From niuli1978 at yahoo.com.cn  Tue May  1 04:07:26 2007
From: niuli1978 at yahoo.com.cn (li niu)
Date: Tue, 1 May 2007 10:07:26 +0800 (CST)
Subject: [Pw_forum] on finite electric methods to calulate vibrational properties
In-Reply-To: <20070430194002.1003.88740.Mailman@democritos.sissa.it>
Message-ID: <46765.88510.qm@web15008.mail.cnb.yahoo.com>

Dear Stefano Baroni ,
   
  I'm sorry for my spelling error. 
   I want to investigate Raman spectra in the case of large   disordered system from first principles and use the finite electric field methods.
The dielectric polarizability tensor can be calculated by taking dinite differences of  atomic forces.
There are several questions to ask you.
  1. We obtained the diagonal terms, by considering values for the electric field of
-2h,-h, 0, h and 2h in the cp.x code[tefield=.true.  
                                                         tcg = .true.,
                                                     epol = 1 or 2 or 3
                                                    efield = -2h,-h, 0, h or 2h],
and by using the five-point formular . Is it right?
   
  2. For the calculation of the off-diagonal terms, two different electric fields 
are required. This need apply electric fields of intensity -2h/1.414,-h/1.414, 
0, h/1.414 and 2h/1.414 along the three different couples of cartesian directions, and apply eauation.
But how can I apply simultaneously finite fields along two different Cartesian directions
in cp.x code?[ESSPRESSO-3.2]
 
3. In this way, we could obtain all the dielectric polarizability tensor. Then the
Raman susceptibilities associated to the normal mode n can be obtianed according to the equation. 
How to implement it ? By a small code?
   
  Best!
  I'm counting on the new version.
  Niu Li

       
---------------------------------
????????3.5G???20M??? 
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From kazempoor2000 at yahoo.com  Tue May  1 10:11:04 2007
From: kazempoor2000 at yahoo.com (ali kazempoor)
Date: Tue, 1 May 2007 01:11:04 -0700 (PDT)
Subject: [Pw_forum] Fwd: nanowire
Message-ID: <20070501081104.44101.qmail@web33103.mail.mud.yahoo.com>

Note: forwarded message attached.


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From ezadshojaee at hotmail.com  Tue May  1 10:28:07 2007
From: ezadshojaee at hotmail.com (Ezad Shojaee)
Date: Tue, 01 May 2007 08:28:07 +0000
Subject: [Pw_forum] LO-TO splitting
Message-ID: <BAY101-F24582DDB040B25C74AD991AA430@phx.gbl>

Hi
i want to know that how could we obtain the splitted modes in for example 
Gamma phonon calculation? because it seems that it does not splitt the LO-TO
thanx

_________________________________________________________________
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From kazempoor2000 at yahoo.com  Tue May  1 10:51:59 2007
From: kazempoor2000 at yahoo.com (ali kazempoor)
Date: Tue, 1 May 2007 01:51:59 -0700 (PDT)
Subject: [Pw_forum] nanowire
Message-ID: <563451.81499.qm@web33114.mail.mud.yahoo.com>

hi all
i want work with MnAs nanowire that has hexagonal
cross section .please comment me in making  which
structure is suitable and how i must make
supercell.also i send input file for bulk for view in
xcryden 
thanks

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From marcel at physik.tu-berlin.de  Tue May  1 12:01:30 2007
From: marcel at physik.tu-berlin.de (Marcel Mohr)
Date: Tue, 1 May 2007 12:01:30 +0200 (CEST)
Subject: [Pw_forum] LO-TO splitting
In-Reply-To: <BAY101-F24582DDB040B25C74AD991AA430@phx.gbl>
References: <BAY101-F24582DDB040B25C74AD991AA430@phx.gbl>
Message-ID: <20070501120036.M23975@rosa.physik-pool.tu-berlin.de>

Hi
I think it is included. Maybe you post your pw.x and ph.x input.

Cheers
Marcel

On Tue, 1 May 2007, Ezad Shojaee wrote:

> Hi
> i want to know that how could we obtain the splitted modes in for example 
> Gamma phonon calculation? because it seems that it does not splitt the LO-TO
> thanx
>
> _________________________________________________________________
> Express yourself instantly with MSN Messenger! Download today it's FREE! 
> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



From ezadshojaee at hotmail.com  Tue May  1 15:08:34 2007
From: ezadshojaee at hotmail.com (Ezad Shojaee)
Date: Tue, 01 May 2007 13:08:34 +0000
Subject: [Pw_forum] LO-TO splitting
Message-ID: <BAY101-F237CAD0927EDCBBFA2BD81AA430@phx.gbl>

Hi
when i use phonon calculation for Gamma point, i do not have splitted modes, 
for example i have E_u mode, not E_u(LO) and E_u(TO).
what's the point?

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From akohlmey at cmm.chem.upenn.edu  Tue May  1 14:54:11 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 1 May 2007 08:54:11 -0400 (EDT)
Subject: [Pw_forum] LO-TO splitting
In-Reply-To: <BAY101-F237CAD0927EDCBBFA2BD81AA430@phx.gbl>
Message-ID: <Pine.LNX.4.44.0705010842210.18695-100000@localhost.localdomain>

On Tue, 1 May 2007, Ezad Shojaee wrote:

ES> Hi
ES> when i use phonon calculation for Gamma point, i do not have splitted modes, 
ES> for example i have E_u mode, not E_u(LO) and E_u(TO).
ES> what's the point?

did you search the pw_forum mailing list archives?
a simple search for 'LO-TO Gamma site:democritos.it'
spits out about 50 hits out of which a third looks
like they are relevant to your question.

have you looked at the user's guide?

this kind of question pops up quite often and i bet 
a pint of your favorate beverage that the answer to 
your question is already there.

axel.

ES> 
ES> _________________________________________________________________
ES> Express yourself instantly with MSN Messenger! Download today it's FREE! 
ES> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
ES> 
ES> _______________________________________________
ES> Pw_forum mailing list
ES> Pw_forum at pwscf.org
ES> http://www.democritos.it/mailman/listinfo/pw_forum
ES> 

-- 
=======================================================================
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 degironc at sissa.it  Tue May  1 16:05:01 2007
From: degironc at sissa.it (degironc)
Date: Tue, 01 May 2007 16:05:01 +0200
Subject: [Pw_forum] LO-TO splitting
In-Reply-To: <BAY101-F237CAD0927EDCBBFA2BD81AA430@phx.gbl>
References: <BAY101-F237CAD0927EDCBBFA2BD81AA430@phx.gbl>
Message-ID: <4637490D.2070008@sissa.it>

The point is explained in Review of Moderm Physiscs 73, 515 (2001).
example06 shows how to take care of if for full phonon dispersions.
another way is to use code dynmat.x on the dynamical matrix generated by
ph.x
stefano


Ezad Shojaee wrote:

> Hi
> when i use phonon calculation for Gamma point, i do not have splitted 
> modes, for example i have E_u mode, not E_u(LO) and E_u(TO).
> what's the point?
>
> _________________________________________________________________
> Express yourself instantly with MSN Messenger! Download today it's 
> FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum




From umari at democritos.it  Wed May  2 10:58:45 2007
From: umari at democritos.it (Paolo Umari)
Date: Wed, 2 May 2007 10:58:45 +0200 (CEST)
Subject: [Pw_forum] Re: on finite electric methods to calulate vibrational properties
In-Reply-To: <20070501065254.29144.46185.Mailman@democritos.sissa.it>
References: <20070501065254.29144.46185.Mailman@democritos.sissa.it>
Message-ID: <Pine.LNX.4.64.0705021045330.16068@democritos.sissa.it>

>Dear Stefano Baroni ,
>
>  I'm sorry for my spelling error.
>   I want to investigate Raman spectra in the case of large   disordered 
>system from first principles and use the finite
>electric field methods.
>The dielectric polarizability tensor can be calculated by taking dinite 
>differences of  atomic forces.

If you want to calculate the raman tensor you need either the 
first derivative
of the dielectric polarizability tensor with respect to the atomic 
displacements or the second derivative of the atomic forces with
respect to twice the electric field.
The second choice is the best one with the finite electric field method

>There are several questions to ask you.
>  1. We obtained the diagonal terms, by considering values for the 
>electric field of
>-2h,-h, 0, h and 2h in the cp.x code[tefield=.true.
>                                                         tcg = .true.,
>                                                     epol = 1 or 2 or 3
>                                                    efield = -2h,-h, 0, h 
>or 2h],
>and by using the five-point formular . Is it right?

It's right, but I should check the convergence by using only the 
three-point formula

>  2. For the calculation of the off-diagonal terms, two different 
>electric 
>fields
>are required. This need apply electric fields of intensity 
>-2h/1.414,-h/1.414,
>0, h/1.414 and 2h/1.414 along the three different couples of cartesian 
>directions, and apply eauation.
>But how can I apply simultaneously finite fields along two different 
>Cartesian directions
>in cp.x code?[ESSPRESSO-3.2]

As the Berry's phase implementation  provides  electric fields along the 
three carthesian  directions, to consider an electric field along an 
arbitrary direction you  should consider its components along the
three cartesian direction.
By now, 2 components are implemented, the second one is defined by
the input variables: tefield2,epol2,efield2 (defined as 
tefield,epol,efield)

Note that only the options epol=3 and epol2=3 are now available in case 
of parallel computing

>3. In this way, we could obtain all the dielectric polarizability tensor. 
>Then the
>Raman susceptibilities associated to the normal mode n can be obtianed 
>according to the equation.
>How to implement it ? By a small code?

For the Raman tensor, you should consider the second derivatives of the 
atomic forces....


Best wishes,

PaoloU


>  Best!
>  I'm counting on the new version.



From wmbmacam at lg.ehu.es  Wed May  2 12:25:20 2007
From: wmbmacam at lg.ehu.es (Miguel Mart=?US-ASCII?Q?=ED?=nez)
Date: Wed, 2 May 2007 12:25:20 +0200 (CEST)
Subject: [Pw_forum] Some electron-phonon questions
Message-ID: <3599472996wmbmacam@ehu.es>

Dear folks,

I've been doing some electron phonon coupling calculations in selected q
points, following a recent discussion between Profs. Floris and
Gianozzi. However, I still have some doubts. 


From ihsanas at yahoo.com  Wed May  2 13:29:00 2007
From: ihsanas at yahoo.com (احسان عريقات)
Date: Wed, 2 May 2007 04:29:00 -0700 (PDT)
Subject: [Pw_forum] transition state
Message-ID: <468074.60485.qm@web52302.mail.re2.yahoo.com>

Dear Stefano Baroni 
I am a new phd student at the university of Jordan ,
in a new growing theoretical group, we are new in this
field . We don`t have supercomputers  so I`m working
on NEB using pc`s computers pentium 4, it`s too slow ,
that`s why I am asking for other options.

Greetings from Dr Bothina Hamad (my supervisor).
best regards
Ihsan -physics department ,Jordan
 

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


From giannozz at nest.sns.it  Wed May  2 14:04:30 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 2 May 2007 14:04:30 +0200
Subject: [Pw_forum] Some electron-phonon questions
In-Reply-To: <3599472996wmbmacam@ehu.es>
References: <3599472996wmbmacam@ehu.es>
Message-ID: <1C0B5360-6FA2-4652-8B51-39DBAAF4E7D4@nest.sns.it>

On May 2, 2007, at 12:25 , Miguel Mart=EDnez wrote:

>> From what I read at PW/a2fmod.f90 (use the source, Luke) it seems to
> save some data from the self-consistent calculations. Is this data- 
> saving
> flag equivalent to the previous way of computing the el-ph coupling  
> with
> a second very dense non self-consistent mesh?

not exactly

> In the case of not being equivalent, how small are the differences?

they should be small when convergence is achieved

> On another ground, are displaced Monkhorst-Pack grids compatible with
> electron phonon calculations?

I don't think they are

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




From giannozz at nest.sns.it  Wed May  2 14:11:48 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 2 May 2007 14:11:48 +0200
Subject: [Pw_forum] iotk_scan_dat & dos.x
In-Reply-To: <002701c788fb$af613260$0301a8c0@w2agz>
References: <00d501c78870$e1535cc0$0301a8c0@w2agz> <Pine.LNX.4.58.0704271727440.18139@bamboo.fisica.unimo.it> <002701c788fb$af613260$0301a8c0@w2agz>
Message-ID: <2F6EA68F-FA9A-45FA-BC80-0E9B190075C1@nest.sns.it>

On Apr 27, 2007, at 20:41 , Paul M. Grant wrote:

> Yeah, I've done a fair amount of nscf post-processing with the PWscf
> package...DOS, band structures, Fermi surfaces, e-p coupling...without
> problems, but all on metals so far.  This is my first "homework  
> problem"
> on a semiconductor

If you have a reproducible error in a specific case, please
post all the information needed to reproduce it, but please
allow me to be a little bit skeptical that such an error exists:
the file format is the same for metals and semiconductors,
the file is read by the same routines for all postprocessing
codes.

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




From akohlmey at cmm.chem.upenn.edu  Wed May  2 14:33:26 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 2 May 2007 08:33:26 -0400 (EDT)
Subject: [Pw_forum] transition state
In-Reply-To: <468074.60485.qm@web52302.mail.re2.yahoo.com>
Message-ID: <Pine.LNX.4.44.0705020806220.18695-100000@localhost.localdomain>

On Wed, 2 May 2007, ????? ?????? wrote:

dear ihsan,

please ask yourself a simple question:

if there _was_ a way to get the same anwer as
you can get it from NEB in a simple, reliable,
and less cpu-time demanding way, do you think
anybody would be still using NEB?

IA> Dear Stefano Baroni 
IA> I am a new phd student at the university of Jordan ,
IA> in a new growing theoretical group, we are new in this
IA> field . We don`t have supercomputers  so I`m working
IA> on NEB using pc`s computers pentium 4, it`s too slow ,

while it can be very frustrating to not have the 
cpu power at your disposal, that other people have,
this is also a chance: you have to think harder before
you can afford to run a calculation and than better 
make sure that it will work. in many cases, finding
good strategies to do this will take significant 
additional time, but you will also aviod many useless
calculations that people with abundant resources will
do without thinking (and thus risking to waste their time).

should you then get access to larger resources, you 
will be able to make so much more efficient use of them, 
that you can have a huge advantage.

a second chance is in picking up problems, that others
have neglected as being not 'big' or 'flashy' enough.
this way you don't even have to 'compete' with others
in terms of available cpu resources.

hope this is of some help,
    axel.

IA> that`s why I am asking for other options.

p.s.: the alternative here of course would be that
_you_ try coming up with a more efficient method...

IA> Greetings from Dr Bothina Hamad (my supervisor).
IA> best regards
IA> Ihsan -physics department ,Jordan
IA>  
IA> 
IA> __________________________________________________
IA> Do You Yahoo!?
IA> Tired of spam?  Yahoo! Mail has the best spam protection around 
IA> http://mail.yahoo.com 
IA> _______________________________________________
IA> Pw_forum mailing list
IA> Pw_forum at pwscf.org
IA> http://www.democritos.it/mailman/listinfo/pw_forum
IA> 

-- 
=======================================================================
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
=======================================================================




From roma at srmp.saclay.cea.fr  Wed May  2 16:26:04 2007
From: roma at srmp.saclay.cea.fr (roma)
Date: Wed, 02 May 2007 16:26:04 +0200
Subject: [Pw_forum] transition state
In-Reply-To: <130578.14058.qm@web52303.mail.re2.yahoo.com>
References: <130578.14058.qm@web52303.mail.re2.yahoo.com>
Message-ID: <1178115964.11236.67.camel@srmp19.saclay.cea.fr>

Hello, 
an alternative for finding a transition state is to do a number of
constrained relaxations one after the other approaching the saddle
point, at first, and then another local minimum. A constraint that, to
my experience, works well in several cases is the Bennett projection
constraint, implemented in PWSCF (sort of drag method, for info and
reference see the Modules/constraints_module.f90, the keyword is
"bennett_proj").
It can be faster than NEB in finding the saddle point and it works even
if you don't know the endpoint.
Of course in special cases it might be more effective to use other type
of constraints (distance, angles, coordination ...)
Regards,

Guido

On Sun, 2007-04-29 at 04:42 -0700, ????? ?????? wrote:
> Hi,
> transition state structures can be determined by
> searching for first order saddle points on the
> potential energy surface ,how we can do this using
> pwscf without using neb .
> thanks
> 
> __________________________________________________
> 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
-- 
Guido Roma <roma${at}cea.fr> -- CEA-Saclay - DEN/DMN/SRMP Bat.520/13
Phone: [+33]-1-69081857 -- Fax: ...6867 -- Mobile: [+33]-6-20069085



From w2agz at pacbell.net  Wed May  2 16:56:16 2007
From: w2agz at pacbell.net (Paul M. Grant)
Date: Wed, 2 May 2007 07:56:16 -0700
Subject: [Pw_forum] iotk_scan_dat & dos.x
In-Reply-To: <2F6EA68F-FA9A-45FA-BC80-0E9B190075C1@nest.sns.it>
References: <00d501c78870$e1535cc0$0301a8c0@w2agz> <Pine.LNX.4.58.0704271727440.18139@bamboo.fisica.unimo.it> <002701c788fb$af613260$0301a8c0@w2agz> <2F6EA68F-FA9A-45FA-BC80-0E9B190075C1@nest.sns.it>
Message-ID: <001a01c78cca$09d624e0$0301a8c0@w2agz>

Paolo, you're probably right.  I haven't had time to revisit the issue...I
had a book review due to Nature this week.  But I will check it out by
Friday.  For "simple silicon," the error is very reproducible, but perhaps
an input format problem.

I thought the question by Martinez on displaced vs. non-displaced MP points
was an interesting one.  For the few tests I've done, not on e-p coupling,
just scf, the choice between them doesn't seem to make much of a difference
in final energy or convergence rate.  The early papers in PR on "special
points" are not much help.  Can you suggest a good up-to-date review of the
subject?

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford University
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com
?
?

-----Original Message-----
From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] On Behalf
Of Paolo Giannozzi
Sent: Wednesday, May 02, 2007 5:12 AM
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] iotk_scan_dat & dos.x


On Apr 27, 2007, at 20:41 , Paul M. Grant wrote:

> Yeah, I've done a fair amount of nscf post-processing with the PWscf
> package...DOS, band structures, Fermi surfaces, e-p coupling...without
> problems, but all on metals so far.  This is my first "homework  
> problem"
> on a semiconductor

If you have a reproducible error in a specific case, please
post all the information needed to reproduce it, but please
allow me to be a little bit skeptical that such an error exists:
the file format is the same for metals and semiconductors,
the file is read by the same routines for all postprocessing
codes.

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


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




From giannozz at nest.sns.it  Wed May  2 17:21:13 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 2 May 2007 17:21:13 +0200
Subject: [Pw_forum] iotk_scan_dat & dos.x
In-Reply-To: <001a01c78cca$09d624e0$0301a8c0@w2agz>
References: <00d501c78870$e1535cc0$0301a8c0@w2agz> <Pine.LNX.4.58.0704271727440.18139@bamboo.fisica.unimo.it> <002701c788fb$af613260$0301a8c0@w2agz> <2F6EA68F-FA9A-45FA-BC80-0E9B190075C1@nest.sns.it> <001a01c78cca$09d624e0$0301a8c0@w2agz>
Message-ID: <1A3406E5-79F0-4E5D-BE48-51D3ED9D1F3C@nest.sns.it>

On May 2, 2007, at 16:56 , Paul M. Grant wrote:

> I thought the question by Martinez on displaced vs. non-displaced  
> MP points
> was an interesting one.  For the few tests I've done, not on e-p  
> coupling,
> just scf, the choice between them doesn't seem to make much of a  
> difference
> in final energy or convergence rate.

if you use coarse grids, i.e. with very few k-points, shifted grids  
are somewhat
more convenient, but the difference quickly vanishes for denser grids

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




From vranjan at ncsu.edu  Wed May  2 17:58:51 2007
From: vranjan at ncsu.edu (Vivek Ranjan)
Date: Wed, 2 May 2007 11:58:51 -0400 (EDT)
Subject: [Pw_forum] compilation problem
In-Reply-To: <1178115964.11236.67.camel@srmp19.saclay.cea.fr>
References: <130578.14058.qm@web52303.mail.re2.yahoo.com>
    <1178115964.11236.67.camel@srmp19.saclay.cea.fr>
Message-ID: <34707.152.14.74.117.1178121531.squirrel@webmail.ncsu.edu>

Hello !

