdn40d2e578acfa5c66@mail.gmail.com> 
 <3837402B-A3D6-4993-8C63-6097CB648AB1@nest.sns.it>
 <1d9d5d9d0706070940i4783b411n29dae27b14c6ad66@mail.gmail.com>
Message-ID: <Pine.GSO.4.64L.0706071324090.29434@home-on-the-dome.mit.edu>

Hi Jess,

This might not address your issue, but from your k-point sampling it looks 
like you are performing calculations for a slab geometry (i.e. with vacuum 
layer in between).  If this is the case, the Fermi energy (and the 
eigenvalues) will all be shifted due to the leaving out of the ill defined 
g=0 term in the solving of the electrostatic potential in Fourier space. 
This shift will depend on the cell dimension (e.g. two calculations with 
different sized vacuum regions will report different Fermi energies).

again, i am not sure that this was the issue.

-Nicholas


On Thu, 7 Jun 2007, Jess Kondor wrote:

> Paolo,
>
> Yes, FFT grid is the same for scf and nscf, only k-point mesh is different
> (13x13x1  -scf vs. 23x23x1 -nscf). But, I repeated again scf calculation and
> funny enough Fermi level is 3.86 eV (not 5.05 eV as before). I will repeat
> nscf again to see what is going on.
>
> cheers,
> J.
>
> On 6/6/07, Paolo Giannozzi <giannozz at nest.sns.it> wrote:
>> 
>> 
>> On Jun 5, 2007, at 22:43 , Jess Kondor wrote:
>> 
>> >  I performed 'scf' and 'nscf' calculations with 'm-v' smearing
>> > method. In the end of both calculations, the Fermi energy is the
>> > same. But if these calculations are performed using 'tetrahedra',
>> > Fermi levels are different ( 5.05 eV from 'scf' and 3.86 eV from
>> > 'nscf'). Is it normal?
>> 
>> are the grid for scf and nscf the same? are you getting the same
>> Kohn-Sham eigenvalues?
>> 
>> 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
>> 
>
>
>
>

*****************************************
Nicholas E. Singh-Miller
Ph.D. Candidate
Prof. Marzari Group (quasiamore.mit.edu)
Materials Science and Engineering
Massachusetts Institute of Technology
13-4066
(617)324-0372
*****************************************


From njuxuyuehua at gmail.com  Fri Jun  8 04:52:23 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 8 Jun 2007 10:52:23 +0800
Subject: [Pw_forum] PHONON errors varies when i use 6 or 2 cpu?
Message-ID: <aca2feb20706071952h74e684b8k8b2904905cce7de0@mail.gmail.com>

hi everyone?
today i met a problem when i compute phonon :first i do scf using 6 cpu
,then i also use 6 cpu to do phono at G,BUT a problem came out in out.file :



 Proc/  planes cols    G   planes cols    G    columns  G
 Pool       (dense grid)      (smooth grid)   (wavefct grid)
  1      5   3284  53988    4   2408  34052  719   5577
  2      4   3283  53987    4   2407  34051  719   5577
  3      4   3283  53987    4   2407  34049  719   5577
  4      4   3283  53987    4   2407  34051  719   5577
  5      4   3283  53987    4   2407  34049  719   5577
  6      4   3283  53987    4   2407  34051  720   5576
  0     25  19699 323923   24  14443 204303 4315  33461


     nbndx  =    20  nbnd   =    20  natomwfc =    30  npwx   =    4282
     nelec  =  40.00  nkb   =    50  ngl    =   10269
p0_9381:  p4_error: net_recv read:  probable EOF on socket: 1
Killed by signal 2.^M
forrtl: error (69): process interrupted (SIGINT)
Killed by signal 2.^M
Killed by signal 2.^M
Killed by signal 2.^M
Killed by signal 2.^M
p0_9381: (12.363281) net_send: could not write to fd=4, errno = 32
Fri Jun  8 09:41:35 CST 2007

because i do not know the reason .and then i try to use 4 cpu to compute
phono  ,this time the error is like this :



Representation    44      1 modes - To be done

     Representation    45      1 modes - To be done
 IOS = 36

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from davcio : error #        20
     i/o error in davcio
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from davcio : error #        20
     i/o error in davcio
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_11006:  p4_error: : 0
Killed by signal 2.^M
forrtl: error (69): process interrupted (SIGINT)
p0_11006: (18.296875) net_send: could not write to fd=4, errno = 32
Fri Jun  8 09:57:22 CST 2007

above two case ,the same input:
phonons of fiveringwater at Gamma
 &inputph
  tr2_ph=1.0d-14,
  prefix='fxx_specify_ibra_500_12+force',
  epsil=.true.,
  amass(1)=1.0,
  amass(2)=15.999,
  outdir='/raid/xx/pwscf/tmp/',
  fildyn='fxx.dynG',
 /
0.0 0.0 0.0





so my question is  why different number of cpu can change the error ?
befor a few days ago ,i use 2 cpu to do relax ,scf and phonon about another
case ,there was well ,but now .....?
i need your  help .thanks

-- 
Xu Yuehua
physics Department of Nanjing university
China
-------------- next part --------------
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From ding at sissa.it  Fri Jun  8 08:27:03 2007
From: ding at sissa.it (Xunlei Ding)
Date: Fri, 08 Jun 2007 08:27:03 +0200
Subject: [Pw_forum] PHONON errors varies when i use 6 or 2 cpu?
In-Reply-To: <aca2feb20706071952h74e684b8k8b2904905cce7de0@mail.gmail.com>
References: <aca2feb20706071952h74e684b8k8b2904905cce7de0@mail.gmail.com>
Message-ID: <4668F6B7.4040501@sissa.it>

Dear Xu,
I think,
error for 6 cpu calculation is just because one of the six nodes is down,
and error for 4 cpu calculation is because you change 6 cpu to 4 cpu.
So my suggestion is, doing the ph calculation with 6 cpu again.

Hope it will works.

Yours,
ding



xu yuehua wrote:

> hi everyone?
> today i met a problem when i compute phonon :first i do scf using 6 
> cpu ,then i also use 6 cpu to do phono at G,BUT a problem came out in 
> out.file :
>  
>  
>
>  Proc/  planes cols    G   planes cols    G    columns  G
>  Pool       (dense grid)      (smooth grid)   (wavefct grid)
>   1      5   3284  53988    4   2408  34052  719   5577
>   2      4   3283  53987    4   2407  34051  719   5577
>   3      4   3283  53987    4   2407  34049  719   5577
>   4      4   3283  53987    4   2407  34051  719   5577
>   5      4   3283  53987    4   2407  34049  719   5577
>   6      4   3283  53987    4   2407  34051  720   5576
>   0     25  19699 323923   24  14443 204303 4315  33461
>
>
>      nbndx  =    20  nbnd   =    20  natomwfc =    30  npwx   =    4282
>      nelec  =  40.00  nkb   =    50  ngl    =   10269
> p0_9381:  p4_error: net_recv read:  probable EOF on socket: 1
> Killed by signal 2.^M
> forrtl: error (69): process interrupted (SIGINT)
> Killed by signal 2.^M
> Killed by signal 2.^M
> Killed by signal 2.^M
> Killed by signal 2.^M
> p0_9381: (12.363281) net_send: could not write to fd=4, errno = 32
> Fri Jun  8 09:41:35 CST 2007
>
> because i do not know the reason .and then i try to use 4 cpu to 
> compute phono  ,this time the error is like this :
>
>  
>  
>  
> Representation    44      1 modes - To be done
>
>      Representation    45      1 modes - To be done
>  IOS = 36
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from davcio : error #        20
>      i/o error in davcio
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
>
>
>      stopping ...
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from davcio : error #        20
>      i/o error in davcio
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
>
>
>      stopping ...
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
> p0_11006:  p4_error: : 0
> Killed by signal 2.^M
> forrtl: error (69): process interrupted (SIGINT)
> p0_11006: (18.296875 ) net_send: could not write to fd=4, errno = 32
> Fri Jun  8 09:57:22 CST 2007
>  
> above two case ,the same input:
> phonons of fiveringwater at Gamma
>  &inputph
>   tr2_ph=1.0d-14,
>   prefix='fxx_specify_ibra_500_12+force',
>   epsil=.true.,
>   amass(1)=1.0,
>   amass(2)=15.999,
>   outdir='/raid/xx/pwscf/tmp/',
>   fildyn='fxx.dynG',
>  /
> 0.0 0.0 0.0
>
>  
>  
>  
>  
> so my question is  why different number of cpu can change the error ?
> befor a few days ago ,i use 2 cpu to do relax ,scf and phonon about 
> another case ,there was well ,but now .....?
> i need your  help .thanks
>
> -- 
> Xu Yuehua
> physics Department of Nanjing university
> China



From njuxuyuehua at gmail.com  Fri Jun  8 09:21:36 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 8 Jun 2007 15:21:36 +0800
Subject: [Pw_forum] PHONON errors varies when i use 6 or 2 cpu?
In-Reply-To: <4668F6B7.4040501@sissa.it>
References: <aca2feb20706071952h74e684b8k8b2904905cce7de0@mail.gmail.com>
	 <4668F6B7.4040501@sissa.it>
Message-ID: <aca2feb20706080021p7c862efbl17093c6998dc9ef1@mail.gmail.com>

Dear Ding:
I think  about your idea , if your idea is correct ,that says:if i use 6 cpu
to do scf ,then i must use the same number of cpu to continue tophonon
calculation .is it right for  me to comprehend your idea ?
need your help thanks a lot


2007/6/8, Xunlei Ding <ding at sissa.it>:
>
> Dear Xu,
> I think,
> error for 6 cpu calculation is just because one of the six nodes is down,
> and error for 4 cpu calculation is because you change 6 cpu to 4 cpu.
> So my suggestion is, doing the ph calculation with 6 cpu again.
>
> Hope it will works.
>
> Yours,
> ding
>
>
>
> xu yuehua wrote:
>
> > hi everyone?
> > today i met a problem when i compute phonon :first i do scf using 6
> > cpu ,then i also use 6 cpu to do phono at G,BUT a problem came out in
> > out.file :
> >
> >
> >
> >  Proc/  planes cols    G   planes cols    G    columns  G
> >  Pool       (dense grid)      (smooth grid)   (wavefct grid)
> >   1      5   3284  53988    4   2408  34052  719   5577
> >   2      4   3283  53987    4   2407  34051  719   5577
> >   3      4   3283  53987    4   2407  34049  719   5577
> >   4      4   3283  53987    4   2407  34051  719   5577
> >   5      4   3283  53987    4   2407  34049  719   5577
> >   6      4   3283  53987    4   2407  34051  720   5576
> >   0     25  19699 323923   24  14443 204303 4315  33461
> >
> >
> >      nbndx  =    20  nbnd   =    20  natomwfc =    30  npwx   =    4282
> >      nelec  =  40.00  nkb   =    50  ngl    =   10269
> > p0_9381:  p4_error: net_recv read:  probable EOF on socket: 1
> > Killed by signal 2.^M
> > forrtl: error (69): process interrupted (SIGINT)
> > Killed by signal 2.^M
> > Killed by signal 2.^M
> > Killed by signal 2.^M
> > Killed by signal 2.^M
> > p0_9381: (12.363281) net_send: could not write to fd=4, errno = 32
> > Fri Jun  8 09:41:35 CST 2007
> >
> > because i do not know the reason .and then i try to use 4 cpu to
> > compute phono  ,this time the error is like this :
> >
> >
> >
> >
> > Representation    44      1 modes - To be done
> >
> >      Representation    45      1 modes - To be done
> >  IOS = 36
> >
>
> >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >      from davcio : error #        20
> >      i/o error in davcio
>
> >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> >
> >      stopping ...
> >
>
> >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >      from davcio : error #        20
> >      i/o error in davcio
>
> >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> >
> >      stopping ...
> > [0] MPI Abort by user Aborting program !
> > [0] Aborting program!
> > p0_11006:  p4_error: : 0
> > Killed by signal 2.^M
> > forrtl: error (69): process interrupted (SIGINT)
> > p0_11006: (18.296875 ) net_send: could not write to fd=4, errno = 32
> > Fri Jun  8 09:57:22 CST 2007
> >
> > above two case ,the same input:
> > phonons of fiveringwater at Gamma
> >  &inputph
> >   tr2_ph=1.0d-14,
> >   prefix='fxx_specify_ibra_500_12+force',
> >   epsil=.true.,
> >   amass(1)=1.0,
> >   amass(2)=15.999,
> >   outdir='/raid/xx/pwscf/tmp/',
> >   fildyn='fxx.dynG',
> >  /
> > 0.0 0.0 0.0
> >
> >
> >
> >
> >
> > so my question is  why different number of cpu can change the error ?
> > befor a few days ago ,i use 2 cpu to do relax ,scf and phonon about
> > another case ,there was well ,but now .....?
> > i need your  help .thanks
> >
> > --
> > Xu Yuehua
> > physics Department of Nanjing university
> > China
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
-------------- next part --------------
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From ding at sissa.it  Fri Jun  8 09:59:10 2007
From: ding at sissa.it (Xunlei Ding)
Date: Fri, 08 Jun 2007 09:59:10 +0200
Subject: [Pw_forum] PHONON errors varies when i use 6 or 2 cpu?
In-Reply-To: <aca2feb20706080021p7c862efbl17093c6998dc9ef1@mail.gmail.com>
References: <aca2feb20706071952h74e684b8k8b2904905cce7de0@mail.gmail.com>	 <4668F6B7.4040501@sissa.it> <aca2feb20706080021p7c862efbl17093c6998dc9ef1@mail.gmail.com>
Message-ID: <46690C4E.30002@sissa.it>

Dear xu,
Yes, you are right because ph.x need to read wfc files of scf 
calculation. So the number of cpu should be the same.
Maybe you can try wf_collect=.true. in scf calculation if you want to 
change the cpu number.

And I suggest you to do some small tests on these questions.

Best wishes,
Ding

xu yuehua wrote:

> Dear Ding:
> I think  about your idea , if your idea is correct ,that says:if i use 
> 6 cpu to do scf ,then i must use the same number of cpu to continue 
> tophonon calculation .is it right for  me to comprehend your idea ?
> need your help thanks a lot
>
>  
> 2007/6/8, Xunlei Ding <ding at sissa.it <mailto:ding at sissa.it>>:
>
>     Dear Xu,
>     I think,
>     error for 6 cpu calculation is just because one of the six nodes
>     is down,
>     and error for 4 cpu calculation is because you change 6 cpu to 4 cpu.
>     So my suggestion is, doing the ph calculation with 6 cpu again.
>
>     Hope it will works.
>
>     Yours,
>     ding
>
>
>
>     xu yuehua wrote:
>
>     > hi everyone?
>     > today i met a problem when i compute phonon :first i do scf using 6
>     > cpu ,then i also use 6 cpu to do phono at G,BUT a problem came
>     out in
>     > out.file :
>     >
>     >
>     >
>     >  Proc/  planes cols    G   planes cols    G    columns  G
>     >  Pool       (dense grid)      (smooth grid)   (wavefct grid)
>     >   1      5   3284  53988    4   2408  34052  719   5577
>     >   2      4   3283  53987    4   2407  34051  719   5577
>     >   3      4   3283  53987    4   2407  34049  719   5577
>     >   4      4   3283  53987    4   2407  34051  719   5577
>     >   5      4   3283  53987    4   2407  34049  719   5577
>     >   6      4   3283  53987    4   2407  34051  720   5576
>     >   0     25  19699 323923   24  14443 204303 4315  33461
>     >
>     >
>     >      nbndx  =    20  nbnd   =    20  natomwfc =    30  npwx  
>     =    4282
>     >      nelec  =  40.00  nkb   =    50  ngl    =   10269
>     > p0_9381:  p4_error: net_recv read:  probable EOF on socket: 1
>     > Killed by signal 2.^M
>     > forrtl: error (69): process interrupted (SIGINT)
>     > Killed by signal 2.^M
>     > Killed by signal 2.^M
>     > Killed by signal 2.^M
>     > Killed by signal 2.^M
>     > p0_9381: (12.363281) net_send: could not write to fd=4, errno = 32
>     > Fri Jun  8 09:41:35 CST 2007
>     >
>     > because i do not know the reason .and then i try to use 4 cpu to
>     > compute phono  ,this time the error is like this :
>     >
>     >
>     >
>     >
>     > Representation    44      1 modes - To be done
>     >
>     >      Representation    45      1 modes - To be done
>     >  IOS = 36
>     >
>     >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     >      from davcio : error #        20
>     >      i/o error in davcio
>     >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     >
>     >
>     >      stopping ...
>     >
>     >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>     >      from davcio : error #        20
>     >      i/o error in davcio
>     >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     >
>     >
>     >      stopping ...
>     > [0] MPI Abort by user Aborting program !
>     > [0] Aborting program!
>     > p0_11006:  p4_error: : 0
>     > Killed by signal 2.^M
>     > forrtl: error (69): process interrupted (SIGINT)
>     > p0_11006: (18.296875 ) net_send: could not write to fd=4, errno
>     = 32
>     > Fri Jun  8 09:57:22 CST 2007
>     >
>     > above two case ,the same input:
>     > phonons of fiveringwater at Gamma
>     >  &inputph
>     >   tr2_ph=1.0d-14,
>     >   prefix='fxx_specify_ibra_500_12+force',
>     >   epsil=.true.,
>     >   amass(1)=1.0,
>     >   amass(2)=15.999,
>     >   outdir='/raid/xx/pwscf/tmp/',
>     >   fildyn='fxx.dynG',
>     >  /
>     > 0.0 0.0 0.0
>     >
>     >
>     >
>     >
>     >
>     > so my question is  why different number of cpu can change the
>     error ?
>     > befor a few days ago ,i use 2 cpu to do relax ,scf and phonon about
>     > another case ,there was well ,but now .....?
>     > i need your  help .thanks
>     >
>     > --
>     > Xu Yuehua
>     > physics Department of Nanjing university
>     > China
>
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> -- 
> Xu Yuehua
> physics Department of Nanjing university
> China 



From stewart at cnf.cornell.edu  Fri Jun  8 16:17:31 2007
From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu)
Date: Fri, 08 Jun 2007 10:17:31 -0400
Subject: [Pw_forum] LDA Ultrasoft pseudopotential for Mg
In-Reply-To: <4667DB45.2040506@cea.fr>
References: <46601330.5090506@cea.fr>
            <F87F14D3-AF61-452D-81E5-8D1145706A83@nest.sns.it>
            <46666B79.3090607@cea.fr>
            <BB28D461-10D0-4D73-9973-FDD80C6113BA@nest.sns.it>
            <4667DB45.2040506@cea.fr>
Message-ID: <20070608141731.5691.qmail@mail.spidergraphics.com>

Hi all, 

I was wondering if anyone had a reliable ultrasoft pseudopotential for Mg in 
the local density approximation.  The periodic table on the PWscf site has 
only norm-conserving and a GGA ultrasoft. 

Thanks, 

Derek 


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


From njuxuyuehua at gmail.com  Fri Jun  8 16:27:49 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 8 Jun 2007 22:27:49 +0800
Subject: [Pw_forum] PHONON errors varies when i use 6 or 2 cpu?
In-Reply-To: <46690C4E.30002@sissa.it>
References: <aca2feb20706071952h74e684b8k8b2904905cce7de0@mail.gmail.com>
	 <4668F6B7.4040501@sissa.it>
	 <aca2feb20706080021p7c862efbl17093c6998dc9ef1@mail.gmail.com>
	 <46690C4E.30002@sissa.it>
Message-ID: <aca2feb20706080727m684a7d3dk93cf35612bc66359@mail.gmail.com>

Dear Ding
 thanks for your help .accoding to suggestion ,i did  some small tests on
these question .
but i find if i use >2 cpu from relax,there is always error ,for example :in
relax outfile:



ATOMIC_POSITIONS (crystal)
H       -0.198038036   0.118658320   0.038439471
H       -0.156238802   0.183672385   0.037451256
O       -0.201997079   0.167103737   0.035109275



     Writing output data file gash2o.save
     Check: negative starting charge=   -0.027067

     second order charge density extrapolation
p3_4229:  p4_error: net_recv read:  probable EOF on socket: 1
p2_4108:  p4_error: net_recv read:  probable EOF on socket: 1
p1_4369:  p4_error: : 8097
[1] MPI Abort by user Aborting program !
[1] Aborting program!
rm_l_3_4346: (16650.921875) net_send: could not write to fd=5, errno = 32
rm_l_2_4225: (16651.347656) net_send: could not write to fd=7, errno = 32
p2_4108: (16657.351562) net_send: could not write to fd=5, errno = 32
p3_4229: (16656.933594) net_send: could not write to fd=5, errno = 32
Fri Jun  8 21:58:05 CST 2007



i check the cpus they are ok not down.because other job is runing on it .i
wonder what happend ? this problem is parallel  issuue ?or others?need your
help .thanks again


2007/6/8, Xunlei Ding <ding at sissa.it>:
>
> Dear xu,
> Yes, you are right because ph.x need to read wfc files of scf
> calculation. So the number of cpu should be the same.
> Maybe you can try wf_collect=.true. in scf calculation if you want to
> change the cpu number.
>
> And I suggest you to do some small tests on these questions.
>
> Best wishes,
> Ding
>
> xu yuehua wrote:
>
> > Dear Ding:
> > I think  about your idea , if your idea is correct ,that says:if i use
> > 6 cpu to do scf ,then i must use the same number of cpu to continue
> > tophonon calculation .is it right for  me to comprehend your idea ?
> > need your help thanks a lot
> >
> >
> > 2007/6/8, Xunlei Ding <ding at sissa.it <mailto:ding at sissa.it>>:
> >
> >     Dear Xu,
> >     I think,
> >     error for 6 cpu calculation is just because one of the six nodes
> >     is down,
> >     and error for 4 cpu calculation is because you change 6 cpu to 4
> cpu.
> >     So my suggestion is, doing the ph calculation with 6 cpu again.
> >
> >     Hope it will works.
> >
> >     Yours,
> >     ding
> >
> >
> >
> >     xu yuehua wrote:
> >
> >     > hi everyone?
> >     > today i met a problem when i compute phonon :first i do scf using
> 6
> >     > cpu ,then i also use 6 cpu to do phono at G,BUT a problem came
> >     out in
> >     > out.file :
> >     >
> >     >
> >     >
> >     >  Proc/  planes cols    G   planes cols    G    columns  G
> >     >  Pool       (dense grid)      (smooth grid)   (wavefct grid)
> >     >   1      5   3284  53988    4   2408  34052  719   5577
> >     >   2      4   3283  53987    4   2407  34051  719   5577
> >     >   3      4   3283  53987    4   2407  34049  719   5577
> >     >   4      4   3283  53987    4   2407  34051  719   5577
> >     >   5      4   3283  53987    4   2407  34049  719   5577
> >     >   6      4   3283  53987    4   2407  34051  720   5576
> >     >   0     25  19699 323923   24  14443 204303 4315  33461
> >     >
> >     >
> >     >      nbndx  =    20  nbnd   =    20  natomwfc =    30  npwx
> >     =    4282
> >     >      nelec  =  40.00  nkb   =    50  ngl    =   10269
> >     > p0_9381:  p4_error: net_recv read:  probable EOF on socket: 1
> >     > Killed by signal 2.^M
> >     > forrtl: error (69): process interrupted (SIGINT)
> >     > Killed by signal 2.^M
> >     > Killed by signal 2.^M
> >     > Killed by signal 2.^M
> >     > Killed by signal 2.^M
> >     > p0_9381: (12.363281) net_send: could not write to fd=4, errno = 32
> >     > Fri Jun  8 09:41:35 CST 2007
> >     >
> >     > because i do not know the reason .and then i try to use 4 cpu to
> >     > compute phono  ,this time the error is like this :
> >     >
> >     >
> >     >
> >     >
> >     > Representation    44      1 modes - To be done
> >     >
> >     >      Representation    45      1 modes - To be done
> >     >  IOS = 36
> >     >
> >
> >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >     >      from davcio : error #        20
> >     >      i/o error in davcio
> >
> >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >     >
> >     >
> >     >      stopping ...
> >     >
> >
> >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> >     >      from davcio : error #        20
> >     >      i/o error in davcio
> >
> >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >     >
> >     >
> >     >      stopping ...
> >     > [0] MPI Abort by user Aborting program !
> >     > [0] Aborting program!
> >     > p0_11006:  p4_error: : 0
> >     > Killed by signal 2.^M
> >     > forrtl: error (69): process interrupted (SIGINT)
> >     > p0_11006: (18.296875 ) net_send: could not write to fd=4, errno
> >     = 32
> >     > Fri Jun  8 09:57:22 CST 2007
> >     >
> >     > above two case ,the same input:
> >     > phonons of fiveringwater at Gamma
> >     >  &inputph
> >     >   tr2_ph=1.0d-14,
> >     >   prefix='fxx_specify_ibra_500_12+force',
> >     >   epsil=.true.,
> >     >   amass(1)=1.0,
> >     >   amass(2)=15.999,
> >     >   outdir='/raid/xx/pwscf/tmp/',
> >     >   fildyn='fxx.dynG',
> >     >  /
> >     > 0.0 0.0 0.0
> >     >
> >     >
> >     >
> >     >
> >     >
> >     > so my question is  why different number of cpu can change the
> >     error ?
> >     > befor a few days ago ,i use 2 cpu to do relax ,scf and phonon
> about
> >     > another case ,there was well ,but now .....?
> >     > i need your  help .thanks
> >     >
> >     > --
> >     > Xu Yuehua
> >     > physics Department of Nanjing university
> >     > China
> >
> >     _______________________________________________
> >     Pw_forum mailing list
> >     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> >     http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> >
> > --
> > Xu Yuehua
> > physics Department of Nanjing university
> > China
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From giannozz at nest.sns.it  Fri Jun  8 17:55:19 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 8 Jun 2007 17:55:19 +0200
Subject: [Pw_forum] PHONON errors varies when i use 6 or 2 cpu?
In-Reply-To: <aca2feb20706080727m684a7d3dk93cf35612bc66359@mail.gmail.com>
References: <aca2feb20706071952h74e684b8k8b2904905cce7de0@mail.gmail.com> <4668F6B7.4040501@sissa.it> <aca2feb20706080021p7c862efbl17093c6998dc9ef1@mail.gmail.com> <46690C4E.30002@sissa.it> <aca2feb20706080727m684a7d3dk93cf35612bc66359@mail.gmail.com>
Message-ID: <380FF45F-B579-4434-86DA-10F77D414999@nest.sns.it>

On Jun 8, 2007, at 16:27 , xu yuehua wrote:

> p3_4229:  p4_error: net_recv read:  probable EOF on socket: 1p2_4108:

the issue of "mysterious crashes in parallel execution" has been
discussed many times here. See the user guide, troubleshooting
(http://www.quantum-espresso.org/wiki/index.php/Troubleshooting_% 
28PWscf%29)
  under "pw.x crashes in parallel execution with an obscure message
related to MPI errors". Unless you have evidence of the opposite,
my opinion is that the problem is in your machine, not in the codes.

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




From ding at sissa.it  Fri Jun  8 18:36:00 2007
From: ding at sissa.it (Xunlei Ding)
Date: Fri, 08 Jun 2007 18:36:00 +0200
Subject: [Pw_forum] PHONON errors varies when i use 6 or 2 cpu?
In-Reply-To: <aca2feb20706080727m684a7d3dk93cf35612bc66359@mail.gmail.com>
References: <aca2feb20706071952h74e684b8k8b2904905cce7de0@mail.gmail.com>	 <4668F6B7.4040501@sissa.it>	 <aca2feb20706080021p7c862efbl17093c6998dc9ef1@mail.gmail.com>	 <46690C4E.30002@sissa.it> <aca2feb20706080727m684a7d3dk93cf35612bc66359@mail.gmail.com>
Message-ID: <46698570.6000201@sissa.it>

Dear xu,
I am confused by your questions.
I suggest you to do:
1. parallel calculation on 4 cpu for a scf calculation from scratch 
(restart_mode='from_scratch').
2. parallel calculation on 4 cpu for a relax calculation from scratch.
If there is error, please put your input and output file here, and tell 
me how you submit your job.

Best wishes,
Ding

xu yuehua wrote:

> Dear Ding
>  thanks for your help .accoding to suggestion ,i did  some small tests 
> on these question .
> but i find if i use >2 cpu from relax,there is always error ,for 
> example :in relax outfile:
>
>  
>
> ATOMIC_POSITIONS (crystal)
> H       -0.198038036   0.118658320   0.038439471
> H       -0.156238802   0.183672385   0.037451256
> O       -0.201997079   0.167103737   0.035109275
>
>  
>
>      Writing output data file gash2o.save
>      Check: negative starting charge=   -0.027067
>
>      second order charge density extrapolation
> p3_4229:  p4_error: net_recv read:  probable EOF on socket: 1
> p2_4108:  p4_error: net_recv read:  probable EOF on socket: 1
> p1_4369:  p4_error: : 8097
> [1] MPI Abort by user Aborting program !
> [1] Aborting program!
> rm_l_3_4346: (16650.921875) net_send: could not write to fd=5, errno = 32
> rm_l_2_4225: (16651.347656) net_send: could not write to fd=7, errno = 32
> p2_4108: (16657.351562) net_send: could not write to fd=5, errno = 32
> p3_4229: (16656.933594) net_send: could not write to fd=5, errno = 32
> Fri Jun  8 21:58:05 CST 2007
>
>  
>
>  
> i check the cpus they are ok not down.because other job is runing on 
> it .i wonder what happend ? this problem is parallel  issuue ?or 
> others?need your help .thanks again 
>
>  
> 2007/6/8, Xunlei Ding <ding at sissa.it <mailto:ding at sissa.it>>:
>
>     Dear xu,
>     Yes, you are right because ph.x need to read wfc files of scf
>     calculation. So the number of cpu should be the same.
>     Maybe you can try wf_collect=.true. in scf calculation if you want to
>     change the cpu number.
>
>     And I suggest you to do some small tests on these questions.
>
>     Best wishes,
>     Ding
>
>     xu yuehua wrote:
>
>     > Dear Ding:
>     > I think  about your idea , if your idea is correct ,that says:if
>     i use
>     > 6 cpu to do scf ,then i must use the same number of cpu to continue
>     > tophonon calculation .is it right for  me to comprehend your idea ?
>     > need your help thanks a lot
>     >
>     >
>     > 2007/6/8, Xunlei Ding <ding at sissa.it <mailto:ding at sissa.it>
>     <mailto:ding at sissa.it <mailto:ding at sissa.it>>>:
>     >
>     >     Dear Xu,
>     >     I think,
>     >     error for 6 cpu calculation is just because one of the six nodes
>     >     is down,
>     >     and error for 4 cpu calculation is because you change 6 cpu
>     to 4 cpu.
>     >     So my suggestion is, doing the ph calculation with 6 cpu again.
>     >
>     >     Hope it will works.
>     >
>     >     Yours,
>     >     ding
>     >
>     >
>     >
>     >     xu yuehua wrote:
>     >
>     >     > hi everyone?
>     >     > today i met a problem when i compute phonon :first i do
>     scf using 6
>     >     > cpu ,then i also use 6 cpu to do phono at G,BUT a problem came
>     >     out in
>     >     > out.file :
>     >     >
>     >     >
>     >     >
>     >     >  Proc/  planes cols    G   planes cols    G    columns  G
>     >     >  Pool       (dense grid)      (smooth grid)   (wavefct grid)
>     >     >   1      5   3284  53988    4   2408  34052  719   5577
>     >     >   2      4   3283  53987    4   2407  34051  719   5577
>     >     >   3      4   3283  53987    4   2407  34049  719   5577
>     >     >   4      4   3283  53987    4   2407  34051  719   5577
>     >     >   5      4   3283  53987    4   2407  34049  719   5577
>     >     >   6      4   3283  53987    4   2407  34051  720   5576
>     >     >   0     25  19699 323923   24  14443 204303 4315  33461
>     >     >
>     >     >
>     >     >      nbndx  =    20  nbnd   =    20  natomwfc =    30  npwx
>     >     =    4282
>     >     >      nelec  =  40.00  nkb   =    50  ngl    =   10269
>     >     > p0_9381:  p4_error: net_recv read:  probable EOF on socket: 1
>     >     > Killed by signal 2.^M
>     >     > forrtl: error (69): process interrupted (SIGINT)
>     >     > Killed by signal 2.^M
>     >     > Killed by signal 2.^M
>     >     > Killed by signal 2.^M
>     >     > Killed by signal 2.^M
>     >     > p0_9381: (12.363281) net_send: could not write to fd=4,
>     errno = 32
>     >     > Fri Jun  8 09:41:35 CST 2007
>     >     >
>     >     > because i do not know the reason .and then i try to use 4
>     cpu to
>     >     > compute phono  ,this time the error is like this :
>     >     >
>     >     >
>     >     >
>     >     >
>     >     > Representation    44      1 modes - To be done
>     >     >
>     >     >      Representation    45      1 modes - To be done
>     >     >  IOS = 36
>     >     >
>     >    
>     >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     >     >      from davcio : error #        20
>     >     >      i/o error in davcio
>     >    
>     >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>     >     >
>     >     >
>     >     >      stopping ...
>     >     >
>     >    
>     >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     >
>     >     >      from davcio : error #        20
>     >     >      i/o error in davcio
>     >    
>     >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     >     >
>     >     >
>     >     >      stopping ...
>     >     > [0] MPI Abort by user Aborting program !
>     >     > [0] Aborting program!
>     >     > p0_11006:  p4_error: : 0
>     >     > Killed by signal 2.^M
>     >     > forrtl: error (69): process interrupted (SIGINT)
>     >     > p0_11006: (18.296875 ) net_send: could not write to fd=4,
>     errno
>     >     = 32
>     >     > Fri Jun  8 09:57:22 CST 2007
>     >     >
>     >     > above two case ,the same input:
>     >     > phonons of fiveringwater at Gamma
>     >     >  &inputph
>     >     >   tr2_ph=1.0d-14,
>     >     >   prefix='fxx_specify_ibra_500_12+force',
>     >     >   epsil=.true.,
>     >     >   amass(1)=1.0,
>     >     >   amass(2)= 15.999,
>     >     >   outdir='/raid/xx/pwscf/tmp/',
>     >     >   fildyn='fxx.dynG',
>     >     >  /
>     >     > 0.0 0.0 0.0
>     >     >
>     >     >
>     >     >
>     >     >
>     >     >
>     >     > so my question is  why different number of cpu can change the
>     >     error ?
>     >     > befor a few days ago ,i use 2 cpu to do relax ,scf and
>     phonon about
>     >     > another case ,there was well ,but now .....?
>     >     > i need your  help .thanks
>     >     >
>     >     > --
>     >     > Xu Yuehua
>     >     > physics Department of Nanjing university
>     >     > China
>     >
>     >     _______________________________________________
>     >     Pw_forum mailing list
>     >     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     <mailto:Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>>
>     >     http://www.democritos.it/mailman/listinfo/pw_forum
>     >
>     >
>     >
>     >
>     > --
>     > Xu Yuehua
>     > physics Department of Nanjing university
>     > China
>
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> -- 
> Xu Yuehua
> physics Department of Nanjing university
> China 



From giannozz at nest.sns.it  Fri Jun  8 18:42:58 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 8 Jun 2007 18:42:58 +0200
Subject: [Pw_forum] error in "vc-relax" calculation
In-Reply-To: <822f4ec80705301053t49ab2569t9decddd727d4f8f0@mail.gmail.com>
References: <822f4ec80705301053t49ab2569t9decddd727d4f8f0@mail.gmail.com>
Message-ID: <8008A45D-3FAD-41C3-9D8B-079159FD9519@nest.sns.it>

On May 30, 2007, at 19:53 , shruba at gmail.com wrote:

> I am running an optimization for SrFeO3 ( a metallic perovskite  
> system )
> the input structure is

...remarkably complicated input data follows.

