From etabel at hotmail.com  Fri Sep  1 02:18:58 2006
From: etabel at hotmail.com (Eric Abel)
Date: Thu, 31 Aug 2006 20:18:58 -0400
Subject: [Pw_forum] Answers and Questions
In-Reply-To: <7b6913e90608311141r1c050f4ama7af37889c1593ef@mail.gmail.com>
Message-ID: <BAY105-F2009D6B6B51229CE2690A7D43C0@phx.gbl>



>From: "Axel Kohlmeyer" <akohlmey at cmm.upenn.edu>
>Reply-To: pw_forum at pwscf.org
>To: pw_forum at pwscf.org
>Subject: Re: [Pw_forum] Answers and Questions
>Date: Thu, 31 Aug 2006 14:41:32 -0400
>
>On 8/31/06, Eric Abel <etabel at hotmail.com> wrote:
>
>[...]
>
>>From my perspective, I would say that some people are too eager to ask
>>questions...the answers they seek are clearly present in the current
>>available resources.   It just takes a little elbow grease to find them.
>>It's much easier to simply post a question to the forum.  I don't support
>>this...researching one's own problem is far more educational than having
>>someone answer it for you.  We all learned this in the 8th grade.  That
>
>yep. but you also have to understand, that people can get carried away.
>my strategy towards this is to gradually provide less direct information
>and move to point out ways to how to obtain the information yourself.
>some people need to be helped across the first big barrier before they
>realize that investing effort into finding the right answers
>themselves pays off.
>the whole thing is a matter of finding the right balance and understanding
>the background.
>
>>said, I feel that these wiki ideas are great, as they would make it easier
>>to find answers.  I don't know if this is planned but the wikis should 
>>also
>>contain the reference papers which disuss the thoery that goes into pwscf.
>
><grin>you should have looked into the mailing list archives, this has
>been discussed recently</grin>
>please head over to:
>http://www.quantum-espresso.org/wiki/index.php/Main_Page
>and ask to get an account (well actually you can probably
>request it in person. ;-) ). i have made the experience, that
>people who have just learned a method or how to use a tool
>(i.e. advanced beginners) write the best documentation.

I would be happy to contribute what I've learned to the PWSCF community.  I 
agree that "advanced beginners" make good teachers, as they tend to be able 
to "dumb the material down" so that the "beginning beginners" can follow.

Eric

>
>cheers,
>  axel.
>
>>As far as the developers are concerned, I am truly impressed with their
>>patience and competence.  It is intimidating enough for a graduate student
>>and pwscf beginner to post to the forum, it would be much worse if those
>>answering the questions were condescending.  Instead, they treat every
>>question more or less equally, and for that I applaud them.
>
>
>>
>>Thank you for all of your hard work and patience.
>>
>>Eric Abel
>>Ph.D. Student, M.I.T.
>>
>>
>
>
>
>--
>=======================================================================
>Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>  Center for Molecular Modeling   --   University of Pennsylvania
>Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
>tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
>=======================================================================
>If you make something idiot-proof, the universe creates a better idiot.
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum




From etabel at hotmail.com  Fri Sep  1 02:35:25 2006
From: etabel at hotmail.com (Eric Abel)
Date: Thu, 31 Aug 2006 20:35:25 -0400
Subject: [Pw_forum] phonon eigenvectors
In-Reply-To: <56DF6181-2682-471B-AC4B-ECCFB8613513@sissa.it>
Message-ID: <BAY105-F276E568AB68518905AD9F7D43C0@phx.gbl>

>From: Stefano Baroni <baroni at sissa.it>
>Reply-To: pw_forum at pwscf.org
>To: pw_forum at pwscf.org
>Subject: Re: [Pw_forum] phonon eigenvectors
>Date: Thu, 31 Aug 2006 22:28:04 +0200
>
>Dear Eric: I feel flattered (and a little guilty) for your taking me  so 
>seriously. Also, I may have had a role in starting the discussion  taken up 
>by Axel and Fernando which, to tell the truth, I do not  fully understand. 
>All in all, forgive my being (involuntarily!)  paternalistic, and let's 
>come to the real stuff!

No worries.  It's hard to portray tone over email.  I guess I assumed your 
tone from reading your responses to other postings (where the post-er was 
clearly not doing their homework) and assumed you thought the same of me...I 
just wanted to clear that up.

>
>>Question: What is the meaning of an eigenvector?
>>Answer:  An eigenvector tells how the atoms are displaced in the  
>>vibration.
>
>OK
>
>>Question: What is the imaginary part?
>>Answer: The imaginary part is a phase factor.
>
>Forgive my fussiness: its is *not* a phase factor. A non zero  imaginary 
>part is *due* to a non zero phase.
>
>>If one atom has a significant imaginary part with respect to the  rest, 
>>then then it's displacement in the vibration will be phase  shifted with 
>>respect to the others.
>
>OK - More precisely: a phase dfference between two different atomic  
>components of a same eigenvectors imply that the motions of the two  atoms 
>are out of phase (i.e. the velocities of the two may vanish at  different 
>times)
>
>>In the case of a completely imaginary eigenvector, the displacement  will 
>>be completely out of phase.
>
>This statement, instead, is meaningless. Ou of phase WITH RESPECT TO  WHAT?

Yeah, poorly chosed words here...I guess I redeem myself below.  I really 
did mean "out of phase with respect to an atom with say a completly real 
eigenvector".

>The only meaningful thing is the phase difference between the  eigenvector 
>components of two different atoms. An overall phase equal  for all the 
>atoms is simply equivalent to a shift of the origin of  time. CAN YOU SEE 
>THIS?

yes.

>
>Can you see the analogies with the well know statement that quantum  
>mechanical wavefunctions (a problem which is conceptually TOTALLY  
>different) are defined to within an overall phase factor?

again, yes.

>
>>Question:  If the imaginary part is a phase factor, then what does  it 
>>mean if all of the components are imaginary?
>>Answer:  First answer: nothing.  If all of the atoms are "out of  phase", 
>>then they are "in phase" with respect to eachother,  therefore, having a 
>>completely imaginary or completely real  eigenvector should be equivalent.
>
>VERY GOOD. YOU GOT IT!
>
>>Question:  Great.  If this is the case, then why does this  eigenvector 
>>come up imaginary when all of the other vectors come up  real?
>>Answer:  Hmmm.  That's a good one.  There must be some reason that  the 
>>code chooses an imaginary eigenvector for this mode...time to  get help on 
>>this one.  We are fresh out of answers.
>
>Very good, Erich. You came to the point. The answer is deceivingly  simple. 
>If the the phase is *physically* irrelevant, how could a  physically sound 
>mathematical algorithm choose it? Answer (deeper  than it may sound at 
>first): AT RANDOM! Actual algorithms may not be  really random, but it 
>wouldn't harm if they were!
>
>>And with this I come first to the pwscf discussion archive.  I  didn't 
>>find any discussion of imaginary eigenvectors with real  eigenvalues.
>
>Hey, hey, hey! Slow down! Real eigenvalues are a consequence of the  
>Hermiticity of the dynamical matrix and have nothing to do with the  
>eigenvector being or not real. A Hermitean matrix may or may not have  
>complex eigenvectors. If the matrix is real, the phases can alwayes  (*not* 
>"must": you see the difference?) in such a way that the  eigenvectors are 
>real. If the matrix is not real (still being  Hermitean), I do not know: 
>eigenvectors are in general complex (i.e.  no overall phase can be chosen  
>so as to make all of their components  real), but they may also be in some 
>particular instance real ...

OK, that makes sense.

>
>>I looked to the literature, with the same result.  There comes a  time 
>>when one asks himself questions to which he doesn't have the  answers, 
>>then it comes time to discuss with his peers.  With that I  come to you 
>>with my question:
>>
>>Why did the code "choose" to make this displacement imaginary.  Is  this 
>>simply an artifact of the matrix diagonalization,
>
>YES
>
>>or is there some physical implications to this?
>
>NO
>
>>Thank you for your time and patience.
>
>Thank you for challenging them! ;-)
>(I am not kidding: it's refreshing and instructive for us to help, no  less 
>that it is for you to be assisted - hopefully ;-)
>
>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

Amen to that...although, Openoffice does quite well at opening these :)

>Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>




From baroni at sissa.it  Fri Sep  1 08:57:32 2006
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 1 Sep 2006 08:57:32 +0200
Subject: [Pw_forum] PWscf can not find out symmetry operations!!!
In-Reply-To: <6398ac910608311454t4dfe1d70me517142c1318d4d5@mail.gmail.com>
References: <6398ac910608311454t4dfe1d70me517142c1318d4d5@mail.gmail.com>
Message-ID: <CDF687A8-6C71-40AA-AC61-5AD5AD083BA3@sissa.it>


On Aug 31, 2006, at 11:54 PM, Yingli Niu wrote:

> I only found this feature at Gamma point, for other points I will  
> test!

gamma is enough. what about non-acoustic phonons?

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 yanmingma at sohu.com  Fri Sep  1 09:17:19 2006
From: yanmingma at sohu.com (yanmingma at sohu.com)
Date: Fri, 1 Sep 2006 15:17:19 +0800 (CST)
Subject: [Pw_forum] PWscf can not find out symmetry operations!!!
Message-ID: <40257.1157095039039.JavaMail.postfix@mx81.mail.sohu.com>

Dear Stefano,<p> <p>I had a case of CuCl [PRB 67, 140301(R) (2003)]. When I increased the ecutrho parameter to a double value of its defualt with the Norm-conserving PPs, the calculation was improved greatly at X point. So, it does make great senses to increase the ecutrho when one stucks in the accuarcy of phonon frequency.<p> <p>Best Regards<p> <p>Yanming<p><p><p>-----  Original Message  -----<p>From: Stefano Baroni <p>To: pw_forum at pwscf.org <p>Subject: Re: [Pw_forum] PWscf can not find out symmetry operations!!!<p>Sent: Fri Sep 01 14:57:32 CST 2006<p><p>> <p>> On Aug 31, 2006, at 11:54 PM, Yingli Niu wrote:<p>> <p>> > I only found this feature at Gamma point, for other points I will  <p>> > test!<p>> <p>> gamma is enough. what about non-acoustic phonons?<p>> <p>> S.<p>> <p>> ---<p>> Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -  <p>> Trieste<p>> [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)<p>> <p>> Please, if possible, don't  send me MS Word or PowerPoint attachments<p>> Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html<p>> <p>> <p>> <p>
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From marcello.rosini at unimore.it  Fri Sep  1 09:32:38 2006
From: marcello.rosini at unimore.it (Marcello Rosini)
Date: Fri, 01 Sep 2006 09:32:38 +0200
Subject: [Pw_forum] charge is wrong
Message-ID: <44F7E216.6080605@unimore.it>

Hi,
I'm new to pwscf, my program stops this way:

>  WARNING: integrated charge=   299.29664324, expected=   300.00000000
>
> %%%%%%%%%%%%%%%%%%%%%%
>     from electrons : error #         1
>     charge is wrong
> %%%%%%%%%%%%%%%%%%%%%%

Can someone help me? I' didn't find the answer in the forum...
Thank you
Marcello

In the following my input file:

 &control
    calculation = 'scf'
    restart_mode='from_scratch',
    verbosity='default',
    prefix='c2.4x4',
    nstep=1,
    pseudo_dir = '../../../PSEUDO/',
    outdir='./'
    etot_conv_thr=1.0e-7,
    forc_conv_thr=1.0e-5,
 /
 &system
      ibrav=0,
      celldm(1)=10.65,
      nat=86,
      ntyp=3,
      ecutwfc =18.0,
 /
 &electrons
    electron_maxstep = 300,
    diagonalization='david'
    mixing_mode = 'plain'
    mixing_beta = 0.55
    conv_thr =  1.0d-8,
    startingpot='atomic',
 /
ATOMIC_SPECIES
 As   74.922    As.TM.UPF
 Ga   69.72     Ga_hamlu.fhi.UPF
 hn   1.008     hn.UPF
CELL_PARAMETERS
      2. 0. 0.
      0. 2. 0.
      0. 0. 4.5
ATOMIC_POSITIONS
Ga       0.250000000   0.250000000  -0.250000000 0 0 0
Ga       1.250000000   0.250000000  -0.250000000 0 0 0
Ga .....
......
K_POINTS automatic
4 4 1 1 1 0
EOF
-- 
------------------------------------------------------------------------
*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 2055292  -  fax +39 059 2055616
------------------------------------------------------------------------



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From giannozz at nest.sns.it  Fri Sep  1 11:21:39 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 1 Sep 2006 11:21:39 +0200
Subject: [Pw_forum] charge is wrong
In-Reply-To: <44F7E216.6080605@unimore.it>
References: <44F7E216.6080605@unimore.it>
Message-ID: <200609011121.39847.giannozz@nest.sns.it>

On Friday 01 September 2006 09:32, Marcello Rosini wrote:

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

> Can someone help me?

no, unless you provide a complete test job (including 
pseudopotentials) and specify the conditions under
which this happens

Paolo
-- 
Paolo Giannozzi             Phone:   +39/050-509876
DEMOCRITOS and SNS          Fax:     +39/050-563513 
Piazza dei Cavalieri 7      I-56126 Pisa, Italy


From giannozz at nest.sns.it  Fri Sep  1 11:43:18 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 1 Sep 2006 11:43:18 +0200
Subject: [Pw_forum] lambda convergence
In-Reply-To: <20060830140917.64925.qmail@web15213.mail.cnb.yahoo.com>
References: <20060830140917.64925.qmail@web15213.mail.cnb.yahoo.com>
Message-ID: <200609011143.18832.giannozz@nest.sns.it>

On Wednesday 30 August 2006 16:09, ?? ? wrote:

>      Before I calculate the electron-phonon coupling constant, I should
> judge the convergence of lambda with k-mesh and Gaussian broadening. But my
> results show that lambda at a choosed q point do not close to be a constant
> with increasing Gaussian broadening at different k-meshs, it continues to
> decrease

the large broadening limit is of no interest to you. You should rather check
the opposite limit and try to extrapolate a meaningful value for sigma->0

Paolo
-- 
Paolo Giannozzi             Phone:   +39/050-509876
DEMOCRITOS and SNS          Fax:     +39/050-563513 
Piazza dei Cavalieri 7      I-56126 Pisa, Italy


From eyvaz_isaev at yahoo.com  Fri Sep  1 12:26:30 2006
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 1 Sep 2006 03:26:30 -0700 (PDT)
Subject: [Pw_forum] charge is wrong
In-Reply-To: <44F7E216.6080605@unimore.it>
Message-ID: <20060901102630.22926.qmail@web60323.mail.yahoo.com>

Hi, 

Very similar question was discussed quite recently,
but for odd number of electrons. Now there are even.
It might be that your system is metallic, but you
consider it as a semicondictor. I.e. you did not
specify  "occupations" keyword.

Bests,
Eyvaz.


--- Marcello Rosini <marcello.rosini at unimore.it>
wrote:

> Hi,
> I'm new to pwscf, my program stops this way:
> 
> >  WARNING: integrated charge=   299.29664324,
> expected=   300.00000000
> >
> > %%%%%%%%%%%%%%%%%%%%%%
> >     from electrons : error #         1
> >     charge is wrong
> > %%%%%%%%%%%%%%%%%%%%%%
> 
> Can someone help me? I' didn't find the answer in
> the forum...
> Thank you
> Marcello
> 
> In the following my input file:
> 
>  &control
>     calculation = 'scf'
>     restart_mode='from_scratch',
>     verbosity='default',
>     prefix='c2.4x4',
>     nstep=1,
>     pseudo_dir = '../../../PSEUDO/',
>     outdir='./'
>     etot_conv_thr=1.0e-7,
>     forc_conv_thr=1.0e-5,
>  /
>  &system
>       ibrav=0,
>       celldm(1)=10.65,
>       nat=86,
>       ntyp=3,
>       ecutwfc =18.0,
>  /
>  &electrons
>     electron_maxstep = 300,
>     diagonalization='david'
>     mixing_mode = 'plain'
>     mixing_beta = 0.55
>     conv_thr =  1.0d-8,
>     startingpot='atomic',
>  /
> ATOMIC_SPECIES
>  As   74.922    As.TM.UPF
>  Ga   69.72     Ga_hamlu.fhi.UPF
>  hn   1.008     hn.UPF
> CELL_PARAMETERS
>       2. 0. 0.
>       0. 2. 0.
>       0. 0. 4.5
> ATOMIC_POSITIONS
> Ga       0.250000000   0.250000000  -0.250000000 0 0
> 0
> Ga       1.250000000   0.250000000  -0.250000000 0 0
> 0
> Ga .....
> ......
> K_POINTS automatic
> 4 4 1 1 1 0
> EOF
> -- 
>
------------------------------------------------------------------------
> *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 2055292  -  fax +39 059 2055616
>
------------------------------------------------------------------------
> 
> 
> 
> 


__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 


From marcello.rosini at unimore.it  Fri Sep  1 15:09:37 2006
From: marcello.rosini at unimore.it (Marcello Rosini)
Date: Fri, 01 Sep 2006 15:09:37 +0200
Subject: [Pw_forum] charge is wrong
Message-ID: <44F83111.6050407@unimore.it>

I put here
http://cdm.unimo.it/home/fisica/rosini.marcello/job.tar.gz
the complete job and the ppfiles
The job was running on the CINECA linux cluster using version 3.1 of
espresso
Thanks
-- 
------------------------------------------------------------------------
*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 2055292  -  fax +39 059 2055616
------------------------------------------------------------------------



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From yanchao.w at gmail.com  Fri Sep  1 17:28:23 2006
From: yanchao.w at gmail.com (Yanchao Wang)
Date: Fri, 1 Sep 2006 23:28:23 +0800
Subject: [Pw_forum] PWscf can not find out symmetry operations!!!
Message-ID: <67a2f1f30609010828r3ac8a1fcm9926f57675610013@mail.gmail.com>

On Sep 1, 2006, at 08:57:32 +0200, Prof. Baroni wrote:
> > I only found this feature at Gamma point, for other points I will
> > test!
>
> gamma is enough. what about non-acoustic phonons?

In  my case  increasing  ecutrho will decrease the acoustic phonon
frequences at Gamma point.
Non-acoustic phonons also decrease but not too much!
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From niuyingli at gmail.com  Fri Sep  1 17:35:49 2006
From: niuyingli at gmail.com (Yingli Niu)
Date: Fri, 1 Sep 2006 23:35:49 +0800
Subject: [Pw_forum] PWscf can not find out symmetry operations!!!
In-Reply-To: <67a2f1f30609010828r3ac8a1fcm9926f57675610013@mail.gmail.com>
References: <67a2f1f30609010828r3ac8a1fcm9926f57675610013@mail.gmail.com>
Message-ID: <6398ac910609010835o39ec4fe3laea8aa96a896cd02@mail.gmail.com>

My case is as the same as Wang's.

On 9/1/06, Yanchao Wang <yanchao.w at gmail.com> wrote:
> On Sep 1, 2006, at 08:57:32 +0200, Prof. Baroni wrote:
> > > I only found this feature at Gamma point, for other points I will
> > > test!
> >
> > gamma is enough. what about non-acoustic phonons?
>
> In  my case  increasing  ecutrho will decrease the acoustic phonon
> frequences at Gamma point.
> Non-acoustic phonons also decrease but not too much!
>
>


From akohlmey at cmm.chem.upenn.edu  Fri Sep  1 17:40:23 2006
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Fri, 1 Sep 2006 11:40:23 -0400
Subject: [Pw_forum] PWscf can not find out symmetry operations!!!
In-Reply-To: <6398ac910609010835o39ec4fe3laea8aa96a896cd02@mail.gmail.com>
References: <67a2f1f30609010828r3ac8a1fcm9926f57675610013@mail.gmail.com>
	 <6398ac910609010835o39ec4fe3laea8aa96a896cd02@mail.gmail.com>
Message-ID: <7b6913e90609010840i21e275fek64fbc4ca5a491cc1@mail.gmail.com>

On 9/1/06, Yingli Niu <niuyingli at gmail.com> wrote:
> My case is as the same as Wang's.

out of curiosity. how much is that related to the _wavefunction_
cutoff? 70ry to the quoted systems seems to be a bit on the
low side for norm-conserving pseudopotentials to me (of course
that will increase the default density cutoff automatically as well).

regards,
    axel.

>
> On 9/1/06, Yanchao Wang <yanchao.w at gmail.com> wrote:
> > On Sep 1, 2006, at 08:57:32 +0200, Prof. Baroni wrote:
> > > > I only found this feature at Gamma point, for other points I will
> > > > test!
> > >
> > > gamma is enough. what about non-acoustic phonons?
> >
> > In  my case  increasing  ecutrho will decrease the acoustic phonon
> > frequences at Gamma point.
> > Non-acoustic phonons also decrease but not too much!
> >
> >
> _______________________________________________
> 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 naromero at gmail.com  Fri Sep  1 18:12:54 2006
From: naromero at gmail.com (Nichols A. Romero)
Date: Fri, 1 Sep 2006 12:12:54 -0400
Subject: [Pw_forum] publishing in JAP
Message-ID: <6ac064b60609010912r46c8d967le6661ccd893875bc@mail.gmail.com>

Dear Colleagues,

This is not a PWSCF question per se, so please forgive me.
I usually publish my work in Phys. Rev. journals, but one recent work ended
up in the Journal of Applied Physics (JAP). They have strict formatting
guidelines
which are different from Phys. Rev., but they accept manuscripts in RevTeX.
However,
there does not seem to be a RevTeX style file that formats according to
there JAP
guidelines.

Does anyone have any experience with this? Or will I have to resort to using
Microsoft Word?

Bests,

-- 
Nichols A. Romero, Ph.D.
1613 Denise Dr. Apt. D
Forest Hill, MD 21050
443-567-8328 (C)
410-306-0709 (O)
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From baroni at sissa.it  Sat Sep  2 08:33:46 2006
From: baroni at sissa.it (Stefano Baroni)
Date: Sat, 2 Sep 2006 08:33:46 +0200
Subject: [Pw_forum] publishing in JAP
In-Reply-To: <6ac064b60609010912r46c8d967le6661ccd893875bc@mail.gmail.com>
References: <6ac064b60609010912r46c8d967le6661ccd893875bc@mail.gmail.com>
Message-ID: <29C036DE-BDC5-40AE-BBB0-55FE15396BED@sissa.it>

Send it prb-style and let 'em change it if they do not like ...
S.

On Sep 1, 2006, at 6:12 PM, Nichols A. Romero wrote:

> Dear Colleagues,
>
> This is not a PWSCF question per se, so please forgive me.
> I usually publish my work in Phys. Rev. journals, but one recent  
> work ended
> up in the Journal of Applied Physics (JAP). They have strict  
> formatting guidelines
> which are different from Phys. Rev., but they accept manuscripts in  
> RevTeX. However,
> there does not seem to be a RevTeX style file that formats  
> according to there JAP
> guidelines.
>
> Does anyone have any experience with this? Or will I have to resort  
> to using
> Microsoft Word?
>
> Bests,
>
> -- 
> Nichols A. Romero, Ph.D.
> 1613 Denise Dr. Apt. D
> Forest Hill, MD 21050
> 443-567-8328 (C)
> 410-306-0709 (O)
>

---
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 yuhailin_79 at msn.com  Sun Sep  3 13:45:08 2006
From: yuhailin_79 at msn.com (hailin yu)
Date: Sun, 03 Sep 2006 19:45:08 +0800
Subject: [Pw_forum] help:free energy under pressure
In-Reply-To: <20060829134001.33829.qmail@web58309.mail.re3.yahoo.com>
Message-ID: <BAY106-F217DB33B52C06CBD86FF4093320@phx.gbl>

Dear all:
       I want to reserach the free energy of alpha-Sn under different 
external pressure. I can calculate the free energy at P=0, but I don't sure 
it is same under non-zero pressure. Can you tell me? Thanks in advance!

Thanks a lot!
yuhailin

_________________________________________________________________
FREE pop-up blocking with the new MSN Toolbar - get it now! 
http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/



From baroni at sissa.it  Sun Sep  3 18:32:47 2006
From: baroni at sissa.it (Stefano Baroni)
Date: Sun, 3 Sep 2006 18:32:47 +0200
Subject: [Pw_forum] help:free energy under pressure
In-Reply-To: <BAY106-F217DB33B52C06CBD86FF4093320@phx.gbl>
References: <BAY106-F217DB33B52C06CBD86FF4093320@phx.gbl>
Message-ID: <3E4E1B7C-BA28-4699-9318-E26FA0A58F53@sissa.it>

On Sep 3, 2006, at 1:45 PM, hailin yu wrote:

> Dear all:
>       I want to reserach the free energy of alpha-Sn under  
> different external pressure. I can calculate the free energy at  
> P=0, but I don't sure it is same under non-zero pressure.

Sure, it is not, even though your statement is a bit confusing (or,  
at least, it denotes some degree of confusion)

What you probably calculate (what is easiest to calculate from the  
ingredients you have) is the Helmholtz free energy, which is the  
thermodinamical potential function of the volume and temperature, F=E- 
TS. The volume derivative of F wrt V is the pressure: P = {\partial F  
over \partial V}. The thermodynamical potential whose independent  
variables are the pressure (instead of the volume) and the  
temperature is the Gibbs free energy, G=E+PV-TS=F+PV. In order to  
calculate G as a function of pressure and temperature, you usually  
have to express V as a function of P by inverting the relation: P =  
{\partial F over \partial V}, which gives P as a function of V and T.  
In practice, this is done numerically.

I would recommend that you take a few hours studying the relevant  
chapter of any textbook of elementary statistical mechanics, such as  
Landau's, Chandler's, or your favorite textbook. If you do not have a  
text in statistical mechanics handy, you may find the relevant  
definitions and formulas by googling "helmholtz gibbs free energy"

hope this helps

Stefano B.



> Can you tell me? Thanks in advance!
>
> Thanks a lot!
> yuhailin
>
> _________________________________________________________________
> FREE pop-up blocking with the new MSN Toolbar - get it now! http:// 
> toolbar.msn.click-url.com/go/onm00200415ave/direct/01/
>
> _______________________________________________
> 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 baroni at sissa.it  Sun Sep  3 18:35:37 2006
From: baroni at sissa.it (Stefano Baroni)
Date: Sun, 3 Sep 2006 18:35:37 +0200
Subject: [Pw_forum] help:free energy under pressure
In-Reply-To: <3E4E1B7C-BA28-4699-9318-E26FA0A58F53@sissa.it>
References: <BAY106-F217DB33B52C06CBD86FF4093320@phx.gbl> <3E4E1B7C-BA28-4699-9318-E26FA0A58F53@sissa.it>
Message-ID: <0CF74EB8-8077-4353-B6D7-C0737C182FDA@sissa.it>

of course, it was:

> P = - {\partial F over \partial V}

SB

---
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 ongphuongvu at yahoo.com  Mon Sep  4 06:40:47 2006
From: ongphuongvu at yahoo.com (vu ongphuong)
Date: Sun, 3 Sep 2006 21:40:47 -0700 (PDT)
Subject: [Pw_forum] I need help
Message-ID: <20060904044047.26653.qmail@web50613.mail.yahoo.com>

Dear users,
   
  In the paper A. Antons et al., Phys. Rev. B 71, 024102 (2005), A. Antons used PWSCF for his caculation.  I want to contact with him via email to ask him some calculation problems. Howerver his email adsress[a.antons at fz-juelich.de] given in the paper is no longer reachable.
  Any body know A. Anton's current-in-use email address, please help me contact with him by sending me the email.
   
  Thank you very much,
  ------------------------------------------------------------------------------------------ 
Ong Phuong Vu 
Semiconductor and Thin Films Devices Lab 
Department of Materials Sciences and Engineering 
SungKyunKwan University 
300 Chunchundong, Jangan gu 
Suwon 440 - 746, South Korea. 
Labroom: 25137 
Labpage: http://web.skku.edu/~std/ 
  Tel: 031-299-4743
Email address: ongphuongvu at yahoo.com
  -------------------------------------------------------------------------------------------

 			
---------------------------------
Get your own web address for just $1.99/1st yr. We'll help. Yahoo! Small Business.
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From niuyingli at gmail.com  Mon Sep  4 07:03:53 2006
From: niuyingli at gmail.com (Yingli Niu)
Date: Mon, 4 Sep 2006 13:03:53 +0800
Subject: [Pw_forum] Force contant matrix elements
Message-ID: <6398ac910609032203h2a2bcad4i549439847c268820@mail.gmail.com>

Dear all,
Excuse me for a simple question.
As we know that force contant matrix elements are stored in the case.fc file.
FC(j1,j2,atom1,atom2,m1,m2,m3)
Question:
j1,j2 is along x,y,z(Cartesian coordinates)
or
j1,j2 is along a,b,c(Crystal coordinates)
Which one is right?


From giannozz at nest.sns.it  Mon Sep  4 10:55:23 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 4 Sep 2006 10:55:23 +0200
Subject: [Pw_forum] Force contant matrix elements
In-Reply-To: <6398ac910609032203h2a2bcad4i549439847c268820@mail.gmail.com>
References: <6398ac910609032203h2a2bcad4i549439847c268820@mail.gmail.com>
Message-ID: <200609041055.23865.giannozz@nest.sns.it>

On Monday 04 September 2006 07:03, Yingli Niu wrote:
>
> As we know that force contant matrix elements are stored in the case.
> fc file. FC(j1,j2,atom1,atom2,m1,m2,m3)
> Question:
> j1,j2 is along x,y,z(Cartesian coordinates)
> or
> j1,j2 is along a,b,c(Crystal coordinates)
> Which one is right?

cartesian, if I remember correctly.

P.
-- 
Paolo Giannozzi             Phone:   +39/050-509876
DEMOCRITOS and SNS          Fax:     +39/050-563513 
Piazza dei Cavalieri 7      I-56126 Pisa, Italy


From niuyingli at gmail.com  Mon Sep  4 12:29:36 2006
From: niuyingli at gmail.com (Yingli Niu)
Date: Mon, 4 Sep 2006 18:29:36 +0800
Subject: [Pw_forum] Force contant matrix elements
In-Reply-To: <200609041055.23865.giannozz@nest.sns.it>
References: <6398ac910609032203h2a2bcad4i549439847c268820@mail.gmail.com>
	 <200609041055.23865.giannozz@nest.sns.it>
Message-ID: <6398ac910609040329q2b930430r8117b10802b0a9fb@mail.gmail.com>

Thank you!

On 9/4/06, Paolo Giannozzi <giannozz at nest.sns.it> wrote:
> On Monday 04 September 2006 07:03, Yingli Niu wrote:
> >
> > As we know that force contant matrix elements are stored in the case.
> > fc file. FC(j1,j2,atom1,atom2,m1,m2,m3)
> > Question:
> > j1,j2 is along x,y,z(Cartesian coordinates)
> > or
> > j1,j2 is along a,b,c(Crystal coordinates)
> > Which one is right?
>
> cartesian, if I remember correctly.
>
> P.
> --
> Paolo Giannozzi             Phone:   +39/050-509876
> DEMOCRITOS and SNS          Fax:     +39/050-563513
> Piazza dei Cavalieri 7      I-56126 Pisa, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


-- 
Yingli Niu


From vdiep at ictp.it  Mon Sep  4 15:20:59 2006
From: vdiep at ictp.it (Diep Quang Vinh)
Date: Mon, 4 Sep 2006 15:20:59 +0200 (CEST)
Subject: [Pw_forum] Distance Constraint relaxation and SIC in QE 3.1.1 (FPMD)
In-Reply-To: <44EE39A7.4090102@mit.edu>
References: <8c9dc66c0608240629m4b2e482ev13ae2324d29d0e96@mail.gmail.com>
    <20060824140315.9721.qmail@xuxa.iecc.com> <44EE39A7.4090102@mit.edu>
Message-ID: <41044.140.105.16.2.1157376059.squirrel@webmail2.ictp.trieste.it>

Dear all,
I am using FPMD and my problems are:

1. I need include the Self-Interaction-Correction (SIC) in the calculation. Actually, I
did it in the version 3.0 and the results are good.
2. Now i want to do some constraint (distance) relaxations (with SIC correction). I
think i should change to version 3.1.1??

Here are my run:


If i use the version 3.1 of QE the code give the the following error:

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from  module setup  : error #         1
      Stress is not yet implemented with SIC
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

ERROR: 0031-250  task 0: Terminated

It seems to me that the code don't understand the SIC. But if I use the previous version
of QE like 3.0 I meet the following error. In this case the code don't understant the
constrain.


 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from init_constraint : error #         1
     constrain type not implemented
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

ERROR: 0031-250  task 0: Terminated

Both of them have the same input like the following:


-------------
&CONTROL
  calculation = 'fpmd',
 title = 'resconstructed and ee',
  prefix='RECON-EE-CON'
  ndr = 60,
  ndw = 61,
  restart_mode = 'restart'
  nstep  = 200
  iprint = 20
  isave  = 20
  tstress = .TRUE.,
  tprnfor = .TRUE.,
  dt    = 4.d0
  etot_conv_thr = 1.d-5,
  pseudo_dir= '/sfs/sanfs/home/userictp/ictpcm01/UPF/'
/

&SYSTEM
    ibrav=  14,
     celldm(1) = 16.972000,
    celldm(2) = 1.,
    celldm(3) = 4.9733070,
    celldm(4) = 0.0,
    celldm(5) = 0.0,
    celldm(6) = -0.5,
    nat=  101,
    ntyp= 4,
    nspin = 2,
    ecutwfc =80.0,
    ecfixed = 68.0,
    q2sigma = 8.0,
    nbnd=145,
    nelec=289,
    nelup = 145.d0,
    neldw = 144.d0,
    sic = 'sic_mac',
    sic_epsilon = 1.d0,
    sic_alpha = 1.d0,
    force_pairing = .TRUE.,
    xc_type = 'BLYP',
/

&ELECTRONS
  emass = 200.d0,
  emass_cutoff = 2.5d0,
  orthogonalization = 'ortho',
  ortho_eps = 5.d-8,
  ortho_max = 28,
  electron_dynamics = 'damp'
  electron_damping=0.1d0
  electron_velocities = 'default'
  electron_temperature = 'not_controlled',
/

&IONS
  ion_dynamics = 'sd'
  !on_damping=0.2d0
  ion_velocities='zero'
  ion_positions='default'
  !ion_temperature='nose'
  !fnosep=30.d0
  !tempw=150.d0
   ion_radius(1) = 0.8d0,
  ion_radius(2) = 0.8d0,
  ion_radius(3) = 0.8d0,
  ion_radius(4) = 0.8d0,
  sic_rloc = 1.d0,

/

&CELL
  cell_dynamics = 'none',
/

ATOMIC_SPECIES
Cl  35.4d0 Cl.blyp-mt.UPF
 O  16.0d0 O.blyp-mt.UPF
 C  12.0d0 C.blyp-mt.UPF
 H   1.0d0 H.blyp-mt.UPF

ATOMIC_POSITIONS (bohr)
Cl      2.61430   7.78152 -34.88870  1 1 1 1
Cl      3.35627   4.05314 -31.36570  1 1 1 1
Cl      6.74509   3.51397 -35.12750  1 1 1 1
Cl      7.44480   8.10866 -32.96470  1 1 1 1
C       5.03399   5.90311 -33.57770  1 1 1 1
H      15.45910  -3.29036 -22.36830  1 1 1 1
...................
CONSTRAINTS
1
'distance' 1 5

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

If you ommit the these last lines(CONSTRAINTS), The version 3.0 work very well (no error
at all) but not the version 3.1.1.