I have been running program on a IBM power4 machine for a while. Recently,
I discovered that the results of the programme are sensitive to the
compilation options. I compiled the programme with three following options
and got three different results :

(1) ./configure
(2) ./configure LDFLAGS="-L/u2/wes/PET_HOME/MATH/IBM/lib64 -llapack -lessl
-q64"
(3) ./configure LDFLAGS="-L/u2/wes/PET_HOME/MATH/IBM/lib64 -lessl -llapack
-q64"

Even with options (2) and (3), "LAPACK_LIBS    = -lessl  -llapack" is set.
The system administrators had suggested me that I keep "-lessl" after
"-llapack" for these machines. The problem is that for versions 3.2 and
the latest cvs versions I can compile only with option (1). For,
options(2) and (3) I get an error message, which runs like this :

*******************************************************************************************************************
       ( cd clib ; if test "make" = "" ; then make  TLDEPS= all ;  else
make  TLDEPS= all ; fi )
       xlc_r -q64 -O2 -D__AIX -D__XLF -D__ESSL -D__MASS -D__MPI -D__PARA
-I../include   -c c_mkdir.c
"c_mkdir.c", line 42.5: 1506-033 (S) Function F77_FUNC_ is not valid.
Function cannot return a function.
"c_mkdir.c", line 49.41: 1506-045 (S) Undeclared identifier length.
"c_mkdir.c", line 51.19: 1506-045 (S) Undeclared identifier dirname.
"c_mkdir.c", line 62.11: 1506-1332 (W) A function with return type
"int(*)(const char*,const int*)" may not return a value of type "int".
"c_mkdir.c", line 74.5: 1506-033 (S) Function F77_FUNC_ is not valid.
Function cannot return a function.
"c_mkdir.c", line 74.5: 1506-343 (S) Redeclaration of F77_FUNC_ differs
from previous declaration on line 42 of "c_mkdir.c".
"c_mkdir.c", line 74.5: 1506-050 (I) Return type "int(const char*,const
int*,const char*,const int*)" in redeclaration is not compatible with the
previous return type "int(const char*,const int*)".
"c_mkdir.c", line 80.45: 1506-045 (S) Undeclared identifier oldlength.
"c_mkdir.c", line 81.45: 1506-045 (S) Undeclared identifier newlength.
"c_mkdir.c", line 83.23: 1506-045 (S) Undeclared identifier oldname.
"c_mkdir.c", line 84.23: 1506-045 (S) Undeclared identifier newname.
make: 1254-004 The error code from the last command is 1.


Stop.
make: 1254-004 The error code from the last command is 2.


Stop.
*********************************************************************************************************

I have also included a note from the system administrator :

*********** Sys Admin note ********************************
Our specialists responded with the following about ordering the -lessl and
-llapack flags:


From giannozz at nest.sns.it  Wed May  2 18:06:00 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 2 May 2007 18:06:00 +0200
Subject: [Pw_forum] compilation problem
In-Reply-To: <34707.152.14.74.117.1178121531.squirrel@webmail.ncsu.edu>
References: <130578.14058.qm@web52303.mail.re2.yahoo.com> <1178115964.11236.67.camel@srmp19.saclay.cea.fr> <34707.152.14.74.117.1178121531.squirrel@webmail.ncsu.edu>
Message-ID: <BF4025FF-F384-4EAC-86B1-313AE6772780@nest.sns.it>

On May 2, 2007, at 17:58 , Vivek Ranjan wrote:

> The problem is that for versions 3.2 and the latest cvs versions
> I can compile only with option (1). For, options(2) and (3) I get
> an error message

then compile with option (1). Where is the problem?
---
Paolo Giannozzi, Democritos and University of Udine, Italy




From ceresoli at sissa.it  Wed May  2 18:23:06 2007
From: ceresoli at sissa.it (Davide Ceresoli)
Date: Wed, 02 May 2007 18:23:06 +0200
Subject: [Pw_forum] compilation problem
In-Reply-To: <34707.152.14.74.117.1178121531.squirrel@webmail.ncsu.edu>
References: <130578.14058.qm@web52303.mail.re2.yahoo.com>    <1178115964.11236.67.camel@srmp19.saclay.cea.fr> <34707.152.14.74.117.1178121531.squirrel@webmail.ncsu.edu>
Message-ID: <4638BAEA.6000204@sissa.it>

Vivek Ranjan wrote:
> Hello !
> 
> I have been running program on a IBM power4 machine for a while. Recently,
> I discovered that the results of the programme are sensitive to the
> compilation options. I compiled the programme with three following options
> and got three different results :
> 
> (1) ./configure
> (2) ./configure LDFLAGS="-L/u2/wes/PET_HOME/MATH/IBM/lib64 -llapack -lessl
> -q64"
> (3) ./configure LDFLAGS="-L/u2/wes/PET_HOME/MATH/IBM/lib64 -lessl -llapack
> -q64"
> 
> Even with options (2) and (3), "LAPACK_LIBS    = -lessl  -llapack" is set.
> The system administrators had suggested me that I keep "-lessl" after
> "-llapack" for these machines. The problem is that for versions 3.2 and
> the latest cvs versions I can compile only with option (1). For,
> options(2) and (3) I get an error message, which runs like this :
> 
> *******************************************************************************************************************
>        ( cd clib ; if test "make" = "" ; then make  TLDEPS= all ;  else
> make  TLDEPS= all ; fi )
>        xlc_r -q64 -O2 -D__AIX -D__XLF -D__ESSL -D__MASS -D__MPI -D__PARA
> -I../include   -c c_mkdir.c
> "c_mkdir.c", line 42.5: 1506-033 (S) Function F77_FUNC_ is not valid.
> Function cannot return a function.

Can you please inspect the file include/c_defs.h ?

Here is as it should look like (for the IBM AIX!):
#define F77_FUNC(name,NAME) name
#define F77_FUNC_(name,NAME) name

Try to configure this way (instead of setting the LDFLAGS)
./configure LIBDIRS="/u2/wes/PET_HOME/MATH/IBM/lib64"

HTH

Davide


From vranjan at ncsu.edu  Wed May  2 17:35:58 2007
From: vranjan at ncsu.edu (Vivek Ranjan)
Date: Wed, 2 May 2007 11:35:58 -0400 (EDT)
Subject: [Pw_forum] compilation problem
Message-ID: <51186.152.14.74.117.1178120158.squirrel@webmail.ncsu.edu>

Hello !

I have been running program on a IBM power4 machine for a while. Recently,
I discovered that the results of the programme are sensitive to the
compilation options. I compiled the programme with three following options
and got three different results :

(1) ./configure
(2) ./configure LDFLAGS="-L/u2/wes/PET_HOME/MATH/IBM/lib64 -llapack -lessl
-q64"
(3) ./configure LDFLAGS="-L/u2/wes/PET_HOME/MATH/IBM/lib64 -lessl -llapack
-q64"

Even with options (2) and (3), "LAPACK_LIBS    = -lessl  -llapack" is set.
The system administrators had suggested me that I keep "-lessl" after
"-llapack" for these machines. The problem is that for versions 3.2 and
the latest cvs versions I can compile only with option (1). For,
options(2) and (3) I get an error message, which runs like this :

*******************************************************************************************************************
       ( cd clib ; if test "make" = "" ; then make  TLDEPS= all ;  else
make  TLDEPS= all ; fi )
       xlc_r -q64 -O2 -D__AIX -D__XLF -D__ESSL -D__MASS -D__MPI -D__PARA
-I../include   -c c_mkdir.c
"c_mkdir.c", line 42.5: 1506-033 (S) Function F77_FUNC_ is not valid.
Function cannot return a function.
"c_mkdir.c", line 49.41: 1506-045 (S) Undeclared identifier length.
"c_mkdir.c", line 51.19: 1506-045 (S) Undeclared identifier dirname.
"c_mkdir.c", line 62.11: 1506-1332 (W) A function with return type
"int(*)(const char*,const int*)" may not return a value of type "int".
"c_mkdir.c", line 74.5: 1506-033 (S) Function F77_FUNC_ is not valid.
Function cannot return a function.
"c_mkdir.c", line 74.5: 1506-343 (S) Redeclaration of F77_FUNC_ differs
from previous declaration on line 42 of "c_mkdir.c".
"c_mkdir.c", line 74.5: 1506-050 (I) Return type "int(const char*,const
int*,const char*,const int*)" in redeclaration is not compatible with the
previous return type "int(const char*,const int*)".
"c_mkdir.c", line 80.45: 1506-045 (S) Undeclared identifier oldlength.
"c_mkdir.c", line 81.45: 1506-045 (S) Undeclared identifier newlength.
"c_mkdir.c", line 83.23: 1506-045 (S) Undeclared identifier oldname.
"c_mkdir.c", line 84.23: 1506-045 (S) Undeclared identifier newname.
make: 1254-004 The error code from the last command is 1.


Stop.
make: 1254-004 The error code from the last command is 2.


Stop.
*********************************************************************************************************

I have also included a note from the system administrator :

*********** Sys Admin note ********************************
Our specialists responded with the following about ordering the -lessl and
-llapack flags:


From kondor.jess at gmail.com  Wed May  2 21:59:05 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Wed, 2 May 2007 14:59:05 -0500
Subject: [Pw_forum] equilibrium lattice parameters
Message-ID: <1d9d5d9d0705021259n560c74b0v81d3775dbaeeece@mail.gmail.com>

Hello,
 I have a tetragonal unit cell with experimental lattice parameters
(a=b=/c). In order to find their theoretical values, I performed variable
cell relaxation (vc-relax). But I want to be sure that I performed these
calculations correctly. I know it is possible to perform several static
calculations for different lattice parameters (or volume) and then fit the
data by EOS. But I only see (for example, ev.f90 from espresso
distribution), that it is possible only for cubic and hexagonal unit cell.
Could anyone tell me can I use such kind of technique in case of tetragonal
unit cell?


cheers,
   Jess
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From hashem.yamani at gmail.com  Thu May  3 18:37:16 2007
From: hashem.yamani at gmail.com (Hashem Al-Yamani)
Date: Thu, 3 May 2007 14:37:16 -0200
Subject: [Pw_forum] Installation error
Message-ID: <82a593400705030937m231e7a7bpda656be2d8c67e09@mail.gmail.com>

Dear All ;

While I were trying to install PWSCF I faced the following error ..... which
I weren't had it before installing the g95 :

checking for Fortran 77 compiler default output file name... configure:
error: Fortran 77 compiler cannot create executables
See `config.log' for more details.


am sending my config.log in case ...... any help would be very appreciaple
...... thanks alot


Regards ;

HAshem
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From ceresoli at sissa.it  Thu May  3 18:59:24 2007
From: ceresoli at sissa.it (Davide Ceresoli)
Date: Thu, 03 May 2007 18:59:24 +0200
Subject: [Pw_forum] Installation error
In-Reply-To: <82a593400705030937m231e7a7bpda656be2d8c67e09@mail.gmail.com>
References: <82a593400705030937m231e7a7bpda656be2d8c67e09@mail.gmail.com>
Message-ID: <463A14EC.7090200@sissa.it>

Hashem Al-Yamani wrote:
> Dear All ;
> 
> While I were trying to install PWSCF I faced the following error ..... 
> which I weren't had it before installing the g95 :
> 
> checking for Fortran 77 compiler default output file name... configure: 
> error: Fortran 77 compiler cannot create executables
> See `config.log' for more details.
> 
> 
> am sending my config.log in case ...... any help would be very 
> appreciaple ...... thanks alot
> 
> 
> Regards ;
> 
> HAshem

Let me guess: did you installed the x86 version of g95 ? (g95-x86-linux.tgz)

You should better install the x86_64 version for your machine
(http://ftp.g95.org/g95-x86_64-32-linux.tgz)

HTH

Davide



From baroni at sissa.it  Thu May  3 20:15:19 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 3 May 2007 19:15:19 +0100
Subject: [Pw_forum] equilibrium lattice parameters
In-Reply-To: <1d9d5d9d0705021259n560c74b0v81d3775dbaeeece@mail.gmail.com>
References: <1d9d5d9d0705021259n560c74b0v81d3775dbaeeece@mail.gmail.com>
Message-ID: <BDE0B83C-E4AD-4CAC-97AC-99192033BB30@sissa.it>

On May 2, 2007, at 8:59 PM, Jess Kondor wrote:

>
> Hello,
>  I have a tetragonal unit cell with experimental lattice parameters  
> (a=b=/c). In order to find their theoretical values, I performed  
> variable cell relaxation (vc-relax). But I want to be sure that I  
> performed these calculations correctly. I know it is possible to  
> perform several static calculations for different lattice  
> parameters (or volume) and then fit the data by EOS. But I only see  
> (for example, ev.f90 from espresso distribution), that it is  
> possible only for cubic and hexagonal unit cell. Could anyone tell  
> me can I use such kind of technique in case of tetragonal unit cell?

YES, with some extra effort. You have to optimize first c/a keeping  
the volume fixed. The discontinuities of the total energy as a  
function of c/a (due to the fact that the number of PWs change as you  
change c/a) are less critical than the discontinuities in E(V). Once  
you have E(V), you can fit it to an equation of state, much in the  
same way you would for a cubic system.

Stefano


>
>
> cheers,
>    Jess

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

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



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From peterwiney at gmail.com  Thu May  3 21:45:39 2007
From: peterwiney at gmail.com (Peter Winey)
Date: Thu, 3 May 2007 15:45:39 -0400
Subject: [Pw_forum] A question about pp.x and potential output
Message-ID: <dac27ff50705031245i1c3cf752g62aa6797930b1239@mail.gmail.com>

Dear all,

I was trying to fit/optimize some parameters of an emperical potential using
DFT calculation
results. I got stuck while using the post-processing code.

It is related to "plot_num" of the pp.x input file. In the manual, I found
three values related
to potential:

1=total potential V_bare +V_H+V_xc
2=local ionic potential
11=the V_bare+V_H potential

Now what I want is the "classical electrostatic energy or Coulombic
potential". I searched
the achive of this discussion list a bit and could not find the answer.
I also read the source
code and could not sort it out. I am wondering if it is possible at all to
seperate the Coulombic
contribution from the total potential?

Thanks in advance!
-Peter
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From fratesi at mater.unimib.it  Fri May  4 07:57:55 2007
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Fri, 4 May 2007 07:57:55 +0200 (CEST)
Subject: [Pw_forum] A question about pp.x and potential output
In-Reply-To: <dac27ff50705031245i1c3cf752g62aa6797930b1239@mail.gmail.com>
References: <dac27ff50705031245i1c3cf752g62aa6797930b1239@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0705040747080.30407@localhost.localdomain>

Dear Peter,

PW> 1=total potential V_bare +V_H+V_xc
PW> 2=local ionic potential
PW> 11=the V_bare+V_H potential
PW> 
PW> Now what I want is the "classical electrostatic energy or Coulombic
PW> potential". I searched
PW> the achive of this discussion list a bit and could not find the answer.
PW> I also read the source
PW> code and could not sort it out. I am wondering if it is possible at all to
PW> seperate the Coulombic
PW> contribution from the total potential?

if you just need the Hartree contribution *due to electronic charge only* 
to the total potential, V_H(r) = \int dr' \rho(r') \frac{1}{r-r'}
where \rho is the electron density, you can either:

1) run twice pp.x with plot_num=2 and plot_num=11 and substract the results;

2) edit PP/punch_plot.f90 so that plot_num=11 plots only v_H:

  ELSEIF (plot_num == 11) THEN

[old]     raux(:) = vltot(:) 
[new]     raux(:) = 0._DP
     IF (nspin == 2) THEN
        rhog(:,1) =  rhog(:,1) +  rhog(:,2)
        rho (:,1) =  rho (:,1) +  rho (:,2)
        nspin = 1
     END IF
     CALL v_h (rhog, ehart, charge, raux)
     IF (tefield.AND.dipfield) CALL add_efield(rho,raux,dummy,1)

(notice that routine "v_h" ADDS the potential V_H to the array raux.

Let me say it again, this gives you the Coulomb contribution from the 
valence charge only.

Cheers,
Guido

-- 
Guido Fratesi

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

Phone: +39 02 6448 5214
email: fratesi at mater.unimib.it


From peterwiney at gmail.com  Fri May  4 15:19:58 2007
From: peterwiney at gmail.com (Peter Winey)
Date: Fri, 4 May 2007 09:19:58 -0400
Subject: [Pw_forum] A question about pp.x and potential output
In-Reply-To: <Pine.LNX.4.64.0705040747080.30407@localhost.localdomain>
References: <dac27ff50705031245i1c3cf752g62aa6797930b1239@mail.gmail.com>
	 <Pine.LNX.4.64.0705040747080.30407@localhost.localdomain>
Message-ID: <dac27ff50705040619y43b47ea1i5584c3c00263a5d4@mail.gmail.com>

Thanks for the help! I really appreciate it.
Best,
-Peter
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From wmbmacam at lg.ehu.es  Fri May  4 15:28:21 2007
From: wmbmacam at lg.ehu.es (=?ISO-8859-1?Q?Miguel_Mart=EDnez_Canales?=)
Date: Fri, 04 May 2007 15:28:21 +0200
Subject: [Pw_forum] Some electron-phonon questions
In-Reply-To: <1C0B5360-6FA2-4652-8B51-39DBAAF4E7D4@nest.sns.it>
References: <3599472996wmbmacam@ehu.es> <1C0B5360-6FA2-4652-8B51-39DBAAF4E7D4@nest.sns.it>
Message-ID: <463B34F5.8090800@lg.ehu.es>

Thank you very much for your answers, Paolo

Paolo Giannozzi escribi?:
> 
> On May 2, 2007, at 12:25 , Miguel Mart=EDnez wrote:
>>  Is this data-saving
>> flag equivalent to the previous way of computing the el-ph coupling with
>> a second very dense non self-consistent mesh?
> 
> not exactly
> 
>> In the case of not being equivalent, how small are the differences?
> 
> they should be small when convergence is achieved
> 
>> On another ground, are displaced Monkhorst-Pack grids compatible with
>> electron phonon calculations?
> 
> I don't think they are
> 
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
-- 
----------------------------------------
Miguel Mart?nez Canales
    Dto. F?sica de la Materia Condensada
    UPV/EHU
    Facultad de Ciencia y Tecnolog?a
    Apdo. 644
    48080 Bilbao (Spain)
Fax:  +34 94 601 3500
Tlf:  +34 94 601 5437
----------------------------------------

  "If you have an apple and I have an apple and
  we exchange these apples then you and I will
  still each have one apple. But if you have an
  idea and I have an idea and we exchange these
  ideas, then each of us will have two ideas."