Unless you know really well what you are doing, you should start
with something simpler. You can't start with the most exotic
techniques of quantum-espresso (variable-cell + ensemble dynamics +
Fermi Dirac smearing of 6000Ry??? + 32 spin up + whatnot), and
pretend that everything runs at the first attempt

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




From eyvaz_isaev at yahoo.com  Fri Jun  8 20:28:46 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 8 Jun 2007 11:28:46 -0700 (PDT)
Subject: [Pw_forum] LDA Ultrasoft pseudopotential for Mg
In-Reply-To: <20070608141731.5691.qmail@mail.spidergraphics.com>
Message-ID: <656368.89227.qm@web60321.mail.yahoo.com>

Hi Derek,

I can try generate it. My US GGA pseudopotential for
Mg works quite well. It will take few days, hopefully,

including tests.

Bests,
Eyvaz. 

--- stewart at cnf.cornell.edu wrote:

> Hi all, 
> 
> I was wondering if anyone had a reliable ultrasoft
> pseudopotential for Mg in 
> the local density approximation.  The periodic table
> on the PWscf site has 
> only norm-conserving and a GGA ultrasoft. 
> 
> Thanks, 
> 
> Derek 
> 
> 
> ################################
> Derek Stewart, Ph. D.
> Scientific Computation Associate
> 250 Duffield Hall
> Cornell Nanoscale Facility (CNF)
> Ithaca, NY 14853
> stewart (at) cnf.cornell.edu
> (607) 255-2856
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 



       
____________________________________________________________________________________
Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out.
http://answers.yahoo.com/dir/?link=list&sid=396545469


From stewart at cnf.cornell.edu  Sat Jun  9 02:55:41 2007
From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu)
Date: Fri, 08 Jun 2007 20:55:41 -0400
Subject: [Pw_forum] LDA Ultrasoft pseudopotential for Mg
In-Reply-To: <656368.89227.qm@web60321.mail.yahoo.com>
References: <656368.89227.qm@web60321.mail.yahoo.com>
Message-ID: <20070609005541.94777.qmail@mail.spidergraphics.com>

Hi Eyvaz, 

That would be a great help!  I look forward to trying it out. 

Thanks, 

Derek 


Eyvaz Isaev writes: 

> Hi Derek, 
> 
> I can try generate it. My US GGA pseudopotential for
> Mg works quite well. It will take few days, hopefully, 
> 
> including tests. 
> 
> Bests,
> Eyvaz.  
> 
> --- stewart at cnf.cornell.edu wrote: 
> 
>> Hi all,  
>> 
>> I was wondering if anyone had a reliable ultrasoft
>> pseudopotential for Mg in 
>> the local density approximation.  The periodic table
>> on the PWscf site has 
>> only norm-conserving and a GGA ultrasoft.  
>> 
>> Thanks,  
>> 
>> Derek  
>> 
>> 
>> ################################
>> Derek Stewart, Ph. D.
>> Scientific Computation Associate
>> 250 Duffield Hall
>> Cornell Nanoscale Facility (CNF)
>> Ithaca, NY 14853
>> stewart (at) cnf.cornell.edu
>> (607) 255-2856
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum 
>> 
>  
> 
> 
>        
> ____________________________________________________________________________________
> Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out.
> http://answers.yahoo.com/dir/?link=list&sid=396545469
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum 
> 
 


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


From asen at iitk.ac.in  Sat Jun  9 11:21:11 2007
From: asen at iitk.ac.in (Sen)
Date: Sat, 9 Jun 2007 14:51:11 +0530 (IST)
Subject: [Pw_forum] structural relaxation for a M-M-M system
Message-ID: <49019.140.109.128.2.1181380871.squirrel@newwebmail.iitk.ac.in>

Dear all,
         After a lot of trials, I am, however, not yet successful in
optimizing a metal-molecule-metal system as the forces are coming
like this:
.........
     Total force =     0.095460     Total SCF correction =     0.000604
     Total force =     0.082488     Total SCF correction =     0.000306
     Total force =     0.046922     Total SCF correction =     0.000911
     Total force =     0.056506     Total SCF correction =     0.000344
     Total force =     0.054621     Total SCF correction =     0.000626
     Total force =     0.065249     Total SCF correction =     0.000466
     Total force =     0.083905     Total SCF correction =     0.000689
     Total force =     0.079088     Total SCF correction =     0.000242
     Total force =     0.062822     Total SCF correction =     0.000331
     Total force =     0.042837     Total SCF correction =     0.000466
     Total force =     0.043863     Total SCF correction =     0.000608
     Total force =     0.060127     Total SCF correction =     0.000548
     Total force =     0.056791     Total SCF correction =     0.000600
     Total force =     0.055846     Total SCF correction =     0.000490
     Total force =     0.048528     Total SCF correction =     0.000801
     Total force =     0.035071     Total SCF correction =     0.000413
     Total force =     0.032172     Total SCF correction =     0.000433
     Total force =     0.039041     Total SCF correction =     0.000416
     Total force =     0.044582     Total SCF correction =     0.000545
     Total force =     0.046444     Total SCF correction =     0.000524
     Total force =     0.054854     Total SCF correction =     0.000818
     Total force =     0.063710     Total SCF correction =     0.000484
     Total force =     0.062717     Total SCF correction =     0.000626
     Total force =     0.065163     Total SCF correction =     0.000812
     Total force =     0.075249     Total SCF correction =     0.001036
     Total force =     0.088846     Total SCF correction =     0.000643
     Total force =     0.105373     Total SCF correction =     0.000338
     Total force =     0.120634     Total SCF correction =     0.000572
     Total force =     0.126982     Total SCF correction =     0.000283
     Total force =     0.113945     Total SCF correction =     0.000450
     Total force =     0.108384     Total SCF correction =     0.000297
     Total force =     0.099096     Total SCF correction =     0.000580
     Total force =     0.077881     Total SCF correction =     0.000668
     Total force =     0.095374     Total SCF correction =     0.000452

 while the stress is the following:
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
34.70
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
34.72
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
35.27
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
35.66
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
35.07
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
33.99
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
32.67
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
31.43
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
31.16
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
31.69
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
32.41
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
33.54
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
33.84
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
34.53
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
34.35
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
34.06
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
33.97
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
34.12
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
34.65
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
34.86
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
34.38
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
33.60
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
32.83
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
32.23
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
32.38
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
32.16
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
32.24
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
32.34
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
32.88
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
34.00
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
33.58
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
33.10
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
32.30
          total   stress  (Ry/bohr**3)                   (kbar)     P=  
31.50

I start my calculations with the following input file:
&CONTROL
  calculation = "relax",
  tstress = .TRUE.,
  tprnfor = .TRUE.,
  dt= 20,
  outdir       = "/work1/tmp",
  prefix       = "6r_md",
  pseudo_dir   = "/work1/pwscf/newwork1/pseudo",
/
&SYSTEM
  nosym = .TRUE.,
  ibrav = 6,
  celldm(1) = 16.0,
  celldm(3) = 6.7,
  nat       = 108,
  ntyp      = 4,
  ecutwfc = 25.0,
  ecutrho  =  200.0 ,
  occupations = "smearing",
  degauss     = 0.01,
  smearing    = "gauss",
/
&ELECTRONS
  conv_thr    = 1.e-7,
  mixing_beta = 0.1,
/
&IONS
  ion_dynamics = "damp",
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
ATOMIC_SPECIES
Au 1.00  Au.pbe-van_ak.UPF
S  1.00  S.pbe-van_ak.UPF
C  1.00  C.pbe-van_ak.UPF
H  1.00  H.pbe-van_ak.UPF
ATOMIC_POSITIONS {bohr}
Au       0.000000000  -4.965200000   0.000000000 0 0 0
Au      -4.319724000  -2.482600000   0.000000000 0 0 0
Au      -4.319724000   2.482600000   0.000000000 0 0 0
.................
Au      -2.774561616   0.031062380  28.596765964 1 1 1
Au       0.041848351  -0.082778583  32.636501628 1 1 1
Au      -0.028301935   1.263362498  37.301572656 1 1 1
.................
C        0.003014820  -0.792207427  45.903314488 1 1 1
H       -1.656592433  -2.071574048  45.925688702 1 1 1
H        1.659769150  -2.074993963  45.925343414 1 1 1
.................
Au       0.002439106   5.120271920  81.897457381 1 1 1
Au      -4.361967945   2.134818447  81.462315449 1 1 1
Au      -5.204105949  -3.027358489  81.522909929 1 1 1
.................
Au      -4.319724000   2.482600000  98.968460000 0 0 0
Au      -4.319724000  -2.482600000  98.968460000 0 0 0
Au       0.000000000  -4.965200000  98.968460000 0 0 0
K_POINTS {Gamma}

I tried with vc-relax as well but could not improve it much. In another
system, I came across the following forces:
     Total force =     0.506859     Total SCF correction =     0.000423
     Total force =     0.501602     Total SCF correction =     0.000666
     Total force =     0.504022     Total SCF correction =     0.000468
     Total force =     0.515807     Total SCF correction =     0.000445
     Total force =     0.531093     Total SCF correction =     0.000497
     Total force =     0.546169     Total SCF correction =     0.000294
     Total force =     0.565997     Total SCF correction =     0.000298
     Total force =     0.594369     Total SCF correction =     0.000437
     Total force =     0.628540     Total SCF correction =     0.000323
     Total force =     0.652224     Total SCF correction =     0.000388
     Total force =     0.636638     Total SCF correction =     0.000299
     Total force =     0.558604     Total SCF correction =     0.000572
     Total force =     0.441045     Total SCF correction =     0.000310
     Total force =     0.331614     Total SCF correction =     0.000424
     Total force =     0.230756     Total SCF correction =     0.000319
     Total force =     0.188110     Total SCF correction =     0.000422
     Total force =     0.160244     Total SCF correction =     0.000236
     Total force =     0.145254     Total SCF correction =     0.000270
     Total force =     0.139637     Total SCF correction =     0.000262
     Total force =     0.125084     Total SCF correction =     0.000424
     Total force =     0.150679     Total SCF correction =     0.000854
     Total force =     0.167059     Total SCF correction =     0.000294
     Total force =     0.172462     Total SCF correction =     0.000478
     Total force =     0.179529     Total SCF correction =     0.000434
     Total force =     0.187906     Total SCF correction =     0.000499
     Total force =     0.191868     Total SCF correction =     0.000428
     Total force =     0.188061     Total SCF correction =     0.000504
     Total force =     0.175147     Total SCF correction =     0.000272
     Total force =     0.159927     Total SCF correction =     0.000273
     Total force =     0.161611     Total SCF correction =     0.000373
     Total force =     0.208462     Total SCF correction =     0.000460
     Total force =     0.280821     Total SCF correction =     0.000192
     Total force =     0.353126     Total SCF correction =     0.000699
     Total force =     0.420761     Total SCF correction =     0.000602
     Total force =     0.486584     Total SCF correction =     0.000230
     Total force =     0.550967     Total SCF correction =     0.000360
     Total force =     0.606887     Total SCF correction =     0.000672
     Total force =     0.640920     Total SCF correction =     0.000602
     Total force =     0.632764     Total SCF correction =     0.000467
     Total force =     0.559615     Total SCF correction =     0.000506
     Total force =     0.526823     Total SCF correction =     0.000464
     Total force =     0.503575     Total SCF correction =     0.000432
.........
Could you please suggest me as to how I could get the "Total force"
something like 0.001 or of that sort?
Best regards,
Sen





From wyanchao at gmail.com  Sat Jun  9 12:46:41 2007
From: wyanchao at gmail.com (wang yanchao)
Date: Sat, 9 Jun 2007 18:46:41 +0800
Subject: [Pw_forum] ask question
Message-ID: <55639d30706090346s4beb456aw62d0ee3eabfc6c40@mail.gmail.com>

Dear all
  I caculate a material which is body centered orthorhombic structure. It
should have 8 operations,but it only find 2 operations! When I used CASTEP
do it,I can find 8 operation,So I redefine teh vecter of lattice,but in
vain.now I don't know what I should do? if someone know it,please tell me!
Thank you in advance!
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From lanhaiping at gmail.com  Sat Jun  9 14:10:41 2007
From: lanhaiping at gmail.com (lan haiping)
Date: Sat, 9 Jun 2007 20:10:41 +0800
Subject: [Pw_forum] ask question
In-Reply-To: <55639d30706090346s4beb456aw62d0ee3eabfc6c40@mail.gmail.com>
References: <55639d30706090346s4beb456aw62d0ee3eabfc6c40@mail.gmail.com>
Message-ID: <c92002fa0706090510u20245ffv2a43a5b8923608ab@mail.gmail.com>

Hi, Mr Wang.

 The symmetry operations given by PW also depend on the cutoff energy
"ecutwfc" and cutoff density grids "ecutrho" you set.

By the way, would you please give your  affiliation ?

Regards,

H.P

On 6/9/07, wang yanchao <wyanchao at gmail.com> wrote:
>
> Dear all
>   I caculate a material which is body centered orthorhombic structure. It
> should have 8 operations,but it only find 2 operations! When I used CASTEP
> do it,I can find 8 operation,So I redefine teh vecter of lattice,but in
> vain.now I don't know what I should do? if someone know it,please tell me!
> Thank you in advance!
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From jonathan.breeze at imperial.ac.uk  Sat Jun  9 14:41:06 2007
From: jonathan.breeze at imperial.ac.uk (Jonathan Breeze)
Date: Sat, 09 Jun 2007 13:41:06 +0100
Subject: [Pw_forum] LDA Ultrasoft pseudopotential for Mg
In-Reply-To: <20070608141731.5691.qmail@mail.spidergraphics.com>
References: <46601330.5090506@cea.fr>
	 <F87F14D3-AF61-452D-81E5-8D1145706A83@nest.sns.it>
	 <46666B79.3090607@cea.fr>
	 <BB28D461-10D0-4D73-9973-FDD80C6113BA@nest.sns.it>
	 <4667DB45.2040506@cea.fr>
	 <20070608141731.5691.qmail@mail.spidergraphics.com>
Message-ID: <1181392866.6373.2.camel@breeze>

Hi Derek,

Have you tried converting a Vanderbilt pseudopotential to UPF format
using the upftools?

Jonathan Breeze
Research Fellow

Department of Materials
Imperial College London
Exhibition Road
London SW7 2AZ


On Fri, 2007-06-08 at 10:17 -0400, stewart at cnf.cornell.edu wrote:
> Hi all, 
> 
> I was wondering if anyone had a reliable ultrasoft pseudopotential for Mg in 
> the local density approximation.  The periodic table on the PWscf site has 
> only norm-conserving and a GGA ultrasoft. 
> 
> Thanks, 
> 
> Derek 
> 
> 
> ################################
> Derek Stewart, Ph. D.
> Scientific Computation Associate
> 250 Duffield Hall
> Cornell Nanoscale Facility (CNF)
> Ithaca, NY 14853
> stewart (at) cnf.cornell.edu
> (607) 255-2856
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From ding at sissa.it  Sat Jun  9 15:32:59 2007
From: ding at sissa.it (Xunlei Ding)
Date: Sat, 09 Jun 2007 15:32:59 +0200
Subject: [Pw_forum] structural relaxation for a M-M-M system
In-Reply-To: <49019.140.109.128.2.1181380871.squirrel@newwebmail.iitk.ac.in>
References: <49019.140.109.128.2.1181380871.squirrel@newwebmail.iitk.ac.in>
Message-ID: <466AAC0B.8010101@sissa.it>

Dear Sen,

 What the directions of the forces, mostly in XY plane or in Z direction?
 Are you using slab model? Where you get the number celldm(1) = 16.0?

Please give more information.

Yours sincerely,
Ding
 
Sen wrote:

>Dear all,
>         After a lot of trials, I am, however, not yet successful in
>optimizing a metal-molecule-metal system as the forces are coming
>like this:
>.........
>     Total force =     0.095460     Total SCF correction =     0.000604
>     Total force =     0.082488     Total SCF correction =     0.000306
>     Total force =     0.046922     Total SCF correction =     0.000911
>     Total force =     0.056506     Total SCF correction =     0.000344
>     Total force =     0.054621     Total SCF correction =     0.000626
>     Total force =     0.065249     Total SCF correction =     0.000466
>     Total force =     0.083905     Total SCF correction =     0.000689
>     Total force =     0.079088     Total SCF correction =     0.000242
>     Total force =     0.062822     Total SCF correction =     0.000331
>     Total force =     0.042837     Total SCF correction =     0.000466
>     Total force =     0.043863     Total SCF correction =     0.000608
>     Total force =     0.060127     Total SCF correction =     0.000548
>     Total force =     0.056791     Total SCF correction =     0.000600
>     Total force =     0.055846     Total SCF correction =     0.000490
>     Total force =     0.048528     Total SCF correction =     0.000801
>     Total force =     0.035071     Total SCF correction =     0.000413
>     Total force =     0.032172     Total SCF correction =     0.000433
>     Total force =     0.039041     Total SCF correction =     0.000416
>     Total force =     0.044582     Total SCF correction =     0.000545
>     Total force =     0.046444     Total SCF correction =     0.000524
>     Total force =     0.054854     Total SCF correction =     0.000818
>     Total force =     0.063710     Total SCF correction =     0.000484
>     Total force =     0.062717     Total SCF correction =     0.000626
>     Total force =     0.065163     Total SCF correction =     0.000812
>     Total force =     0.075249     Total SCF correction =     0.001036
>     Total force =     0.088846     Total SCF correction =     0.000643
>     Total force =     0.105373     Total SCF correction =     0.000338
>     Total force =     0.120634     Total SCF correction =     0.000572
>     Total force =     0.126982     Total SCF correction =     0.000283
>     Total force =     0.113945     Total SCF correction =     0.000450
>     Total force =     0.108384     Total SCF correction =     0.000297
>     Total force =     0.099096     Total SCF correction =     0.000580
>     Total force =     0.077881     Total SCF correction =     0.000668
>     Total force =     0.095374     Total SCF correction =     0.000452
>
> while the stress is the following:
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>34.70
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>34.72
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>35.27
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>35.66
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>35.07
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>33.99
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>32.67
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>31.43
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>31.16
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>31.69
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>32.41
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>33.54
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>33.84
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>34.53
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>34.35
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>34.06
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>33.97
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>34.12
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>34.65
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>34.86
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>34.38
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>33.60
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>32.83
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>32.23
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>32.38
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>32.16
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>32.24
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>32.34
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>32.88
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>34.00
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>33.58
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>33.10
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>32.30
>          total   stress  (Ry/bohr**3)                   (kbar)     P=  
>31.50
>
>I start my calculations with the following input file:
>&CONTROL
>  calculation = "relax",
>  tstress = .TRUE.,
>  tprnfor = .TRUE.,
>  dt= 20,
>  outdir       = "/work1/tmp",
>  prefix       = "6r_md",
>  pseudo_dir   = "/work1/pwscf/newwork1/pseudo",
>/
>&SYSTEM
>  nosym = .TRUE.,
>  ibrav = 6,
>  celldm(1) = 16.0,
>  celldm(3) = 6.7,
>  nat       = 108,
>  ntyp      = 4,
>  ecutwfc = 25.0,
>  ecutrho  =  200.0 ,
>  occupations = "smearing",
>  degauss     = 0.01,
>  smearing    = "gauss",
>/
>&ELECTRONS
>  conv_thr    = 1.e-7,
>  mixing_beta = 0.1,
>/
>&IONS
>  ion_dynamics = "damp",
>  pot_extrapolation = "second_order",
>  wfc_extrapolation = "second_order",
>ATOMIC_SPECIES
>Au 1.00  Au.pbe-van_ak.UPF
>S  1.00  S.pbe-van_ak.UPF
>C  1.00  C.pbe-van_ak.UPF
>H  1.00  H.pbe-van_ak.UPF
>ATOMIC_POSITIONS {bohr}
>Au       0.000000000  -4.965200000   0.000000000 0 0 0
>Au      -4.319724000  -2.482600000   0.000000000 0 0 0
>Au      -4.319724000   2.482600000   0.000000000 0 0 0
>.................
>Au      -2.774561616   0.031062380  28.596765964 1 1 1
>Au       0.041848351  -0.082778583  32.636501628 1 1 1
>Au      -0.028301935   1.263362498  37.301572656 1 1 1
>.................
>C        0.003014820  -0.792207427  45.903314488 1 1 1
>H       -1.656592433  -2.071574048  45.925688702 1 1 1
>H        1.659769150  -2.074993963  45.925343414 1 1 1
>.................
>Au       0.002439106   5.120271920  81.897457381 1 1 1
>Au      -4.361967945   2.134818447  81.462315449 1 1 1
>Au      -5.204105949  -3.027358489  81.522909929 1 1 1
>.................
>Au      -4.319724000   2.482600000  98.968460000 0 0 0
>Au      -4.319724000  -2.482600000  98.968460000 0 0 0
>Au       0.000000000  -4.965200000  98.968460000 0 0 0
>K_POINTS {Gamma}
>
>I tried with vc-relax as well but could not improve it much. In another
>system, I came across the following forces:
>     Total force =     0.506859     Total SCF correction =     0.000423
>     Total force =     0.501602     Total SCF correction =     0.000666
>     Total force =     0.504022     Total SCF correction =     0.000468
>     Total force =     0.515807     Total SCF correction =     0.000445
>     Total force =     0.531093     Total SCF correction =     0.000497
>     Total force =     0.546169     Total SCF correction =     0.000294
>     Total force =     0.565997     Total SCF correction =     0.000298
>     Total force =     0.594369     Total SCF correction =     0.000437
>     Total force =     0.628540     Total SCF correction =     0.000323
>     Total force =     0.652224     Total SCF correction =     0.000388
>     Total force =     0.636638     Total SCF correction =     0.000299
>     Total force =     0.558604     Total SCF correction =     0.000572
>     Total force =     0.441045     Total SCF correction =     0.000310
>     Total force =     0.331614     Total SCF correction =     0.000424
>     Total force =     0.230756     Total SCF correction =     0.000319
>     Total force =     0.188110     Total SCF correction =     0.000422
>     Total force =     0.160244     Total SCF correction =     0.000236
>     Total force =     0.145254     Total SCF correction =     0.000270
>     Total force =     0.139637     Total SCF correction =     0.000262
>     Total force =     0.125084     Total SCF correction =     0.000424
>     Total force =     0.150679     Total SCF correction =     0.000854
>     Total force =     0.167059     Total SCF correction =     0.000294
>     Total force =     0.172462     Total SCF correction =     0.000478
>     Total force =     0.179529     Total SCF correction =     0.000434
>     Total force =     0.187906     Total SCF correction =     0.000499
>     Total force =     0.191868     Total SCF correction =     0.000428
>     Total force =     0.188061     Total SCF correction =     0.000504
>     Total force =     0.175147     Total SCF correction =     0.000272
>     Total force =     0.159927     Total SCF correction =     0.000273
>     Total force =     0.161611     Total SCF correction =     0.000373
>     Total force =     0.208462     Total SCF correction =     0.000460
>     Total force =     0.280821     Total SCF correction =     0.000192
>     Total force =     0.353126     Total SCF correction =     0.000699
>     Total force =     0.420761     Total SCF correction =     0.000602
>     Total force =     0.486584     Total SCF correction =     0.000230
>     Total force =     0.550967     Total SCF correction =     0.000360
>     Total force =     0.606887     Total SCF correction =     0.000672
>     Total force =     0.640920     Total SCF correction =     0.000602
>     Total force =     0.632764     Total SCF correction =     0.000467
>     Total force =     0.559615     Total SCF correction =     0.000506
>     Total force =     0.526823     Total SCF correction =     0.000464
>     Total force =     0.503575     Total SCF correction =     0.000432
>.........
>Could you please suggest me as to how I could get the "Total force"
>something like 0.001 or of that sort?
>Best regards,
>Sen
>
>
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>
>  
>


From marzari at MIT.EDU  Sat Jun  9 17:53:12 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Sat, 09 Jun 2007 11:53:12 -0400
Subject: [Pw_forum] structural relaxation for a M-M-M system
In-Reply-To: <49019.140.109.128.2.1181380871.squirrel@newwebmail.iitk.ac.in>
References: <49019.140.109.128.2.1181380871.squirrel@newwebmail.iitk.ac.in>
Message-ID: <466ACCE8.8000306@mit.edu>


Dear Sen,


here are a few suggestions, from the more general ones to ones
specific to your system.

1) list your affiliation. PWSCF has a long history of misbehaving
with anonymous users.

2) when things do not work, always try a smaller and simple system,
and try to figure out one problem at a time.

3) even if in your case it won't make a difference, I would feel
more comfortable if you used a slightly larger smearing (0.025 Ry),
"m-v" smearing, and one order of magnitude tighter threshold on the
electronic convergence.

4) with these parameters in hand, and with a fixed unit cell, let the 
code run for a few atomic iterations, starting from the coordinates
that were giving you

>      Total force =     0.095460     Total SCF correction =     0.000604
>      Total force =     0.082488     Total SCF correction =     0.000306
>      Total force =     0.046922     Total SCF correction =     0.000911

[...] etc...

Does the total energy goes down ? (note that the code is calling total 
energy your variational quantity in the presence of a fictitious 
smearing temperature, i.e. E-TS).

If it does, things are moving in the right direction, and the ions are 
being relaxed. Note that since you have always a certain amount of noise 
in the forces (due to imperfect convergence), and because the total free
energy as a function of ionic positions is not perfectly quadratic, it
would probably be wise to do only 20 to 50 ionic iterations, and then 
restart the problem from scratch with the new relaxed ionic coordinates.

If the total energy goes up even at the very first steps, the reasons 
could be two:

1) your forces have too much noise (unlikely, given your small "Total
SCF correction"). Note that you can always specify a desired threshold 
for the convergence of forces.

2) the step that pwscf takes in the search direction for ionic 
minimization is too large (or too small), and thus it is difficult to 
guess correctly the minimum along the search direction. Change the trust
radius, either the min or the max ones (assuming you are doing relax in
the default bfgs mode). All the parameters are described in INPUT_PW, in
the Doc directory.

3) switch to a more robust but less efficient ionic minimization - the
other option in pw is damped dyanmics

4) once you know how to relax the ions, repeat the calculations with 
different celldm(1), and find the one that gives you the minimum in 
energy as a function of celldm(1). If your energy cutoff is high enough,
that should also give a trace of the stress tensor that is roughly
equal to zero.

5) try hard, before asking again for help on the list. In this field, 
you learn by doing more calculations, and thinking what could have gone 
wrong. Once you have solved the problem, post a short message that
summarizes what made a difference and solved the problem.

Best luck,

			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 giannozz at nest.sns.it  Sun Jun 10 19:13:51 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Sun, 10 Jun 2007 19:13:51 +0200
Subject: [Pw_forum] ask question
In-Reply-To: <55639d30706090346s4beb456aw62d0ee3eabfc6c40@mail.gmail.com>
References: <55639d30706090346s4beb456aw62d0ee3eabfc6c40@mail.gmail.com>
Message-ID: <B7D2B6EF-AACB-4DC5-ACD0-BA4CA93B2DB1@nest.sns.it>

On Jun 9, 2007, at 12:46 , wang yanchao wrote:

>   I caculate a material which is body centered orthorhombic  
> structure. It should have 8 operations,but it only find 2  
> operations! When I used CASTEP do it,I can find 8 operation,So I  
> redefine teh vecter of lattice,but in vain.now I don't know what I  
> should do?

In the user guide, "Troubleshooting" section:
http://www.quantum-espresso.org/wiki/index.php/Troubleshooting_% 
28PWscf%29
you should locate the two fields
- ?warning: symmetry operation # N not allowed?
- pw.x doesn?t ?nd all the symmetries you expected.
and read them

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




From murda at sissa.it  Mon Jun 11 20:22:02 2007
From: murda at sissa.it (Garold Murdachaew)
Date: Mon, 11 Jun 2007 20:22:02 +0200 (CEST)
Subject: [Pw_forum] discrepancy in molecular binding energy between pwscf and localized
 basis set program
Message-ID: <Pine.LNX.4.64.0706112017490.22187@shannon-01.sissa.it>

Dear pwscf users,

I am doing some calculations for relatively weakly interacting species and 
decided to compare to what I obtained with localized wavefunction based 
programs such as molpro.  For example, I did calculations of the binding 
energy of Xenon dimer (at the minimum separation of 4.42 Angstroms).
I obtained (in meV):

 	molpro	pwscf3.2
LDA	-34	-34
PBE	 -4	-11

As can be seen, the LDA calculations agree perfectly but the PBE pwscf 
calculation gives an interaction energy almost three times more negative. 
(I realize that for most pwscf users who are usually only concerned about 
energies on the eV rather than on the meV scale these differences may seem 
insignificant.)

Here is my PBE pwscf input file for the Xe dimer (the monomer and the LDA 
inputs are similar):

&CONTROL
   calculation   = 'scf',
   prefix        = '$HEAD',
   title         = '$HEAD',
   restart_mode  = 'from_scratch',
   outdir        = '$TMPDIR/',
   PSEUDO_DIR    = '$PSEUDODIR/',
/
&SYSTEM
     ibrav     = 0,
     celldm(1) = 25.d0,
     nat       = 2,
     ntyp      = 1,
     ecutwfc   = 30.0d0,
     ecutrho   = 300.0d0,
     occupations = 'smearing',
     degauss     = 0.001D0,
     smearing    = 'mp',
     nbnd        = 12,
/
&ELECTRONS
     conv_thr    = 1.0d-8,
     mixing_mode = 'plain',
     mixing_beta = 0.3d0,
/
ATOMIC_SPECIES
Xe 131.30   Xet2tPBE.RRKJ3
ATOMIC_POSITIONS { angstrom }
Xe     .000000000    .000000000    .000000000  0  0  0
Xe     .000000000    .000000000   4.420000000  0  0  0
K_POINTS { gamma }
CELL_PARAMETERS { cubic }
    1.00000    0.00000    0.00000
    0.00000    1.00000    0.00000
    0.00000    0.00000    1.00000

As can be seen, the molecule is in a cubic box of edge length 25 bohr and 
thus there is sufficient vacuum to minimize the spurious interactions with 
its periodic images.  I played with the convergence setting conv_thr but 
setting it to a factor of 100 tighter had very small effect.  Changing the 
degauss setting had no effect on energy (only Fermi level was changed.) 
However, when I increased  ecutwfc and ecutrho to 70 and 700 respectively, 
I obtained a slight change (-10 meV rather than -11 meV).  Can somebody 
please tell me how I can reproduce my PBE  localized basis sets 
calculation.  Do I need to make some changes to the pseudos?  Or is this 
what I can expect from gradient-corrected calculations (such as PBE) due 
to some sort of errors in estimating the gradients (which are not needed 
in the LDA calculation)?

Thank you for you assistance.

Best regards,
Garold Murdachaew

ps:  Here are the details of the pseudo I used in pwscf:

LDA pseudo: XeLDA.RRKJ3.UPF: nonrel, nc, nlcc=t, valence=8, maxl=2
PBE pseudo: Xet2tPBE.RRKJ3 : nonrel, nc, nlcc=t, valence=8, maxl=2

--
Garold Murdachaew
Postdoctoral Fellow - Condensed Matter Sector
SISSA-ISAS (International School for Advanced Studies)
New Building Room 208
Via Beirut 2-4, 34014 Trieste, Italy

tel   : +39 040 3787 477
fax   : +39 040 3787 528
email : murda at sissa.it




From akohlmey at cmm.chem.upenn.edu  Tue Jun 12 00:55:01 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 11 Jun 2007 18:55:01 -0400 (EDT)
Subject: [Pw_forum] discrepancy in molecular binding energy between pwscf
 and localized basis set program
In-Reply-To: <Pine.LNX.4.64.0706112017490.22187@shannon-01.sissa.it>
Message-ID: <Pine.LNX.4.44.0706111850070.11699-100000@localhost.localdomain>

On Mon, 11 Jun 2007, Garold Murdachaew wrote:

GM> Dear pwscf users,
GM> 
GM> I am doing some calculations for relatively weakly interacting species and 
GM> decided to compare to what I obtained with localized wavefunction based 
GM> programs such as molpro.  For example, I did calculations of the binding 
GM> energy of Xenon dimer (at the minimum separation of 4.42 Angstroms).
GM> I obtained (in meV):
GM> 
GM>  	molpro	pwscf3.2
GM> LDA	-34	-34
GM> PBE	 -4	-11

garold,

one stupid question: how is your basis set convergence 
in molpro and more importantly, did you correct for BSSE?

i found that BSSE can be very large for weakly binding
systems, even with large basis sets.

axel.

GM> 
GM> As can be seen, the LDA calculations agree perfectly but the PBE pwscf 
GM> calculation gives an interaction energy almost three times more negative. 
GM> (I realize that for most pwscf users who are usually only concerned about 
GM> energies on the eV rather than on the meV scale these differences may seem 
GM> insignificant.)
GM> 
GM> Here is my PBE pwscf input file for the Xe dimer (the monomer and the LDA 
GM> inputs are similar):
GM> 
GM> &CONTROL
GM>    calculation   = 'scf',
GM>    prefix        = '$HEAD',
GM>    title         = '$HEAD',
GM>    restart_mode  = 'from_scratch',
GM>    outdir        = '$TMPDIR/',
GM>    PSEUDO_DIR    = '$PSEUDODIR/',
GM> /
GM> &SYSTEM
GM>      ibrav     = 0,
GM>      celldm(1) = 25.d0,
GM>      nat       = 2,
GM>      ntyp      = 1,
GM>      ecutwfc   = 30.0d0,
GM>      ecutrho   = 300.0d0,
GM>      occupations = 'smearing',
GM>      degauss     = 0.001D0,
GM>      smearing    = 'mp',
GM>      nbnd        = 12,
GM> /
GM> &ELECTRONS
GM>      conv_thr    = 1.0d-8,
GM>      mixing_mode = 'plain',
GM>      mixing_beta = 0.3d0,
GM> /
GM> ATOMIC_SPECIES
GM> Xe 131.30   Xet2tPBE.RRKJ3
GM> ATOMIC_POSITIONS { angstrom }
GM> Xe     .000000000    .000000000    .000000000  0  0  0
GM> Xe     .000000000    .000000000   4.420000000  0  0  0
GM> K_POINTS { gamma }
GM> CELL_PARAMETERS { cubic }
GM>     1.00000    0.00000    0.00000
GM>     0.00000    1.00000    0.00000
GM>     0.00000    0.00000    1.00000
GM> 
GM> As can be seen, the molecule is in a cubic box of edge length 25 bohr and 
GM> thus there is sufficient vacuum to minimize the spurious interactions with 
GM> its periodic images.  I played with the convergence setting conv_thr but 
GM> setting it to a factor of 100 tighter had very small effect.  Changing the 
GM> degauss setting had no effect on energy (only Fermi level was changed.) 
GM> However, when I increased  ecutwfc and ecutrho to 70 and 700 respectively, 
GM> I obtained a slight change (-10 meV rather than -11 meV).  Can somebody 
GM> please tell me how I can reproduce my PBE  localized basis sets 
GM> calculation.  Do I need to make some changes to the pseudos?  Or is this 
GM> what I can expect from gradient-corrected calculations (such as PBE) due 
GM> to some sort of errors in estimating the gradients (which are not needed 
GM> in the LDA calculation)?
GM> 
GM> Thank you for you assistance.
GM> 
GM> Best regards,
GM> Garold Murdachaew
GM> 
GM> ps:  Here are the details of the pseudo I used in pwscf:
GM> 
GM> LDA pseudo: XeLDA.RRKJ3.UPF: nonrel, nc, nlcc=t, valence=8, maxl=2
GM> PBE pseudo: Xet2tPBE.RRKJ3 : nonrel, nc, nlcc=t, valence=8, maxl=2
GM> 
GM> --
GM> Garold Murdachaew
GM> Postdoctoral Fellow - Condensed Matter Sector
GM> SISSA-ISAS (International School for Advanced Studies)
GM> New Building Room 208
GM> Via Beirut 2-4, 34014 Trieste, Italy
GM> 
GM> tel   : +39 040 3787 477
GM> fax   : +39 040 3787 528
GM> email : murda at sissa.it
GM> 
GM> 
GM> _______________________________________________
GM> Pw_forum mailing list
GM> Pw_forum at pwscf.org
GM> http://www.democritos.it/mailman/listinfo/pw_forum
GM> 

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



From murda at sissa.it  Tue Jun 12 12:16:14 2007
From: murda at sissa.it (Garold Murdachaew)
Date: Tue, 12 Jun 2007 12:16:14 +0200 (CEST)
Subject: [Pw_forum] discrepancy in molecular binding energy between pwscf
 and localized basis set program
In-Reply-To: <1181612259.466df8e386b57@webmail.unimore.it>
References: <Pine.LNX.4.64.0706112017490.22187@shannon-01.sissa.it>
 <1181612259.466df8e386b57@webmail.unimore.it>
Message-ID: <Pine.LNX.4.64.0706121209370.31779@shannon-01.sissa.it>

Dear Stefano, Axel, and Agostino,

I should have mentioned that the molpro calculation is done with a large
basis set (I checked for convergence), and, as always necessary for these
types of calculations, the counterpoise correction for BSSE.  The fact 
that the LDA calculations (where the same basis set and CP correction was 
also used in molpro) agree show that the disagreement in the PBE values 
between the programs is not due to a basis set problem in the molpro 
calculation.