So it seems to me that the version 3.1.1 don't incoporate the SIC correction ? Am i right?


Thank you very much

Best regards.

Vinh
















From vdiep at ictp.it  Mon Sep  4 15:37:38 2006
From: vdiep at ictp.it (Diep Quang Vinh)
Date: Mon, 4 Sep 2006 15:37:38 +0200 (CEST)
Subject: [Pw_forum] [Fwd: Re: Contraint relaxation and SIC in version 3.1.1]
Message-ID: <47457.140.105.16.2.1157377058.squirrel@webmail2.ictp.trieste.it>

Dear all,

The following suggestions (set tstress=.false.) fixed my problems

Thank you very much

Vinh

----------------------------------- Original Message -----------------------------------
Subject: Re: Contraint relaxation and SIC in version 3.1.1
From:    "Carlo Cavazzoni" <c.cavazzoni at cineca.it>
Date:    Mon, September 4, 2006 3:26 pm
To:      "Diep Quang Vinh" <vdiep at ictp.it>
----------------------------------------------------------------------------------------

dear Vinh

let's try to fix 3.1.1.
First of all you have to exclude the computation of stress:
tstress = .false.

since stress with SIC has not been implemented, neither in the 3.0 the stress was
implemented, it was siply wrong, now we have added the message. Then you have to check
the type of costraint.
Distance should be implemented, then there is an error in the input or a bug in the code.

In conclusion try first 3.1.1 without tstress,
then we will check for the constraint type

ciao
carlo

----- Original Message -----
From: "Diep Quang Vinh" <vdiep at ictp.it>
To: "Carlo Cavazzoni" <c.cavazzoni at cineca.it>
Sent: Monday, September 04, 2006 3:18 PM
Subject: Contraint relaxation and SIC in version 3.1.1


> Dear all,
> My problems are:
>
> 1. I need include the Self-Interaction-Correction (SIC) in the calculation. Actually,
I did it in the version 3.0 and the results are good.
> 2. Now i want to do some constraint (distance) relaxations (with SIC correction). I
think i should change to version 3.1.1??
>
> Here are my run:
>
>
> If i use the version 3.1 of QE the code give the the following error:
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     from  module setup  : error #         1
>      Stress is not yet implemented with SIC
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> ERROR: 0031-250  task 0: Terminated
>
> It seems to me that the code don't understand the SIC. But if I use the previous
version of QE like 3.0 I meet the following error. In this case the code don't
understant the constrain.
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     from init_constraint : error #         1
>     constrain type not implemented
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> ERROR: 0031-250  task 0: Terminated
>
> Both of them have the same input like the following:
>
>
> -------------
> &CONTROL
>  calculation = 'fpmd',
> title = 'resconstructed and ee',
>  prefix='RECON-EE-CON'
>  ndr = 60,
>  ndw = 61,
>  restart_mode = 'restart'
>  nstep  = 200
>  iprint = 20
>  isave  = 20
>  tstress = .TRUE.,
>  tprnfor = .TRUE.,
>  dt    = 4.d0
>  etot_conv_thr = 1.d-5,
>  pseudo_dir= '/sfs/sanfs/home/userictp/ictpcm01/UPF/'
> /
>
> &SYSTEM
>    ibrav=  14,
>     celldm(1) = 16.972000,
>    celldm(2) = 1.,
>    celldm(3) = 4.9733070,
>    celldm(4) = 0.0,
>    celldm(5) = 0.0,
>    celldm(6) = -0.5,
>    nat=  101,
>    ntyp= 4,
>    nspin = 2,
>    ecutwfc =80.0,
>    ecfixed = 68.0,
>    q2sigma = 8.0,
>    nbnd=145,
>    nelec=289,
>    nelup = 145.d0,
>    neldw = 144.d0,
>    sic = 'sic_mac',
>    sic_epsilon = 1.d0,
>    sic_alpha = 1.d0,
>    force_pairing = .TRUE.,
>    xc_type = 'BLYP',
> /
>
> &ELECTRONS
>  emass = 200.d0,
>  emass_cutoff = 2.5d0,
>  orthogonalization = 'ortho',
>  ortho_eps = 5.d-8,
>  ortho_max = 28,
>  electron_dynamics = 'damp'
>  electron_damping=0.1d0
>  electron_velocities = 'default'
>  electron_temperature = 'not_controlled',
> /
>
> &IONS
>  ion_dynamics = 'sd'
>  !on_damping=0.2d0
>  ion_velocities='zero'
>  ion_positions='default'
>  !ion_temperature='nose'
>  !fnosep=30.d0
>  !tempw=150.d0
>   ion_radius(1) = 0.8d0,
>  ion_radius(2) = 0.8d0,
>  ion_radius(3) = 0.8d0,
>  ion_radius(4) = 0.8d0,
>  sic_rloc = 1.d0,
>
> /
>
> &CELL
>  cell_dynamics = 'none',
> /
>
> ATOMIC_SPECIES
> Cl  35.4d0 Cl.blyp-mt.UPF
> O  16.0d0 O.blyp-mt.UPF
> C  12.0d0 C.blyp-mt.UPF
> H   1.0d0 H.blyp-mt.UPF
>
> ATOMIC_POSITIONS (bohr)
> Cl      2.61430   7.78152 -34.88870  1 1 1 1
> Cl      3.35627   4.05314 -31.36570  1 1 1 1
> Cl      6.74509   3.51397 -35.12750  1 1 1 1
> Cl      7.44480   8.10866 -32.96470  1 1 1 1
> C       5.03399   5.90311 -33.57770  1 1 1 1
> H      15.45910  -3.29036 -22.36830  1 1 1 1
> ...................
> CONSTRAINTS
> 1
> 'distance' 1 5
>
> --------------
>
> If you ommit the these last lines(CONSTRAINTS), The version 3.0 work very well (no
error at all) but not the version 3.1.1.
>
>
> So it seems to me that the version 3.1.1 don't incoporate the SIC correction ? Am i
right?
>
>
> Thank you very much
>
> Best regards.
>
> Vinh
>
>
>
>
>
>
>
>
>
>
>
>







From yuhailin_79 at msn.com  Mon Sep  4 16:00:19 2006
From: yuhailin_79 at msn.com (hailin yu)
Date: Mon, 04 Sep 2006 22:00:19 +0800
Subject: [Pw_forum] help:Sn phase transition
In-Reply-To: <0CF74EB8-8077-4353-B6D7-C0737C182FDA@sissa.it>
Message-ID: <BAY106-F271CF927306D0FEACA4E1293330@phx.gbl>

Dear Stefano Baroni :
       Thank you for your reply.
       I have another question want to ask you. Can you tell me? Thank you 
in advance!
       In your paper ??PRB??57??10421??1998??????you have discussed the 
phase transition of alpha-Sn to beta-Sn by compared their free energy. Now, 
I want to research the effect of pressure on the transition temperature. So 
I want to know, it is feasible to research the effect of pressure on the 
transition temperature by compare the free energy  under different pressure?
    Thanks a lot!
yuhailin

_________________________________________________________________
FREE pop-up blocking with the new MSN Toolbar - get it now! 
http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/



From baroni at sissa.it  Mon Sep  4 18:09:55 2006
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 4 Sep 2006 18:09:55 +0200
Subject: [Pw_forum] help:Sn phase transition
In-Reply-To: <BAY106-F271CF927306D0FEACA4E1293330@phx.gbl>
References: <BAY106-F271CF927306D0FEACA4E1293330@phx.gbl>
Message-ID: <726A2BE2-D0DC-485A-95A6-420BC9D682FD@sissa.it>

Yes - SB

On Sep 4, 2006, at 4:00 PM, hailin yu wrote:

> Dear Stefano Baroni :
>       Thank you for your reply.
>       I have another question want to ask you. Can you tell me?  
> Thank you in advance!
>       In your paper ??PRB??57??10421??1998??????you have discussed  
> the phase transition of alpha-Sn to beta-Sn by compared their free  
> energy. Now, I want to research the effect of pressure on the  
> transition temperature. So I want to know, it is feasible to  
> research the effect of pressure on the transition temperature by  
> compare the free energy  under different pressure?
>    Thanks a lot!
> yuhailin
>
> _________________________________________________________________
> FREE pop-up blocking with the new MSN Toolbar - get it now! http:// 
> toolbar.msn.click-url.com/go/onm00200415ave/direct/01/
>
> _______________________________________________
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> 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
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From ssaarti at jncasr.ac.in  Tue Sep  5 16:11:21 2006
From: ssaarti at jncasr.ac.in (aarti srirangarajan)
Date: Tue, 5 Sep 2006 19:41:21 +0530 (IST)
Subject: [Pw_forum] help needed with projwfc.x
Message-ID: <57185.202.41.111.151.1157465481.squirrel@202.41.111.151>

Dear PWSCF developers,


Could anyone please explain the output of the program projwfc.x?
My question is how the values for m = 1,2,3,4,5 are assigned ( m should be
-2 to +2) ? And in the output files for the PDOS for d-orbitals, what is
the sequence of the data listed in it.(in terms of dxy,dxz,dyz etc.).
Thanking you in anticipation
Aarti
TSU,JNCASR


From giannozz at nest.sns.it  Tue Sep  5 19:21:01 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 5 Sep 2006 19:21:01 +0200
Subject: [Pw_forum] help needed with projwfc.x
In-Reply-To: <57185.202.41.111.151.1157465481.squirrel@202.41.111.151>
References: <57185.202.41.111.151.1157465481.squirrel@202.41.111.151>
Message-ID: <200609051921.01232.giannozz@nest.sns.it>

On Tuesday 05 September 2006 16:11, aarti srirangarajan wrote:

> Could anyone please explain the output of the program projwfc.x?
> My question is how the values for m = 1,2,3,4,5 are assigned ( m should be
> -2 to +2) ? And in the output files for the PDOS for d-orbitals, what is
> the sequence of the data listed in it.(in terms of dxy,dxz,dyz etc.).

I am not sure I can "explain", but I can point out where to look for
explanations: the index "m" runs on real combinations of spherical 
harmonics, as defined in flib/ylmr2.f90 

Paolo
-- 
Paolo Giannozzi             Phone:   +39/050-509876
DEMOCRITOS and SNS          Fax:     +39/050-563513 
Piazza dei Cavalieri 7      I-56126 Pisa, Italy


From likedew at phys.ksu.edu  Wed Sep  6 07:27:30 2006
From: likedew at phys.ksu.edu (Hong, SamPyo)
Date: Wed, 6 Sep 2006 00:27:30 -0500
Subject: [Pw_forum] frequency of NO molecule
Message-ID: <F0712C28C5E30740A5F81252A97E6F32E5F347@isis.phys.ksu.edu>

Hello, everyone,

I have a supercell of 32 atoms, 2 of which are a NO molecule adsorbed on
a metallic surface of 30 atoms.
I want to calculate frequencies of adsorbed NO molecule only, not those
for substrate atoms.

How can I do this?


My sincere thanks in advance.

 Sampyo Hong
______________________________
 Research Associate
 Department of Physics, Kansas State University, Manhattan, KS 66506,
USA.
 E-Mail: likedew at phys.ksu.edu   WEB:
http://www.phys.ksu.edu/personal/likedew 
 Phone: +1-785-532-1642           FAX:   +1-785-532-6806
 Favorite quotation: 
 "God demonstrates his own love for us in this: While we were still
sinners, Christ died for us."
_______________________________
 


From rui_zhi_zhang at yahoo.com  Wed Sep  6 11:09:06 2006
From: rui_zhi_zhang at yahoo.com (ruizhi zhang)
Date: Wed, 6 Sep 2006 02:09:06 -0700 (PDT)
Subject: [Pw_forum] Re: how to get Interatomic force constants
Message-ID: <20060906090906.42157.qmail@web39813.mail.mud.yahoo.com>

Yes, I am sure I correctly followed example 06. But even in example06, I donot know how to get IFC's from the results. 
  The README in example06 says the IFC's is contained in the file named  alas444.fc . But there are only three matrix. i.e.
  
 T
     13.7439584      0.0000000      0.0000000
      0.0000000     13.7439584      0.0000000
      0.0000000      0.0000000     13.7439584
    1
      2.5582108      0.0000000      0.0000000
      0.0000000      2.5582108      0.0000000
      0.0000000      0.0000000      2.5582108
    2
     -2.5582108      0.0000000      0.0000000
      0.0000000     -2.5582108      0.0000000
      0.0000000      0.0000000     -2.5582108
  
  and the sum of matrix1 and matrix 2 is zero. It looks like they are effective charges.
  However, the README says " The output file containing the force constants in a format suitable    for program matdyn.x is alas444.fc." 
  So can we know IFC's from these matrix? If they are not IFC matrix.
   

 		
---------------------------------
Do you Yahoo!?
 Get on board. You're invited to try the new Yahoo! Mail.
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From jibiaoli at gmail.com  Wed Sep  6 11:56:06 2006
From: jibiaoli at gmail.com (Clark Lee)
Date: Wed, 6 Sep 2006 17:56:06 +0800
Subject: [Pw_forum] frequency of NO molecule
In-Reply-To: <F0712C28C5E30740A5F81252A97E6F32E5F347@isis.phys.ksu.edu>
References: <F0712C28C5E30740A5F81252A97E6F32E5F347@isis.phys.ksu.edu>
Message-ID: <b8b82da20609060256g7e9380b6k418507773649f198@mail.gmail.com>

Yes ! I want to know any methods for solving this problem too. Anyone know
the answer?

On 9/6/06, Hong, SamPyo <likedew at phys.ksu.edu> wrote:
>
>
> Hello, everyone,
>
> I have a supercell of 32 atoms, 2 of which are a NO molecule adsorbed on
> a metallic surface of 30 atoms.
> I want to calculate frequencies of adsorbed NO molecule only, not those
> for substrate atoms.
>
> How can I do this?
>
>
> My sincere thanks in advance.
>
> Sampyo Hong
> ______________________________
> Research Associate
> Department of Physics, Kansas State University, Manhattan, KS 66506,
> USA.
> E-Mail: likedew at phys.ksu.edu   WEB:
> http://www.phys.ksu.edu/personal/likedew
> Phone: +1-785-532-1642           FAX:   +1-785-532-6806
> Favorite quotation:
> "God demonstrates his own love for us in this: While we were still
> sinners, Christ died for us."
> _______________________________
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Standing on the shoulders of Newton
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From giannozz at nest.sns.it  Wed Sep  6 12:48:43 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 6 Sep 2006 12:48:43 +0200
Subject: [Pw_forum] Re: how to get Interatomic force constants
In-Reply-To: <20060906090906.42157.qmail@web39813.mail.mud.yahoo.com>
References: <20060906090906.42157.qmail@web39813.mail.mud.yahoo.com>
Message-ID: <200609061248.43562.giannozz@nest.sns.it>

On Wednesday 06 September 2006 11:09, ruizhi zhang wrote:

> [...] I do not know how to get IFC's from the results. 
> The README in example06 says the IFC's is contained
> in the file named  alas444.fc .
> But there are only three matrix. i.e. [...] 

the matrix elements of the IFC are written after these matrices 
(respectively the dielectric tensor and the effective charges). 
The format is for internal usage of the code matdyn.x, may
change at any time, is undocumented and will ever be, unless
somebody volunteers to document it
-- 
Paolo Giannozzi             Phone:   +39/050-509876
DEMOCRITOS and SNS          Fax:     +39/050-563513 
Piazza dei Cavalieri 7      I-56126 Pisa, Italy


From ezadshojaee at hotmail.com  Wed Sep  6 13:15:05 2006
From: ezadshojaee at hotmail.com (Ezad Shojaee)
Date: Wed, 06 Sep 2006 11:15:05 +0000
Subject: [Pw_forum] about phonon calculation
Message-ID: <BAY101-F19EA93BA1F8B13D799EAABAA310@phx.gbl>

hi
i wonder if anyone could tell me where can i find a lecture about 
"representations"  ( for the use in phonon calculation ?

_________________________________________________________________
FREE pop-up blocking with the new MSN Toolbar - get it now! 
http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/



From chen_shao_hua197 at yahoo.com.tw  Wed Sep  6 14:41:14 2006
From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=)
Date: Wed, 6 Sep 2006 20:41:14 +0800 (CST)
Subject: [Pw_forum] where to get correct Bi Norm-Conserving PP ?
Message-ID: <20060906124114.42794.qmail@web18208.mail.tpe.yahoo.com>

Dear all,
Does anyone know where to get correct Bi
Norm-Conserving PP ?
Thanks

Best Regards
Max Chen

___________________________________________________ 
 ??????? ? ???????????????? 
 http://messenger.yahoo.com.tw/


From akohlmey at cmm.chem.upenn.edu  Wed Sep  6 16:34:41 2006
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 6 Sep 2006 10:34:41 -0400
Subject: [Pw_forum] frequency of NO molecule
In-Reply-To: <b8b82da20609060256g7e9380b6k418507773649f198@mail.gmail.com>
References: <F0712C28C5E30740A5F81252A97E6F32E5F347@isis.phys.ksu.edu>
	 <b8b82da20609060256g7e9380b6k418507773649f198@mail.gmail.com>
Message-ID: <7b6913e90609060734h319b535i51a4b95238ee4e12@mail.gmail.com>

On 9/6/06, Clark Lee <jibiaoli at gmail.com> wrote:
> Yes ! I want to know any methods for solving this problem too. Anyone know
> the answer?

well, you basically just have to do the displacement perturbation
only for the atoms you are interested in. i have done this with a
different code (CPMD), which cannot handle metals well for that
kind of calculations, but have a look at 'nat_todo' in Doc/INPUT_PH
looks quite similar to me.

if i am guessing wronge here, feel free to implement that feature
into the code (and submit it for inclusion into the next release).
it should be pretty straightforward...

cheers,
   axel.

>
>
> On 9/6/06, Hong, SamPyo < likedew at phys.ksu.edu> wrote:
> >
> > Hello, everyone,
> >
> > I have a supercell of 32 atoms, 2 of which are a NO molecule adsorbed on
> > a metallic surface of 30 atoms.
> > I want to calculate frequencies of adsorbed NO molecule only, not those
> > for substrate atoms.
> >
> > How can I do this?
> >
> >
> > My sincere thanks in advance.
> >
> > Sampyo Hong
> > ______________________________
> > Research Associate
> > Department of Physics, Kansas State University, Manhattan, KS 66506,
> > USA.
> > E-Mail: likedew at phys.ksu.edu   WEB:
> > http://www.phys.ksu.edu/personal/likedew
> > Phone: +1-785-532-1642           FAX:   +1-785-532-6806
> > Favorite quotation:
> > "God demonstrates his own love for us in this: While we were still
> > sinners, Christ died for us."
> > _______________________________
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Standing on the shoulders of Newton


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


From giannozz at nest.sns.it  Wed Sep  6 17:50:39 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 6 Sep 2006 17:50:39 +0200
Subject: [Pw_forum] about phonon calculation
In-Reply-To: <BAY101-F19EA93BA1F8B13D799EAABAA310@phx.gbl>
References: <BAY101-F19EA93BA1F8B13D799EAABAA310@phx.gbl>
Message-ID: <200609061750.39960.giannozz@nest.sns.it>

On Wednesday 06 September 2006 13:15, Ezad Shojaee wrote:

> i wonder if anyone could tell me where can i find a lecture about
> "representations"  ( for the use in phonon calculation) ?

it depends. For irreducible representations in general,
any textbook in group theory. For their specific usage 
in the phonon code, there isn't much more that the 
code itself and comments in the code, unfortunately

Paolo
-- 
Paolo Giannozzi             Phone:   +39/050-509876
DEMOCRITOS and SNS          Fax:     +39/050-563513 
Piazza dei Cavalieri 7      I-56126 Pisa, Italy


From likedew at phys.ksu.edu  Wed Sep  6 21:12:46 2006
From: likedew at phys.ksu.edu (Hong, SamPyo)
Date: Wed, 6 Sep 2006 14:12:46 -0500
Subject: [Pw_forum] frequency of NO molecule
In-Reply-To: <b8b82da20609060256g7e9380b6k418507773649f198@mail.gmail.com>
Message-ID: <F0712C28C5E30740A5F81252A97E6F32E5F34B@isis.phys.ksu.edu>

Hello,
 
As I looked into the code, I found that that can be done very easily.
Here is a sample script:
 
phonons of NO on metal Ru at Gamma
 &inputph
 tr2_ph=1.0d-14,
 prefix='NO',
 epsil=.false.,
 amass(1)=101.07000,
 amass(2)=14.0,
 amass(3)=16.0,
 outdir='./tmp/',
 fildyn='NO.dynG',
 nat_todo=2, <== Here we specify number of atoms to be displaced.
 /
 0.0 0.0 0.0
 31 32 <== Here we specify atom index in our supercell.
 
That's it. Later I found that INPUT_PH has a mention regarding this.
I wish that this procedure could be explained very clearly in the manual
in coming verion.
 
Thanks.

 Sampyo Hong
______________________________
 Research Associate
 Department of Physics, Kansas State University, Manhattan, KS 66506,
USA.
 E-Mail: likedew at phys.ksu.edu   WEB:
http://www.phys.ksu.edu/personal/likedew
 Phone: +1-785-532-1642           FAX:   +1-785-532-6806
 Favorite quotation:
 "God demonstrates his own love for us in this: While we were still
sinners, Christ died for us."
_______________________________
  

	-----Original Message-----
	From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org]
On Behalf Of Clark Lee
	Sent: Wednesday, September 06, 2006 4:56 AM
	To: pw_forum at pwscf.org
	Subject: Re: [Pw_forum] frequency of NO molecule
	
	
	Yes ! I want to know any methods for solving this problem too.
Anyone know the answer?
	
	
	On 9/6/06, Hong, SamPyo < likedew at phys.ksu.edu
<mailto:likedew at phys.ksu.edu> > wrote: 


		Hello, everyone,
		
		I have a supercell of 32 atoms, 2 of which are a NO
molecule adsorbed on 
		a metallic surface of 30 atoms.
		I want to calculate frequencies of adsorbed NO molecule
only, not those
		for substrate atoms.
		
		How can I do this?
		
		
		My sincere thanks in advance.
		
		Sampyo Hong 
		______________________________
		Research Associate
		Department of Physics, Kansas State University,
Manhattan, KS 66506,
		USA.
		E-Mail: likedew at phys.ksu.edu   WEB:
		http://www.phys.ksu.edu/personal/likedew
		Phone: +1-785-532-1642           FAX:   +1-785-532-6806
		Favorite quotation:
		"God demonstrates his own love for us in this: While we
were still 
		sinners, Christ died for us."
		_______________________________
		
		_______________________________________________
		Pw_forum mailing list
		Pw_forum at pwscf.org
		http://www.democritos.it/mailman/listinfo/pw_forum
		




	-- 
	Standing on the shoulders of Newton 

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From akohlmey at cmm.chem.upenn.edu  Wed Sep  6 22:00:16 2006
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 6 Sep 2006 16:00:16 -0400
Subject: [Pw_forum] frequency of NO molecule
In-Reply-To: <F0712C28C5E30740A5F81252A97E6F32E5F34B@isis.phys.ksu.edu>
References: <b8b82da20609060256g7e9380b6k418507773649f198@mail.gmail.com>
	 <F0712C28C5E30740A5F81252A97E6F32E5F34B@isis.phys.ksu.edu>
Message-ID: <7b6913e90609061300r6f450350p53ff3af3d011a55b@mail.gmail.com>

On 9/6/06, Hong, SamPyo <likedew at phys.ksu.edu> wrote:
>
>
> Hello,
>
> As I looked into the code, I found that that can be done very easily.
> Here is a sample script:
>
> phonons of NO on metal Ru at Gamma
>  &inputph
>  tr2_ph=1.0d-14,
>  prefix='NO',
>  epsil=.false.,
>  amass(1)=101.07000,
>  amass(2)=14.0,
>  amass(3)=16.0,
>  outdir='./tmp/',
>  fildyn='NO.dynG',
>  nat_todo=2, <== Here we specify number of atoms to be displaced.
>  /
>  0.0 0.0 0.0
>  31 32 <== Here we specify atom index in our supercell.
>
> That's it. Later I found that INPUT_PH has a mention regarding this.
> I wish that this procedure could be explained very clearly in the manual in
> coming verion.

since quantum espresso is a community project, this is _your_
chance to 'pay your debts to the community' by adding a description
of what you found out to the manual.

on average most of the time _users_ are much better qualified to
write documentation (since it is for other users) than developers
(who are better off implementing new features).

and many developers tend to only write documentation if there
are _so_ many people asking questions, that they just want to
get them off their respective backs.

cheers,
    axel.

>
> Thanks.
>
>
>  Sampyo Hong
> ______________________________
>  Research Associate
>  Department of Physics, Kansas State University, Manhattan, KS 66506, USA.
>  E-Mail: likedew at phys.ksu.edu   WEB:
> http://www.phys.ksu.edu/personal/likedew
>  Phone: +1-785-532-1642           FAX:   +1-785-532-6806
>  Favorite quotation:
>  "God demonstrates his own love for us in this: While we were still sinners,
> Christ died for us."
> _______________________________
>
>
>
[...]

-- 
=======================================================================
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 ajoshi at mines.edu  Wed Sep  6 23:45:58 2006
From: ajoshi at mines.edu (Ameya Joshi)
Date: Wed, 6 Sep 2006 15:45:58 -0600
Subject: [Pw_forum] Bond dissociation energy of CO (gas-phase)
Message-ID: <004701c6d1fd$d7fde6b0$3b20438a@brucite>

Hi all,

I'm a recent convert to Espresso. I've computed the bond dissociation energy (BDE) of the CO molecule ( CO --> C + O ) using several available pseudos for C and O, but do not find good agreement with the experimental value of 256 kcal/mol. Attached, please find a summary of the calculations using the various pseudos. 

Most calculations overpredict the BDE  by almost 15 kcal/mol, while the one using the BLYP pseudo underpredicts it by 11.6 kcal/mol. The BDE obtained using the pseudos included in example03 and that using the PZ (LDA) pseudo give the worst result (almost 40 kcal/mol too high). For reference, I have also included the value obtained by using CASTEP and the PW91 functional, which yields a value within 5 kcal/mol of the experimental value. 

I'd like to clarify that I am using the triplet states for both O and C in these calculations. I realize that there might be some errors in my input files, so include a typical input file towards the end of this mail. (the only change in the other files is the name of the pseudo) 

Finally, I'd like to share my ultimate motive behind these calculations - I'm looking to calculate the binding energies of small molecules on nickel surfaces. I find that in case of CO, the binding energy is lower by about 15 kcal/mol - the same difference as the BDE - as compared to CASTEP. So my guess is that the absolute energy of CO molecule is not being calculated correctly with my current settings.

Any thoughts will be appreciated. Also, I should add that I have browsed the archive carefully and found no reference to this or similar problems there, but apologize if I've missed any relevant information (in which case please give a pointer to that discussion thread). 

*********
Input file
*********

&CONTROL

calculation = "relax",

prefix = "CO",

pseudo_dir = "c:/Ameya/Espresso/espresso-3.1.1/pseudo",

outdir = "c:/Ameya/Espresso/espresso-3.1.1/tmp",

/

&SYSTEM

ibrav = 1,

celldm(1) = 20.D0, 

nat = 2, 

ntyp = 2,

ecutwfc = 29.105D0,

ecutrho = 144.D0,

/

&ELECTRONS

conv_thr = 1.D-7,

mixing_beta = 0.7D0,

/

&IONS

pot_extrapolation = "second_order",

wfc_extrapolation = "second_order",

/

ATOMIC_SPECIES

O 16.00 O.pbe-van_bm.UPF

C 12.01 C.pbe-van_bm.UPF

ATOMIC_POSITIONS {angstrom}

C 0.000 0.0 0.000

O 0.000 0.0 1.100 

K_POINTS {Gamma}

*********
End of Input file
*********


Ameya Joshi, Postdoc
----------------------------------------
Chemical Engineering Department
Colorado School of Mines 
Ph. (303)-273-3192
----------------------------------------
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From akohlmey at cmm.chem.upenn.edu  Thu Sep  7 00:12:16 2006
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 6 Sep 2006 18:12:16 -0400
Subject: [Pw_forum] Bond dissociation energy of CO (gas-phase)
In-Reply-To: <004701c6d1fd$d7fde6b0$3b20438a@brucite>
References: <004701c6d1fd$d7fde6b0$3b20438a@brucite>
Message-ID: <7b6913e90609061512x563dbfe2q30b2bd3d1a2e1c54@mail.gmail.com>

On 9/6/06, Ameya Joshi <ajoshi at mines.edu> wrote:
>
>
> Hi all,

hi!

> Most calculations overpredict the BDE  by almost 15 kcal/mol, while the one
> using the BLYP pseudo underpredicts it by 11.6 kcal/mol. The BDE obtained

one comment on this:
your table does not indicate, what plane wave cutoff you were using
for the different pseudopotentials. in the case of the norm-conserving
potentials, you used for BLYP, this makes a huge difference, as ~30Ry
are far from convergence for that type of pseudopotential.

generally, i would suggest checking for basis set convergence (i.e.
convergence with respect to ecutwfc) for all sets of psps. the same
goes for the box size dependence.

cheers,
   axel.

> using the pseudos included in example03 and that using the PZ (LDA) pseudo
> give the worst result (almost 40 kcal/mol too high). For reference, I have
> also included the value obtained by using CASTEP and the PW91 functional,
> which yields a value within 5 kcal/mol of the experimental value.
>
> I'd like to clarify that I am using the triplet states for both O and C in
> these calculations. I realize that there might be some errors in my input
> files, so include a typical input file towards the end of this mail. (the
> only change in the other files is the name of the pseudo)
>
> Finally, I'd like to share my ultimate motive behind these calculations -
> I'm looking to calculate the binding energies of small molecules on nickel
> surfaces. I find that in case of CO, the binding energy is lower by about 15
> kcal/mol - the same difference as the BDE - as compared to CASTEP. So my
> guess is that the absolute energy of CO molecule is not being calculated
> correctly with my current settings.
>
> Any thoughts will be appreciated. Also, I should add that I have browsed the
> archive carefully and found no reference to this or similar problems there,
> but apologize if I've missed any relevant information (in which case please
> give a pointer to that discussion thread).
>
> *********
> Input file
> *********
>
>
>
> &CONTROL
>
> calculation = "relax",
>
> prefix = "CO",
>
> pseudo_dir = "c:/Ameya/Espresso/espresso-3.1.1/pseudo",
>
> outdir = "c:/Ameya/Espresso/espresso-3.1.1/tmp",
>
> /
>
> &SYSTEM
>
> ibrav = 1,
>
> celldm(1) = 20.D0,
>
> nat = 2,
>
> ntyp = 2,
>
> ecutwfc = 29.105D0,
>
> ecutrho = 144.D0,
>
> /
>
> &ELECTRONS
>
> conv_thr = 1.D-7,
>
> mixing_beta = 0.7D0,
>
> /
>
> &IONS
>
> pot_extrapolation = "second_order",
>
> wfc_extrapolation = "second_order",
>
> /
>
> ATOMIC_SPECIES
>
> O 16.00 O.pbe-van_bm.UPF
>
> C 12.01 C.pbe-van_bm.UPF
>
> ATOMIC_POSITIONS {angstrom}
>
> C 0.000 0.0 0.000
>
> O 0.000 0.0 1.100
>
> K_POINTS {Gamma}
>
> *********
> End of Input file
> *********
>
>
> Ameya Joshi, Postdoc
> ----------------------------------------
> Chemical Engineering Department
> Colorado School of Mines
> Ph. (303)-273-3192
> ----------------------------------------
>


-- 
=======================================================================
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 konstantin_kudin at yahoo.com  Thu Sep  7 00:20:45 2006
From: konstantin_kudin at yahoo.com (Konstantin Kudin)
Date: Wed, 6 Sep 2006 15:20:45 -0700 (PDT)
Subject: [Pw_forum] Bond dissociation energy of CO (gas-phase)
In-Reply-To: <004701c6d1fd$d7fde6b0$3b20438a@brucite>
Message-ID: <20060906222045.15017.qmail@web52012.mail.yahoo.com>

--- Ameya Joshi <ajoshi at mines.edu> wrote:

 Hi Ameya,

> I'm a recent convert to Espresso.

 Yes, it is about time that this crusade has started to bring in some
fresh converts :-) Now, if only people could get converted away from
using Microsoft formats such as *.xls ...

>...
>...
>...

> Finally, I'd like to share my ultimate motive behind these
> calculations - I'm looking to calculate the binding energies of small
> molecules on nickel surfaces. I find that in case of CO, the binding
> energy is lower by about 15 kcal/mol - the same difference as the BDE
> - as compared to CASTEP. So my guess is that the absolute energy of
> CO molecule is not being calculated correctly with my current
> settings.

 It seems that you could always compute the energy of CO on the nickel
surface, as well as a few Angstroms away from the surface. Then you get
the energy difference from an identical setup, just different
geometries. See if you still get the 15 kcal/mol difference. Now, if
you computing the energy of Ni-CO with respect to (Ni+C+O), that one
can easily find this 15 kcal error coming from the improperly handled
reference substances.

 Anyway, BDEs are often rather challenging to compute correctly (one
has to deal with reference atomic states and such), so try to avoid
doing that if possible, and stick to the smallest possible changes.