  George Bernard Shaw



From kazempoor2000 at yahoo.com  Sat May  5 10:01:25 2007
From: kazempoor2000 at yahoo.com (ali kazempoor)
Date: Sat, 5 May 2007 01:01:25 -0700 (PDT)
Subject: [Pw_forum] supercell
Message-ID: <205.57087.qm@web33114.mail.mud.yahoo.com>

hi all
I want to bring a nanowire structure to the center of
big supercell and set vaccum on circumestance in
supercell.how can i make this? which parameter in
input file must be settled?
thanks


 
____________________________________________________________________________________
No need to miss a message. Get email on-the-go 
with Yahoo! Mail for Mobile. Get started.
http://mobile.yahoo.com/mail 


From ding at sissa.it  Sat May  5 09:47:29 2007
From: ding at sissa.it (Xunlei Ding)
Date: Sat, 05 May 2007 09:47:29 +0200
Subject: [Pw_forum] supercell
In-Reply-To: <205.57087.qm@web33114.mail.mud.yahoo.com>
References: <205.57087.qm@web33114.mail.mud.yahoo.com>
Message-ID: <463C3691.9030402@sissa.it>

Dear ali,
You can use ATOMIC_POSITIONS {crystal}, and then set all the x,y around 
0.50 (supposing z is the direction along the nanowire).
I don't know whether this is the best way.

best wishes,
Ding


ali kazempoor wrote:

>hi all
>I want to bring a nanowire structure to the center of
>big supercell and set vaccum on circumestance in
>supercell.how can i make this? which parameter in
>input file must be settled?
>thanks
>
>
> 
>____________________________________________________________________________________
>No need to miss a message. Get email on-the-go 
>with Yahoo! Mail for Mobile. Get started.
>http://mobile.yahoo.com/mail 
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>
>  
>


From jhashemifar at gmail.com  Sat May  5 20:48:52 2007
From: jhashemifar at gmail.com (Javad hashemifar)
Date: Sat, 5 May 2007 20:48:52 +0200
Subject: [Pw_forum] Fermi Energy
Message-ID: <2fb18d9f0705051148w1e95b89apaf8859fc95c648fb@mail.gmail.com>

Dear pwscf users,

During partial DOS calculation for a metallic compound I found a
difference of about 0.7 eV between the Fermi energies obtained by scf
and nscf calculations. Although the origin of this difference is not
clear to me but I guess the one that is obtained by nscf should be
considered for DOS plotting. Your kind advises in this regard is
highly appreciated.

thanks in advance
Javad Hashemifar
University of Duisburg


======================================
Seyed Javad  Hashemifar,    Ph.D.
[current:]
Tel:+49-203-3794743        Fax:+49-203-3794742
Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen
47048 Dusiburg, Germany
[permanent:]
Tel:  +98-311-3912375       Fax: +98-311-3912376
Physics Department, Isfahan University of Technology
84156 Isfahan, Iran
---------------------------------------------------------------------------


From kazempoor2000 at yahoo.com  Sun May  6 09:17:14 2007
From: kazempoor2000 at yahoo.com (ali kazempoor)
Date: Sun, 6 May 2007 00:17:14 -0700 (PDT)
Subject: [Pw_forum] optimization
Message-ID: <997684.4242.qm@web33105.mail.mud.yahoo.com>

Hi
 i make super cell that
its situation is in the center of big tetragonal cell
  and has hexagonal (wurtzite structure),
but i dont  know about the number of k-point, vaccum
and other detail 
if you can ,help me in these subject.(i attach my
input file)
thank you 
regards

__________________________________________________
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From amos at errno.com  Sun May  6 17:24:46 2007
From: amos at errno.com (Amos Leffler)
Date: Sun, 06 May 2007 09:24:46 -0600
Subject: [Pw_forum] CO and N2 Crystals
In-Reply-To: <Pine.LNX.4.64.0705040747080.30407@localhost.localdomain>
References: <dac27ff50705031245i1c3cf752g62aa6797930b1239@mail.gmail.com> <Pine.LNX.4.64.0705040747080.30407@localhost.localdomain>
Message-ID: <463DF33E.2050006@errno.com>

Dear Forum,
          I would like to calculate the properties of the CO and N2 
structures.  Example03 calculates the scf for CO but does nothing about 
the crystal.  The problem is whether to use ibrav=0 to place each atom 
or to use CO units with ibrav=2.  Little is said in the Users Guide 
about either of these approaches and I have looked at some of Forum 
records but haven't found anything about either of these methods.  
Hopefully someone can point me to references or suggestions.  There 
appears to be nothing about using polyatom elements for crystalline 
structure but this would be a very useful ability since there are many 
cases where it could be applied.
                                                                         
                     Amos Leffler


From marzari at MIT.EDU  Sun May  6 18:46:09 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Sun, 06 May 2007 12:46:09 -0400
Subject: [Pw_forum] CO and N2 Crystals
In-Reply-To: <463DF33E.2050006@errno.com>
References: <dac27ff50705031245i1c3cf752g62aa6797930b1239@mail.gmail.com> <Pine.LNX.4.64.0705040747080.30407@localhost.localdomain> <463DF33E.2050006@errno.com>
Message-ID: <463E0651.7010306@mit.edu>

Dear Amos,

ibrav specifies the 3-dimensional repetition pattern (i.e. the Bravais 
lattice) that you apply to the individual atoms you specify.

E.g., an infinite fcc crystal of Al can be described as one Al atom
repeated according to the translational symmetry of a fcc Bravais
lattive, or as 4 atoms repeated in a simple cubic Bravais
lattice, or in many other ways. One atom repeated fcc is the least
expensive approach.

A crystal of CO would typically have 2 atoms specified, and the
ibrav of the crystal you think CO has. Of course molecular crystals can
have unit cells that contain more than one inequivalent molecule - so 
you would have to specify more than 2 atoms. An isolated CO molecule 
would be described by a crystal with a lattice parameter large enought 
where the CO - CO interactions have become negligible.

Having said this, this is a question that is not appropriate to the
forum - it's really about crystals et al. Ashcroft Mermin chap 4-7 could
be a good start, or the material in
http://ocw.mit.edu/OcwWeb/Materials-Science-and-Engineering/3-320Spring-2005/CourseHome/index.htm

				nicola

Amos Leffler wrote:
> Dear Forum,
>          I would like to calculate the properties of the CO and N2 
> structures.  Example03 calculates the scf for CO but does nothing about 
> the crystal.  The problem is whether to use ibrav=0 to place each atom 
> or to use CO units with ibrav=2.  Little is said in the Users Guide 
> about either of these approaches and I have looked at some of Forum 
> records but haven't found anything about either of these methods.  
> Hopefully someone can point me to references or suggestions.  There 
> appears to be nothing about using polyatom elements for crystalline 
> structure but this would be a very useful ability since there are many 
> cases where it could be applied.
>                                                                         
>                     Amos Leffler
> _______________________________________________
> 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 akohlmey at cmm.chem.upenn.edu  Sun May  6 20:05:19 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sun, 6 May 2007 14:05:19 -0400 (EDT)
Subject: [Pw_forum] optimization
In-Reply-To: <997684.4242.qm@web33105.mail.mud.yahoo.com>
Message-ID: <Pine.LNX.4.44.0705061332370.18695-100000@localhost.localdomain>

On Sun, 6 May 2007, ali kazempoor wrote:

ali,

please note, that there is no 'ultimate wisdom' on
how to setup a specific calculation. you usually have 
to run a few tests and figure it out for yourself (i.e.
everybody has, with some experience people can make good
guesses, but that does not mean, they have to test it). 
what may work well in one case may produce (large) errors 
in other cases.

please have a look through the mailing list archives
and see the various recommendations on how to approach
finding out the proper supercell size, number of k-points,
smearing parameter, wavefunction/density cutoff. 
all of which can affect the quality of your results.

for people with limited experience (either with the system
they are investigating or the method altogether), it is 
usually a good idea to first try to reproduce results from
some other, similar but (computationally) much simpler system
and then try to understand why which parameter works in its
special way and what influences the accuracy. you can see 
quite a few of that kind of questions here in the archives.
so don't hesitate to ask if you have a question about a
particular detail, but don't expect that somebody will
eplain your whole project to you, or simply give you
his 'blessing' on your inputs.

best regards,
    axel.

AK> Hi
AK>  i make super cell that
AK> its situation is in the center of big tetragonal cell
AK>   and has hexagonal (wurtzite structure),
AK> but i dont  know about the number of k-point, vaccum
AK> and other detail 
AK> if you can ,help me in these subject.(i attach my
AK> input file)
AK> thank you 
AK> regards
AK> 
AK> __________________________________________________
AK> Do You Yahoo!?
AK> Tired of spam?  Yahoo! Mail has the best spam protection around 
AK> http://mail.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 amos at errno.com  Sun May  6 22:03:42 2007
From: amos at errno.com (Amos Leffler)
Date: Sun, 06 May 2007 14:03:42 -0600
Subject: [Pw_forum] CO and N2 Crystals
In-Reply-To: <463E0651.7010306@mit.edu>
References: <dac27ff50705031245i1c3cf752g62aa6797930b1239@mail.gmail.com> <Pine.LNX.4.64.0705040747080.30407@localhost.localdomain> <463DF33E.2050006@errno.com> <463E0651.7010306@mit.edu>
Message-ID: <463E349E.2000404@errno.com>

Dear Nicola,
       My thanks for such a rapid reply especially on Sunday!
I will look at the download as soon as possible.
                                                                         
         Amos Leffler
P.S. I enjoyed your video courses.

Nicola Marzari wrote:
>
> Dear Amos,
>
> ibrav specifies the 3-dimensional repetition pattern (i.e. the Bravais 
> lattice) that you apply to the individual atoms you specify.
>
> E.g., an infinite fcc crystal of Al can be described as one Al atom
> repeated according to the translational symmetry of a fcc Bravais
> lattive, or as 4 atoms repeated in a simple cubic Bravais
> lattice, or in many other ways. One atom repeated fcc is the least
> expensive approach.
>
> A crystal of CO would typically have 2 atoms specified, and the
> ibrav of the crystal you think CO has. Of course molecular crystals can
> have unit cells that contain more than one inequivalent molecule - so 
> you would have to specify more than 2 atoms. An isolated CO molecule 
> would be described by a crystal with a lattice parameter large enought 
> where the CO - CO interactions have become negligible.
>
> Having said this, this is a question that is not appropriate to the
> forum - it's really about crystals et al. Ashcroft Mermin chap 4-7 could
> be a good start, or the material in
> http://ocw.mit.edu/OcwWeb/Materials-Science-and-Engineering/3-320Spring-2005/CourseHome/index.htm 
>
>
>                 nicola
>
> Amos Leffler wrote:
>> Dear Forum,
>>          I would like to calculate the properties of the CO and N2 
>> structures.  Example03 calculates the scf for CO but does nothing 
>> about the crystal.  The problem is whether to use ibrav=0 to place 
>> each atom or to use CO units with ibrav=2.  Little is said in the 
>> Users Guide about either of these approaches and I have looked at 
>> some of Forum records but haven't found anything about either of 
>> these methods.  Hopefully someone can point me to references or 
>> suggestions.  There appears to be nothing about using polyatom 
>> elements for crystalline structure but this would be a very useful 
>> ability since there are many cases where it could be applied.
>>                                                                         
>>                     Amos Leffler
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>



From kazempoor2000 at yahoo.com  Mon May  7 14:36:11 2007
From: kazempoor2000 at yahoo.com (ali kazempoor)
Date: Mon, 7 May 2007 05:36:11 -0700 (PDT)
Subject: [Pw_forum] ecut
Message-ID: <587626.78467.qm@web33111.mail.mud.yahoo.com>

hi
i run scf input file for MnAs that has NiAs -type
(hexagonal)and i use ultrasoft pseudopotentials for Mn
and As from espersso  and optimize k point but my run
don't converge at 50 ,55 ,.. rydberg for ecut.please
correct my input file.
 &CONTROL
                       title = MnAs ,
                 calculation = 'scf' ,
                restart_mode = 'from_scratch' ,
                      outdir =
'/scratch/kazempour/tmp/MnAs/' ,
                  pseudo_dir =
'/home/akazem/espresso-3.2/pseudo/' ,
                      prefix = MnAs ,
 /
 &SYSTEM
                       ibrav = 4,
                   celldm(1) = 7.0373,
                   celldm(3) = 1.5318,
                         nat = 4,
                        ntyp = 2,
                     ecutwfc = 20,
                     occupations = 'smearing' ,
                     degauss = 0.05 ,
                    smearing = 'methfessel-paxton' ,
                       nspin = 2 ,
   starting_magnetization(1) = 1.0,
   starting_magnetization(2) = 0.1,
 /
 &ELECTRONS
            electron_maxstep = 100,
                    conv_thr = .00001 ,
 /
ATOMIC_SPECIES
   Mn  54.93   Mn.pbe-sp-van.UPF 
   As  74.92   As.pbe-n-van.UPF 
ATOMIC_POSITIONS crystal 
   Mn      0.000000000    0.000000000    0.000000000  
 
   Mn      0.000000000    0.000000000    0.500000000  
 
   As      0.333333333    0.666666666    0.250000000  
 
   As      0.666666666    0.333333333    0.750000000  
 
K_POINTS automatic 
  11 11 9   1 1 1 




 
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From matteo at umn.edu  Mon May  7 16:20:28 2007
From: matteo at umn.edu (Matteo Cococcioni)
Date: Mon, 07 May 2007 09:20:28 -0500
Subject: [Pw_forum] ecut
In-Reply-To: <587626.78467.qm@web33111.mail.mud.yahoo.com>
References: <587626.78467.qm@web33111.mail.mud.yahoo.com>
Message-ID: <463F35AC.5070401@umn.edu>

Hi,

one thing missing in your input file is ecutrho (the energy cutoff for 
the charge density) (read INPUT_PW).
If you use ultrasoft pseudopotential you need to specify this parameter 
besides the ecutwfc.
It is needed to reconstruct the "hard" (augmentation) part of the charge 
density that you won't obtain
from the square of (soft) wavefunction. Typically, for ultrasoft 
pseudopotential, this parameter is
8 to 12 times the cut-off for the wavefunctions but it can even be 
bigger. If you don't specify
its value the code probably assumes you are using norm conserving 
pseudos and puts
ecutrho = 4.0 * ecutwfc which is not big enough.
I hope this will help.

Matteo


ali kazempoor wrote:
> hi
> i run scf input file for MnAs that has NiAs -type
> (hexagonal)and i use ultrasoft pseudopotentials for Mn
> and As from espersso  and optimize k point but my run
> don't converge at 50 ,55 ,.. rydberg for ecut.please
> correct my input file.
>  &CONTROL
>                        title = MnAs ,
>                  calculation = 'scf' ,
>                 restart_mode = 'from_scratch' ,
>                       outdir =
> '/scratch/kazempour/tmp/MnAs/' ,
>                   pseudo_dir =
> '/home/akazem/espresso-3.2/pseudo/' ,
>                       prefix = MnAs ,
>  /
>  &SYSTEM
>                        ibrav = 4,
>                    celldm(1) = 7.0373,
>                    celldm(3) = 1.5318,
>                          nat = 4,
>                         ntyp = 2,
>                      ecutwfc = 20,
>                      occupations = 'smearing' ,
>                      degauss = 0.05 ,
>                     smearing = 'methfessel-paxton' ,
>                        nspin = 2 ,
>    starting_magnetization(1) = 1.0,
>    starting_magnetization(2) = 0.1,
>  /
>  &ELECTRONS
>             electron_maxstep = 100,
>                     conv_thr = .00001 ,
>  /
> ATOMIC_SPECIES
>    Mn  54.93   Mn.pbe-sp-van.UPF 
>    As  74.92   As.pbe-n-van.UPF 
> ATOMIC_POSITIONS crystal 
>    Mn      0.000000000    0.000000000    0.000000000  
>  
>    Mn      0.000000000    0.000000000    0.500000000  
>  
>    As      0.333333333    0.666666666    0.250000000  
>  
>    As      0.666666666    0.333333333    0.750000000  
>  
> K_POINTS automatic 
>   11 11 9   1 1 1 
>
>
>
>
>  
> ____________________________________________________________________________________
> No need to miss a message. Get email on-the-go 
> with Yahoo! Mail for Mobile. Get started.
> http://mobile.yahoo.com/mail 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   



From giannozz at nest.sns.it  Mon May  7 21:28:47 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 7 May 2007 21:28:47 +0200
Subject: [Pw_forum] Fermi Energy
In-Reply-To: <2fb18d9f0705051148w1e95b89apaf8859fc95c648fb@mail.gmail.com>
References: <2fb18d9f0705051148w1e95b89apaf8859fc95c648fb@mail.gmail.com>
Message-ID: <14EB9EA7-F063-4765-B7EC-A768980A7A63@nest.sns.it>

On May 5, 2007, at 20:48 , Javad hashemifar wrote:

> During partial DOS calculation for a metallic compound I found a
> difference of about 0.7 eV between the Fermi energies obtained
> by scf and nscf calculations. Although the origin of this difference
> is not clear to me

...you should try to make it clear in the first place. If you are  
performing
a 'nscf' calculation, with a uniform grid, you should find the same  
results,
apart from minor numerical differences, than in the corresponding 'scf'
calculation. Beware: the atomic positions in a 'nscf' or 'band'  
calculation
are read from input, not from file

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




From etabel at hotmail.com  Tue May  8 21:38:33 2007
From: etabel at hotmail.com (Eric Abel)
Date: Tue, 08 May 2007 15:38:33 -0400
Subject: [Pw_forum] Compilation Error
Message-ID: <BAY105-F3048A83898CEBF52BAD6DFD4440@phx.gbl>

Forum members,

I have successfully configured pwscf using g95, glibc-2.5 and kernel 2.6.20. 
  When I try to "make all", I get the following error:

g95 -O3 -cpp -D__FFTW -D__USE_INTERNAL_FFTW -I../include  -I./  -I../Modules 
  -I../iotk/src -I../PW  -I../PH  -I../CPV -c fft_scalar.f90
Fatal Error: While reading module 'kinds' found module version 0, expected 
5.
make[1]: *** [fft_scalar.o] Error 1

I have been unable to find any of these key words in neither the pwscf 
forum, nor google.  My instincts tell me it may be an incompatibility 
problem with the compiler and my glibc and/or kernel, but I was wondering if 
anyone had any thoughts on this.

Eric Abel,
Ph.D.




From ferretti.andrea at unimore.it  Tue May  8 22:16:00 2007
From: ferretti.andrea at unimore.it (Andrea Ferretti)
Date: Tue, 8 May 2007 22:16:00 +0200 (CEST)
Subject: [Pw_forum] Compilation Error
In-Reply-To: <BAY105-F3048A83898CEBF52BAD6DFD4440@phx.gbl>
References: <BAY105-F3048A83898CEBF52BAD6DFD4440@phx.gbl>
Message-ID: <Pine.LNX.4.58.0705082209410.8723@bamboo.fisica.unimo.it>

> Forum members,
> 
> I have successfully configured pwscf using g95, glibc-2.5 and kernel 2.6.20.
> When I try to "make all", I get the following error:
> 
> g95 -O3 -cpp -D__FFTW -D__USE_INTERNAL_FFTW -I../include  -I./  -I../Modules
> -I../iotk/src -I../PW  -I../PH  -I../CPV -c fft_scalar.f90
> Fatal Error: While reading module 'kinds' found module version 0, expected 5.
> make[1]: *** [fft_scalar.o] Error 1

Did you try with a different compiler before ??
in case, do a "make clean" and then restart the compilation from the 
beginning with "make all"

andrea

> 
> I have been unable to find any of these key words in neither the pwscf forum,
> nor google.  My instincts tell me it may be an incompatibility problem with
> the compiler and my glibc and/or kernel, but I was wondering if anyone had any
> thoughts on this.
> 
> Eric Abel,
> Ph.D.
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


From etabel at hotmail.com  Wed May  9 02:34:34 2007
From: etabel at hotmail.com (Eric Abel)
Date: Tue, 08 May 2007 20:34:34 -0400
Subject: [Pw_forum] Compilation Error
In-Reply-To: <Pine.LNX.4.58.0705082209410.8723@bamboo.fisica.unimo.it>
Message-ID: <BAY105-F24632056E3DF41664222BAD43B0@phx.gbl>

Thank you Andrea.  This was the solution to my problem.