By the way, I realize that DFT cannot describe this van der Waals
interaction: the correct result from molpro at CCSD(T) level is -21 meV
while a more accurate ab initio calculation of Slavicek et al. gives -22 
meV and the very accurate Aziz empirical potential fitted to rovibrational
spectra of Xe dimer gives -24 meV; note that all of these numbers are
without ZPE.  However, since I am trying to assemble a hybrid method which
relies on some calculations from pwscf (for Xe/Cu(111) physisorption),
supplemented with the neglected van der Waals corrections from molpro, it 
is important to be able to reproduce the same DFT numbers in both 
programs.  This is especially necessary since pwscf with PBE gives -40 
meV/atom and -34 meV/atom for the V3xV3 Xe/Cu(111) physisorption energy 
for top and fcc sites respectively.  Thus, differences of a few meV become 
important in this problem.  I am hoping that all the van der Waals-type 
corrections will bring the PBE top-site value down to something close to 
the experimentally measured value of about -183 meV/atom, as well shifting 
the minimum of the binding energy curve to something close to that 
measured experimentally.

Thanks to all of you for your comments.  The question still remains open, 
however...

Best regards,
Garold



On Tue, 12 Jun 2007, smigliore at unimo.it wrote:

> Dear Garold,
>
> let me say that I am in complete agreement with what suggested by Axel. BSSE can
> also account for a so large reduction in the binding energy; see, e.g., Chem.
> Phys. 324, 455 (2006).
>
> Best Regards,
> Agostino Migliore
> PS: There are also many PWscf users concerned with energies on the meV scale.
>
> Quoting Garold Murdachaew <murda at sissa.it>:
>
>> Dear pwscf users,
>>
>> I am doing some calculations for relatively weakly interacting species and
>> decided to compare to what I obtained with localized wavefunction based
>> programs such as molpro.  For example, I did calculations of the binding
>> energy of Xenon dimer (at the minimum separation of 4.42 Angstroms).
>> I obtained (in meV):
>>
>>  	molpro	pwscf3.2
>> LDA	-34	-34
>> PBE	 -4	-11
>>
>> As can be seen, the LDA calculations agree perfectly but the PBE pwscf
>> calculation gives an interaction energy almost three times more negative.
>> (I realize that for most pwscf users who are usually only concerned about
>> energies on the eV rather than on the meV scale these differences may seem
>> insignificant.)
>>
>> Here is my PBE pwscf input file for the Xe dimer (the monomer and the LDA
>> inputs are similar):
>>
>> &CONTROL
>>    calculation   = 'scf',
>>    prefix        = '$HEAD',
>>    title         = '$HEAD',
>>    restart_mode  = 'from_scratch',
>>    outdir        = '$TMPDIR/',
>>    PSEUDO_DIR    = '$PSEUDODIR/',
>> /
>> &SYSTEM
>>      ibrav     = 0,
>>      celldm(1) = 25.d0,
>>      nat       = 2,
>>      ntyp      = 1,
>>      ecutwfc   = 30.0d0,
>>      ecutrho   = 300.0d0,
>>      occupations = 'smearing',
>>      degauss     = 0.001D0,
>>      smearing    = 'mp',
>>      nbnd        = 12,
>> /
>> &ELECTRONS
>>      conv_thr    = 1.0d-8,
>>      mixing_mode = 'plain',
>>      mixing_beta = 0.3d0,
>> /
>> ATOMIC_SPECIES
>> Xe 131.30   Xet2tPBE.RRKJ3
>> ATOMIC_POSITIONS { angstrom }
>> Xe     .000000000    .000000000    .000000000  0  0  0
>> Xe     .000000000    .000000000   4.420000000  0  0  0
>> K_POINTS { gamma }
>> CELL_PARAMETERS { cubic }
>>     1.00000    0.00000    0.00000
>>     0.00000    1.00000    0.00000
>>     0.00000    0.00000    1.00000
>>
>> As can be seen, the molecule is in a cubic box of edge length 25 bohr and
>> thus there is sufficient vacuum to minimize the spurious interactions with
>> its periodic images.  I played with the convergence setting conv_thr but
>> setting it to a factor of 100 tighter had very small effect.  Changing the
>> degauss setting had no effect on energy (only Fermi level was changed.)
>> However, when I increased  ecutwfc and ecutrho to 70 and 700 respectively,
>> I obtained a slight change (-10 meV rather than -11 meV).  Can somebody
>> please tell me how I can reproduce my PBE  localized basis sets
>> calculation.  Do I need to make some changes to the pseudos?  Or is this
>> what I can expect from gradient-corrected calculations (such as PBE) due
>> to some sort of errors in estimating the gradients (which are not needed
>> in the LDA calculation)?
>>
>> Thank you for you assistance.
>>
>> Best regards,
>> Garold Murdachaew
>>
>> ps:  Here are the details of the pseudo I used in pwscf:
>>
>> LDA pseudo: XeLDA.RRKJ3.UPF: nonrel, nc, nlcc=t, valence=8, maxl=2
>> PBE pseudo: Xet2tPBE.RRKJ3 : nonrel, nc, nlcc=t, valence=8, maxl=2
>>
>> --
>> Garold Murdachaew
>> Postdoctoral Fellow - Condensed Matter Sector
>> SISSA-ISAS (International School for Advanced Studies)
>> New Building Room 208
>> Via Beirut 2-4, 34014 Trieste, Italy
>>
>> tel   : +39 040 3787 477
>> fax   : +39 040 3787 528
>> email : murda at sissa.it
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
>

-- 
Garold Murdachaew
Postdoctoral Fellow - Condensed Matter Sector
SISSA-ISAS (International School for Advanced Studies)
New Building Room 208
Via Beirut 2-4, 34014 Trieste, Italy

tel   : +39 040 3787 477
fax   : +39 040 3787 528
email : murda at sissa.it


From giannozz at nest.sns.it  Tue Jun 12 13:17:57 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 12 Jun 2007 13:17:57 +0200
Subject: [Pw_forum] discrepancy in molecular binding energy between pwscf and localized basis set program
In-Reply-To: <Pine.LNX.4.64.0706112017490.22187@shannon-01.sissa.it>
References: <Pine.LNX.4.64.0706112017490.22187@shannon-01.sissa.it>
Message-ID: <CEFA1D1C-CF77-4FA8-89B4-4D90F2D49CF5@nest.sns.it>

On Jun 11, 2007, at 20:22 , Garold Murdachaew wrote:
>
> [...] I did calculations of the binding energy of Xenon dimer
> (at the minimum separation of 4.42 Angstroms). I obtained (in meV):
>
> 	molpro	pwscf3.2
> LDA	-34	-34
> PBE	 -4	-11
>
> As can be seen, the LDA calculations agree perfectly but the PBE  
> pwscf calculation gives an interaction energy almost three times  
> more negative.

in French, there is a nice way to say that something is negligibly  
small:
"c'est trois fois rien" = "it is three times nothing". It perfectly  
describes
the above situation :-).

Seriously: gradient-corrected functionals are ill-defined in the
rho=>0 limit . In pwscf, they are cut when rho < small, defined
in Modules/functionals.f90. In molpro, I don't know. This is the
first thing I would check.

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




From eclee at kyungwon.ac.kr  Tue Jun 12 17:09:04 2007
From: eclee at kyungwon.ac.kr (=?EUC-KR?B?IsDMwLrDtiI=?=)
Date: Wed, 13 Jun 2007 00:09:04 +0900
Subject: [Pw_forum] =?EUC-KR?B?U2VyaW91cyBwcm9ibGVtIGluIHRvdGFsIGVuZXJneSBjYWxjdWxhdA==?=
 =?EUC-KR?B?aW9uID8=?=
Message-ID: <1181660944837946.18333@mail>

Dear advanced users and developers of PWSCF;

I recently installed Quantum Espresso code, ver 3.2.2, and 
performed simple calculations for tests using PWSCF. 
Today, I have found that total energy of a single oxygen atom
calculated in PWSCF is different from that generated in  Vanderbilt's 
pseudopotential code (ver. 7.3.6). I surely remember that the total
energies of single atom  in pseudopotential generation program
and in plane wave code are almost same within small errors, when
I used Berkely code made by S. Froyen. Please inform me if I make
any mistake in using PWSCF code, after seeing following results.

1. Total energy of a single oxygen atom calculated by Vanderbilt's 
pseudopotential code;

You can easily find it in the header of the oxygen pseudopotential file
O.pbe-van_bm.UPF at PWSCF webpage, as follows. 

<PP_HEADER>
   0                   Version Number
   O                   Element
   US                  Ultrasoft pseudopotential
    F                  Nonlinear Core Correction
 SLA  PW   PBE  PBE    PBE  Exchange-Correlation functional
    6.00000000000      Z valence
  -31.58339463984      Total energy
 25.000000 100.0000000 Suggested cutoff for wfc and rho
    1                  Max angular momentum component
  737                  Number of points in mesh

Thus, this file indicate that the total energy of single oxygen atom is 
-31.58339463984 Ry. 

2. PWSCF calculation
     
I used following input file. 

&control
    calculation='relax',
    restart_mode='from_scratch',
    prefix='o',
    pseudo_dir = '/home/kgna0022/pseudo/',
    outdir='/scratch2/kgna0022/tmp/',
    nstep=1,
 /
 &system
    ibrav= 1,
    celldm(1)=20.0
    nat= 1, ntyp= 1,
    ecutwfc =30.0,
    ecutrho =210.0,
    nbnd=6,
    occupations='from_input',
 /
 &electrons
    conv_thr =  1.0D-8,
    mixing_beta = 0.7D0,
/
&IONS
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
/
ATOMIC_SPECIES
 O   16.00  O.pbe-van_bm.UPF
ATOMIC_POSITIONS (bohr)
O        0.00000000000   0.000000000   0.000000000
K_POINTS (Gamma)
OCCUPATIONS
2.0  1.333333333333333    1.333333333333333   1.333333333333333  0.0 0.0

After running PWSCF, I obtained following results.

     total energy              =   -31.53644545 Ry
     total energy              =   -31.53655807 Ry
     total energy              =   -31.53657629 Ry
!    total energy              =   -31.53657705 Ry

Thus, the total energy is -31.53657705 Ry, diffent from
the result of Vanderbilt's code, -31.58339463984 Ry. 

If you teach me my mistake during the calculations, I will
be happy. However, if you don't find my mistake, I cordially ask 
developers of PWSCF code to solve this problem.
Thank you very much.

Best regards,

Eun-Cheol Lee, Ph. D.
Assistant Professor,
Dept. of BioNano Tech., 
Kyungwon University, Korea.
E-mail : eclee at kyungwon.ac.kr
TEL : +82-31-750-8752
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From cyrille.barreteau at cea.fr  Tue Jun 12 19:44:54 2007
From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille)
Date: Tue, 12 Jun 2007 19:44:54 +0200
Subject: [Pw_forum] three times nothing :-)
References: <Pine.LNX.4.64.0706112017490.22187@shannon-01.sissa.it> <CEFA1D1C-CF77-4FA8-89B4-4D90F2D49CF5@nest.sns.it>
Message-ID: <18E4AC9C2FAC504E994A6759DE5ABE8D20F136@DIODON.extra.cea.fr>

Dear Paolo,

There is a famous french humorist (Raymond Devos)
who made an whole sketch on this "trois fois rien" he said that
"trois fois rien c'est d?j? quelque chose!"
"three times nothing it is already something":-)
Maybe it does not apply to this situation!

 cyrille


On Jun 11, 2007, at 20:22 , Garold Murdachaew wrote:
>
> [...] I did calculations of the binding energy of Xenon dimer
> (at the minimum separation of 4.42 Angstroms). I obtained (in meV):
>
> 	molpro	pwscf3.2
> LDA	-34	-34
> PBE	 -4	-11
>
> As can be seen, the LDA calculations agree perfectly but the PBE  
> pwscf calculation gives an interaction energy almost three times  
> more negative.

in French, there is a nice way to say that something is negligibly  
small:
"c'est trois fois rien" = "it is three times nothing". It perfectly  
describes
the above situation :-).


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


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

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From shruba at gmail.com  Wed Jun 13 16:44:20 2007
From: shruba at gmail.com (shruba at gmail.com)
Date: Wed, 13 Jun 2007 10:44:20 -0400
Subject: [Pw_forum] error msg -previous MD history got lost
Message-ID: <822f4ec80706130744o196cb906hcc1bdbc5cec5e1ed@mail.gmail.com>

Hi all,
 I was running a vc-relax calculation , it was completed several steps but
it stopped with the error messeage

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from vcsmd : error #         1
     previous MD history got lost
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 if you can help me to fix this preoblem that will be great.
 thanks
                         shruba
                        graduate student
                        department of chemistry
                         university of central florida
                         orlando , Fl-32826

-- 
'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
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From giannozz at nest.sns.it  Wed Jun 13 17:56:20 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 13 Jun 2007 17:56:20 +0200
Subject: [Pw_forum] Serious problem in total energy calculation ?
In-Reply-To: <1181660944837946.18333@mail>
References: <1181660944837946.18333@mail>
Message-ID: <5A9677FE-8402-47F1-B872-1DD59E52B490@nest.sns.it>

On Jun 12, 2007, at 17:09 , ??? wrote:

> Thus, the total energy is -31.53657705 Ry, different from the  
> result of Vanderbilt's code, -31.58339463984 Ry.

reproducing atomic results (typically obtained using real-space
radial grids) with plane waves is tricky: you have to really push
the convergence of the PW calculation. In your example, the PW
energy seems to converge to E=-31.5525 or so (ecutwfc=70,
ecutrho=280). I don't know where the remaining 0.03 Ry difference
may come from, but the usual suspect is the presence of a small
amount of negative charge. Different codes may follow different
recipes on how to deal in that case with the exchange-correlation
potential and energy, and this might well explain the difference in
total energy.

Please post simple text, not html.

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




From eclee at kyungwon.ac.kr  Thu Jun 14 03:08:08 2007
From: eclee at kyungwon.ac.kr (Eun-Cheol Lee)
Date: Thu, 14 Jun 2007 10:08:08 +0900
Subject: [Pw_forum] Serious problem in total energy calculation ?
References: <1181660944837946.18333@mail> <5A9677FE-8402-47F1-B872-1DD59E52B490@nest.sns.it>
Message-ID: <002f01c7ae20$781d96a0$9aba66d2@HAKOCA>

Dear Paolo,

Thank you for kind explanation.
I didn't know this kind of problem in  norm-conserving
pseudopotential, where sufficient kinetic energy
cutoffs are used and negative charge does not exist.
If the relative difference of total energies is not affected,
this is not serious problem. I will check the situation.

In addition, I am sorry for my html mail. I never expected
that my mail is seen broken.

Eun-Cheol Lee

Kyungwon Univ., Korea


----- Original Message ----- 
From: "Paolo Giannozzi" <giannozz at nest.sns.it>
To: <pw_forum at pwscf.org>
Sent: Thursday, June 14, 2007 12:56 AM
Subject: Re: [Pw_forum] Serious problem in total energy calculation ?



On Jun 12, 2007, at 17:09 , ?????? wrote:

> Thus, the total energy is -31.53657705 Ry, different from the  result of 
> Vanderbilt's code, -31.58339463984 Ry.

reproducing atomic results (typically obtained using real-space
radial grids) with plane waves is tricky: you have to really push
the convergence of the PW calculation. In your example, the PW
energy seems to converge to E=-31.5525 or so (ecutwfc=70,
ecutrho=280). I don't know where the remaining 0.03 Ry difference
may come from, but the usual suspect is the presence of a small
amount of negative charge. Different codes may follow different
recipes on how to deal in that case with the exchange-correlation
potential and energy, and this might well explain the difference in
total energy.

Please post simple text, not html.

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


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





From colin.mcmurtrie at canterbury.ac.nz  Thu Jun 14 05:44:58 2007
From: colin.mcmurtrie at canterbury.ac.nz (Colin John McMurtrie)
Date: Thu, 14 Jun 2007 15:44:58 +1200
Subject: [Pw_forum] makedeps.sh problems
Message-ID: <10AB4C0B-A50D-44A4-81E0-E9B3DE439875@canterbury.ac.nz>

Dear Pw_scf community,

There appears to be a minor problem with the makedeps.sh script.   
When I  run it I receive the following warning:
./makedeps.sh
directory Modules : ok
directory clib : ok
directory PW : ok
directory CPV : ok
directory flib : ok
directory pwtools : ok
directory upftools : ok
pw2wannier90.o : @wannier@
WARNING: dependencies not found in directory PP
directory PWCOND : ok
directory Gamma : ok
directory PH : ok
directory D3 : ok
directory atomic : ok
directory Nmr : ok
directory VIB : ok
directory VdW : ok

Furthermore if I look at the file PP/make.depend there appears to be  
an invalid entry, namely @wannier@:
pw2wannier90.o : ../Modules/cell_base.o
pw2wannier90.o : ../Modules/constants.o
pw2wannier90.o : ../Modules/io_files.o
pw2wannier90.o : ../Modules/io_global.o
pw2wannier90.o : ../Modules/ions_base.o
pw2wannier90.o : ../Modules/kind.o
pw2wannier90.o : ../Modules/mp.o
pw2wannier90.o : ../Modules/mp_global.o
pw2wannier90.o : ../Modules/random_numbers.o
pw2wannier90.o : ../Modules/uspp.o
pw2wannier90.o : ../Modules/wannier.o
pw2wannier90.o : ../Modules/wavefunctions.o
pw2wannier90.o : ../PW/becmod.o
pw2wannier90.o : ../PW/noncol.o
pw2wannier90.o : ../PW/pwcom.o
pw2wannier90.o : @wannier@

Compilation chokes when it gets to this stage of the build.  If I  
remove the entry things proceed normally.

Our system is an IBM p575 running AIX5.3 with XL family compilers.   
Our targets of interest are power5-aix-parallel and bgl.

Cheers,

Colin

-- 
Colin McMurtrie,
UCSC Application Development Consultant and Systems Engineer,
University of Canterbury Te Whare Wananga o Waitaha
Private Bag 4800,
Christchurch,
New Zealand

http://www.ucsc.canterbury.ac.nz
mailto:colin.mcmurtrie at canterbury.ac.nz



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From giannozz at nest.sns.it  Thu Jun 14 10:11:46 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 14 Jun 2007 10:11:46 +0200
Subject: [Pw_forum] makedeps.sh problems
In-Reply-To: <10AB4C0B-A50D-44A4-81E0-E9B3DE439875@canterbury.ac.nz>
References: <10AB4C0B-A50D-44A4-81E0-E9B3DE439875@canterbury.ac.nz>
Message-ID: <A135FC01-C8A3-4B84-BE5E-D381DF31ADAB@nest.sns.it>

On Jun 14, 2007, at 5:44 , Colin John McMurtrie wrote:

> pw2wannier90.o : @wannier@
> WARNING: dependencies not found in directory PP

remove the DOS ^M characters in pw2wannier.f90,
or (better) install the patches (this should be fixed in v.3.2.1)

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




From giannozz at nest.sns.it  Thu Jun 14 10:23:07 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 14 Jun 2007 10:23:07 +0200
Subject: [Pw_forum] Serious problem in total energy calculation ?
In-Reply-To: <002f01c7ae20$781d96a0$9aba66d2@HAKOCA>
References: <1181660944837946.18333@mail> <5A9677FE-8402-47F1-B872-1DD59E52B490@nest.sns.it> <002f01c7ae20$781d96a0$9aba66d2@HAKOCA>
Message-ID: <1757FE58-1BA0-443B-A7CB-D527A2E53F1B@nest.sns.it>

On Jun 14, 2007, at 3:08 , Eun-Cheol Lee wrote:

> I didn't know this kind of problem in  norm-conserving
> pseudopotential, where sufficient kinetic energy
> cutoffs are used and negative charge does not exist.

the charge density with norm-conserving pseudopotentials is
positive by definition. Unfortunately ultrasoft pseudopotentials
may have a small amount of negative charge, typically because
the cutoff is not sufficiently high, but also because the charge
density is not guaranteed to be positive (although, at least in
the atomic configuration used to produce the pseudopotential,
it should).

Anyway: with a LDA ultrasoft pseudopotential for O, also having
some negative charge, the difference between PW and atomic
calculations is much smaller than with the PBE pseudopotential,
so it is more likely that differences in the numerical implementation
of gradient-corrected functionals are to be blamed for the difference.

Anyway: I don't think such differences have any effect on the
quality of the results. If you have any evidence of the opposite,
please let us know

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




From afloris at physik.fu-berlin.de  Thu Jun 14 16:39:16 2007
From: afloris at physik.fu-berlin.de (Andrea Floris)
Date: Thu, 14 Jun 2007 16:39:16 +0200 (CEST)
Subject: [Pw_forum] phonons of bcc iron bulk in parallel
Message-ID: <Pine.LNX.4.58.0706141638090.29061@g32.physik.fu-berlin.de>


Dear Espresso community,

I am running a phonon calculation for iron bulk (bcc structure),
using nspin=2, i.e. a collinear spin polarized calculation.

I am running the version 3.2 *with applied 3.2.1 and 3.2.2. patches*.

If I run in serial, I can reproduce the results
obtained by Dal Corso and de Gironcoli [PRB 62, 273 (2000)].
But if I run in parallel, with the same input except for the number of
processors,
the code runs but the phonons, e.g. at H point, are a disaster (i.e. -940
cm-1,
nonsense, they should be around +295 cm-1).
I attach the relavent inputs/outputs.

It is important to note that if I run an UNpolarized calculation, the
serial and parallel
runs agree very well. This doesn't seem a problem of unlucky combination
of compiler/mpi/machine. Anyhow, I am using:

espresso 3.2 with 3.2.1 and 3.2.2. patches
compiler:  pgi 6.1
mpi     :  /opt/pgi/mpich2/bin/mpif90
machine :  opteron amachine dual or four core


Does anyone have a clue of what is happening?
I would appreciate very much any suggestions,
ciao

Andrea

---------------
 Dr. Andrea Floris
 Institut f"ur Theoretische Physik
 Freie Universit"at Berlin
 Arnimallee 14
 D-14195 Berlin
 Germany
 Tel +49-30-838-53029
 Fax +49-30-838-55258
 e-mail: afloris at physik.fu-berlin.de
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From giannozz at nest.sns.it  Thu Jun 14 17:01:09 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 14 Jun 2007 17:01:09 +0200
Subject: [Pw_forum] phonons of bcc iron bulk in parallel
In-Reply-To: <Pine.LNX.4.58.0706141638090.29061@g32.physik.fu-berlin.de>
References: <Pine.LNX.4.58.0706141638090.29061@g32.physik.fu-berlin.de>
Message-ID: <6BEEA64E-FCC6-4030-A249-1BD88EF4DBBF@nest.sns.it>

On Jun 14, 2007, at 16:39 , Andrea Floris wrote:

> [...] if I run in parallel, with the same input except for the  
> number of
> processors, the code runs but the phonons, e.g. at H point, are a  
> disaster

with pools? there was a number of problems with phonons+pools+lsda
in 3.2. I though they were all fixed by the two patches, but maybe they
were not...

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




From kondor.jess at gmail.com  Thu Jun 14 17:14:16 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Thu, 14 Jun 2007 10:14:16 -0500
Subject: [Pw_forum] a question
Message-ID: <1d9d5d9d0706140814w6ed9e56ase7aeec931e35945e@mail.gmail.com>

 Dear espresso community,

  I have a question. I relaxed a surface (periodic in x and y direction)
with criteria for forces 4.0d-4. I wanted to calculate a polarization via
Berry phase in x-direction, however the code (berry phase) works in parallel
only for z-direction ( I need to use a parallel version due to large number
of atoms). So, I had to exchange the axes (z-> x , x->z) for both atomic
coordinates and for cell parameters:

before:
CELL_PARAMETERS cubic
   5.65402582   0.00000000   0.00000000
   0.00000000   5.65402582   0.00000000
   0.00000000   0.00000000  30.74000000

and after:
CELL_PARAMETERS cubic
 30.74000000    0.00000000   0.00000000
   0.00000000   5.65402582   0.00000000
   0.00000000   0.00000000   5.65402582

The code found 4 symmetry operations as before. The strange thing - after
those operations I performed scf calculations with the same parameters and
output forces are huge ~ 0.02 Ry/au. So, it looks like a system is not
relaxed. Did I do something wrong?

cheers,
 jess


-- 
=====================================
Jess Kondor

PICYT, Av. Venustiano Carranza 2425-A,
San Luis Potos? 78210, M?xico
=====================================
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From giannozz at nest.sns.it  Thu Jun 14 17:42:33 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 14 Jun 2007 17:42:33 +0200
Subject: [Pw_forum] a question
In-Reply-To: <1d9d5d9d0706140814w6ed9e56ase7aeec931e35945e@mail.gmail.com>
References: <1d9d5d9d0706140814w6ed9e56ase7aeec931e35945e@mail.gmail.com>
Message-ID: <5BC4F900-5173-4EBB-8C71-C5609994AE40@nest.sns.it>

On Jun 14, 2007, at 17:14 , Jess Kondor wrote:

> I had to exchange the axes (z-> x , x->z) for both atomic coordinates
> and for cell parameters

and for k-points as well if you want to find the same results

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




From kondor.jess at gmail.com  Thu Jun 14 18:08:28 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Thu, 14 Jun 2007 11:08:28 -0500
Subject: [Pw_forum] a question
In-Reply-To: <5BC4F900-5173-4EBB-8C71-C5609994AE40@nest.sns.it>
References: <1d9d5d9d0706140814w6ed9e56ase7aeec931e35945e@mail.gmail.com>
	 <5BC4F900-5173-4EBB-8C71-C5609994AE40@nest.sns.it>
Message-ID: <1d9d5d9d0706140908i7708ab15y8ddb4912145ad97f@mail.gmail.com>

>
> and for k-points as well if you want to find the same results
>

Yes, I did it too (forgot to mention). 12 12 1  1 1 0 -> (1 12 12  0 1 1).

jess
-- 
=====================================
Jess Kondor

PICYT, Av. Venustiano Carranza 2425-A,
San Luis Potos? 78210, M?xico

=====================================
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From afloris at physik.fu-berlin.de  Thu Jun 14 18:46:38 2007
From: afloris at physik.fu-berlin.de (Andrea Floris)
Date: Thu, 14 Jun 2007 18:46:38 +0200 (CEST)
Subject: [Pw_forum] phonons of bcc iron bulk in parallel
In-Reply-To: <6BEEA64E-FCC6-4030-A249-1BD88EF4DBBF@nest.sns.it>
References: <Pine.LNX.4.58.0706141638090.29061@g32.physik.fu-berlin.de>
 <6BEEA64E-FCC6-4030-A249-1BD88EF4DBBF@nest.sns.it>
Message-ID: <Pine.LNX.4.58.0706141708260.29061@g32.physik.fu-berlin.de>

On Thu, 14 Jun 2007, Paolo Giannozzi wrote:

>
> On Jun 14, 2007, at 16:39 , Andrea Floris wrote:
>
> > [...] if I run in parallel, with the same input except for the
> > number of
> > processors, the code runs but the phonons, e.g. at H point, are a
> > disaster
>
> with pools? there was a number of problems with phonons+pools+lsda
> in 3.2. I though they were all fixed by the two patches, but maybe they
> were not...

Yes, with npool = 4 . Inspired by your question I run a parallel job with
npool=1 (i.e.
with no pools) and everything is fine.    So  also after applying the
patch 3.2.2, the problem arises when  pools are used.

Thank you Paolo, your answer was very useful.
Andrea

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


From ackollias at gmail.com  Thu Jun 14 18:48:27 2007
From: ackollias at gmail.com (sasha)
Date: Thu, 14 Jun 2007 12:48:27 -0400
Subject: [Pw_forum] lda+u low spin question
Message-ID: <1181839707.3218.6.camel@cryptonomicon>

Greetings,
	For a low spin (non-magnetic) LDA+U calculation of MgFeO, the following
Hubbard matrix occupations were obtained:

  z2-1/3   zx    zy    x2-y2   xy
 0.384  0.000  0.000  0.000  0.002
 0.000  0.993  0.000  0.001  0.000
 0.000  0.000  0.993 -0.001  0.000
 0.000  0.001 -0.001  0.380  0.000
 0.002  0.000  0.000  0.000  0.993

For the low-spin solution the eg orbitals should have near zero
occupancies however above it's clear that while the t2g have the
correction occupancy (near 1) the occupancy of the eg seems to be too
large.  The basic question I have is am I computing the low-spin
solution properly?  Any pointers are greatly appreciated. The input file
used to obtain the above occupations is given below.
regards,
	Sasha

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

FeO 
FeO Wustite whithin LDA+U using standard initial ns matrices
 &control
    calculation = 'scf'
    restart_mode='from_scratch',
    verbosity='high',
    tstress=.true.,
    prefix='mgfeo-a-7.28-low-initial-444-0.6',
    pseudo_dir = '/home/akollias/espresso-3.2/pseudo/',
    outdir='/home/scratch/akollias'
 /
 &system
    ibrav=  0, celldm(1)=7.28, nat=  16, ntyp= 6,
    ecutwfc = 60.0, ecutrho = 480.0, nbnd=53
    occupations='smearing', smearing='gauss', degauss=0.01,
    nspin=1,
    lda_plus_u=.true.  Hubbard_U(1)=5.0, Hubbard_U(2)=5.0,
Hubbard_U(3)=5.0, Hubbard_U(4)=5.0,
    report=1
 /
 &electrons
    mixing_mode      = 'plain'
    mixing_beta      = 0.30
    mixing_ndim      = 8  
    mixing_fixed_ns  = 0
    conv_thr         =  1.0d-6
    electron_maxstep = 300

 /
CELL_PARAMETERS
 0.50 -0.50  0.00
 1.00  0.50 -0.50
 1.00  1.00  2.00
ATOMIC_SPECIES
 Fe1  1.  Fe.pz-nd-rrkjus.UPF
 Fe2  1.  Fe.pz-nd-rrkjus.UPF
 Fe3  1.  Fe.pz-nd-rrkjus.UPF
 Fe4  1.  Fe.pz-nd-rrkjus.UPF
 Mg1  1.  Mg.pz-n-vbc.UPF
 O1   1.  O.LDA.US.RRKJ3.UPF
ATOMIC_POSITIONS {alat}
Fe1 0.5  0.5  1.0 
Fe2 1.0  0.0  0.0 
Fe3 1.5  1.0  1.5 
Fe4 0.0  0.0  0.0 
Mg1 1.5  0.5  0.0 
Mg1 1.0  0.5  1.5 
Mg1 1.0  0.5  0.5 
Mg1 1.5  0.5  1.0 
O1  1.0  0.5  0.0 
O1  1.5  0.5  1.5 
O1  0.5  0.0  0.0 
O1  2.0  1.0  1.5 
O1  1.5  0.5  0.5 
O1  1.0  0.5  1.0 
O1  1.5  1.0  1.0 
O1  1.0  0.0  0.5 
K_POINTS {automatic}
4 4 4 0 0 0




From liyanpcl at yahoo.com.cn  Fri Jun 15 03:20:59 2007
From: liyanpcl at yahoo.com.cn (li yan)
Date: Fri, 15 Jun 2007 09:20:59 +0800 (CST)
Subject: [Pw_forum] Re:about the displacive instabilities
Message-ID: <158075.99290.qm@web15605.mail.cnb.yahoo.com>

Dear Stefano
       I'm so sorry and giving my delayed thanks to you, 
       I am not sure if i can continue the discussion of my previous question. I have read the papers you suggested. And the authors proposed that the softening mode coupled with the lattice strain can induced a second or a slightly first order pahse transition. But I stil have doubts in the displacive instabilitis. 
     The character of the  transition from NaCl to CsCl is thougt to be  first order in experiment. May I cosider this  transition to be induced by the lattice instability if I found the softening mode in the  NaCl phase at the pressure which is consitent with the experiment? 
    Best regards. 
        
   
   
  Hi, Li Yan. This is a good question which, I am sure, has been =20
addressed many times in many places. There are for sure a number of =20
textbook references. The only one that occurs to me by heart is =20
unfortunately in French [N. Boccara, Symmetries brisees (Hermann, =20
Paris, 1976)]. Any textbook dealing with Landau's theory of phase =20
transitions would do. The literature in the field looks often more =20
complicated than it actually should. You may want to take a glance at =20=

a pair of old papers of mine where your issue is addressed using =20
minimum theoretical background.

NARDELLI MB, BARONI S, GIANNOZZI P
HIGH-PRESSURE LOW-SYMMETRY PHASES OF CESIUM-HALIDES
PHYSICAL REVIEW B 51 (13): 8060-8068 APR 1 1995

NARDELLI MB, BARONI S, GIANNOZZI P
PHONON SOFTENING AND HIGH-PRESSURE LOW-SYMMETRY PHASES OF CESIUM IODIDE
PHYSICAL REVIEW LETTERS 69 (7): 1069-1072 AUG 17 1992

Hope you will find something useful in them. If not, I will try to =20
write a short explanation, but for this you will have to wait for me =20
to find 1-2 hours of spare time, which is not going to be tomorrow ...

Cheers - Stefano


On Jan 9, 2007, at 8:54 AM, li yan wrote:

> Dear all,
>       Since the displacive phase transition is second order, why =20
> some first order transitions are considered to be induced by the =20
> displacive instabilities? would you please give me some advices or =20
> some reference papers about this?
>                                                                       =20=

>               best regards
> __________________________________________________

    

       
---------------------------------
????????3.5G???20M??? 
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From degironc at sissa.it  Fri Jun 15 10:08:30 2007
From: degironc at sissa.it (degironc)
Date: Fri, 15 Jun 2007 10:08:30 +0200
Subject: [Pw_forum] a question
In-Reply-To: <1d9d5d9d0706140908i7708ab15y8ddb4912145ad97f@mail.gmail.com>
References: <1d9d5d9d0706140814w6ed9e56ase7aeec931e35945e@mail.gmail.com>	 <5BC4F900-5173-4EBB-8C71-C5609994AE40@nest.sns.it> <1d9d5d9d0706140908i7708ab15y8ddb4912145ad97f@mail.gmail.com>
Message-ID: <467248FE.9010301@sissa.it>

... and (relaxed) atomic positions as well...  sorry if it is a trivial 
suggestion.
Could you post your two input files, if they are  not too large ?
stefano
-
Stefano de Gironcoli, SISSA & DEMOCRITOS

Jess Kondor wrote:
>
>     and for k-points as well if you want to find the same results
>
>
> Yes, I did it too (forgot to mention). 12 12 1  1 1 0 -> (1 12 12  0 1 1).
>
> jess
> -- 
> =====================================
> Jess Kondor
>
> PICYT, Av. Venustiano Carranza 2425-A,
> San Luis Potos? 78210, M?xico
>
> ===================================== 



From calderin at physics.queensu.ca  Fri Jun 15 14:01:31 2007
From: calderin at physics.queensu.ca (Lazaro Calderin)
Date: Fri, 15 Jun 2007 14:01:31 +0200
Subject: [Pw_forum] ultra soft psps (ld1 vs uspp)
Message-ID: <1181908891.2688.1.camel@localhost.localdomain>

Hi every one,

I wonder if someone could point me to a reference or provide some hints
on how ultra-soft pseudo potentials are calculated in ld1.x as compared
to Vanderbilt's code.