 And, if you really want to learn about minimizing errors for chemical
reactions, check out the definition of "isodesmic" :
http://en.wikipedia.org/wiki/Isodesmic_reaction

 Kostya

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 


From jzwanzig at dal.ca  Thu Sep  7 02:45:31 2006
From: jzwanzig at dal.ca (Josef Zwanziger)
Date: Wed, 6 Sep 2006 21:45:31 -0300
Subject: [Pw_forum] Status of NMR Project
Message-ID: <EBEJLEGBCGBNDNDDHFOFIEACCAAA.jzwanzig@dal.ca>

Dear Colleagues,

can someone provide an update to the status of incorporating GIPAW into
pwscf? Last fall the information was that the project was back on after a
pause, I wonder how things are going now?

Thanks much,

Joe Zwanziger
Dept. of Chemistry
Dalhousie University



From ajoshi at mines.edu  Thu Sep  7 03:22:31 2006
From: ajoshi at mines.edu (Ameya Joshi)
Date: Wed, 6 Sep 2006 19:22:31 -0600
Subject: [Pw_forum] Bond dissociation energy of CO (gas-phase)
References: <20060906222045.15017.qmail@web52012.mail.yahoo.com>
Message-ID: <001701c6d21c$1869c520$3b20438a@brucite>

Axel and Kostya,

Thanks for the suggestions. My first concern was convergence, and as pointed 
out by Axel, I did try increasing the cutoff, but even after increasing the 
cutoff from 30 to 50 Ryd, the BDE changes only by 0.5 kcal/mol (and makes it 
worse), so its safe to say its converged with respect to that. I've also 
confirmed that increasing the box size has no further effect.

Ameya




----- Original Message ----- 
From: "Konstantin Kudin" <konstantin_kudin at yahoo.com>
To: <pw_forum at pwscf.org>
Sent: Wednesday, September 06, 2006 4:20 PM
Subject: Re: [Pw_forum] Bond dissociation energy of CO (gas-phase)


> --- Ameya Joshi <ajoshi at mines.edu> wrote:
>
> Hi Ameya,
>
>> I'm a recent convert to Espresso.
>
> Yes, it is about time that this crusade has started to bring in some
> fresh converts :-) Now, if only people could get converted away from
> using Microsoft formats such as *.xls ...
>
>>...
>>...
>>...
>
>> Finally, I'd like to share my ultimate motive behind these
>> calculations - I'm looking to calculate the binding energies of small
>> molecules on nickel surfaces. I find that in case of CO, the binding
>> energy is lower by about 15 kcal/mol - the same difference as the BDE
>> - as compared to CASTEP. So my guess is that the absolute energy of
>> CO molecule is not being calculated correctly with my current
>> settings.
>
> It seems that you could always compute the energy of CO on the nickel
> surface, as well as a few Angstroms away from the surface. Then you get
> the energy difference from an identical setup, just different
> geometries. See if you still get the 15 kcal/mol difference. Now, if
> you computing the energy of Ni-CO with respect to (Ni+C+O), that one
> can easily find this 15 kcal error coming from the improperly handled
> reference substances.
>
> Anyway, BDEs are often rather challenging to compute correctly (one
> has to deal with reference atomic states and such), so try to avoid
> doing that if possible, and stick to the smallest possible changes.
>
> And, if you really want to learn about minimizing errors for chemical
> reactions, check out the definition of "isodesmic" :
> http://en.wikipedia.org/wiki/Isodesmic_reaction
>
> Kostya
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum 



From prasenjit.jnc at gmail.com  Thu Sep  7 09:15:54 2006
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Thu, 7 Sep 2006 12:45:54 +0530
Subject: [Pw_forum] Bond dissociation energy of CO (gas-phase)
In-Reply-To: <004701c6d1fd$d7fde6b0$3b20438a@brucite>
References: <004701c6d1fd$d7fde6b0$3b20438a@brucite>
Message-ID: <627e0ffa0609070015p71971fb3k92386ee36f76a758@mail.gmail.com>

Hi Ameya,

I did similar calculations some time back with PWscf & got reasonably good
results compared with expt.( atomization energy/dissociation energy=264
KCal/mole and C-O bond length=1.14 A) with pbe-rrkjus psp's for both O & C
with cutoffs:
ecutwfc= 32.0, ecutrho=192 and box length of 20 bohr. I also used a degauss
of 0.03 Ry.

May be u can try this.
Prasenjit.





-- 
PRASENJIT GHOSH,
Ph. D STUDENT,
THEORETICAL SCIENCES UNIT,
JNCASR,
BANGALORE-560064,
INDIA.

PHONE:
OFFICE : +91-80-22082835/34
MOBILE:  +91-9880519401
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From niuyingli at gmail.com  Thu Sep  7 09:22:30 2006
From: niuyingli at gmail.com (Yingli Niu)
Date: Thu, 7 Sep 2006 15:22:30 +0800
Subject: [Pw_forum] Can I get dVscf without scf-consistent procedure in the el-ph calculation?
Message-ID: <6398ac910609070022p4adbab3dwfaff2d6089205c53@mail.gmail.com>

Dear all,
  I use espresso-3.0.
  I ran example07 step by step, calculated Gamma q-point
electron-phonon interaction.
  Part of my script was
cat > al.ph.in << EOF
phonons of Al at Gamma
 &inputph
  tr2_ph=1.0d-14,
  prefix='al',
  amass(1)=26.98,
  outdir='$TMP_DIR/',
  fildyn='al.dyn'
 /
 0.0 0.0 1.0
EOF

  That is to say, I didn't write:
    fildvscf='aldv'
due to my carelessness.

  So there was I/O preblem in el-ph calculation.
cat > al.elph.in << EOF
Al el-phonon at X
 &inputph
  tr2_ph=1.0d-14,
  prefix='al',
  fildvscf='aldv',
  amass(1)=26.98,
  outdir='$TMP_DIR/',
  fildyn='al.dyn',
  elph=.true.,
  trans=.false.,
 /
 0.0 0.0 1.0
EOF

  because it did not find the file aldv.

  I know I should rerun the whole script.

  Since the the linear response equations of phonon calculations had
been self-consistent. So I had got the wave functions and their
one-order correction in case.wfc and case.dwf files.
  Can I make use of file case.wfc case.dwf or charge density file to
get aldv file (deltaVscf) without recalculate in the self-consistent
cycles?
-- 
Yingli Niu


From giannozz at nest.sns.it  Thu Sep  7 09:34:18 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 7 Sep 2006 09:34:18 +0200
Subject: [Pw_forum] frequency of NO molecule
In-Reply-To: <F0712C28C5E30740A5F81252A97E6F32E5F34B@isis.phys.ksu.edu>
References: <F0712C28C5E30740A5F81252A97E6F32E5F34B@isis.phys.ksu.edu>
Message-ID: <200609070934.18827.giannozz@nest.sns.it>

On Wednesday 06 September 2006 21:12, Hong, SamPyo wrote:

> As I looked into the code, I found that that can be done very easily.
> [...]
>  nat_todo=2, <== Here we specify number of atoms to be displaced.
>  /
>  0.0 0.0 0.0
>  31 32 <== Here we specify atom index in our supercell.
>
> That's it. Later I found that INPUT_PH has a mention regarding this.

in this way you just calculate and diagonalize the 6 x 6 submatrix of the
dynamical matrix. 

In principle it should be possible to reconstruct an approximate dynamical
matrix from the above calculation and the dynamical matrix of the surface
without NO. I don't know how useful this would be, though.

> I wish that this procedure could be explained very clearly in the manual
> in coming version.

it is not clearly explained right now because it is a seldom-used feature
(and one that should be carefully used). If you have any specific suggestions
to improve the manual, feel free to suggest them

Paolo
-- 
Paolo Giannozzi             Phone:   +39/050-509876
DEMOCRITOS and SNS          Fax:     +39/050-563513 
Piazza dei Cavalieri 7      I-56126 Pisa, Italy


From giannozz at nest.sns.it  Thu Sep  7 09:54:59 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 7 Sep 2006 09:54:59 +0200
Subject: [Pw_forum] Can I get dVscf without scf-consistent procedure in the el-ph calculation?
In-Reply-To: <6398ac910609070022p4adbab3dwfaff2d6089205c53@mail.gmail.com>
References: <6398ac910609070022p4adbab3dwfaff2d6089205c53@mail.gmail.com>
Message-ID: <200609070954.59325.giannozz@nest.sns.it>

On Thursday 07 September 2006 09:22, Yingli Niu wrote:

>   I know I should rerun the whole script [..]
>   Can I make use of file case.wfc case.dwf or charge density file to
> get aldv file (deltaVscf) without recalculate in the self-consistent
> cycles?

I am afraid you cannot: what is left on disk is the linear response
(*.dwf files) from which the Delta V_scf could be in principle
reconstructed; however only one mode (irrep) at the time is 
written to disk and overwritten by the following mode. Writing
all Delta\psi for all modes would require a large disk space.
The columns of the dynamical matrix are calculated and saved
to file in order to allow restarting from an interrupted calculation,
but this is not sufficient to recalculate Delta V_scf

Paolo
-- 
Paolo Giannozzi             Phone:   +39/050-509876
DEMOCRITOS and SNS          Fax:     +39/050-563513 
Piazza dei Cavalieri 7      I-56126 Pisa, Italy


From niuyingli at gmail.com  Thu Sep  7 11:44:04 2006
From: niuyingli at gmail.com (Yingli Niu)
Date: Thu, 7 Sep 2006 17:44:04 +0800
Subject: [Pw_forum] Can I get dVscf without scf-consistent procedure in the el-ph calculation?
In-Reply-To: <200609070954.59325.giannozz@nest.sns.it>
References: <6398ac910609070022p4adbab3dwfaff2d6089205c53@mail.gmail.com>
	 <200609070954.59325.giannozz@nest.sns.it>
Message-ID: <6398ac910609070244r426ec8d1u73291ee4700094ac@mail.gmail.com>

Dear Paolo,
Thank you!
I have only to rerun the script!

Best regards!
Yingli Niu

On 9/7/06, Paolo Giannozzi <giannozz at nest.sns.it> wrote:
> On Thursday 07 September 2006 09:22, Yingli Niu wrote:
>
> >   I know I should rerun the whole script [..]
> >   Can I make use of file case.wfc case.dwf or charge density file to
> > get aldv file (deltaVscf) without recalculate in the self-consistent
> > cycles?
>
> I am afraid you cannot: what is left on disk is the linear response
> (*.dwf files) from which the Delta V_scf could be in principle
> reconstructed; however only one mode (irrep) at the time is
> written to disk and overwritten by the following mode. Writing
> all Delta\psi for all modes would require a large disk space.
> The columns of the dynamical matrix are calculated and saved
> to file in order to allow restarting from an interrupted calculation,
> but this is not sufficient to recalculate Delta V_scf
>
> Paolo
> --
> Paolo Giannozzi             Phone:   +39/050-509876
> DEMOCRITOS and SNS          Fax:     +39/050-563513
> Piazza dei Cavalieri 7      I-56126 Pisa, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


From akohlmey at cmm.chem.upenn.edu  Thu Sep  7 15:42:46 2006
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 7 Sep 2006 09:42:46 -0400
Subject: [Pw_forum] Bond dissociation energy of CO (gas-phase)
In-Reply-To: <001701c6d21c$1869c520$3b20438a@brucite>
References: <20060906222045.15017.qmail@web52012.mail.yahoo.com>
	 <001701c6d21c$1869c520$3b20438a@brucite>
Message-ID: <7b6913e90609070642sbae97e7p2236d775e2cecf31@mail.gmail.com>

On 9/6/06, Ameya Joshi <ajoshi at mines.edu> wrote:
> Axel and Kostya,
>
> Thanks for the suggestions. My first concern was convergence, and as pointed
> out by Axel, I did try increasing the cutoff, but even after increasing the
> cutoff from 30 to 50 Ryd, the BDE changes only by 0.5 kcal/mol (and makes it
> worse), so its safe to say its converged with respect to that. I've also

i agree for the ultra-soft potentials (and even there are differences, as one
can kindof define during psp generation, how soft the potential should be)
but for the norm-conserving ones used with BLYP, you'll need 70-90ry.
and in general you always have to find the optimal cutoff for each pair
as the 'hardest' pseudopotential determines the required cutoff.

cheers,
   axel.
> confirmed that increasing the box size has no further effect.
>
> Ameya
>
>
>
>
> ----- Original Message -----
> From: "Konstantin Kudin" <konstantin_kudin at yahoo.com>
> To: <pw_forum at pwscf.org>
> Sent: Wednesday, September 06, 2006 4:20 PM
> Subject: Re: [Pw_forum] Bond dissociation energy of CO (gas-phase)
>
>
> > --- Ameya Joshi <ajoshi at mines.edu> wrote:
> >
> > Hi Ameya,
> >
> >> I'm a recent convert to Espresso.
> >
> > Yes, it is about time that this crusade has started to bring in some
> > fresh converts :-) Now, if only people could get converted away from
> > using Microsoft formats such as *.xls ...
> >
> >>...
> >>...
> >>...
> >
> >> Finally, I'd like to share my ultimate motive behind these
> >> calculations - I'm looking to calculate the binding energies of small
> >> molecules on nickel surfaces. I find that in case of CO, the binding
> >> energy is lower by about 15 kcal/mol - the same difference as the BDE
> >> - as compared to CASTEP. So my guess is that the absolute energy of
> >> CO molecule is not being calculated correctly with my current
> >> settings.
> >
> > It seems that you could always compute the energy of CO on the nickel
> > surface, as well as a few Angstroms away from the surface. Then you get
> > the energy difference from an identical setup, just different
> > geometries. See if you still get the 15 kcal/mol difference. Now, if
> > you computing the energy of Ni-CO with respect to (Ni+C+O), that one
> > can easily find this 15 kcal error coming from the improperly handled
> > reference substances.
> >
> > Anyway, BDEs are often rather challenging to compute correctly (one
> > has to deal with reference atomic states and such), so try to avoid
> > doing that if possible, and stick to the smallest possible changes.
> >
> > And, if you really want to learn about minimizing errors for chemical
> > reactions, check out the definition of "isodesmic" :
> > http://en.wikipedia.org/wiki/Isodesmic_reaction
> >
> > Kostya
> >
> > __________________________________________________
> > Do You Yahoo!?
> > Tired of spam?  Yahoo! Mail has the best spam protection around
> > http://mail.yahoo.com
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
=======================================================================
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 Sep  7 16:01:52 2006
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 7 Sep 2006 10:01:52 -0400
Subject: [Pw_forum] frequency of NO molecule
In-Reply-To: <200609070934.18827.giannozz@nest.sns.it>
References: <F0712C28C5E30740A5F81252A97E6F32E5F34B@isis.phys.ksu.edu>
	 <200609070934.18827.giannozz@nest.sns.it>
Message-ID: <7b6913e90609070701j2a340ed5r91e25815b5487584@mail.gmail.com>

> >  nat_todo=2, <== Here we specify number of atoms to be displaced.
> >  /
> >  0.0 0.0 0.0
> >  31 32 <== Here we specify atom index in our supercell.
> >
> > That's it. Later I found that INPUT_PH has a mention regarding this.
>
> in this way you just calculate and diagonalize the 6 x 6 submatrix of the
> dynamical matrix.
>
> In principle it should be possible to reconstruct an approximate dynamical
> matrix from the above calculation and the dynamical matrix of the surface
> without NO. I don't know how useful this would be, though.

how about including several atoms in the neighborhood of the adsorbed
molecule? this is how it works in CPMD: you pick an atoms (or pick a
reference coordinate) and set a radius and then do the vibrational analysis
for those atoms and keep the rest fixed. this way you include at least the
contributions from the near neighbors, have the rest as 'static background',
and still save a lot of (cpu) time.

ciao,
   axel.

> > I wish that this procedure could be explained very clearly in the manual
> > in coming version.
>
> it is not clearly explained right now because it is a seldom-used feature
> (and one that should be carefully used). If you have any specific suggestions
> to improve the manual, feel free to suggest them


>
> Paolo
> --
> Paolo Giannozzi             Phone:   +39/050-509876
> DEMOCRITOS and SNS          Fax:     +39/050-563513
> Piazza dei Cavalieri 7      I-56126 Pisa, Italy
> _______________________________________________
> 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 wmbmacam at lg.ehu.es  Thu Sep  7 16:50:20 2006
From: wmbmacam at lg.ehu.es (=?ISO-8859-1?Q?Miguel_Mart=EDnez_Canales?=)
Date: Thu, 07 Sep 2006 16:50:20 +0200
Subject: [Pw_forum] Bond dissociation energy of CO (gas-phase)
In-Reply-To: <7b6913e90609070642sbae97e7p2236d775e2cecf31@mail.gmail.com>
References: <20060906222045.15017.qmail@web52012.mail.yahoo.com> 	<001701c6d21c$1869c520$3b20438a@brucite> <7b6913e90609070642sbae97e7p2236d775e2cecf31@mail.gmail.com>
Message-ID: <450031AC.80601@lg.ehu.es>

Hello everybody,

I have a small naive question with respect to the discrepancies Ameya is 
getting. Being C and O pretty light elements, and because the dissociation 
energies he is getting is always (except for BLYP) around 10-15 kcal/mol, 
?could this be caused because he is neglecting the zero-point energy?

-- 
----------------------------------------
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're a mad scientist, you can use
   GPLv2'd software for your evil plans to
   take over the world"

Linus Torvalds



From giannozz at nest.sns.it  Thu Sep  7 17:31:34 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 7 Sep 2006 17:31:34 +0200
Subject: [Pw_forum] frequency of NO molecule
In-Reply-To: <7b6913e90609070701j2a340ed5r91e25815b5487584@mail.gmail.com>
References: <F0712C28C5E30740A5F81252A97E6F32E5F34B@isis.phys.ksu.edu> <200609070934.18827.giannozz@nest.sns.it> <7b6913e90609070701j2a340ed5r91e25815b5487584@mail.gmail.com>
Message-ID: <200609071731.34283.giannozz@nest.sns.it>

On Thursday 07 September 2006 16:01, Axel Kohlmeyer wrote:
>
> how about including several atoms in the neighborhood of the 
> adsorbed molecule? this is how it works in CPMD: you pick an
> atom (or pick a reference coordinate) and set a radius and then 
> do the vibrational analysis for those atoms and keep the rest fixed. 
> this way you include at least the contributions from the near 
> neighbors, have the rest as 'static background', and still save
> a lot of (cpu) time. 

the problem I see in this approach is that the vibrations of 
surface atoms close to the adsorbed molecule may be 
strongly correlated to vibrations of other atoms in the 
surface; i.e., taking only a few surface atoms close to 
the molecule will produce rather bogus displacement
patterns for those atoms. 

Paolo
-- 
Paolo Giannozzi             Phone:   +39/050-509876
DEMOCRITOS and SNS          Fax:     +39/050-563513 
Piazza dei Cavalieri 7      I-56126 Pisa, Italy


From akohlmey at cmm.chem.upenn.edu  Thu Sep  7 17:41:52 2006
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 7 Sep 2006 11:41:52 -0400
Subject: [Pw_forum] frequency of NO molecule
In-Reply-To: <200609071731.34283.giannozz@nest.sns.it>
References: <F0712C28C5E30740A5F81252A97E6F32E5F34B@isis.phys.ksu.edu>
	 <200609070934.18827.giannozz@nest.sns.it>
	 <7b6913e90609070701j2a340ed5r91e25815b5487584@mail.gmail.com>
	 <200609071731.34283.giannozz@nest.sns.it>
Message-ID: <7b6913e90609070841t3d5877baxc51c29658a656eae@mail.gmail.com>

On 9/7/06, Paolo Giannozzi <giannozz at nest.sns.it> wrote:
> On Thursday 07 September 2006 16:01, Axel Kohlmeyer wrote:
> >
> > how about including several atoms in the neighborhood of the
> > adsorbed molecule? this is how it works in CPMD: you pick an
> > atom (or pick a reference coordinate) and set a radius and then
> > do the vibrational analysis for those atoms and keep the rest fixed.
> > this way you include at least the contributions from the near
> > neighbors, have the rest as 'static background', and still save
> > a lot of (cpu) time.
>
> the problem I see in this approach is that the vibrations of
> surface atoms close to the adsorbed molecule may be
> strongly correlated to vibrations of other atoms in the
> surface; i.e., taking only a few surface atoms close to
> the molecule will produce rather bogus displacement
> patterns for those atoms.

ok, makes sense. it would still be interesting to see
how much this can actually affect the internal(!) vibrations
of the adsorbed molecule (which is what this was about).
would make a nice undergrad project, too bad i have
nobody around to assign this to. :(

ciao,
  axel.

>
> Paolo
> --
> Paolo Giannozzi             Phone:   +39/050-509876
> DEMOCRITOS and SNS          Fax:     +39/050-563513
> Piazza dei Cavalieri 7      I-56126 Pisa, Italy
> _______________________________________________
> 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 marzari at MIT.EDU  Thu Sep  7 18:58:09 2006
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 07 Sep 2006 12:58:09 -0400
Subject: [Pw_forum] frequency of NO molecule
In-Reply-To: <200609071731.34283.giannozz@nest.sns.it>
References: <F0712C28C5E30740A5F81252A97E6F32E5F34B@isis.phys.ksu.edu> <200609070934.18827.giannozz@nest.sns.it> <7b6913e90609070701j2a340ed5r91e25815b5487584@mail.gmail.com> <200609071731.34283.giannozz@nest.sns.it>
Message-ID: <45004FA1.2050802@mit.edu>


We have done this in the past for CO on Pt (since that
Pt is very heavy, only 3 force constants are neeeded
(Pt-C, C-O, Pt-O)), and you diagonalize a 2x2 matrix
(instead of 6x6, for a molecule standing upright, with only
z as a degree of freedom). Compared to a full phonon calculation,
the discrepancies on the stretching mode of CO were of 50-70 cm-1,
i.e. 5%.

Of course, it depends on how heavy the metal is, and how
things are bonded, as Paolo points out.

				nicola




Paolo Giannozzi wrote:
> On Thursday 07 September 2006 16:01, Axel Kohlmeyer wrote:
>> how about including several atoms in the neighborhood of the 
>> adsorbed molecule? this is how it works in CPMD: you pick an
>> atom (or pick a reference coordinate) and set a radius and then 
>> do the vibrational analysis for those atoms and keep the rest fixed. 
>> this way you include at least the contributions from the near 
>> neighbors, have the rest as 'static background', and still save
>> a lot of (cpu) time. 
> 
> the problem I see in this approach is that the vibrations of 
> surface atoms close to the adsorbed molecule may be 
> strongly correlated to vibrations of other atoms in the 
> surface; i.e., taking only a few surface atoms close to 
> the molecule will produce rather bogus displacement
> patterns for those atoms. 
> 
> Paolo


-- 
---------------------------------------------------------------------
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 ajoshi at mines.edu  Thu Sep  7 20:56:42 2006
From: ajoshi at mines.edu (Ameya Joshi)
Date: Thu, 7 Sep 2006 12:56:42 -0600
Subject: [Pw_forum] Bond dissociation energy of CO (gas-phase)
References: <20060906222045.15017.qmail@web52012.mail.yahoo.com> 	<001701c6d21c$1869c520$3b20438a@brucite> <7b6913e90609070642sbae97e7p2236d775e2cecf31@mail.gmail.com> <450031AC.80601@lg.ehu.es>
Message-ID: <005801c6d2af$5cd6f960$3b20438a@brucite>

Hi all,

First of all Axel : using a much greater cutoff (90 Ryd) with BLYP, the BDE 
increased by 20 kcal/mol (!!) to 264 kcal/mol, bringing the value within 8 
kcal/mol of the experimental. Thanks for your valuable input ! I'll try 
increasing the cutoff for other pseudos as well and report if there is any 
improvement. Also I plan to increase the cutoff further with BLYP and check 
for convergence and hopefully a further improvement in the BDE value.

Miguel, the vibrational frequency of CO is about 2200 cm-1, which relates to 
a zero-point correction of 3.1 kcal/mol (ZPE = 0.5*h*nu), so that is 
definitely not the reason for the huge discrepancy.

Prasenjit, I did try the settings you suggested, but got a BDE of 271.6 
kcal/mol (the only change between your input file and mine was a upward 
revision of ecutrho, and the BDE changed by only 0.1 kcal/mol).

Thanks everyone for your inputs.


----- Original Message ----- 
From: "Miguel Mart?nez Canales" <wmbmacam at lg.ehu.es>
To: <pw_forum at pwscf.org>
Sent: Thursday, September 07, 2006 8:50 AM
Subject: Re: [Pw_forum] Bond dissociation energy of CO (gas-phase)


> Hello everybody,
>
> I have a small naive question with respect to the discrepancies Ameya is 
> getting. Being C and O pretty light elements, and because the dissociation 
> energies he is getting is always (except for BLYP) around 10-15 kcal/mol, 
> ?could this be caused because he is neglecting the zero-point energy?
>
> -- 
> ----------------------------------------
> 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're a mad scientist, you can use
>   GPLv2'd software for your evil plans to
>   take over the world"
>
> Linus Torvalds
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum 



From babazade at gmail.com  Fri Sep  8 09:38:04 2006
From: babazade at gmail.com (Amin Babazadeh)
Date: Fri, 8 Sep 2006 11:08:04 +0330
Subject: [Pw_forum] help
Message-ID: <b25d3a170609080038n737f2cd8of5b6c64f3e382671@mail.gmail.com>

Dear users
I want to simulate a nanostructure with using espresso code so I give this
structure

&CONTROL
                 calculation = 'nscf' ,
                restart_mode = 'from_scratch' ,
                      outdir = '/home/zareh/espresso- 2.1.3/work/zns_nano/'
,
                  pseudo_dir = '/home/zareh/espresso-2.1.3/pseudo/' ,
                      prefix = zns ,
               etot_conv_thr = 1.D-6 ,
               forc_conv_thr = 1.D-5 ,
 /
 &SYSTEM
                       ibrav = 2,
                   celldm(1) = 30.670266,
                         nat = 10,
                        ntyp = 2,
                     ecutwfc = 20. ,
                       nosym = .true. ,
                 occupations = 'smearing' ,
                     degauss = 0.002 ,
                       nspin = 1 ,
 /
 &ELECTRONS
             diagonalization = 'cg' ,
 /
ATOMIC_SPECIES
   Zn   65.40900  Zn.pw91-van_ak.UPF
    S   32.06600  S.pw91-van_ak.UPF
ATOMIC_POSITIONS crystal
   Zn      0.166666670    0.166666670     0.000000000
   Zn      0.166666670    0.166666670    0.333333330
   Zn      0.166666670    0.000000000    0.166666670
   Zn      0.166666670    0.333333330    0.166666670
   Zn      0.000000000     0.166666670    0.166666670
   Zn      0.333333330    0.166666670     0.166666670
    S      0.083333330    0.083333330    0.083333330
    S      0.250000000    0.250000000    0.083333330
    S      0.250000000    0.083333330    0.250000000
    S      0.083333330     0.250000000    0.250000000


The calculation for pw.x was good but my problem is in finding band
structures.I don't know what k-points is good for this structure.I will
appreciate if tell me what k-point is good for this structure or give me a
recommend that how usually  we  choose k-point for any structure because I
usually use automatic generation k-point and I don't know how manually i can
choose the k-points.
Sincerely yours

-- 
AMIN
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From ustunel at sissa.it  Fri Sep  8 15:11:20 2006
From: ustunel at sissa.it (Hande Ustunel)
Date: Fri, 8 Sep 2006 15:11:20 +0200 (CEST)
Subject: [Pw_forum] Sn pseudopotential
In-Reply-To: <44BFB4E8.2060506@lg.ehu.es>
References: <44BFB4E8.2060506@lg.ehu.es>
Message-ID: <Pine.LNX.4.64.0609081412530.11733@shannon-02.sissa.it>

Dear pwscf users,

Has anyone ever used the pw91 Sn pseudopotential from the web site with
success?  I'm failing to verify the experimental lattice constants c and a
for the beta-Sn structure for this pseudopotential and I'm wondering if I'm
making a silly mistake that I can't see. The alpha-Sn lattice constant on
the other hand seems fine and is overestimated by only a 3% difference. I
include my input script to which the input parameters were

     nk=4
     ecutwfc=50
     ecutrho=400

Thank you very much in advance,
Hande

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From giannozz at nest.sns.it  Fri Sep  8 15:51:33 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 8 Sep 2006 15:51:33 +0200
Subject: [Pw_forum] help
In-Reply-To: <b25d3a170609080038n737f2cd8of5b6c64f3e382671@mail.gmail.com>
References: <b25d3a170609080038n737f2cd8of5b6c64f3e382671@mail.gmail.com>
Message-ID: <200609081551.33285.giannozz@nest.sns.it>

On Friday 08 September 2006 09:38, Amin Babazadeh wrote:

> I want to simulate a nanostructure with using espresso code so I give 
> this structure [...]
> The calculation for pw.x was good but my problem is in finding band
> structures. I don't know what k-points is good for this structure.

are you sure k-points are "good" (i.e. a useful concept) for this
structure? It looks like you are studying a small ZnS clusters using 
a fcc supercell.

Paolo
-- 
Paolo Giannozzi             Phone:   +39/050-509876
DEMOCRITOS and SNS          Fax:     +39/050-563513 
Piazza dei Cavalieri 7      I-56126 Pisa, Italy


From schwegler at llnl.gov  Sat Sep  9 01:59:25 2006
From: schwegler at llnl.gov (Eric Schwegler)
Date: Fri, 8 Sep 2006 16:59:25 -0700
Subject: [Pw_forum] Postdoctoral Positions in LLNL's Quantum Simulation Group
Message-ID: <1b2ba425349cd6c8432198b9730b5144@llnl.gov>

Lawrence Livermore National Laboratory?s (LLNL) Quantum Simulation 
Group is looking to fill one or more Postdoctoral Research Positions in 
the field of electronic structure simulations of materials.  The 
positions are available immediately and renewable for up to 3 years.

We are seeking applicants with a strong background in solid-state 
physics or chemistry and experience with electronic structure 
simulation techniques such as Density Functional Theory and Quantum 
Monte Carlo. Candidates with experience studying nanostructured 
materials, electron transport in semiconductors, or radiation detector 
materials are particularly encouraged to apply.

The Quantum Simulation Group currently consists of ten Ph.D.'s in 
condensed matter physics and chemistry.  It has extensive 
collaborations with a broad range of international theoretical and 
experimental groups.  The group makes extensive use of the world 
leading high performance computational facilities at LLNL.  More 
information on the QSG group, its research, publications, and personnel 
can be found on the group website, www.llnl.gov/qsg

Interested candidates should send their curriculum vitae and list of 
references to:

Dr. Eric Schwegler, schwegler1 at llnl.gov

LLNL offers a challenging environment and a competitive salary/benefits 
package. When contacting us, please mention where you saw this ad. LLNL 
is operated by the University of California for the National Nuclear 
Security Administration/Department of Energy. We are proud to be an 
equal opportunity employer with a commitment to workforce diversity.



From baroni at sissa.it  Sat Sep  9 14:42:55 2006
From: baroni at sissa.it (Stefano Baroni)
Date: Sat, 9 Sep 2006 14:42:55 +0200
Subject: [Pw_forum] Sn pseudopotential
In-Reply-To: <Pine.LNX.4.64.0609081412530.11733@shannon-02.sissa.it>
References: <44BFB4E8.2060506@lg.ehu.es> <Pine.LNX.4.64.0609081412530.11733@shannon-02.sissa.it>
Message-ID: <FB247B9E-E75A-4CDA-86C5-CFBBB13457B9@sissa.it>

Hande: beta tin is a metal. You'll need (much?) more k points and  
Gaussian smearing.
The wfc cutoff seems to me to large for an US PP. If it is really  
neede, I would say that the PP is not very optimized.
Also, I kind of remember that the number of atom per unit cell is 4,  
and not 2 ...

S.

On Sep 8, 2006, at 3:11 PM, Hande Ustunel wrote:

> Dear pwscf users,
>
> Has anyone ever used the pw91 Sn pseudopotential from the web site  
> with
> success?  I'm failing to verify the experimental lattice constants  
> c and a
> for the beta-Sn structure for this pseudopotential and I'm  
> wondering if I'm
> making a silly mistake that I can't see. The alpha-Sn lattice  
> constant on
> the other hand seems fine and is overestimated by only a 3%  
> difference. I
> include my input script to which the input parameters were
>
>     nk=4
>     ecutwfc=50
>     ecutrho=400
>
> Thank you very much in advance,
> Hande
>
> <lattice_constant_white_tin.sh>

---
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 etabel at hotmail.com  Sun Sep 10 04:56:20 2006
From: etabel at hotmail.com (Eric Abel)
Date: Sat, 09 Sep 2006 22:56:20 -0400
Subject: [Pw_forum] vc-relax
Message-ID: <BAY105-F19E819A023C42CEA16209FD4350@phx.gbl>

Hello all,

I have just performed a vc-relax calculation, and the program finished 
without complaints, but now I'm not sure how to decrypt the output file.  
Unlike 'relax' where the new atomic positions and forces are given, no such 
information seems to be given for vc-relax.  From browsing the forum 
archives, it seems that not many people use vc-relax so there is little or 
no documentation on it.  If I am successful with my results I will gladly 
contribute a short how-to.

Eric
Graduate Student, M.I.T.




From babazade at gmail.com  Sun Sep 10 15:05:46 2006
From: babazade at gmail.com (Amin Babazadeh)
Date: Sun, 10 Sep 2006 17:35:46 +0430
Subject: [Pw_forum] help
In-Reply-To: <200609081551.33285.giannozz@nest.sns.it>
References: <b25d3a170609080038n737f2cd8of5b6c64f3e382671@mail.gmail.com>
	 <200609081551.33285.giannozz@nest.sns.it>
Message-ID: <b25d3a170609100605ga70ce59tc973385d8638b740@mail.gmail.com>

Dear Dr.Paolo
I want to simulate a nanostructure with using espresso code.For doing it i
made a zns supercell, and after that i omitted some of the atoms .After
omitting i think the crystal looks a nanostructure.
Do you think I could simulate nanostructure with using this method.
I should say that the pw.x command run without any error for this structure.
I will appreciate if you say your idea about my job.