Eric


>From: Andrea Ferretti <ferretti.andrea at unimore.it>
>Reply-To: pw_forum at pwscf.org
>To: pw_forum at pwscf.org
>Subject: Re: [Pw_forum] Compilation Error
>Date: Tue, 8 May 2007 22:16:00 +0200 (CEST)
>
>
> > Forum members,
> >
> > I have successfully configured pwscf using g95, glibc-2.5 and kernel 
>2.6.20.
> > When I try to "make all", I get the following error:
> >
> > g95 -O3 -cpp -D__FFTW -D__USE_INTERNAL_FFTW -I../include  -I./  
>-I../Modules
> > -I../iotk/src -I../PW  -I../PH  -I../CPV -c fft_scalar.f90
> > Fatal Error: While reading module 'kinds' found module version 0, 
>expected 5.
> > make[1]: *** [fft_scalar.o] Error 1
>
>Did you try with a different compiler before ??
>in case, do a "make clean" and then restart the compilation from the
>beginning with "make all"
>
>andrea
>
> >
> > I have been unable to find any of these key words in neither the pwscf 
>forum,
> > nor google.  My instincts tell me it may be an incompatibility problem 
>with
> > the compiler and my glibc and/or kernel, but I was wondering if anyone 
>had any
> > thoughts on this.
> >
> > Eric Abel,
> > Ph.D.
> >
> >
> > _______________________________________________
> > 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 ezadshojaee at hotmail.com  Wed May  9 16:20:33 2007
From: ezadshojaee at hotmail.com (Ezad Shojaee)
Date: Wed, 9 May 2007 14:20:33 +0000
Subject: [Pw_forum] monkhorst-pack grid
Message-ID: <BAY101-W139103155772046768C64DAA3B0@phx.gbl>


hi
i have an amateur question !
when i read the monkhorst-pack article, i can not realize what is the input of the algorithme except 'q' which is the # of special points of the lattice. so does this algorithme needs the # of special points?! i thought that when we specify n1 n2 n3 in the auto-K_POINTS in the code, these #'s are going to make the grid !
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From conor.hogan at roma2.infn.it  Thu May 10 13:09:05 2007
From: conor.hogan at roma2.infn.it (Conor Hogan)
Date: Thu, 10 May 2007 13:09:05 +0200 (CEST)
Subject: [Pw_forum] pw.x configuration on AMD opteron with ifort/pgi/mkl/acml (CASPUR)
Message-ID: <48312.141.108.248.231.1178795345.squirrel@141.108.248.231>

Dear forum,
Before I spend a few weeks trying every possible combination of compiler
and library, does anyone have any recommendations for how best to compile
pw.x on an AMD Opteron 246/250/280 cluster (at CASPUR, if that helps)?

The available compilers are ifort9.1 and pgi6.2. ACML is available for
both compilers; MKL 8.2 is available for ifort (both Infiniband and Gb
ethernet are available)

I've no idea how pgi+acml compares with ifort+mkl on an opteron, for
instance. Perhaps someone out there knows, or even better, has a
high-performance make.sys for CASPUR to share...

Best regards,
Conor

----

Dr. Conor Hogan                                --- -----  ---   ---
Dipartimento di Fisica e CNR-INFM             |      :   |     :
Universita' di Roma "Tor Vergata"             |--    :    ---  |---
Tel: +39 06 72594908                          |      :       | :
Fax: +39 06 2023507                            ---   :    ---  :
http://www.fisica.uniroma2.it/~cmtheo-group/  European Theoretical
                                              Spectroscopy Facility
                                              http://www.etsf.eu

Q. What do you call a fish with no eyes?
A. A fsh.   (Tommy Cooper)

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 akohlmey at cmm.chem.upenn.edu  Thu May 10 16:01:51 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 10 May 2007 10:01:51 -0400 (EDT)
Subject: [Pw_forum] pw.x configuration on AMD opteron with ifort/pgi/mkl/acml
 (CASPUR)
In-Reply-To: <48312.141.108.248.231.1178795345.squirrel@141.108.248.231>
Message-ID: <Pine.LNX.4.44.0705100952240.26197-100000@localhost.localdomain>

On Thu, 10 May 2007, Conor Hogan wrote:

dear conor,

i would definitely recommend using ifort. pgi is know to occasionally
miscompile (large scientific) codes. i've had trouble with pgi-6.2 on
some machines that went away when moving to either intel 8.1 or 9.1
or pgi-7.0.2. as for ACML vs. MKL. you need to try it out. for single
core, mkl tends to be a little bit better, for multi-core ACML.

here is an excerpt from my make.sys that seems to work well.
since i usually work off the cvs code, i generally prefer
less aggressive optimization to be more confident, that problems
are caused by the code and not the compiler. nevertheless, on opteron
and intel cpus higher and cpu specific optimizations rarely bring
an improvement and frequently even slow the code down (due to the
overhead cause by switching betwee the regular floating point unit
and the SSE unit).

MPIF90         = mpif90
CC             = gcc
F77            = ifort
CPP            = cpp
CPPFLAGS       = -P -traditional $(DFLAGS) $(IFLAGS)
CFLAGS         = -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS       = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS         = -O2 -assume byterecl -tpp6 -pc64 -unroll
FFLAGS_NOOPT   = -O0 -assume byterecl
LD             = mpif90
LDFLAGS        = -i-static -openmp
BLAS_LIBS      = -L/opt/intel/mkl/9.0/lib/em64t -lmkl_em64t 
LAPACK_LIBS    = -L/opt/intel/mkl/9.0/lib/em64t -lmkl_lapack
FFT_LIBS       =  -lfftw 

hope this helps,
   axel.

CH> Dear forum,
CH> Before I spend a few weeks trying every possible combination of compiler
CH> and library, does anyone have any recommendations for how best to compile
CH> pw.x on an AMD Opteron 246/250/280 cluster (at CASPUR, if that helps)?
CH> 
CH> The available compilers are ifort9.1 and pgi6.2. ACML is available for
CH> both compilers; MKL 8.2 is available for ifort (both Infiniband and Gb
CH> ethernet are available)
CH> 
CH> I've no idea how pgi+acml compares with ifort+mkl on an opteron, for
CH> instance. Perhaps someone out there knows, or even better, has a
CH> high-performance make.sys for CASPUR to share...
CH> 
CH> Best regards,
CH> Conor
CH> 
CH> ----
CH> 
CH> Dr. Conor Hogan                                --- -----  ---   ---
CH> Dipartimento di Fisica e CNR-INFM             |      :   |     :
CH> Universita' di Roma "Tor Vergata"             |--    :    ---  |---
CH> Tel: +39 06 72594908                          |      :       | :
CH> Fax: +39 06 2023507                            ---   :    ---  :
CH> http://www.fisica.uniroma2.it/~cmtheo-group/  European Theoretical
CH>                                               Spectroscopy Facility
CH>                                               http://www.etsf.eu
CH> 
CH> Q. What do you call a fish with no eyes?
CH> A. A fsh.   (Tommy Cooper)
CH> 
CH> The early bird gets the worm, but the second mouse gets the cheese. - S.
CH> Wright
CH> 
CH> If you go through a lot of hammers each month, I don't think it necessarily
CH> means you're a hard worker. It may just mean that you have a lot to learn
CH> about proper hammer maintenance - J. Handey
CH> _______________________________________________
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CH> http://www.democritos.it/mailman/listinfo/pw_forum
CH> 

-- 
=======================================================================
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 chen_shao_hua197 at yahoo.com.tw  Thu May 10 20:51:20 2007
From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=)
Date: Fri, 11 May 2007 02:51:20 +0800 (CST)
Subject: [Pw_forum] configure error
Message-ID: <311123.85169.qm@web73010.mail.tp2.yahoo.com>

Dear members,

I had compiled the MPI-version  QE-3.0 successfully
before in the server.But when I tried to compile 
QE-3.2 .It showed "Parallel environment not detected
(is this a parallel machine?) "
I tried to compare the difference between them.But I
can't figure out the key settings in MPI environment.
I just show the mpi-related informations which
produced after ./configure  command

QE-3.0/configure
then showed
checking for library containing mpi_init... none
required
setting MPI_LIBS...
 . 
 .
 .
checking for library containing mpi_init... (cached)
none required
 .
 .
 .
Parallel environment detected successfully.

QE-3.2/configure
then showed
checking for library containing mpi_init... no
setting MPI_LIBS...
checking for library containing mpi_init... (cached)
no
 .
 .
 .
Parallel environment not detected (is this a parallel
machine?).

Where is going wrong ? How to fix it ?
Thanks for your advice.

max


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


From peterwiney at gmail.com  Fri May 11 00:21:57 2007
From: peterwiney at gmail.com (Peter Winey)
Date: Thu, 10 May 2007 18:21:57 -0400
Subject: [Pw_forum] a question about nbnd setting in band structure calculation
Message-ID: <dac27ff50705101521t71be67a6h479b1aa28efe1293@mail.gmail.com>

Dear all,

I had a little trouble with band calculation for a metallic material, so I
revisited example01.

When I run the "bands" calculation for Al, I found that the results depend
on the setting
of "nbnd". I tried nbnd=8 (the value used in the example) and nbnd=10. The
bands below
the Fermi level are the same in both cases, however, some of the empty bands
are clearly
different.

I am puzzled by this. Is there any physics that I missed?

-Peter
-------------- next part --------------
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From mmarques at staffmail.ed.ac.uk  Fri May 11 17:11:39 2007
From: mmarques at staffmail.ed.ac.uk (Miriam Marques)
Date: Fri, 11 May 2007 16:11:39 +0100
Subject: [Pw_forum] Redhat linux PCs ESPRESSO compilation
Message-ID: <20070511161139.0mticjfbggw4kcsc@www.staffmail.ed.ac.uk>

  Hello,

  I am trying to compile the ESPRESO package in  Redhat linux PCs
  build system type: i686-pc-linux-gnu, architecture: ia32)

I am using the NagWare f95 compiler (but I have also tried with the  
gfortran compiler).
  When I write ./configure it seems to work
, but it is unable to detect FFTW libraries. In the make.sys the line  
FFT_LIBS is empty as well as the line corresponding to the pgplot  
libraries and MPI_LIBS.

  Writing locate fftw, I can see that the machines have by default  
fftw3, but it
is not recognised by the program. I have tried to indicate where it is  
located,
but it does not work.

  I do not know if I should  install another fftw library. I was  
trying to install a fftw-2.1.5 library (I downloaded it from  
http://www.fftw.org/)
, but I do not know if it is suitable for Redhat linux.
When using it, the line:
FFT_LIBS       = -L/Home/mmarques/fftw-2.1.5/lib -lfftw
appears,
but when executing make all, the error:

make[1]: Entering directory `/phys/linux/mmarques/espresso-3.2/iotk'
cd src ; make libiotk.a
make[2]: Entering directory `/phys/linux/mmarques/espresso-3.2/iotk/src'
cpp -P -traditional -D__FFTW -I../include  
-I/Home/mmarques/fftw-2.1.5/include /Home/mmarques/fftw-2.1.5/include  
iotk_base.f90 -o iotk_base.F90
cc1: error: output filename specified twice
(null):0: confused by earlier errors, bailing out
make[2]: *** [iotk_base.o] Error 1
make[2]: Leaving directory `/phys/linux/mmarques/espresso-3.2/iotk/src'
make[1]: *** [libiotk.a] Error 2
make[1]: Leaving directory `/phys/linux/mmarques/espresso-3.2/iotk'
make: *** [libiotk] Error 2

appears.

On the other hand, when I use FFT_LIBS="/Home/mmarques/fftw-2.1.5/lib"

the line
checking for library containing fftwnd... no
appears.

and the error when executing make all is:

if test -d iotk ; then \
( cd iotk ; if test "make" = "" ; then make  TLDEPS= libiotk.a ; \
else make  TLDEPS= libiotk.a ; fi ) ; fi
make[1]: Entering directory `/phys/linux/mmarques/espresso-3.2/iotk'
cd src ; make libiotk.a
make[2]: Entering directory `/phys/linux/mmarques/espresso-3.2/iotk/src'
cpp -P -traditional -D__FFTW -D__USE_INTERNAL_FFTW -I../include   
iotk_base.f90 -o iotk_base.F90
f95 -O -D__FFTW -D__USE_INTERNAL_FFTW -I../include  -I./  -I../Modules  
  -I../iotk/src -I../PW  -I../PH  -I../CPV -c iotk_base.F90 -o  
iotk_base.o
Error: iotk_base.F90, line 1: syntax error
        detected at end of file
***Malformed statement
[f95 fatal error termination]
make[2]: *** [iotk_base.o] Error 2
make[2]: Leaving directory `/phys/linux/mmarques/espresso-3.2/iotk/src'
make[1]: *** [libiotk.a] Error 2
make[1]: Leaving directory `/phys/linux/mmarques/espresso-3.2/iotk'
make: *** [libiotk] Error 2




Thank you very much for your help,

  Miriam.




From giannozz at nest.sns.it  Fri May 11 17:42:25 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 11 May 2007 17:42:25 +0200
Subject: [Pw_forum] configure error
In-Reply-To: <311123.85169.qm@web73010.mail.tp2.yahoo.com>
References: <311123.85169.qm@web73010.mail.tp2.yahoo.com>
Message-ID: <84F2A9F7-A617-4732-9A73-78E1EC846CB7@nest.sns.it>

On May 10, 2007, at 20:51 , ? ?? wrote:

> Parallel environment not detected (is this a parallel
> machine?).
>
> Where is going wrong ? How to fix it ?

the answer is (hidden) in the config.log files. All versions of
configure are available here:
http://www.democritos.it:8888/O-sesame/rlog?f=O-sesame/configure
but notice that different versions may generate different versions of
make.sys or may require different versions of other configuration files

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




From ceresoli at sissa.it  Fri May 11 17:43:02 2007
From: ceresoli at sissa.it (Davide Ceresoli)
Date: Fri, 11 May 2007 17:43:02 +0200
Subject: [Pw_forum] Redhat linux PCs ESPRESSO compilation
In-Reply-To: <20070511161139.0mticjfbggw4kcsc@www.staffmail.ed.ac.uk>
References: <20070511161139.0mticjfbggw4kcsc@www.staffmail.ed.ac.uk>
Message-ID: <46448F06.8070206@sissa.it>

Miriam Marques wrote:

>  I do not know if I should  install another fftw library. I was trying 
> to install a fftw-2.1.5 library (I downloaded it from http://www.fftw.org/)
> , but I do not know if it is suitable for Redhat linux.
> When using it, the line:
> FFT_LIBS       = -L/Home/mmarques/fftw-2.1.5/lib -lfftw
> appears,
> but when executing make all, the error:
> 
> make[1]: Entering directory `/phys/linux/mmarques/espresso-3.2/iotk'
> cd src ; make libiotk.a
> make[2]: Entering directory `/phys/linux/mmarques/espresso-3.2/iotk/src'
> cpp -P -traditional -D__FFTW -I../include 
> -I/Home/mmarques/fftw-2.1.5/include /Home/mmarques/fftw-2.1.5/include 
> iotk_base.f90 -o iotk_base.F90
> cc1: error: output filename specified twice
Can you inspect the file make.sys?
Most likely it will contain a line:

IFLAGS         = -I../include -I/Home/mmarques/fftw-2.1.5/include
                  /Home/mmarques/fftw-2.1.5/include

So, delete the second occurrence of '/Home/mmarques/fftw-2.1.5/include'.

We'll try to fix this configure error in the CVS and in the next release.

HTH.

Davide


From giannozz at nest.sns.it  Fri May 11 17:54:54 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 11 May 2007 17:54:54 +0200
Subject: [Pw_forum] a question about nbnd setting in band structure calculation
In-Reply-To: <dac27ff50705101521t71be67a6h479b1aa28efe1293@mail.gmail.com>
References: <dac27ff50705101521t71be67a6h479b1aa28efe1293@mail.gmail.com>
Message-ID: <63581D42-7BBD-45F4-9C27-A7397409526D@nest.sns.it>

On May 11, 2007, at 24:21 , Peter Winey wrote:

>  When I run the "bands" calculation for Al, I found that the  
> results depend on the setting of "nbnd". I tried nbnd=8 (the value  
> used in the example) and nbnd=10.
> The bands below the Fermi level are the same in both cases,  
> however, some
> of the empty bands are clearly different.

if you want to be sure to get all the N bands you want, you need to  
calculate
a few more than N. Iterative diagonalization requires a good starting  
point.
If for some reason the final bands are not present in the starting  
manifold,
you can easily miss them. This never happens (with the notable exception
of some ferroelectric perovskites) in scf calculations, even if you  
use the
strict minimum of bands, because sooner or later the 'good' bands  
find their
way into the lowest-energy manifold. In non-scf calculation it may  
happen
that a few of the highest bands are not what they are supposed to be,  
though.

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




From giannozz at nest.sns.it  Fri May 11 18:01:14 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 11 May 2007 18:01:14 +0200
Subject: [Pw_forum] Redhat linux PCs ESPRESSO compilation
In-Reply-To: <20070511161139.0mticjfbggw4kcsc@www.staffmail.ed.ac.uk>
References: <20070511161139.0mticjfbggw4kcsc@www.staffmail.ed.ac.uk>
Message-ID: <9A133B3F-2F02-4665-9D73-D1AE90C945E3@nest.sns.it>

On May 11, 2007, at 17:11 , Miriam Marques wrote:

> I am using the NagWare f95 compiler (but I have also tried with the  
> gfortran compiler).

gfortran doesn't work (or at least it didn't the last time I tried).  
If you do
not manage to have NagWare f95 working, try g95.

>  When I write ./configure it seems to work, but it is unable to  
> detect FFTW libraries.