I was able to design a large cutoff ultra-soft pseudo potential for Hg
using ld1.x (espresso 3.2), but I could not reproduce the same pseudo
using Vanderbilt's code (uspp 7.3.6).

I have started digging into the code but in the mean time any info would
be very helpful.

Thanks, Lazaro

-- 
=============================================================
Dr. Lazaro Calderin, Ph.D.                        
Dpt. of Theoretical, Atomic and Optical Physics        
Univ. of Valladolid, 47005 Valladolid. Spain 
Phone: +34 983 423891   Fax: +34 983 423013   
E-mails: calderin at fta.uva.es  or  calderin at physics.queensu.ca



From stirling at chemres.hu  Fri Jun 15 17:12:53 2007
From: stirling at chemres.hu (stirling andras)
Date: Fri, 15 Jun 2007 17:12:53 +0200
Subject: [Pw_forum] phonon calculation, gamma point
Message-ID: <1181920373.19399.33.camel@geronimo.mta-kk>

Dear Espresso users,

I have encountered a problem during the phonon calculation
of bulk pyrite, which I am not able to resolve.

The way I do the calculation is the following:
I remove all the old restarts from my working directory.
I do an SCF calculation using K point sampling (see attached input).
It runs without problem.
Then I submit the phonon calculation using the attached (second) input.

The error message I receive right at the start of the calculation is the
following:
-------------------------------------------------
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from find_group : error #         1
     incompatible operations
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
------------------------------------------------
looking into the source files i have understood that the problem is related to the fact that
no symmetry element has been found during the restart but  I have not gone further
hoping that you might help.

Thanks for any suggestion in anticipation.

Andras Stirling

--------------------------
Andras Stirling
Department of Theoretical Chemistry,
Chemical Research Center, Budapest, Hungary


-------------- next part --------------
 &control
    calculation = 'scf'
    restart_mode='from_scratch',
    prefix='pyrit',
    pseudo_dir='/home/andras/espresso-3.2/pseudo'
    outdir='/home/andras/espresso/test/test3' 
 /
 &system
    ibrav=  1,
    celldm(1) = 10.18702
    nat= 12
    ntyp= 2
    ecutwfc = 25.0
    ecutrho = 200.D0
 /
 &electrons
  conv_thr    = 1.D-6,
  mixing_beta = 0.5D0
 /
ATOMIC_SPECIES
  Fe   56.0  Fe.pbe-sp-van_mit.UPF
   S   32.0  S.pbe-van_bm.UPF            
ATOMIC_POSITIONS 
Fe      -0.000000000   0.000000000  -0.000000000
Fe       0.500000000   0.000000000   0.500000000
Fe      -0.000000000   0.500000000   0.500000000
Fe       0.500000000   0.500000000   0.000000000
S        0.382544247   0.382544247   0.382544247
S        0.117455753   0.617455753   0.882544247
S        0.617455753   0.882544247   0.117455753
S        0.882544247   0.117455753   0.617455753
S        0.617455753   0.617455753   0.617455753
S        0.882544247   0.382544247   0.117455753
S        0.382544247   0.117455753   0.882544247
S        0.117455753   0.882544247   0.382544247
K_POINTS AUTOMATIC
4 4 4 0 0 0
-------------- next part --------------
phonons of pyrite at Gamma
 &inputph
  tr2_ph=1.0d-14,
  epsil=.true.
  prefix='pyrit',
  amass(1)=56.0,  amass(2)=32.0
  outdir='/home/andras/espresso/test/test3'
  fildyn='pyrit_dynG',
 /
0.0 0.0 0.0


From dalcorso at sissa.it  Fri Jun 15 15:38:11 2007
From: dalcorso at sissa.it (Dal Corso Andrea)
Date: Fri, 15 Jun 2007 15:38:11 +0200
Subject: [Pw_forum] phonon calculation, gamma point
In-Reply-To: <1181920373.19399.33.camel@geronimo.mta-kk>
References: <1181920373.19399.33.camel@geronimo.mta-kk>
Message-ID: <1181914692.14939.16.camel@dhpc-5-01.sissa.it>

There was a bug in the routine PW/find_group.f90 that was corrected some
time ago. The routine was not able to identify the T_h point group.
Please check if your version is correct.
Line 102 of this routine should be:

      IF (noperation(5)==3) code_group=29                   ! T_h

If it is: 
      IF (noperation(5)==6) code_group=29                   ! T_h

correct the 6 to 3.

Hope this helps,

Andrea



On Fri, 2007-06-15 at 17:12 +0200, stirling andras wrote:
> Dear Espresso users,
> 
> I have encountered a problem during the phonon calculation
> of bulk pyrite, which I am not able to resolve.
> 
> The way I do the calculation is the following:
> I remove all the old restarts from my working directory.
> I do an SCF calculation using K point sampling (see attached input).
> It runs without problem.
> Then I submit the phonon calculation using the attached (second) input.
> 
> The error message I receive right at the start of the calculation is the
> following:
> -------------------------------------------------
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from find_group : error #         1
>      incompatible operations
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
>      stopping ...
> ------------------------------------------------
> looking into the source files i have understood that the problem is related to the fact that
> no symmetry element has been found during the restart but  I have not gone further
> hoping that you might help.
> 
> Thanks for any suggestion in anticipation.
> 
> Andras Stirling
> 
> --------------------------
> Andras Stirling
> Department of Theoretical Chemistry,
> Chemical Research Center, Budapest, Hungary
> 
> 
-- 



From stirling at chemres.hu  Fri Jun 15 18:25:11 2007
From: stirling at chemres.hu (stirling andras)
Date: Fri, 15 Jun 2007 18:25:11 +0200
Subject: [Pw_forum] phonon calculation, gamma point
In-Reply-To: <1181914692.14939.16.camel@dhpc-5-01.sissa.it>
References: <1181920373.19399.33.camel@geronimo.mta-kk>
	 <1181914692.14939.16.camel@dhpc-5-01.sissa.it>
Message-ID: <1181924711.19399.41.camel@geronimo.mta-kk>

Thanks for the help.
Indeed in my version (the latest available) contained the wrong line.
However after having edited this line and recompiling the code ("make
all")
the immediate stop still occurs.

Is there any further idea?

Thanks,
Andras Stirling.

On Fri, 2007-06-15 at 15:38 +0200, Dal Corso Andrea wrote:
> There was a bug in the routine PW/find_group.f90 that was corrected some
> time ago. The routine was not able to identify the T_h point group.
> Please check if your version is correct.
> Line 102 of this routine should be:
> 
>       IF (noperation(5)==3) code_group=29                   ! T_h
> 
> If it is: 
>       IF (noperation(5)==6) code_group=29                   ! T_h
> 
> correct the 6 to 3.
> 
> Hope this helps,
> 
> Andrea
> 
> 
> 
> On Fri, 2007-06-15 at 17:12 +0200, stirling andras wrote:
> > Dear Espresso users,
> > 
> > I have encountered a problem during the phonon calculation
> > of bulk pyrite, which I am not able to resolve.
> > 
> > The way I do the calculation is the following:
> > I remove all the old restarts from my working directory.
> > I do an SCF calculation using K point sampling (see attached input).
> > It runs without problem.
> > Then I submit the phonon calculation using the attached (second) input.
> > 
> > The error message I receive right at the start of the calculation is the
> > following:
> > -------------------------------------------------
> >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >      from find_group : error #         1
> >      incompatible operations
> >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > 
> >      stopping ...
> > ------------------------------------------------
> > looking into the source files i have understood that the problem is related to the fact that
> > no symmetry element has been found during the restart but  I have not gone further
> > hoping that you might help.
> > 
> > Thanks for any suggestion in anticipation.
> > 
> > Andras Stirling
> > 
> > --------------------------
> > Andras Stirling
> > Department of Theoretical Chemistry,
> > Chemical Research Center, Budapest, Hungary
> > 
> > 
-- 
stirling andras <stirling at chemres.hu>



From dalcorso at sissa.it  Fri Jun 15 16:28:26 2007
From: dalcorso at sissa.it (Dal Corso Andrea)
Date: Fri, 15 Jun 2007 16:28:26 +0200
Subject: [Pw_forum] phonon calculation, gamma point
In-Reply-To: <1181924711.19399.41.camel@geronimo.mta-kk>
References: <1181920373.19399.33.camel@geronimo.mta-kk>
	 <1181914692.14939.16.camel@dhpc-5-01.sissa.it>
	 <1181924711.19399.41.camel@geronimo.mta-kk>
Message-ID: <1181917706.14939.25.camel@dhpc-5-01.sissa.it>

Remove the executable PH/ph.x before doing make all, otherwise
the corrected routine is not linked to the phonon code.

Andrea


On Fri, 2007-06-15 at 18:25 +0200, stirling andras wrote:
> Thanks for the help.
> Indeed in my version (the latest available) contained the wrong line.
> However after having edited this line and recompiling the code ("make
> all")
> the immediate stop still occurs.
> 
> Is there any further idea?
> 
> Thanks,
> Andras Stirling.
> 
> On Fri, 2007-06-15 at 15:38 +0200, Dal Corso Andrea wrote:
> > There was a bug in the routine PW/find_group.f90 that was corrected some
> > time ago. The routine was not able to identify the T_h point group.
> > Please check if your version is correct.
> > Line 102 of this routine should be:
> > 
> >       IF (noperation(5)==3) code_group=29                   ! T_h
> > 
> > If it is: 
> >       IF (noperation(5)==6) code_group=29                   ! T_h
> > 
> > correct the 6 to 3.
> > 
> > Hope this helps,
> > 
> > Andrea
> > 
> > 
> > 
> > On Fri, 2007-06-15 at 17:12 +0200, stirling andras wrote:
> > > Dear Espresso users,
> > > 
> > > I have encountered a problem during the phonon calculation
> > > of bulk pyrite, which I am not able to resolve.
> > > 
> > > The way I do the calculation is the following:
> > > I remove all the old restarts from my working directory.
> > > I do an SCF calculation using K point sampling (see attached input).
> > > It runs without problem.
> > > Then I submit the phonon calculation using the attached (second) input.
> > > 
> > > The error message I receive right at the start of the calculation is the
> > > following:
> > > -------------------------------------------------
> > >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > >      from find_group : error #         1
> > >      incompatible operations
> > >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > > 
> > >      stopping ...
> > > ------------------------------------------------
> > > looking into the source files i have understood that the problem is related to the fact that
> > > no symmetry element has been found during the restart but  I have not gone further
> > > hoping that you might help.
> > > 
> > > Thanks for any suggestion in anticipation.
> > > 
> > > Andras Stirling
> > > 
> > > --------------------------
> > > Andras Stirling
> > > Department of Theoretical Chemistry,
> > > Chemical Research Center, Budapest, Hungary
> > > 
> > > 
-- 



From degironc at sissa.it  Fri Jun 15 17:07:48 2007
From: degironc at sissa.it (degironc)
Date: Fri, 15 Jun 2007 17:07:48 +0200
Subject: [Pw_forum] a question
In-Reply-To: <1d9d5d9d0706150741i52952350ha81567cce25536d4@mail.gmail.com>
References: <1d9d5d9d0706140814w6ed9e56ase7aeec931e35945e@mail.gmail.com>	 <5BC4F900-5173-4EBB-8C71-C5609994AE40@nest.sns.it>	 <1d9d5d9d0706140908i7708ab15y8ddb4912145ad97f@mail.gmail.com>	 <467248FE.9010301@sissa.it> <1d9d5d9d0706150741i52952350ha81567cce25536d4@mail.gmail.com>
Message-ID: <4672AB44.4070701@sissa.it>

Dear Jess,
   thank you for sending me the input/output files. The structure of the 
two calculations should indeed be equivalent , however the number of 
band are different and in particular the second input has many less 
bands than the first one so that the occupations of the highest computed 
bands in the output have not yet vanished has they should for a 
metallic  calculation.
   Try to repeat the calculation with the same number of bands as the 
first one and let me know.
   stefano

Jess Kondor wrote:
> Dear Stefano,
>
>  Yes, sure, I used relaxed atomic positions as well. I attach my 
> input/output files (1 - x and y are periodic, 2 - x->z; z-> x). 
> Pseudos are attached as well. I send it to you directly due to their 
> big size (sorry!).
>
>  jess
>
> On 6/15/07, *degironc* <degironc at sissa.it <mailto:degironc at sissa.it>> 
> wrote:
>
>     ... and (relaxed) atomic positions as well...  sorry if it is a
>     trivial
>     suggestion.
>     Could you post your two input files, if they are  not too large ?
>     stefano
>     -
>     Stefano de Gironcoli, SISSA & DEMOCRITOS
>
>     Jess Kondor wrote:
>     >
>     >     and for k-points as well if you want to find the same results
>     >
>     >
>     > Yes, I did it too (forgot to mention). 12 12 1  1 1 0 -> (1 12
>     12  0 1 1).
>     >
>     > jess
>     > --
>     > =====================================
>     > Jess Kondor
>     >
>     > PICYT, Av. Venustiano Carranza 2425-A,
>     > San Luis Potos? 78210, M?xico
>     >
>     > =====================================
>
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>     <http://www.democritos.it/mailman/listinfo/pw_forum>
>
>
>
>
> -- 
> =====================================
> Jess Kondor
>
> PICYT, Av. Venustiano Carranza 2425-A,
> San Luis Potos? 78210, M?xico
> ===================================== 



From stirling at chemres.hu  Fri Jun 15 19:28:25 2007
From: stirling at chemres.hu (stirling andras)
Date: Fri, 15 Jun 2007 19:28:25 +0200
Subject: [Pw_forum] phonon calculation, gamma point
In-Reply-To: <1181917706.14939.25.camel@dhpc-5-01.sissa.it>
References: <1181920373.19399.33.camel@geronimo.mta-kk>
	 <1181914692.14939.16.camel@dhpc-5-01.sissa.it>
	 <1181924711.19399.41.camel@geronimo.mta-kk>
	 <1181917706.14939.25.camel@dhpc-5-01.sissa.it>
Message-ID: <1181928505.19399.45.camel@geronimo.mta-kk>

Dear Andrea,

Now it  has indeed started normally.

Thank you for your help,
Regards,
Andras 


--------------------------
Andras Stirling
Department of Theoretical Chemistry,
Chemical Research Center, Budapest, Hungary


On Fri, 2007-06-15 at 16:28 +0200, Dal Corso Andrea wrote:
> Remove the executable PH/ph.x before doing make all, otherwise
> the corrected routine is not linked to the phonon code.
> 
> Andrea
> 
> 
> On Fri, 2007-06-15 at 18:25 +0200, stirling andras wrote:
> > Thanks for the help.
> > Indeed in my version (the latest available) contained the wrong line.
> > However after having edited this line and recompiling the code ("make
> > all")
> > the immediate stop still occurs.
> > 
> > Is there any further idea?
> > 
> > Thanks,
> > Andras Stirling.
> > 
> > On Fri, 2007-06-15 at 15:38 +0200, Dal Corso Andrea wrote:
> > > There was a bug in the routine PW/find_group.f90 that was corrected some
> > > time ago. The routine was not able to identify the T_h point group.
> > > Please check if your version is correct.
> > > Line 102 of this routine should be:
> > > 
> > >       IF (noperation(5)==3) code_group=29                   ! T_h
> > > 
> > > If it is: 
> > >       IF (noperation(5)==6) code_group=29                   ! T_h
> > > 
> > > correct the 6 to 3.
> > > 
> > > Hope this helps,
> > > 
> > > Andrea
> > > 
> > > 
> > > 
> > > On Fri, 2007-06-15 at 17:12 +0200, stirling andras wrote:
> > > > Dear Espresso users,
> > > > 
> > > > I have encountered a problem during the phonon calculation
> > > > of bulk pyrite, which I am not able to resolve.
> > > > 
> > > > The way I do the calculation is the following:
> > > > I remove all the old restarts from my working directory.
> > > > I do an SCF calculation using K point sampling (see attached input).
> > > > It runs without problem.
> > > > Then I submit the phonon calculation using the attached (second) input.
> > > > 
> > > > The error message I receive right at the start of the calculation is the
> > > > following:
> > > > -------------------------------------------------
> > > >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > > >      from find_group : error #         1
> > > >      incompatible operations
> > > >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > > > 
> > > >      stopping ...
> > > > ------------------------------------------------
> > > > looking into the source files i have understood that the problem is related to the fact that
> > > > no symmetry element has been found during the restart but  I have not gone further
> > > > hoping that you might help.
> > > > 
> > > > Thanks for any suggestion in anticipation.
> > > > 
> > > > Andras Stirling
> > > > 
> > > > --------------------------
> > > > Andras Stirling
> > > > Department of Theoretical Chemistry,
> > > > Chemical Research Center, Budapest, Hungary
> > > > 
> > > > 
-- 
stirling andras <stirling at chemres.hu>



From giannozz at nest.sns.it  Fri Jun 15 18:54:12 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 15 Jun 2007 18:54:12 +0200
Subject: [Pw_forum] phonons of bcc iron bulk in parallel
In-Reply-To: <Pine.LNX.4.58.0706141708260.29061@g32.physik.fu-berlin.de>
References: <Pine.LNX.4.58.0706141638090.29061@g32.physik.fu-berlin.de> <6BEEA64E-FCC6-4030-A249-1BD88EF4DBBF@nest.sns.it> <Pine.LNX.4.58.0706141708260.29061@g32.physik.fu-berlin.de>
Message-ID: <8E7A540F-D11A-467C-8B30-6D04ED598CF0@nest.sns.it>


On Jun 14, 2007, at 18:46 , Andrea Floris wrote:

>> with pools? there was a number of problems with phonons+pools+lsda
>> in 3.2. I though they were all fixed by the two patches, but maybe  
>> they
>> were not...
>
> Yes, with npool = 4 . Inspired by your question I run a parallel  
> job with
> npool=1 (i.e. with no pools) and everything is fine. So also after  
> applying
> the patch 3.2.2, the problem arises when  pools are used.

in fact one needed correction was missing from the patch (the cvs  
version
works fine). Thanks to AdC who found it. Attached please find yet  
another
(and final!) patch. Go into the directory containing the qe  
distribution,
espresso-3.2/ or something like that, and from there:
    patch -p1 < /path/to/the/diff/file/espresso-3.2.1.diff
Paolo

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



From niuli1978 at yahoo.com.cn  Sat Jun 16 04:08:13 2007
From: niuli1978 at yahoo.com.cn (li niu)
Date: Sat, 16 Jun 2007 10:08:13 +0800 (CST)
Subject: [Pw_forum] the difference between the linear response method and finite differences of the atomic forces
Message-ID: <710169.43556.qm@web15015.mail.cnb.yahoo.com>

dear all,
 I found there are two methods to obtain the vibarational modes and frequencies by diagonalizing the dymamical matrix. One is the linear response method and the other other is finite differences of the atomic forces by displacing each atom and computing the resulting forces.
 My question is that what's the difference between these two methods? And what's the advantage of respective method?
 
 Thank you in advance!
 
 Best wishes,
 
  Niu Li
 
  Harbin Institue of Technology 
                                                                     
  China
 		
---------------------------------
 ??????-3.5G???20M??
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From degironc at sissa.it  Sat Jun 16 11:57:24 2007
From: degironc at sissa.it (degironc)
Date: Sat, 16 Jun 2007 11:57:24 +0200
Subject: [Pw_forum] the difference between the linear response method
 and finite differences of the atomic forces
In-Reply-To: <710169.43556.qm@web15015.mail.cnb.yahoo.com>
References: <710169.43556.qm@web15015.mail.cnb.yahoo.com>
Message-ID: <4673B404.1070803@sissa.it>

numerical derivative vs analytic ones.
If well done they agree.
Advantages of numerical derivatives: relative simplicity of coding,
access to non-linear anharminic terms.
Disadvantages of numerical derivatives: needs care in order to isolate
the harmonic terms from the anharmonic one, limited to zone-center modes
(electric fields require extra coding/care), non-zone center modes
requires supercells which imply extra computational effort, especially
for small/low symmetry q-points.
Advantages of analytical derivates: direct access to harmonic terms, not
limited to zone-center modes, used to be the only way to deal properly
with macroscopic electric fields but this is not so much true nowadays.
Disadvantage of anaylital derivatves: anharmonic terms require extra coding.
hope this helps.
Stefano de Gironcoli, SISSA and DEMOCRITOS

li niu wrote:
> dear all,
> I found there are two methods to obtain the vibarational modes and
> frequencies by diagonalizing the dymamical matrix. One is the linear
> response method and the other other is finite differences of the
> atomic forces by displacing each atom and computing the resulting forces.
> My question is that what's the difference between these two methods?
> And what's the advantage of respective method?
>
> Thank you in advance!
>
> Best wishes,
>
> Niu Li
>
> Harbin Institue of Technology
>
> China
>
> ------------------------------------------------------------------------
> ??????-3.5G???20M?? <http://cn.mail.yahoo.com/> 



From hashem.yamani at gmail.com  Sat Jun 16 15:12:22 2007
From: hashem.yamani at gmail.com (Hashem Al-Yamani)
Date: Sat, 16 Jun 2007 11:12:22 -0200
Subject: [Pw_forum] nscf error
Message-ID: <82a593400706160612j6114ddc9id18f8b0bd16f0b0b@mail.gmail.com>

Dear All ;

While doing a nscf calculation  in order to plot PDOS for IrO2 by using
K_POINTS [automatic] option, it gave the following error :


 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from efermit : error #         1
     unexpected error
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...



Any one has any Ideas ???



Thanks alot ;

Regards ;
Hashem
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From giannozz at nest.sns.it  Sat Jun 16 19:48:29 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Sat, 16 Jun 2007 19:48:29 +0200
Subject: [Pw_forum] nscf error
In-Reply-To: <82a593400706160612j6114ddc9id18f8b0bd16f0b0b@mail.gmail.com>
References: <82a593400706160612j6114ddc9id18f8b0bd16f0b0b@mail.gmail.com>
Message-ID: <DCE3362F-43EF-4096-A851-96F1670E1453@nest.sns.it>

On Jun 16, 2007, at 15:12 , Hashem Al-Yamani wrote:

> While doing a nscf calculation  in order to plot PDOS for IrO2 by  
> using
> K_POINTS [automatic] option, it gave the following error :
> [...]
> from efermit : error # 1
> unexpected error

did you specify enough bands?

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




From alcantar at phys.ksu.edu  Sun Jun 17 18:55:58 2007
From: alcantar at phys.ksu.edu (Alcantara Ortigoza, Marisol)
Date: Sun, 17 Jun 2007 11:55:58 -0500
Subject: [Pw_forum] about the number of bands
References: <82a593400706160612j6114ddc9id18f8b0bd16f0b0b@mail.gmail.com> <DCE3362F-43EF-4096-A851-96F1670E1453@nest.sns.it>
Message-ID: <F0712C28C5E30740A5F81252A97E6F3201C89BD6@isis.phys.ksu.edu>

Dear all,
 
I understand that to solve the eigenvalue problem one uses the available subroutines to diagonalize the Hamiltonian matrix and usually, for convinience, we request to find only the lowest eigenvectors (occupied plus a few unoccupied bands). However, is there any reason why increasing the number of eigenvalues (bands) to be computed improves or speeds the convergence of these, curing the warnings saying that such and such eigenvectors did not convege (usually the highest ones, I read in the forum)? 
 
Thank you very much.
Marisol
 
...................................................................................................................
Marisol Alc?ntara Ortigoza   Phone: + (407) 823 1543,  Fax: +(407) 823-5112 Cel + (407) 844 3052

Kansas State University  
116 Cardwell Hall    
Manhattan, Kansas 66506, USA
 
University of Central Florida
4000 Central Florida Boulevard
Building 12 Room 418
Orlando, Florida 32816-2385 
 

________________________________

From: pw_forum-admin at pwscf.org on behalf of Paolo Giannozzi
Sent: Sat 6/16/2007 12:48 PM
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] nscf error




On Jun 16, 2007, at 15:12 , Hashem Al-Yamani wrote:

> While doing a nscf calculation  in order to plot PDOS for IrO2 by 
> using
> K_POINTS [automatic] option, it gave the following error :
> [...]
> from efermit : error # 1
> unexpected error

did you specify enough bands?

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


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




From shruba at gmail.com  Sun Jun 17 19:56:40 2007
From: shruba at gmail.com (shruba at gmail.com)
Date: Sun, 17 Jun 2007 13:56:40 -0400
Subject: [Pw_forum] Problem with vc -relax
Message-ID: <822f4ec80706171056w6f0673abre672c69445a895d3@mail.gmail.com>

Hi all,
     I was trying to run vc-relax calculation for srfeo3 ( antiferromagnetic
mettalic ) system,  the problem I was facing for a unit cell it is running
for 3-4 days in processor , where as a single point 'scf' calculation is
taking only 5 minutes, the scf calculation is giving very nice agreement
with experimental data , but for vc -relax  i checked the cell volume was
decresing first then it started exapnding after a certain point, this is my
input file . If any one can help me in this matter that will be really great
help, I am using same cutoff and other parameters required for scf

&CONTROL

calculation = 'vc-relax',

restart_mode = 'from_scratch',

tstress = .TRUE.,

tprnfor = .TRUE.,

prefix = 'relax',

pseudo_dir = '/............./',

outdir='/................../'

/

&SYSTEM

ibrav = 1,

celldm(1) = 7.3

nat =5,

ntyp =3,

ecutwfc = 45,

ecutrho = 360,

nspin=2,

nelec=44

nelup=26,

neldw=18,

nbnd=52,

occupations = 'smearing',

smearing ='marzari-vanderbilt',

degauss=0.03,

qcutz=150., q2sigma=2.0,ecfixed=10.0

/

&ELECTRONS

electron_maxstep =200,

emass =1000.d0,

emass_cutoff = 4.d0,

orthogonalization = 'Gram-Schmidt',

startingwfc ='atomic',

n_inner = 8,

tcg = .TRUE.,

passop=0.3,

maxiter = 250,

conv_thr=1.d-6,

/

&IONS

ion_dynamics = 'damp',

ion_damping = 0.,

ion_positions = 'from_input',

ion_temperature = 'not_controlled',

/

&CELL

cell_dynamics = 'damp-w'

/

ATOMIC_SPECIES

Fe 55.85 Fe.pbe-sp-van.UPF

Sr 87.62 Sr.pbe-nsp-van.UPF

O 16.00 O.pbe-van-bm.UPF

ATOMIC_POSITIONS

Sr 0.000 0.000 0.010

Fe 0.500 0.500 0.500

O 0.000 0.500 0.500

O 0.500 0.500 0.000

O 0.500 0.000 0.500

K_POINTS {automatic}

8 8 8 1 1 1

Thanks in advance , looking forward for your reply
                                shruba

-- 
shruba gangopadhyay
graduate student
department of chemistry
university of central florida
orlando, FL-32826
'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
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From degironc at sissa.it  Sun Jun 17 22:36:53 2007
From: degironc at sissa.it (degironc)
Date: Sun, 17 Jun 2007 22:36:53 +0200
Subject: [Pw_forum] Postdoctoral position available
Message-ID: <46759B65.10607@sissa.it>

A 2-year post-doctoral position is available at the Condensed Matter 
Theory Sector of the International School for Advanced Studies in 
Trieste (Italy) to work in the field of Theoretical Heterogeneous 
Catalysis and Surface Science under my supervision.

The successful candidate will mainly work on theoretical understanding 
of the mechanism of ammonia synthesis and/or on models for reactivity at 
the interface between solid surfaces and solutions.

The preferred starting date is mid September or early October.

The announcement (deadline July 16th) can be found at the page 
http://www.sissa.it/main/?p=A3_B4&what=tpd

Applications should be sent by e-mail to degironc at sissa.it, with 
complete CV in attachment.

Stefano de Gironcoli
degironc at sissa.it,  SISSA and DEMOCRITOS, Trieste (Italy).


From adrainzhou at yahoo.com.cn  Mon Jun 18 06:10:36 2007
From: adrainzhou at yahoo.com.cn (Adrain Zhou)
Date: Mon, 18 Jun 2007 12:10:36 +0800 (CST)
Subject: [Pw_forum] The calcualtion of static dielectric constant using espresso!
Message-ID: <475588.26461.qm@web15804.mail.cnb.yahoo.com>

Dear all,

I am trying to do the static dielectric constant for
TiO2 systetm. It seems example30 provides a
calcualtion of static dielectric constant for MgO.
This mainly involves CP dynamics. Here I just want to
know whether the static dielectric constant can be
obtained using linear response method. Could anybody
please give me more details on how to calcualte it?

Another question: is it possible to study the effect
of temperature on the static dielectric constant?


Many thanks in advance!

With regards,
Adrian


      ___________________________________________________________ 
??????3.5G???20M??? 
http://cn.mail.yahoo.com/


From giannozz at nest.sns.it  Mon Jun 18 09:16:24 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 18 Jun 2007 09:16:24 +0200
Subject: [Pw_forum] about the number of bands
In-Reply-To: <F0712C28C5E30740A5F81252A97E6F3201C89BD6@isis.phys.ksu.edu>
References: <82a593400706160612j6114ddc9id18f8b0bd16f0b0b@mail.gmail.com> <DCE3362F-43EF-4096-A851-96F1670E1453@nest.sns.it> <F0712C28C5E30740A5F81252A97E6F3201C89BD6@isis.phys.ksu.edu>
Message-ID: <522F6014-D91F-40C8-8335-EA0F5D26B0F7@nest.sns.it>

On Jun 17, 2007, at 18:55 , Alcantara Ortigoza, Marisol wrote:

> is there any reason why increasing the number of eigenvalues  
> (bands) to be computed improves or speeds the convergence of these,  
> curing the warnings saying that such and such eigenvectors did not  
> convege (usually the highest ones, I read in the forum)?

Davidson diagonalization performs a (conventional) diagonalization in a
subspace containing the trial wavefunctions (the current estimate) and
the estimated corrections ((only for unconverged eigenvectors). If the
subspace is larger, you have more freedom to find the correct ground
state manifold.

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




From giannozz at nest.sns.it  Mon Jun 18 09:20:45 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 18 Jun 2007 09:20:45 +0200
Subject: [Pw_forum] The calcualtion of static dielectric constant using espresso!
In-Reply-To: <475588.26461.qm@web15804.mail.cnb.yahoo.com>
References: <475588.26461.qm@web15804.mail.cnb.yahoo.com>
Message-ID: <6BC1E8A1-DFC8-4DDD-A375-D62CAF3F0D89@nest.sns.it>

On Jun 18, 2007, at 6:10 , Adrain Zhou wrote:
>
> Here I just want to know whether the static dielectric constant
> can be obtained using linear response method. Could anybody
> please give me more details on how to calculate it?

use option 'epsil' of code ph.x (or cgph.x)

> Another question: is it possible to study the effect
> of temperature on the static dielectric constant?

if the main effect of the temperature is via the change of volume,
it can be easily calculated; other effects may be much less obvious

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




From marcello.rosini at unimore.it  Mon Jun 18 10:30:50 2007
From: marcello.rosini at unimore.it (Marcello Rosini)
Date: Mon, 18 Jun 2007 10:30:50 +0200
Subject: [Pw_forum] H 0.75 pseudopotential
Message-ID: <467642BA.102@unimore.it>

Good morning everybody
For my calculation I need a pseudopotential for H, of charge 0.75. Since
I wasn't able to find it anywhere, I tried to generate by myself, using
the ld1.x program. It seems to me that ld1 cannot work with charge <1...
when running it says "wrong zed"...
so I have two questions:
    1. is this a limitation of ld1 or someone can give me some help?
    2. Does anybody can indicate me such a pseudopotential?

tanks a lot
Marcello
-- 
------------------------------------------------------------------------
*Dr. ROSINI MARCELLO*
rosini.marcello at unimo.it <mailto:rosini.marcello at unimo.it>
---------------------------------------------------
dipartimento di fisica <http://www.fisica.unimo.it>
Universit? degli studi di Modena e Reggio Emilia

via campi 213/a, 41100 Modena, Italy
tel +39 059 2055312  -  fax +39 059 2055616
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From giannozz at nest.sns.it  Mon Jun 18 11:23:10 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 18 Jun 2007 11:23:10 +0200
Subject: [Pw_forum] H 0.75 pseudopotential
In-Reply-To: <467642BA.102@unimore.it>
References: <467642BA.102@unimore.it>
Message-ID: <498A2AD4-CBA2-4C9E-A983-B8002D414C89@nest.sns.it>

On Jun 18, 2007, at 10:30 , Marcello Rosini wrote:

> It seems to me that ld1 cannot work with charge <1... when running  
> it says "wrong zed"... so I have two questions:
>     1. is this a limitation of ld1 or someone can give me some help?

no, it is just a check

>     2. Does anybody can indicate me such a pseudopotential?

once upon a time I did some bogus H PP with fractionary charge.
They were used with satisfactory results (by people in your
department, by the way). I'll send them to you

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




From chen_shao_hua197 at yahoo.com.tw  Mon Jun 18 16:04:32 2007
From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=)
Date: Mon, 18 Jun 2007 22:04:32 +0800 (CST)
Subject: [Pw_forum] H 0.75 pseudopotential
In-Reply-To: <498A2AD4-CBA2-4C9E-A983-B8002D414C89@nest.sns.it>
Message-ID: <257265.92133.qm@web73011.mail.tp2.yahoo.com>

Dear Paolo,

Could you send them to me, too ? 
I want to create another In PP with fractionary charge
.
So I think maybe I could try it from fellow this
successful example.Or you could tell me what is
keypoint to create such  PP with fractionary charge .
Thanks in advance 

max
Department of Physics ,National Taiwan
University,Taiwan
E-mail : D92222009 at ntu.edu.tw  
           
--- Paolo Giannozzi <giannozz at nest.sns.it> ??

> 
> On Jun 18, 2007, at 10:30 , Marcello Rosini wrote:
> 
> > It seems to me that ld1 cannot work with charge
> <1... when running  
> > it says "wrong zed"... so I have two questions:
> >     1. is this a limitation of ld1 or someone can
> give me some help?
> 
> no, it is just a check
> 
> >     2. Does anybody can indicate me such a
> pseudopotential?
> 
> once upon a time I did some bogus H PP with
> fractionary charge.
> They were used with satisfactory results (by people
> in your
> department, by the way). I'll send them to you
> 
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine,
> Italy
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 



      ____________________________________________________________________________________
????????????? - ???? Yahoo!??????http://tw.info.yahoo.com/seal/index.html


From cesards at msi.umn.edu  Mon Jun 18 19:00:49 2007
From: cesards at msi.umn.edu (cesards at msi.umn.edu)
Date: Mon, 18 Jun 2007 12:00:49 -0500 (CDT)
Subject: [Pw_forum] Re: Problem with vc -relax
In-Reply-To: <20070618053817.14332.33633.Mailman@democritos.sissa.it>
References: <20070618053817.14332.33633.Mailman@democritos.sissa.it>
Message-ID: <50518.209.162.14.191.1182186049.squirrel@www.msi.umn.edu>

Dear Shruba,


I notice that your input doe not contains the varables "dt" in &CONTROL
namelist (dt = 80.0 is recommended for start) and "wmass" in &CELL
namelist (wmass =  0.001 , for example). If get large negative stresses in
the first MD step, try to reduce celldm(1).