On 9/8/06, Paolo Giannozzi <giannozz at nest.sns.it> wrote:
>
> On Friday 08 September 2006 09:38, Amin Babazadeh wrote:
>
> > I want to simulate a nanostructure with using espresso code so I give
> > this structure [...]
> > The calculation for pw.x was good but my problem is in finding band
> > structures. I don't know what k-points is good for this structure.
>
> are you sure k-points are "good" ( i.e. a useful concept) for this
> structure? It looks like you are studying a small ZnS clusters using
> a fcc supercell.
>
> Paolo
> --
> Paolo Giannozzi             Phone:   +39/050-509876
> DEMOCRITOS and SNS          Fax:     +39/050-563513
> Piazza dei Cavalieri 7      I-56126 Pisa, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
AMIN
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From akohlmey at cmm.chem.upenn.edu  Sun Sep 10 19:40:39 2006
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sun, 10 Sep 2006 13:40:39 -0400
Subject: [Pw_forum] help
In-Reply-To: <b25d3a170609100605ga70ce59tc973385d8638b740@mail.gmail.com>
References: <b25d3a170609080038n737f2cd8of5b6c64f3e382671@mail.gmail.com>
	 <200609081551.33285.giannozz@nest.sns.it>
	 <b25d3a170609100605ga70ce59tc973385d8638b740@mail.gmail.com>
Message-ID: <7b6913e90609101040y126c3015n37e3bb06b44330b9@mail.gmail.com>

On 9/10/06, Amin Babazadeh <babazade at gmail.com> wrote:
>
> Dear Dr.Paolo

dear amin,

> I want to simulate a nanostructure with using espresso code.For doing it i
> made a zns supercell, and after that i omitted some of the atoms .After
> omitting i think the crystal looks a nanostructure.

it is some kind of a nanostructure, in the sense that it is a cluster.
however, you seem to be not paying enough attention to both the
chemistry (with a Zn:S ratio of 6:4 your cluster is either charged or
you'll have to have_very_ unusual bonding) and the physics (with a
cell size of > 30 a.u. the irreducible brillouine zone is small and
thus the need for extensive k-point sampling not very high, especially
with a compound like ZnS).

>  Do you think I could simulate nanostructure with using this method.
> I should say that the pw.x command run without any error for this structure.
> I will appreciate if you say your idea about my job.

the main suggestion would be that you first get more knowledgable
about the theory behind plane-wave pseudopotential calculations
in periodic systems. there are a number of fine text books available
(just search through the mailing list archives for some recommendations).
on that topic.

cheers,
    axel.
>
>
>
> On 9/8/06, Paolo Giannozzi <giannozz at nest.sns.it > wrote:
> > On Friday 08 September 2006 09:38, Amin Babazadeh wrote:
> >
> > > I want to simulate a nanostructure with using espresso code so I give
> > > this structure [...]
> > > The calculation for pw.x was good but my problem is in finding band
> > > structures. I don't know what k-points is good for this structure.
> >
> > are you sure k-points are "good" ( i.e. a useful concept) for this
> > structure? It looks like you are studying a small ZnS clusters using
> > a fcc supercell.
> >
> > Paolo
> > --
> > Paolo Giannozzi             Phone:   +39/050-509876
> > DEMOCRITOS and SNS          Fax:     +39/050-563513
> > Piazza dei Cavalieri 7      I-56126 Pisa, Italy
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> AMIN


-- 
=======================================================================
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 cesards at msi.umn.edu  Mon Sep 11 01:11:12 2006
From: cesards at msi.umn.edu (cesards at msi.umn.edu)
Date: Sun, 10 Sep 2006 18:11:12 -0500 (CDT)
Subject: [Pw_forum] vc-relax
Message-ID: <62365.128.101.191.226.1157929872.squirrel@www.msi.umn.edu>

Hi Eric,


with     verbosity = 'default'     pwscf will report new cell vectors in
units of a_0, and atomic positions relative to the new cell vector at the
end of standard output, just before the cpu time breakdow report.

Search for the keywords CELL_PARAMETERS and ATOMIC_POSITIONS.


Cesar R.S. da Silva.



From etabel at hotmail.com  Mon Sep 11 08:41:02 2006
From: etabel at hotmail.com (Eric Abel)
Date: Mon, 11 Sep 2006 02:41:02 -0400
Subject: [Pw_forum] vc-relax
In-Reply-To: <62365.128.101.191.226.1157929872.squirrel@www.msi.umn.edu>
Message-ID: <BAY105-F2738967C665570091C2024D42A0@phx.gbl>

Cesar,

Thank you for your response.  Unfortunately if it were that simple, I 
wouldn't have had the need to post to the forum.

my output file contains a series of scf calculations, which is to be 
expected, after each scf convergence it lists the atomic forces followed by 
the stress:

total energy              =  -357.37450532 ryd
     estimated scf accuracy    <        2.2E-11 ryd

     convergence has been achieved

     Forces acting on atoms (Ry/au):

     atom   1 type  1   force =     0.00000000    0.00000000    0.00682942
     atom   2 type  1   force =     0.00000000    0.00000000   -0.00682942
     atom   3 type  2   force =     0.00000000    0.00000000    0.20546159
     atom   4 type  2   force =     0.00000000    0.00000000   -0.20546159
     atom   5 type  3   force =     0.00000000    0.00000000   -0.08327844
     atom   6 type  3   force =     0.00000000    0.00000000    0.08327844


     entering subroutine stress ...

          total   stress  (ryd/bohr**3)                  (kbar)     P=  
-82.53
  -0.00135974   0.00000000   0.00000000       -200.02      0.00      0.00
   0.00000000  -0.00071001   0.00000000          0.00   -104.45      0.00
   0.00000000   0.00000000   0.00038671          0.00      0.00     56.89

after the last iteration, it lists a set of k-points followed by:

     Writing file     tiocl.save for program phonon

     PWSCF        :    13h57m CPU time

     init_run     :    66.55s CPU
     electrons    : 44803.10s CPU (      50 calls, 896.062 s avg)
     forces       :  1319.61s CPU (      50 calls,  26.392 s avg)
     stress       :  2795.36s CPU (      50 calls,  55.907 s avg)

     electrons    : 44803.10s CPU (      50 calls, 896.062 s avg)
     c_bands      : 37432.39s CPU (     343 calls, 109.132 s avg)
     sum_band     :  6668.94s CPU (     343 calls,  19.443 s avg)
     v_of_rho     :    70.93s CPU (     688 calls,   0.103 s avg)
     newd         :   669.21s CPU (     345 calls,   1.940 s avg)
     mix_rho      :    48.63s CPU (     343 calls,   0.142 s avg)

     c_bands      : 37432.39s CPU (     343 calls, 109.132 s avg)
     init_us_2    :   514.48s CPU (   59025 calls,   0.009 s avg)
     cegterg      : 36838.34s CPU (   25725 calls,   1.432 s avg)

     sum_band     :  6668.94s CPU (     343 calls,  19.443 s avg)
     becsum       :     5.02s CPU (   25725 calls,   0.000 s avg)
     addusdens    :   625.36s CPU (     343 calls,   1.823 s avg)

     wfcrot       :    44.03s CPU (      75 calls,   0.587 s avg)
     cegterg      : 36838.34s CPU (   25725 calls,   1.432 s avg)
     h_psi        : 24259.17s CPU (   85747 calls,   0.283 s avg)
     g_psi        :   203.06s CPU (   59947 calls,   0.003 s avg)
     overlap      :  3791.19s CPU (   59947 calls,   0.063 s avg)
     cdiaghg      :  1084.00s CPU (   60022 calls,   0.018 s avg)
     update       :  1402.85s CPU (   59947 calls,   0.023 s avg)
     last         :  1466.98s CPU (   26082 calls,   0.056 s avg)

     h_psi        : 24259.17s CPU (   85747 calls,   0.283 s avg)
     init         :    96.39s CPU (   85747 calls,   0.001 s avg)
     firstfft     :  8568.69s CPU ( 1932983 calls,   0.004 s avg)
     secondfft    :  8659.88s CPU ( 1932983 calls,   0.004 s avg)
     add_vuspsi   :  2826.23s CPU (   85747 calls,   0.033 s avg)
     s_psi        :  2548.22s CPU (   85747 calls,   0.030 s avg)

     General routines
     ccalbec      :  4178.90s CPU (  118972 calls,   0.035 s avg)
     cft3         :   128.72s CPU (    4378 calls,   0.029 s avg)
     cft3s        : 18657.11s CPU ( 4638404 calls,   0.004 s avg)
     interpolate  :    33.71s CPU (     688 calls,   0.049 s avg)
     davcio       :   147.96s CPU (   84750 calls,   0.002 s avg)

There are a few additional lines, but I don't find the words CELL_PARAMETERS 
or ATOMIC_POSITIONS anywhere.  My instinct tells me that perhaps something 
went wrong, but the program completed without complaint.  I never set the 
verbosity level, so I assume it's set at the default.  Like I said in my 
original post, in the 'relax' calculation, the relevant information was 
present.

Any ideas from anyone?

Eric

>From: cesards at msi.umn.edu
>Reply-To: pw_forum at pwscf.org
>To: pw_forum at pwscf.org
>Subject: Re:[Pw_forum] vc-relax
>Date: Sun, 10 Sep 2006 18:11:12 -0500 (CDT)
>
>Hi Eric,
>
>
>with     verbosity = 'default'     pwscf will report new cell vectors in
>units of a_0, and atomic positions relative to the new cell vector at the
>end of standard output, just before the cpu time breakdow report.
>
>Search for the keywords CELL_PARAMETERS and ATOMIC_POSITIONS.
>
>
>Cesar R.S. da Silva.
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum




From ceresoli at sissa.it  Mon Sep 11 08:56:26 2006
From: ceresoli at sissa.it (Davide Ceresoli)
Date: Mon, 11 Sep 2006 08:56:26 +0200
Subject: [Pw_forum] Status of NMR Project
In-Reply-To: <EBEJLEGBCGBNDNDDHFOFIEACCAAA.jzwanzig@dal.ca>
References: <EBEJLEGBCGBNDNDDHFOFIEACCAAA.jzwanzig@dal.ca>
Message-ID: <4505089A.90500@sissa.it>

Josef Zwanziger wrote:
> Dear Colleagues,
> 
> can someone provide an update to the status of incorporating GIPAW into
> pwscf? Last fall the information was that the project was back on after a
> pause, I wonder how things are going now?
> 
> Thanks much,
> 
> Joe Zwanziger
> Dept. of Chemistry
> Dalhousie University

Yes, in June we've put in the Pickard-Mauri GIPAW method for computing
the NMR and EPR. It's in the CVS version, in the NMR_new directory.
Right now, only the "bare" term is implemented. A. Seitsonen and U. 
Gerstmann have just implemented the reconstruction part. The code needs
to be cleaned up and tested extensively. We are 2-3 ppm off
the reference calculations done with an other code and we are
currently investigating. I hope everything will be fixed within
2-3 weeks.

Davide



From roma at srmp.saclay.cea.fr  Mon Sep 11 09:00:21 2006
From: roma at srmp.saclay.cea.fr (roma)
Date: Mon, 11 Sep 2006 09:00:21 +0200
Subject: [Pw_forum] vc-relax
In-Reply-To: <BAY105-F19E819A023C42CEA16209FD4350@phx.gbl>
References: <BAY105-F19E819A023C42CEA16209FD4350@phx.gbl>
Message-ID: <1157958022.21139.141.camel@srmp19.saclay.cea.fr>

Hello,

I have used vc-relax, the last time it was a couple of months ago with
PWSCF 3.1. In the input I had no verbosity flag (so it was the default
one) but I had:
    tstress = .true.,
    tprnfor = .true.,
In the output file (with no change of the verbosity flag) after the last
converged electronic iteration, I had forces, stresses, and then the
following:

     Wentzcovitch Damped Dynamics: convergence achieved, Efinal=
-1737.31382172

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

     Final estimate of lattice vectors (input alat units)
   0.972922012  -0.013290460  -0.011135071
  -0.011550462   0.849853383   0.014077965
  -0.013003053   0.018275504   1.104881947
  final unit-cell volume =   5650.6710 (a.u.)^3
  input alat =      18.3600 (a.u.)

CELL_PARAMETERS (alat)
   0.972922012  -0.013290460  -0.011135071
  -0.011550462   0.849853383   0.014077965
  -0.013003053   0.018275504   1.104881947

ATOMIC_POSITIONS (alat)
Si       0.213353153  -0.005371958   0.176573325
Si       0.356286914   0.189018144   0.370648864
... etc.

Writing output data file ISi73_+2.save-new

Then the usual info on timing.
I wasn't asking to write files for a phonon calculation, as it seems
you're doing. Hope it helps.

Guido




 
On Sat, 2006-09-09 at 22:56 -0400, Eric Abel wrote:
> Hello all,
> 
> I have just performed a vc-relax calculation, and the program finished 
> without complaints, but now I'm not sure how to decrypt the output file.  
> Unlike 'relax' where the new atomic positions and forces are given, no such 
> information seems to be given for vc-relax.  From browsing the forum 
> archives, it seems that not many people use vc-relax so there is little or 
> no documentation on it.  If I am successful with my results I will gladly 
> contribute a short how-to.
> 
> Eric
> Graduate Student, M.I.T.
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
-- 
Guido Roma <roma${at}cea.fr> -- CEA-Saclay - DEN/DMN/SRMP Bat.520/130
Phone: [+33]-1-69085738 -- Fax: ...6867 -- Mobile: [+33]-6-20069085




From etabel at hotmail.com  Mon Sep 11 10:01:49 2006
From: etabel at hotmail.com (Eric Abel)
Date: Mon, 11 Sep 2006 04:01:49 -0400
Subject: [Pw_forum] vc-relax
In-Reply-To: <1157958022.21139.141.camel@srmp19.saclay.cea.fr>
Message-ID: <BAY105-F90CB9CC66A88B5521F1E2D42A0@phx.gbl>

Hi roma,

Do you mind posting your input file...if you'd rather keep the material 
composition under wraps, I understand...just omit the ATOMIC SPECIES card.

Eric


>From: roma <roma at srmp.saclay.cea.fr>
>Reply-To: pw_forum at pwscf.org
>To: pw_forum at pwscf.org
>Subject: Re: [Pw_forum] vc-relax
>Date: Mon, 11 Sep 2006 09:00:21 +0200
>
>Hello,
>
>I have used vc-relax, the last time it was a couple of months ago with
>PWSCF 3.1. In the input I had no verbosity flag (so it was the default
>one) but I had:
>     tstress = .true.,
>     tprnfor = .true.,
>In the output file (with no change of the verbosity flag) after the last
>converged electronic iteration, I had forces, stresses, and then the
>following:
>
>      Wentzcovitch Damped Dynamics: convergence achieved, Efinal=
>-1737.31382172
>
>------------------------------------------------------------------------
>
>      Final estimate of lattice vectors (input alat units)
>    0.972922012  -0.013290460  -0.011135071
>   -0.011550462   0.849853383   0.014077965
>   -0.013003053   0.018275504   1.104881947
>   final unit-cell volume =   5650.6710 (a.u.)^3
>   input alat =      18.3600 (a.u.)
>
>CELL_PARAMETERS (alat)
>    0.972922012  -0.013290460  -0.011135071
>   -0.011550462   0.849853383   0.014077965
>   -0.013003053   0.018275504   1.104881947
>
>ATOMIC_POSITIONS (alat)
>Si       0.213353153  -0.005371958   0.176573325
>Si       0.356286914   0.189018144   0.370648864
>... etc.
>
>Writing output data file ISi73_+2.save-new
>
>Then the usual info on timing.
>I wasn't asking to write files for a phonon calculation, as it seems
>you're doing. Hope it helps.
>
>Guido
>
>
>
>
>
>On Sat, 2006-09-09 at 22:56 -0400, Eric Abel wrote:
> > Hello all,
> >
> > I have just performed a vc-relax calculation, and the program finished
> > without complaints, but now I'm not sure how to decrypt the output file.
> > Unlike 'relax' where the new atomic positions and forces are given, no 
>such
> > information seems to be given for vc-relax.  From browsing the forum
> > archives, it seems that not many people use vc-relax so there is little 
>or
> > no documentation on it.  If I am successful with my results I will 
>gladly
> > contribute a short how-to.
> >
> > Eric
> > Graduate Student, M.I.T.
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>--
>Guido Roma <roma${at}cea.fr> -- CEA-Saclay - DEN/DMN/SRMP Bat.520/130
>Phone: [+33]-1-69085738 -- Fax: ...6867 -- Mobile: [+33]-6-20069085
>
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum




From roma at srmp.saclay.cea.fr  Mon Sep 11 10:48:07 2006
From: roma at srmp.saclay.cea.fr (roma)
Date: Mon, 11 Sep 2006 10:48:07 +0200
Subject: [Pw_forum] vc-relax
In-Reply-To: <BAY105-F90CB9CC66A88B5521F1E2D42A0@phx.gbl>
References: <BAY105-F90CB9CC66A88B5521F1E2D42A0@phx.gbl>
Message-ID: <1157964488.21139.144.camel@srmp19.saclay.cea.fr>

On Mon, 2006-09-11 at 04:01 -0400, Eric Abel wrote:
> Hi roma,
> 
> Do you mind posting your input file...if you'd rather keep the material 
> composition under wraps, I understand...just omit the ATOMIC SPECIES card.

No problem, I haven't discovered any miraculous material whatsoever,
it's simply silicon dioxide ;-)
Guido



-- 
Guido Roma <roma${at}cea.fr> -- CEA-Saclay - DEN/DMN/SRMP Bat.520/130
Phone: [+33]-1-69085738 -- Fax: ...6867 -- Mobile: [+33]-6-20069085

-------------- next part --------------
SiO2
ISi73_+2
 &control
    calculation = 'vc-relax'
    restart_mode='from_scratch',
    prefix='ISi73_+2',
    disk_io='high',
    tstress = .true.,
    tprnfor = .true.,
    nstep=900,
    dt=50
    pseudo_dir = '/home/roma/O-sesame/pseudo//',
    outdir='./'
 /
 &system    
    ibrav=  0, celldm(1) =18.36,
    nat=  73, ntyp= 2, ecutwfc =80, 
    nosym=.true., nbnd=225,nelec=386
 /
 &electrons
    mixing_beta = 0.05 
    conv_thr =  5.0d-8
    diagonalization='cg'
 /
 &ions
 /
 &cell
 wmass=0.01
 press=0
 cell_dynamics='damp-w'
 press_conv_thr=2
 /
ATOMIC_SPECIES
 Si  28.086  Si.vbc.UPF
 O  15.999  O.mt.UPF
ATOMIC_POSITIONS (alat)
Si       0.215833604  -0.005149972   0.178195694
Si       0.360689499   0.190381795   0.371998571
Si       0.141546082   0.225884958  -0.009624532
O        0.122663860   0.119125789   0.117006117
O        0.301709669   0.046605337   0.312556712
O        0.263305651   0.263152943   0.486870074
O        0.017718471   0.195068423   0.415654998
O        0.378159059   0.293383515   0.238191554
O        0.072271300   0.368705240   0.053737987
Si       0.693471988  -0.013757077   0.174823651
Si       0.837355173   0.190665079   0.366774426
Si       0.635218478   0.195456730  -0.035929509
O        0.603367406   0.108038034   0.104591621
O        0.781561394   0.049818837   0.302942140
O        0.750772597   0.268730687   0.482914272
O        0.511101418   0.170328280   0.438997584
O        0.827945665   0.307321202   0.225060087
O        0.629450866   0.359392746   0.006512732
Si       0.457373790   0.438409785   0.227818103
Si       0.110713776   0.628668120   0.374294040
Si       0.370122449   0.652563218   0.003722566
O        0.374137083   0.532483866   0.121351013
O        0.061619618   0.476305094   0.313966622
O        0.011565036   0.682461079   0.494891096
O        0.263719509   0.620694097   0.433271801
O        0.102108142   0.726445111   0.238955083
O        0.312161817   0.793148865   0.071472570
Si       0.964149082   0.410412613   0.173498984
Si       0.583135122   0.637645712   0.396591077
Si       0.851531218   0.650605041  -0.010430668
Si       0.687218121   0.412812697   0.152278405
O        0.835556611   0.517127335   0.112759633
O        0.488326347   0.500316400   0.377833870
O        0.506216667   0.722735719   0.516158788
O        0.739913052   0.590505806   0.429444757
O        0.587420101   0.717175512   0.247107284
O        0.793961289   0.778565897   0.074069288
Si       0.195424165   0.014990628   0.736428394
Si       0.362136683   0.203062053   0.912793044
Si       0.110185747   0.246902892   0.549622272
O        0.097059614   0.136166865   0.675019578
O        0.294208083   0.059442986   0.864200367
O        0.290974273   0.264622463   1.053112260
O        0.054643047   0.186582938   0.960726551
O        0.344014794   0.311222100   0.786642743
O        0.054986166   0.392913349   0.608917543
Si       0.707239403  -0.001637623   0.720969894
Si       0.875991600   0.175798691   0.897584747
Si       0.602933100   0.240701507   0.559906792
O        0.618594831   0.133881828   0.685463691
O        0.826133016   0.029176505   0.836131888
O        0.787145316   0.195708020   1.037574386
O        0.523281646   0.174600671   0.949402393
O        0.847279606   0.297934790   0.787079987
O        0.547385271   0.385380932   0.618595054
Si       0.442047950   0.437252551   0.737773042
Si       0.111586805   0.630272748   0.928743879
Si       0.349875586   0.680804789   0.564479915
O        0.348795851   0.563825236   0.683351419
O        0.055207789   0.484214527   0.872028762
O        0.022735585   0.681931951   1.065295746
O        0.267191698   0.613148788   0.984636359
O        0.094229759   0.741002670   0.805082366
O        0.282515465   0.821645426   0.619472727
Si       0.939432932   0.426834063   0.733665473
Si       0.595728811   0.629137396   0.919951019
Si       0.839252008   0.652252916   0.551340997
O        0.838332128   0.550092219   0.683179695
O        0.531670145   0.484608321   0.871148997
O        0.516141949   0.692974665   1.053870961
O        0.753558719   0.605821285   0.973049301
O        0.594621514   0.735845118   0.792825084
O        0.779784218   0.801824190   0.594525881
K_POINTS
1
0.0 0.0 0.0 1.0
CELL_PARAMETERS (alat)
   0.978694875  -0.009470492  -0.008079682
  -0.008212973   0.852389532   0.011820621
  -0.009049098   0.015265495   1.107706317


From etabel at hotmail.com  Mon Sep 11 21:16:16 2006
From: etabel at hotmail.com (Eric Abel)
Date: Mon, 11 Sep 2006 15:16:16 -0400
Subject: [Pw_forum] vc-relax
In-Reply-To: <1157964488.21139.144.camel@srmp19.saclay.cea.fr>
Message-ID: <BAY105-F2823F7BE74ABC4C0F7D8ED42A0@phx.gbl>

PWSCF Users

I am running the vc-relax calculation again, with more or less the same 
parameters as
Guido (roma at srmp.saclay.cea.fr), but I am noticing (as I did with the first 
time I tried tha calculation) that neither the force nor the stress is 
changing from iteration to iteration.  This makes me think that perhaps the 
program reached a maximum number of iterations the first time I tried the 
calculation and therefore there were not lattice or cell parameters to 
report.

The relevant parts of my input file are the following:

                 calculation = 'vc-relax' ,
                restart_mode = 'from_scratch' ,
                      outdir = './tmp/' ,
                  pseudo_dir = '/home/eric/espresso/pseudo/' ,
                      prefix = 'tiocl' ,
                     tstress = .true.,
                     tprnfor = .true.,

/
&SYSTEM
                       ibrav = 8,
                   celldm(1) = 7.1544654,
                   celldm(2) = .8877443,
                   celldm(3) = 2.1249340,
                         nat = 6,
                        ntyp = 3,
                     ecutwfc = 30.0 ,
                     ecutrho = 240 ,
                 occupations = 'smearing' ,
                     degauss = .02 ,
                    smearing = 'methfessel-paxton' ,
                       nspin = 1 ,
/
&ELECTRONS
                    conv_thr = 1.0e-10 ,
                 mixing_beta = 0.7 ,
             diagonalization = 'david' ,
/
&IONS
/
&CELL
               cell_dynamics = 'damp-w' ,
                       wmass = .01,
                       press = 0,
/

This is really the first problem I have encountered using PWSCF where things 
didn't behave as they should.  Could it be that I am using 2.1?

Eric


>Subject: Re: [Pw_forum] vc-relax
>Date: Mon, 11 Sep 2006 10:48:07 +0200
>
>On Mon, 2006-09-11 at 04:01 -0400, Eric Abel wrote:
> > Hi roma,
> >
> > Do you mind posting your input file...if you'd rather keep the material
> > composition under wraps, I understand...just omit the ATOMIC SPECIES 
>card.
>
>No problem, I haven't discovered any miraculous material whatsoever,
>it's simply silicon dioxide ;-)
>Guido
>
>
>
>--
>Guido Roma <roma${at}cea.fr> -- CEA-Saclay - DEN/DMN/SRMP Bat.520/130
>Phone: [+33]-1-69085738 -- Fax: ...6867 -- Mobile: [+33]-6-20069085
>


><< ISi73__2.in >>




From likedew at phys.ksu.edu  Mon Sep 11 21:37:22 2006
From: likedew at phys.ksu.edu (Hong, SamPyo)
Date: Mon, 11 Sep 2006 14:37:22 -0500
Subject: [Pw_forum] Calculations for  local density of states  within the Wigner-Seitz radius
References: <F0712C28C5E30740A5F81252A97E6F32E5F34B@isis.phys.ksu.edu> <200609070934.18827.giannozz@nest.sns.it> <7b6913e90609070701j2a340ed5r91e25815b5487584@mail.gmail.com> <200609071731.34283.giannozz@nest.sns.it>
Message-ID: <F0712C28C5E30740A5F81252A97E6F32017E2217@isis.phys.ksu.edu>

Hello, dear users
 
It is often interesting and physically important to calculate local density of states (or charge density) within the Wigner-Seitz Radius around a given atom, despite the fact that the radius cannot be determined unambiguously.
 
How can this be done in the code? Or any suggestions?
 
Thanks.
 
Sampyo Hong
______________________________
 Research Associate
 Department of Physics, Kansas State University, Manhattan, KS 66506, USA.
 E-Mail: likedew at phys.ksu.edu   WEB: http://www.phys.ksu.edu/personal/likedew 
 Phone: +1-785-532-1642            FAX:   +1-785-532-6806
 Favorite quotation: 
      "God demonstrates his own love for us in this: While we were still sinners, Christ died for us."
_______________________________
 
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From akohlmey at cmm.chem.upenn.edu  Mon Sep 11 21:45:01 2006
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 11 Sep 2006 15:45:01 -0400
Subject: [Pw_forum] vc-relax
In-Reply-To: <BAY105-F2823F7BE74ABC4C0F7D8ED42A0@phx.gbl>
References: <1157964488.21139.144.camel@srmp19.saclay.cea.fr>
	 <BAY105-F2823F7BE74ABC4C0F7D8ED42A0@phx.gbl>
Message-ID: <7b6913e90609111245n2a5d8addy84e8d8bb08c6a95d@mail.gmail.com>

> This is really the first problem I have encountered using PWSCF where things
> didn't behave as they should.  Could it be that I am using 2.1?

do you have a specific reason to use version 2.1?
did you check with the current version?

please don't expect people to fix problems in obsolete
versions of the package.

cheers,
   axel.


ps: when reporting problems, please _always_ report the version of the code
your are using and the platform you are running on. this makes isolating the
problem _so_ much easier. there is nothing more frustrating than locating a
bug and then seeing that this bug has already been fixed in a later version
of the code or that the code was compiled with a compiler that is known to
miscompile the code.
>
> Eric
>
>


-- 
=======================================================================
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 likedew at phys.ksu.edu  Mon Sep 11 21:50:00 2006
From: likedew at phys.ksu.edu (Hong, SamPyo)
Date: Mon, 11 Sep 2006 14:50:00 -0500
Subject: [Pw_forum] Calculations of work-function of slab
References: <BAY105-F2823F7BE74ABC4C0F7D8ED42A0@phx.gbl>
Message-ID: <F0712C28C5E30740A5F81252A97E6F32017E2219@isis.phys.ksu.edu>

Hi,
 
As the subject title says, I am intereted in calculations of workfunction for a given slab (surface). (I'm afraid that this topic may have been covered, but as I did some search on the pw_forum archive, I couldn't find a result though.)
 
How can workfunction be calculated in the code?  As the total potential can be calculated using pp.x (plot_num=1), can work-function be the difference between the potential energy at the vacuum (in a supercell) and the Fermi energy which is given by the code?
 
Thanks.
 
Sampyo Hong
______________________________
 Research Associate
 Department of Physics, Kansas State University, Manhattan, KS 66506, USA.
 E-Mail: likedew at phys.ksu.edu   WEB: http://www.phys.ksu.edu/personal/likedew 
 Phone: +1-785-532-1642            FAX:   +1-785-532-6806
 Favorite quotation: 
      "God demonstrates his own love for us in this: While we were still sinners, Christ died for us."
_______________________________

 
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From marzari at MIT.EDU  Mon Sep 11 22:02:21 2006
From: marzari at MIT.EDU (Nicola Marzari)
Date: Mon, 11 Sep 2006 16:02:21 -0400
Subject: [Pw_forum] Calculations of work-function of slab
In-Reply-To: <F0712C28C5E30740A5F81252A97E6F32017E2219@isis.phys.ksu.edu>
References: <BAY105-F2823F7BE74ABC4C0F7D8ED42A0@phx.gbl> <F0712C28C5E30740A5F81252A97E6F32017E2219@isis.phys.ksu.edu>
Message-ID: <4505C0CD.9040901@mit.edu>


Hong, SamPyo wrote:
> Hi,
>  
> As the subject title says, I am intereted in calculations of workfunction for a given slab (surface). (I'm afraid that this topic may have been covered, but as I did some search on the pw_forum archive, I couldn't find a result though.)
>  
> How can workfunction be calculated in the code?  As the total potential can be calculated using pp.x (plot_num=1), can work-function be the difference between the potential energy at the vacuum (in a supercell) and the Fermi energy which is given by the code?
>  
> Thanks.
>  
> Sampyo Hong
> _______


Hi Sampyo,

here is the link:

http://www.democritos.it/pipermail/pw_forum/2006-April/003887.html

			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 etabel at hotmail.com  Mon Sep 11 22:15:28 2006
From: etabel at hotmail.com (Eric Abel)
Date: Mon, 11 Sep 2006 16:15:28 -0400
Subject: [Pw_forum] vc-relax
In-Reply-To: <7b6913e90609111245n2a5d8addy84e8d8bb08c6a95d@mail.gmail.com>
Message-ID: <BAY105-F142E404720BEA1151696ACD42A0@phx.gbl>

Sorry Axel,

I actually didn't think this was a bug in the program, but rather a bug in 
myself.  I had no expectations of anyone to fix anything, just to point me 
in the right direction, even if that means upgrading the software.  I will 
do this, and if the problem persists, I'll be back.

Eric


>From: "Axel Kohlmeyer" <akohlmey at cmm.chem.upenn.edu>
>Reply-To: pw_forum at pwscf.org
>To: pw_forum at pwscf.org
>Subject: Re: [Pw_forum] vc-relax
>Date: Mon, 11 Sep 2006 15:45:01 -0400
>
>>This is really the first problem I have encountered using PWSCF where 
>>things
>>didn't behave as they should.  Could it be that I am using 2.1?
>
>do you have a specific reason to use version 2.1?
>did you check with the current version?
>
>please don't expect people to fix problems in obsolete
>versions of the package.
>
>cheers,
>   axel.
>
>
>ps: when reporting problems, please _always_ report the version of the code
>your are using and the platform you are running on. this makes isolating 
>the
>problem _so_ much easier. there is nothing more frustrating than locating a
>bug and then seeing that this bug has already been fixed in a later version
>of the code or that the code was compiled with a compiler that is known to
>miscompile the code.
>>
>>Eric
>>
>>
>
>
>--
>=======================================================================
>Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>  Center for Molecular Modeling   --   University of Pennsylvania
>Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
>tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
>=======================================================================
>If you make something idiot-proof, the universe creates a better idiot.
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum




From likedew at phys.ksu.edu  Mon Sep 11 23:50:53 2006
From: likedew at phys.ksu.edu (Hong, SamPyo)
Date: Mon, 11 Sep 2006 16:50:53 -0500
Subject: [Pw_forum] Calculations of work-function of slab
In-Reply-To: <4505C0CD.9040901@mit.edu>
Message-ID: <F0712C28C5E30740A5F81252A97E6F32E5F34F@isis.phys.ksu.edu>

Dear Prof. Marzari, 

>here is the link:
>http://www.democritos.it/pipermail/pw_forum/2006-April/003887.html

 Thank you very much for your help!

 Sampyo Hong



From giannozz at nest.sns.it  Tue Sep 12 00:02:10 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 12 Sep 2006 00:02:10 +0200
Subject: [Pw_forum] vc-relax
In-Reply-To: <BAY105-F2823F7BE74ABC4C0F7D8ED42A0@phx.gbl>
References: <BAY105-F2823F7BE74ABC4C0F7D8ED42A0@phx.gbl>
Message-ID: <200609120002.10333.giannozz@nest.sns.it>

On Monday 11 September 2006 21:16, Eric Abel wrote:

> This is really the first problem I have encountered using PWSCF where
> things didn't behave as they should.  Could it be that I am using 2.1?

it could. Several problems in variable-cell calculations have been
fixed in recent versions. From file Doc/BUGS:
...
Fixed in version 2.1.3:
...
  *  damped variable-cell dynamics in PWscf was not working properly
...
Fixed in version 2.1.2:
...
  *  variable-cell dynamics and optimization was not working in parallel
...

Paolo
-- 
Paolo Giannozzi             Phone:   +39/050-509876
DEMOCRITOS and SNS          Fax:     +39/050-563513 
Piazza dei Cavalieri 7      I-56126 Pisa, Italy


From jasonsun98 at hotmail.com  Tue Sep 12 03:23:21 2006
From: jasonsun98 at hotmail.com (sun jian)
Date: Tue, 12 Sep 2006 01:23:21 +0000
Subject: [Pw_forum] vc-relax
In-Reply-To: <20060911193801.3515.21054.Mailman@democritos.sissa.it>
Message-ID: <BAY107-F247BAE3E815A677B308B2BDF2B0@phx.gbl>

Hi Eric,

It seems that your vc-relax calculation is not finished, it just terminate. 
because it not get convergence for the tress tensor or pressure when it get 
the max step (n=50).

the way solve this problem is get a more good start geometry or largen the 
step maximum.
please specify nstep = 100 or larger in the input file.

good luck!