FFTW v.3 are not detected by configure. If nothing is found, the  
internal
library is used. I never observed any significant speedup from external
fftw libraries.
>
> f95 -O -D__FFTW -D__USE_INTERNAL_FFTW -I../include  -I./  -I../ 
> Modules  -I../iotk/src -I../PW  -I../PH  -I../CPV -c iotk_base.F90 - 
> o iotk_base.o
> Error: iotk_base.F90, line 1: syntax error
>        detected at end of file
> ***Malformed statement

an empty or bad file has been created by the previous failed attempt.
"make clean" first

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




From kazempoor2000 at yahoo.com  Sat May 12 06:33:31 2007
From: kazempoor2000 at yahoo.com (ali kazempoor)
Date: Fri, 11 May 2007 21:33:31 -0700 (PDT)
Subject: [Pw_forum] correct pseudopotentials
Message-ID: <471834.82511.qm@web33101.mail.mud.yahoo.com>

hi
i run scf input file for MnAs that has NiAs -type
(hexagonal)and i use ultrasoft pseudopotentials for Mn
and As from espersso  and optimize k point and also
ecutrho in my case was converged but my run
don't converge at 50 ,55 ,.. rydberg for ecut.please
correct my input file.
 &CONTROL
                       title = MnAs ,
                 calculation = 'scf' ,
                restart_mode = 'from_scratch' ,
                      outdir =
'/scratch/kazempour/tmp/MnAs/' ,
                  pseudo_dir =
'/home/akazem/espresso-3.2/pseudo/' ,
                      prefix = MnAs ,
 /
 &SYSTEM
                       ibrav = 4,
                   celldm(1) = 7.0373,
                   celldm(3) = 1.5318,
                         nat = 4,
                        ntyp = 2,
                     ecutwfc = 40,
                     ecutrho = 350 
                     occupations = 'smearing' ,
                     degauss = 0.02 ,
                    smearing = 'methfessel-paxton' ,
                       nspin = 2 ,
   starting_magnetization(1) = 1.0,
   starting_magnetization(2) = 0.1,
 /
 &ELECTRONS
            electron_maxstep = 100,
                    conv_thr = .00001 ,
 /
ATOMIC_SPECIES
   Mn  54.93   Mn.pbe-sp-van.UPF 
   As  74.92   As.pbe-n-van.UPF 
ATOMIC_POSITIONS crystal 
   Mn      0.000000000    0.000000000    0.000000000  
 
   Mn      0.000000000    0.000000000    0.500000000  
 
   As      0.333333333    0.666666666    0.250000000  
 
   As      0.666666666    0.333333333    0.750000000  
 
K_POINTS automatic 
  11 11 9   1 1 1 

i get pseudopotentials for Mn and As from pwscf
website.
thanks





      ____________________________________________________________________________________
Park yourself in front of a world of choices in alternative vehicles. Visit the Yahoo! Auto Green Center.
http://autos.yahoo.com/green_center/ 


From degironc at sissa.it  Sat May 12 09:23:47 2007
From: degironc at sissa.it (degironc)
Date: Sat, 12 May 2007 09:23:47 +0200
Subject: [Pw_forum] correct pseudopotentials
In-Reply-To: <471834.82511.qm@web33101.mail.mud.yahoo.com>
References: <471834.82511.qm@web33101.mail.mud.yahoo.com>
Message-ID: <46456B83.1080103@sissa.it>

might not be related but prefix is a string and as such should be quoted.
stefano

ali kazempoor wrote:

>hi
>i run scf input file for MnAs that has NiAs -type
>(hexagonal)and i use ultrasoft pseudopotentials for Mn
>and As from espersso  and optimize k point and also
>ecutrho in my case was converged but my run
>don't converge at 50 ,55 ,.. rydberg for ecut.please
>correct my input file.
> &CONTROL
>                       title = MnAs ,
>                 calculation = 'scf' ,
>                restart_mode = 'from_scratch' ,
>                      outdir =
>'/scratch/kazempour/tmp/MnAs/' ,
>                  pseudo_dir =
>'/home/akazem/espresso-3.2/pseudo/' ,
>                      prefix = MnAs ,
> /
> &SYSTEM
>                       ibrav = 4,
>                   celldm(1) = 7.0373,
>                   celldm(3) = 1.5318,
>                         nat = 4,
>                        ntyp = 2,
>                     ecutwfc = 40,
>                     ecutrho = 350 
>                     occupations = 'smearing' ,
>                     degauss = 0.02 ,
>                    smearing = 'methfessel-paxton' ,
>                       nspin = 2 ,
>   starting_magnetization(1) = 1.0,
>   starting_magnetization(2) = 0.1,
> /
> &ELECTRONS
>            electron_maxstep = 100,
>                    conv_thr = .00001 ,
> /
>ATOMIC_SPECIES
>   Mn  54.93   Mn.pbe-sp-van.UPF 
>   As  74.92   As.pbe-n-van.UPF 
>ATOMIC_POSITIONS crystal 
>   Mn      0.000000000    0.000000000    0.000000000  
> 
>   Mn      0.000000000    0.000000000    0.500000000  
> 
>   As      0.333333333    0.666666666    0.250000000  
> 
>   As      0.666666666    0.333333333    0.750000000  
> 
>K_POINTS automatic 
>  11 11 9   1 1 1 
>
>i get pseudopotentials for Mn and As from pwscf
>website.
>thanks
>
>
>
>
>
>      ____________________________________________________________________________________
>Park yourself in front of a world of choices in alternative vehicles. Visit the Yahoo! Auto Green Center.
>http://autos.yahoo.com/green_center/ 
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>  
>



From akohlmey at cmm.chem.upenn.edu  Sun May 13 00:22:31 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 12 May 2007 18:22:31 -0400 (EDT)
Subject: [Pw_forum] correct pseudopotentials
In-Reply-To: <471834.82511.qm@web33101.mail.mud.yahoo.com>
Message-ID: <Pine.LNX.4.44.0705121808340.12078-100000@localhost.localdomain>

On Fri, 11 May 2007, ali kazempoor wrote:

hi!

your input works for me (QE 3.2cvs version, 
intel em64t cpu, intel 9.1 compiler, intel mkl 9.0).

you did not specify what version of the code
i would recommend you run some of the test examples
and check the results against the reference output.
perhaps your compiler miscompiles the code or creates
less accurate code.

cheers,

  axel.

AK> hi
AK> i run scf input file for MnAs that has NiAs -type
AK> (hexagonal)and i use ultrasoft pseudopotentials for Mn
AK> and As from espersso  and optimize k point and also
AK> ecutrho in my case was converged but my run
AK> don't converge at 50 ,55 ,.. rydberg for ecut.please
AK> correct my input file.
AK>  &CONTROL
AK>                        title = MnAs ,
AK>                  calculation = 'scf' ,
AK>                 restart_mode = 'from_scratch' ,
AK>                       outdir =
AK> '/scratch/kazempour/tmp/MnAs/' ,
AK>                   pseudo_dir =
AK> '/home/akazem/espresso-3.2/pseudo/' ,
AK>                       prefix = MnAs ,
AK>  /
AK>  &SYSTEM
AK>                        ibrav = 4,
AK>                    celldm(1) = 7.0373,
AK>                    celldm(3) = 1.5318,
AK>                          nat = 4,
AK>                         ntyp = 2,
AK>                      ecutwfc = 40,
AK>                      ecutrho = 350 
AK>                      occupations = 'smearing' ,
AK>                      degauss = 0.02 ,
AK>                     smearing = 'methfessel-paxton' ,
AK>                        nspin = 2 ,
AK>    starting_magnetization(1) = 1.0,
AK>    starting_magnetization(2) = 0.1,
AK>  /
AK>  &ELECTRONS
AK>             electron_maxstep = 100,
AK>                     conv_thr = .00001 ,
AK>  /
AK> ATOMIC_SPECIES
AK>    Mn  54.93   Mn.pbe-sp-van.UPF 
AK>    As  74.92   As.pbe-n-van.UPF 
AK> ATOMIC_POSITIONS crystal 
AK>    Mn      0.000000000    0.000000000    0.000000000  
AK>  
AK>    Mn      0.000000000    0.000000000    0.500000000  
AK>  
AK>    As      0.333333333    0.666666666    0.250000000  
AK>  
AK>    As      0.666666666    0.333333333    0.750000000  
AK>  
AK> K_POINTS automatic 
AK>   11 11 9   1 1 1 
AK> 
AK> i get pseudopotentials for Mn and As from pwscf
AK> website.
AK> thanks
AK> 
AK> 
AK> 
AK> 
AK> 
AK>       ____________________________________________________________________________________
AK> Park yourself in front of a world of choices in alternative vehicles. Visit the Yahoo! Auto Green Center.
AK> http://autos.yahoo.com/green_center/ 
AK> _______________________________________________
AK> Pw_forum mailing list
AK> Pw_forum at pwscf.org
AK> http://www.democritos.it/mailman/listinfo/pw_forum
AK> 

-- 
=======================================================================
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 kazempoor2000 at yahoo.com  Sun May 13 10:56:08 2007
From: kazempoor2000 at yahoo.com (ali kazempoor)
Date: Sun, 13 May 2007 01:56:08 -0700 (PDT)
Subject: [Pw_forum] Mn pseudopotential
Message-ID: <620694.3015.qm@web33110.mail.mud.yahoo.com>

hi all
Could anyone contribute the pseudopotential for Mn for
share?
thanks


       
____________________________________________________________________________________Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online.
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From ackollias at gmail.com  Sun May 13 17:22:31 2007
From: ackollias at gmail.com (sasha)
Date: Sun, 13 May 2007 11:22:31 -0400
Subject: [Pw_forum] MgFeO LDA+U convergence problem
Message-ID: <1179069751.5546.20.camel@cryptonomicon>

Greetings,
          I am having difficulties converging an insulating AFM solution
for (Mg,Fe)O using LDA+U.  The starting ns_eigenvalues are manually set,
see input file below, based on the eigenvalues from a standard LDA+U
calculation ( similar to the calculations found in example25 that comes
with pwscf), i.e. from a "standard" lda+u calculation the eigenvalues at
the first iteration for each Fe atom and spin are:
 
atom  1  spin  1   0.9963065 0.9965670 0.9992693 1.0013531 1.0014491
atom  1  spin  2   0.0596477 0.0599690 0.1193848 0.1515851 0.1529077

atom  2  spin  1   0.0596467 0.0599706 0.1193259 0.1496419 0.1509636
atom  2  spin  2   0.9963062 0.9965635 0.9992686 1.0013520 1.0014480

atom  3  spin  1   0.9963065 0.9965668 0.9992693 1.0013532 1.0014491
atom  3  spin  2   0.0596468 0.0599704 0.1193283 0.1497012 0.1511213

atom  4  spin  1   0.0596478 0.0599688 0.1193870 0.1516467 0.1530634
atom  4  spin  2   0.9963069 0.9965703 0.9992700 1.0013546 1.0014500

	Initially the calculation proceeds normally however after a number of
iterations the SCF accuracy no longer improves and in fact begins to
increase, see output snippet below:

   Energy              SCF accuracy
 -484.47448064 	      10.17038034 
 -485.86491483 	       0.86693260 
  ...                    ....
 -486.21197435 	       0.00002051 
 -486.21199031 	       0.00002066 
 -486.21190314 	       0.00002043 
 -486.21186241 	       0.00002073 
 -486.21188439 	       0.00002073 
 -486.21185625 	       0.00002089 

I have tried various combinations of degauss values and increasing the
number of bands with no success.  Which values or input setting could be
used to achieve convergence in this system For the clarity's sake my
input file is included below. Any help or suggestions are greatly
appreciated.

regards,
	Sasha

Input file:

 &system
    ibrav=  0, celldm(1)=8.19, nat=  16, ntyp= 6,
    ecutwfc = 30.0, ecutrho = 240.0, nbnd=53
    starting_magnetization(1)= 0.5, 
    starting_magnetization(2)=-0.5,
    starting_magnetization(3)= 0.5, 
    starting_magnetization(4)=-0.5,
    starting_magnetization(5)= 0.0, 
    starting_magnetization(6)= 0.0,
    occupations='smearing', smearing='gauss', degauss=0.01,
    nspin=2,
    lda_plus_u=.true.  Hubbard_U(1)=5.0, Hubbard_U(2)=5.0,
Hubbard_U(3)=5.0, Hubbard_U(4)=5.0,
    starting_ns_eigenvalue(3,2,1) = 1.d0
    starting_ns_eigenvalue(3,1,2) = 1.d0
    starting_ns_eigenvalue(3,1,3) = 1.d0
    starting_ns_eigenvalue(3,2,4) = 1.d0
    report=1
 /
 &electrons
    mixing_mode      = 'plain'
    mixing_beta      = 0.20
    mixing_ndim      = 5  
    mixing_fixed_ns  = 0
    conv_thr         =  1.0d-6
    electron_maxstep = 100

 /
CELL_PARAMETERS
1.00 1.00 0.00
1.00 0.00 1.00
0.00 1.00 1.00
ATOMIC_SPECIES
 Fe1  1.  Fe.pz-nd-rrkjus.UPF
 Fe2  1.  Fe.pz-nd-rrkjus.UPF
 Fe3  1.  Fe.pz-nd-rrkjus.UPF
 Fe4  1.  Fe.pz-nd-rrkjus.UPF
 Mg1  1.  Mg.pz-n-vbc.UPF
 O1   1.  O.LDA.US.RRKJ3.UPF
ATOMIC_POSITIONS {alat}
 Fe1 0.00 0.00 0.00
 Fe2 1.00 0.50 0.50
 Fe3 0.50 0.50 1.00
 Fe4 0.50 1.00 0.50
 Mg1 0.50 0.50 0.00
 Mg1 0.50 0.00 0.50
 Mg1 0.00 0.50 0.50
 Mg1 1.00 1.00 1.00
 O1  0.50 0.00 0.00
 O1  0.50 0.50 0.50
 O1  1.00 0.50 0.00
 O1  1.00 0.00 0.50
 O1  1.50 0.50 0.50
 O1  1.00 0.50 1.00
 O1  1.00 1.00 0.50
 O1  1.50 1.00 1.00
K_POINTS {automatic}
2 2 2 0 0 0




From matteo at umn.edu  Mon May 14 16:48:55 2007
From: matteo at umn.edu (Matteo Cococcioni)
Date: Mon, 14 May 2007 09:48:55 -0500
Subject: [Pw_forum] MgFeO LDA+U convergence problem
In-Reply-To: <1179069751.5546.20.camel@cryptonomicon>
References: <1179069751.5546.20.camel@cryptonomicon>
Message-ID: <464876D7.40004@umn.edu>


Dear Sasha

looking at your input (in particular at the spin arrangement you fixed) 
I think the starting_ns should be something like:

    starting_ns_eigenvalue(3,2,1) = 1.d0
    starting_ns_eigenvalue(3,1,2) = 1.d0
    starting_ns_eigenvalue(3,2,3) = 1.d0
    starting_ns_eigenvalue(3,1,4) = 1.d0

Maybe it would also make sense to have different starting magnetization 
on the Fe iron so that the breaking of their equivalence is more
complete from the beginning:

    starting_magnetization(1)= 0.8, 
    starting_magnetization(2)=-0.7,
    starting_magnetization(3)= 0.4, 
    starting_magnetization(4)=-0.5,


 Another possibility is to (slightly) move the Fe iron from their 
positions. Residual symmetries would be lost and maybe the code is able to
find the ground state and the occupation pattern you are trying to impose.

Hope this helps,

Matteo





sasha wrote:
> Greetings,
>           I am having difficulties converging an insulating AFM solution
> for (Mg,Fe)O using LDA+U.  The starting ns_eigenvalues are manually set,
> see input file below, based on the eigenvalues from a standard LDA+U
> calculation ( similar to the calculations found in example25 that comes
> with pwscf), i.e. from a "standard" lda+u calculation the eigenvalues at
> the first iteration for each Fe atom and spin are:
>  
> atom  1  spin  1   0.9963065 0.9965670 0.9992693 1.0013531 1.0014491
> atom  1  spin  2   0.0596477 0.0599690 0.1193848 0.1515851 0.1529077
>
> atom  2  spin  1   0.0596467 0.0599706 0.1193259 0.1496419 0.1509636
> atom  2  spin  2   0.9963062 0.9965635 0.9992686 1.0013520 1.0014480
>
> atom  3  spin  1   0.9963065 0.9965668 0.9992693 1.0013532 1.0014491
> atom  3  spin  2   0.0596468 0.0599704 0.1193283 0.1497012 0.1511213
>
> atom  4  spin  1   0.0596478 0.0599688 0.1193870 0.1516467 0.1530634
> atom  4  spin  2   0.9963069 0.9965703 0.9992700 1.0013546 1.0014500
>
> 	Initially the calculation proceeds normally however after a number of
> iterations the SCF accuracy no longer improves and in fact begins to
> increase, see output snippet below:
>
>    Energy              SCF accuracy
>  -484.47448064 	      10.17038034 
>  -485.86491483 	       0.86693260 
>   ...                    ....
>  -486.21197435 	       0.00002051 
>  -486.21199031 	       0.00002066 
>  -486.21190314 	       0.00002043 
>  -486.21186241 	       0.00002073 
>  -486.21188439 	       0.00002073 
>  -486.21185625 	       0.00002089 
>
> I have tried various combinations of degauss values and increasing the
> number of bands with no success.  Which values or input setting could be
> used to achieve convergence in this system For the clarity's sake my
> input file is included below. Any help or suggestions are greatly
> appreciated.
>
> regards,
> 	Sasha
>
> Input file:
>
>  &system
>     ibrav=  0, celldm(1)=8.19, nat=  16, ntyp= 6,
>     ecutwfc = 30.0, ecutrho = 240.0, nbnd=53
>     starting_magnetization(1)= 0.5, 
>     starting_magnetization(2)=-0.5,
>     starting_magnetization(3)= 0.5, 
>     starting_magnetization(4)=-0.5,
>     starting_magnetization(5)= 0.0, 
>     starting_magnetization(6)= 0.0,
>     occupations='smearing', smearing='gauss', degauss=0.01,
>     nspin=2,
>     lda_plus_u=.true.  Hubbard_U(1)=5.0, Hubbard_U(2)=5.0,
> Hubbard_U(3)=5.0, Hubbard_U(4)=5.0,
>     starting_ns_eigenvalue(3,2,1) = 1.d0
>     starting_ns_eigenvalue(3,1,2) = 1.d0
>     starting_ns_eigenvalue(3,1,3) = 1.d0
>     starting_ns_eigenvalue(3,2,4) = 1.d0
>     report=1
>  /
>  &electrons
>     mixing_mode      = 'plain'
>     mixing_beta      = 0.20
>     mixing_ndim      = 5  
>     mixing_fixed_ns  = 0
>     conv_thr         =  1.0d-6
>     electron_maxstep = 100
>
>  /
> CELL_PARAMETERS
> 1.00 1.00 0.00
> 1.00 0.00 1.00
> 0.00 1.00 1.00
> ATOMIC_SPECIES
>  Fe1  1.  Fe.pz-nd-rrkjus.UPF
>  Fe2  1.  Fe.pz-nd-rrkjus.UPF
>  Fe3  1.  Fe.pz-nd-rrkjus.UPF
>  Fe4  1.  Fe.pz-nd-rrkjus.UPF
>  Mg1  1.  Mg.pz-n-vbc.UPF
>  O1   1.  O.LDA.US.RRKJ3.UPF
> ATOMIC_POSITIONS {alat}
>  Fe1 0.00 0.00 0.00
>  Fe2 1.00 0.50 0.50
>  Fe3 0.50 0.50 1.00
>  Fe4 0.50 1.00 0.50
>  Mg1 0.50 0.50 0.00
>  Mg1 0.50 0.00 0.50
>  Mg1 0.00 0.50 0.50
>  Mg1 1.00 1.00 1.00
>  O1  0.50 0.00 0.00
>  O1  0.50 0.50 0.50
>  O1  1.00 0.50 0.00
>  O1  1.00 0.00 0.50
>  O1  1.50 0.50 0.50
>  O1  1.00 0.50 1.00
>  O1  1.00 1.00 0.50
>  O1  1.50 1.00 1.00
> K_POINTS {automatic}
> 2 2 2 0 0 0
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   

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From brad.malone at gmail.com  Mon May 14 22:24:51 2007
From: brad.malone at gmail.com (Brad Malone)
Date: Mon, 14 May 2007 13:24:51 -0700
Subject: [Pw_forum] Getting the points for the bandstructure path
Message-ID: <bf16929a0705141324q3ba71c0vb9d9ac4f6209019b@mail.gmail.com>

Hi, I was wondering if there was any script included in pwSCF which could be
used to generated the set of points along the line that one wanted to plot
the bandstructure.  In example 5 I see that the points have to be given
explicitly in order to calculate the BS, and I just want to know if pwSCF
has any tools to calculate those points or whether I should just write the
script myself.