It is normal for the cell volume to oscilate. Things are going wrong only
if the amplitude of oscilations are increasing.


Yours,


Cesar R.S. da Silva




> ------=_Part_75233_9601271.1182103000930
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Content-Transfer-Encoding: 7bit
> Content-Disposition: inline
>
> Hi all,
>      I was trying to run vc-relax calculation for srfeo3 (
> antiferromagnetic
> mettalic ) system,  the problem I was facing for a unit cell it is running
> for 3-4 days in processor , where as a single point 'scf' calculation is
> taking only 5 minutes, the scf calculation is giving very nice agreement
> with experimental data , but for vc -relax  i checked the cell volume was
> decresing first then it started exapnding after a certain point, this is
> my
> input file . If any one can help me in this matter that will be really
> great
> help, I am using same cutoff and other parameters required for scf
>
> &CONTROL
>
> calculation = 'vc-relax',
>
> restart_mode = 'from_scratch',
>
> tstress = .TRUE.,
>
> tprnfor = .TRUE.,
>
> prefix = 'relax',
>
> pseudo_dir = '/............./',
>
> outdir='/................../'
>
> /
>
> &SYSTEM
>
> ibrav = 1,
>
> celldm(1) = 7.3
>
> nat =5,
>
> ntyp =3,
>
> ecutwfc = 45,
>
> ecutrho = 360,
>
> nspin=2,
>
> nelec=44
>
> nelup=26,
>
> neldw=18,
>
> nbnd=52,
>
> occupations = 'smearing',
>
> smearing ='marzari-vanderbilt',
>
> degauss=0.03,
>
> qcutz=150., q2sigma=2.0,ecfixed=10.0
>
> /
>
> &ELECTRONS
>
> electron_maxstep =200,
>
> emass =1000.d0,
>
> emass_cutoff = 4.d0,
>
> orthogonalization = 'Gram-Schmidt',
>
> startingwfc ='atomic',
>
> n_inner = 8,
>
> tcg = .TRUE.,
>
> passop=0.3,
>
> maxiter = 250,
>
> conv_thr=1.d-6,
>
> /
>
> &IONS
>
> ion_dynamics = 'damp',
>
> ion_damping = 0.,
>
> ion_positions = 'from_input',
>
> ion_temperature = 'not_controlled',
>
> /
>
> &CELL
>
> cell_dynamics = 'damp-w'
>
> /
>
> ATOMIC_SPECIES
>
> Fe 55.85 Fe.pbe-sp-van.UPF
>
> Sr 87.62 Sr.pbe-nsp-van.UPF
>
> O 16.00 O.pbe-van-bm.UPF
>
> ATOMIC_POSITIONS
>
> Sr 0.000 0.000 0.010
>
> Fe 0.500 0.500 0.500
>
> O 0.000 0.500 0.500
>
> O 0.500 0.500 0.000
>
> O 0.500 0.000 0.500
>
> K_POINTS {automatic}
>
> 8 8 8 1 1 1
>
> Thanks in advance , looking forward for your reply
>                                 shruba
>
> --
> shruba gangopadhyay
> graduate student
> department of chemistry
> university of central florida
> orlando, FL-32826
> 'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
>




From haskell.vivian.mcphail at gmail.com  Tue Jun 19 05:43:37 2007
From: haskell.vivian.mcphail at gmail.com (Vivian McPhail)
Date: Tue, 19 Jun 2007 15:43:37 +1200
Subject: [Pw_forum] Memory allocation in linux using mpirun
Message-ID: <7b03b3c60706182043t5d9c2261qa7424f60e452fa89@mail.gmail.com>

Hi,

I can successfully run all the examples provided with espresso using mpirun,
however, when I attempt to run my own calculations the program crashes with
a memory allocation failure.  This occurs when real memory is exhausted.

From adrainzhou at yahoo.com.cn  Tue Jun 19 06:42:54 2007
From: adrainzhou at yahoo.com.cn (Adrain Zhou)
Date: Tue, 19 Jun 2007 12:42:54 +0800 (CST)
Subject: [Pw_forum] =?gb2312?q?=BB=D8=B8=B4=A3=BA=20Re:=20[Pw=5Fforum]=20The=20calcualtion=20?=
 =?gb2312?q?of=20static=20dielectric=20constant=20using=20espresso!?=
In-Reply-To: <6BC1E8A1-DFC8-4DDD-A375-D62CAF3F0D89@nest.sns.it>
Message-ID: <464696.35279.qm@web15814.mail.cnb.yahoo.com>

Dear Paolo, 

I just read the definition of dielectric constant from
http://www.quantum-espresso.org/wiki/index.php/Dielectric_constant
. I am not sure whether the contribution to dielectric
constant from clamped-ion polarization conrresponds to
static response. That is why espresso is unable to
deal with dynamics response.

As for the study of temperature effect on the static
dielectric constant, I am not sure whether what you
mean is to run MD at fix temperature first and then
calculate dielectric constant by sampling different
configurations. Could you please give me more details?

Many thanks!

Regards,
Adrian




--- Paolo Giannozzi <giannozz at nest.sns.it> witten:

> 
> On Jun 18, 2007, at 6:10 , Adrain Zhou wrote:
> >
> > Here I just want to know whether the static
> dielectric constant
> > can be obtained using linear response method.
> Could anybody
> > please give me more details on how to calculate
> it?
> 
> use option 'epsil' of code ph.x (or cgph.x)
> 
> > Another question: is it possible to study the
> effect
> > of temperature on the static dielectric constant?
> 
> if the main effect of the temperature is via the
> change of volume,
> it can be easily calculated; other effects may be
> much less obvious
> 
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine,
> Italy
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 



      ___________________________________________________________ 
????????3.5G???20M??? 
http://cn.mail.yahoo.com


From adrainzhou at yahoo.com.cn  Tue Jun 19 10:00:34 2007
From: adrainzhou at yahoo.com.cn (Adrain Zhou)
Date: Tue, 19 Jun 2007 16:00:34 +0800 (CST)
Subject: [Pw_forum] Wrong Static dielectric constant for TiO2
Message-ID: <778881.597.qm@web15805.mail.cnb.yahoo.com>

Dear all,

I have tried to calculte the static dielectric
constant for TiO2 by using pw.x and ph.x. I got the
following results for output of ph.x.
 
End of electric fields calculation

          Dielectric constant in cartesian axis

          (       7.855837978      -0.051415295     
-0.008755542 )
          (      -0.051415295       7.855837978     
-0.008755542 )
          (      -0.008755520      -0.008755520      
8.995713377 )

The static dielectric constant for TiO2 is around 110.
It seems these values are very close to high frequency
dielectric constant. Am I wrong?

Any comments and suggestions will be highly
appreciated!

Regards,
Adrian


		
___________________________________________________________ 
????????-3.5G???20M??? 
http://cn.mail.yahoo.com


From yuwen_66 at yahoo.com  Tue Jun 19 11:22:41 2007
From: yuwen_66 at yahoo.com (W. YU)
Date: Tue, 19 Jun 2007 02:22:41 -0700 (PDT)
Subject: [Pw_forum] _intel_cpu_indicator error
Message-ID: <120956.83978.qm@web51004.mail.re2.yahoo.com>

Dear PW users,

I have met a problem when running in pc clusters.

The environment is: x86 amd64 cluster. I use 
espresso-3.2. Configure found this system and 
set the makefile. It also compiled well. But when
I run in either serial or paralell, the following 
problem arose: undefined symbol, _intel_cpu_indicator.

I browsed the web and found someone mentioned it is
caused by the version of mkl used. I used mkl8.0,
someone suggested mkl8.1. But I have no control of 
this pc cluster. So I don't know whether it comes
here.

I would appreciate it very much if anybody can help
me?

Wen Yu


       
____________________________________________________________________________________
Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. 
http://mobile.yahoo.com/go?refer=1GNXIC


From paulatto at sissa.it  Tue Jun 19 12:25:58 2007
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 19 Jun 2007 12:25:58 +0200 (CEST)
Subject: [Pw_forum] _intel_cpu_indicator error
In-Reply-To: <120956.83978.qm@web51004.mail.re2.yahoo.com>
References: <120956.83978.qm@web51004.mail.re2.yahoo.com>
Message-ID: <13420.147.122.5.194.1182248758.squirrel@webmail.sissa.it>

On Tue, June 19, 2007 11:22, W. YU wrote:
> I would appreciate it very much if anybody can help
> me?

Hi,
using this discussion:
<http://softwarecommunity.intel.com/isn/Community/en-US/forums/thread/5460914.aspx>
as a starting point I think that seeing you make.sys file could help. You
will find it in the root directory of pwscf source.

Bye

-- 
Lorenzo Paulatto
+39 040 3787 312
http://people.sissa.it/~paulatto/


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From giannozz at nest.sns.it  Tue Jun 19 12:53:02 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 19 Jun 2007 12:53:02 +0200
Subject: [Pw_forum] The calcualtion of static dielectric constant using espresso!
In-Reply-To: <464696.35279.qm@web15814.mail.cnb.yahoo.com>
References: <464696.35279.qm@web15814.mail.cnb.yahoo.com>
Message-ID: <107D4585-E851-48AD-BE57-E13E7B3A62F9@nest.sns.it>

On Jun 19, 2007, at 6:42 , Adrain Zhou wrote:

> I just read the definition of dielectric constant from
> http://www.quantum-espresso.org/wiki/index.php/Dielectric_constant.
> I am not sure whether the contribution to dielectric constant from
> clamped-ion polarization corresponds to static response.

what QE calculates is the dielectric tensor at clamped ions
(often referred to as \epsilon_\infty). The ionic contribution
must be calculated and added to this in order to obtain the
static dielectric tensor (\epsilon_0)

>  That is why espresso is unable to deal with dynamics response.

???

> As for the study of temperature effect on the static
> dielectric constant, I am not sure whether what you
> mean is to run MD at fix temperature first and then
> calculate dielectric constant by sampling different
> configurations.

I didn't mean anything like this. The dielectric tensor should
depend upon the temperature via the volume expansion (and
this should be the easy part), but also at constant volume via
anharmonic terms (and this will be less easy).

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




From giannozz at nest.sns.it  Tue Jun 19 13:06:52 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 19 Jun 2007 13:06:52 +0200
Subject: [Pw_forum] H 0.75 pseudopotential
In-Reply-To: <257265.92133.qm@web73011.mail.tp2.yahoo.com>
References: <257265.92133.qm@web73011.mail.tp2.yahoo.com>
Message-ID: <7830E57A-676D-4D75-9156-D1956DCDA095@nest.sns.it>

On Jun 18, 2007, at 16:04 , ? ?? wrote:

> I want to create another In PP with fractionary charge.
> So I think maybe I could try it from fellow this
> successful example.Or you could tell me what is
> keypoint to create such  PP with fractionary charge.

there is no keypoint, actually. I just took a H pseudopotential
in the old analytical format and changed Z to 0.75, then converted
to the new format (it cannot be done in the new format because
it contains Vloc in numerical form). Of course one could produce
a real PP for a bogus atom with Z=0.75, but I don't think it is
worth the effort.

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




From emenendez at macul.ciencias.uchile.cl  Tue Jun 19 15:55:39 2007
From: emenendez at macul.ciencias.uchile.cl (Eduardo Ariel Menendez P)
Date: Tue, 19 Jun 2007 09:55:39 -0400 (CLT)
Subject: [Pw_forum] H 0.75 pseudopotential
In-Reply-To: <20070619053826.959.78221.Mailman@democritos.sissa.it>
References: <20070619053826.959.78221.Mailman@democritos.sissa.it>
Message-ID: <Pine.LNX.4.58.0706190952540.30117@macul.ciencias.uchile.cl>

Hi Paolo,
Would you better put the pseudo-H PP in the web site, please?
Cheers
Eduardo
>
> Dear Paolo,
>
> Could you send them to me, too ?
> I want to create another In PP with fractionary charge
> .
> So I think maybe I could try it from fellow this
> successful example.Or you could tell me what is
> keypoint to create such  PP with fractionary charge .
> Thanks in advance
>
> max
> Department of Physics ,National Taiwan
> University,Taiwan
> E-mail : D92222009 at ntu.edu.tw
>
> --- Paolo Giannozzi <giannozz at nest.sns.it> ???G
>
> >
> > On Jun 18, 2007, at 10:30 , Marcello Rosini wrote:
> >
> > > It seems to me that ld1 cannot work with charge
> > <1... when running
> > > it says "wrong zed"... so I have two questions:
> > >     1. is this a limitation of ld1 or someone can
> > give me some help?
> >
> > no, it is just a check
> >
> > >     2. Does anybody can indicate me such a
> > pseudopotential?
> >
> > once upon a time I did some bogus H PP with
> > fractionary charge.
> > They were used with satisfactory results (by people
> > in your
> > department, by the way). I'll send them to you
> >
> > Paolo
> > ---


From baroni at sissa.it  Tue Jun 19 18:41:39 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Tue, 19 Jun 2007 18:41:39 +0200
Subject: [Pw_forum] signature
Message-ID: <C62CD084-99B8-4DF0-9A1B-C36CE4396888@sissa.it>

This is just to remind everybody that a complete signature of the  
posts to this mailing list (including the current affiliation of the  
poster) would be much appreciated by the community and would actually  
encourage people to respond. Many thanks to all those who contribute  
to this forum, particularly to those who have chosen to follow  
similar recommendations made in the past. Stefano

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

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 akohlmey at cmm.chem.upenn.edu  Tue Jun 19 18:15:06 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 19 Jun 2007 12:15:06 -0400 (EDT)
Subject: [Pw_forum] Memory allocation in linux using mpirun
In-Reply-To: <7b03b3c60706182043t5d9c2261qa7424f60e452fa89@mail.gmail.com>
Message-ID: <Pine.LNX.4.44.0706191209030.12063-100000@localhost.localdomain>

On Tue, 19 Jun 2007, Vivian McPhail wrote:


vivian,

VM> Hi,
VM> 
VM> I can successfully run all the examples provided with espresso using mpirun,

even the big water CP-MD examples with cp.x?

VM> however, when I attempt to run my own calculations the program crashes with
VM> a memory allocation failure.  This occurs when real memory is exhausted.

well, your application should _never_ exhaust the physical memory 
and/or go significantly into swap, or else performance will be horrible.

this means, that you either have some serious error in your input
(which we cannot tell, since you didn't post it) or you may simply 
need to use more nodes (whether that will work, we cannot tell, since
you did not tell us which machine you are running on). 

VM> >From examining "top" output, I can see that no virtual memory gets allocated
VM> (swap space is on).

if your application is already heavily swapping, you may not see it
with top in default mode. try 'shift-M' to sort by memory.

cheers,
   axel.

VM> Has anyone had a similar problem?
VM> 
VM> Cheers,
VM> 
VM> Vivian

p.s.: please see stefano's e-mail about adding a signature.
that (and providing more details about your calculations)
will increase your chances of getting help significantly.


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



From njuxuyuehua at gmail.com  Wed Jun 20 10:12:32 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Wed, 20 Jun 2007 16:12:32 +0800
Subject: [Pw_forum] phonon question :how to get improved frequency ? lo-to can change the relative strength of IR peak ?
Message-ID: <aca2feb20706200112h6039672er9ebf32a39df5d3@mail.gmail.com>

hello all :
i have some problem about phonon at  G point .
firstly ,i use the same major parameter as the literuture listed when
compute the phonon at G
BUT my results are a bit smaller than literature :
the relax section:
&CONTROL
calculation  = "relax",
  prefix       = "relax_specify_ibra_408_6_20+force_nogauss",
  pseudo_dir   = "/home/xx/intel_espresso-3.2/pseudo",
  outdir       = "/raid/xx/pwscf/tmp/",
  etot_conv_thr=1.D-6
  forc_conv_thr=1.D-6
/
&SYSTEM
  ibrav     = 4,
  a=20,b=20,c=2.9,cosab=-0.5,cosac=0,cosbc=0,
  nat       = 15,
  ntyp      = 2,
  ecutwfc   = 29.98744D0,
  ecutrho   =200
/
&ELECTRONS
  conv_thr    = 1.D-9,
  mixing_beta = 0.2D0,
/
&IONS
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
/
 ATOMIC_SPECIES
H  1.0  H.pbe-van_bm.UPF
O 15.999 O.pbe-van_bm.UPF
ATOMIC_POSITIONS { crystal }......
.....
...--------------------------------------------------------------------
scf section:
&CONTROL
calculation  = "scf",
  prefix       = "fiveringwater_specify_ibra_408_6_20_force_noguass",
  pseudo_dir   = "/home/xx/intel_espresso-3.2/pseudo",
  outdir       = "/raid/xx/pwscf/tmp/",
  /
&SYSTEM
  ibrav     = 4,
  a=20,b=20,c=2.9,cosab=-0.5,cosac=0,cosbc=0,
  nat       = 15,
  ntyp      = 2,
  ecutwfc   =29.98744D0,
  ecutrho   =200
/
&ELECTRONS
  conv_thr    = 1.D-9,
  mixing_beta = 0.2D0,
/
 ATOMIC_SPECIES
H  1.0  H.pbe-van_bm.UPF
O 15.999 O.pbe-van_bm.UPF
ATOMIC_POSITIONS { crystal }..........
------------------------------------------------------------------------------------.......
phonons of h2o at Gamma
 &inputph
  tr2_ph=1.0d-14,
  prefix='fiveringwater_specify_ibra_408_6_20_force_noguass',
  epsil=.true.,
  amass(1)=1.0,
  amass(2)=15.999,
  outdir='/raid/xx/pwscf/tmp/',
  fildyn='fiveringwater.dynG',
 /
0.0 0.0 0.0
------------------------------------------------------------------------------

my results:(cm -1)(via lo-to split)



3539.38

 3540.60

 3541.95

 3544.93
 3553.70

the not via lo-to results are :

3538.754218

3539.743464

3541.102871

3541.989623
3543.425339

but the literature results are :
3547
3553
3555
3558
3559
 you may my results are acceptable .but i think if i use the same  parameter
to compute phonon as literature  and
Energy cutoff:408ev
Monkhorst-Pack
k-point grid:1*1*6
and the same PBE-USPP,the cell shape and size,
(the literature only lists these parameters)

 the above difference are rising from the relax and scf section, in these
work ,i use the same k-points and the energy cut as phonon .
 i have changed a lot parameter in relax and scf.but the result are lower
than the literature:
i  enlarge the encut to 500ev,k points to 1,1,12
ecutrho to 300RY,
ALSO I have change tr2_ph to  tr2_ph=1.0d-18,but the results are the same
general .
my question ,is there any solution to lift my frequency?because i am a
newer.,i have no idea.

another question is if i use the lo-to split ,the big strength of  IR peak
shifts to higher frequency,for example : 3538 peak is the tallest in not via
lo-to ,but after lo-to spilt the
biggest strength is 3553
what the cause ?
please help me about above two question .thanks a lot






Xu Yuehua
physics Department of Nanjing university
China
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From helen at fh.huji.ac.il  Wed Jun 20 13:26:43 2007
From: helen at fh.huji.ac.il (Helen)
Date: Wed, 20 Jun 2007 14:26:43 +0300
Subject: [Pw_forum] SIGSEGV (was Re:[Pw-forum] example01 errors
Message-ID: <005101c7b32d$e10f1230$cd604084@fh.huji.ac.il>

I solved the error I was getting for the example01 code.
Reminder: the error occured when ZGEMM was called:
forrtl: severe (174): SIGSEGV, segmentation fault occurred

Stack trace terminated abnormally

I fixed the error by writing my own ZGEMM code (written by slightly modifiying the ZGEMM code found on the internet which blas uses). I then altered f_defs.h to write 
#define ZGEMM    C_NAME(repzgemm)
and I placed repzgemm in the flib directory.
I had checked that the library ZGEMM worked by writing a little test code.
All this suggests that there is a memory leak problem.
Now example01 works fine, but the same error message occurs with example03.

I tried the sigsegv.diff patch that Paolo sent and I tried changing ulimit, but none of these solutions works. I also tried using the local blas library.

I'd appreciate any insights into this problem and any comments on the partial solution I found,
Thanks,
Dr. Helen Eisenberg 
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From giannozz at nest.sns.it  Wed Jun 20 16:16:04 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 20 Jun 2007 16:16:04 +0200
Subject: [Pw_forum] SIGSEGV (was Re:[Pw-forum] example01 errors
In-Reply-To: <005101c7b32d$e10f1230$cd604084@fh.huji.ac.il>
References: <005101c7b32d$e10f1230$cd604084@fh.huji.ac.il>
Message-ID: <A9BED1BA-3BD1-489B-8B0E-1B3D9EDF7234@nest.sns.it>

On Jun 20, 2007, at 13:26 , Helen wrote:

> I fixed the error by writing my own ZGEMM code (written by slightly
> modifiying the ZGEMM code found on the internet which blas uses)
> [...]
> Now example01 works fine, but the same error message occurs with
> example03.

so this was not the solution

>  I tried the sigsegv.diff patch that Paolo sent and I tried  
> changing ulimit,
> but none of these solutions works. I also tried using the local  
> blas library

if it was a problem with blas and lapack libraries, it should have  
been solved
by loading the local copy. My opinion is that the machine you are  
working on
has some glitch (presumably in the software).

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




From shruba at gmail.com  Wed Jun 20 23:01:06 2007
From: shruba at gmail.com (shruba at gmail.com)
Date: Wed, 20 Jun 2007 17:01:06 -0400
Subject: [Pw_forum] Re: Problem with vc -relax
In-Reply-To: <50518.209.162.14.191.1182186049.squirrel@www.msi.umn.edu>
References: <20070618053817.14332.33633.Mailman@democritos.sissa.it>
	 <50518.209.162.14.191.1182186049.squirrel@www.msi.umn.edu>
Message-ID: <822f4ec80706201401k49b3f040kbc52e1cc615aaae5@mail.gmail.com>

Thanks a lot Cesar.
  That works,  still I am facing a problem because the single point optimum
lattice parameter and the vc-relax optimum one is quite different
around 0.1angstrom, I tried changing cell _factor and wmass parameter
but those are
not affecting much on optimum lattice paraneter.
         if anybody can provide me any hints or  suggest some references on
this topic then it will be real helpful.
thanks in advance
                         shruba ganaygopadhy


shruba gangopadhyay
graduate student
department of chemistry
university of central florida
orlando, FL-32826



On 6/18/07, cesards at msi.umn.edu <cesards at msi.umn.edu> wrote:
>
> Dear Shruba,
>
>
> I notice that your input doe not contains the varables "dt" in &CONTROL
> namelist (dt = 80.0 is recommended for start) and "wmass" in &CELL
> namelist (wmass =  0.001 , for example). If get large negative stresses in
> the first MD step, try to reduce celldm(1).
>
> It is normal for the cell volume to oscilate. Things are going wrong only
> if the amplitude of oscilations are increasing.
>
>
> Yours,
>
>
> Cesar R.S. da Silva
>
>
>
>
> > ------=_Part_75233_9601271.1182103000930
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> > Content-Transfer-Encoding: 7bit
> > Content-Disposition: inline
> >
> > Hi all,
> >      I was trying to run vc-relax calculation for srfeo3 (
> > antiferromagnetic
> > mettalic ) system,  the problem I was facing for a unit cell it is
> running
> > for 3-4 days in processor , where as a single point 'scf' calculation is
> > taking only 5 minutes, the scf calculation is giving very nice agreement
> > with experimental data , but for vc -relax  i checked the cell volume
> was
> > decresing first then it started exapnding after a certain point, this is
> > my
> > input file . If any one can help me in this matter that will be really
> > great
> > help, I am using same cutoff and other parameters required for scf
> >
> > &CONTROL
> >
> > calculation = 'vc-relax',
> >
> > restart_mode = 'from_scratch',
> >
> > tstress = .TRUE.,
> >
> > tprnfor = .TRUE.,
> >
> > prefix = 'relax',
> >
> > pseudo_dir = '/............./',
> >
> > outdir='/................../'
> >
> > /
> >
> > &SYSTEM
> >
> > ibrav = 1,
> >
> > celldm(1) = 7.3
> >
> > nat =5,
> >
> > ntyp =3,
> >
> > ecutwfc = 45,
> >
> > ecutrho = 360,
> >
> > nspin=2,
> >
> > nelec=44
> >
> > nelup=26,
> >
> > neldw=18,
> >
> > nbnd=52,
> >
> > occupations = 'smearing',
> >
> > smearing ='marzari-vanderbilt',
> >
> > degauss=0.03,
> >
> > qcutz=150., q2sigma=2.0,ecfixed=10.0
> >
> > /
> >
> > &ELECTRONS
> >
> > electron_maxstep =200,
> >
> > emass =1000.d0,
> >
> > emass_cutoff = 4.d0,
> >
> > orthogonalization = 'Gram-Schmidt',
> >
> > startingwfc ='atomic',
> >
> > n_inner = 8,
> >
> > tcg = .TRUE.,
> >
> > passop=0.3,
> >
> > maxiter = 250,
> >
> > conv_thr=1.d-6,
> >
> > /
> >
> > &IONS
> >
> > ion_dynamics = 'damp',
> >
> > ion_damping = 0.,
> >
> > ion_positions = 'from_input',
> >
> > ion_temperature = 'not_controlled',
> >
> > /
> >
> > &CELL
> >
> > cell_dynamics = 'damp-w'
> >
> > /
> >
> > ATOMIC_SPECIES
> >
> > Fe 55.85 Fe.pbe-sp-van.UPF
> >
> > Sr 87.62 Sr.pbe-nsp-van.UPF
> >
> > O 16.00 O.pbe-van-bm.UPF
> >
> > ATOMIC_POSITIONS
> >
> > Sr 0.000 0.000 0.010
> >
> > Fe 0.500 0.500 0.500
> >
> > O 0.000 0.500 0.500
> >
> > O 0.500 0.500 0.000
> >
> > O 0.500 0.000 0.500
> >
> > K_POINTS {automatic}
> >
> > 8 8 8 1 1 1
> >
> > Thanks in advance , looking forward for your reply
> >                                 shruba
> >
> > --
> > shruba gangopadhyay
> > graduate student
> > department of chemistry
> > university of central florida
> > orlando, FL-32826
> > 'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
> >
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
shruba gangopadhyay
graduate student
department of chemistry
university of central florida
orlando, FL-32826
'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
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From jibiaoli at gmail.com  Thu Jun 21 08:10:26 2007
From: jibiaoli at gmail.com (Clark Lee)
Date: Thu, 21 Jun 2007 14:10:26 +0800
Subject: [Pw_forum] How to convert CPMD pseudopotential to UPF format
Message-ID: <b8b82da20706202310m1b3e8235re468b9b5834a5f8c@mail.gmail.com>

Dear all,

Does anyone know how to convert a pseudopotential in CPMD format(*.psp) UPF
format that can be used in PWSCF code. Thanks


Regards

-- 
Yours sincerely,

Clark Lee

State Key Lab of Corrosion and Protection (SKLCP)
Institute of Metal Research (IMR)
Chinese Academy of Sciences (CAS), China
Phone: 024-23971339
Email: jibiaoli at imr.ac.cn or jibiaoli at gmail.com
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From njuxuyuehua at gmail.com  Thu Jun 21 09:03:52 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Thu, 21 Jun 2007 15:03:52 +0800
Subject: [Pw_forum] how to add the asr="one-dim''
Message-ID: <aca2feb20706210003t15b65e64sc15b410ba5a1c50@mail.gmail.com>

hello all
i want to add asr-"one-dim", the cartesian axis is along c,how to specify c
in input.
thanks a lot



asr ="one-dim'3 translational asr + 1 rotational asr
!                     imposed by optimized correction of the dyn. mat. (the
!                     rotation axis is the direction of periodicity; it
!                     will work only if this axis considered is one of
!                     the cartesian axis).

-- 
Xu Yuehua
physics Department of Nanjing university
China
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From shruba at gmail.com  Thu Jun 21 09:45:33 2007
From: shruba at gmail.com (shruba at gmail.com)
Date: Thu, 21 Jun 2007 03:45:33 -0400
Subject: [Pw_forum] vc -relax vs single point
Message-ID: <822f4ec80706210045u44894dabj58bf888ca2d23f05@mail.gmail.com>

 Thanks a lot Cesar,
   Your suggestion was really helpful.
Still in vc -relax calculation I am facing some issues, the optimum lattice
parameter shows a 0.1 Angstrom difference in the calculation, though I used
same K points and cut off and other parameter, anyone please suggest me some
clues or references for that, I checked cell_factor parameter and wmass
parameter those are not making much difference.
Thanks in advance
                                                    shruba gangopadhyay
-- 
shruba gangopadhyay
graduate student
department of chemistry
university of central florida
orlando, FL-32826
'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
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From helen at fh.huji.ac.il  Thu Jun 21 11:17:43 2007
From: helen at fh.huji.ac.il (Helen)
Date: Thu, 21 Jun 2007 12:17:43 +0300
Subject: [Pw_forum] SIGSEGV (was Re:[Pw-forum] example01 errors
References: <005101c7b32d$e10f1230$cd604084@fh.huji.ac.il> <A9BED1BA-3BD1-489B-8B0E-1B3D9EDF7234@nest.sns.it>
Message-ID: <007701c7b3e5$064dc070$cd604084@fh.huji.ac.il>

Hi,

I finally fixed the problem, and I have a bit of an apology to make because 
I found out I didn't previuosly implement properly what Paolo advised. I had 
tried linking to the local blas library which is where the ZGEMM routine 
which wasn't working is contained, but I didn't try to also link to the 
local lapack libraries. Today I tried to link locally to both blas and 
lapack and now everything works. Do you think there is a way to correct the 
problem with the linking between the code and the mkl libraries on my 
computer? Or should I just use the local libraries?
Thanks for your help,
Helen

----- Original Message ----- 
From: "Paolo Giannozzi" <giannozz at nest.sns.it>
To: <pw_forum at pwscf.org>
Sent: Wednesday, June 20, 2007 5:16 PM
Subject: Re: [Pw_forum] SIGSEGV (was Re:[Pw-forum] example01 errors


> On Jun 20, 2007, at 13:26 , Helen wrote:
>
>> I fixed the error by writing my own ZGEMM code (written by slightly
>> modifiying the ZGEMM code found on the internet which blas uses)
>> [...]
>> Now example01 works fine, but the same error message occurs with
>> example03.
>
> so this was not the solution
>
>>  I tried the sigsegv.diff patch that Paolo sent and I tried  changing 
>> ulimit,
>> but none of these solutions works. I also tried using the local  blas 
>> library
>
> if it was a problem with blas and lapack libraries, it should have  been 
> solved
> by loading the local copy. My opinion is that the machine you are  working 
> on
> has some glitch (presumably in the software).
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 



From shang.yi at hotmail.com  Thu Jun 21 11:26:22 2007
From: shang.yi at hotmail.com (mashangyi)
Date: Thu, 21 Jun 2007 17:26:22 +0800
Subject: [Pw_forum] help on q2r.x error!
Message-ID: <BAY117-W54BE12EDCE2C818CE705B82100@phx.gbl>

Dear all:  I encounter a problem when I use the q2r.x transform the dynamical matrix of gamma point to interatomic force constants in real space.  The system in my calculation is a Si-supercell composed of 64 Si atoms. I want to get some properties of it, like phdos, vibrational energy, entropy and so on. Following example02 and 06 indication, I calculate the dynamical matrix at the gamma point of the supercell after scf calculation( scf use 2x2x2 k_points). When I call q2r.x to calculate IFC's in real space, it complains the follow errors:+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++   transforming Si-bulk.q2r.in C(q) => C(R)...forrtl: severe (19): invalid reference to variable in NAMELIST input, unit 5, file stdin, line 5, position 5Image              PC        Routine            Line        Sourceq2r.x              083C4220  Unknown               Unknown  Unknownq2r.x              083C2721  Unknown               Unknown  Unknownq2r.x              083996D6  Unknown               Unknown  Unknownq2r.x              0835F4FC  Unknown               Unknown  Unknownq2r.x              0837AA50  Unknown               Unknown  Unknownq2r.x              0804D3AE  Unknown               Unknown  Unknownq2r.x              0804D206  Unknown               Unknown  Unknownlibc.so.6          B7E1687C  Unknown               Unknown  Unknownq2r.x              0804D141  Unknown               Unknown  Unknown+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++   It look likes like that the errors come from some mistakes in my input files.Following are the input files of ph.x and q2r.x:ph.x input-file:
phonons of Si at gamma&inputph tr2_ph = 1.0d-12 outdir = '/tmp/tmp_1' prefix = 'si-ph' epsil  = .true. amass(1) = 28.0855 fildyn = 'si-bulk.dynG'/0.0  0.0  0.0
 
and q2r.x input-file:
&input fildyn = 'si-bulk.dynG' zasr   = 'simple' flfrc  = 'si-bulk.fc' nr1=2, nr2=2, nr3=2 nfile  = 1 filin  = 'si-bulk.dynG'/
 
   I am still troubled with the errors though I searched some topics related it through the maillist. Would you help me solve it? Any suggestions are appreciated!
Best regards!
yours, shangyi
ps: the q2r.x works well in example06
 
 
Graduate school of China academy of science 
_________________________________________________________________
??????????
http://search.msn.com/results.aspx?q=%E4%B8%AD%E5%9B%BD%E5%8D%81%E5%A4%A7%E9%A3%8E%E6%99%AF&mkt=zh-CN&form=QBRE
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From jibiaoli at gmail.com  Thu Jun 21 13:51:34 2007
From: jibiaoli at gmail.com (Clark Lee)
Date: Thu, 21 Jun 2007 19:51:34 +0800
Subject: [Pw_forum] Problem of pseudopotential file
Message-ID: <b8b82da20706210451idf62389i8e1932a4f6dfedae@mail.gmail.com>

Hi All,
In a recent disscution with M. Pozzo, I learned that the Ni pseudopotential
files available from the PWSCF web-page had some convergency issue with
respect to the plane-wave and charge density cutoffs. I got a Ni
pseudopotential file (PBE) by which M.Pozzo et.al.reasonablely obtained
parameters including adsorption energy of water on Ni(111) [JCP,126, 164706
2007] using QE 3.2 code.   M.Pozzo Said the PP was working fine for them
with version 3.2.  However,  my  calculations  always  stop with an error
below:

     Program PWSCF     v.3.0    starts ...
     Today is 17Jan2008 at 19:40:58

     Parallel version (MPI)

     Number of processors in use:       2
     K-points division:     npool     =    2

     Ultrasoft (Vanderbilt) Pseudopotentials

     Current dimensions of program pwscf are:

     ntypx = 10   npk = 40000  lmax =  3
     nchix =  6  ndmx =  2000  nbrx = 14  nqfx =  8

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from readvan : error #        59
     error reading pseudo file
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...



THe first part of the PP is shown below:
    7    3    4   12    3 2004
Ni (US s-loc)          28.000000000   10.000000000    5.000000000
    3  939 -9.53855345677E+01
  320    8.000000000   -0.652240294
  400    2.000000000   -0.414755227
  410    0.000000000   -0.090035867
    3    1    1.200000000
    3    0 -0.41475    3    8 10.00000
  1.20000000000E+00  1.20000000000E+00  1.20000000000E+00  1.20000000000E+00
  1.20000000000E+00
    2
  2.03000000000E+00  2.22802202189E+00  2.00000000000E+00
    3  677
    1
 -9.00366252122E-02  0.00000000000E+00 -7.19962583407E-13 -2.92845340520E-12
 -6.70053286789E-12 -1.21142191010E-11 -1.92505951636E-11 -2.81939199977E-11
 -3.90317432609E-11 -5.18550241718E-11 -6.67582545070E-11 -8.38395858919E-11
 -1.03200961533E-10 -1.24948252542E-10 -1.49191399020E-10 -1.76044556043E-10
 -2.05626244746E-10 -2.38059508658E-10 -2.73472075477E-10 -3.11996524474E-10
... ...

Any suggestions?