Best regards,
=============================================== 
Jian SUN 
Physics Dept. of Nanjing University 
National Lab. of Solid State Microstructures 
22 Hankou Road, Gulou District 
Nanjing, Jiangsu Province 
210093 
China 
===============================================  


Message: 1
From: "Eric Abel" <etabel at hotmail.com>
To: pw_forum at pwscf.org
Subject: Re:[Pw_forum] vc-relax
Date: Mon, 11 Sep 2006 02:41:02 -0400
Reply-To: pw_forum at pwscf.org

Cesar,

Thank you for your response.  Unfortunately if it were that simple, I 
wouldn't have had the need to post to the forum.

my output file contains a series of scf calculations, which is to be 
expected, after each scf convergence it lists the atomic forces followed by 

the stress:

total energy              =  -357.37450532 ryd
     estimated scf accuracy    <        2.2E-11 ryd

     convergence has been achieved

     Forces acting on atoms (Ry/au):

     atom   1 type  1   force =     0.00000000    0.00000000    0.00682942
     atom   2 type  1   force =     0.00000000    0.00000000   -0.00682942
     atom   3 type  2   force =     0.00000000    0.00000000    0.20546159
     atom   4 type  2   force =     0.00000000    0.00000000   -0.20546159
     atom   5 type  3   force =     0.00000000    0.00000000   -0.08327844
     atom   6 type  3   force =     0.00000000    0.00000000    0.08327844


     entering subroutine stress ...

          total   stress  (ryd/bohr**3)                  (kbar)     P=  
-82.53
  -0.00135974   0.00000000   0.00000000       -200.02      0.00      0.00
   0.00000000  -0.00071001   0.00000000          0.00   -104.45      0.00
   0.00000000   0.00000000   0.00038671          0.00      0.00     56.89

after the last iteration, it lists a set of k-points followed by:

     Writing file     tiocl.save for program phonon

     PWSCF        :    13h57m CPU time

     init_run     :    66.55s CPU
     electrons    : 44803.10s CPU (      50 calls, 896.062 s avg)
     forces       :  1319.61s CPU (      50 calls,  26.392 s avg)
     stress       :  2795.36s CPU (      50 calls,  55.907 s avg)

     electrons    : 44803.10s CPU (      50 calls, 896.062 s avg)
     c_bands      : 37432.39s CPU (     343 calls, 109.132 s avg)
     sum_band     :  6668.94s CPU (     343 calls,  19.443 s avg)
     v_of_rho     :    70.93s CPU (     688 calls,   0.103 s avg)
     newd         :   669.21s CPU (     345 calls,   1.940 s avg)
     mix_rho      :    48.63s CPU (     343 calls,   0.142 s avg)

     c_bands      : 37432.39s CPU (     343 calls, 109.132 s avg)
     init_us_2    :   514.48s CPU (   59025 calls,   0.009 s avg)
     cegterg      : 36838.34s CPU (   25725 calls,   1.432 s avg)

     sum_band     :  6668.94s CPU (     343 calls,  19.443 s avg)
     becsum       :     5.02s CPU (   25725 calls,   0.000 s avg)
     addusdens    :   625.36s CPU (     343 calls,   1.823 s avg)

     wfcrot       :    44.03s CPU (      75 calls,   0.587 s avg)
     cegterg      : 36838.34s CPU (   25725 calls,   1.432 s avg)
     h_psi        : 24259.17s CPU (   85747 calls,   0.283 s avg)
     g_psi        :   203.06s CPU (   59947 calls,   0.003 s avg)
     overlap      :  3791.19s CPU (   59947 calls,   0.063 s avg)
     cdiaghg      :  1084.00s CPU (   60022 calls,   0.018 s avg)
     update       :  1402.85s CPU (   59947 calls,   0.023 s avg)
     last         :  1466.98s CPU (   26082 calls,   0.056 s avg)

     h_psi        : 24259.17s CPU (   85747 calls,   0.283 s avg)
     init         :    96.39s CPU (   85747 calls,   0.001 s avg)
     firstfft     :  8568.69s CPU ( 1932983 calls,   0.004 s avg)
     secondfft    :  8659.88s CPU ( 1932983 calls,   0.004 s avg)
     add_vuspsi   :  2826.23s CPU (   85747 calls,   0.033 s avg)
     s_psi        :  2548.22s CPU (   85747 calls,   0.030 s avg)

     General routines
     ccalbec      :  4178.90s CPU (  118972 calls,   0.035 s avg)
     cft3         :   128.72s CPU (    4378 calls,   0.029 s avg)
     cft3s        : 18657.11s CPU ( 4638404 calls,   0.004 s avg)
     interpolate  :    33.71s CPU (     688 calls,   0.049 s avg)
     davcio       :   147.96s CPU (   84750 calls,   0.002 s avg)

There are a few additional lines, but I don't find the words 
CELL_PARAMETERS 
or ATOMIC_POSITIONS anywhere.  My instinct tells me that perhaps something 
went wrong, but the program completed without complaint.  I never set the 
verbosity level, so I assume it's set at the default.  Like I said in my 
original post, in the 'relax' calculation, the relevant information was 
present.

Any ideas from anyone?

Eric




From cesards at msi.umn.edu  Tue Sep 12 03:37:18 2006
From: cesards at msi.umn.edu (cesards at msi.umn.edu)
Date: Mon, 11 Sep 2006 20:37:18 -0500 (CDT)
Subject: [Pw_forum] Re:Re:vc-relax (Eric Abel)
Message-ID: <64881.128.101.191.226.1158025038.squirrel@www.msi.umn.edu>

Hi Eric,

It is OK, I understand your problem now: Your damped dynamics cicle heve
NOT converged. If dt parameter in &CONTROL, wmass in  &CELL namelist and
atomic masses are not set properly damped wc-dynamics takes too long to
converge. If you are not running in damped mode, the keywords tosearch are
"new lattice vectors (alat unit) :" and "new positions in cryst coord".
The program will report those at end of every MD step.

Also remember to set nstep in &CONTROL namelist to an appropriate number,
depending on the numbers of degrees of freedom, and the fine tunning of
paremeters above.

If you want to learn how to optimize dt, wmass and atomic masses, take a
look at the several tutorials at

http://www.vlab.msi.umn.edu/events/tutorials.shtml


Yours,

Cesar R.S. da Silva.




From babazade at gmail.com  Tue Sep 12 08:37:52 2006
From: babazade at gmail.com (Amin Babazadeh)
Date: Tue, 12 Sep 2006 11:07:52 +0430
Subject: [Pw_forum] help
In-Reply-To: <7b6913e90609101040y126c3015n37e3bb06b44330b9@mail.gmail.com>
References: <b25d3a170609080038n737f2cd8of5b6c64f3e382671@mail.gmail.com>
	 <200609081551.33285.giannozz@nest.sns.it>
	 <b25d3a170609100605ga70ce59tc973385d8638b740@mail.gmail.com>
	 <7b6913e90609101040y126c3015n37e3bb06b44330b9@mail.gmail.com>
Message-ID: <b25d3a170609112337p3792ae0bucdcebcba75c10d9d@mail.gmail.com>

Dear Dr.Axel
Thanks a lot for your helping.
As I said before, I wanted to simulate a nanostructure and I began my job
with Wien2k code but this software takes a long time to run and for reducing
the time i  need supercomputers that i don't have. So i decided to change my
software. And now i start to do it with espresso code.My first problem is
that I don't know whether the espresso code  could simulate it or
not.Youare an expert.  would you please tell me, if it  is possible to
simulate a
nanostructure with using espresso code until I began my study about PWscf
and espresso code or i  have to change it again.
Cheers
Amin

On 9/10/06, Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu> wrote:
>
> On 9/10/06, Amin Babazadeh <babazade at gmail.com> wrote:
> >
> > Dear Dr.Paolo
>
> dear amin,
>
> > I want to simulate a nanostructure with using espresso code.For doing it
> i
> > made a zns supercell, and after that i omitted some of the atoms .After
> > omitting i think the crystal looks a nanostructure.
>
> it is some kind of a nanostructure, in the sense that it is a cluster.
> however, you seem to be not paying enough attention to both the
> chemistry (with a Zn:S ratio of 6:4 your cluster is either charged or
> you'll have to have_very_ unusual bonding) and the physics (with a
> cell size of > 30 a.u. the irreducible brillouine zone is small and
> thus the need for extensive k-point sampling not very high, especially
> with a compound like ZnS).
>
> >  Do you think I could simulate nanostructure with using this method.
> > I should say that the pw.x command run without any error for this
> structure.
> > I will appreciate if you say your idea about my job.
>
> the main suggestion would be that you first get more knowledgable
> about the theory behind plane-wave pseudopotential calculations
> in periodic systems. there are a number of fine text books available
> (just search through the mailing list archives for some recommendations).
> on that topic.
>
> cheers,
>     axel.
> >
> >
> >
> > On 9/8/06, Paolo Giannozzi <giannozz at nest.sns.it > wrote:
> > > On Friday 08 September 2006 09:38, Amin Babazadeh wrote:
> > >
> > > > I want to simulate a nanostructure with using espresso code so I
> give
> > > > this structure [...]
> > > > The calculation for pw.x was good but my problem is in finding band
> > > > structures. I don't know what k-points is good for this structure.
> > >
> > > are you sure k-points are "good" ( i.e. a useful concept) for this
> > > structure? It looks like you are studying a small ZnS clusters using
> > > a fcc supercell.
> > >
> > > Paolo
> > > --
> > > Paolo Giannozzi             Phone:   +39/050-509876
> > > DEMOCRITOS and SNS          Fax:     +39/050-563513
> > > Piazza dei Cavalieri 7      I-56126 Pisa, Italy
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> >
> >
> >
> > --
> > AMIN
>
>
> --
> =======================================================================
> Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>   Center for Molecular Modeling   --   University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
AMIN
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From Conor.Hogan at roma2.infn.it  Tue Sep 12 11:48:53 2006
From: Conor.Hogan at roma2.infn.it (Conor Hogan)
Date: Tue, 12 Sep 2006 10:48:53 +0100 (GMT+0100)
Subject: [Pw_forum] Relativistics PPs + pp.x problems
Message-ID: <Pine.OSF.3.95a.1060912104745.25812C-100000@axroma2.roma2.infn.it>

Dear developers,
I'm having some problems using pp.x with fully relativistic pseudopotentials, but with lspinorb=.false. (I just want to plot the potential: I generally calculate the charge density in this way, before switching on SO for the bandstructure) )
The code gives me a segmentation fault here:

PW/init_us_1.f90 : line 175 or so
     if (so(nt)) then
       [...]
       fcoef(ih,kh,is1,is2,nt)=coeff
       [...]
     endif
because fcoef is not allocated. This appears to be because fcoef is only allocated if lspinorb=.true. :

PW/allocate_nlpot.f90
  if (lspinorb) then
    [...]
    allocate (fcoef(nhm,nhm,2,2,nsp))
    [...]
  else
    [...]
  endif

perhaps the distinction between so(nt) and lspinorb=.true. hasn't been 
looked after properly here? But then I dont know how the pw.x works ok...
Some quick hacks didn't fix the problem, after that I'm out of my depth.

Using ifort 9.0 on linux, PW 3.1 and 3.1.1 (routines are the same).

Best regards and thanks for all the general help in the forums.
Conor
PS Should I send problems like these direct to developers rather than the forum?


----

Dr. Conor Hogan                                --- -----  ---   --- 
Dipartimento di Fisica e CNR-INFM             |      :   |     :    
Universita' di Roma "Tor Vergata"             |--    :    ---  |---
Tel: +39 06 72594908 (NEW!)                   |      :       | :    
Fax: +39 06 2023507                            ---   :    ---  :    
http://www.fisica.uniroma2.it/~cmtheo-group/  European Theoretical  
                                              Spectroscopy Facility 
                                              http://www.etsf.eu    
 
The early bird gets the worm, but the second mouse gets the cheese. - S. Wright

If you go through a lot of hammers each month, I don't think it necessarily 
means you're a hard worker. It may just mean that you have a lot to learn 
about proper hammer maintenance - J. Handey




From Conor.Hogan at roma2.infn.it  Tue Sep 12 12:49:57 2006
From: Conor.Hogan at roma2.infn.it (Conor Hogan)
Date: Tue, 12 Sep 2006 11:49:57 +0100 (GMT+0100)
Subject: [Pw_forum] Relativistics PPs + pp.x problems
In-Reply-To: <Pine.OSF.3.95a.1060912104745.25812C-100000@axroma2.roma2.infn.it>
Message-ID: <Pine.OSF.3.95a.1060912114655.25812D-100000@axroma2.roma2.infn.it>

Just realised that the problem is so(nt) should not be .true. when
lspinorb=.false. in the scf run: a quick fix is setting so(nt)=.false. in
init_is_1.f90 for this run - of course the bug is still present for some
reason, but I can at least stop banging my head off the wall for today.
Regards,
Conor

> Dear developers,
> I'm having some problems using pp.x with fully relativistic pseudopotentials, but with lspinorb=.false. (I just want to plot the potential: I generally calculate the charge density in this way, before switching on SO for the bandstructure) )
> The code gives me a segmentation fault here:
> 
> PW/init_us_1.f90 : line 175 or so
>      if (so(nt)) then
>        [...]
>        fcoef(ih,kh,is1,is2,nt)=coeff
>        [...]
>      endif
> because fcoef is not allocated. This appears to be because fcoef is only allocated if lspinorb=.true. :
> 
> PW/allocate_nlpot.f90
>   if (lspinorb) then
>     [...]
>     allocate (fcoef(nhm,nhm,2,2,nsp))
>     [...]
>   else
>     [...]
>   endif
> 
> perhaps the distinction between so(nt) and lspinorb=.true. hasn't been 
> looked after properly here? But then I dont know how the pw.x works ok...
> Some quick hacks didn't fix the problem, after that I'm out of my depth.
> 
> Using ifort 9.0 on linux, PW 3.1 and 3.1.1 (routines are the same).
> 
> Best regards and thanks for all the general help in the forums.
> Conor
> PS Should I send problems like these direct to developers rather than the forum?
> 
> 
> ----
> 
> Dr. Conor Hogan                                --- -----  ---   --- 
> Dipartimento di Fisica e CNR-INFM             |      :   |     :    
> Universita' di Roma "Tor Vergata"             |--    :    ---  |---
> Tel: +39 06 72594908 (NEW!)                   |      :       | :    
> Fax: +39 06 2023507                            ---   :    ---  :    
> http://www.fisica.uniroma2.it/~cmtheo-group/  European Theoretical  
>                                               Spectroscopy Facility 
>                                               http://www.etsf.eu    
>  
> The early bird gets the worm, but the second mouse gets the cheese. - S. Wright
> 
> If you go through a lot of hammers each month, I don't think it necessarily 
> means you're a hard worker. It may just mean that you have a lot to learn 
> about proper hammer maintenance - J. Handey
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 



From L.Boeri at fkf.mpg.de  Tue Sep 12 13:39:10 2006
From: L.Boeri at fkf.mpg.de (Lilia Boeri)
Date: Tue, 12 Sep 2006 13:39:10 +0200 (CEST)
Subject: [Pw_forum] Compilation Problem
In-Reply-To: <44ED5ED5.80902@cea.fr>
References: <44ED5ED5.80902@cea.fr>
Message-ID: <Pine.LNX.4.61.0609121332140.3715@pcand23.mpi-stuttgart.mpg.de>

Dear PWSCF users,

I am trying to compile Quantum Expresso 3.1.1 on a powerpc machine with 
xlf compiler. I ran the configure script without problem, and then issued 
the 'make all' command. The compilation crashed at some point with the 
message:

"1501-510  Compilation successful for file iotk_write.f90.
xlf90_r -q64 -qalias=noaryovrlp -O3 -qstrict -qarch=auto -qtune=auto -qdpc 
-Q -qalias=nointptr -qsuffix=cpp=f90 -qfree=f90 -WF,-D__AIX,-D__ESSL 
-I../include  -I. -I../Modules -I../PW -I../PH -I../iotk/src -I../CPV -c 
iotk_xtox.f90
** iotk_atol_x   === End of Compilation 1 ===
"iotk_xtox.spp", line 78.65: 1517-005 (U) Error in Conform.  Call service 
representative.
1501-511  Compilation failed for file iotk_xtox.f90.
make[3]: *** [iotk_xtox.o] Error 1
make[3]: Leaving directory 
`/home/users/xiewh/program/pwscf/espresso-3.1.1/iotk/src'
make[2]: *** [libiotk.a] Error 2
make[2]: Leaving directory 
`/home/users/xiewh/program/pwscf/espresso-3.1.1/iotk'
make[1]: *** [libiotk] Error 2
make[1]: Leaving directory 
`/home/users/xiewh/program/pwscf/espresso-3.1.1'
xlf90_r -q64 -qalias=noaryovrlp -O3 -qstrict -qarch=auto -qtune=auto -qdpc 
-Q -qalias=nointptr -qsuffix=cpp=f90 -qfree=f90 -WF,-D__AIX,-D__ESSL 
-I../include  -I. -I../Modules -I../PW -I../PH -I../iotk/src -I../CPV -c 
../Modules/check_stop.f90
"../Modules/check_stop.f90", line 19.7: 1514-219 (S) Unable to access 
module symbol file for module kinds. Check path and file permissions of 
file. Use association not done for this module.
1501-511  Compilation failed for file check_stop.f90.
make: *** [../Modules/check_stop.o] Error 1
"
Do you know what the problem might be?
Thanks a lot,
Lilia


From giannozz at nest.sns.it  Tue Sep 12 14:05:23 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 12 Sep 2006 14:05:23 +0200
Subject: [Pw_forum] Compilation Problem
In-Reply-To: <Pine.LNX.4.61.0609121332140.3715@pcand23.mpi-stuttgart.mpg.de>
References: <44ED5ED5.80902@cea.fr> <Pine.LNX.4.61.0609121332140.3715@pcand23.mpi-stuttgart.mpg.de>
Message-ID: <200609121405.23193.giannozz@nest.sns.it>

On Tuesday 12 September 2006 13:39, Lilia Boeri wrote:

> "iotk_xtox.spp", line 78.65: 1517-005 (U) Error in Conform.  
> Call service representative. 

did you ? and what did the service representative say :-) ?

Seriously: this kind of messages is clearly due to some
compiler bug, so you should either find a workaround
or change/upgrade compiler. In this particular case, 
it is line 78 (column 65) of iotk/src/iotk_xtox.spp that 
confuses your compiler:

#ifdef __IOTK_WORKAROUND5
  integer(kind=__IOTK_INTEGER$kind) :: limit(0:9)
  integer(kind=__IOTK_INTEGER$kind) :: hug
  hug = huge(j)
  limit(0:9) = (/ ((hug-j)/10,j=0,9) /)
#else
==>  integer(kind=__IOTK_INTEGER$kind), parameter :: limit(0:9) = (/ 
((huge(j)-j)/10,j=0,9) /)
#endif

Apparently it has confused scores of other compilers as well:
#define __IOTK_WORKAROUND5 in iotk/include/iotk_config.h 
and it might work, without calling a service representative 

Notice that recent IBM machines seem to need xlf95 
instead of xlf90

Paolo
-- 
Paolo Giannozzi             Phone:   +39/050-509876
DEMOCRITOS and SNS          Fax:     +39/050-563513 
Piazza dei Cavalieri 7      I-56126 Pisa, Italy


From etabel at hotmail.com  Tue Sep 12 18:17:10 2006
From: etabel at hotmail.com (Eric Abel)
Date: Tue, 12 Sep 2006 12:17:10 -0400
Subject: [Pw_forum] Re:Re:vc-relax (Eric Abel)
In-Reply-To: <64881.128.101.191.226.1158025038.squirrel@www.msi.umn.edu>
Message-ID: <BAY105-F22015439FCAAB67F9EFD00D42B0@phx.gbl>

Thank you all for your tips.  It turns out the real fix was to upgrade to 
the latest stable version.  Now the program is behaving as I would expect.

Cesar, you mention the parameters wmass and dt...I was wondering if there is 
a way to get an initial estimate for these values.  Unfortunately the 
documentation on this is sketchy at best.

Right now I am running with wmass=0.1, and I didn't set dt, so it must be 
using the default.  Things are converging slowly...the atomic forces are 
creeping down.

Eric

>From: cesards at msi.umn.edu
>Reply-To: pw_forum at pwscf.org
>To: pw_forum at pwscf.org
>Subject: [Pw_forum] Re:Re:vc-relax (Eric Abel)
>Date: Mon, 11 Sep 2006 20:37:18 -0500 (CDT)
>
>Hi Eric,
>
>It is OK, I understand your problem now: Your damped dynamics cicle heve
>NOT converged. If dt parameter in &CONTROL, wmass in  &CELL namelist and
>atomic masses are not set properly damped wc-dynamics takes too long to
>converge. If you are not running in damped mode, the keywords tosearch are
>"new lattice vectors (alat unit) :" and "new positions in cryst coord".
>The program will report those at end of every MD step.
>
>Also remember to set nstep in &CONTROL namelist to an appropriate number,
>depending on the numbers of degrees of freedom, and the fine tunning of
>paremeters above.
>
>If you want to learn how to optimize dt, wmass and atomic masses, take a
>look at the several tutorials at
>
>http://www.vlab.msi.umn.edu/events/tutorials.shtml
>
>
>Yours,
>
>Cesar R.S. da Silva.
>
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum




From akohlmey at cmm.chem.upenn.edu  Tue Sep 12 21:20:43 2006
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 12 Sep 2006 15:20:43 -0400
Subject: [Pw_forum] help
In-Reply-To: <b25d3a170609112337p3792ae0bucdcebcba75c10d9d@mail.gmail.com>
References: <b25d3a170609080038n737f2cd8of5b6c64f3e382671@mail.gmail.com>
	 <200609081551.33285.giannozz@nest.sns.it>
	 <b25d3a170609100605ga70ce59tc973385d8638b740@mail.gmail.com>
	 <7b6913e90609101040y126c3015n37e3bb06b44330b9@mail.gmail.com>
	 <b25d3a170609112337p3792ae0bucdcebcba75c10d9d@mail.gmail.com>
Message-ID: <7b6913e90609121220l299bc4e2l5e712b9fe6532f67@mail.gmail.com>

On 9/12/06, Amin Babazadeh <babazade at gmail.com> wrote:
> Dear Dr.Axel
> Thanks a lot for your helping.
> As I said before, I wanted to simulate a nanostructure and I began my job
> with Wien2k code but this software takes a long time to run and for reducing
> the time i  need supercomputers that i don't have. So i decided to change my
> software. And now i start to do it with espresso code.My first problem is
> that I don't know whether the espresso code  could simulate it or not.You
> are an expert.  would you please tell me, if it  is possible to simulate a
> nanostructure with using espresso code until I began my study about PWscf
> and espresso code or i  have to change it again.

dear amin,

sorry, i cannot give you a direct answer for that. you'd first have to
tell us _what_ kind of nanostructure you want to investigate. how many
atoms, what elements, etc. secondly, the computational effort depends
on what kind of properties you want to calculate (comparing single point
energies, optimal geometries, minimum energy paths, phonons, phonon
dispersion curves, statistical averages from molecular dynamics). all of
these have different requirements in terms of computer times.

with QE you can do calculations of systems, that are fast on a single pc
but also calculations that require hundreds of processors (the largest
job i ran so far with pw.x, was across almost 1000 processors...).

cheers,
   axel.

> Cheers
> Amin
>
>

-- 
=======================================================================
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  Tue Sep 12 21:34:03 2006
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 12 Sep 2006 15:34:03 -0400
Subject: [Pw_forum] Re:Re:vc-relax (Eric Abel)
In-Reply-To: <BAY105-F22015439FCAAB67F9EFD00D42B0@phx.gbl>
References: <64881.128.101.191.226.1158025038.squirrel@www.msi.umn.edu>
	 <BAY105-F22015439FCAAB67F9EFD00D42B0@phx.gbl>
Message-ID: <7b6913e90609121234w163410cby2d258d925cdce907@mail.gmail.com>

On 9/12/06, Eric Abel <etabel at hotmail.com> wrote:
> Thank you all for your tips.  It turns out the real fix was to upgrade to
> the latest stable version.  Now the program is behaving as I would expect.
>
> Cesar, you mention the parameters wmass and dt...I was wondering if there is
> a way to get an initial estimate for these values.  Unfortunately the
> documentation on this is sketchy at best.

eric,

please have a look at the tutorial material that cesar recommended, e.g.,
http://www.vlab.msi.umn.edu/events/download/VCS_tutorial.pdf
it contains a lot of examples. usually one needs to get 'a feeling' for
what effect the various parameters have, and in the tutorial pages you
have a large number of examples that you can run easily and then
you should modify individual parameters to see how it affects convergence.

cheers,
   axel.

> Right now I am running with wmass=0.1, and I didn't set dt, so it must be
> using the default.  Things are converging slowly...the atomic forces are
> creeping down.


>
> Eric
>



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


From lanhaiping at gmail.com  Wed Sep 13 09:49:15 2006
From: lanhaiping at gmail.com (lan haiping)
Date: Wed, 13 Sep 2006 15:49:15 +0800
Subject: [Pw_forum] Confusion between PWCOND and WANT
Message-ID: <c92002fa0609130049j1b028f5k2b7385ae90b9bc65@mail.gmail.com>

Dear all,

   Basically, both PWCOND and WANT  are post-process tools for  analyzing
conductance and complex bandstructure. Is it right ?
While i donot know much the differenc between them, though i read some
seminal papers about MLWFs and NEGF techniques used in WanT  package.   I
tried to dig out the Doc for PWCOND , but failed . Would you  please give me
some hints and help ?

 Regards,

Hai-Ping
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From dalcorso at sissa.it  Wed Sep 13 10:04:06 2006
From: dalcorso at sissa.it (Andrea Dal Corso)
Date: Wed, 13 Sep 2006 10:04:06 +0200
Subject: [Pw_forum] Confusion between PWCOND and WANT
In-Reply-To: <c92002fa0609130049j1b028f5k2b7385ae90b9bc65@mail.gmail.com>
References: <c92002fa0609130049j1b028f5k2b7385ae90b9bc65@mail.gmail.com>
Message-ID: <1158134647.4007.7.camel@dhpc-5-50.sissa.it>

Dear Hai-Ping,

The use of PWCOND is illustrated in examples 13 and 22 and in the
following papers:


Surf. Sci. 532-535, 549 (2003)
J. Phys.: Cond. Mat. 15, 3731 (2003)
Phys. Rev. B 70, 045417 (2004)
Phys. Rev. B 73, 075418 (2006)
Phys. Rev. B 74, 045429 (2006)

Best Regards,

Andrea



On Wed, 2006-09-13 at 15:49 +0800, lan haiping wrote:
> Dear all,
>  
>    Basically, both PWCOND and WANT  are post-process tools for
> analyzing conductance and complex bandstructure. Is it right ?
> While i donot know much the differenc between them, though i read some
> seminal papers about MLWFs and NEGF techniques used in WanT  package.
> I tried to dig out the Doc for PWCOND , but failed . Would you  please
> give me some hints and help ?
>  
>  Regards,
>  
> Hai-Ping
-- 
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 ferretti.andrea at unimore.it  Wed Sep 13 11:55:57 2006
From: ferretti.andrea at unimore.it (Andrea Ferretti)
Date: Wed, 13 Sep 2006 11:55:57 +0200 (CEST)
Subject: [Pw_forum] Confusion between PWCOND and WANT
In-Reply-To: <c92002fa0609130049j1b028f5k2b7385ae90b9bc65@mail.gmail.com>
References: <c92002fa0609130049j1b028f5k2b7385ae90b9bc65@mail.gmail.com>
Message-ID: <Pine.LNX.4.58.0609131121380.25866@bamboo.fisica.unimo.it>

Dear Hai-Ping,

> Basically, both PWCOND and WANT  are post-process tools for  analyzing
> conductance and complex bandstructure. Is it right ?
> While i donot know much the differenc between them, though i read some
> seminal papers about MLWFs and NEGF techniques used in WanT  package.   
>

a small aside note:
the complex band structure calculation is performed only by PWCOND, which 
then solves the scattering problem for the system under study and 
evaluates the transmittance (as you can find better explained in the papers cited by 
Andrea).
WanT solves the same problem but using the "maximally localized" Wannier 
function basis + a matrix green function approach (no need here for the 
complex band structure) 

a short description of the difference between the two approaches can 
be also found in a previous post to this forum

http://www.democritos.it/pipermail/pw_forum/2006-January/003479.html 

cheers
Andrea


-- 
Andrea Ferretti
National Research Center S3, CNR-INFM  ( http://s3.infm.it )
Dipartimento di Fisica, Universita' di Modena e Reggio Emilia
Via Campi 213/A I-41100 Modena, Italy
Tel:     +39 059 2055301
Fax:     +39 059 374794
E-mail:  ferretti.andrea at unimore.it
URL:     http://www.nanoscience.unimo.it

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


On Wed, 13 Sep 2006, lan haiping wrote:

> Dear all,
> 
>   Basically, both PWCOND and WANT  are post-process tools for  analyzing
> conductance and complex bandstructure. Is it right ?
> While i donot know much the differenc between them, though i read some
> seminal papers about MLWFs and NEGF techniques used in WanT  package.   I
> tried to dig out the Doc for PWCOND , but failed . Would you  please give me
> some hints and help ?
> 
> Regards,
> 
> Hai-Ping
> 


From L.Boeri at fkf.mpg.de  Wed Sep 13 13:28:28 2006
From: L.Boeri at fkf.mpg.de (Lilia Boeri)
Date: Wed, 13 Sep 2006 13:28:28 +0200 (CEST)
Subject: [Pw_forum] Compilation Problem
In-Reply-To: <200609121405.23193.giannozz@nest.sns.it>
References: <44ED5ED5.80902@cea.fr> <Pine.LNX.4.61.0609121332140.3715@pcand23.mpi-stuttgart.mpg.de>
 <200609121405.23193.giannozz@nest.sns.it>
Message-ID: <Pine.LNX.4.61.0609131141440.3715@pcand23.mpi-stuttgart.mpg.de>

Dear Paolo,

thanks a lot for replying.
> 
> did you ? and what did the service representative say :-) ?

he is on holiday ;)
We managed to compile the code by editing iotk_config.h
and adding the line you suggest.
Changing the compiler was not needed!
Thanks,
Lilia

> Apparently it has confused scores of other compilers as well:
> #define __IOTK_WORKAROUND5 in iotk/include/iotk_config.h 
> and it might work, without calling a service representative 
> 
> Notice that recent IBM machines seem to need xlf95 
> instead of xlf90
> 
> Paolo
> -- 
> Paolo Giannozzi             Phone:   +39/050-509876
> DEMOCRITOS and SNS          Fax:     +39/050-563513 
> Piazza dei Cavalieri 7      I-56126 Pisa, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


From lanhaiping at gmail.com  Wed Sep 13 14:18:40 2006
From: lanhaiping at gmail.com (lan haiping)
Date: Wed, 13 Sep 2006 20:18:40 +0800
Subject: [Pw_forum] Confusion between PWCOND and WANT
In-Reply-To: <1158134647.4007.7.camel@dhpc-5-50.sissa.it>
References: <c92002fa0609130049j1b028f5k2b7385ae90b9bc65@mail.gmail.com>
	 <1158134647.4007.7.camel@dhpc-5-50.sissa.it>
Message-ID: <c92002fa0609130518k31652485qa737cb6fc6dffc2b@mail.gmail.com>

Thank you , Andrea !

:)

Regards

hai-ping


On 9/13/06, Andrea Dal Corso <dalcorso at sissa.it> wrote:
>
> Dear Hai-Ping,
>
> The use of PWCOND is illustrated in examples 13 and 22 and in the
> following papers:
>
>
> Surf. Sci. 532-535, 549 (2003)
> J. Phys.: Cond. Mat. 15, 3731 (2003)
> Phys. Rev. B 70, 045417 (2004)
> Phys. Rev. B 73, 075418 (2006)
> Phys. Rev. B 74, 045429 (2006)
>
> Best Regards,
>
> Andrea
>
>
>
> On Wed, 2006-09-13 at 15:49 +0800, lan haiping wrote:
> > Dear all,
> >
> >    Basically, both PWCOND and WANT  are post-process tools for
> > analyzing conductance and complex bandstructure. Is it right ?
> > While i donot know much the differenc between them, though i read some
> > seminal papers about MLWFs and NEGF techniques used in WanT  package.
> > I tried to dig out the Doc for PWCOND , but failed . Would you  please
> > give me some hints and help ?
> >
> >  Regards,
> >
> > Hai-Ping
> --
> 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
>
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From lanhaiping at gmail.com  Wed Sep 13 15:19:47 2006
From: lanhaiping at gmail.com (lan haiping)
Date: Wed, 13 Sep 2006 21:19:47 +0800
Subject: [Pw_forum] Confusion between PWCOND and WANT
In-Reply-To: <Pine.LNX.4.58.0609131121380.25866@bamboo.fisica.unimo.it>
References: <c92002fa0609130049j1b028f5k2b7385ae90b9bc65@mail.gmail.com>
	 <Pine.LNX.4.58.0609131121380.25866@bamboo.fisica.unimo.it>
Message-ID: <c92002fa0609130619p435759d5v96589609cd725ead@mail.gmail.com>

Thank you ,Andrea !
 regards,
hai-ping


On 9/13/06, Andrea Ferretti <ferretti.andrea at unimore.it> wrote:
>
>
> Dear Hai-Ping,
>
> > Basically, both PWCOND and WANT  are post-process tools for  analyzing
> > conductance and complex bandstructure. Is it right ?
> > While i donot know much the differenc between them, though i read some
> > seminal papers about MLWFs and NEGF techniques used in WanT  package.
> >
>
> a small aside note:
> the complex band structure calculation is performed only by PWCOND, which
> then solves the scattering problem for the system under study and
> evaluates the transmittance (as you can find better explained in the
> papers cited by
> Andrea).
> WanT solves the same problem but using the "maximally localized" Wannier
> function basis + a matrix green function approach (no need here for the
> complex band structure)
>
> a short description of the difference between the two approaches can
> be also found in a previous post to this forum
>
> http://www.democritos.it/pipermail/pw_forum/2006-January/003479.html
>
> cheers
> Andrea
>
>
> --
> Andrea Ferretti
> National Research Center S3, CNR-INFM  ( http://s3.infm.it )
> Dipartimento di Fisica, Universita' di Modena e Reggio Emilia
> Via Campi 213/A I-41100 Modena, Italy
> Tel:     +39 059 2055301
> Fax:     +39 059 374794
> E-mail:  ferretti.andrea at unimore.it
> URL:     http://www.nanoscience.unimo.it
>
> Please, if possible, don't send me MS Word or PowerPoint attachments
> Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html
>
>
> On Wed, 13 Sep 2006, lan haiping wrote:
>
> > Dear all,
> >
> >   Basically, both PWCOND and WANT  are post-process tools for  analyzing
> > conductance and complex bandstructure. Is it right ?
> > While i donot know much the differenc between them, though i read some
> > seminal papers about MLWFs and NEGF techniques used in WanT  package.
> I
> > tried to dig out the Doc for PWCOND , but failed . Would you  please
> give me
> > some hints and help ?
> >
> > Regards,
> >
> > Hai-Ping
> >
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From lanhaiping at gmail.com  Wed Sep 13 17:40:10 2006
From: lanhaiping at gmail.com (lan haiping)
Date: Wed, 13 Sep 2006 23:40:10 +0800
Subject: [Pw_forum] Confusion between PWCOND and WANT
In-Reply-To: <Pine.LNX.4.58.0609131121380.25866@bamboo.fisica.unimo.it>
References: <c92002fa0609130049j1b028f5k2b7385ae90b9bc65@mail.gmail.com>
	 <Pine.LNX.4.58.0609131121380.25866@bamboo.fisica.unimo.it>
Message-ID: <c92002fa0609130840i6aa367d1j75657146c9fa82eb@mail.gmail.com>

Dear Andrea:

 Tonight , i tried to derive the generalized Landauer-like formula you gave
in *PRB 72 125114*  . While, with result of Eq(15), I cannot obtain the
final result of Eq(17). I then checked it again, I found Eq(15) may be given
with print error, omitting  subscript 0 in this expression *[\Sigma_L^{<,>}
+ \Sigma_R^{<,>} ]* , which should be with a form like this :
*[\Sigma_{0L}^{<,>}
+ \Sigma_[0R]^{<,>} ] .  *It could also be obtained by inserting Eq(12) into
Eq(9). would you please confirm it for me ?