Thanks for the help,
Brad
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From ackollias at gmail.com  Tue May 15 16:30:21 2007
From: ackollias at gmail.com (sasha)
Date: Tue, 15 May 2007 10:30:21 -0400
Subject: [Pw_forum] MgFeO LDA+U convergence problem
In-Reply-To: <464876D7.40004@umn.edu>
References: <1179069751.5546.20.camel@cryptonomicon>
	 <464876D7.40004@umn.edu>
Message-ID: <1179239421.3203.4.camel@cryptonomicon>

Greetings Matteo,
	Thanks for the advice, your suggestion in fact works very well.  It
turns out that I should have more closely examined my input.  I have
another quick question regarding the starting_ns_eigenvalue, in the
previous example (below) from the eigenvalues at the first iteration of
the "standard" lda+u calculation it is clear how to set the
ns_eigenvalues however what does one do if the starting eigenvalues are
as follows:

atom  1  spin  1   0.9985560 0.9998587 1.0007556 1.0013322 1.0057882
atom  1  spin  2   0.0484071 0.0493657 0.0578860 0.1216687 0.1308162 

atom  2  spin  1   0.0535213 0.0592929 0.1256650 0.1321563 0.1439048 
atom  2  spin  2   0.9979128 0.9993943 1.0004671 1.0010265 1.0058542

atom  3  spin  1   0.9947113 0.9953027 0.9992115 0.9997585 1.0044052
atom  3  spin  2   0.0693133 0.1280564 0.1459512 0.1547219 0.4858838

atom  4  spin  1   0.0637767 0.0681158 0.1421888 0.1436934 0.2272403 
atom  4  spin  2   0.9965028 0.9979222 0.9991654 1.0005289 1.0054916

where only some of the eigenvalues for certain atoms and spins are
degenerate?  Once again thank you in advance for any advice or
suggestions.
regards,
	Sasha
On Mon, 2007-05-14 at 09:48 -0500, Matteo Cococcioni wrote:
> Dear Sasha
> 
> looking at your input (in particular at the spin arrangement you fixed) 
> I think the starting_ns should be something like:
> 
>     starting_ns_eigenvalue(3,2,1) = 1.d0
>     starting_ns_eigenvalue(3,1,2) = 1.d0
>     starting_ns_eigenvalue(3,2,3) = 1.d0
>     starting_ns_eigenvalue(3,1,4) = 1.d0
> 
> Maybe it would also make sense to have different starting magnetization 
> on the Fe iron so that the breaking of their equivalence is more
> complete from the beginning:
> 
>     starting_magnetization(1)= 0.8, 
>     starting_magnetization(2)=-0.7,
>     starting_magnetization(3)= 0.4, 
>     starting_magnetization(4)=-0.5,
> 
> 
>  Another possibility is to (slightly) move the Fe iron from their 
> positions. Residual symmetries would be lost and maybe the code is able to
> find the ground state and the occupation pattern you are trying to impose.
> 
> Hope this helps,
> 
> Matteo
> 
> 
> 
> 
> 
> sasha wrote:
> > Greetings,
> >           I am having difficulties converging an insulating AFM solution
> > for (Mg,Fe)O using LDA+U.  The starting ns_eigenvalues are manually set,
> > see input file below, based on the eigenvalues from a standard LDA+U
> > calculation ( similar to the calculations found in example25 that comes
> > with pwscf), i.e. from a "standard" lda+u calculation the eigenvalues at
> > the first iteration for each Fe atom and spin are:
> >  
> > atom  1  spin  1   0.9963065 0.9965670 0.9992693 1.0013531 1.0014491
> > atom  1  spin  2   0.0596477 0.0599690 0.1193848 0.1515851 0.1529077
> >
> > atom  2  spin  1   0.0596467 0.0599706 0.1193259 0.1496419 0.1509636
> > atom  2  spin  2   0.9963062 0.9965635 0.9992686 1.0013520 1.0014480
> >
> > atom  3  spin  1   0.9963065 0.9965668 0.9992693 1.0013532 1.0014491
> > atom  3  spin  2   0.0596468 0.0599704 0.1193283 0.1497012 0.1511213
> >
> > atom  4  spin  1   0.0596478 0.0599688 0.1193870 0.1516467 0.1530634
> > atom  4  spin  2   0.9963069 0.9965703 0.9992700 1.0013546 1.0014500
> >
> > 	Initially the calculation proceeds normally however after a number of
> > iterations the SCF accuracy no longer improves and in fact begins to
> > increase, see output snippet below:
> >
> >    Energy              SCF accuracy
> >  -484.47448064 	      10.17038034 
> >  -485.86491483 	       0.86693260 
> >   ...                    ....
> >  -486.21197435 	       0.00002051 
> >  -486.21199031 	       0.00002066 
> >  -486.21190314 	       0.00002043 
> >  -486.21186241 	       0.00002073 
> >  -486.21188439 	       0.00002073 
> >  -486.21185625 	       0.00002089 
> >
> > I have tried various combinations of degauss values and increasing the
> > number of bands with no success.  Which values or input setting could be
> > used to achieve convergence in this system For the clarity's sake my
> > input file is included below. Any help or suggestions are greatly
> > appreciated.
> >
> > regards,
> > 	Sasha
> >
> > Input file:
> >
> >  &system
> >     ibrav=  0, celldm(1)=8.19, nat=  16, ntyp= 6,
> >     ecutwfc = 30.0, ecutrho = 240.0, nbnd=53
> >     starting_magnetization(1)= 0.5, 
> >     starting_magnetization(2)=-0.5,
> >     starting_magnetization(3)= 0.5, 
> >     starting_magnetization(4)=-0.5,
> >     starting_magnetization(5)= 0.0, 
> >     starting_magnetization(6)= 0.0,
> >     occupations='smearing', smearing='gauss', degauss=0.01,
> >     nspin=2,
> >     lda_plus_u=.true.  Hubbard_U(1)=5.0, Hubbard_U(2)=5.0,
> > Hubbard_U(3)=5.0, Hubbard_U(4)=5.0,
> >     starting_ns_eigenvalue(3,2,1) = 1.d0
> >     starting_ns_eigenvalue(3,1,2) = 1.d0
> >     starting_ns_eigenvalue(3,1,3) = 1.d0
> >     starting_ns_eigenvalue(3,2,4) = 1.d0
> >     report=1
> >  /
> >  &electrons
> >     mixing_mode      = 'plain'
> >     mixing_beta      = 0.20
> >     mixing_ndim      = 5  
> >     mixing_fixed_ns  = 0
> >     conv_thr         =  1.0d-6
> >     electron_maxstep = 100
> >
> >  /
> > CELL_PARAMETERS
> > 1.00 1.00 0.00
> > 1.00 0.00 1.00
> > 0.00 1.00 1.00
> > ATOMIC_SPECIES
> >  Fe1  1.  Fe.pz-nd-rrkjus.UPF
> >  Fe2  1.  Fe.pz-nd-rrkjus.UPF
> >  Fe3  1.  Fe.pz-nd-rrkjus.UPF
> >  Fe4  1.  Fe.pz-nd-rrkjus.UPF
> >  Mg1  1.  Mg.pz-n-vbc.UPF
> >  O1   1.  O.LDA.US.RRKJ3.UPF
> > ATOMIC_POSITIONS {alat}
> >  Fe1 0.00 0.00 0.00
> >  Fe2 1.00 0.50 0.50
> >  Fe3 0.50 0.50 1.00
> >  Fe4 0.50 1.00 0.50
> >  Mg1 0.50 0.50 0.00
> >  Mg1 0.50 0.00 0.50
> >  Mg1 0.00 0.50 0.50
> >  Mg1 1.00 1.00 1.00
> >  O1  0.50 0.00 0.00
> >  O1  0.50 0.50 0.50
> >  O1  1.00 0.50 0.00
> >  O1  1.00 0.00 0.50
> >  O1  1.50 0.50 0.50
> >  O1  1.00 0.50 1.00
> >  O1  1.00 1.00 0.50
> >  O1  1.50 1.00 1.00
> > K_POINTS {automatic}
> > 2 2 2 0 0 0
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >   
> 



From swblelia at ehu.es  Tue May 15 18:11:16 2007
From: swblelia at ehu.es (Aritz Leonardo Liceranzu)
Date: Tue, 15 May 2007 18:11:16 +0200
Subject: [Pw_forum] l, m pdos
Message-ID: <B91C24D7-87C6-4E76-83AB-8201649D237C@ehu.es>




Hello all,

I am drawing the some projected states and I would like somebody to  
confirm the following about the output:

l=1 m=1 --> factor*(z/r)
l=1 m=2 --> factor*(x/r)
l=1 m=3 --> factor*(y/r)

l=2 m=1 --> factor*(-1+z2/r2)
l=2 m=2 --> factor*(xz/r2)
l=2 m=3 --> factor*(yz/r2)

Thank you!!
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From konstantin_kudin at yahoo.com  Tue May 15 18:56:16 2007
From: konstantin_kudin at yahoo.com (Konstantin Kudin)
Date: Tue, 15 May 2007 09:56:16 -0700 (PDT)
Subject: [Pw_forum] Single precision FFTs on GPUs for QE ?
In-Reply-To: <1179239421.3203.4.camel@cryptonomicon>
Message-ID: <566770.25127.qm@web57714.mail.re3.yahoo.com>

 Hi all,

 With all the hype surrounding the recent graphics cards and how fast
they are supposed to be, the following question arises.

 If QE were to do everything in double precision, but the FFTs in
single precision, will it hurt too much? FFTs kind of do few
operations, so the error accumulation could be tolerable. Of course,
another issue if the few digits of single precision are really enough
...

 With multicore cpus it is increasingly difficult to transfer the data
between the boxes for FFTs, it sure would be easier (in principle) to
send the data locally to the super fast (tm) GPU.
 
 Anyway, from the implementation perspective, FFTs are currectly
reasonably well localized in the code, so in principle the hassle of
using GPUs would be only local in terms of coding :-) 

 Ideas? 

 Kostya


       
____________________________________________________________________________________Give spam the boot. Take control with tough spam protection in the all-new Yahoo! Mail Beta.
http://advision.webevents.yahoo.com/mailbeta/newmail_html.html 


From akohlmey at cmm.chem.upenn.edu  Tue May 15 18:04:01 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 15 May 2007 12:04:01 -0400 (EDT)
Subject: [Pw_forum] Single precision FFTs on GPUs for QE ?
In-Reply-To: <566770.25127.qm@web57714.mail.re3.yahoo.com>
Message-ID: <Pine.LNX.4.44.0705151159100.12088-100000@localhost.localdomain>

On Tue, 15 May 2007, Konstantin Kudin wrote:

hi kostya,

i would suggest waiting until the end of summer as nvidia is
supposed to release cards that actually can handle double precision
(and will have accellerated FFT _and_ BLAS).

however, it should also be straightforward to test single precision
ffts with the existing codes, just change the FFTW code to call
the respective single precision subroutines. you have to convert
all data from double to single and back which will cost some
performance and i'm not so sure whether the resulting noise will
be negligible.

cheers,
   axel.

KK>  Hi all,
KK> 
KK>  With all the hype surrounding the recent graphics cards and how fast
KK> they are supposed to be, the following question arises.
KK> 
KK>  If QE were to do everything in double precision, but the FFTs in
KK> single precision, will it hurt too much? FFTs kind of do few
KK> operations, so the error accumulation could be tolerable. Of course,
KK> another issue if the few digits of single precision are really enough
KK> ...
KK> 
KK>  With multicore cpus it is increasingly difficult to transfer the data
KK> between the boxes for FFTs, it sure would be easier (in principle) to
KK> send the data locally to the super fast (tm) GPU.
KK>  
KK>  Anyway, from the implementation perspective, FFTs are currectly
KK> reasonably well localized in the code, so in principle the hassle of
KK> using GPUs would be only local in terms of coding :-) 
KK> 
KK>  Ideas? 
KK> 
KK>  Kostya
KK> 
KK> 
KK>        
KK> ____________________________________________________________________________________Give spam the boot. Take control with tough spam protection in the all-new Yahoo! Mail Beta.
KK> http://advision.webevents.yahoo.com/mailbeta/newmail_html.html 
KK> _______________________________________________
KK> Pw_forum mailing list
KK> Pw_forum at pwscf.org
KK> http://www.democritos.it/mailman/listinfo/pw_forum
KK> 

-- 
=======================================================================
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  Tue May 15 19:11:00 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 15 May 2007 19:11:00 +0200
Subject: [Pw_forum] Getting the points for the bandstructure path
In-Reply-To: <bf16929a0705141324q3ba71c0vb9d9ac4f6209019b@mail.gmail.com>
References: <bf16929a0705141324q3ba71c0vb9d9ac4f6209019b@mail.gmail.com>
Message-ID: <73945695-D671-49A9-AB57-21FAE895D5A9@nest.sns.it>

On May 14, 2007, at 22:24 , Brad Malone wrote:

> Hi, I was wondering if there was any script included in pwSCF which  
> could be used to generated the set of points along the line that  
> one wanted to plot the bandstructure.  In example 5 I see that the  
> points have to be given explicitly in order to calculate the BS,  
> and I just want to know if pwSCF has any tools to calculate those  
> points or whether I should just write the script myself.

I think there is some facility in XCrysDen that allows to produce a list
of k-points along selected high-symmetry lines

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




From giannozz at nest.sns.it  Tue May 15 19:21:01 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 15 May 2007 19:21:01 +0200
Subject: [Pw_forum] l, m pdos
In-Reply-To: <B91C24D7-87C6-4E76-83AB-8201649D237C@ehu.es>
References: <B91C24D7-87C6-4E76-83AB-8201649D237C@ehu.es>
Message-ID: <3CC6DE9C-60C3-4C07-A01C-FEB64655A1F4@nest.sns.it>

On May 15, 2007, at 18:11 , Aritz Leonardo Liceranzu wrote:

> I am drawing the some projected states and I would like somebody to  
> confirm the following about the output:
>
> l=1 m=1 --> factor*(z/r)
> l=1 m=2 --> factor*(x/r)
> l=1 m=3 --> factor*(y/r)
>
> l=2 m=1 --> factor*(-1+z2/r2)
> l=2 m=2 --> factor*(xz/r2)
> l=2 m=3 --> factor*(yz/r2)

this doesn't sound new to me: in fact it is even in the FAQ
http://www.quantum-espresso.org/wiki/index.php/ 
Frequently_Asked_Questions
towards the end

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




From mmarques at staffmail.ed.ac.uk  Tue May 15 19:24:52 2007
From: mmarques at staffmail.ed.ac.uk (Miriam Marques)
Date: Tue, 15 May 2007 18:24:52 +0100
Subject: [Pw_forum] Redhat linux PCs ESPRESSO compilation
In-Reply-To: <9A133B3F-2F02-4665-9D73-D1AE90C945E3@nest.sns.it>
References: <20070511161139.0mticjfbggw4kcsc@www.staffmail.ed.ac.uk>
	<9A133B3F-2F02-4665-9D73-D1AE90C945E3@nest.sns.it>
Message-ID: <20070515182452.xzu746qps0o4o0wo@www.staffmail.ed.ac.uk>

  Dear PWSCF users,

  I have also tried to compile ESPRESSO with g95, but it is also unable
  to detect the internal FFTW library. In the make.sys the line FFT_LIBS is
empty as well as the line corresponding to the pgplot libraries and MPI_LIBS.
  I was trying to install a fftw-2.1.5 library (I downloaded it from  
http://www.fftw.org), but I do not know if it is suitable for Redhat  
linux
Writing locate, linux is unable to detect it.

Executing make pw, the following error appears:

In file path_io_routines.F90:430

              CALL spline_interpolation( pos,      1, nim, nim_inp )
                   1
Error: Cannot CALL procedure 'spline_interpolation' that returns a type at (1)
In file path_io_routines.F90:431

              CALL spline_interpolation( pes,      1, nim, nim_inp )
                   1
Error: Cannot CALL procedure 'spline_interpolation' that returns a type at (1)
In file path_io_routines.F90:432

              CALL spline_interpolation( grad_pes, 1, nim, nim_inp )
                   1
Error: Cannot CALL procedure 'spline_interpolation' that returns a type at (1)
In file path_io_routines.F90:436

                 CALL spline_interpolation( posold, 1, nim, nim_inp )
                      1
Error: Cannot CALL procedure 'spline_interpolation' that returns a type at (1)
make[1]: *** [path_io_routines.o] Error 1
make[1]: Leaving directory `/phys/linux/mmarques/espresso-3.2/Modules'
make: *** [mods] Error 2

And, including the external library, the same problem remains.

Thank you very much,

Miriam.


Quoting Paolo Giannozzi <giannozz at nest.sns.it>:

>
> On May 11, 2007, at 17:11 , Miriam Marques wrote:
>
>> I am using the NagWare f95 compiler (but I have also tried with the  
>>  gfortran compiler).
>
> gfortran doesn't work (or at least it didn't the last time I tried).  
>  If you do
> not manage to have NagWare f95 working, try g95.
>
>> When I write ./configure it seems to work, but it is unable to   
>> detect FFTW libraries.
>
> FFTW v.3 are not detected by configure. If nothing is found, the internal
> library is used. I never observed any significant speedup from external
> fftw libraries.
>>
>> f95 -O -D__FFTW -D__USE_INTERNAL_FFTW -I../include  -I./    
>> -I../Modules -I../iotk/src -I../PW  -I../PH  -I../CPV -c   
>> iotk_base.F90 -o iotk_base.o
>> Error: iotk_base.F90, line 1: syntax error
>>       detected at end of file
>> ***Malformed statement
>
> an empty or bad file has been created by the previous failed attempt.
> "make clean" first
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum





From konstantin_kudin at yahoo.com  Tue May 15 20:30:48 2007
From: konstantin_kudin at yahoo.com (Konstantin Kudin)
Date: Tue, 15 May 2007 11:30:48 -0700 (PDT)
Subject: [Pw_forum] Single precision FFTs on GPUs for QE ?
In-Reply-To: <Pine.LNX.4.44.0705151159100.12088-100000@localhost.localdomain>
Message-ID: <165505.22506.qm@web57701.mail.re3.yahoo.com>

--- Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu> wrote:

> On Tue, 15 May 2007, Konstantin Kudin wrote:
> 
> hi kostya,
> 
> i would suggest waiting until the end of summer as nvidia is
> supposed to release cards that actually can handle double precision
> (and will have accellerated FFT _and_ BLAS).

 Axel,

 Thanks for the note! I was not aware that the double precision GPU
hardware was so close. It then seems that reasonably soon the cluster
money previously used on the interconnect will seemlessly flow into the
graphics boards. :-)

 Kostya


       
____________________________________________________________________________________
Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games.
http://sims.yahoo.com/  


From akohlmey at cmm.chem.upenn.edu  Tue May 15 20:46:22 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 15 May 2007 14:46:22 -0400 (EDT)
Subject: [Pw_forum] Single precision FFTs on GPUs for QE ?
In-Reply-To: <165505.22506.qm@web57701.mail.re3.yahoo.com>
Message-ID: <Pine.LNX.4.44.0705151443580.12088-100000@localhost.localdomain>

On Tue, 15 May 2007, Konstantin Kudin wrote:

KK> > supposed to release cards that actually can handle double precision
KK> > (and will have accellerated FFT _and_ BLAS).
KK> 
KK>  Axel,
KK> 
KK>  Thanks for the note! I was not aware that the double precision GPU
KK> hardware was so close. It then seems that reasonably soon the cluster
KK> money previously used on the interconnect will seemlessly flow into the
KK> graphics boards. :-)

naaaw, faster computation will need even faster communication, 
so you'll need both. but unlike the interconnect, you can recycle 
the graphics boards for visualization once they are obsolete 
for computation. so in a couple of years everybody will have
excellent 3d-graphics on the desktop. :-)

a.

KK> 
KK>  Kostya
KK> 
KK> 
KK>        
KK> ____________________________________________________________________________________
KK> Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games.
KK> http://sims.yahoo.com/  
KK> _______________________________________________
KK> Pw_forum mailing list
KK> Pw_forum at pwscf.org
KK> http://www.democritos.it/mailman/listinfo/pw_forum
KK> 

-- 
=======================================================================
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 aryjunior at gmail.com  Wed May 16 02:18:08 2007
From: aryjunior at gmail.com (Ary Junior)
Date: Tue, 15 May 2007 21:18:08 -0300
Subject: [Pw_forum] Running the examples
Message-ID: <4c9c61c20705151718x591ad832y3023241a62d25637@mail.gmail.com>

Hi, I'm trying to run the examples included on espresso-3.2. I have a Intel
Xeon 64 bits processor and I've used the Make.pc_ifc for compilation. When I
execute "run_examples" I get:

...
  running the scf calculation...At line 103 of file error.f90
Traceback: not available, compile with -ftrace=frame or -ftrace=full
STOP 2
 done
...