Yours sincerely,

Clark Lee

State Key Lab of Corrosion and Protection (SKLCP)
Institute of Metal Research (IMR)
Chinese Academy of Sciences (CAS), China
Phone: 024-23971339
Email: jibiaoli at imr.ac.cn or jibiaoli at gmail.com
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From giannozz at nest.sns.it  Thu Jun 21 14:18:22 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 21 Jun 2007 14:18:22 +0200
Subject: [Pw_forum] Problem of pseudopotential file
In-Reply-To: <b8b82da20706210451idf62389i8e1932a4f6dfedae@mail.gmail.com>
References: <b8b82da20706210451idf62389i8e1932a4f6dfedae@mail.gmail.com>
Message-ID: <99FEC90B-1C63-4E15-8CBC-F1E87791BACA@nest.sns.it>

On Jun 21, 2007, at 13:51 , Clark Lee wrote:

> M.Pozzo Said the PP was working fine for them with version 3.2.   
> However,
> my  calculations  always  stop with an error below:
>
>      Program PWSCF     v.3.0    starts ...

try v. 3.2

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




From giannozz at nest.sns.it  Thu Jun 21 14:27:26 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 21 Jun 2007 14:27:26 +0200
Subject: [Pw_forum] help on q2r.x error!
In-Reply-To: <BAY117-W54BE12EDCE2C818CE705B82100@phx.gbl>
References: <BAY117-W54BE12EDCE2C818CE705B82100@phx.gbl>
Message-ID: <C85F24ED-2F90-43A4-BEC4-306B535BF16E@nest.sns.it>

On Jun 21, 2007, at 11:26 , mashangyi wrote:

> invalid reference to variable in NAMELIST input, unit 5, file stdin,
> line 5, position 5

since your compiler that has the good habit of saying where the
error has occurred, you should read the error message. The
variables in the last three lines of your data are not in the namelist.

> ps: the q2r.x works well in example06

of course it does: in example06 the input data is correct

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




From eyvaz_isaev at yahoo.com  Thu Jun 21 14:31:49 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 21 Jun 2007 05:31:49 -0700 (PDT)
Subject: [Pw_forum] help on q2r.x error!
In-Reply-To: <BAY117-W54BE12EDCE2C818CE705B82100@phx.gbl>
Message-ID: <224386.45695.qm@web60317.mail.yahoo.com>

Hi,

--- mashangyi <shang.yi at hotmail.com> wrote:

> Dear all:  I encounter a problem when I use the
> q2r.x transform the dynamical matrix of gamma point
> to interatomic force constants in real space.  The
> system in my calculation is a Si-supercell composed
> of 64 Si atoms. I want to get some properties of it,
> like phdos, vibrational energy, entropy and so on.
> Following example02 and 06 indication, I calculate
> the dynamical matrix at the gamma point of the
> supercell after scf calculation( scf use 2x2x2
> k_points). When I call q2r.x to calculate IFC's in
> real space, it complains the follow
>
errors:+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>   transforming Si-bulk.q2r.in C(q) => C(R)...forrtl:
> severe (19): invalid reference to variable in
> NAMELIST input, unit 5, file stdin, line 5, position

There is very clean indication what is wrong: you
specified a parameter which does not exist in
NAMELIST.
 
> and q2r.x input-file:
> &input fildyn = 'si-bulk.dynG' zasr   = 'simple'
> flfrc  = 'si-bulk.fc' nr1=2, nr2=2, nr3=2 nfile  = 1

> filin  = 'si-bulk.dynG'/

There is no keyword "filin" in NAMELIST. That is your
problem, so, remove this line.

Besides, I did not understand you did scf-calculations
using 2x2x2 k-mesh, and then made phonon calculations.
If so, nr1=2 and etc. is not correct. 
Here you have to specify q-points mesh different of
k-points used in scf-calculations. Then q2r will be
able to do FFT F(q)=>F(R). So, you should put here 
nr1=1 etc. as you used only the Gamma point. Is the
use only the Gamma point is OK for FFT, some doubts.  

Probably, you have an enormous computational resource
and are very ambitious to calculate phonons for 64
atoms supercell. For ideal case these properties you
would like to calculate is just 32 times that these
for 2 atomic cell. 

Bests,
Eyvaz.

>  
>    I am still troubled with the errors though I
> searched some topics related it through the
> maillist. Would you help me solve it? Any
> suggestions are appreciated!
> Best regards!
> yours, shangyi
> ps: the q2r.x works well in example06
>  
>  
> Graduate school of China academy of science 
>
_________________________________________________________________
> ????????????????????
>
http://search.msn.com/results.aspx?q=%E4%B8%AD%E5%9B%BD%E5%8D%81%E5%A4%A7%E9%A3%8E%E6%99%AF&mkt=zh-CN&form=QBRE


-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and 
Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com


       
____________________________________________________________________________________
Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. 
http://mobile.yahoo.com/go?refer=1GNXIC


From giannozz at nest.sns.it  Thu Jun 21 14:32:00 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 21 Jun 2007 14:32:00 +0200
Subject: [Pw_forum] vc -relax vs single point
In-Reply-To: <822f4ec80706210045u44894dabj58bf888ca2d23f05@mail.gmail.com>
References: <822f4ec80706210045u44894dabj58bf888ca2d23f05@mail.gmail.com>
Message-ID: <54DF2C23-8169-4942-8053-3C33D36151C7@nest.sns.it>

On Jun 21, 2007, at 9:45 , shruba at gmail.com wrote:

> Still in vc -relax calculation I am facing some issues, the optimum  
> lattice parameter shows a 0.1 Angstrom difference in the  
> calculation, though I
> used same K points and cut off and other parameter

the usage of the modified kinetic functional may make a sizable
difference

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




From giannozz at nest.sns.it  Thu Jun 21 14:34:08 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 21 Jun 2007 14:34:08 +0200
Subject: [Pw_forum] How to convert CPMD pseudopotential to UPF format
In-Reply-To: <b8b82da20706202310m1b3e8235re468b9b5834a5f8c@mail.gmail.com>
References: <b8b82da20706202310m1b3e8235re468b9b5834a5f8c@mail.gmail.com>
Message-ID: <BC370C68-1EAA-40D6-B736-8B3DC4277CB8@nest.sns.it>

On Jun 21, 2007, at 8:10 , Clark Lee wrote:

> Does anyone know how to convert a pseudopotential in CPMD format 
> (*.psp)
>  UPF format that can be used in PWSCF code. Thanks

upftools/cpmd2upf.x
---
Paolo Giannozzi, Democritos and University of Udine, Italy




From giannozz at nest.sns.it  Thu Jun 21 14:35:54 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 21 Jun 2007 14:35:54 +0200
Subject: [Pw_forum] how to add the asr="one-dim''
In-Reply-To: <aca2feb20706210003t15b65e64sc15b410ba5a1c50@mail.gmail.com>
References: <aca2feb20706210003t15b65e64sc15b410ba5a1c50@mail.gmail.com>
Message-ID: <B8A2680B-326D-41D2-9493-6DD9AC3A6D1D@nest.sns.it>

On Jun 21, 2007, at 9:03 , xu yuehua wrote:

> i want to add asr-"one-dim", the cartesian axis is along c,how to  
> specify c in input.

c is fixed and is along the z axis: see file INPUT_PW towards the end

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




From jibiaoli at gmail.com  Thu Jun 21 15:01:05 2007
From: jibiaoli at gmail.com (Clark Lee)
Date: Thu, 21 Jun 2007 21:01:05 +0800
Subject: [Pw_forum] Problem of pseudopotential file
In-Reply-To: <99FEC90B-1C63-4E15-8CBC-F1E87791BACA@nest.sns.it>
References: <b8b82da20706210451idf62389i8e1932a4f6dfedae@mail.gmail.com>
	 <99FEC90B-1C63-4E15-8CBC-F1E87791BACA@nest.sns.it>
Message-ID: <b8b82da20706210601p131e8b6kbcdea37f3281054c@mail.gmail.com>

Hello Paolo
The same error appeared with v3.2.


     Program PWSCF     v.3.2    starts ...
     Today is 17Jan2008 at 20:55:29

     Parallel version (MPI)

     Number of processors in use:       1

     Ultrasoft (Vanderbilt) Pseudopotentials

     Current dimensions of program pwscf are:

     ntypx = 10   npk = 40000  lmax =  3
     nchix =  6  ndmx =  2000  nbrx = 14  nqfx =  8

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from readvan : error #        59
     error reading pseudo file
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...


I wondered whether the format of the PP is correct

THe first part of the PP is shown below:
    7    3    4   12    3 2004
Ni (US s-loc)          28.000000000   10.000000000    5.000000000
    3  939 -9.53855345677E+01
  320    8.000000000   -0.652240294
  400    2.000000000   -0.414755227
  410    0.000000000   -0.090035867
    3    1    1.200000000
    3    0 -0.41475    3    8 10.00000
  1.20000000000E+00  1.20000000000E+00  1.20000000000E+00  1.20000000000E+00
  1.20000000000E+00
    2
  2.03000000000E+00  2.22802202189E+00  2.00000000000E+00
    3  677
    1
 -9.00366252122E-02  0.00000000000E+00 -7.19962583407E-13 -2.92845340520E-12
 -6.70053286789E-12 -1.21142191010E-11 -1.92505951636E-11 -2.81939199977E-11
 -3.90317432609E-11 -5.18550241718E-11 -6.67582545070E-11 -8.38395858919E-11
 -1.03200961533E-10 -1.24948252542E-10 -1.49191399020E-10 -1.76044556043E-10
 -2.05626244746E-10 -2.38059508658E-10 -2.73472075477E-10 -3.11996524474E-10



Yours sincerely,

Clark Lee

State Key Lab of Corrosion and Protection (SKLCP)
Institute of Metal Research (IMR)
Chinese Academy of Sciences (CAS), China
Phone: 024-23971339
Email: jibiaoli at imr.ac.cn or jibiaoli at gmail.com
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From stewart at cnf.cornell.edu  Thu Jun 21 15:55:00 2007
From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu)
Date: Thu, 21 Jun 2007 09:55:00 -0400
Subject: [Pw_forum] Problem of pseudopotential file
In-Reply-To: <b8b82da20706210601p131e8b6kbcdea37f3281054c@mail.gmail.com>
References: <b8b82da20706210451idf62389i8e1932a4f6dfedae@mail.gmail.com>
            <99FEC90B-1C63-4E15-8CBC-F1E87791BACA@nest.sns.it>
            <b8b82da20706210601p131e8b6kbcdea37f3281054c@mail.gmail.com>
Message-ID: <20070621135500.40646.qmail@mail.spidergraphics.com>

Hi Clark, 

You might want to check that the file is not in dos format.  Dos/windows and 
linux handle line returns differently.  This could occur if you transferred 
the psp file over from a Windows machine.  To check this, just run your psp 
file through the linux utility, dos2unix, and this should put the line 
returns to the proper format. 

Best regards, 

Derek
 


Clark Lee writes: 

> Hello Paolo
> The same error appeared with v3.2. 
> 
> 
>     Program PWSCF     v.3.2    starts ...
>     Today is 17Jan2008 at 20:55:29 
> 
>     Parallel version (MPI) 
> 
>     Number of processors in use:       1 
> 
>     Ultrasoft (Vanderbilt) Pseudopotentials 
> 
>     Current dimensions of program pwscf are: 
> 
>     ntypx = 10   npk = 40000  lmax =  3
>     nchix =  6  ndmx =  2000  nbrx = 14  nqfx =  8 
> 
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
> %%%%
>     from readvan : error #        59
>     error reading pseudo file
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
> %%%% 
> 
>     stopping ... 
> 
> 
> I wondered whether the format of the PP is correct 
> 
> THe first part of the PP is shown below:
>    7    3    4   12    3 2004
> Ni (US s-loc)          28.000000000   10.000000000    5.000000000
>    3  939 -9.53855345677E+01
>  320    8.000000000   -0.652240294
>  400    2.000000000   -0.414755227
>  410    0.000000000   -0.090035867
>    3    1    1.200000000
>    3    0 -0.41475    3    8 10.00000
> 1.20000000000E+00  1.20000000000E+00  1.20000000000E+00  1.20000000000E+00
>  1.20000000000E+00
>    2
>  2.03000000000E+00  2.22802202189E+00  2.00000000000E+00
>    3  677
>    1
> -9.00366252122E-02  0.00000000000E+00 -7.19962583407E-13 
> -2.92845340520E-12
> -6.70053286789E-12 -1.21142191010E-11 -1.92505951636E-11 
> -2.81939199977E-11
> -3.90317432609E-11 -5.18550241718E-11 -6.67582545070E-11 
> -8.38395858919E-11
> -1.03200961533E-10 -1.24948252542E-10 -1.49191399020E-10 
> -1.76044556043E-10
> -2.05626244746E-10 -2.38059508658E-10 -2.73472075477E-10 
> -3.11996524474E-10 
> 
>  
> 
> Yours sincerely, 
> 
> Clark Lee 
> 
> State Key Lab of Corrosion and Protection (SKLCP)
> Institute of Metal Research (IMR)
> Chinese Academy of Sciences (CAS), China
> Phone: 024-23971339
> Email: jibiaoli at imr.ac.cn or jibiaoli at gmail.com
 


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


From giannozz at nest.sns.it  Thu Jun 21 17:42:46 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 21 Jun 2007 17:42:46 +0200
Subject: [Pw_forum] Problem of pseudopotential file
In-Reply-To: <b8b82da20706210601p131e8b6kbcdea37f3281054c@mail.gmail.com>
References: <b8b82da20706210451idf62389i8e1932a4f6dfedae@mail.gmail.com> <99FEC90B-1C63-4E15-8CBC-F1E87791BACA@nest.sns.it> <b8b82da20706210601p131e8b6kbcdea37f3281054c@mail.gmail.com>
Message-ID: <80706DA6-2DFD-45EC-9D4D-91DAB8544360@nest.sns.it>

On Jun 21, 2007, at 15:01 , Clark Lee wrote:

> The same error appeared with v3.2.

Modules/read_uspp.f90, routine readvan. Put a print before
and after all lines
     read(iunps, *, err=100 ) ...
and see where it stops. It must be something trivial

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




From giannozz at nest.sns.it  Thu Jun 21 17:46:48 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 21 Jun 2007 17:46:48 +0200
Subject: [Pw_forum] SIGSEGV (was Re:[Pw-forum] example01 errors
In-Reply-To: <007701c7b3e5$064dc070$cd604084@fh.huji.ac.il>
References: <005101c7b32d$e10f1230$cd604084@fh.huji.ac.il> <A9BED1BA-3BD1-489B-8B0E-1B3D9EDF7234@nest.sns.it> <007701c7b3e5$064dc070$cd604084@fh.huji.ac.il>
Message-ID: <F67E4071-F021-4808-80F9-BC1D4535CF5C@nest.sns.it>

On Jun 21, 2007, at 11:17 , Helen wrote:

> Do you think there is a way to correct the problem with the linking  
> between
> the code and the mkl libraries on my computer?

ask your system manager to install a different version of mkl.
You didn't link to a hardware-specific version that does not work
with your hardware, did you?

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




From akohlmey at cmm.chem.upenn.edu  Thu Jun 21 20:03:12 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 21 Jun 2007 14:03:12 -0400 (EDT)
Subject: [Pw_forum] How to convert CPMD pseudopotential to UPF format
In-Reply-To: <BC370C68-1EAA-40D6-B736-8B3DC4277CB8@nest.sns.it>
Message-ID: <Pine.LNX.4.44.0706211359080.12753-100000@localhost.localdomain>

On Thu, 21 Jun 2007, Paolo Giannozzi wrote:

PG> 
PG> On Jun 21, 2007, at 8:10 , Clark Lee wrote:
PG> 
PG> > Does anyone know how to convert a pseudopotential in CPMD format 
PG> > (*.psp)
PG> >  UPF format that can be used in PWSCF code. Thanks
PG> 
PG> upftools/cpmd2upf.x

...with some restrictions!

it does not work for goedecker pseudopotentials,
and also there are quite a few cpmd potential files
'in the wild' that work correctly in cpmd but are
not fully conformant to the format that cpmd2upf.x
is expecting. there is no way that this can be fixed
consistently within cpmd2upf.x. 

so all converted cpmd pseudopotentials, need to be 
carefully tested.

the safer way is to take the parameters from the &INFO
section of the cpmd potential and try to re-create the
it with the integrated atomic code of QE.

cheers,
   axel.

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

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



From akohlmey at cmm.chem.upenn.edu  Thu Jun 21 20:07:01 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 21 Jun 2007 14:07:01 -0400 (EDT)
Subject: [Pw_forum] Problem of pseudopotential file
In-Reply-To: <b8b82da20706210451idf62389i8e1932a4f6dfedae@mail.gmail.com>
Message-ID: <Pine.LNX.4.44.0706211405310.12753-100000@localhost.localdomain>

On Thu, 21 Jun 2007, Clark Lee wrote:

clark,

CL> 
CL> THe first part of the PP is shown below:
CL>     7    3    4   12    3 2004
CL> Ni (US s-loc)          28.000000000   10.000000000    5.000000000

try changing this line into (i.e. no blanks in between the ascii text): 
  Ni_(US_s-loc)          28.000000000   10.000000000    5.000000000

cheers,
   axel.

CL>     3  939 -9.53855345677E+01
CL>   320    8.000000000   -0.652240294
CL>   400    2.000000000   -0.414755227
CL>   410    0.000000000   -0.090035867
CL>     3    1    1.200000000
CL>     3    0 -0.41475    3    8 10.00000
CL>   1.20000000000E+00  1.20000000000E+00  1.20000000000E+00  1.20000000000E+00
CL>   1.20000000000E+00
CL>     2
CL>   2.03000000000E+00  2.22802202189E+00  2.00000000000E+00
CL>     3  677
CL>     1
CL>  -9.00366252122E-02  0.00000000000E+00 -7.19962583407E-13 -2.92845340520E-12
CL>  -6.70053286789E-12 -1.21142191010E-11 -1.92505951636E-11 -2.81939199977E-11
CL>  -3.90317432609E-11 -5.18550241718E-11 -6.67582545070E-11 -8.38395858919E-11
CL>  -1.03200961533E-10 -1.24948252542E-10 -1.49191399020E-10 -1.76044556043E-10
CL>  -2.05626244746E-10 -2.38059508658E-10 -2.73472075477E-10 -3.11996524474E-10
CL> ... ...
CL> 
CL> Any suggestions?
CL> 
CL> 
CL> 
CL> 
CL> Yours sincerely,
CL> 
CL> Clark Lee
CL> 
CL> State Key Lab of Corrosion and Protection (SKLCP)
CL> Institute of Metal Research (IMR)
CL> Chinese Academy of Sciences (CAS), China
CL> Phone: 024-23971339
CL> Email: jibiaoli at imr.ac.cn or jibiaoli at gmail.com
CL> 

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



From shruba at gmail.com  Fri Jun 22 05:00:10 2007
From: shruba at gmail.com (shruba at gmail.com)
Date: Thu, 21 Jun 2007 23:00:10 -0400
Subject: [Pw_forum] vc -relax vs single point
In-Reply-To: <54DF2C23-8169-4942-8053-3C33D36151C7@nest.sns.it>
References: <822f4ec80706210045u44894dabj58bf888ca2d23f05@mail.gmail.com>
	 <54DF2C23-8169-4942-8053-3C33D36151C7@nest.sns.it>
Message-ID: <822f4ec80706212000je7c4b1em7d81cf23f95ec5fa@mail.gmail.com>

Thanks Paolo.
             shruba


On 6/21/07, Paolo Giannozzi <giannozz at nest.sns.it> wrote:
>
>
> On Jun 21, 2007, at 9:45 , shruba at gmail.com wrote:
>
> > Still in vc -relax calculation I am facing some issues, the optimum
> > lattice parameter shows a 0.1 Angstrom difference in the
> > calculation, though I
> > used same K points and cut off and other parameter
>
> the usage of the modified kinetic functional may make a sizable
> difference
>
> 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
>



-- 
shruba gangopadhyay
graduate student
department of chemistry
university of central florida
orlando, FL-32826
'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
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From shang.yi at hotmail.com  Fri Jun 22 10:52:48 2007
From: shang.yi at hotmail.com (shangyi)
Date: Fri, 22 Jun 2007 16:52:48 +0800
Subject: [Pw_forum] help on q2r.x error!
Message-ID: <BAY117-W75E954F55B0D5CA472F0482170@phx.gbl>

Dear Eyvaz and Paolo:
  Thanks for your kind reply! With your advice, I get the results of interatomic force constants in real space at gamma point.> Hi,> > --- mashangyi <shang.yi at hotmail.com> wrote:> > > Dear all: I encounter a problem when I use the> > q2r.x transform the dynamical matrix of gamma point> > to interatomic force constants in real space. The> > system in my calculation is a Si-supercell composed> > of 64 Si atoms. I want to get some properties of it,> > like phdos, vibrational energy, entropy and so on.> > Following example02 and 06 indication, I calculate> > the dynamical matrix at the gamma point of the> > supercell after scf calculation( scf use 2x2x2> > k_points). When I call q2r.x to calculate IFC's in> > real space, it complains the follow> >> errors:+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++> > transforming Si-bulk.q2r.in C(q) => C(R)...forrtl:> > severe (19): invalid reference to variable in> > NAMELIST input, unit 5, file stdin, line 5, position> > There is very clean indication what is wrong: you> specified a parameter which does not exist in> NAMELIST.> > > and q2r.x input-file:> > &input fildyn = 'si-bulk.dynG' zasr = 'simple'> > flfrc = 'si-bulk.fc' nr1=2, nr2=2, nr3=2 nfile = 1> > > filin = 'si-bulk.dynG'/> > There is no keyword "filin" in NAMELIST. That is your> problem, so, remove this line.> > Besides, I did not understand you did scf-calculations> using 2x2x2 k-mesh, and then made phonon calculations.> If so, nr1=2 and etc. is not correct. > Here you have to specify q-points mesh different of> k-points used in scf-calculations. Then q2r will be> able to do FFT F(q)=>F(R). So, you should put here > nr1=1 etc. as you used only the Gamma point. Is the> use only the Gamma point is OK for FFT, some doubts. > > Probably, you have an enormous computational resource> and are very ambitious to calculate phonons for 64> atoms supercell. For ideal case these properties you> would like to calculate is just 32 times that these> for 2 atomic cell. 
;( No, I haven't enormous eomputational resource and I'm just a little novice on phonons calculation. I find the resource the phonon calculation needed is out of my expection when I first touch it. For the aim of obtaining some properties of point-defects in Si-supercell, I try to make the perfect Si-bulk as reference. And for consistency I use the same k-points, supercell and cutoffs as initial geometry optimization. The phonons calculation is so expensive that I have to just calculate the dynamical matrix at the gamma point of the supercell.
> Bests,> Eyvaz.> 
yours, shangyi
Best regards!
 Graduate school of China academy of science 
_________________________________________________________________
?? Windows Vista ???
http://search.live.com/results.aspx?q=windows+vista&mkt=zh-cn&FORM=LIVSOP
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From ihsanas at yahoo.com  Sat Jun 23 17:35:14 2007
From: ihsanas at yahoo.com (احسان عريقات)
Date: Sat, 23 Jun 2007 08:35:14 -0700 (PDT)
Subject: [Pw_forum] max time
Message-ID: <420258.87086.qm@web52302.mail.re2.yahoo.com>

Hi 
Is there any way to increase the max time of cpu .
best regard 
Ihsan
physics department -Jordan


       
____________________________________________________________________________________
Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase.
http://farechase.yahoo.com/


From akohlmey at cmm.chem.upenn.edu  Sat Jun 23 16:55:03 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 23 Jun 2007 10:55:03 -0400 (EDT)
Subject: [Pw_forum] max time
In-Reply-To: <420258.87086.qm@web52302.mail.re2.yahoo.com>
Message-ID: <Pine.LNX.4.44.0706231051540.11261-100000@localhost.localdomain>

On Sat, 23 Jun 2007, ????? ?????? wrote:

> Hi 
> Is there any way to increase the max time of cpu .

the default value of max_seconds in pw.x (i assume,
you're using that code) is 150 days according to
the documentation. you can always checkpoint and
restart a calculation (by creating an EXIT.prefix file).

so i guess, you are more likely to have a problem 
in your queueing system, which is completely independent
from the QE code.

cheers,
   axel.

> best regard 
> Ihsan
> physics department -Jordan
> 
> 
>        
> ____________________________________________________________________________________
> Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase.
> http://farechase.yahoo.com/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

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



From ihsanas at yahoo.com  Sat Jun 23 18:48:47 2007
From: ihsanas at yahoo.com (احسان عريقات)
Date: Sat, 23 Jun 2007 09:48:47 -0700 (PDT)
Subject: [Pw_forum] max time
Message-ID: <188426.16228.qm@web52304.mail.re2.yahoo.com>

Thank`s alot for replaying ,but why my scf calculation
by using pw.x stops after 7 days
best regard 
Ihsan 
physics department -Jordan


      ____________________________________________________________________________________
Fussy? Opinionated? Impossible to please? Perfect.  Join Yahoo!'s user panel and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 



From eyvaz_isaev at yahoo.com  Sat Jun 23 19:15:46 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sat, 23 Jun 2007 10:15:46 -0700 (PDT)
Subject: [Pw_forum] max time
In-Reply-To: <188426.16228.qm@web52304.mail.re2.yahoo.com>
Message-ID: <527652.4294.qm@web60322.mail.yahoo.com>

Hi,

--- ????? ?????? <ihsanas at yahoo.com> wrote:

> Thank`s alot for replaying ,but why my scf
> calculation by using pw.x stops after 7 days
> best regard 

Presumably it is due to a queueing system installed on
your local system. Ask your system administrator about
maximally allowed time per process.  
By the way how is complex your system? Are you sure
everything is OK with your input?
 
Bests,
Eyvaz.

> Ihsan 
> physics department -Jordan
> 
> 
>      
>
____________________________________________________________________________________
> Fussy? Opinionated? Impossible to please? Perfect. 
> Join Yahoo!'s user panel and lay it on us.
>
http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and 
Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com


      ____________________________________________________________________________________
Fussy? Opinionated? Impossible to please? Perfect.  Join Yahoo!'s user panel and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 



From srijan.india at gmail.com  Sun Jun 24 14:36:44 2007
From: srijan.india at gmail.com (Srijan Kumar Saha)
Date: Sun, 24 Jun 2007 18:06:44 +0530
Subject: [Pw_forum] spin dope
Message-ID: <3fcc7e670706240536g3d6da239o8a15def90dd46d5@mail.gmail.com>

  Dear pwscf users,

  Is it possible in PWSCF to add a certain number of free carriers with a
given spin
  (say only up spin electrons) in a particular metal???
  Which input flags I have to tune for that???

  Looking forawrd to your kind reply.
  With best regards,
  Srijan

  Dept. of Physics
  Center of Condensed Matter Theory.
  India
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From giannozz at nest.sns.it  Sun Jun 24 19:26:12 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Sun, 24 Jun 2007 19:26:12 +0200
Subject: [Pw_forum] spin dope
In-Reply-To: <3fcc7e670706240536g3d6da239o8a15def90dd46d5@mail.gmail.com>
References: <3fcc7e670706240536g3d6da239o8a15def90dd46d5@mail.gmail.com>
Message-ID: <D4771F51-C340-4572-9EC6-05BCF1857405@nest.sns.it>

On Jun 24, 2007, at 14:36 , Srijan Kumar Saha wrote:

>   Is it possible in PWSCF to add a certain number of free carriers
>   with a given spin (say only up spin electrons) in a particular  
> metal???
>   Which input flags I have to tune for that???

tot_magnetization (or, as an alternative, multiplicity) + tot_charge.
Obsolete but still working: nelup/neldw + nelec

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




From shruba at gmail.com  Sun Jun 24 19:37:57 2007
From: shruba at gmail.com (shruba at gmail.com)
Date: Sun, 24 Jun 2007 13:37:57 -0400
Subject: [Pw_forum] problem with uspp2upf tools
Message-ID: <822f4ec80706241037n57827330i93915fe1e3044ec@mail.gmail.com>

Dear alll
I was trying to convert uspp files to upf format , I am using uspp files
which I got  inside vanderbilt uspp package
I used the command
../upftools/uspp2upf.x   filename.uspp
 but I am getting the error message
forrtl: severe (67): input statement requires too much data, unit 1, file
/home/shruba/espresso-3.2
/uspp-736/Work/028-Ni/028-Ni-gpw-n-campos/Ni_ps.uspp
Image              PC        Routine            Line        Source
uspp2upf.x         080A01CA  Unknown               Unknown  Unknown
uspp2upf.x         0809E89D  Unknown               Unknown  Unknown
uspp2upf.x         08080449  Unknown               Unknown  Unknown
uspp2upf.x         0805589E  Unknown               Unknown  Unknown
uspp2upf.x         080555CE  Unknown               Unknown  Unknown
uspp2upf.x         080690CA  Unknown               Unknown  Unknown
uspp2upf.x         08049A05  Unknown               Unknown  Unknown
uspp2upf.x         08049704  Unknown               Unknown  Unknown
uspp2upf.x         08049651  Unknown               Unknown  Unknown
libc.so.6          00BACE23  Unknown               Unknown  Unknown
uspp2upf.x         08049591  Unknown               Unknown  Unknown

I tried couple other  uspp files also but getting same problem, I noticed
the uspp files I am using is binary files. is it creating problem.
Can you please suggest me how to solve this problem.
 reagards
                      shruba

-- 
shruba gangopadhyay
graduate student
department of chemistry
university of central florida
orlando, FL-32826
'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
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From giannozz at nest.sns.it  Sun Jun 24 20:04:49 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Sun, 24 Jun 2007 20:04:49 +0200
Subject: [Pw_forum] problem with uspp2upf tools
In-Reply-To: <822f4ec80706241037n57827330i93915fe1e3044ec@mail.gmail.com>
References: <822f4ec80706241037n57827330i93915fe1e3044ec@mail.gmail.com>
Message-ID: <E430FDD7-1F75-4D69-A499-D00C6563AB85@nest.sns.it>

On Jun 24, 2007, at 19:37 , shruba at gmail.com wrote:

> I tried couple other  uspp files also but getting same problem,
> I noticed the uspp files I am using is binary files. is it creating  
> problem.

binary files produced on one machine are readable on another machine
if and only if:
- they use the same representation of numbers (most machines do)
- they use the same "big-endian" or "little-endian" logic (i.e. most
significant bits first or last, which is which I don't know and it  
doesn't
matter as long as they are the same; according to Murphy's law,
typically they are not the same).

> Can you please suggest me how to solve this problem

do everything on the same machine, or try compiler options to
instruct the compiler to read the format you have.

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




From niuli1978 at yahoo.com.cn  Mon Jun 25 08:18:44 2007
From: niuli1978 at yahoo.com.cn (li niu)
Date: Mon, 25 Jun 2007 14:18:44 +0800 (CST)
Subject: [Pw_forum] about decomoposition of the atomic contribution to the vibrational density of states
Message-ID: <139462.39484.qm@web15004.mail.cnb.yahoo.com>

Dear PWSCF co-users,
 
 I am facing the following  confusion in using PWSCF.
 Some papers mention about decomoposition of the atomic contribution to the vibrational density of states in stretching, bending and rocking components.[PRB 69,235102(2004)]
 how does one extract the density of states accociated to the C-C bond stretching and bending?
 APPLED PHYSICS LETTERS 75,644(1999)
 
 I am looking forward to your reply.Thank you very much.
 
 Best regards,
 
 Sincerely,
 Niu Li
 harbin Institute of Technology
 China
 
       
---------------------------------
????????3.5G???20M??? 
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From shruba at gmail.com  Mon Jun 25 08:19:32 2007
From: shruba at gmail.com (shruba at gmail.com)
Date: Mon, 25 Jun 2007 02:19:32 -0400
Subject: [Pw_forum] problem with uspp2upf tools
In-Reply-To: <E430FDD7-1F75-4D69-A499-D00C6563AB85@nest.sns.it>
References: <822f4ec80706241037n57827330i93915fe1e3044ec@mail.gmail.com>
	 <E430FDD7-1F75-4D69-A499-D00C6563AB85@nest.sns.it>
Message-ID: <822f4ec80706242319h11ee8463hefa4787210230f75@mail.gmail.com>

Thanks Paolo,
 I tried that option also,
 I cleaned the old files , and did everything in same machine but still that
is not working, In the Vanderbilt code I am getting another file "
filename.out"  do i need to convert those instead of uspp,
or Can i use any other pseudopotential format instead of UPF in pwscf?

Regards
       shruba

On 6/24/07, Paolo Giannozzi <giannozz at nest.sns.it> wrote:
>
>
> On Jun 24, 2007, at 19:37 , shruba at gmail.com wrote:
>
> > I tried couple other  uspp files also but getting same problem,
> > I noticed the uspp files I am using is binary files. is it creating
> > problem.
>
> binary files produced on one machine are readable on another machine
> if and only if:
> - they use the same representation of numbers (most machines do)
> - they use the same "big-endian" or "little-endian" logic (i.e. most
> significant bits first or last, which is which I don't know and it
> doesn't
> matter as long as they are the same; according to Murphy's law,
> typically they are not the same).
>
> > Can you please suggest me how to solve this problem
>
> do everything on the same machine, or try compiler options to
> instruct the compiler to read the format you have.
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
shruba gangopadhyay
graduate student
department of chemistry
university of central florida
orlando, FL-32826
'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
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From dalcorso at sissa.it  Mon Jun 25 09:06:13 2007
From: dalcorso at sissa.it (Dal Corso Andrea)
Date: Mon, 25 Jun 2007 09:06:13 +0200
Subject: [Pw_forum] problem with uspp2upf tools
In-Reply-To: <822f4ec80706242319h11ee8463hefa4787210230f75@mail.gmail.com>
References: <822f4ec80706241037n57827330i93915fe1e3044ec@mail.gmail.com>
	 <E430FDD7-1F75-4D69-A499-D00C6563AB85@nest.sns.it>
	 <822f4ec80706242319h11ee8463hefa4787210230f75@mail.gmail.com>
Message-ID: <1182755173.3286.6.camel@dhpc-5-01.sissa.it>

On Mon, 2007-06-25 at 02:19 -0400, shruba at gmail.com wrote:
> Thanks Paolo,
>  I tried that option also,
>  I cleaned the old files , and did everything in same machine but
> still that is not working, In the Vanderbilt code I am getting another
> file "filename.out"  do i need to convert those instead of uspp, 
> or Can i use any other pseudopotential format instead of UPF in
> pwscf? 
>  

There is an utility program reform.x in the Vanderbilt distribution that
converts the pseudopotential to a formatted file. I would try to use 
this program first and then convert the formatted file into UPF with
uspp2upf.