Regards,
hai-ping



On 9/13/06, Andrea Ferretti <ferretti.andrea at unimore.it> wrote:
>
>
> Dear Hai-Ping,
>
> > Basically, both PWCOND and WANT  are post-process tools for  analyzing
> > conductance and complex bandstructure. Is it right ?
> > While i donot know much the differenc between them, though i read some
> > seminal papers about MLWFs and NEGF techniques used in WanT  package.
> >
>
> a small aside note:
> the complex band structure calculation is performed only by PWCOND, which
> then solves the scattering problem for the system under study and
> evaluates the transmittance (as you can find better explained in the
> papers cited by
> Andrea).
> WanT solves the same problem but using the "maximally localized" Wannier
> function basis + a matrix green function approach (no need here for the
> complex band structure)
>
> a short description of the difference between the two approaches can
> be also found in a previous post to this forum
>
> http://www.democritos.it/pipermail/pw_forum/2006-January/003479.html
>
> cheers
> Andrea
>
>
> --
> Andrea Ferretti
> National Research Center S3, CNR-INFM  ( http://s3.infm.it )
> Dipartimento di Fisica, Universita' di Modena e Reggio Emilia
> Via Campi 213/A I-41100 Modena, Italy
> Tel:     +39 059 2055301
> Fax:     +39 059 374794
> E-mail:  ferretti.andrea at unimore.it
> URL:     http://www.nanoscience.unimo.it
>
> Please, if possible, don't send me MS Word or PowerPoint attachments
> Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html
>
>
> On Wed, 13 Sep 2006, lan haiping wrote:
>
> > Dear all,
> >
> >   Basically, both PWCOND and WANT  are post-process tools for  analyzing
> > conductance and complex bandstructure. Is it right ?
> > While i donot know much the differenc between them, though i read some
> > seminal papers about MLWFs and NEGF techniques used in WanT  package.
> I
> > tried to dig out the Doc for PWCOND , but failed . Would you  please
> give me
> > some hints and help ?
> >
> > Regards,
> >
> > Hai-Ping
> >
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From giannozz at nest.sns.it  Wed Sep 13 18:59:54 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 13 Sep 2006 18:59:54 +0200
Subject: [Pw_forum] Mac OS-X + XLF problems
Message-ID: <200609131859.54599.giannozz@nest.sns.it>

I learnt from Pascal Thibaudeau that XLF v.8.1 for
Mac OS-X (powerpc processor) does not produce a 
working iotk library. As a quick workaround,
replace "../iotk/src/libiotk.a" with "../iotk/src/*.o" 
in file make.sys. This is fixed in the CVS version
(I hope): a dynamical iotk library is generated.
This requires to set the DYLD_LIBRARY_PATH
environment variable to run the codes.

I don't know if there is a similar problem in IBM 
machines running AIX.

Paolo
-- 
Paolo Giannozzi             Phone:   +39/050-509876
DEMOCRITOS and SNS          Fax:     +39/050-563513 
Piazza dei Cavalieri 7      I-56126 Pisa, Italy


From cesards at msi.umn.edu  Thu Sep 14 02:39:48 2006
From: cesards at msi.umn.edu (cesards at msi.umn.edu)
Date: Wed, 13 Sep 2006 19:39:48 -0500 (CDT)
Subject: [Pw_forum] Re:Re:vc-relax (Eric Abel)
Message-ID: <52054.128.101.191.226.1158194388.squirrel@www.msi.umn.edu>

Dear Eric,


Supposing you set the atomic masses to the average of real atomic masses
in amu (for faster convergence, all atoms must have equal masses),
reasonable dt is in the range 50 to 100. wmass is 10^(-2) or smaller.


Cesar.



From liyanpcl at yahoo.com.cn  Thu Sep 14 04:37:16 2006
From: liyanpcl at yahoo.com.cn (li yan)
Date: Thu, 14 Sep 2006 10:37:16 +0800 (CST)
Subject: [Pw_forum] about the generation of the pseudopotential with ld1.x
Message-ID: <20060914023716.4003.qmail@web15603.mail.cnb.yahoo.com>

Dear all,
        i wanna to generate the pseudopotential with ld1.x. 
        the input file is in the fowllowing part:
   &input
        title='Au',
        zed=79.0,
        rel=2,
        iswitch=3,
        rlderiv=2.50,
        eminld=-4.0,
        emaxld=4.0,
        deld=0.02,
        nld=3,
        config='[Xe]4f14 5d10 6s1',
        dft='PW'
 /
 &inputp
        pseudotype=2,
        lloc=0,
        file_pseudopw='Au.UPF',
        nlcc=.true.,
        rcore=1.2,
        rcloc=2.5
 /
3
5D 3   2  4.00  0.00  2.50 2.5  1.50
5D 3   2  6.00  0.00  2.50 2.5  2.50
6S 1   0  1.00  0.00  2.60 2.6  0.50

  If I choose dft='LDA' or 'PZ', it works well. But when dft= 'PW91' , 'PBE' or 'BP', it dosen't work. Why? 
   
  best regards

 		
---------------------------------
????????-3.5G???20M??? 
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From giannozz at nest.sns.it  Thu Sep 14 10:02:40 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 14 Sep 2006 10:02:40 +0200
Subject: [Pw_forum] Relativistics PPs + pp.x problems
In-Reply-To: <Pine.OSF.3.95a.1060912104745.25812C-100000@axroma2.roma2.infn.it>
References: <Pine.OSF.3.95a.1060912104745.25812C-100000@axroma2.roma2.infn.it>
Message-ID: <200609141002.40315.giannozz@nest.sns.it>

On Tuesday 12 September 2006 11:48, Conor Hogan wrote:

> I'm having some problems using pp.x with fully relativistic
> pseudopotentials, but with lspinorb=.false.

it should be fixed now in the CVS version. 
Thank you for bringing this to our attention

Paolo
-- 
Paolo Giannozzi             Phone:   +39/050-509876
DEMOCRITOS and SNS          Fax:     +39/050-563513 
Piazza dei Cavalieri 7      I-56126 Pisa, Italy


From duan at physics.usyd.edu.au  Fri Sep 15 07:48:07 2006
From: duan at physics.usyd.edu.au (Xiangmei Duan)
Date: Fri, 15 Sep 2006 15:48:07 +1000 (EST)
Subject: [Pw_forum] pseudopotential for Indium
Message-ID: <Pine.LNX.4.62.0609151542550.18021@cmt.physics.usyd.edu.au>

Dear all,

I'm using the pseudopotential for In with nlcc (In.pz-n-bhs.UPF), and 
would like to test the effect of the 4d electron.
Does anyone has a pseudopotential for In includingthe 4d electrons as 
vakence ?

Thanks in advance,
Best wishes,
Xiangmei
___________________________
X.M. DUAN
School of Physics, A28
The University of sydney
NSW, Sydney 2006
Tel: 02 9036 5389
Fax: 02 9351 7726
Email: duan at physics.usyd.edu.au
_____________________________________


From lyw1983 at 163.com  Sat Sep 16 11:54:11 2006
From: lyw1983 at 163.com (lyw1983)
Date: Sat, 16 Sep 2006 17:54:11 +0800 (CST)
Subject: [Pw_forum] The stress in the output of the scf.
Message-ID: <450BC9C3.000029.05162@bj163app74.163.com>

Dear all,
   when I test the ecutwfc for CrO2, I found that the stress at the end of the output file change largely with differenr ecutwfc values, I choose the ultrasoft pseudopotential for Cr and O, the pseudopotential as follow:
  Cr  Cr.pbe-sp-van.UPF
  O   O.pbe-rrkjus.UPF
   what can cause this result and who can tell me?
   The input file as below:


. ../../environment/environment_2
for ecut in 30 35 40 45 50  
do
 rm -rf $TMP_DIR/*

cat > cro2.scf.in << EOF
 &control
    calculation = 'scf'
    restart_mode='from_scratch',
    prefix='cro2',
    tstress = .true.
    tprnfor = .true.
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
 /
 &system
       ibrav=  6, celldm(1) = 8.3544825, celldm(3) =0.65957928, nat= 6, ntyp= 2,
    nspin = 2,  starting_magnetization6(1)=0.7,starting_magnetization(2)=0.0,ecutwfc =$ecut,ecutrho=400,
    occupations = 'smearing',smearing = 'methfessel-paxton',degauss = 0.03

 /
 &electrons
      mixing_beta = 0.7
    conv_thr =  1.0d-8
 /
ATOMIC_SPECIES
 Cr  52.000  Cr.pbe-sp-van.UPF 
 O   15.999  O.pbe-rrkjus.UPF
ATOMIC_POSITIONS {crystal}
Cr 0.000000  0.000000  0.000000
Cr 0.500000  0.500000  0.500000
O  0.301000  0.301000  0.000000
O  0.699000  0.699000  0.000000
O  0.199000  0.801000  0.500000
O  0.801000  0.199000  0.500000
K_POINTS {automatic}
4 4 6 0 0 0

EOF

$PARA_PREFIX /home/pwscf/pwscf_215/bin/pw.x $PARA_POSTFIX < cro2.scf.in >cro2.scf.out_$ecut
done
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From akohlmey at cmm.chem.upenn.edu  Sat Sep 16 14:59:35 2006
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 16 Sep 2006 08:59:35 -0400 (EDT)
Subject: [Pw_forum] The stress in the output of the scf.
In-Reply-To: <450BC9C3.000029.05162@bj163app74.163.com>
Message-ID: <Pine.LNX.4.44.0609160846150.11962-100000@localhost.localdomain>

On Sat, 16 Sep 2006, lyw1983 wrote:

> Dear all,
>    when I test the ecutwfc for CrO2, I found that the stress at the end of the output file change largely with differenr ecutwfc values, I choose the ultrasoft pseudopotential for Cr and O, the pseudopotential as follow:
>   Cr  Cr.pbe-sp-van.UPF
>   O   O.pbe-rrkjus.UPF
>    what can cause this result and who can tell me?

hi,

this behavior is normal. the stress tensor is a quantity that 
converges rather slowly with the wavefunction cutoff.

please check the mailing list archives.

axel.


>    The input file as below:
> 
> 
> . ../../environment/environment_2
> for ecut in 30 35 40 45 50  
> do
>  rm -rf $TMP_DIR/*
> 
> cat > cro2.scf.in << EOF
>  &control
>     calculation = 'scf'
>     restart_mode='from_scratch',
>     prefix='cro2',
>     tstress = .true.
>     tprnfor = .true.
>     pseudo_dir = '$PSEUDO_DIR/',
>     outdir='$TMP_DIR/'
>  /
>  &system
>        ibrav=  6, celldm(1) = 8.3544825, celldm(3) =0.65957928, nat= 6, ntyp= 2,
>     nspin = 2,  starting_magnetization6(1)=0.7,starting_magnetization(2)=0.0,ecutwfc =$ecut,ecutrho=400,
>     occupations = 'smearing',smearing = 'methfessel-paxton',degauss = 0.03
> 
>  /
>  &electrons
>       mixing_beta = 0.7
>     conv_thr =  1.0d-8
>  /
> ATOMIC_SPECIES
>  Cr  52.000  Cr.pbe-sp-van.UPF 
>  O   15.999  O.pbe-rrkjus.UPF
> ATOMIC_POSITIONS {crystal}
> Cr 0.000000  0.000000  0.000000
> Cr 0.500000  0.500000  0.500000
> O  0.301000  0.301000  0.000000
> O  0.699000  0.699000  0.000000
> O  0.199000  0.801000  0.500000
> O  0.801000  0.199000  0.500000
> K_POINTS {automatic}
> 4 4 6 0 0 0
> 
> EOF
> 
> $PARA_PREFIX /home/pwscf/pwscf_215/bin/pw.x $PARA_POSTFIX < cro2.scf.in >cro2.scf.out_$ecut
> done
> 

-- 
=======================================================================
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 yuhailin_79 at msn.com  Sun Sep 17 15:13:35 2006
From: yuhailin_79 at msn.com (hailin yu)
Date: Sun, 17 Sep 2006 21:13:35 +0800
Subject: [Pw_forum] help: Pt phonon calculation
In-Reply-To: <FB247B9E-E75A-4CDA-86C5-CFBBB13457B9@sissa.it>
Message-ID: <BAY106-F22BE3612FE572FA3AE1082932C0@phx.gbl>

Dear all:
       I have some questions about the phonon calculation of Pt.
       1). Is it reasonable to calculate the phonon dispersion of Pt by 
using the Pt.pbe-rrkjus.UPF pseudopotentials?
       2). For the value of degauss, how it is reasonable? And for the 
kpoint?
Thanks in advance!
Thanks a lot!
yuhailin

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE! 
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From baroni at sissa.it  Sun Sep 17 17:26:54 2006
From: baroni at sissa.it (Stefano Baroni)
Date: Sun, 17 Sep 2006 17:26:54 +0200
Subject: [Pw_forum] help: Pt phonon calculation
In-Reply-To: <BAY106-F22BE3612FE572FA3AE1082932C0@phx.gbl>
References: <BAY106-F22BE3612FE572FA3AE1082932C0@phx.gbl>
Message-ID: <37C3CD20-F0FC-4925-B4F7-827CA9F14AEB@sissa.it>


On Sep 17, 2006, at 3:13 PM, hailin yu wrote:

> Dear all:
>       I have some questions about the phonon calculation of Pt.
>       1). Is it reasonable to calculate the phonon dispersion of Pt  
> by using the Pt.pbe-rrkjus.UPF pseudopotentials?

why not?

>       2). For the value of degauss, how it is reasonable? And for  
> the kpoint?

Only you can tell. This is not so difficult to assess. Take a few  
representative points in the BZ and calculate the phonon frequencies  
as functions of degauss. For each value of degauss, keep increasing  
the number of k points until you reach convergence. Note: (1) the  
resulting number of k-pts should increase with decreasing degauss;  
(2) this is the order to follow (i.e. degauss first, convergence wrt  
to k-points for each given value of degauss: not the other way  
around). Finally choose the value of degauss (and the corresponding  
number of k-pts) which gives you the accuracy you desire.

In normal circumstances, such as Pt, I would say, the optimal value  
of degauss should not depend on the phonon wavevector. At a Kohn  
anomaly, instead, a much smaller degauss (and a correspondingly  
larger number of k-pts) than at "ordinary" phonon wave-vectors is  
usually needed. Can you see why? (if you understand this you  
understand a lot of the fine details of phonon calculations in metals).

Take care
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 stargmoon at yahoo.com  Sun Sep 17 22:23:09 2006
From: stargmoon at yahoo.com (stargmoon)
Date: Sun, 17 Sep 2006 13:23:09 -0700 (PDT)
Subject: [Pw_forum] parallel compiling
In-Reply-To: <BAY106-F22BE3612FE572FA3AE1082932C0@phx.gbl>
Message-ID: <20060917202309.61494.qmail@web33213.mail.mud.yahoo.com>

Dear pwscf community,
 
 I tried to compile Espresso-3.1.1 recently on our PC cluster (AMD64). However, after I run ./configure, I am told that "Parallel environment not detected". I checked the config.log, since there is no problem in seaching for the MPI compilers (mpif90, mpif77 and mpicc), I think it must be the MPI library problem. Therefore, I tried to set "MPI_LIBS" (there is only libmpich.a in there) in the ./configure command line, but it did not work either. Could anybody please tell me what kind of MPI libraries I have to point to the "configure" in order to get parallel compilation?
 
 Thanks in advance!
 
 stargmoon

 		
---------------------------------
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From akohlmey at cmm.chem.upenn.edu  Sun Sep 17 22:43:36 2006
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sun, 17 Sep 2006 16:43:36 -0400
Subject: [Pw_forum] parallel compiling
In-Reply-To: <20060917202309.61494.qmail@web33213.mail.mud.yahoo.com>
References: <BAY106-F22BE3612FE572FA3AE1082932C0@phx.gbl>
	 <20060917202309.61494.qmail@web33213.mail.mud.yahoo.com>
Message-ID: <7b6913e90609171343v6f28ffft43837c23803b7266@mail.gmail.com>

On 9/17/06, stargmoon <stargmoon at yahoo.com> wrote:
> Dear pwscf community,
>
>  I tried to compile Espresso-3.1.1 recently on our PC cluster (AMD64).
> However, after I run ./configure, I am told that "Parallel environment not
> detected". I checked the config.log, since there is no problem in seaching
> for the MPI compilers (mpif90, mpif77 and mpicc), I think it must be the MPI

there are two stages of the search. a) whether the executables exists
and b) whether they can produce working binaries.

> library problem. Therefore, I tried to set "MPI_LIBS" (there is only
> libmpich.a in there) in the ./configure command line, but it did not work

i would have expected a libfmpich.a, too.

> either. Could anybody please tell me what kind of MPI libraries I have to
> point to the "configure" in order to get parallel compilation?

this is impossible to tell, without knowing any details about your system.

what parallel software are you using (it looks like MPICH) and did you
install it yourself or was it bundled with the system? do mpif77 and
mpif90 point to a sufficient fortran

can you compile and run any of the (trivial) MPI example programs
that usually ship with MPI packages, and if yes, please describe the
commandline you use for that. based on that information, we may
be able to help you.

especially on linux machines, there are almost always a few kinks
to be worked out in the installation.

regards,
  axel.

>
>  Thanks in advance!
>
>  stargmoon
>
>
>  ________________________________
> Get your email and more, right on the new Yahoo.com
>
>


-- 
=======================================================================
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 stargmoon at yahoo.com  Mon Sep 18 15:16:42 2006
From: stargmoon at yahoo.com (stargmoon)
Date: Mon, 18 Sep 2006 06:16:42 -0700 (PDT)
Subject: [Pw_forum] parallel compiling
In-Reply-To: <7b6913e90609171343v6f28ffft43837c23803b7266@mail.gmail.com>
Message-ID: <20060918131642.58122.qmail@web33201.mail.mud.yahoo.com>

Dear Dr.Kohlmeyer,
 
 Thanks for your reply. 
 
 I am just one user of our cluster, that is, I am not the system administrator. I do not know the detail of the installation of softwares there. But MPICH was there, and can be launched by "module add".  And I was told that MPICH was installed ourselves, not bundled with the machines.
 
The command line I used to do "configure" is "./configure MPI_LIBS="-L/opt/mpi/tcp/mpich-pgi/lib -lmpich -lfmpich"
 
 Could you please give me more hints what I should do to figure out this problem?
 
 By the way, have you ever used pathscale to compile espresso? It seems to be possible from the update information for espresso3.1.1. We have pathscale and mpich for pathscale work for VASP on our cluster.
 
 Best,
 
 Stargmoon
 
Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu> wrote: On 9/17/06, stargmoon  wrote:
> Dear pwscf community,
>
>  I tried to compile Espresso-3.1.1 recently on our PC cluster (AMD64).
> However, after I run ./configure, I am told that "Parallel environment not
> detected". I checked the config.log, since there is no problem in seaching
> for the MPI compilers (mpif90, mpif77 and mpicc), I think it must be the MPI

there are two stages of the search. a) whether the executables exists
and b) whether they can produce working binaries.

> library problem. Therefore, I tried to set "MPI_LIBS" (there is only
> libmpich.a in there) in the ./configure command line, but it did not work

i would have expected a libfmpich.a, too.

> either. Could anybody please tell me what kind of MPI libraries I have to
> point to the "configure" in order to get parallel compilation?

this is impossible to tell, without knowing any details about your system.

what parallel software are you using (it looks like MPICH) and did you
install it yourself or was it bundled with the system? do mpif77 and
mpif90 point to a sufficient fortran

can you compile and run any of the (trivial) MPI example programs
that usually ship with MPI packages, and if yes, please describe the
commandline you use for that. based on that information, we may
be able to help you.

especially on linux machines, there are almost always a few kinks
to be worked out in the installation.

regards,
  axel.

>
>  Thanks in advance!
>
>  stargmoon
>
>
>  ________________________________
> Get your email and more, right on the new Yahoo.com
>
>


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


 		
---------------------------------
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From akohlmey at cmm.chem.upenn.edu  Mon Sep 18 17:02:38 2006
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 18 Sep 2006 11:02:38 -0400
Subject: [Pw_forum] parallel compiling
In-Reply-To: <20060918131642.58122.qmail@web33201.mail.mud.yahoo.com>
References: <7b6913e90609171343v6f28ffft43837c23803b7266@mail.gmail.com>
	 <20060918131642.58122.qmail@web33201.mail.mud.yahoo.com>
Message-ID: <7b6913e90609180802u74eaae07l63ccbee076a0dd0a@mail.gmail.com>

On 9/18/06, stargmoon <stargmoon at yahoo.com> wrote:
> Dear Dr.Kohlmeyer,
>
>  Thanks for your reply.
>
>  I am just one user of our cluster, that is, I am not the system
> administrator. I do not know the detail of the installation of softwares

so please _ask_ your sysadmin, this is the person 'in the know'
about the details. as i wrote before, all machines/clusters are
slightly different, so there is no way to predict what might be a problem.

> there. But MPICH was there, and can be launched by "module add".  And I was
> told that MPICH was installed ourselves, not bundled with the machines.

so then your sysadmin _has_ to know...

> The command line I used to do "configure" is "./configure
> MPI_LIBS="-L/opt/mpi/tcp/mpich-pgi/lib -lmpich -lfmpich"
>
>  Could you please give me more hints what I should do to figure out this
> problem?

as i wrote before, please try to compile and run _another_ MPI program,
best one of the MPI tutorial examples, as they are rather trivial.
once you get that working, let us know what command line you needed
for the successful compile that produced a usable executable,
we can look into getting QE compiled.

>
>  By the way, have you ever used pathscale to compile espresso? It seems to
> be possible from the update information for espresso3.1.1. We have pathscale
> and mpich for pathscale work for VASP on our cluster.

i managed to do it a long time ago (including a few manual hacks).
but i didn't have access to a machine with pathscale for quite a while.
with the addition of the iotk library, probably a few more tweaks are/were
needed. i would not expect a large difference between pathscale and PGI
on AMD64 machines. most of the speed comes from the design of the
cpu itself and usually numerical codes like QE are faster, if you _lower_
the optimization (and especially avoid IPA/IPO and heuristic vectorization).
QE already takes a lot of advantage of SIMD instructions through the
use of optimized BLAS/LAPACK libraries (i.e. ACML on AMD64).

cheers,
    axel.

>
>  Best,
>
>  Stargmoon
>
> Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu> wrote:
>  On 9/17/06, stargmoon wrote:
> > Dear pwscf community,
> >
> > I tried to compile Espresso-3.1.1 recently on our PC cluster (AMD64).
> > However, after I run ./configure, I am told that "Parallel environment not
> > detected". I checked the config.log, since there is no problem in seaching
> > for the MPI compilers (mpif90, mpif77 and mpicc), I think it must be the
> MPI
>
> there are two stages of the search. a) whether the executables exists
> and b) whether they can produce working binaries.
>
> > library problem. Therefore, I tried to set "MPI_LIBS" (there is only
> > libmpich.a in there) in the ./configure command line, but it did not work
>
> i would have expected a libfmpich.a, too.
>
> > either. Could anybody please tell me what kind of MPI libraries I have to
> > point to the "configure" in order to get parallel compilation?
>
> this is impossible to tell, without knowing any details about your system.
>
> what parallel software are you using (it looks like MPICH) and did you
> install it yourself or was it bundled with the system? do mpif77 and
> mpif90 point to a sufficient fortran
>
> can you compile and run any of the (trivial) MPI example programs
> that usually ship with MPI packages, and if yes, please describe the
> commandline you use for that. based on that information, we may
> be able to help you.
>
> especially on linux machines, there are almost always a few kinks
> to be worked out in the installation.
>
> regards,
>  axel.
>
> >
> > Thanks in advance!
> >
> > stargmoon
> >
> >
> > ________________________________
> > Get your email and more, right on the new Yahoo.com
> >
> >
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
>  Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>  ________________________________
> Stay in the know. Pulse on the new Yahoo.com. Check it out.
>
>


-- 
=======================================================================
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 stargmoon at yahoo.com  Mon Sep 18 17:37:22 2006
From: stargmoon at yahoo.com (stargmoon)
Date: Mon, 18 Sep 2006 08:37:22 -0700 (PDT)
Subject: [Pw_forum] parallel compiling
In-Reply-To: <7b6913e90609180802u74eaae07l63ccbee076a0dd0a@mail.gmail.com>
Message-ID: <20060918153722.17903.qmail@web33206.mail.mud.yahoo.com>

Thanks a lot Dr.Kohlmeyer, I will ask our sysadmin and let you know if I can successfully compile the parallel version.
 
 Best regards,
 
 Stargmoon

Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu> wrote: On 9/18/06, stargmoon  wrote:
> Dear Dr.Kohlmeyer,
>
>  Thanks for your reply.
>
>  I am just one user of our cluster, that is, I am not the system
> administrator. I do not know the detail of the installation of softwares

so please _ask_ your sysadmin, this is the person 'in the know'
about the details. as i wrote before, all machines/clusters are
slightly different, so there is no way to predict what might be a problem.

> there. But MPICH was there, and can be launched by "module add".  And I was
> told that MPICH was installed ourselves, not bundled with the machines.

so then your sysadmin _has_ to know...

> The command line I used to do "configure" is "./configure
> MPI_LIBS="-L/opt/mpi/tcp/mpich-pgi/lib -lmpich -lfmpich"
>
>  Could you please give me more hints what I should do to figure out this
> problem?

as i wrote before, please try to compile and run _another_ MPI program,
best one of the MPI tutorial examples, as they are rather trivial.
once you get that working, let us know what command line you needed
for the successful compile that produced a usable executable,
we can look into getting QE compiled.

>
>  By the way, have you ever used pathscale to compile espresso? It seems to
> be possible from the update information for espresso3.1.1. We have pathscale
> and mpich for pathscale work for VASP on our cluster.

i managed to do it a long time ago (including a few manual hacks).
but i didn't have access to a machine with pathscale for quite a while.
with the addition of the iotk library, probably a few more tweaks are/were
needed. i would not expect a large difference between pathscale and PGI
on AMD64 machines. most of the speed comes from the design of the
cpu itself and usually numerical codes like QE are faster, if you _lower_
the optimization (and especially avoid IPA/IPO and heuristic vectorization).
QE already takes a lot of advantage of SIMD instructions through the
use of optimized BLAS/LAPACK libraries (i.e. ACML on AMD64).

cheers,
    axel.

>
>  Best,
>
>  Stargmoon
>
> Axel Kohlmeyer  wrote:
>  On 9/17/06, stargmoon wrote:
> > Dear pwscf community,
> >
> > I tried to compile Espresso-3.1.1 recently on our PC cluster (AMD64).
> > However, after I run ./configure, I am told that "Parallel environment not
> > detected". I checked the config.log, since there is no problem in seaching
> > for the MPI compilers (mpif90, mpif77 and mpicc), I think it must be the
> MPI
>
> there are two stages of the search. a) whether the executables exists
> and b) whether they can produce working binaries.
>
> > library problem. Therefore, I tried to set "MPI_LIBS" (there is only
> > libmpich.a in there) in the ./configure command line, but it did not work
>
> i would have expected a libfmpich.a, too.
>
> > either. Could anybody please tell me what kind of MPI libraries I have to
> > point to the "configure" in order to get parallel compilation?
>
> this is impossible to tell, without knowing any details about your system.
>
> what parallel software are you using (it looks like MPICH) and did you
> install it yourself or was it bundled with the system? do mpif77 and
> mpif90 point to a sufficient fortran
>
> can you compile and run any of the (trivial) MPI example programs
> that usually ship with MPI packages, and if yes, please describe the
> commandline you use for that. based on that information, we may
> be able to help you.
>
> especially on linux machines, there are almost always a few kinks
> to be worked out in the installation.
>
> regards,
>  axel.
>
> >
> > Thanks in advance!
> >
> > stargmoon
> >
> >
> > ________________________________
> > Get your email and more, right on the new Yahoo.com
> >
> >
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
>  Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>  ________________________________
> Stay in the know. Pulse on the new Yahoo.com. Check it out.
>
>


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


 		
---------------------------------
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From lathiot at physik.fu-berlin.de  Mon Sep 18 18:38:48 2006
From: lathiot at physik.fu-berlin.de (Nektarios Lathiotakis)
Date: Mon, 18 Sep 2006 18:38:48 +0200
Subject: [Pw_forum] Supercell- gamma point calculation reliability
Message-ID: <450ECB98.9070501@physik.fu-berlin.de>

Hi all,

I want to calculate the energy difference of FM and AFM states of two
isolated
magnetic impurities in a semiconductor, optionaly with the presence of
native
impurities.

The supercell has to be  fairly large, of the order of 100 atoms, so I
can only
afford Gamma-point calculation. The difference in the energy of
different magnetic states might be of the order of mRyd.

My question concerns the convergence parameters and especially degauss.
Right now I use degauss=5.d-4 and thats the smallest I can  use without
serious oscillation problems. That is 0.5mRyd so it is probably fine.

A second concern is the realiability of the Gamma point calculation itself.
My worry is that increasing the mumber of k-points will lower all the
energies
by much more than the mRyd differences I am obtaining.  In other words,
I am worrying that the error of restricting the k-space to the gamma point
is much larger than the energy differences I get.  What is the
experience on that
issue? Is a supercell of 100 atoms big enough to guarantee that a
gamma-point
calculation will have accuracy of the order of miliRydberg? And if not
are the
energy differences of any value or it is just crap?

Here are the convergence parameters I use right now:
etot_conv_thr = 1.d-5
degauss = 5.d-4
conv_thr = 1.0d-6

Thanks
Nektarios


From eyvaz_isaev at yahoo.com  Mon Sep 18 19:29:09 2006
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 18 Sep 2006 10:29:09 -0700 (PDT)
Subject: [Pw_forum] parallel compiling
In-Reply-To: <20060918153722.17903.qmail@web33206.mail.mud.yahoo.com>
Message-ID: <20060918172909.52415.qmail@web60315.mail.yahoo.com>

Hi,

My apologies interfering. It might be that I did not
read the threat completely.

The problem looks like the same I had before on a
Linux cluster. It turned out that I had to load some
moduli before typing "./configure". They were mpich,
blas, lapack, fftw, and ifort. Sure, compiled
libraries have to be compatible with a compiler you
would like to use. 
I.e. if you like ifort compiler choose intel_mpich,
but not gnu_mpich. 

So, try the command "module available" and choose
these what you need using "module load XXXXXX". Then
./configure
It worked perfectly in my case.

Bests,
Eyvaz.