For all the examples. How can I solve it?

Thanks very much!

Ary Junior
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From giannozz at nest.sns.it  Wed May 16 09:55:10 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 16 May 2007 09:55:10 +0200
Subject: [Pw_forum] Running the examples
In-Reply-To: <4c9c61c20705151718x591ad832y3023241a62d25637@mail.gmail.com>
References: <4c9c61c20705151718x591ad832y3023241a62d25637@mail.gmail.com>
Message-ID: <02F94C31-2F46-48AE-BAB6-136C4F2AAABF@nest.sns.it>

On May 16, 2007, at 2:18 , Ary Junior wrote:

> When I execute "run_examples" I get:
> ...
>   running the scf calculation...At line 103 of file error.f90
> Traceback: not available, compile with -ftrace=frame or -ftrace=full
> STOP 2
>  done
> ...
>
> For all the examples. How can I solve it?

look into the output
---
Paolo Giannozzi, Democritos and University of Udine, Italy




From giannozz at nest.sns.it  Wed May 16 09:59:25 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 16 May 2007 09:59:25 +0200
Subject: [Pw_forum] Redhat linux PCs ESPRESSO compilation
In-Reply-To: <20070515182452.xzu746qps0o4o0wo@www.staffmail.ed.ac.uk>
References: <20070511161139.0mticjfbggw4kcsc@www.staffmail.ed.ac.uk> <9A133B3F-2F02-4665-9D73-D1AE90C945E3@nest.sns.it> <20070515182452.xzu746qps0o4o0wo@www.staffmail.ed.ac.uk>
Message-ID: <42EB050B-923B-49A3-8244-A2D58246010E@nest.sns.it>

On May 15, 2007, at 19:24 , Miriam Marques wrote:

>  I have also tried to compile ESPRESSO with g95, but it is also unable
>  to detect the internal FFTW library.

this is not a problem: the code will load the internal FFTW library

> Executing make pw, the following error appears:
>
> In file path_io_routines.F90:430
>
>              CALL spline_interpolation( pos,      1, nim, nim_inp )
>                   1
> Error: Cannot CALL procedure 'spline_interpolation' that returns a  
> type at (1)

'make clean' first. If the error persists, check the version of your
g95 compiler (g95 -v) . Try the stable version (0.9).

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




From xu11249249 at gmail.com  Wed May 16 16:22:24 2007
From: xu11249249 at gmail.com (xu yuehua)
Date: Wed, 16 May 2007 22:22:24 +0800
Subject: [Pw_forum] Single precision FFTs on GPUs for QE ?
In-Reply-To: <566770.25127.qm@web57714.mail.re3.yahoo.com>
References: <1179239421.3203.4.camel@cryptonomicon>
	 <566770.25127.qm@web57714.mail.re3.yahoo.com>
Message-ID: <426b166e0705160722s73c6d7c8n7ec4ee63aa7d9007@mail.gmail.com>

can you help me about downloading the
http://www.democritos.it/pipermail/pw_forum/     the full raw archive ( 31
MB )
i can not get it now.i am in a hurry to use it .thanks


2007/5/16, Konstantin Kudin <konstantin_kudin at yahoo.com>:
>
> Hi all,
>
> With all the hype surrounding the recent graphics cards and how fast
> they are supposed to be, the following question arises.
>
> If QE were to do everything in double precision, but the FFTs in
> single precision, will it hurt too much? FFTs kind of do few
> operations, so the error accumulation could be tolerable. Of course,
> another issue if the few digits of single precision are really enough
> ...
>
> With multicore cpus it is increasingly difficult to transfer the data
> between the boxes for FFTs, it sure would be easier (in principle) to
> send the data locally to the super fast (tm) GPU.
>
> Anyway, from the implementation perspective, FFTs are currectly
> reasonably well localized in the code, so in principle the hassle of
> using GPUs would be only local in terms of coding :-)
>
> Ideas?
>
> Kostya
>
>
>
> ____________________________________________________________________________________Give
> spam the boot. Take control with tough spam protection in the all-new Yahoo!
> Mail Beta.
> http://advision.webevents.yahoo.com/mailbeta/newmail_html.html
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
lalala lalala
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From daijiayu at nudt.edu.cn  Thu May 17 14:17:39 2007
From: daijiayu at nudt.edu.cn (=?gb2312?B?tPe80e7a?=)
Date: Thu, 17 May 2007 20:17:39 +0800
Subject: [Pw_forum] where can i find the code VDW?
Message-ID: <379404259.21643@nudt.edu.cn>

Dear users,
     When i complete the installaion of Quantum-espresso, i find i can no find the
program vdw.x. And i can not find the directory of VDW. So, where can i find it?
 Thank you very much.

Jiayu




From wmbmacam at lg.ehu.es  Thu May 17 16:30:25 2007
From: wmbmacam at lg.ehu.es (=?UTF-8?B?TWlndWVsIE1hcnTDrW5leiBDYW5hbGVz?=)
Date: Thu, 17 May 2007 16:30:25 +0200
Subject: [Pw_forum] Na phonon issues
Message-ID: <464C6701.7040501@lg.ehu.es>

Dear folks,

I've been doing some phonon calculations on Na lately, and I've got an 
issue with the Na.pw91-n-mt.UPF pseudopotential. Well, it might be an issue 
with the input, so I also attach them.

When doing a phonon calculation at q=(0 -0.1 0.1) for bcc Na, which is the 
same as na.dyn2 in the enclosed input, I get the following frequencies:

$ tail na.dyn2
      q = (    0.000000000  -0.100000000   0.100000000 )

  **************************************************************************
      omega( 1) =      -0.102259 [THz] =      -3.411026 [cm-1]
  (  0.000000  0.000000 -0.707107  0.000000 -0.707107  0.000000 )
      omega( 2) =       0.766410 [THz] =      25.564857 [cm-1]
  (  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000 )
      omega( 3) =       1.171147 [THz] =      39.065511 [cm-1]
  (  0.000000  0.000000 -0.707107  0.000000  0.707107  0.000000 )
  **************************************************************************

If I use the LDA pseudo Na.pz-n-vbc.UPF near equilibrium (a=7.738a_0) with 
ecut=30 Ry and 18 18 18 shifted M-P grid, I get the following omegas:
      omega( 1) =       0.273215 [THz] =       9.113532 [cm-1]
      omega( 2) =       0.835358 [THz] =      27.864728 [cm-1]
      omega( 3) =       1.264994 [THz] =      42.195940 [cm-1]

While the Na.pbe-sp-van_ak.UPF pseudo, with the same grid as the enclosed 
input (20 20 20 shifted M-P), ecut=35 and ecutrho=300 Ry, I get also 
sensible results (with 7.932 a_0 as lattice parametre):
      omega( 1) =       0.390200 [THz] =      13.015753 [cm-1]
      omega( 2) =       0.857166 [THz] =      28.592182 [cm-1]
      omega( 3) =       1.238921 [THz] =      41.326237 [cm-1]

So I have the following question: Is the mechanical instability I see a 
product of my input or a product of the pseudopotential?

Thanks a lot,

Miguel


============= input follows ==============
# self-consistent run
cat > na.scf.in << EOF
  &control
     calculation='scf'
     restart_mode='from_scratch',
     tstress = .true.
     tprnfor = .true.
     prefix='na',
     pseudo_dir = '$PSEUDO_DIR/',
     outdir='$TMP_DIR/'
  /
  &system
     ibrav=  3, celldm(1) = 7.8956 , nat=  1, ntyp= 1,
     ecutwfc = 35.0,
     occupations='smearing', smearing='m-p', degauss= 0.010
  /
  &electrons
     conv_thr =  1.0d-8
     mixing_beta = 0.7
  /
ATOMIC_SPECIES
  Na  22.989768  Na.pw91-n-mt.UPF
ATOMIC_POSITIONS
  Na 0.00 0.00 0.00
K_POINTS {automatic}
  20 20 20   1 1 1
EOF


# phonon calculation
cat > na.ph.in << EOF
phonons of Na
  &inputph
   tr2_ph=1.0d-16,
   prefix='na',
   ldisp=.true.,
   nq1=10, nq2=10, nq3=10
   amass(1)=22.989768,
   outdir='$TMP_DIR/',
   fildyn='na.dyn',
  /
EOF


-- 
----------------------------------------
Miguel Mart?nez Canales
Dto. F?sica de la Materia Condensada
UPV/EHU
Facultad de Ciencia y Tecnolog?a
Apdo. 644
48080 Bilbao (Spain)
Fax:  +34 94 601 3500
Tlf:  +34 94 601 5437
----------------------------------------

  "If you have an apple and I have an apple and
  we exchange these apples then you and I will
  still each have one apple. But if you have an
  idea and I have an idea and we exchange these
  ideas, then each of us will have two ideas."

    George Bernard Shaw



From marzari at MIT.EDU  Thu May 17 16:37:10 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 17 May 2007 10:37:10 -0400
Subject: [Pw_forum] Na phonon issues
In-Reply-To: <464C6701.7040501@lg.ehu.es>
References: <464C6701.7040501@lg.ehu.es>
Message-ID: <464C6896.7030605@mit.edu>

Miguel Mart?nez Canales wrote:
> Dear folks,


Dear Miguel,

search the archives, for negative phonon .

			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 matteo at umn.edu  Thu May 17 16:42:58 2007
From: matteo at umn.edu (Matteo Cococcioni)
Date: Thu, 17 May 2007 09:42:58 -0500
Subject: [Pw_forum] MgFeO LDA+U convergence problem
In-Reply-To: <1179239421.3203.4.camel@cryptonomicon>
References: <1179069751.5546.20.camel@cryptonomicon>	 <464876D7.40004@umn.edu> <1179239421.3203.4.camel@cryptonomicon>
Message-ID: <464C69F2.1020506@umn.edu>


Dear Sasha,

I'm not sure you got my reply (the message seemed to be too big for some 
reasons...) so I will try again.

I think you can get a good idea on how to choose the starting 
occupations looking at the eigenvectors of the occupation matrix (from the
first iteration). another thing you can do is decrease the initial 
magnetization on atoms 1 and 2 (that seem the most problematic ones): 
try to use
for example 0.4 and -0.3.

hope this helps.

Matteo



sasha wrote:
> Greetings Matteo,
> 	Thanks for the advice, your suggestion in fact works very well.  It
> turns out that I should have more closely examined my input.  I have
> another quick question regarding the starting_ns_eigenvalue, in the
> previous example (below) from the eigenvalues at the first iteration of
> the "standard" lda+u calculation it is clear how to set the
> ns_eigenvalues however what does one do if the starting eigenvalues are
> as follows:
>
> atom  1  spin  1   0.9985560 0.9998587 1.0007556 1.0013322 1.0057882
> atom  1  spin  2   0.0484071 0.0493657 0.0578860 0.1216687 0.1308162 
>
> atom  2  spin  1   0.0535213 0.0592929 0.1256650 0.1321563 0.1439048 
> atom  2  spin  2   0.9979128 0.9993943 1.0004671 1.0010265 1.0058542
>
> atom  3  spin  1   0.9947113 0.9953027 0.9992115 0.9997585 1.0044052
> atom  3  spin  2   0.0693133 0.1280564 0.1459512 0.1547219 0.4858838
>
> atom  4  spin  1   0.0637767 0.0681158 0.1421888 0.1436934 0.2272403 
> atom  4  spin  2   0.9965028 0.9979222 0.9991654 1.0005289 1.0054916
>
> where only some of the eigenvalues for certain atoms and spins are
> degenerate?  Once again thank you in advance for any advice or
> suggestions.
> regards,
> 	Sasha
> On Mon, 2007-05-14 at 09:48 -0500, Matteo Cococcioni wrote:
>   
>

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From eyvaz_isaev at yahoo.com  Thu May 17 16:54:32 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 17 May 2007 07:54:32 -0700 (PDT)
Subject: [Pw_forum] Running the examples
In-Reply-To: <4c9c61c20705151718x591ad832y3023241a62d25637@mail.gmail.com>
Message-ID: <831507.55162.qm@web60315.mail.yahoo.com>

Hi,

Did you try ./Configure before Make.pc_ifc? The latter
seems to be for 32bits Intel CPUs (see $LIBS in the
makefile), but you have 64bits one.

Bests,
Eyvaz.

--- Ary Junior <aryjunior at gmail.com> wrote:

> Hi, I'm trying to run the examples included on
> espresso-3.2. I have a Intel
> Xeon 64 bits processor and I've used the Make.pc_ifc
> for compilation. When I
> execute "run_examples" I get:
> 
> ...
>   running the scf calculation...At line 103 of file
> error.f90
> Traceback: not available, compile with -ftrace=frame
> or -ftrace=full
> STOP 2
>  done
> ...
> 
> For all the examples. How can I solve it?
> 
> Thanks very much!
> 
> Ary Junior
> 



       
____________________________________________________________________________________Pinpoint customers who are looking for what you sell. 
http://searchmarketing.yahoo.com/


From eyvaz_isaev at yahoo.com  Thu May 17 17:25:53 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 17 May 2007 08:25:53 -0700 (PDT)
Subject: [Pw_forum] where can i find the code VDW?
In-Reply-To: <379404259.21643@nudt.edu.cn>
Message-ID: <903889.21484.qm@web60319.mail.yahoo.com>

Hi,

Try CVS version of the code. Read README.cvs how to
get it.

Bests,
Eyvaz.
 

--- ?????? <daijiayu at nudt.edu.cn> wrote:

> Dear users,
>      When i complete the installaion of
> Quantum-espresso, i find i can no find the
> program vdw.x. And i can not find the directory of
> VDW. So, where can i find it?
>  Thank you very much.
> 
> Jiayu
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 



 
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From wmbmacam at lg.ehu.es  Thu May 17 17:56:30 2007
From: wmbmacam at lg.ehu.es (=?UTF-8?B?TWlndWVsIE1hcnTDrW5leiBDYW5hbGVz?=)
Date: Thu, 17 May 2007 17:56:30 +0200
Subject: [Pw_forum] Na phonon issues
In-Reply-To: <464C6896.7030605@mit.edu>
References: <464C6701.7040501@lg.ehu.es> <464C6896.7030605@mit.edu>
Message-ID: <464C7B2E.8040604@lg.ehu.es>

Nicola Marzari escribi?:
> Dear Miguel,
> 
> search the archives, for negative phonon .

Dear Nicola,

thanks for your advice. I've been reading this, as well as the 
troubleshooting part of the manual. Please note that I am *not* talking 
about \Gamma. I have, then, increased the K_POINTS to 30 30 30, which seems 
pretty dense to me, unless I were to do electron-phonon calculations. This 
still yields the following omegas:
      omega( 1) =      -0.102074 [THz] =      -3.404853 [cm-1]
      omega( 2) =       0.766422 [THz] =      25.565257 [cm-1]
      omega( 3) =       1.200480 [THz] =      40.043969 [cm-1]

These aren't really that different from the ones I got with a 20 20 20 grid 
(although the longitudinal mode is 2.5% higher). Just in case, I'm running 
the script with an increased degauss value, because it's a bit too small.

The thing is, the pseudopotential is norm-conserving (or so it says on the 
header), and thus it's not an issue of not setting ecutrho. And the 
positive values are close to the numbers I get with the other pseudos. I am 
also reading the correct file, as I delete the temporary dir at the 
beginning and the end of my script. Am I being to harsh or lenient with the 
phonon threshold?

Thanks again for your comments,

Miguel

-- 
----------------------------------------
Miguel Mart?nez Canales
Dto. F?sica de la Materia Condensada
UPV/EHU
Facultad de Ciencia y Tecnolog?a
Apdo. 644
48080 Bilbao (Spain)
Fax:  +34 94 601 3500
Tlf:  +34 94 601 5437
----------------------------------------

  "If you have an apple and I have an apple and
  we exchange these apples then you and I will
  still each have one apple. But if you have an
  idea and I have an idea and we exchange these
  ideas, then each of us will have two ideas."

    George Bernard Shaw



From marzari at MIT.EDU  Thu May 17 18:20:04 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 17 May 2007 12:20:04 -0400
Subject: [Pw_forum] Na phonon issues
In-Reply-To: <464C7B2E.8040604@lg.ehu.es>
References: <464C6701.7040501@lg.ehu.es> <464C6896.7030605@mit.edu> <464C7B2E.8040604@lg.ehu.es>
Message-ID: <464C80B4.60108@mit.edu>


Dear Miguel,

I do not think we have ever managed, even for very high-thresholds
everywhere , to converge the lowest frequencies so that at Gamma
or close to Gamma they would come out "right" in a direct phononq
calculation. In other words, it does seem that the converged values that
phonon gives, for the lowest frequency at Gamma or nearby, it's not the
value that you would expect, i.e. sitting on a linear dispersion from
Gamma, with slopes determined by the elastic constants (if the q is on
a high symmetry direction).

Diamond carbon was the worst case, with a converged value at Gamma that
(if I recall correctly - Nicola B ?) could be anywhere between -10
and 50 cm^-1 , depending on the pseudo (note that these numbers are
small, compared to the optical frequencies of diamond, around 1500
cm-1).

Why is that ? Not sure - Stefano de Gironcoli advice was to try
and remove the xc part, to see if that was the culprit, but we never
tried.

The only solution is to calculate the dynamical matrix explicitly on a
homogeneous q grid that is not too fine (so that the q closest to gamma
but not gamma has all frequencies well converged), then transform in
real space, impose acoustic sum rules, and then obtain the phonon
dispersions everywhere from the fourier transform and diagonalization of 
the interatomic force constants.

But it's true that it's only partially satisfactory, and I wouldn't mind
figuring out a solution, especially because accurate results at long
wavelengths are very important for thermal transport.

One additional note about worst case scenarios: when two dispersions are 
degenerate, but maybe numerically slightly different, we found an 
instability in the back-transform (I think because diagonalization and 
ft do not commute) with the two degenerate branches being degenerate at 
the original q's, and mostly everywhere, but with one of the two
displaying a infinite derivative at a critical q close to gamma, in 
between gamma and one of the original q's. This was the case for CNTs.

				nicola



> Dear Nicola,
> 
> thanks for your advice. I've been reading this, as well as the 
> troubleshooting part of the manual. Please note that I am *not* talking 
> about \Gamma. I have, then, increased the K_POINTS to 30 30 30, which 
> seems pretty dense to me, unless I were to do electron-phonon 
> calculations. This still yields the following omegas:
>      omega( 1) =      -0.102074 [THz] =      -3.404853 [cm-1]
>      omega( 2) =       0.766422 [THz] =      25.565257 [cm-1]
>      omega( 3) =       1.200480 [THz] =      40.043969 [cm-1]
> 
> These aren't really that different from the ones I got with a 20 20 20 
> grid (although the longitudinal mode is 2.5% higher). Just in case, I'm 
> running the script with an increased degauss value, because it's a bit 
> too small.
> 
> The thing is, the pseudopotential is norm-conserving (or so it says on 
> the header), and thus it's not an issue of not setting ecutrho. And the 
> positive values are close to the numbers I get with the other pseudos. I 
> am also reading the correct file, as I delete the temporary dir at the 
> beginning and the end of my script. Am I being to harsh or lenient with 
> the phonon threshold?
> 
> Thanks again for your comments,
> 
> Miguel
> 


-- 
---------------------------------------------------------------------
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 ongphuongvu at yahoo.com  Fri May 18 10:14:47 2007
From: ongphuongvu at yahoo.com (vu ongphuong)
Date: Fri, 18 May 2007 01:14:47 -0700 (PDT)
Subject: [Pw_forum] Compilation Problem
Message-ID: <257234.96962.qm@web50604.mail.re2.yahoo.com>

Dear users,
   
  During install PWSCF, I encounter the following error message:
   
  cpp -P -traditional -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include  wannier.f90 -o wannier.F90 
  
wannier.f90:8: #include expects "fname" or <fname>
make[1]: *** [wannier.o] Error 1
make[1]: Leaving directory `/home2/x190ljc/opvu/PWscf/espresso-3.2/Modules'
   
  Please help me fix this error.
   