Hope this helps,

Andrea 


> Regards
>        shruba
>  
> On 6/24/07, Paolo Giannozzi <giannozz at nest.sns.it> wrote: 
>         
>         On Jun 24, 2007, at 19:37 , shruba at gmail.com wrote:
>         
>         > I tried couple other  uspp files also but getting same
>         problem, 
>         > I noticed the uspp files I am using is binary files. is it
>         creating
>         > problem.
>         
>         binary files produced on one machine are readable on another
>         machine
>         if and only if:
>         - they use the same representation of numbers (most machines
>         do) 
>         - they use the same "big-endian" or "little-endian" logic
>         (i.e. most
>         significant bits first or last, which is which I don't know
>         and it
>         doesn't
>         matter as long as they are the same; according to Murphy's
>         law, 
>         typically they are not the same).
>         
>         > Can you please suggest me how to solve this problem
>         
>         do everything on the same machine, or try compiler options to
>         instruct the compiler to read the format you have. 
>         
>         Paolo
>         ---
>         Paolo Giannozzi, Democritos and University of Udine, Italy
>         
>         
>         _______________________________________________
>         Pw_forum mailing list
>         Pw_forum at pwscf.org
>         http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> 
> -- 
> shruba gangopadhyay
> graduate student
> department of chemistry 
> university of central florida
> orlando, FL-32826
> 'friendship doubles joys and reduces sorrows by half' (Francis
> Bacon). 
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
34014 Trieste (Italy)               e-mail: dalcorso at sissa.it




From srijan.india at gmail.com  Mon Jun 25 09:24:58 2007
From: srijan.india at gmail.com (Srijan Kumar Saha)
Date: Mon, 25 Jun 2007 12:54:58 +0530
Subject: [Pw_forum] spin dope
In-Reply-To: <D4771F51-C340-4572-9EC6-05BCF1857405@nest.sns.it>
References: <3fcc7e670706240536g3d6da239o8a15def90dd46d5@mail.gmail.com>
	 <D4771F51-C340-4572-9EC6-05BCF1857405@nest.sns.it>
Message-ID: <3fcc7e670706250024r735807adw7b4f1afd69e9b8f1@mail.gmail.com>

  Dear Paolo,
  Thank you very much for your helpful reply.
  Regards,
  Srijan

  Department of Physics
  CCMT
  India

  P.S.  Could anybody please give me some useful references of
  the published papers on spin-dpoed calculation in metal using PWSCF????
  or which particular code infact calculate "Total Magnetization" in
PWSCF????
  or any good tutorial  on  the usage example and algorithm
  for "Total Magnetization"  calculations??????????????



On 6/24/07, Paolo Giannozzi <giannozz at nest.sns.it> wrote:
>
>
> On Jun 24, 2007, at 14:36 , Srijan Kumar Saha wrote:
>
> >   Is it possible in PWSCF to add a certain number of free carriers
> >   with a given spin (say only up spin electrons) in a particular
> > metal???
> >   Which input flags I have to tune for that???
>
> tot_magnetization (or, as an alternative, multiplicity) + tot_charge.
> Obsolete but still working: nelup/neldw + nelec
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
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From yuwen_66 at yahoo.com  Mon Jun 25 10:03:18 2007
From: yuwen_66 at yahoo.com (W. YU)
Date: Mon, 25 Jun 2007 01:03:18 -0700 (PDT)
Subject: [Pw_forum] symmetry identification
Message-ID: <40915.46590.qm@web51012.mail.re2.yahoo.com>

Dear PW users,

I met a problem when doing some calculation on a body
centered tetragonal structure. The space group no. is
139 (I4/mmm). There are all together 16 symmetry
operations, but pw can only identify 8 symmetry
operations without inversion. So in a follow up phonon
calculation, the given phonon symmetry modes are not
consistent with the space analysis. I an not sure
whether the lost symmetry operations are caused by the
input coordinates. I tried it with wie2k package, it
could identify all the symmetry operations. So what
could be the cause for this problem? The input file is
attached. Any help would be much appreciated. Thanks.

Wen Yu

 =====================================================
The following is my  input file:

 &system
    ibrav = 7, celldm(1) =7.1747,celldm(3)=3.2818,
    nat= 7, ntyp= 3,
    ecutwfc = 50.0,ecutrho = 400.0,
    occupations = 'smearing',
    smearing = 'methfessel-paxton', 
    degauss = 0.02,
  /
 &electrons
    mixing_beta = 0.2
 /
ATOMIC_SPECIES
 Sr  87.62  Sr.pbe-nsp-van.UPF
 Cu  63.55  Cu.pbe-n-van_ak.UPF
 O   16.0   O.pbe-van_ak.UPF
ATOMIC_POSITIONS bohr
 Sr 0.0 0.0  8.341471850
 Sr 0.0 0.0  15.20471415
 Cu 0.0 0.0  0.0
 O  0.000000 3.587363  0.0
 O  3.587363 0.000000  0.0
 O  0.0 0.0   3.64071128
 O  0.0 0.0  19.90547472
K_POINTS automatic
8 8 8 0 0 0
EOF
 


 
____________________________________________________________________________________
Bored stiff? Loosen up... 
Download and play hundreds of games for free on Yahoo! Games.
http://games.yahoo.com/games/front


From baroni at sissa.it  Mon Jun 25 10:34:42 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 25 Jun 2007 10:34:42 +0200
Subject: [Pw_forum] symmetry identification
In-Reply-To: <40915.46590.qm@web51012.mail.re2.yahoo.com>
References: <40915.46590.qm@web51012.mail.re2.yahoo.com>
Message-ID: <3EE44792-B795-43D4-9DB2-4771F8A2D040@sissa.it>

Dear W Yu: this problem has been discussed zillions of times in this  
forum, and has to do with the commensurability of fractional  
translations with the FFT grid. Please, refer to archive where, I am  
sure, you will find the answer to your question. Also, please note  
that we really appreciate those posts to this mailing list which are  
thoroughly signed (name, current affiliation). Thanks a lot for using  
QE and for posting to this mailing list. Stefano Baroni

On Jun 25, 2007, at 10:03 AM, W. YU wrote:

> Dear PW users,
>
> I met a problem when doing some calculation on a body
> centered tetragonal structure. The space group no. is
> 139 (I4/mmm). There are all together 16 symmetry
> operations, but pw can only identify 8 symmetry
> operations without inversion. So in a follow up phonon
> calculation, the given phonon symmetry modes are not
> consistent with the space analysis. I an not sure
> whether the lost symmetry operations are caused by the
> input coordinates. I tried it with wie2k package, it
> could identify all the symmetry operations. So what
> could be the cause for this problem? The input file is
> attached. Any help would be much appreciated. Thanks.
>
> Wen Yu
>
>  =====================================================
> The following is my  input file:
>
>  &system
>     ibrav = 7, celldm(1) =7.1747,celldm(3)=3.2818,
>     nat= 7, ntyp= 3,
>     ecutwfc = 50.0,ecutrho = 400.0,
>     occupations = 'smearing',
>     smearing = 'methfessel-paxton',
>     degauss = 0.02,
>   /
>  &electrons
>     mixing_beta = 0.2
>  /
> ATOMIC_SPECIES
>  Sr  87.62  Sr.pbe-nsp-van.UPF
>  Cu  63.55  Cu.pbe-n-van_ak.UPF
>  O   16.0   O.pbe-van_ak.UPF
> ATOMIC_POSITIONS bohr
>  Sr 0.0 0.0  8.341471850
>  Sr 0.0 0.0  15.20471415
>  Cu 0.0 0.0  0.0
>  O  0.000000 3.587363  0.0
>  O  3.587363 0.000000  0.0
>  O  0.0 0.0   3.64071128
>  O  0.0 0.0  19.90547472
> K_POINTS automatic
> 8 8 8 0 0 0
> EOF
>
>
>
>
> ______________________________________________________________________ 
> ______________
> Bored stiff? Loosen up...
> Download and play hundreds of games for free on Yahoo! Games.
> http://games.yahoo.com/games/front
> _______________________________________________
> 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
[+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

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 ihsanas at yahoo.com  Mon Jun 25 14:25:25 2007
From: ihsanas at yahoo.com (احسان عريقات)
Date: Mon, 25 Jun 2007 05:25:25 -0700 (PDT)
Subject: [Pw_forum] max time
Message-ID: <2313.39623.qm@web52308.mail.re2.yahoo.com>

Dear Axel
I`m not using any queing system,I`m  running the jobs
interactively " means on the computer directly not
through a queing system" eventhough it stops ,may be
this problem becouse I am using old version 2.1.2 .
best regard 
Ihsan 


       
____________________________________________________________________________________
Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase.
http://farechase.yahoo.com/


From gnkrumah at ictp.it  Mon Jun 25 15:54:25 2007
From: gnkrumah at ictp.it (Nkrumah-Buandoh George_Kofi)
Date: Mon, 25 Jun 2007 15:54:25 +0200 (CEST)
Subject: [Pw_forum] Pseudopotential for Nd
Message-ID: <56975.10.2.0.25.1182779665.squirrel@webmail2.ictp.trieste.it>

I need an Ultrasoft Vanderbilt pseudopotentials for Neodymium. It is
available at the pwscf web site. I would be grateful if any one could be
of help.
Thanks.

George K. Nkrumah-Buandoh

The Abdus Salam
International Centre for Theoretical Physics
Strada Costiera 11, 34014 Trieste, Italy.



From akohlmey at cmm.chem.upenn.edu  Mon Jun 25 17:51:45 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 25 Jun 2007 11:51:45 -0400
Subject: [Pw_forum] max time
In-Reply-To: <2313.39623.qm@web52308.mail.re2.yahoo.com>
References: <2313.39623.qm@web52308.mail.re2.yahoo.com>
Message-ID: <7b6913e90706250851x73d040d0u77ce4500e9b33a8d@mail.gmail.com>

On 6/25/07, ????? ?????? <ihsanas at yahoo.com> wrote:
> Dear Axel
> I`m not using any queing system,I`m  running the jobs
> interactively " means on the computer directly not
> through a queing system" eventhough it stops ,may be
> this problem becouse I am using old version 2.1.2 .

dear ihsan,

i admire your optimisim.
expecting a machine to run reliably for over a week
under full load is asking for a lot, even if you have the
perfect hardward and machine room (do you?).

it is most likely, that some machine setup related issue
terminated your job (running out of memory?, max cputime
limit on the shell level), but if it was a problem with QE,
please try again with the current release version. nobody
will help you to correct a problem in an deprecated version
of the code.

regardless, QE calculations are generally restartable, and
you can also set up your jobs to terminate cleanly after
a certain time is expired. in the typical enviroment, people
can rarely expect to run jobs longer than 24 hours, so it
might be a good thing to practice how to restart jobs.

> best regard
> Ihsan


please remember the forum policy of stating your
full name and affiliation. thanks.


cheers,
   axel.
>
>
> ____________________________________________________________________________________
> Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase.
> http://farechase.yahoo.com/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


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


From akohlmey at cmm.chem.upenn.edu  Mon Jun 25 17:44:17 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 25 Jun 2007 11:44:17 -0400
Subject: [Pw_forum] problem with uspp2upf tools
In-Reply-To: <1182755173.3286.6.camel@dhpc-5-01.sissa.it>
References: <822f4ec80706241037n57827330i93915fe1e3044ec@mail.gmail.com>
	 <E430FDD7-1F75-4D69-A499-D00C6563AB85@nest.sns.it>
	 <822f4ec80706242319h11ee8463hefa4787210230f75@mail.gmail.com>
	 <1182755173.3286.6.camel@dhpc-5-01.sissa.it>
Message-ID: <7b6913e90706250844t49a3329h91415cbf9720fc41@mail.gmail.com>

On 6/25/07, Dal Corso Andrea <dalcorso at sissa.it> wrote:
> On Mon, 2007-06-25 at 02:19 -0400, shruba at gmail.com wrote:
> > Thanks Paolo,
> >  I tried that option also,
> >  I cleaned the old files , and did everything in same machine but
> > still that is not working, In the Vanderbilt code I am getting another
> > file "filename.out"  do i need to convert those instead of uspp,
> > or Can i use any other pseudopotential format instead of UPF in
> > pwscf?

the use of UPF is highly recommended, since it can be read on
all platforms and contains all relevant information. for backward
compatibility, QE can in principle read text format uspp files (i.e.
processed with reform), if their name ends in .van or .vdb.

two more comments:
1) if you build your own pseudopotential files, you should know what
you are doing, i.e. read the documentation, which will tell you what
files are needed and what are not.

2) as paolo already mentioned, the binary format can change between
machines, but also between compilers. if you use the same compiler
with the same flags for QE and the uspp code, they should be readable.
for a couple more details, see e.g.:
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-linux.html#endian

cheers,
   axel.

>
> There is an utility program reform.x in the Vanderbilt distribution that
> converts the pseudopotential to a formatted file. I would try to use
> this program first and then convert the formatted file into UPF with
> uspp2upf.
>
> Hope this helps,
>
> Andrea
>
>
> > Regards
> >        shruba
> >
> > On 6/24/07, Paolo Giannozzi <giannozz at nest.sns.it> wrote:
> >
> >         On Jun 24, 2007, at 19:37 , shruba at gmail.com wrote:
> >
> >         > I tried couple other  uspp files also but getting same
> >         problem,
> >         > I noticed the uspp files I am using is binary files. is it
> >         creating
> >         > problem.
> >
> >         binary files produced on one machine are readable on another
> >         machine
> >         if and only if:
> >         - they use the same representation of numbers (most machines
> >         do)
> >         - they use the same "big-endian" or "little-endian" logic
> >         (i.e. most
> >         significant bits first or last, which is which I don't know
> >         and it
> >         doesn't
> >         matter as long as they are the same; according to Murphy's
> >         law,
> >         typically they are not the same).
> >
> >         > Can you please suggest me how to solve this problem
> >
> >         do everything on the same machine, or try compiler options to
> >         instruct the compiler to read the format you have.
> >
> >         Paolo
> >         ---
> >         Paolo Giannozzi, Democritos and University of Udine, Italy
> >
> >
> >         _______________________________________________
> >         Pw_forum mailing list
> >         Pw_forum at pwscf.org
> >         http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> > --
> > shruba gangopadhyay
> > graduate student
> > department of chemistry
> > university of central florida
> > orlando, FL-32826
> > 'friendship doubles joys and reduces sorrows by half' (Francis
> > Bacon).
> --
> Andrea Dal Corso                    Tel. 0039-040-3787428
> SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
> 34014 Trieste (Italy)               e-mail: dalcorso at sissa.it
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


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


From jiaanyan at gmail.com  Mon Jun 25 23:52:19 2007
From: jiaanyan at gmail.com (Jia-An Yan)
Date: Mon, 25 Jun 2007 17:52:19 -0400
Subject: [Pw_forum] questions about the phonon calculation
Message-ID: <6581de880706251452s382b0613x87d3979440644921@mail.gmail.com>

Dear PWscf users,

I have some questions during my phonon calculations using PWscf 3.2.2.

1) If I switch the iverbosity=.true. in the input file, the output of
ph.xwill list  the eigenvectors for each mode before entering the scf
iterations. If I understand correctly, the code can determine an initial
displacement patterns even WITHOUT solving the linear system. I looked into
the source code and found that this is done in the set_irr.f90 subroutine.
The comment line says:

!    This subroutine computes a basis for all the irreducible
!     representations of the small group of q, which are contained
!     in the representation which has as basis the displacement vectors.
!     This is achieved by building a random hermitean matrix,
!     symmetrizing it and diagonalizing the result. The eigenvectors
!     give a basis for the irreducible representations of the
!     small group of q.

I noticed that the calculation of the first-order perturbation dVscf also
needs the initial displacement pattern for each mode to calculate the
contribution of the local potential (in dvqpsi_us.f90).  Can anybody here
provide me more details about the algorithm? thanks

2)  I try to output the dVscf for each mode from the solve_linter.f90 after
the convergence has been reached. However, it seems that the output value
will change when I increase the Ecut (the FFT grid and also the symmetry
operations will be different comparing with previous case). In fact, in all
cases the Ecut has been already converged.  I believe there should be
something missed in my output of dVscf. Can anybody here give me some hints
about that?  Thanks!

Best,
Jia-An Yan

---------------------------------------------------------------------------------------------------------
School of Physics,
Georgia Institute of Technology
837 State Street,
Atlanta, Georgia 30332
U.S.A.
---------------------------------------------------------------------------------------------------------
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From kondor.jess at gmail.com  Tue Jun 26 00:45:09 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Mon, 25 Jun 2007 17:45:09 -0500
Subject: [Pw_forum] ultrasoft pseudopotential for Mn
Message-ID: <1d9d5d9d0706251545rcabafcft4f78549e9878ea3@mail.gmail.com>

Dear community,

 Does anybody have an ultrasoft (LDA) pseudopotential for Mn? I see only PBE
pseudo on pwscf web page, but there are original parameters (even in
uspp-7.3.6 package).

 Regards,
   jess

-- 
=====================================
Jess Kondor

PICYT, Av. Venustiano Carranza 2425-A,
San Luis Potos? 78210, M?xico
=====================================
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From changhuacas at hotmail.com  Tue Jun 26 05:41:20 2007
From: changhuacas at hotmail.com (=?gb2312?B?zuIgu6q7qg==?=)
Date: Tue, 26 Jun 2007 11:41:20 +0800
Subject: [Pw_forum] **some confusion about spin related knobs**
Message-ID: <BAY133-F347223BCC59CA1BC57A1A0A10B0@phx.gbl>

Hi,every pwscf experts and users in this community .

It has been almost one year since I abandoned VASP. In the past one year , 
I learned much from the community of pwscf, which is a free world full of 
many gifted men.



I am reproducing the published study of the high spin (HS)/low spin (LS) 
transition in low solute concentration magnesiowustite (Mw), 
(Mg(1-x)Fe(x))O, (x < 20%), by Tsuchiya T etc.

Under the guide of  INPUT_PW file ,I know some knobs that control spin 
related calculation,such as  nspin , 
starting_magnetization(i),tot_magnetization etc.

In order to contain the Fe with the desired proportion,supercell is needed.
I did not use the primitive fcc cell,for it reduces the number of Fe x 
proportion, instead a conventional cubic supercell is used,as you can see 
in my input file below.
You know, when there is only one Fe in the supercell ,things come much 
easy.
But 5 Fe atoms is another story.




Let's hit the point.

1.the main puzzle is that 
 I can only controll the tot_magnetization of all the atoms in the 
supercell ,but not the respective Fe ? which  prevents  me assembling HS 
and LS Fe atoms.
 starting_magnetization(i)  seems to have the capacity to control each Fe? 
but from the literal meaning, it seems to only give a initial status , and 
from my testing calculation it does evolve with the relax calculation.

2.another minor puzzle is that
How to spread the Fe atoms in the supercell,which satisfied the following 
requirement:
give the Fe atoms as mamy symmetries as possible
keep th Fe atoms as far as possible to avoid the 3d electrons interactions
I have write several possible assemblings with the help of XCrySDen and my 
own eyes! But I do not satisfied with them.   is there any routines or 
special techniques to handle them?


I will be much appreciated, if  my confusion  could be cleared .

input file for  HS 
///////////////////////////////////////
&CONTROL
                 calculation = 'relax' ,
                restart_mode = 'from_scratch' ,
                      outdir = './tmp/' ,
                  pseudo_dir = '/home/wu/mpich2/espresso-3.2/pseudo/MgFeO/' 
,
                      prefix = 'MgFeO_super_cubic' ,
                     tstress = .TRUE. ,
                     tprnfor = .TRUE.,
                    etot_conv_thr=1.0d-6,  forc_conv_thr=1.0D-4 
                      
 /
 &SYSTEM
                       ibrav = 0,
                         nat = 64,
                        ntyp = 6,
                      ecutwfc = 30 ,
                     ecutrho  = 144,
                     nbnd = 400,
                     nspin = 2, 
       starting_magnetization(3) = 1.0 
       angle1(3) = 90.0
       angle2(3) =  0.0 
       starting_magnetization(4) = 1.0
       angle1(4) = 90.0
       angle2(4) =  0.0 
       starting_magnetization(5) = 1.0
       angle1(5) = 90.0
       angle2(5) =  0.0    
       starting_magnetization(6) = 1.0 
       angle1(6) = 90.0
       angle2(6) =  0.0     
       tot_magnetization = 16          
       lda_plus_u=.true.  Hubbard_U(3)=5.0, Hubbard_U(4)=5.0,
                          Hubbard_U(5)=5.0 ,  Hubbard_U(6)=5.0
                   
 /
 &ELECTRONS
                    conv_thr = 1.0d-6 ,
                 mixing_mode = 'plain' ,
                 mixing_beta = 0.7 ,   
/
&IONS
  ion_dynamics = 'bfgs',
  pot_extrapolation =  "second_order",
  wfc_extrapolation = "second_order",
/
CELL_PARAMETERS cubic
16.2  0.0  0.0
 0.0 16.2  0.0
 0.0  0.0 16.2
ATOMIC_SPECIES
   Mg   24.30500  Mg.pw91-np-van.UPF 
    O   15.99940  O.pw91-van_ak.UPF
   Fe1    55.8452  Fe.pw91-sp-van_ak.UPF
   Fe2    55.8452  Fe.pw91-sp-van_ak.UPF
   Fe3    55.8452  Fe.pw91-sp-van_ak.UPF
   Fe4    55.8452  Fe.pw91-sp-van_ak.UPF
ATOMIC_POSITIONS {crystal}
Mg 0.00000 0.00000 0.00000
Fe1 0.00000 0.00000 0.50000
Fe2 0.00000 0.50000 0.00000
Mg 0.00000 0.50000 0.50000
Fe3 0.50000 0.00000 0.00000
Mg 0.50000 0.00000 0.50000
Mg 0.50000 0.50000 0.00000
Fe4 0.50000 0.50000 0.50000   
Mg 0.00000 0.25000 0.25000
Mg 0.00000 0.25000 0.75000
Mg 0.00000 0.75000 0.25000
Mg 0.00000 0.75000 0.75000
Mg 0.50000 0.25000 0.25000
Mg 0.50000 0.25000 0.75000
Mg 0.50000 0.75000 0.25000
Mg 0.50000 0.75000 0.75000
Mg 0.25000 0.00000 0.25000
Mg 0.25000 0.00000 0.75000
Mg 0.25000 0.50000 0.25000
Mg 0.25000 0.50000 0.75000
Mg 0.75000 0.00000 0.25000
Mg 0.75000 0.00000 0.75000
Mg 0.75000 0.50000 0.25000
Mg 0.75000 0.50000 0.75000
Mg 0.25000 0.25000 0.00000
Mg 0.25000 0.25000 0.50000
Mg 0.25000 0.75000 0.00000
Mg 0.25000 0.75000 0.50000
Mg 0.75000 0.25000 0.00000
Mg 0.75000 0.25000 0.50000
Mg 0.75000 0.75000 0.00000
Mg 0.75000 0.75000 0.50000
O 0.25000 0.25000 0.25000
O 0.25000 0.25000 0.75000
O 0.25000 0.75000 0.25000
O 0.25000 0.75000 0.75000
O 0.75000 0.25000 0.25000
O 0.75000 0.25000 0.75000
O 0.75000 0.75000 0.25000
O 0.75000 0.75000 0.75000
O 0.25000 0.00000 0.00000
O 0.25000 0.00000 0.50000
O 0.25000 0.50000 0.00000
O 0.25000 0.50000 0.50000
O 0.75000 0.00000 0.00000
O 0.75000 0.00000 0.50000
O 0.75000 0.50000 0.00000
O 0.75000 0.50000 0.50000
O 0.00000 0.25000 0.00000
O 0.00000 0.25000 0.50000
O 0.00000 0.75000 0.00000
O 0.00000 0.75000 0.50000
O 0.50000 0.25000 0.00000
O 0.50000 0.25000 0.50000
O 0.50000 0.75000 0.00000
O 0.50000 0.75000 0.50000
O 0.00000 0.00000 0.25000
O 0.00000 0.00000 0.75000
O 0.00000 0.50000 0.25000
O 0.00000 0.50000 0.75000
O 0.50000 0.00000 0.25000
O 0.50000 0.00000 0.75000
O 0.50000 0.50000 0.25000
O 0.50000 0.50000 0.75000
K_POINTS automatic
5 5 5 0 0 0 
/////////////////////////////////////////////////////////





***********************************************
Wu Changhua , 
Institute of Geology and Geophysics, 
CAS , POB.9825  Beijing 100029  China

Email:  changhuacas at hotmail.com

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

_________________________________________________________________
???? MSN Explorer:   http://explorer.msn.com/lccn  



From giannozz at nest.sns.it  Tue Jun 26 09:55:10 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 26 Jun 2007 09:55:10 +0200
Subject: [Pw_forum] Pseudopotential for Nd
In-Reply-To: <56975.10.2.0.25.1182779665.squirrel@webmail2.ictp.trieste.it>
References: <56975.10.2.0.25.1182779665.squirrel@webmail2.ictp.trieste.it>
Message-ID: <BC7580F6-8D0E-4E16-98D2-E5FD2C587943@nest.sns.it>

On Jun 25, 2007, at 15:54 , Nkrumah-Buandoh George_Kofi wrote:

> I need an Ultrasoft Vanderbilt pseudopotentials for Neodymium.
> It is available at the pwscf web site.

no it isn't, and it is not trivial to generate one. Also note that DFT
may easily yield an incorrect f electron configuration. LDA+U may
be needed.

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




From giannozz at nest.sns.it  Tue Jun 26 10:04:28 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 26 Jun 2007 10:04:28 +0200
Subject: [Pw_forum] ultrasoft pseudopotential for Mn
In-Reply-To: <1d9d5d9d0706251545rcabafcft4f78549e9878ea3@mail.gmail.com>
References: <1d9d5d9d0706251545rcabafcft4f78549e9878ea3@mail.gmail.com>
Message-ID: <42A4A04B-8C28-43D0-88E0-19DAC7212129@nest.sns.it>

On Jun 26, 2007, at 24:45 , Jess Kondor wrote:

> Does anybody have an ultrasoft (LDA) pseudopotential for Mn?
> I see only PBE pseudo on pwscf web page, but there are original
> parameters (even in uspp-7.3.6 package).

if there are original parameters, you can easily rebuild a  
pseudopotential
with a different XC functional. It may not work, but it is easy.

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




From kondor.jess at gmail.com  Tue Jun 26 16:41:25 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Tue, 26 Jun 2007 09:41:25 -0500
Subject: [Pw_forum] ultrasoft pseudopotential for Mn
In-Reply-To: <42A4A04B-8C28-43D0-88E0-19DAC7212129@nest.sns.it>
References: <1d9d5d9d0706251545rcabafcft4f78549e9878ea3@mail.gmail.com>
	 <42A4A04B-8C28-43D0-88E0-19DAC7212129@nest.sns.it>
Message-ID: <1d9d5d9d0706260741x5934f991pea93af31a4593b5@mail.gmail.com>

Paolo,

 There are indeed no original parameters for Mn in uspp-7.3.6 package (I
made a typo in my e-mail). I see PBE pseudo on pwscf web page generated by
you - do you have those parameters?

 regards,
   jess

On 6/26/07, Paolo Giannozzi <giannozz at nest.sns.it> wrote:
>
>
> On Jun 26, 2007, at 24:45 , Jess Kondor wrote:
>
> > Does anybody have an ultrasoft (LDA) pseudopotential for Mn?
> > I see only PBE pseudo on pwscf web page, but there are original
> > parameters (even in uspp-7.3.6 package).
>
> if there are original parameters, you can easily rebuild a
> pseudopotential
> with a different XC functional. It may not work, but it is easy.
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
=====================================
 Jess Kondor

PICYT, Av. Venustiano Carranza 2425-A,
 San Luis Potos? 78210, M?xico

=====================================
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From giannozz at nest.sns.it  Tue Jun 26 17:16:48 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 26 Jun 2007 17:16:48 +0200
Subject: [Pw_forum] ultrasoft pseudopotential for Mn
In-Reply-To: <1d9d5d9d0706260741x5934f991pea93af31a4593b5@mail.gmail.com>
References: <1d9d5d9d0706251545rcabafcft4f78549e9878ea3@mail.gmail.com> <42A4A04B-8C28-43D0-88E0-19DAC7212129@nest.sns.it> <1d9d5d9d0706260741x5934f991pea93af31a4593b5@mail.gmail.com>
Message-ID: <2955A882-FF30-44E0-9B46-8A0189CA0995@nest.sns.it>

On Jun 26, 2007, at 16:41 , Jess Kondor wrote:

> There are indeed no original parameters for Mn in uspp-7.3.6 package
> (I made a typo in my e-mail). I see PBE pseudo on pwscf web page
> generated by you - do you have those parameters?

http://www.fisica.uniud.it/~giannozz/public/mn.tar.gz . There is also
a LDA PP that should have been generated with the same data by
changing the XC functional. No warranty. Several people reported
crappy results from Mn + LDA (for instance, badly underestimated
lattice parameters in materials like MnAs)

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




From kondor.jess at gmail.com  Tue Jun 26 17:53:11 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Tue, 26 Jun 2007 10:53:11 -0500
Subject: [Pw_forum] ultrasoft pseudopotential for Mn
In-Reply-To: <2955A882-FF30-44E0-9B46-8A0189CA0995@nest.sns.it>
References: <1d9d5d9d0706251545rcabafcft4f78549e9878ea3@mail.gmail.com>
	 <42A4A04B-8C28-43D0-88E0-19DAC7212129@nest.sns.it>
	 <1d9d5d9d0706260741x5934f991pea93af31a4593b5@mail.gmail.com>
	 <2955A882-FF30-44E0-9B46-8A0189CA0995@nest.sns.it>
Message-ID: <1d9d5d9d0706260853r36abd784ud5fd778f679561e4@mail.gmail.com>

Thank you, Paolo!

Jess

On 6/26/07, Paolo Giannozzi <giannozz at nest.sns.it> wrote:
>
>
> On Jun 26, 2007, at 16:41 , Jess Kondor wrote:
>
> > There are indeed no original parameters for Mn in uspp-7.3.6 package
> > (I made a typo in my e-mail). I see PBE pseudo on pwscf web page
> > generated by you - do you have those parameters?
>
> http://www.fisica.uniud.it/~giannozz/public/mn.tar.gz . There is also
> a LDA PP that should have been generated with the same data by
> changing the XC functional. No warranty. Several people reported
> crappy results from Mn + LDA (for instance, badly underestimated
> lattice parameters in materials like MnAs)
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
=====================================
Jess Kondor

PICYT, Av. Venustiano Carranza 2425-A,
San Luis Potos? 78210, M?xico

=====================================
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From amos at errno.com  Wed Jun 27 01:21:14 2007
From: amos at errno.com (Amos Leffler)
Date: Tue, 26 Jun 2007 17:21:14 -0600
Subject: [Pw_forum] Example21 Problem
Message-ID: <46819F6A.6030307@errno.com>

Dear Forum,
         Attached  are the details of a problem I ran into trying to  
execute  example21.  I am using SuSE  Linux 10.2 which has worked well 
up to this point so I think the problem is in the  run_example file.
                                                                        
   Amos Leffler
                                                                        
    Walnut Creek, CA.
                                                                        
       unaffiliated

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From akohlmey at cmm.chem.upenn.edu  Wed Jun 27 02:05:44 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 26 Jun 2007 20:05:44 -0400 (EDT)
Subject: [Pw_forum] Example21 Problem
In-Reply-To: <46819F6A.6030307@errno.com>
Message-ID: <Pine.LNX.4.44.0706262000360.12112-100000@localhost.localdomain>

On Tue, 26 Jun 2007, Amos Leffler wrote:

AL> Dear Forum,
AL>          Attached  are the details of a problem I ran into trying to  
AL> execute  example21.  I am using SuSE  Linux 10.2 which has worked well 
AL> up to this point so I think the problem is in the  run_example file.

well, i would say the problem is in your using of -ftrace=full. why?
example21 is special and requires as an argument the maximum number
of water molecules that you want to run (32-512). if you provide

the error message stems from the numerical compares of the first 
argument of the script, $1, with the corresponding number of waters.
the way it is done, allows to have a default value of '0' (i.e.
don't run any of those tests). your -ftrace=full argument expands
to a non-numerical value, hence the error messages. in all other
scripts it will be ignored, anyways.

cheers,
   axel.


AL>                                                                         
AL>    Amos Leffler
AL>                                                                         
AL>     Walnut Creek, CA.
AL>                                                                         
AL>        unaffiliated
AL> 
AL> 

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



From srijan.india at gmail.com  Wed Jun 27 06:54:18 2007
From: srijan.india at gmail.com (Srijan Kumar Saha)
Date: Wed, 27 Jun 2007 10:24:18 +0530
Subject: [Pw_forum] spin dope
In-Reply-To: <3fcc7e670706250024r735807adw7b4f1afd69e9b8f1@mail.gmail.com>
References: <3fcc7e670706240536g3d6da239o8a15def90dd46d5@mail.gmail.com>
	 <D4771F51-C340-4572-9EC6-05BCF1857405@nest.sns.it>
	 <3fcc7e670706250024r735807adw7b4f1afd69e9b8f1@mail.gmail.com>
Message-ID: <3fcc7e670706262154iadb46b4g3555c4adc3606875@mail.gmail.com>

      Dear  pwscf developers,

      It's written in the input documentation that
      nelup and  neldw  are REAL. The sum must yield nelec that is also
real.
      Then why
      tot_magnetization (nelup - neldw) is INTEGER ( default = -1
[unspecified] )????
      What will somebody do if he wants to fix a fractional
tot_magnetization for
      his system??? In the output files pwscf gives total magnetization as
a  real
      parameter ( unit Bohr mag/ cell). So  tot_magnetization and  total
magnetization
      are not same. Am I right????  In the code,   total  magnetization
      is divided by  omega/ (nr1 nr2 nr3). What does it mean????
      I mean what is omega????

      Looking forward to your kind  reply.
      With best regards,
      Srijan
      Department of Physics
      CCMT
      India


tot_magnetization (or, as an alternative, multiplicity) + tot_charge.
> > Obsolete but still working: nelup/neldw + nelec
> >
> > Paolo
> > ---
> > Paolo Giannozzi, Democritos and University of Udine, Italy
> >
> >
> >
>
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From giannozz at nest.sns.it  Wed Jun 27 11:02:04 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 27 Jun 2007 11:02:04 +0200
Subject: [Pw_forum] spin dope
In-Reply-To: <3fcc7e670706262154iadb46b4g3555c4adc3606875@mail.gmail.com>
References: <3fcc7e670706240536g3d6da239o8a15def90dd46d5@mail.gmail.com> <D4771F51-C340-4572-9EC6-05BCF1857405@nest.sns.it> <3fcc7e670706250024r735807adw7b4f1afd69e9b8f1@mail.gmail.com> <3fcc7e670706262154iadb46b4g3555c4adc3606875@mail.gmail.com>
Message-ID: <2099A05C-FB43-4CE4-8356-7684F536F465@nest.sns.it>

On Jun 27, 2007, at 6:54 , Srijan Kumar Saha wrote:

>       It's written in the input documentation that nelup and neldw  
> are REAL.
>       The sum must yield nelec that is also real. Then why
>       tot_magnetization (nelup - neldw) is INTEGER ( default = -1  
> [unspecified] )?

because whoever implemented this feature didn't need a fractional
total magnetization

>       In the code, total magnetization is divided by  omega/ (nr1  
> nr2 nr3).
>       What does it mean???? I mean what is omega????

omega is the volume of the unit cell, (nr1 nr2 nr3) is the total number
of grid points in real space, omega/(nr1 nr2 nr3) = Delta V in the
integration

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




From amos at errno.com  Wed Jun 27 16:19:29 2007
From: amos at errno.com (Amos Leffler)
Date: Wed, 27 Jun 2007 08:19:29 -0600
Subject: [Pw_forum] Example21 Problem
In-Reply-To: <Pine.LNX.4.44.0706262000360.12112-100000@localhost.localdomain>
References: <Pine.LNX.4.44.0706262000360.12112-100000@localhost.localdomain>
Message-ID: <468271F1.3060202@errno.com>

Dear Forum,
       I found later after sending this note that the program ran (in 
background) but did the calculation for all of the numbers of water 
molecules.  The original input did have as the last entry a number (64) 
so there still is a problem.
                                                                      
Amos Leffler

Axel Kohlmeyer wrote:
> On Tue, 26 Jun 2007, Amos Leffler wrote:
>
> AL> Dear Forum,
> AL>          Attached  are the details of a problem I ran into trying to  
> AL> execute  example21.  I am using SuSE  Linux 10.2 which has worked well 
> AL> up to this point so I think the problem is in the  run_example file.
>
> well, i would say the problem is in your using of -ftrace=full. why?
> example21 is special and requires as an argument the maximum number
> of water molecules that you want to run (32-512). if you provide
>
> the error message stems from the numerical compares of the first 
> argument of the script, $1, with the corresponding number of waters.
> the way it is done, allows to have a default value of '0' (i.e.
> don't run any of those tests). your -ftrace=full argument expands
> to a non-numerical value, hence the error messages. in all other
> scripts it will be ignored, anyways.
>
> cheers,
>    axel.
>
>
> AL>                                                                         
> AL>    Amos Leffler
> AL>                                                                         
> AL>     Walnut Creek, CA.
> AL>                                                                         
> AL>        unaffiliated
> AL> 
> AL> 
>
>   



From akohlmey at cmm.chem.upenn.edu  Wed Jun 27 17:33:14 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 27 Jun 2007 11:33:14 -0400
Subject: [Pw_forum] Example21 Problem
In-Reply-To: <468271F1.3060202@errno.com>
References: <Pine.LNX.4.44.0706262000360.12112-100000@localhost.localdomain>
	 <468271F1.3060202@errno.com>
Message-ID: <7b6913e90706270833r7ed6f8e6tc3518752fe22699a@mail.gmail.com>

On 6/27/07, Amos Leffler <amos at errno.com> wrote:
> Dear Forum,
>        I found later after sending this note that the program ran (in
> background) but did the calculation for all of the numbers of water
> molecules.  The original input did have as the last entry a number (64)
> so there still is a problem.

i disagree. please explain first the existence of the -ftrace=full
which is obviously causing the problems you see. omit it and
the script will run fine.

axel.