--- stargmoon <stargmoon at yahoo.com> wrote:

> Thanks a lot Dr.Kohlmeyer, I will ask our sysadmin
> and let you know if I can successfully compile the
> parallel version.
>  
>  Best regards,
>  
>  Stargmoon
> 
> Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu> wrote:
> On 9/18/06, stargmoon  wrote:
> > Dear Dr.Kohlmeyer,
> >
> >  Thanks for your reply.
> >
> >  I am just one user of our cluster, that is, I am
> not the system
> > administrator. I do not know the detail of the
> installation of softwares
> 
> so please _ask_ your sysadmin, this is the person
> 'in the know'
> about the details. as i wrote before, all
> machines/clusters are
> slightly different, so there is no way to predict
> what might be a problem.
> 
> > there. But MPICH was there, and can be launched by
> "module add".  And I was
> > told that MPICH was installed ourselves, not
> bundled with the machines.
> 
> so then your sysadmin _has_ to know...
> 
> > The command line I used to do "configure" is
> "./configure
> > MPI_LIBS="-L/opt/mpi/tcp/mpich-pgi/lib -lmpich
> -lfmpich"
> >
> >  Could you please give me more hints what I should
> do to figure out this
> > problem?
> 
> as i wrote before, please try to compile and run
> _another_ MPI program,
> best one of the MPI tutorial examples, as they are
> rather trivial.
> once you get that working, let us know what command
> line you needed
> for the successful compile that produced a usable
> executable,
> we can look into getting QE compiled.
> 
> >
> >  By the way, have you ever used pathscale to
> compile espresso? It seems to
> > be possible from the update information for
> espresso3.1.1. We have pathscale
> > and mpich for pathscale work for VASP on our
> cluster.
> 
> i managed to do it a long time ago (including a few
> manual hacks).
> but i didn't have access to a machine with pathscale
> for quite a while.
> with the addition of the iotk library, probably a
> few more tweaks are/were
> needed. i would not expect a large difference
> between pathscale and PGI
> on AMD64 machines. most of the speed comes from the
> design of the
> cpu itself and usually numerical codes like QE are
> faster, if you _lower_
> the optimization (and especially avoid IPA/IPO and
> heuristic vectorization).
> QE already takes a lot of advantage of SIMD
> instructions through the
> use of optimized BLAS/LAPACK libraries (i.e. ACML on
> AMD64).
> 
> cheers,
>     axel.
> 
> >
> >  Best,
> >
> >  Stargmoon
> >
> > Axel Kohlmeyer  wrote:
> >  On 9/17/06, stargmoon wrote:
> > > Dear pwscf community,
> > >
> > > I tried to compile Espresso-3.1.1 recently on
> our PC cluster (AMD64).
> > > However, after I run ./configure, I am told that
> "Parallel environment not
> > > detected". I checked the config.log, since there
> is no problem in seaching
> > > for the MPI compilers (mpif90, mpif77 and
> mpicc), I think it must be the
> > MPI
> >
> > there are two stages of the search. a) whether the
> executables exists
> > and b) whether they can produce working binaries.
> >
> > > library problem. Therefore, I tried to set
> "MPI_LIBS" (there is only
> > > libmpich.a in there) in the ./configure command
> line, but it did not work
> >
> > i would have expected a libfmpich.a, too.
> >
> > > either. Could anybody please tell me what kind
> of MPI libraries I have to
> > > point to the "configure" in order to get
> parallel compilation?
> >
> > this is impossible to tell, without knowing any
> details about your system.
> >
> > what parallel software are you using (it looks
> like MPICH) and did you
> > install it yourself or was it bundled with the
> system? do mpif77 and
> > mpif90 point to a sufficient fortran
> >
> > can you compile and run any of the (trivial) MPI
> example programs
> > that usually ship with MPI packages, and if yes,
> please describe the
> > commandline you use for that. based on that
> information, we may
> > be able to help you.
> >
> > especially on linux machines, there are almost
> always a few kinks
> > to be worked out in the installation.
> >
> > regards,
> >  axel.
> >
> > >
> > > Thanks in advance!
> > >
> > > stargmoon
> > >
> > >
> > > ________________________________
> > > Get your email and more, right on the new
> Yahoo.com
> > >
> > >
> >
> >
> > --
> >
>
=======================================================================
> > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu
> http://www.cmm.upenn.edu
> >  Center for Molecular Modeling -- University of
> Pennsylvania
> > Department of Chemistry, 231 S.34th Street,
> Philadelphia, PA 19104-6323
> > tel: 1-215-898-1582, fax: 1-215-573-6233,
> office-tel: 1-215-898-5425
> >
>
=======================================================================
> > If you make something idiot-proof, the universe
> creates a better idiot.
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> >  ________________________________
> > Stay in the know. Pulse on the new Yahoo.com.
> Check it out.
> >
> >
> 
> 
> -- 
>
=======================================================================
> Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu  
> http://www.cmm.upenn.edu
>   Center for Molecular Modeling   --   University of
> Pennsylvania
> Department of Chemistry, 231 S.34th Street,
> Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233, 
> office-tel: 1-215-898-5425
>
=======================================================================
> If you make something idiot-proof, the universe
> creates a better idiot.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
=== message truncated ===


__________________________________________________
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From stargmoon at yahoo.com  Mon Sep 18 19:58:02 2006
From: stargmoon at yahoo.com (stargmoon)
Date: Mon, 18 Sep 2006 10:58:02 -0700 (PDT)
Subject: [Pw_forum] parallel compiling
In-Reply-To: <20060918172909.52415.qmail@web60315.mail.yahoo.com>
Message-ID: <20060918175802.11916.qmail@web33207.mail.mud.yahoo.com>

Thanks a lot Eyvaz for your reminder. Actually, every time before I run ./configure I load moduli "pgi52 and mpich-pgi". 
 
 Best

Eyvaz Isaev <eyvaz_isaev at yahoo.com> wrote: Hi,

My apologies interfering. It might be that I did not
read the threat completely.

The problem looks like the same I had before on a
Linux cluster. It turned out that I had to load some
moduli before typing "./configure". They were mpich,
blas, lapack, fftw, and ifort. Sure, compiled
libraries have to be compatible with a compiler you
would like to use. 
I.e. if you like ifort compiler choose intel_mpich,
but not gnu_mpich. 

So, try the command "module available" and choose
these what you need using "module load XXXXXX". Then
./configure
It worked perfectly in my case.

Bests,
Eyvaz.



--- stargmoon  wrote:

> Thanks a lot Dr.Kohlmeyer, I will ask our sysadmin
> and let you know if I can successfully compile the
> parallel version.
>  
>  Best regards,
>  
>  Stargmoon
> 
> Axel Kohlmeyer  wrote:
> On 9/18/06, stargmoon  wrote:
> > Dear Dr.Kohlmeyer,
> >
> >  Thanks for your reply.
> >
> >  I am just one user of our cluster, that is, I am
> not the system
> > administrator. I do not know the detail of the
> installation of softwares
> 
> so please _ask_ your sysadmin, this is the person
> 'in the know'
> about the details. as i wrote before, all
> machines/clusters are
> slightly different, so there is no way to predict
> what might be a problem.
> 
> > there. But MPICH was there, and can be launched by
> "module add".  And I was
> > told that MPICH was installed ourselves, not
> bundled with the machines.
> 
> so then your sysadmin _has_ to know...
> 
> > The command line I used to do "configure" is
> "./configure
> > MPI_LIBS="-L/opt/mpi/tcp/mpich-pgi/lib -lmpich
> -lfmpich"
> >
> >  Could you please give me more hints what I should
> do to figure out this
> > problem?
> 
> as i wrote before, please try to compile and run
> _another_ MPI program,
> best one of the MPI tutorial examples, as they are
> rather trivial.
> once you get that working, let us know what command
> line you needed
> for the successful compile that produced a usable
> executable,
> we can look into getting QE compiled.
> 
> >
> >  By the way, have you ever used pathscale to
> compile espresso? It seems to
> > be possible from the update information for
> espresso3.1.1. We have pathscale
> > and mpich for pathscale work for VASP on our
> cluster.
> 
> i managed to do it a long time ago (including a few
> manual hacks).
> but i didn't have access to a machine with pathscale
> for quite a while.
> with the addition of the iotk library, probably a
> few more tweaks are/were
> needed. i would not expect a large difference
> between pathscale and PGI
> on AMD64 machines. most of the speed comes from the
> design of the
> cpu itself and usually numerical codes like QE are
> faster, if you _lower_
> the optimization (and especially avoid IPA/IPO and
> heuristic vectorization).
> QE already takes a lot of advantage of SIMD
> instructions through the
> use of optimized BLAS/LAPACK libraries (i.e. ACML on
> AMD64).
> 
> cheers,
>     axel.
> 
> >
> >  Best,
> >
> >  Stargmoon
> >
> > Axel Kohlmeyer  wrote:
> >  On 9/17/06, stargmoon wrote:
> > > Dear pwscf community,
> > >
> > > I tried to compile Espresso-3.1.1 recently on
> our PC cluster (AMD64).
> > > However, after I run ./configure, I am told that
> "Parallel environment not
> > > detected". I checked the config.log, since there
> is no problem in seaching
> > > for the MPI compilers (mpif90, mpif77 and
> mpicc), I think it must be the
> > MPI
> >
> > there are two stages of the search. a) whether the
> executables exists
> > and b) whether they can produce working binaries.
> >
> > > library problem. Therefore, I tried to set
> "MPI_LIBS" (there is only
> > > libmpich.a in there) in the ./configure command
> line, but it did not work
> >
> > i would have expected a libfmpich.a, too.
> >
> > > either. Could anybody please tell me what kind
> of MPI libraries I have to
> > > point to the "configure" in order to get
> parallel compilation?
> >
> > this is impossible to tell, without knowing any
> details about your system.
> >
> > what parallel software are you using (it looks
> like MPICH) and did you
> > install it yourself or was it bundled with the
> system? do mpif77 and
> > mpif90 point to a sufficient fortran
> >
> > can you compile and run any of the (trivial) MPI
> example programs
> > that usually ship with MPI packages, and if yes,
> please describe the
> > commandline you use for that. based on that
> information, we may
> > be able to help you.
> >
> > especially on linux machines, there are almost
> always a few kinks
> > to be worked out in the installation.
> >
> > regards,
> >  axel.
> >
> > >
> > > Thanks in advance!
> > >
> > > stargmoon
> > >
> > >
> > > ________________________________
> > > Get your email and more, right on the new
> Yahoo.com
> > >
> > >
> >
> >
> > --
> >
>
=======================================================================
> > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu
> http://www.cmm.upenn.edu
> >  Center for Molecular Modeling -- University of
> Pennsylvania
> > Department of Chemistry, 231 S.34th Street,
> Philadelphia, PA 19104-6323
> > tel: 1-215-898-1582, fax: 1-215-573-6233,
> office-tel: 1-215-898-5425
> >
>
=======================================================================
> > If you make something idiot-proof, the universe
> creates a better idiot.
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> >  ________________________________
> > Stay in the know. Pulse on the new Yahoo.com.
> Check it out.
> >
> >
> 
> 
> -- 
>
=======================================================================
> Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu  
> http://www.cmm.upenn.edu
>   Center for Molecular Modeling   --   University of
> Pennsylvania
> Department of Chemistry, 231 S.34th Street,
> Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233, 
> office-tel: 1-215-898-5425
>
=======================================================================
> If you make something idiot-proof, the universe
> creates a better idiot.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
=== message truncated ===


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From akohlmey at cmm.chem.upenn.edu  Mon Sep 18 20:44:25 2006
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 18 Sep 2006 14:44:25 -0400
Subject: [Pw_forum] parallel compiling
In-Reply-To: <20060918175802.11916.qmail@web33207.mail.mud.yahoo.com>
References: <20060918172909.52415.qmail@web60315.mail.yahoo.com>
	 <20060918175802.11916.qmail@web33207.mail.mud.yahoo.com>
Message-ID: <7b6913e90609181144i5b093e7cs38422304b2c2e48e@mail.gmail.com>

On 9/18/06, stargmoon <stargmoon at yahoo.com> wrote:
> Thanks a lot Eyvaz for your reminder. Actually, every time before I run
> ./configure I load moduli "pgi52 and mpich-pgi".

wait. regardless of whether you can get a successful compile
or not. pgi version 5.2 is known to miscompile QE (and other
similar codes). so you should try a different options.

furthermore, as i was trying to say. even with using the modules
utility, packages are usually installed differently on most machines
and sometime the slightest difference can be the reason for
configure to pick up the right flags or not.

axel.

>
>  Best
>
>
[...]


-- 
=======================================================================
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 marzari at MIT.EDU  Mon Sep 18 22:17:32 2006
From: marzari at MIT.EDU (Nicola Marzari)
Date: Mon, 18 Sep 2006 16:17:32 -0400
Subject: [Pw_forum] Supercell- gamma point calculation reliability
In-Reply-To: <450ECB98.9070501@physik.fu-berlin.de>
References: <450ECB98.9070501@physik.fu-berlin.de>
Message-ID: <450EFEDC.7090202@mit.edu>


Nektarios,


1) the "dispersion" from the magnetic impurities should be flat,
and the difference in energy that you look at is within two
cells that have the same sampling. That is good.

2) a simple test would be to still use 1 k-point, but the Baldereschi
(PRB 1973) point instead of Gamma. For an orthorombic cell, I generally
use 1/4 1/4 1/4 . PWSCf would automatically try to replicate it to
recover full symmetry (i.e. would want to use all of the 2 2 2 1 1 1
Monhorst-Pack mesh that are not related by any point-group operation),
but using no_sym (or nosym ?) you can force the code to just use that
single k-point. 1/4 1/4 1/4 is often more accurate than Gamma, and
any difference you find would hint at insufficient sampling.

3) degauss, generally speaking, should be larger than what you used if
you were dealing with a metal. In your case, though, you probably use it
just to smooth the path to selfconsistency, and at the ground state you
still want integer occupations everywhere, correct ?

4) what I would worry is haivng very good ionic relaxations, since these
can be different  in the FM and AFM states. Using the same cell for the
two calculations (same cell parameters, same cutoff, same kpoints) helps
a lot with the electronic accuracy, since in the energy difference you
have cancellation of terms that might have needed more kpoints.

5) of course, if you need for some reason absolute k-point convergence,
than you need to increase the number of k-points, but as long as you
compare unit cells that are identical, you might easily get away with
lower sampling. Still, gamma can be slow to converge - have a look
at the literature on the vacancy formation energy in silicon.

			nicola



> Hi all,
> 
> I want to calculate the energy difference of FM and AFM states of two
> isolated
> magnetic impurities in a semiconductor, optionaly with the presence of
> native
> impurities.
> 
> The supercell has to be  fairly large, of the order of 100 atoms, so I
> can only
> afford Gamma-point calculation. The difference in the energy of
> different magnetic states might be of the order of mRyd.
> 
> My question concerns the convergence parameters and especially degauss.
> Right now I use degauss=5.d-4 and thats the smallest I can  use without
> serious oscillation problems. That is 0.5mRyd so it is probably fine.
> 
> A second concern is the realiability of the Gamma point calculation itself.
> My worry is that increasing the mumber of k-points will lower all the
> energies
> by much more than the mRyd differences I am obtaining.  In other words,
> I am worrying that the error of restricting the k-space to the gamma point
> is much larger than the energy differences I get.  What is the
> experience on that
> issue? Is a supercell of 100 atoms big enough to guarantee that a
> gamma-point
> calculation will have accuracy of the order of miliRydberg? And if not
> are the
> energy differences of any value or it is just crap?
> 
> Here are the convergence parameters I use right now:
> etot_conv_thr = 1.d-5
> degauss = 5.d-4
> conv_thr = 1.0d-6
> 
> Thanks
> Nektarios
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 
---------------------------------------------------------------------
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 stargmoon at yahoo.com  Tue Sep 19 00:00:55 2006
From: stargmoon at yahoo.com (stargmoon)
Date: Mon, 18 Sep 2006 15:00:55 -0700 (PDT)
Subject: [Pw_forum] parallel compiling
In-Reply-To: <7b6913e90609181144i5b093e7cs38422304b2c2e48e@mail.gmail.com>
Message-ID: <20060918220055.23097.qmail@web33214.mail.mud.yahoo.com>

Thanks a lot for your reminder, I do not know this before. But I know it seems that pgi6.1 does not work for WIEN2k. That is why I chose pgi5.2 here.
 
 Best,
 
 Stargmoon

Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu> wrote: On 9/18/06, stargmoon  wrote:
> Thanks a lot Eyvaz for your reminder. Actually, every time before I run
> ./configure I load moduli "pgi52 and mpich-pgi".

wait. regardless of whether you can get a successful compile
or not. pgi version 5.2 is known to miscompile QE (and other
similar codes). so you should try a different options.

furthermore, as i was trying to say. even with using the modules
utility, packages are usually installed differently on most machines
and sometime the slightest difference can be the reason for
configure to pick up the right flags or not.

axel.

>
>  Best
>
>
[...]


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


 		
---------------------------------
Stay in the know. Pulse on the new Yahoo.com.  Check it out. 
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From lathiot at physik.fu-berlin.de  Tue Sep 19 19:28:03 2006
From: lathiot at physik.fu-berlin.de (Nektarios Lathiotakis)
Date: Tue, 19 Sep 2006 19:28:03 +0200
Subject: [Pw_forum] Supercell- gamma point calculation reliability
In-Reply-To: <450EFEDC.7090202@mit.edu>
References: <450ECB98.9070501@physik.fu-berlin.de> <450EFEDC.7090202@mit.edu>
Message-ID: <451028A3.3080507@physik.fu-berlin.de>

Nicola Marzari wrote:

>
>
> Nektarios,
>
>
> 1) the "dispersion" from the magnetic impurities should be flat,
> and the difference in energy that you look at is within two
> cells that have the same sampling. That is good.
>
> 2) a simple test would be to still use 1 k-point, but the Baldereschi
> (PRB 1973) point instead of Gamma. For an orthorombic cell, I generally
> use 1/4 1/4 1/4 . PWSCf would automatically try to replicate it to
> recover full symmetry (i.e. would want to use all of the 2 2 2 1 1 1
> Monhorst-Pack mesh that are not related by any point-group operation),
> but using no_sym (or nosym ?) you can force the code to just use that
> single k-point. 1/4 1/4 1/4 is often more accurate than Gamma, and
> any difference you find would hint at insufficient sampling.

Thanks, that is a great idea!

>
> 3) degauss, generally speaking, should be larger than what you used if
> you were dealing with a metal. In your case, though, you probably use it
> just to smooth the path to selfconsistency, and at the ground state you
> still want integer occupations everywhere, correct ?

At the very end (after ion relaxation also) I would like degauss=0. I
guess if the
variation has lead to a semiconducting structure that should be OK. If the
structure has a metalic character then the oscillation effects will not
allow
for convergence with degaus=0. But I havent tried sofar.

>
> 4) what I would worry is haivng very good ionic relaxations, since these
> can be different  in the FM and AFM states. Using the same cell for the
> two calculations (same cell parameters, same cutoff, same kpoints) helps
> a lot with the electronic accuracy, since in the energy difference you
> have cancellation of terms that might have needed more kpoints.

I am thinking to allow for relaxation of the first neighbohrs of the
deffects
(impurities / native deffects).

>
>
> 5) of course, if you need for some reason absolute k-point convergence,
> than you need to increase the number of k-points, but as long as you
> compare unit cells that are identical, you might easily get away with
> lower sampling. Still, gamma can be slow to converge - have a look
> at the literature on the vacancy formation energy in silicon.
>
>             nicola
>
Thank you very much for the advice
Nektarios

>
>
>> Hi all,
>>
>> I want to calculate the energy difference of FM and AFM states of two
>> isolated
>> magnetic impurities in a semiconductor, optionaly with the presence of
>> native
>> impurities.
>>
>> The supercell has to be  fairly large, of the order of 100 atoms, so I
>> can only
>> afford Gamma-point calculation. The difference in the energy of
>> different magnetic states might be of the order of mRyd.
>>
>> My question concerns the convergence parameters and especially degauss.
>> Right now I use degauss=5.d-4 and thats the smallest I can  use without
>> serious oscillation problems. That is 0.5mRyd so it is probably fine.
>>
>> A second concern is the realiability of the Gamma point calculation
>> itself.
>> My worry is that increasing the mumber of k-points will lower all the
>> energies
>> by much more than the mRyd differences I am obtaining.  In other words,
>> I am worrying that the error of restricting the k-space to the gamma
>> point
>> is much larger than the energy differences I get.  What is the
>> experience on that
>> issue? Is a supercell of 100 atoms big enough to guarantee that a
>> gamma-point
>> calculation will have accuracy of the order of miliRydberg? And if not
>> are the
>> energy differences of any value or it is just crap?
>>
>> Here are the convergence parameters I use right now:
>> etot_conv_thr = 1.d-5
>> degauss = 5.d-4
>> conv_thr = 1.0d-6
>>
>> Thanks
>> Nektarios
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>



From reboredofa at ornl.gov  Tue Sep 19 23:23:52 2006
From: reboredofa at ornl.gov (Fernando A Reboredo)
Date: Tue, 19 Sep 2006 17:23:52 -0400
Subject: [Pw_forum] small bug zmesh=0
References: <450ECB98.9070501@physik.fu-berlin.de> <450EFEDC.7090202@mit.edu>
 <451028A3.3080507@physik.fu-berlin.de>
Message-ID: <019401c6dc31$e77bb430$b7305ba0@ornl.gov>

I found a problem in PP/pw2casino zmesh is set to zero



Syntoms

Line 262 of PP/pw2casino.f90



WRITE(io,'(i6,3f20.14)') INT(zmesh(ityp(na))), (alat*tau(j,na),j=1,3)



Is supposed to write the atomic number  Z of the atom "na".



However the vector zmesh (defined in Modules/atom.f90) is zero.



It seams that my problem is that my pseudopotential is in UPF format. It 
appears to me that in that format the only way to set values for zmesh is to 
include a

<PP_ADDNFO> tag with additional parameters in the pseudopotential file

According to the soubroutine read_pseudo_upf,  zmesh appears to be read 
under that tag. But if i add the <PP_ADDINFO> tag I will leave

upf%has_so=.true.

And I would also have to set spin-orbit information into the pseudopotential 
file with uncertain outcome for me.



The quit fix for me has been to change pw2casino in the following way



Add atm to line 63 that is

USE ions_base, ONLY : nat, ntyp => nsp, ityp, tau, zv,atm

Change line 262 by

  write(io,'(a6,3f20.14)') atm(ityp(na)), (alat*tau(j,na),j=1,3)



In this way I have the atoms identified and I can replace the symbols for 
the atomic number before running CASINO.



This is not an important problem, only for the large systems with different 
atoms that I am running it is tedious replace. However, there might be other 
routines or post-processing tools that use zmesh.



Please let me know if there is another way to fix this.



Hopping to be a little usefull



Fernando Reboredo



From lyw1983 at 163.com  Wed Sep 20 06:34:32 2006
From: lyw1983 at 163.com (lyw1983)
Date: Wed, 20 Sep 2006 12:34:32 +0800 (CST)
Subject: [Pw_forum] The stress in the outp
 ut of the scf.
In-Reply-To: <Pine.LNX.4.44.0609160846150.11962-100000@localhost.localdomain>
References: <Pine.LNX.4.44.0609160846150.11962-100000@localhost.localdomain>
Message-ID: <4510C4D8.000073.21651@bj163app105.163.com>

hi,
  Thanks for you answer and advice!
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From hsd22 at hermes.cam.ac.uk  Wed Sep 20 12:25:51 2006
From: hsd22 at hermes.cam.ac.uk (H.S.Domingos)
Date: Wed, 20 Sep 2006 11:25:51 +0100 (BST)
Subject: [Pw_forum] Magnetization Question
Message-ID: <Pine.LNX.4.64.0609201119470.16735@hermes-2.csi.cam.ac.uk>

Dear All,

I have been using the constrained_magnetization = 'atomic' option on a 
system with a lot of magnetic atoms. The problem that I am getting is that 
the starting_magnetization can only be imposed on 10 atoms at most.
Is it possible to impose starting magnetizations on an arbitrary number of 
atoms ?
How can that be done ?

Thank you very much and best regards,

Helder


=======================================================================
|  Dr. Helder S. Domingos                                             |
|                                                                     |
| INESC Microsyst & Nanotechnol, Lisbon, P-1000 Portugal              |
| and                                                                 |
| R&D unit for  Molecular Chemical Physics                            |
| Chemistry Department, University of Coimbra                         |
=======================================================================



From giannozz at nest.sns.it  Wed Sep 20 15:52:49 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 20 Sep 2006 15:52:49 +0200
Subject: [Pw_forum] small bug zmesh=0
In-Reply-To: <019401c6dc31$e77bb430$b7305ba0@ornl.gov>
References: <450ECB98.9070501@physik.fu-berlin.de> <450EFEDC.7090202@mit.edu> <451028A3.3080507@physik.fu-berlin.de> <019401c6dc31$e77bb430$b7305ba0@ornl.gov>
Message-ID: <1888A339-F10A-4B7F-8A50-DBE0D724EF75@nest.sns.it>

On Sep 19, 2006, at 23:23 , Fernando A Reboredo wrote:

> I found a problem in PP/pw2casino

only one ? not bad for a piece of code that was last tested two years
ago. It has been updated several times since then.

> WRITE(io,'(i6,3f20.14)') INT(zmesh(ityp(na))), (alat*tau(j,na),j=1,3)
>
> Is supposed to write the atomic number  Z of the atom "na".

not a good idea anyway: zmesh is a parameter defining the atomic
radial grid, which happens to be traditionally equal to Z. It is however
not necessarily so, and not always defined or available. Unfortunately,
Z is written nowhere in pseudopotential files.

> The quit fix for me has been to change pw2casino in the following way
> [...] Please let me know if there is another way to fix this.

the best you can do is the following. Define

   integer, external:: atomic_number
   integer :: at_num

then

   DO na = 1, nat
      nt = ityp(na)
      at_num = atomic_number(TRIM(atm(nt)))
      WRITE(io,'(i6,3f20.14)') at_num, (alat*tau(j,na),j=1,3)
   ENDDO

if atm(nt) happens to be the symbol of an element, you will get Z.

Paolo





From reboredofa at ornl.gov  Wed Sep 20 18:58:25 2006
From: reboredofa at ornl.gov (Fernando A Reboredo)
Date: Wed, 20 Sep 2006 12:58:25 -0400
Subject: [Pw_forum] small bug zmesh=0
References: <450ECB98.9070501@physik.fu-berlin.de> <450EFEDC.7090202@mit.edu>
 <451028A3.3080507@physik.fu-berlin.de>
 <019401c6dc31$e77bb430$b7305ba0@ornl.gov>
 <1888A339-F10A-4B7F-8A50-DBE0D724EF75@nest.sns.it>
Message-ID: <03ae01c6dcd5$fd339a00$b7305ba0@ornl.gov>

Thanks Paolo!
Fernando
----- Original Message ----- 
From: "Paolo Giannozzi" <giannozz at nest.sns.it>
To: <pw_forum at pwscf.org>
Sent: Wednesday, September 20, 2006 9:52 AM
Subject: Re: [Pw_forum] small bug zmesh=0


> 
> On Sep 19, 2006, at 23:23 , Fernando A Reboredo wrote:
> 
>> I found a problem in PP/pw2casino
> 
> only one ? not bad for a piece of code that was last tested two years
> ago. It has been updated several times since then.
> 
>> WRITE(io,'(i6,3f20.14)') INT(zmesh(ityp(na))), (alat*tau(j,na),j=1,3)
>>
>> Is supposed to write the atomic number  Z of the atom "na".
> 
> not a good idea anyway: zmesh is a parameter defining the atomic
> radial grid, which happens to be traditionally equal to Z. It is however
> not necessarily so, and not always defined or available. Unfortunately,
> Z is written nowhere in pseudopotential files.
> 
>> The quit fix for me has been to change pw2casino in the following way
>> [...] Please let me know if there is another way to fix this.
> 
> the best you can do is the following. Define
> 
>   integer, external:: atomic_number
>   integer :: at_num
> 
> then
> 
>   DO na = 1, nat
>      nt = ityp(na)
>      at_num = atomic_number(TRIM(atm(nt)))
>      WRITE(io,'(i6,3f20.14)') at_num, (alat*tau(j,na),j=1,3)
>   ENDDO
> 
> if atm(nt) happens to be the symbol of an element, you will get Z.
> 
> Paolo
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From rui_zhi_zhang at yahoo.com  Fri Sep 22 13:40:09 2006
From: rui_zhi_zhang at yahoo.com (ruizhi zhang)
Date: Fri, 22 Sep 2006 04:40:09 -0700 (PDT)
Subject: [Pw_forum] Can USPP and NCPP be used together?
In-Reply-To: <20060920053744.31279.33545.Mailman@democritos.sissa.it>
Message-ID: <20060922114009.2128.qmail@web39814.mail.mud.yahoo.com>

Dear all
   
  I want to calculate PMN, which contains Nb, Mg, Pb, O, within LDA.  However,  there is only norm-consevring pseudopotential(NCPP) for Mg.  There is ultrasoft pseudopotentials(USPP) for Pb, O, Nb,  i.e.  Pb.vdb.UPF, O.vdb.UPF(as used in example10) and Nb.vdb.UPF( which I generated using vanderbilt's code), 
  Can I use Mg's NCPP and other three's USPP together ?
   
  As a test, I modified Exampel10, changed the Pb.vdb.UPF to Pb.bz-bhs.UPF, and it gave good results, which is somewhat different from the result of original exampel. Can these result be considered reliable?
   
  Thanks in advance
   
  sincerely
  ruizhi zhang

 		
---------------------------------
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 Get on board. You're invited to try the new Yahoo! Mail.
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From lanhaiping at gmail.com  Fri Sep 22 13:56:24 2006
From: lanhaiping at gmail.com (lan haiping)
Date: Fri, 22 Sep 2006 19:56:24 +0800
Subject: [Pw_forum] Can USPP and NCPP be used together?
In-Reply-To: <20060922114009.2128.qmail@web39814.mail.mud.yahoo.com>
References: <20060920053744.31279.33545.Mailman@democritos.sissa.it>
	 <20060922114009.2128.qmail@web39814.mail.mud.yahoo.com>
Message-ID: <c92002fa0609220456wd8b0b3m1a652b7fec6b02b1@mail.gmail.com>

as far as i know, you cannot use different PP for the same calculation..
Also, you shouldnot use different functional for the same calculation

regards,

Hai-Ping


On 9/22/06, ruizhi zhang <rui_zhi_zhang at yahoo.com> wrote:
>
> Dear all
>
> I want to calculate PMN, which contains Nb, Mg, Pb, O, within LDA.
> However,  there is only norm-consevring pseudopotential(NCPP) for Mg.  There
> is ultrasoft pseudopotentials(USPP) for Pb, O, Nb,  i.e.  Pb.vdb.UPF,
> O.vdb.UPF(as used in example10) and Nb.vdb.UPF( which I generated using
> vanderbilt's code),
> Can I use Mg's NCPP and other three's USPP together ?
>
> As a test, I modified Exampel10, changed the Pb.vdb.UPF to Pb.bz-bhs.UPF,
> and it gave good results, which is somewhat different from the result of
> original exampel. Can these result be considered reliable?
>
> Thanks in advance
>
> sincerely
> ruizhi zhang
>
> ------------------------------
> Do you Yahoo!?
> Get on board. You're invited<http://us.rd.yahoo.com/evt=40791/*http://advision.webevents.yahoo.com/mailbeta>to try the new Yahoo! Mail.
>
>
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From giannozz at nest.sns.it  Fri Sep 22 14:09:48 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 22 Sep 2006 14:09:48 +0200
Subject: [Pw_forum] Can USPP and NCPP be used together?
In-Reply-To: <c92002fa0609220456wd8b0b3m1a652b7fec6b02b1@mail.gmail.com>
References: <20060920053744.31279.33545.Mailman@democritos.sissa.it> <20060922114009.2128.qmail@web39814.mail.mud.yahoo.com> <c92002fa0609220456wd8b0b3m1a652b7fec6b02b1@mail.gmail.com>
Message-ID: <789BA91F-2729-4F1D-A0A0-6BA18F5978F7@nest.sns.it>

On Sep 22, 2006, at 13:56 , lan haiping wrote:

> as far as i know, you cannot use different PP for the same  
> calculation..
> Also, you should not use different functional for the same calculation

the latter statement is correct, the former is not. In CP there is a
restriction on the order of PP (ultrasoft must come first)

Paolo




From stewart at cnf.cornell.edu  Mon Sep 25 15:11:49 2006
From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu)
Date: Mon, 25 Sep 2006 09:11:49 -0400
Subject: [Pw_forum] Calculating generalized susceptibility with PWscf
In-Reply-To: <Pine.LNX.4.64.0609201119470.16735@hermes-2.csi.cam.ac.uk>
References: <Pine.LNX.4.64.0609201119470.16735@hermes-2.csi.cam.ac.uk>
Message-ID: <20060925131149.15499.qmail@xuxa.iecc.com>

Hi everyone, 

  I was wondering if it is possible to calculate the generalized 
susceptibility, chi(q), with the PWscf code.  If someone could point me to 
the relevant documentation or examples, I would greatly appreciate it. 

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 lijun_physics at yahoo.com.cn  Tue Sep 26 09:33:06 2006
From: lijun_physics at yahoo.com.cn (Lijun Zhang)
Date: Tue, 26 Sep 2006 15:33:06 +0800 (CST)
Subject: [Pw_forum] About diamagnetic calculation
Message-ID: <20060926073306.23274.qmail@web15608.mail.cnb.yahoo.com>

Dear all,
   
  I want to perform the phonon calculations of  ZnF2, which is diamagnetic.
  Should I think of  spin polarization?
   
  Best regards
   
  Lijun Zhang
  National Lab of Superhard Materials
Jilin University
Changchun,130012
P.R.China
Email: lijun_physics at yahoo.com.cn

 		
---------------------------------
 Mp3???-???????   
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From rui_zhi_zhang at yahoo.com  Tue Sep 26 11:00:06 2006
From: rui_zhi_zhang at yahoo.com (ruizhi zhang)
Date: Tue, 26 Sep 2006 02:00:06 -0700 (PDT)
Subject: [Pw_forum] Problem with Xcrysden when ibrav=0
Message-ID: <20060926090006.40978.qmail@web39812.mail.mud.yahoo.com>

Dear all
   
  When I try to use Xcrysden to show the structure of PbTiO3(the input file has been attached below), the Xcrysden does not work and shows a message : 
  ERROR: while executing 
  exeu.sh
  /home/zrz/pto/pto.rl.in
   
  But when I modify the input file, change ibrav=0 to ibrav=1, and remove the CELL_PARAMETERS card. Then the Xcrysden works well. 
  Is there something wrong? Or the format of CELL_PARAMETERS card is improper?
   
  Thanks in advance
  Regards, ruizhi
   
  ****************************************
  Here is the input file
  &control
    calculation  = 'vc-relax'
    restart_mode = 'from_scratch'
    pseudo_dir   = '/home/zrz/espresso-3.1.1/pseudo/'
    outdir       = '/home/zrz/taisuanqian/tmp/'
 /
 &system
    ibrav=0
    celldm(1)=7.50,
    nat=5
    ntyp=3
    nbnd=25
    ecutwfc=30.0
    occupations = 'fixed'
 /
 &electrons
    conv_thr = 1e-8,
    mixing_beta=0.3,
 /
&IONS
  ion_dynamics = 'damp',
 /
 &CELL
  cell_dynamics ='damp-pr'
   /
ATOMIC_SPECIES
  Pb    207.2      Pb.vdb.UPF
  Ti    47.867    Ti.vdb.UPF
  O     15.9994   O.vdb.UPF
ATOMIC_POSITIONS
  Pb    0.000    0.000    0.000 
  Ti    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}
  4 4 4 0 0 0
CELL_PARAMETERS 
  1.0   0      0
  0     1.0    0
  0     0       1.0

   

 		
---------------------------------
Stay in the know. Pulse on the new Yahoo.com.  Check it out. 
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From eyvaz_isaev at yahoo.com  Tue Sep 26 20:59:29 2006
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 26 Sep 2006 11:59:29 -0700 (PDT)
Subject: [Pw_forum] About diamagnetic calculation
In-Reply-To: <20060926073306.23274.qmail@web15608.mail.cnb.yahoo.com>
Message-ID: <20060926185929.94774.qmail@web60311.mail.yahoo.com>

Hi,

Presumably, you should read a textbook before posting
the question. Even you might have a look at Wikipedia.


From baroni at sissa.it  Tue Sep 26 21:41:40 2006
From: baroni at sissa.it (Stefano Baroni)
Date: Tue, 26 Sep 2006 21:41:40 +0200
Subject: [Pw_forum] Calculating generalized susceptibility with PWscf
In-Reply-To: <20060925131149.15499.qmail@xuxa.iecc.com>
References: <Pine.LNX.4.64.0609201119470.16735@hermes-2.csi.cam.ac.uk> <20060925131149.15499.qmail@xuxa.iecc.com>
Message-ID: <5C16D90B-92E5-4BAB-8E88-F7047A531702@sissa.it>


On Sep 25, 2006, at 3:11 PM, stewart at cnf.cornell.edu wrote:

> Hi everyone,
>  I was wondering if it is possible to calculate the generalized  
> susceptibility, chi(q), with the PWscf code.

what is a "generalized susceptipility"?

PHONON can calculate the macroscopic dielectric constant "out of the  
box". With little work one could obtain the G/=0 components of the  
response to an applied electric field (q->0). With some more work, it  
would not be difficult to calculate epsilon^{-1}(q,q) (I understand  
that my notation may not be more clear than yours ;-)

S.

> If someone could point me to the relevant documentation or  
> examples, I would greatly appreciate it.
> 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

---
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  Tue Sep 26 21:48:06 2006
From: baroni at sissa.it (Stefano Baroni)
Date: Tue, 26 Sep 2006 21:48:06 +0200
Subject: [Pw_forum] About diamagnetic calculation
In-Reply-To: <20060926073306.23274.qmail@web15608.mail.cnb.yahoo.com>
References: <20060926073306.23274.qmail@web15608.mail.cnb.yahoo.com>
Message-ID: <FF7D7152-3E53-425D-92BE-AF644AC0AABC@sissa.it>

Dear Lijun:

may I suggest that you make a step back and answer yourself your own  
question?

Are molecular orbitals in diamagnetic materials singly or doubly  
occupied .?...

hint. here is an excerpts from http://en.wikipedia.org/wiki/Diamagnetism

  ... Materials that are said to be diamagnetic are those which are  
usually considered by non-physicists as "non magnetic" ...


SB

On Sep 26, 2006, at 9:33 AM, Lijun Zhang wrote:

> Dear all,
>
> I want to perform the phonon calculations of  ZnF2, which is  
> diamagnetic.
> Should I think of  spin polarization?
>
> Best regards
>
> Lijun Zhang
> National Lab of Superhard Materials
> Jilin University
> Changchun,130012
> P.R.China
> Email: lijun_physics at yahoo.com.cn
>
> Mp3???-???????

---
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 rudrabnrj at gmail.com  Wed Sep 27 07:49:10 2006
From: rudrabnrj at gmail.com (rudra banerjee)
Date: Wed, 27 Sep 2006 11:19:10 +0530
Subject: [Pw_forum] About diamagnetic calculation
In-Reply-To: <FF7D7152-3E53-425D-92BE-AF644AC0AABC@sissa.it>
References: <20060926073306.23274.qmail@web15608.mail.cnb.yahoo.com>
	 <FF7D7152-3E53-425D-92BE-AF644AC0AABC@sissa.it>
Message-ID: <2e36f8e50609262249w1eef7d9s71c8310ff495cd0a@mail.gmail.com>

hello everyone
i am a new user of PWscf.i am getting a very basic problem...plz help.
the problem is what is abt the weughtage of coordinates? can any1 help me hw
to decalir the weightage???
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From baroni at sissa.it  Wed Sep 27 08:33:59 2006
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 27 Sep 2006 08:33:59 +0200
Subject: [Pw_forum] About diamagnetic calculation
In-Reply-To: <2e36f8e50609262249w1eef7d9s71c8310ff495cd0a@mail.gmail.com>
References: <20060926073306.23274.qmail@web15608.mail.cnb.yahoo.com> <FF7D7152-3E53-425D-92BE-AF644AC0AABC@sissa.it> <2e36f8e50609262249w1eef7d9s71c8310ff495cd0a@mail.gmail.com>
Message-ID: <E667003D-12B7-4795-A5BC-3BEFB79E1F68@sissa.it>

Hi Rudra: we would gladly (try to) help if we only could understand  
what the problem is.
What is the "weughtage of coordinates?"
SB

On Sep 27, 2006, at 7:49 AM, rudra banerjee wrote:

> hello everyone
> i am a new user of PWscf.i am getting a very basic problem...plz help.
> the problem is what is abt the weughtage of coordinates? can any1  
> help me hw to decalir the weightage???

---
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 lijun_physics at yahoo.com.cn  Wed Sep 27 15:15:15 2006
From: lijun_physics at yahoo.com.cn (Lijun Zhang)
Date: Wed, 27 Sep 2006 21:15:15 +0800 (CST)
Subject: [Pw_forum] Re:About diamagnetic calculation
Message-ID: <20060927131515.53068.qmail@web15604.mail.cnb.yahoo.com>

Dear Eyvaz and Stefano,
   
  I think I have got the answer.
  Thanks very much for the patient explanation about my obvious question.
  Especially Stefano, have helped me on the physical principles many times.
   
  Best regards


Lijun Zhang 
National Lab of Superhard Materials
Jilin University
Changchun,130012
P.R.China
Email: lijun_physics at yahoo.com.cn
 		
---------------------------------
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From stewart at cnf.cornell.edu  Wed Sep 27 22:20:33 2006
From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu)
Date: Wed, 27 Sep 2006 16:20:33 -0400
Subject: [Pw_forum] Re: Calculating generalized susceptibility with PWscf
In-Reply-To: <5C16D90B-92E5-4BAB-8E88-F7047A531702@sissa.it>
References: <Pine.LNX.4.64.0609201119470.16735@hermes-2.csi.cam.ac.uk>
            <20060925131149.15499.qmail@xuxa.iecc.com>
            <5C16D90B-92E5-4BAB-8E88-F7047A531702@sissa.it>
Message-ID: <20060927202033.12370.qmail@xuxa.iecc.com>

Hi Stefano, 

The generalized susceptiblity I'm interested in appears in discussions of 
nesting vectors in Fermi surfaces.  It can be expressed in rough latex 
format as 

Chi(q) = \Sum_{ij,k} \frac{f(\eta_{k,i})[1-f(\eta_{k+q,j})]} {\eta_{k+q,j - 
\eta_{k,i}} 

where f is the Fermi function, \eta is the energy for the given band and k 
point, i and j are band indices.  Only bands that cross the Fermi energy are 
included in the sum.  I can send you a pdf file with the equation if the 
above is still unclear. 

I am putting together a small code to calculate this based on PWscf results, 
but I wanted to make sure that this wasn't available as a feature of PWscf.  
No sense in reinventing the wheel... 

Thanks, 

Derek
 

Stefano Baroni writes: 

> 
> On Sep 25, 2006, at 3:11 PM, stewart at cnf.cornell.edu wrote: 
> 
>> Hi everyone,
>>  I was wondering if it is possible to calculate the generalized  
>> susceptibility, chi(q), with the PWscf code.
> 
> what is a "generalized susceptipility"? 
> 
> PHONON can calculate the macroscopic dielectric constant "out of the  
> box". With little work one could obtain the G/=0 components of the  
> response to an applied electric field (q->0). With some more work, it  
> would not be difficult to calculate epsilon^{-1}(q,q) (I understand  that 
> my notation may not be more clear than yours ;-) 
> 
> S. 
> 
>> If someone could point me to the relevant documentation or  examples, I 
>> would greatly appreciate it.
>> 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
> 
> ---
> 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 
> 
>  
> 
 


################################
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 proffess at yandex.ru  Thu Sep 28 01:58:37 2006
From: proffess at yandex.ru (Sergey Lisenkov)
Date: Thu, 28 Sep 2006 03:58:37 +0400 (MSD)
Subject: [Pw_forum] reading pot file
Message-ID: <451B102D.000002.26250@colgate.yandex.ru>

 Dear all,

  I am a little bit confused how to force the code read potential file in beginning of calculation. I use the next option in my input file:

 startingpot='file'

But in output file I see :

 ....

  writing wfc files to a dedicated directory
     Cannot read rho : file not found
 
     Initial potential from superposition of free atoms
 
     starting charge   96.99814, renormalised to   98.00000
     Starting wfc are atomic
 
     total cpu time spent up to now is     10.64 secs
 
     Self-consistent Calculation
 
     iteration #  1     ecut=    35.00 ryd     beta=0.10
     Davidson diagonalization with overlap
     ethr =  1.00E-05,  avg # of iterations =  8.3
 
     total cpu time spent up to now is     35.77 secs
 
     total energy              =  -977.61653338 ryd
     estimated scf accuracy    <    12.50806875 ryd

Is it possible that this behaviour is caused by using local disks on each node and I copied *.save dir only on the first node? I am using 3.1.1 version.

  Thanks,
    Sergey


From baroni at sissa.it  Thu Sep 28 09:08:00 2006
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 28 Sep 2006 09:08:00 +0200
Subject: [Pw_forum] Re: Calculating generalized susceptibility with PWscf
In-Reply-To: <20060927202033.12370.qmail@xuxa.iecc.com>
References: <Pine.LNX.4.64.0609201119470.16735@hermes-2.csi.cam.ac.uk> <20060925131149.15499.qmail@xuxa.iecc.com> <5C16D90B-92E5-4BAB-8E88-F7047A531702@sissa.it> <20060927202033.12370.qmail@xuxa.iecc.com>
Message-ID: <0788BB92-5B8A-4A68-9CAE-B783E4410237@sissa.it>

Hi Derek: that looks like the "kinematic" part of a susceptibility  
(i.e. a susceptibility with all the matrrix elements set equal to  
one). I do not think that anyting similar is already calculated  
anywhere in Quantum ESPRESSO. It would be good to have it! Thanks -  
Stefano

On Sep 27, 2006, at 10:20 PM, stewart at cnf.cornell.edu wrote:

> Chi(q) = \Sum_{ij,k} \frac{f(\eta_{k,i})[1-f(\eta_{k+q,j})]} {\eta_ 
> {k+q,j - \eta_{k,i}}

---
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 giannozz at nest.sns.it  Thu Sep 28 16:41:03 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 28 Sep 2006 16:41:03 +0200
Subject: [Pw_forum] reading pot file
In-Reply-To: <451B102D.000002.26250@colgate.yandex.ru>
References: <451B102D.000002.26250@colgate.yandex.ru>
Message-ID: <49178B5C-6C09-482A-9BF6-A010E06F2B8D@nest.sns.it>

On Sep 28, 2006, at 1:58 , Sergey Lisenkov wrote:

> I am a little bit confused how to force the code read potential file
> in beginning of calculation. I use the next option in my input file:
>
>  startingpot='file'
>
> But in output file I see :
> [ ...]
>      Cannot read rho : file not found
> [....]
> Is it possible that this behaviour is caused by using local disks on
> each node and I copied *.save dir only on the first node?

See routine "PW/potinit.f90". Assuming that the file is really there
with the expected name, the only possible reason is that process 0
of the second run (when the file is read) does not see the *.save
directory, because it is executed on a different processor with
respect to the first run (when the file was written). It is a known
problem if you use local filesystems and there is little one can do,
other than copying the needed files to a place where they can
be found.

Paolo




From vdiep at ictp.it  Thu Sep 28 16:51:40 2006
From: vdiep at ictp.it (Diep Quang Vinh)
Date: Thu, 28 Sep 2006 16:51:40 +0200 (CEST)
Subject: [Pw_forum] About *.grd in charge density
Message-ID: <43598.140.105.16.2.1159455100.squirrel@webmail2.ictp.trieste.it>

Dear all,

I would like to ask you something about the post processing in CP.

I have a problem with the format of the output in charge density calculation (version
3.1.1 or before in CLX system in CINECA). I would like to plot the KS state of a given
sytem by declaring, for example, in the input file:

KSOUT
1
145
1
144

But the code give me the output like "KS_145.xml" and it is in the binary format. On top
of that, if i use the cppp.x to create the charge density of this state, the output is
always in *.grd format. Does anyone know how to plot the *.grd file? Or can you have any
suggestions that i can plot the charge density of a specific KS state by Xcrydens?

Thank you very much in advance.


Vinh




From giannozz at nest.sns.it  Thu Sep 28 17:35:04 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 28 Sep 2006 17:35:04 +0200
Subject: [Pw_forum] About *.grd in charge density
In-Reply-To: <43598.140.105.16.2.1159455100.squirrel@webmail2.ictp.trieste.it>
References: <43598.140.105.16.2.1159455100.squirrel@webmail2.ictp.trieste.it>
Message-ID: <B328655C-657F-47C8-A9B6-98D70EEB1DCC@nest.sns.it>

On Sep 28, 2006, at 16:51 , Diep Quang Vinh wrote:

> can you have any suggestions that i can plot the charge density
> of a specific KS state by Xcrydens?

Carlo Cavazzoni suggests to specify keyword
    output    = 'xsf'
in namelist &inputpp of cppp.x

Paolo




From vdiep at ictp.it  Thu Sep 28 18:44:27 2006
From: vdiep at ictp.it (Diep Quang Vinh)
Date: Thu, 28 Sep 2006 18:44:27 +0200 (CEST)
Subject: [Pw_forum] About *.grd in charge density
In-Reply-To: <B328655C-657F-47C8-A9B6-98D70EEB1DCC@nest.sns.it>
References: <43598.140.105.16.2.1159455100.squirrel@webmail2.ictp.trieste.it>
    <B328655C-657F-47C8-A9B6-98D70EEB1DCC@nest.sns.it>
Message-ID: <56489.140.105.16.2.1159461867.squirrel@webmail2.ictp.trieste.it>

Dear Paolo,

I totally agree with you.  With the keyword " output = 'xsf' ", we can plot the charge
density of with the option

charge_density="full"   or

charge_density='spin'

With these two option, we can plot them by xcrysden because the code give the *.xsf
format. It work very well. However, the problems arise when and only when i want to plot
the specfic KS state. The code give the output in *.grd format regardless " output is
'xsf' or not".

I think the problem is in the following code: fpmdpp.f90 which is responsible for
cppp.x: They said:
--------------------------------------------
 IF ( print_state /= ' ' ) THEN
     CALL read_density( TRIM( print_state ) // '.xml', dunit, nr1, nr2, nr3, rho_in )
     CALL scale_charge( rho_in, rho_out, nr1, nr2, nr3, ns1, ns2, ns3, np1, np2, np3 )
     OPEN( unit = dunit, file = TRIM( print_state ) // '.grd' )
     CALL write_grd( dunit, at, rho_out, ns1, ns2, ns3 )
     CLOSE( dunit )
  END IF
--------------------------------------------
And in my case (print_state=KS_145)

Thank you very much

Regrads.

Vinh



>
> On Sep 28, 2006, at 16:51 , Diep Quang Vinh wrote:
>
>> can you have any suggestions that i can plot the charge density
>> of a specific KS state by Xcrydens?
>
> Carlo Cavazzoni suggests to specify keyword
>     output    = 'xsf'
> in namelist &inputpp of cppp.x
>
> Paolo
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>






From vdiep at ictp.it  Thu Sep 28 18:49:34 2006
From: vdiep at ictp.it (Diep Quang Vinh)
Date: Thu, 28 Sep 2006 18:49:34 +0200 (CEST)
Subject: [Pw_forum] About *.grd in charge density
In-Reply-To: 
     <56489.140.105.16.2.1159461867.squirrel@webmail2.ictp.trieste.it>
References: <43598.140.105.16.2.1159455100.squirrel@webmail2.ictp.trieste.it>
       <B328655C-657F-47C8-A9B6-98D70EEB1DCC@nest.sns.it>
    <56489.140.105.16.2.1159461867.squirrel@webmail2.ictp.trieste.it>
Message-ID: <58003.140.105.16.2.1159462174.squirrel@webmail2.ictp.trieste.it>

Dear Paolo,

Here is my input for cppp.x


&inputpp
  prefix = 'CC',
  output='xsf'
  lcharge = .true.,
  lforces = .false.,
  ldynamics = .false.,
  nframes =1,
  ns1 = 114,
  ns2 = 114,
  ns3 = 114,
  charge_density='spin'
  atomic_number(1) = 17,
  atomic_number(2) = 6,
  print_state = 'KS_17'
/


Regards.
Vinh


> Dear Paolo,
>
> I totally agree with you.  With the keyword " output = 'xsf' ", we can plot the charge
> density of with the option
>
> charge_density="full"   or
>
> charge_density='spin'
>
> With these two option, we can plot them by xcrysden because the code give the *.xsf
> format. It work very well. However, the problems arise when and only when i want to plot
> the specfic KS state. The code give the output in *.grd format regardless " output is
> 'xsf' or not".
>
> I think the problem is in the following code: fpmdpp.f90 which is responsible for
> cppp.x: They said:
> --------------------------------------------
>  IF ( print_state /= ' ' ) THEN
>      CALL read_density( TRIM( print_state ) // '.xml', dunit, nr1, nr2, nr3, rho_in )
>      CALL scale_charge( rho_in, rho_out, nr1, nr2, nr3, ns1, ns2, ns3, np1, np2, np3 )
>      OPEN( unit = dunit, file = TRIM( print_state ) // '.grd' )
>      CALL write_grd( dunit, at, rho_out, ns1, ns2, ns3 )
>      CLOSE( dunit )
>   END IF
> --------------------------------------------
> And in my case (print_state=KS_145)
>
> Thank you very much
>
> Regrads.
>
> Vinh
>
>
>
>>
>> On Sep 28, 2006, at 16:51 , Diep Quang Vinh wrote:
>>
>>> can you have any suggestions that i can plot the charge density
>>> of a specific KS state by Xcrydens?
>>
>> Carlo Cavazzoni suggests to specify keyword
>>     output    = 'xsf'
>> in namelist &inputpp of cppp.x
>>
>> Paolo
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>






From d.alfe at ucl.ac.uk  Thu Sep 28 21:35:00 2006
From: d.alfe at ucl.ac.uk (Dario Alfe`)
Date: Thu, 28 Sep 2006 20:35:00 +0100
Subject: [Pw_forum] anybody has a working Ir potential ?
Message-ID: <001801c6e335$305d71c0$0200a8c0@vesuvioda>

Does anybody have a working potential for Ir? I tried the ones on the pwscf
web-page with no luck.

thanks.

Dario

---------------------------------------------------------------------
Dario Alfe` (d.alfe at ucl.ac.uk)  http://chianti.geol.ucl.ac.uk/~dario
Dept. of Earth Sciences and Dept. of Physics and Astronomy
University College London, Gower Street, London, WC1E 6BT, U.K.
Tel. +44-(0)20-76792361              Fax +44-(0)20-76794166
---------------------------------------------------------------------




From naromero at gmail.com  Thu Sep 28 22:02:41 2006
From: naromero at gmail.com (Nichols A. Romero)
Date: Thu, 28 Sep 2006 16:02:41 -0400
Subject: [Pw_forum] anybody has a working Ir potential ?
In-Reply-To: <001801c6e335$305d71c0$0200a8c0@vesuvioda>
References: <001801c6e335$305d71c0$0200a8c0@vesuvioda>
Message-ID: <6ac064b60609281302u60a0a2c4rf455c42aae49b985@mail.gmail.com>

Dario,

I generated some Ir pseudopotentials about a year ago for use with
ABINIT. I used it for some benchmark tests on one-atom cells. The
pseudopotential was incredibly hard, too hard for most applications.
It was a norm-conserving pseudpotential. I had planned on generating a
softer one, but never got around to it because I had to defend my
thesis at that time.

If you know how to use FHI98PP, I can suggest the appropriate r_c for
generating it. There were some tricky things with the unoccupied f and
the local potential. I meant to publish the results but never got
around to it.

On 9/28/06, Dario Alfe` <d.alfe at ucl.ac.uk> wrote:
> Does anybody have a working potential for Ir? I tried the ones on the pwscf
> web-page with no luck.
>
> thanks.
>
> Dario
>
> ---------------------------------------------------------------------
> Dario Alfe` (d.alfe at ucl.ac.uk)  http://chianti.geol.ucl.ac.uk/~dario
> Dept. of Earth Sciences and Dept. of Physics and Astronomy
> University College London, Gower Street, London, WC1E 6BT, U.K.
> Tel. +44-(0)20-76792361              Fax +44-(0)20-76794166
> ---------------------------------------------------------------------
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


-- 
Nichols A. Romero, Ph.D.
1613 Denise Dr. Apt. D
Forest Hill, MD 21050
443-567-8328 (C)
410-306-0709 (O)


From liquan777 at gmail.com  Fri Sep 29 08:21:00 2006
From: liquan777 at gmail.com (li quan)
Date: Fri, 29 Sep 2006 14:21:00 +0800
Subject: [Pw_forum] a question about electron-phonon coupling
Message-ID: <cb7648fa0609282321i39de79c6n5cbec5acf4d08dfe@mail.gmail.com>

Dear all,
    I'm doing the electron-phonon coupling calculation. I find that in the
source file *elphon.f90* it writes as follows:


*parameter (eps = 20.d0/13.6058d0/8065.5d0)*
*........*
*.......*
*.......*
*if (sqrt(abs(w2(nu)) .gt. eps ) then*
*    lambda = gamma/3.1415926/w2(nu)/dosef*
*else*
*    lambda = 0.0*
*.......*
*.......*
**
So I want to know why it sets *eps=20,* can we change the value of *eps*?

Best wishes!



                 a
pwscf user

gao
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From wierzbom at ts.infn.it  Fri Sep 29 11:49:53 2006
From: wierzbom at ts.infn.it (Malgorzata Wierzbowska)
Date: Fri, 29 Sep 2006 11:49:53 +0200 (CEST)
Subject: [Pw_forum] a question about electron-phonon coupling
In-Reply-To: <cb7648fa0609282321i39de79c6n5cbec5acf4d08dfe@mail.gmail.com>
References: <cb7648fa0609282321i39de79c6n5cbec5acf4d08dfe@mail.gmail.com>
Message-ID: <Pine.LNX.4.61.0609291125340.12069@dawn.ts.infn.it>

On Fri, 29 Sep 2006, li quan wrote:

> Dear all,
>   I'm doing the electron-phonon coupling calculation. I find that in the
> source file *elphon.f90* it writes as follows:
>
>
> *parameter (eps = 20.d0/13.6058d0/8065.5d0)*
> *........*
> *.......*
> *.......*
> *if (sqrt(abs(w2(nu)) .gt. eps ) then*
> *    lambda = gamma/3.1415926/w2(nu)/dosef*
> *else*
> *    lambda = 0.0*
> *.......*
> *.......*
> **
> So I want to know why it sets *eps=20,* can we change the value of *eps?


  This is only for writing "an approximate" lambda_q, for given q-phonon,
to the output file which concerns everything for the one "recently calculated"
phonon vector. The epsilon has an arbitrarily small value to avoid 
contribution from phonons with small frequencies.

The problem with small frequency phonons comes from the fact that the 
phonon linewidths (gamma) may decrease with frequency slower than
the frequency itself. And the contribution of such phonons blows
the el-ph to infinity. This is a numerical problem correlated with
the problem of nonzero phonons (and phonon linewidths) at the Gamma point.

The remedy to this problem is to impose the accustic sum rule (which says
that phonons, and the phonon linewidths at the Gamma point are zero).
The sum rule is programmed in the part of the espresso package
where we sum over the q-phonons
(this is in pwtools in q2r and matdy;
zasr='simple' if you look at example07).

So after summation of all phonons, the el-ph comes without any
"approximation" with epsilon you mentioned.

Unfortunately nobody so far succeded to obtain good results for
the phonon vectors q which are very close to the Gamma point
without imposing anything "ad hoc".

Actually the part of elphon.f90 with the epsilon which you mentioned is 
written by Francesco Mauri and probably he could give you a better
explanation of the use of 20Ry as a cutoff.

     Gosia




From giannozz at nest.sns.it  Fri Sep 29 12:35:43 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 29 Sep 2006 12:35:43 +0200
Subject: [Pw_forum] a question about electron-phonon coupling
In-Reply-To: <Pine.LNX.4.61.0609291125340.12069@dawn.ts.infn.it>
References: <cb7648fa0609282321i39de79c6n5cbec5acf4d08dfe@mail.gmail.com> <Pine.LNX.4.61.0609291125340.12069@dawn.ts.infn.it>
Message-ID: <FB12E913-4116-42BB-82CD-68DB6BCFEA75@nest.sns.it>

On Sep 29, 2006, at 11:49 , Malgorzata Wierzbowska wrote:

> Actually the part of elphon.f90 with the epsilon which you mentioned
> is written by Francesco Mauri and probably he could give you a better
> explanation of the use of 20Ry as a cutoff.

20 cm^-1, actually: electron-phonon coefficients are seto to zero
for phonons whose frequency is smaller than 20 cm^-1

Paolo


From wierzbom at ts.infn.it  Fri Sep 29 12:42:08 2006
From: wierzbom at ts.infn.it (Malgorzata Wierzbowska)
Date: Fri, 29 Sep 2006 12:42:08 +0200 (CEST)
Subject: [Pw_forum] a question about electron-phonon coupling
In-Reply-To: <FB12E913-4116-42BB-82CD-68DB6BCFEA75@nest.sns.it>
References: <cb7648fa0609282321i39de79c6n5cbec5acf4d08dfe@mail.gmail.com>
 <Pine.LNX.4.61.0609291125340.12069@dawn.ts.infn.it>
 <FB12E913-4116-42BB-82CD-68DB6BCFEA75@nest.sns.it>
Message-ID: <Pine.LNX.4.61.0609291239570.19026@dawn.ts.infn.it>

On Fri, 29 Sep 2006, Paolo Giannozzi wrote:



>
> On Sep 29, 2006, at 11:49 , Malgorzata Wierzbowska wrote:
>
>> Actually the part of elphon.f90 with the epsilon which you mentioned
>> is written by Francesco Mauri and probably he could give you a better
>> explanation of the use of 20Ry as a cutoff.
>
> 20 cm^-1, actually: electron-phonon coefficients are seto to zero
> for phonons whose frequency is smaller than 20 cm^-1
>
> Paolo
>

  Yes, sorry, 20Ry would be "above" the spectrum !!!

  Anyway after summation there is no "set" for anything.

  Gosia


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


From liquan777 at gmail.com  Fri Sep 29 13:31:48 2006
From: liquan777 at gmail.com (li quan)
Date: Fri, 29 Sep 2006 19:31:48 +0800
Subject: [Pw_forum] a question about electron-phonon coupling
In-Reply-To: <Pine.LNX.4.61.0609291239570.19026@dawn.ts.infn.it>
References: <cb7648fa0609282321i39de79c6n5cbec5acf4d08dfe@mail.gmail.com>
	 <Pine.LNX.4.61.0609291125340.12069@dawn.ts.infn.it>
	 <FB12E913-4116-42BB-82CD-68DB6BCFEA75@nest.sns.it>
	 <Pine.LNX.4.61.0609291239570.19026@dawn.ts.infn.it>
Message-ID: <cb7648fa0609290431m3ced865aw44bf137daac5969b@mail.gmail.com>

Dear Polo,
   Thanks for your and others' answers, you say that
>electron-phonon coefficients are seto to zero
> for phonons whose frequency is smaller than 20 cm^-1

But, if I want to get the value of electron-phonon coefficients for phonons
whose frequency is smaller than 20 cm^-1. What should I do? Could I reduce
the value of "eps"?

Thanks in advance.

gao
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From wierzbom at ts.infn.it  Fri Sep 29 13:36:30 2006
From: wierzbom at ts.infn.it (Malgorzata Wierzbowska)
Date: Fri, 29 Sep 2006 13:36:30 +0200 (CEST)
Subject: [Pw_forum] a question about electron-phonon coupling
In-Reply-To: <cb7648fa0609290431m3ced865aw44bf137daac5969b@mail.gmail.com>
References: <cb7648fa0609282321i39de79c6n5cbec5acf4d08dfe@mail.gmail.com> 
 <Pine.LNX.4.61.0609291125340.12069@dawn.ts.infn.it> 
 <FB12E913-4116-42BB-82CD-68DB6BCFEA75@nest.sns.it> 
 <Pine.LNX.4.61.0609291239570.19026@dawn.ts.infn.it>
 <cb7648fa0609290431m3ced865aw44bf137daac5969b@mail.gmail.com>
Message-ID: <Pine.LNX.4.61.0609291333280.19813@dawn.ts.infn.it>

On Fri, 29 Sep 2006, li quan wrote:


  No, if you reduce eps, for smaller frequency phonons you will get
el-ph in which you cannot trust, too large - as I wrote before.
It is better to calculate some "grid" of phonons and use q2r and matdyn.
Than you will get also small frequency phonons with a good result.
You need to apply the accustic phonon sum rule.
For optical phonons no problem.

  Gosia


> Dear Polo,
>  Thanks for your and others' answers, you say that
>> electron-phonon coefficients are seto to zero
>> for phonons whose frequency is smaller than 20 cm^-1
>
> But, if I want to get the value of electron-phonon coefficients for phonons
> whose frequency is smaller than 20 cm^-1. What should I do? Could I reduce
> the value of "eps"?
>
> Thanks in advance.
>
> gao
>


From giannozz at nest.sns.it  Fri Sep 29 13:54:22 2006
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 29 Sep 2006 13:54:22 +0200
Subject: [Pw_forum] a question about electron-phonon coupling
In-Reply-To: <cb7648fa0609290431m3ced865aw44bf137daac5969b@mail.gmail.com>
References: <cb7648fa0609282321i39de79c6n5cbec5acf4d08dfe@mail.gmail.com> <Pine.LNX.4.61.0609291125340.12069@dawn.ts.infn.it> <FB12E913-4116-42BB-82CD-68DB6BCFEA75@nest.sns.it> <Pine.LNX.4.61.0609291239570.19026@dawn.ts.infn.it> <cb7648fa0609290431m3ced865aw44bf137daac5969b@mail.gmail.com>
Message-ID: <7B99B5DA-005A-4DE8-9DE7-B2DB1F83580E@nest.sns.it>

On Sep 29, 2006, at 13:31 , li quan wrote:

> Dear Polo,
>    Thanks for your and others' answers, you say that
> >electron-phonon coefficients are seto to zero
> > for phonons whose frequency is smaller than 20 cm^-1
>
> But, if I want to get the value of electron-phonon coefficients for  
> phonons whose frequency is smaller than 20 cm^-1. What should I do?  
> Could I reduce the value of "eps"?

the idea behind the cutoff at 20 cm^-1 is to get rid of acoustic phonons
at q=0 (whose contribution to the el-ph coupling is zero anyway).
If you have "real" phonons with frequency < 20 cm^-1 , you may try
to reduce the value of eps, but I guess it will be hard to get an
accurate value.

Paolo


From liquan777 at gmail.com  Fri Sep 29 14:10:06 2006
From: liquan777 at gmail.com (li quan)
Date: Fri, 29 Sep 2006 20:10:06 +0800
Subject: [Pw_forum] a question about electron-phonon coupling
In-Reply-To: <Pine.LNX.4.61.0609291333280.19813@dawn.ts.infn.it>
References: <cb7648fa0609282321i39de79c6n5cbec5acf4d08dfe@mail.gmail.com>
	 <Pine.LNX.4.61.0609291125340.12069@dawn.ts.infn.it>
	 <FB12E913-4116-42BB-82CD-68DB6BCFEA75@nest.sns.it>
	 <Pine.LNX.4.61.0609291239570.19026@dawn.ts.infn.it>
	 <cb7648fa0609290431m3ced865aw44bf137daac5969b@mail.gmail.com>
	 <Pine.LNX.4.61.0609291333280.19813@dawn.ts.infn.it>
Message-ID: <cb7648fa0609290510x580b1152s882fd62ec639c24c@mail.gmail.com>

>
> Dear Gosia,


          What's your meaning of "calculate some "grid" of phonons and use
q2r and matdyn"? I can not understand it quite clearly. Would you explain it
more explicitly?
How to apply the acoustic sum rule in the el-ph calculation? Is it
suitable for acoustic phonons?




gao
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From liquan777 at gmail.com  Fri Sep 29 17:01:34 2006
From: liquan777 at gmail.com (li quan)
Date: Fri, 29 Sep 2006 23:01:34 +0800
Subject: [Pw_forum] a question about electron-phonon coupling
In-Reply-To: <cb7648fa0609290510x580b1152s882fd62ec639c24c@mail.gmail.com>
References: <cb7648fa0609282321i39de79c6n5cbec5acf4d08dfe@mail.gmail.com>
	 <Pine.LNX.4.61.0609291125340.12069@dawn.ts.infn.it>
	 <FB12E913-4116-42BB-82CD-68DB6BCFEA75@nest.sns.it>
	 <Pine.LNX.4.61.0609291239570.19026@dawn.ts.infn.it>
	 <cb7648fa0609290431m3ced865aw44bf137daac5969b@mail.gmail.com>
	 <Pine.LNX.4.61.0609291333280.19813@dawn.ts.infn.it>
	 <cb7648fa0609290510x580b1152s882fd62ec639c24c@mail.gmail.com>
Message-ID: <cb7648fa0609290801n6524e73dwfd6fd72aa1ce2fe6@mail.gmail.com>

Dear Polo,
  I tried reducing the value of eps, but the result of lambda(q,mu) is still
zero.(q is not the center of Brillouin zone). So I do not know why, but I
still want to get the value of lamba(q,mu). Please tell me how to do?
 Best wishes!
                                                                       gao
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From baroni at sissa.it  Wed Sep 27 08:33:59 2006
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 27 Sep 2006 08:33:59 +0200
Subject: [Pw_forum] About diamagnetic calculation
In-Reply-To: <2e36f8e50609262249w1eef7d9s71c8310ff495cd0a@mail.gmail.com>
References: <20060926073306.23274.qmail@web15608.mail.cnb.yahoo.com> <FF7D7152-3E53-425D-92BE-AF644AC0AABC@sissa.it> <2e36f8e50609262249w1eef7d9s71c8310ff495cd0a@mail.gmail.com>
Message-ID: <E667003D-12B7-4795-A5BC-3BEFB79E1F68@sissa.it>

Hi Rudra: we would gladly (try to) help if we only could understand  
what the problem is.
What is the "weughtage of coordinates?"
SB

On Sep 27, 2006, at 7:49 AM, rudra banerjee wrote:

> hello everyone
> i am a new user of PWscf.i am getting a very basic problem...plz help.
> the problem is what is abt the weughtage of coordinates? can any1  
> help me hw to decalir the weightage???

---
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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