>
> Amos Leffler
>
> Axel Kohlmeyer wrote:
> > On Tue, 26 Jun 2007, Amos Leffler wrote:
> >
> > AL> Dear Forum,
> > AL>          Attached  are the details of a problem I ran into trying to
> > AL> execute  example21.  I am using SuSE  Linux 10.2 which has worked well
> > AL> up to this point so I think the problem is in the  run_example file.
> >
> > well, i would say the problem is in your using of -ftrace=full. why?
> > example21 is special and requires as an argument the maximum number
> > of water molecules that you want to run (32-512). if you provide
> >
> > the error message stems from the numerical compares of the first
> > argument of the script, $1, with the corresponding number of waters.
> > the way it is done, allows to have a default value of '0' (i.e.
> > don't run any of those tests). your -ftrace=full argument expands
> > to a non-numerical value, hence the error messages. in all other
> > scripts it will be ignored, anyways.
> >
> > cheers,
> >    axel.
> >
> >
> > AL>
> > AL>    Amos Leffler
> > AL>
> > AL>     Walnut Creek, CA.
> > AL>
> > AL>        unaffiliated
> > AL>
> > AL>
> >
> >
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


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


From ihsanas at yahoo.com  Wed Jun 27 17:49:10 2007
From: ihsanas at yahoo.com (احسان عريقات)
Date: Wed, 27 Jun 2007 08:49:10 -0700 (PDT)
Subject: [Pw_forum] max_time
Message-ID: <561926.68578.qm@web52303.mail.re2.yahoo.com>

Dear Axel 
thank you for your patient and replaying ,I can
restart the jobs if it is relaxation by replacing
restart instead of from_scratch ,but I can`t do so if
the job is scf ,am I wrong ,what is EXIT.prefix file
,can you give some references to read about.
best regard 
Ihsan
physics department-Jordan university 


       
____________________________________________________________________________________
Boardwalk for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! Games.
http://get.games.yahoo.com/proddesc?gamekey=monopolyherenow  


From akohlmey at cmm.chem.upenn.edu  Thu Jun 28 00:38:02 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 27 Jun 2007 18:38:02 -0400 (EDT)
Subject: [Pw_forum] max_time
In-Reply-To: <561926.68578.qm@web52303.mail.re2.yahoo.com>
Message-ID: <Pine.LNX.4.44.0706271102430.12112-100000@localhost.localdomain>

On Wed, 27 Jun 2007, ????? ?????? wrote:

I> Dear Axel 
I> thank you for your patient and replaying ,I can
I> restart the jobs if it is relaxation by replacing
I> restart instead of from_scratch ,but I can`t do so if
I> the job is scf ,am I wrong ,what is EXIT.prefix file
I> ,can you give some references to read about.

what kind of calculations are you running, when 
you cannot complete a single point calculation within 
a week? what kind of machine are you running on?
are you running efficiently (i.e. not constantly
swapping?).

in that case, you may be better off, to either
investigate whether a less expensive method
(DFT-TB) can give you similar quality results 
or whether you can get access to a more powerful
machine/cluster.

to learn about the so-called softexit have a look
at the user's guide. e.g. at (right before 'Phonon calculations'):

http://www.quantum-espresso.org/wiki/index.php/Using_PWscf#Typical_cases

cheers,
   axel.

p.s.: first of all you should of course upgrade to the latest
version of quantum espresso.


I> best regard 
I> Ihsan
I> physics department-Jordan university 
I> 
I> 
I>        
I> ____________________________________________________________________________________
I> Boardwalk for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! Games.
I> http://get.games.yahoo.com/proddesc?gamekey=monopolyherenow  
I> _______________________________________________
I> Pw_forum mailing list
I> Pw_forum at pwscf.org
I> http://www.democritos.it/mailman/listinfo/pw_forum
I> 

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




From baroni at sissa.it  Thu Jun 28 11:18:23 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 28 Jun 2007 11:18:23 +0200
Subject: [Pw_forum] Re:about the displacive instabilities
In-Reply-To: <158075.99290.qm@web15605.mail.cnb.yahoo.com>
References: <158075.99290.qm@web15605.mail.cnb.yahoo.com>
Message-ID: <38226797-F160-4FCE-A07B-5F1ED5B433C3@sissa.it>


On Jun 15, 2007, at 3:20 AM, li yan wrote:

> Dear Stefano
>      I'm so sorry and giving my delayed thanks to you,
>      I am not sure if i can continue the discussion of my previous  
> question. I have read the papers you suggested. And the authors  
> proposed that the softening mode coupled with the lattice strain  
> can induced a second or a slightly first order pahse transition.  
> But I stil have doubts in the displacive instabilitis.
>    The character of the  transition from NaCl to CsCl is thougt to  
> be  first order in experiment. May I cosider this  transition to be  
> induced by the lattice instability if I found the softening mode in  
> the  NaCl phase at the pressure which is consitent with the  
> experiment?

which normal-mode displacement would bring the NaCl structure to  
CsCl? what would be the order parameter of the transition?

S.

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

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 wyanchao at gmail.com  Thu Jun 28 14:37:59 2007
From: wyanchao at gmail.com (wang yanchao)
Date: Thu, 28 Jun 2007 20:37:59 +0800
Subject: [Pw_forum] ack question
Message-ID: <55639d30706280537r7b42260bke0f6742f2c305d9@mail.gmail.com>

Dear users,
  When I caculate the body center orthorhombic phonon spectrum,
I met a question,which I use pwtools/kpoint.x to generate 5 qpoints(nr is 2
3 2)then run ph.x, all  *.dyn  is  OK!  but when I run q2r.x,the error is "q
not allowed",I think program is due to primtive and convetional cell is not
the same! So I use run scf kpoint set 2 3 2 then there 10 kpoints,then I use
this to do phonon ! *.dyn is also OK! but run q2r.x,the error is the same as
before! Now I do not know how to do next ! if someone know Please tell me
how to deal with it ! thank you in advance!!!!
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From baroni at sissa.it  Thu Jun 28 15:29:21 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 28 Jun 2007 15:29:21 +0200
Subject: [Pw_forum] ack question
In-Reply-To: <55639d30706280537r7b42260bke0f6742f2c305d9@mail.gmail.com>
References: <55639d30706280537r7b42260bke0f6742f2c305d9@mail.gmail.com>
Message-ID: <ADCD1529-F18C-4116-AEFA-09F4D87C96DB@sissa.it>

please, sign you post indicating your current affiliation (or append  
a signature file)
thanks - SB

On Jun 28, 2007, at 2:37 PM, wang yanchao wrote:

> Dear users,
>   When I caculate the body center orthorhombic phonon spectrum,
> I met a question,which I use pwtools/kpoint.x to generate 5 qpoints 
> (nr is 2 3 2)then run ph.x, all  *.dyn  is  OK!  but when I run  
> q2r.x,the error is "q not allowed",I think program is due to  
> primtive and convetional cell is not the same! So I use run scf  
> kpoint set 2 3 2 then there 10 kpoints,then I use this to do  
> phonon ! *.dyn is also OK! but run q2r.x,the error is the same as  
> before! Now I do not know how to do next ! if someone know Please  
> tell me how to deal with it ! thank you in advance!!!!

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

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 eyvaz_isaev at yahoo.com  Thu Jun 28 16:33:13 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 28 Jun 2007 07:33:13 -0700 (PDT)
Subject: [Pw_forum] ack question
In-Reply-To: <55639d30706280537r7b42260bke0f6742f2c305d9@mail.gmail.com>
Message-ID: <748793.16885.qm@web60311.mail.yahoo.com>

Hi,

Please follow Stefano's comment and do not forget 
specify your affiliation. 

There is not enough information provided to make a
conclusion why it happens. Please post your input
files.

Bests,
Eyvaz.

--- wang yanchao <wyanchao at gmail.com> wrote:

> Dear users,
>   When I caculate the body center orthorhombic
> phonon spectrum,
> I met a question,which I use pwtools/kpoint.x to
> generate 5 qpoints(nr is 2
> 3 2)then run ph.x, all  *.dyn  is  OK!  but when I
> run q2r.x,the error is "q
> not allowed",I think program is due to primtive and
> convetional cell is not
> the same! So I use run scf kpoint set 2 3 2 then
> there 10 kpoints,then I use
> this to do phonon ! *.dyn is also OK! but run
> q2r.x,the error is the same as
> before! Now I do not know how to do next ! if
> someone know Please tell me
> how to deal with it ! thank you in advance!!!!
> 


-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and 
Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com


       
____________________________________________________________________________________
Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase.
http://farechase.yahoo.com/


From lmoreira at fc.unesp.br  Fri Jun 29 13:28:32 2007
From: lmoreira at fc.unesp.br (Leandro Moreira de Campos Pinto)
Date: Fri, 29 Jun 2007 08:28:32 -0300
Subject: [Pw_forum] DOS projections with PWscf
Message-ID: <20070629082832.j35ucluxw4gss0sc@webmail.fc.unesp.br>

Dears,

I'm having problems in ploting the DOS projections. I've already set  
the input to run the scf calculations but now I don't know what I  
should do to obtain the DOS.

Thanks in advanced.

Leandro

-- 
**************************************************
* Leandro Moreira de Campos Pinto                *
* Grupo de Eletrocat?lise e Rea??es Superficiais *
* Departamento de Qu?mica                        *
* Faculdades de Ci?ncias, UNESP, C.P. 473        *
* Bauru, SP, CEP 17033-360, Brasil               *
* lmoreira at fc.unesp.br                           *
* http://www.fc.unesp.br/grupo_dafc              *
**************************************************

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



From eyvaz_isaev at yahoo.com  Fri Jun 29 13:41:23 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 29 Jun 2007 04:41:23 -0700 (PDT)
Subject: [Pw_forum] DOS projections with PWscf
In-Reply-To: <20070629082832.j35ucluxw4gss0sc@webmail.fc.unesp.br>
Message-ID: <137301.42076.qm@web60324.mail.yahoo.com>

Hi, 

All you need are described in /example08.

Bests,
Eyvaz.

--- Leandro Moreira de Campos Pinto
<lmoreira at fc.unesp.br> wrote:

> Dears,
> 
> I'm having problems in ploting the DOS projections.
> I've already set  
> the input to run the scf calculations but now I
> don't know what I  
> should do to obtain the DOS.
> 
> Thanks in advanced.
> 
> Leandro
> 
> -- 
> **************************************************
> * Leandro Moreira de Campos Pinto                *
> * Grupo de Eletrocat?lise e Rea??es Superficiais *
> * Departamento de Qu?mica                        *
> * Faculdades de Ci?ncias, UNESP, C.P. 473        *
> * Bauru, SP, CEP 17033-360, Brasil               *
> * lmoreira at fc.unesp.br                           *
> * http://www.fc.unesp.br/grupo_dafc              *
> **************************************************
> 
>
----------------------------------------------------------------
> 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
> 


-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and 
Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com


       
____________________________________________________________________________________
Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase.
http://farechase.yahoo.com/


From mashao_jie at 163.com  Fri Jun 29 16:40:09 2007
From: mashao_jie at 163.com (mashaojie163)
Date: Fri, 29 Jun 2007 22:40:09 +0800
Subject: [Pw_forum] Want test crash
References: <137301.42076.qm@web60324.mail.yahoo.com>
Message-ID: <016301c7ba5b$64e136e0$d245c0de@masj>

Dear Sir:
            I am a newbie for pwscf and want. I have compiled the parallel  version of PWSCF(espresso-3.2) and WANT(want-2.1-RC1). I excute the tests of  PWSCF and everything is OK! However, when I excute the tests of WANT,  the error appeared .
          when I excute test01 for run.sh bands, the bands.x crashed and the error in bands.out as following. 
  
DFT-data fmt automaticaly detected: qexml

 *** from PE    :     0
 *** in routine : lattice_read_ext
 *** error msg. : reading lattice
 *** error code :     1
 *** aborting ***


 *** from PE    :     0
 *** in routine : lattice_read_ext
 *** error msg. : reading lattice
 *** error code :     1
 *** aborting ***


From amos at errno.com  Fri Jun 29 17:17:11 2007
From: amos at errno.com (Amos Leffler)
Date: Fri, 29 Jun 2007 09:17:11 -0600
Subject: [Pw_forum] Example21 Problem
In-Reply-To: <7b6913e90706270833r7ed6f8e6tc3518752fe22699a@mail.gmail.com>
References: <Pine.LNX.4.44.0706262000360.12112-100000@localhost.localdomain>	 <468271F1.3060202@errno.com> <7b6913e90706270833r7ed6f8e6tc3518752fe22699a@mail.gmail.com>
Message-ID: <46852277.2030503@errno.com>

Dear Forum,
       Attached is the result of the following input in example 21:
                   ./run_example 256
It calculates values for all sizes up to 256 and skips the remainder.  
However, I am puzzled that the calculations take very little time 
certainly less than a minute for each one.  The "README" note says it 
takes a long time and should include more than what is shown.  There may 
be more to this than I understand.
                                                                      
Amos Leffler
Axel Kohlmeyer wrote:
> On 6/27/07, Amos Leffler <amos at errno.com> wrote:
>> Dear Forum,
>>        I found later after sending this note that the program ran (in
>> background) but did the calculation for all of the numbers of water
>> molecules.  The original input did have as the last entry a number (64)
>> so there still is a problem.
>
> i disagree. please explain first the existence of the -ftrace=full
> which is obviously causing the problems you see. omit it and
> the script will run fine.
>
> axel.
>
>>
>> Amos Leffler
>>
>> Axel Kohlmeyer wrote:
>> > On Tue, 26 Jun 2007, Amos Leffler wrote:
>> >
>> > AL> Dear Forum,
>> > AL>          Attached  are the details of a problem I ran into 
>> trying to
>> > AL> execute  example21.  I am using SuSE  Linux 10.2 which has 
>> worked well
>> > AL> up to this point so I think the problem is in the  run_example 
>> file.
>> >
>> > well, i would say the problem is in your using of -ftrace=full. why?
>> > example21 is special and requires as an argument the maximum number
>> > of water molecules that you want to run (32-512). if you provide
>> >
>> > the error message stems from the numerical compares of the first
>> > argument of the script, $1, with the corresponding number of waters.
>> > the way it is done, allows to have a default value of '0' (i.e.
>> > don't run any of those tests). your -ftrace=full argument expands
>> > to a non-numerical value, hence the error messages. in all other
>> > scripts it will be ignored, anyways.
>> >
>> > cheers,
>> >    axel.
>> >
>> >
>> > AL>
>> > AL>    Amos Leffler
>> > AL>
>> > AL>     Walnut Creek, CA.
>> > AL>
>> > AL>        unaffiliated
>> > AL>
>> > AL>
>> >
>> >
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>

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From eyvaz_isaev at yahoo.com  Fri Jun 29 19:56:09 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 29 Jun 2007 10:56:09 -0700 (PDT)
Subject: [Pw_forum] Example21 Problem
In-Reply-To: <46852277.2030503@errno.com>
Message-ID: <211793.17296.qm@web60322.mail.yahoo.com>

Hi,

Inspecting your output file have shown that you have
memory allocation problem with all 32, 64, 128 and 256
atoms calculations (that is why just a few seconds),
and others were skipped as it was expected.

There is an advice to compile the program using with a
keyword -ftrace=frame or -ftrace=full, though I do not
know how it is useful, and presumably, compiler
dependent. At least, you can try recompile the code
using these keywords. 

Bests,
Eyvaz.

--- Amos Leffler <amos at errno.com> wrote:

> Dear Forum,
>        Attached is the result of the following input
> in example 21:
>                    ./run_example 256
> It calculates values for all sizes up to 256 and
> skips the remainder.  
> However, I am puzzled that the calculations take
> very little time 
> certainly less than a minute for each one.  The
> "README" note says it 
> takes a long time and should include more than what
> is shown.  There may 
> be more to this than I understand.
>                                                     
>                  
> Amos Leffler
> Axel Kohlmeyer wrote:
> > On 6/27/07, Amos Leffler <amos at errno.com> wrote:
> >> Dear Forum,
> >>        I found later after sending this note that
> the program ran (in
> >> background) but did the calculation for all of
> the numbers of water
> >> molecules.  The original input did have as the
> last entry a number (64)
> >> so there still is a problem.
> >
> > i disagree. please explain first the existence of
> the -ftrace=full
> > which is obviously causing the problems you see.
> omit it and
> > the script will run fine.
> >
> > axel.
> >
> >>
> >> Amos Leffler
> >>
> >> Axel Kohlmeyer wrote:
> >> > On Tue, 26 Jun 2007, Amos Leffler wrote:
> >> >
> >> > AL> Dear Forum,
> >> > AL>          Attached  are the details of a
> problem I ran into 
> >> trying to
> >> > AL> execute  example21.  I am using SuSE  Linux
> 10.2 which has 
> >> worked well
> >> > AL> up to this point so I think the problem is
> in the  run_example 
> >> file.
> >> >
> >> > well, i would say the problem is in your using
> of -ftrace=full. why?
> >> > example21 is special and requires as an
> argument the maximum number
> >> > of water molecules that you want to run
> (32-512). if you provide
> >> >
> >> > the error message stems from the numerical
> compares of the first
> >> > argument of the script, $1, with the
> corresponding number of waters.
> >> > the way it is done, allows to have a default
> value of '0' (i.e.
> >> > don't run any of those tests). your
> -ftrace=full argument expands
> >> > to a non-numerical value, hence the error
> messages. in all other
> >> > scripts it will be ignored, anyways.
> >> >
> >> > cheers,
> >> >    axel.
> >> >
> >> >
> >> > AL>
> >> > AL>    Amos Leffler
> >> > AL>
> >> > AL>     Walnut Creek, CA.
> >> > AL>
> >> > AL>        unaffiliated
> >> > AL>
> >> > AL>
> >> >
> >> >
> >>
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >>
> http://www.democritos.it/mailman/listinfo/pw_forum
> >>
> >>
> >
> >
> 
> 


-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and 
Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com


      ____________________________________________________________________________________
Fussy? Opinionated? Impossible to please? Perfect.  Join Yahoo!'s user panel and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 



From akohlmey at cmm.chem.upenn.edu  Fri Jun 29 20:56:31 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Fri, 29 Jun 2007 14:56:31 -0400 (EDT)
Subject: [Pw_forum] Example21 Problem
In-Reply-To: <46852277.2030503@errno.com>
Message-ID: <Pine.LNX.4.44.0706291453560.18200-100000@localhost.localdomain>

On Fri, 29 Jun 2007, Amos Leffler wrote:


amos,

how much memory do you have on the machine that you are running on?
how large are your ulimit settings?

the 32 water example requires about 1.2GB address space and 
about 400MB physical memory to run. for the larger systems
accordingly more. 

when a job stops complaining about not being able to allocate
memory, it is likely that you either do not have enough memory
or address space available, or that your account settings 
prohibit that.

cheers,
   axel.

AL> Dear Forum,
AL>        Attached is the result of the following input in example 21:
AL>                    ./run_example 256
AL> It calculates values for all sizes up to 256 and skips the remainder.  
AL> However, I am puzzled that the calculations take very little time 
AL> certainly less than a minute for each one.  The "README" note says it 
AL> takes a long time and should include more than what is shown.  There may 
AL> be more to this than I understand.
AL>                                                                       
AL> Amos Leffler
AL> Axel Kohlmeyer wrote:
AL> > On 6/27/07, Amos Leffler <amos at errno.com> wrote:
AL> >> Dear Forum,
AL> >>        I found later after sending this note that the program ran (in
AL> >> background) but did the calculation for all of the numbers of water
AL> >> molecules.  The original input did have as the last entry a number (64)
AL> >> so there still is a problem.
AL> >
AL> > i disagree. please explain first the existence of the -ftrace=full
AL> > which is obviously causing the problems you see. omit it and
AL> > the script will run fine.
AL> >
AL> > axel.
AL> >
AL> >>
AL> >> Amos Leffler
AL> >>
AL> >> Axel Kohlmeyer wrote:
AL> >> > On Tue, 26 Jun 2007, Amos Leffler wrote:
AL> >> >
AL> >> > AL> Dear Forum,
AL> >> > AL>          Attached  are the details of a problem I ran into 
AL> >> trying to
AL> >> > AL> execute  example21.  I am using SuSE  Linux 10.2 which has 
AL> >> worked well
AL> >> > AL> up to this point so I think the problem is in the  run_example 
AL> >> file.
AL> >> >
AL> >> > well, i would say the problem is in your using of -ftrace=full. why?
AL> >> > example21 is special and requires as an argument the maximum number
AL> >> > of water molecules that you want to run (32-512). if you provide
AL> >> >
AL> >> > the error message stems from the numerical compares of the first
AL> >> > argument of the script, $1, with the corresponding number of waters.
AL> >> > the way it is done, allows to have a default value of '0' (i.e.
AL> >> > don't run any of those tests). your -ftrace=full argument expands
AL> >> > to a non-numerical value, hence the error messages. in all other
AL> >> > scripts it will be ignored, anyways.
AL> >> >
AL> >> > cheers,
AL> >> >    axel.
AL> >> >
AL> >> >
AL> >> > AL>
AL> >> > AL>    Amos Leffler
AL> >> > AL>
AL> >> > AL>     Walnut Creek, CA.
AL> >> > AL>
AL> >> > AL>        unaffiliated
AL> >> > AL>
AL> >> > AL>
AL> >> >
AL> >> >
AL> >>
AL> >> _______________________________________________
AL> >> Pw_forum mailing list
AL> >> Pw_forum at pwscf.org
AL> >> http://www.democritos.it/mailman/listinfo/pw_forum
AL> >>
AL> >>
AL> >
AL> >
AL> 
AL> 

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



From akohlmey at cmm.chem.upenn.edu  Fri Jun 29 20:58:24 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Fri, 29 Jun 2007 14:58:24 -0400 (EDT)
Subject: [Pw_forum] Example21 Problem
In-Reply-To: <211793.17296.qm@web60322.mail.yahoo.com>
Message-ID: <Pine.LNX.4.44.0706291456400.18200-100000@localhost.localdomain>

On Fri, 29 Jun 2007, Eyvaz Isaev wrote:

EI> Hi,
EI> 
EI> Inspecting your output file have shown that you have
EI> memory allocation problem with all 32, 64, 128 and 256
EI> atoms calculations (that is why just a few seconds),
EI> and others were skipped as it was expected.
EI> 
EI> There is an advice to compile the program using with a
EI> keyword -ftrace=frame or -ftrace=full, though I do not
EI> know how it is useful, and presumably, compiler

eyvaz,

this is not an output from the run_example script, but
the default error message, that g95 compiled executables
spit out in case of crashes. g95 can be quite quirky at times.
i don't think that there is much use to that, unless you
have a lot of experience in debugging...

cheers,
  axel.

EI> dependent. At least, you can try recompile the code
EI> using these keywords. 
EI> 
EI> Bests,
EI> Eyvaz.
EI> 
EI> --- Amos Leffler <amos at errno.com> wrote:
EI> 
EI> > Dear Forum,
EI> >        Attached is the result of the following input
EI> > in example 21:
EI> >                    ./run_example 256
EI> > It calculates values for all sizes up to 256 and
EI> > skips the remainder.  
EI> > However, I am puzzled that the calculations take
EI> > very little time 
EI> > certainly less than a minute for each one.  The
EI> > "README" note says it 
EI> > takes a long time and should include more than what
EI> > is shown.  There may 
EI> > be more to this than I understand.
EI> >                                                     
EI> >                  
EI> > Amos Leffler
EI> > Axel Kohlmeyer wrote:
EI> > > On 6/27/07, Amos Leffler <amos at errno.com> wrote:
EI> > >> Dear Forum,
EI> > >>        I found later after sending this note that
EI> > the program ran (in
EI> > >> background) but did the calculation for all of
EI> > the numbers of water
EI> > >> molecules.  The original input did have as the
EI> > last entry a number (64)
EI> > >> so there still is a problem.
EI> > >
EI> > > i disagree. please explain first the existence of
EI> > the -ftrace=full
EI> > > which is obviously causing the problems you see.
EI> > omit it and
EI> > > the script will run fine.
EI> > >
EI> > > axel.
EI> > >
EI> > >>
EI> > >> Amos Leffler
EI> > >>
EI> > >> Axel Kohlmeyer wrote:
EI> > >> > On Tue, 26 Jun 2007, Amos Leffler wrote:
EI> > >> >
EI> > >> > AL> Dear Forum,
EI> > >> > AL>          Attached  are the details of a
EI> > problem I ran into 
EI> > >> trying to
EI> > >> > AL> execute  example21.  I am using SuSE  Linux
EI> > 10.2 which has 
EI> > >> worked well
EI> > >> > AL> up to this point so I think the problem is
EI> > in the  run_example 
EI> > >> file.
EI> > >> >
EI> > >> > well, i would say the problem is in your using
EI> > of -ftrace=full. why?
EI> > >> > example21 is special and requires as an
EI> > argument the maximum number
EI> > >> > of water molecules that you want to run
EI> > (32-512). if you provide
EI> > >> >
EI> > >> > the error message stems from the numerical
EI> > compares of the first
EI> > >> > argument of the script, $1, with the
EI> > corresponding number of waters.
EI> > >> > the way it is done, allows to have a default
EI> > value of '0' (i.e.
EI> > >> > don't run any of those tests). your
EI> > -ftrace=full argument expands
EI> > >> > to a non-numerical value, hence the error
EI> > messages. in all other
EI> > >> > scripts it will be ignored, anyways.
EI> > >> >
EI> > >> > cheers,
EI> > >> >    axel.
EI> > >> >
EI> > >> >
EI> > >> > AL>
EI> > >> > AL>    Amos Leffler
EI> > >> > AL>
EI> > >> > AL>     Walnut Creek, CA.
EI> > >> > AL>
EI> > >> > AL>        unaffiliated
EI> > >> > AL>
EI> > >> > AL>
EI> > >> >
EI> > >> >
EI> > >>
EI> > >> _______________________________________________
EI> > >> Pw_forum mailing list
EI> > >> Pw_forum at pwscf.org
EI> > >>
EI> > http://www.democritos.it/mailman/listinfo/pw_forum
EI> > >>
EI> > >>
EI> > >
EI> > >
EI> > 
EI> > 
EI> 
EI> 
EI> -------------------------------------------------------------------
EI> Prof. Eyvaz Isaev, 
EI> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and 
EI> Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com
EI> 
EI> 
EI>       ____________________________________________________________________________________
EI> Fussy? Opinionated? Impossible to please? Perfect.  Join Yahoo!'s user panel and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 
EI> 
EI> _______________________________________________
EI> Pw_forum mailing list
EI> Pw_forum at pwscf.org
EI> http://www.democritos.it/mailman/listinfo/pw_forum
EI> 

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



From eyvaz_isaev at yahoo.com  Fri Jun 29 22:32:04 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 29 Jun 2007 13:32:04 -0700 (PDT)
Subject: [Pw_forum] Example21 Problem
In-Reply-To: <Pine.LNX.4.44.0706291456400.18200-100000@localhost.localdomain>
Message-ID: <649480.16024.qm@web60311.mail.yahoo.com>

Hi Axel,

--- Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu>
wrote:

> On Fri, 29 Jun 2007, Eyvaz Isaev wrote:
> 
> EI> Hi,
> EI> 
> EI> Inspecting your output file have shown that you
> have
> EI> memory allocation problem with all 32, 64, 128
> and 256
> EI> atoms calculations (that is why just a few
> seconds),
> EI> and others were skipped as it was expected.
> EI> 
> EI> There is an advice to compile the program using
> with a
> EI> keyword -ftrace=frame or -ftrace=full, though I
> do not
> EI> know how it is useful, and presumably, compiler
> 
> eyvaz,
> 
> this is not an output from the run_example script,
> but the default error message, that g95 compiled
> executables  spit out in case of crashes. g95 can be
> quite quirky  at times.  

Yes, of course, the message obviously comes from a
compiled used. The only thing I didn't understand
looking at the message whch compiler was used. Now
thanks you I am aware it was g95. 

> i don't think that there is much use to that, 
> unless you  have a lot of experience in debugging...

I would add plenty of time, too.

Very bests,
Eyvaz.


> 
> cheers,
>   axel.
> 
> EI> dependent. At least, you can try recompile the
> code
> EI> using these keywords. 
> EI> 
> EI> Bests,
> EI> Eyvaz.
> EI> 
> EI> --- Amos Leffler <amos at errno.com> wrote:
> EI> 
> EI> > Dear Forum,
> EI> >        Attached is the result of the following
> input
> EI> > in example 21:
> EI> >                    ./run_example 256
> EI> > It calculates values for all sizes up to 256
> and
> EI> > skips the remainder.  
> EI> > However, I am puzzled that the calculations
> take
> EI> > very little time 
> EI> > certainly less than a minute for each one. 
> The
> EI> > "README" note says it 
> EI> > takes a long time and should include more than
> what
> EI> > is shown.  There may 
> EI> > be more to this than I understand.
> EI> >                                               
>      
> EI> >                  
> EI> > Amos Leffler
> EI> > Axel Kohlmeyer wrote:
> EI> > > On 6/27/07, Amos Leffler <amos at errno.com>
> wrote:
> EI> > >> Dear Forum,
> EI> > >>        I found later after sending this
> note that
> EI> > the program ran (in
> EI> > >> background) but did the calculation for all
> of
> EI> > the numbers of water
> EI> > >> molecules.  The original input did have as
> the
> EI> > last entry a number (64)
> EI> > >> so there still is a problem.
> EI> > >
> EI> > > i disagree. please explain first the
> existence of
> EI> > the -ftrace=full
> EI> > > which is obviously causing the problems you
> see.
> EI> > omit it and
> EI> > > the script will run fine.
> EI> > >
> EI> > > axel.
> EI> > >
> EI> > >>
> EI> > >> Amos Leffler
> EI> > >>
> EI> > >> Axel Kohlmeyer wrote:
> EI> > >> > On Tue, 26 Jun 2007, Amos Leffler wrote:
> EI> > >> >
> EI> > >> > AL> Dear Forum,
> EI> > >> > AL>          Attached  are the details of
> a
> EI> > problem I ran into 
> EI> > >> trying to
> EI> > >> > AL> execute  example21.  I am using SuSE 
> Linux
> EI> > 10.2 which has 
> EI> > >> worked well
> EI> > >> > AL> up to this point so I think the
> problem is
> EI> > in the  run_example 
> EI> > >> file.
> EI> > >> >
> EI> > >> > well, i would say the problem is in your
> using
> EI> > of -ftrace=full. why?
> EI> > >> > example21 is special and requires as an
> EI> > argument the maximum number
> EI> > >> > of water molecules that you want to run
> EI> > (32-512). if you provide
> EI> > >> >
> EI> > >> > the error message stems from the
> numerical
> EI> > compares of the first
> EI> > >> > argument of the script, $1, with the
> EI> > corresponding number of waters.
> EI> > >> > the way it is done, allows to have a
> default
> EI> > value of '0' (i.e.
> EI> > >> > don't run any of those tests). your
> EI> > -ftrace=full argument expands
> EI> > >> > to a non-numerical value, hence the error
> EI> > messages. in all other
> EI> > >> > scripts it will be ignored, anyways.
> EI> > >> >
> EI> > >> > cheers,
> EI> > >> >    axel.
> EI> > >> >
> EI> > >> >
> EI> > >> > AL>
> EI> > >> > AL>    Amos Leffler
> EI> > >> > AL>
> EI> > >> > AL>     Walnut Creek, CA.
> EI> > >> > AL>
> EI> > >> > AL>        unaffiliated
> EI> > >> > AL>
> EI> > >> > AL>
> EI> > >> >
> EI> > >> >
> EI> > >>
> EI> > >>
> _______________________________________________
> EI> > >> Pw_forum mailing list
> EI> > >> Pw_forum at pwscf.org
> EI> > >>
> EI> >
> http://www.democritos.it/mailman/listinfo/pw_forum
> EI> > >>
> EI> > >>
> EI> > >
> EI> > >
> EI> > 
> EI> > 
> EI> 
> EI> 
> EI>
>
-------------------------------------------------------------------
> EI> Prof. Eyvaz Isaev, 
> EI> Theoretical Physics Department, Moscow State
> Institute of Steel & Alloys, Russia, and 
> EI> Condensed Matter Theory Group, Uppsala
> University, Sweden Eyvaz.Isaev at fysik.uu.se,
> eyvaz_isaev at yahoo.com
> EI> 
> EI> 
> EI>      
>
____________________________________________________________________________________
> EI> Fussy? Opinionated? Impossible to please?
> Perfect.  Join Yahoo!'s user panel and lay it on us.
>
http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7
> 
> EI> 
> EI> _______________________________________________
> EI> Pw_forum mailing list
> EI> Pw_forum at pwscf.org
> EI>
> http://www.democritos.it/mailman/listinfo/pw_forum
> EI> 
> 
> -- 
>
=======================================================================
> Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu  
> http://www.cmm.upenn.edu
>    Center for Molecular Modeling   --   University
> of Pennsylvania
> Department of Chemistry, 231 S.34th Street,
> Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233, 
> office-tel: 1-215-898-5425
>
=======================================================================
> If you make something idiot-proof, the universe
> creates a better idiot.
> 
> _______________________________________________
> Pw_forum mailing list
> 
=== message truncated ===


-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and 
Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com


       
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From njuxuyuehua at gmail.com  Sat Jun 30 04:34:18 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Sat, 30 Jun 2007 10:34:18 +0800
Subject: [Pw_forum] vc-relax:i want to relax cell only along one direction ,such c
Message-ID: <aca2feb20706291934u3d993e6epb9a95fbebf4d4318@mail.gmail.com>

hello ALL
following the subject , can i realize ir in pwscf ?how to do with it ? if
not ,what other choice ?thanks

-- 
Xu Yuehua
physics Department of Nanjing university
China
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From akohlmey at cmm.chem.upenn.edu  Sat Jun 30 06:08:26 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 30 Jun 2007 00:08:26 -0400 (EDT)
Subject: [Pw_forum] vc-relax:i want to relax cell only along one direction
 ,such c
In-Reply-To: <aca2feb20706291934u3d993e6epb9a95fbebf4d4318@mail.gmail.com>
Message-ID: <Pine.LNX.4.44.0706300006120.11976-100000@localhost.localdomain>

On Sat, 30 Jun 2007, xu yuehua wrote:



XY> hello ALL
XY> following the subject , can i realize ir in pwscf ?how to do with it ? if
XY> not ,what other choice ?thanks

please have a look at the documentation in Doc/INPUT_PW

in the namelist &CELL there is the parameter cell_dofree
which should do exactly what you want. however, if you
only want to relax a single cell parameter, you may be
much better off with a number of single point calculations
and a fit to an equation of state. please see the many 
previous discussions on this subject in the mailing list
archives.

cheers,
   axel.

XY> 
XY> 

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