  Thank you very much,
   
  O.P. Vu

 __________________________________________________
Do You Yahoo!?
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From wmbmacam at lg.ehu.es  Fri May 18 12:00:37 2007
From: wmbmacam at lg.ehu.es (=?UTF-8?B?TWlndWVsIE1hcnTDrW5leiBDYW5hbGVz?=)
Date: Fri, 18 May 2007 12:00:37 +0200
Subject: [Pw_forum] Na phonon issues
In-Reply-To: <464C80B4.60108@mit.edu>
References: <464C6701.7040501@lg.ehu.es> <464C6896.7030605@mit.edu> 	<464C7B2E.8040604@lg.ehu.es> <464C80B4.60108@mit.edu>
Message-ID: <464D7945.1000504@lg.ehu.es>

Dear Nicola,

Thank you very much for your detailed answer, I am very grateful indeed. I 
didn't know there would be such issues outside gamma, and was further 
mislead by the fact that the other pseudopotentials seemed to give a 
similar and sensible answer.

Nicola Marzari escribi?:
> The only solution is to calculate the dynamical matrix explicitly on a
> homogeneous q grid that is not too fine (so that the q closest to gamma
> but not gamma has all frequencies well converged), then transform in
> real space, impose acoustic sum rules, and then obtain the phonon
> dispersions everywhere from the fourier transform and diagonalization of 
> the interatomic force constants.

What would one do in case long range effects are not negligible? For 
example, fcc Li at 30 GPa has a soft phonon in the \Gamma-K branch. 
Reproducing it via the IFC matrix seems to require a not so coarse q point 
grid. What would one do? Calculate the elastic constants from classic 
lattice distortions? Introduce phonons from the soft region to include in 
the q2r.x list? Forget about getting accurate or even physical results with 
matdyn?

> One additional note about worst case scenarios: when two dispersions are 
> degenerate, but maybe numerically slightly different, we found an 
> instability in the back-transform (I think because diagonalization and 
> ft do not commute) with the two degenerate branches being degenerate at 
> the original q's, and mostly everywhere, but with one of the two
> displaying a infinite derivative at a critical q close to gamma, in 
> between gamma and one of the original q's. This was the case for CNTs.

Oh, well, this gives another meaning to "treacherous computing". Thanks 
again for your kind answer,

Miguel

PS: Increasing the degauss only yielded negligible differences in the 
phonons at 0 1/10 1/10.

-- 
----------------------------------------
Miguel Mart?nez Canales
Dto. F?sica de la Materia Condensada
UPV/EHU
Facultad de Ciencia y Tecnolog?a
Apdo. 644
48080 Bilbao (Spain)
Fax:  +34 94 601 3500
Tlf:  +34 94 601 5437
----------------------------------------

  "If you have an apple and I have an apple and
  we exchange these apples then you and I will
  still each have one apple. But if you have an
  idea and I have an idea and we exchange these
  ideas, then each of us will have two ideas."

    George Bernard Shaw



From marzari at MIT.EDU  Fri May 18 12:13:40 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Fri, 18 May 2007 06:13:40 -0400
Subject: [Pw_forum] Na phonon issues
In-Reply-To: <464D7945.1000504@lg.ehu.es>
References: <464C6701.7040501@lg.ehu.es> <464C6896.7030605@mit.edu> 	<464C7B2E.8040604@lg.ehu.es> <464C80B4.60108@mit.edu> <464D7945.1000504@lg.ehu.es>
Message-ID: <464D7C54.3040701@mit.edu>

Miguel Mart?nez Canales wrote:

> What would one do in case long range effects are not negligible? For 
> example, fcc Li at 30 GPa has a soft phonon in the \Gamma-K branch. 
> Reproducing it via the IFC matrix seems to require a not so coarse q 
> point grid. What would one do? Calculate the elastic constants from 
> classic lattice distortions? Introduce phonons from the soft region to 
> include in the q2r.x list? Forget about getting accurate or even 
> physical results with matdyn?


Not exactly sure - but a P=0 calculation as discussed before
would give you the right phonon dispersions (with the acoustic
sum rules) say on the Gamma-K branch, and a phonon calculation
explicitly done on the Gamma-K line would give you a sense of the
numerical error at Gamma and outside Gamma.

So, you might discover that the error at Gamma for the lowest
frequency is 10 cm^-1, 10% outside gamma is 3 cm^-1, and 20%
outside gamma is 1 cm^-1.

This gives you a ballpark for what to do at P=30 GPa - i.e. what are
the q where the error is really small. Note that in this I'm making the 
implicit suggestion that the "errors" are taking place mostly at gamma 
due to the long-wavelength nature of the modes, and would not be there
at a finite q, even if the phonon frequencies were getting close to zero.

Also, you could use extrapolations from calculations at higher
pressures (where the phonon frequency would have gone strongly
imaginary, at a given q), to make sure it's all consistent.

Still, it would be great to understand what is the origin
ofthis discrepancy, and why it is not cured by increasing the
cutoffs and k-point sampling - rather converging smoothly to a non-zero
value.

			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 yukihiro_okuno at fujifilm.co.jp  Fri May 18 13:31:44 2007
From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp)
Date: Fri, 18 May 2007 20:31:44 +0900
Subject: [Pw_forum] problem LDA+U with Cr  ( In tabd.f90 )
Message-ID: <OF18024774.636A0552-ON492572DF.003DDFFF-492572DF.003F54C2@mta.fujifilm.co.jp>

Dear PWscf Users.

I'm now calculating the magnetic system with Cr ion, and
want to use LDA+U for Cr.
But the error occurs in the calculation.

The error says that
"initial potential from superposition of free atoms"
###
from tabd
pseudo potential not yet inseted.

I see tabd.f90, and actually certain that  occ_loc is not defined for Cr.
Then, if i want to use Cr with LDA+U,  I must add Cr case in
tabd.f90 with occ_loc=5 ( with Cr occ_loc=5 ? the occupation Cr d
electron number), and recompile the pw.x ?

Sincerely.





From matteo at umn.edu  Fri May 18 16:59:59 2007
From: matteo at umn.edu (Matteo Cococcioni)
Date: Fri, 18 May 2007 09:59:59 -0500
Subject: [Pw_forum] problem LDA+U with Cr  ( In tabd.f90 )
In-Reply-To: <OF18024774.636A0552-ON492572DF.003DDFFF-492572DF.003F54C2@mta.fujifilm.co.jp>
References: <OF18024774.636A0552-ON492572DF.003DDFFF-492572DF.003F54C2@mta.fujifilm.co.jp>
Message-ID: <464DBF6F.2030406@umn.edu>


Dear Yukihiro,

yes this is exactly what you should do. you should also update 
set_hubbard_l.f90 and put Cr in the same group
of Fe and Ni. This is needed so that the code knows that the Hubbard 
orbitals of Cr are the d ones (l = 2).

Regards,

Matteo


yukihiro_okuno at fujifilm.co.jp wrote:
> Dear PWscf Users.
>
> I'm now calculating the magnetic system with Cr ion, and
> want to use LDA+U for Cr.
> But the error occurs in the calculation.
>
> The error says that
> "initial potential from superposition of free atoms"
> ###
> from tabd
> pseudo potential not yet inseted.
>
> I see tabd.f90, and actually certain that  occ_loc is not defined for Cr.
> Then, if i want to use Cr with LDA+U,  I must add Cr case in
> tabd.f90 with occ_loc=5 ( with Cr occ_loc=5 ? the occupation Cr d
> electron number), and recompile the pw.x ?
>
> Sincerely.
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   

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From ongphuongvu at yahoo.com  Fri May 18 17:43:16 2007
From: ongphuongvu at yahoo.com (vu ongphuong)
Date: Fri, 18 May 2007 08:43:16 -0700 (PDT)
Subject: [Pw_forum] Need help for compilation
Message-ID: <109291.95334.qm@web50608.mail.re2.yahoo.com>

Dear users,
   
  I use g95 for PWSCF compilation. Because I only have rights to work on my directory, I can not install g95 into /usr/local/. How can I make PWSCF know where is my g95? In other words, how to set path leading PWSCF to the g95 directory?
   
  Thank you very much for your help,
   
  O. P. Vu

       
---------------------------------
Got a little couch potato? 
Check out fun summer activities for kids.
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From wmbmacam at lg.ehu.es  Fri May 18 18:32:55 2007
From: wmbmacam at lg.ehu.es (=?ISO-8859-1?Q?Miguel_Mart=EDnez_Canales?=)
Date: Fri, 18 May 2007 18:32:55 +0200
Subject: [Pw_forum] Need help for compilation
In-Reply-To: <109291.95334.qm@web50608.mail.re2.yahoo.com>
References: <109291.95334.qm@web50608.mail.re2.yahoo.com>
Message-ID: <464DD537.4000406@lg.ehu.es>

Dear Vu,

If you are on a cluster, $HOME/bin is probably in your PATH, and moving the 
binary there would do it. Else, supposing you have the g95 binary in 
~/g95-install/bin, you could try the following (in bash):

export PATH=$PATH:~/g95-install/bin

However, these changes will only last for the current session. If you want 
these changes to persist, you should add it to your .bashrc file.

Another option is to kindly ask your "root" to install it systemwide (or 
ifort, for that matter).

vu ongphuong escribi?:
> Dear users,
>  
> I use g95 for PWSCF compilation. Because I only have rights to work on 
> my directory, I can not install g95 into /usr/local/. How can I make 
> PWSCF know where is my g95? In other words, how to set path leading 
> PWSCF to the g95 directory?
>  
> Thank you very much for your help,

-- 
----------------------------------------
Miguel Mart?nez Canales
Dto. F?sica de la Materia Condensada
UPV/EHU
Facultad de Ciencia y Tecnolog?a
Apdo. 644
48080 Bilbao (Spain)
Fax:  +34 94 601 3500
Tlf:  +34 94 601 5437
----------------------------------------

  "If you have an apple and I have an apple and
  we exchange these apples then you and I will
  still each have one apple. But if you have an
  idea and I have an idea and we exchange these
  ideas, then each of us will have two ideas."

    George Bernard Shaw



From eyvaz_isaev at yahoo.com  Sat May 19 00:57:20 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 18 May 2007 15:57:20 -0700 (PDT)
Subject: [Pw_forum] Need help for compilation
In-Reply-To: <109291.95334.qm@web50608.mail.re2.yahoo.com>
Message-ID: <278050.43685.qm@web60324.mail.yahoo.com>

Hi,

Quite easily. Have a look at your home directory and
find .basrc or .cshrc or something like that   
depending on your Unix (Linux) version. 
Just add your g95 binary directory to PATH, i.e. for
.bashrc

PATH=$PATH:/your_g95_bin_directory
export PATH

Then type "source .bashrc" and everything should work.

For your convinient make a link to g95 binary file
ln -s /your_g95_bin_path/g95_binary_file g95
Now g95 is a name for your compiler.

Bests,
Eyvaz.



--- vu ongphuong <ongphuongvu at yahoo.com> wrote:

> Dear users,
>    
>   I use g95 for PWSCF compilation. Because I only
> have rights to work on my directory, I can not
> install g95 into /usr/local/. How can I make PWSCF
> know where is my g95? In other words, how to set
> path leading PWSCF to the g95 directory?
>    
>   Thank you very much for your help,
>    
>   O. P. Vu
> 
>        
> ---------------------------------
> Got a little couch potato? 
> Check out fun summer activities for kids.



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


From helen at fh.huji.ac.il  Mon May 21 08:27:21 2007
From: helen at fh.huji.ac.il (Helen)
Date: Mon, 21 May 2007 09:27:21 +0300
Subject: [Pw_forum] example01 errors;conjugate-gradient algorithm;changing code functionals
Message-ID: <00e301c79b71$16c5cce0$cd604084@fh.huji.ac.il>

I have recently downloaded PWscf and I have several questions.

1. I have compiled PWscf and tried to run example01. During the running of 
espresso-3.2/bin/pw.x <si.scf.cg.in>si.scf.cg.out

I obtain the error message 

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

Stack trace terminated abnormally.

The output file seems fine but I cannot run the band program (si.bands.out):

from pp_check_file : error # 1

file /home2/helen/tmp/silicon.save not found

Any ideas about what is going wrong?

2. I would like to carry out an ion relax on an Si crystal. I see from INPUT_PW that the method is a quasi-Newton algorithm, is it possible to use a conjugate-gradient algorithm? Is the quasi-Newton algorithm efficient is the initial ion positions are not so close to the equilibrium structure?

3. I am exploring the possibility of running PWscf with modified functionals, specifically modifiying the exchange and correlation energy functionals to include a descreened two-body interaction. Is this possible? Which parts of the code include the functional forms? Which sub routines should be modified?

Thank you for your help,
Dr. Helen Eisenberg
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From akohlmey at cmm.chem.upenn.edu  Mon May 21 15:15:23 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 21 May 2007 09:15:23 -0400 (EDT)
Subject: [Pw_forum] example01 errors;conjugate-gradient algorithm;changing
 code functionals
In-Reply-To: <00e301c79b71$16c5cce0$cd604084@fh.huji.ac.il>
Message-ID: <Pine.LNX.4.44.0705210903040.6382-100000@localhost.localdomain>

On Mon, 21 May 2007, Helen wrote:

helen,

HE> I have recently downloaded PWscf and I have several questions.
HE> 
HE> 1. I have compiled PWscf and tried to run example01. During the running of 
HE> espresso-3.2/bin/pw.x <si.scf.cg.in>si.scf.cg.out
HE> 
HE> I obtain the error message 
HE> 
HE> forrtl: severe (174): SIGSEGV, segmentation fault occurred
HE> 
HE> Stack trace terminated abnormally.
HE> 
HE> The output file seems fine but I cannot run the band program (si.bands.out):

is it really complete? 
did you compare with the reference output in the results directory?

HE> from pp_check_file : error # 1
HE> 
HE> file /home2/helen/tmp/silicon.save not found
HE> 
HE> Any ideas about what is going wrong?

it might be that your compiler miscompiled the iotk library.
what platform (os/cpu/compiler/libraries) are you running on?

HE> 2. I would like to carry out an ion relax on an Si crystal. I see
HE> from INPUT_PW that the method is a quasi-Newton algorithm, is it
HE> possible to use a conjugate-gradient algorithm? Is the quasi-Newton
HE> algorithm efficient is the initial ion positions are not so close to
HE> the equilibrium structure?

the damped dynamics should be pretty efficient in 
that situation. you can switch to BFGS later.

HE> 3. I am exploring the possibility of running PWscf with modified
HE> functionals, specifically modifiying the exchange and correlation
HE> energy functionals to include a descreened two-body interaction. Is
HE> this possible? Which parts of the code include the functional forms?
HE> Which sub routines should be modified?

there are several places related to functionals. also pseudopotentials
have to be consistent with the functionals. i would start by looking
at the file Modules/functionals.f90 (which is pretty good commented) 
and then at flib/functionals.f90, flib/lsda_functionals.f90, and 
flib/more_functionals.f90 which provide the low level implementations.

cheers,
   axel.

HE> Thank you for your help, 
HE> Dr. Helen Eisenberg

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



From njuxuyuehua at gmail.com  Tue May 22 09:04:03 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Tue, 22 May 2007 15:04:03 +0800
Subject: [Pw_forum] phonon at G error : from phq_readin : error # 1 no elec. field with metals
Message-ID: <aca2feb20705220004m42e6a8e2w79b1db09b0c9f590@mail.gmail.com>

hello all
i am now compute the phonon calculation at G of h2o, but it has a error in
*out as following: i do not kown what is the meaning?would you tell me what
happened ?


Tue May 22 14:56:04 CST 2007

     Program PHONON    v.3.2    starts ...
     Today is 22May2007 at 14:56: 5

     Parallel version (MPI)

     Number of processors in use:       2
     R & G space division:  proc/pool =    2

     Ultrasoft (Vanderbilt) Pseudopotentials

     Planes per process (thick) : nr3 = 25 npp =  13 ncplane =32400

     Planes per process (smooth): nr3s= 20 npps=  10 ncplanes=18225

 Proc/  planes cols    G   planes cols    G    columns  G
 Pool       (dense grid)      (smooth grid)   (wavefct grid)
  1     13  10033 165487   10   6024  76934 1839  12969
  2     12  10032 165486   10   6025  76937 1840  12968
  0     25  20065 330973   20  12049 153871 3679  25937


     nbndx  =    24  nbnd   =    24  natomwfc =    30  npwx   =    9644
     nelec  =  40.00  nkb   =    50  ngl    =   44065

     negative rho (up, down):  0.367E-01 0.000E+00

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from phq_readin : error #         1
     no elec. field with metals
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
[0] MPI Abort by user Aborting program !
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From marzari at MIT.EDU  Tue May 22 09:15:11 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Tue, 22 May 2007 03:15:11 -0400
Subject: [Pw_forum] phonon at G error : from phq_readin : error # 1 no
 elec. field with metals
In-Reply-To: <aca2feb20705220004m42e6a8e2w79b1db09b0c9f590@mail.gmail.com>
References: <aca2feb20705220004m42e6a8e2w79b1db09b0c9f590@mail.gmail.com>
Message-ID: <4652987F.200@mit.edu>

xu yuehua wrote:
> hello all
> i am now compute the phonon calculation at G of h2o, but it has a error 
> in *out as following: i do not kown what is the meaning?would you tell 
> me what happened ?
>  
> 
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from phq_readin : error #         1
>      no elec. field with metals
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 


One possibility is that your calculation was set up as if it
were a metallic system, with fractional occupations and smearing.

Is this the case ?

As I've mentioned before, I'll stop answering to anyone
that doesn't sign their emails in full, with name and
affiliation.

				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 njuxuyuehua at gmail.com  Tue May 22 09:28:08 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Tue, 22 May 2007 15:28:08 +0800
Subject: [Pw_forum] phonon at G error : from phq_readin : error # 1 no elec. field with metals
In-Reply-To: <4652987F.200@mit.edu>
References: <aca2feb20705220004m42e6a8e2w79b1db09b0c9f590@mail.gmail.com>
	 <4652987F.200@mit.edu>
Message-ID: <aca2feb20705220028q35416ee3g15fdd014f48afc8c@mail.gmail.com>

yes,before pho calculation ,i have computed "scf" .the water. in is this
 &system
ibrav     = 0,
  nat       = 15,
  ntyp      = 2,
  ecutwfc   = 29.98744D0,
  ecutrho   =200
  occupations = "smearing",
  smearing    = "gauss",
  degauss     = 0.003D0,
if it is unsuitable ,i have no idea to use what occupations and so on
.please help me .thanks
my name is xu yuehua
affilation: physics depatment
 nanjing university china.




2007/5/22, Nicola Marzari <marzari at mit.edu>:
>
> xu yuehua wrote:
> > hello all
> > i am now compute the phonon calculation at G of h2o, but it has a error
> > in *out as following: i do not kown what is the meaning?would you tell
> > me what happened ?
> >
> >
>
> >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >      from phq_readin : error #         1
> >      no elec. field with metals
>
> >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>
> One possibility is that your calculation was set up as if it
> were a metallic system, with fractional occupations and smearing.
>
> Is this the case ?
>
> As I've mentioned before, I'll stop answering to anyone
> that doesn't sign their emails in full, with name and
> affiliation.
>
>                                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
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From marzari at MIT.EDU  Tue May 22 11:18:44 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Tue, 22 May 2007 05:18:44 -0400
Subject: [Pw_forum] phonon at G error : from phq_readin : error # 1 no
 elec. field with metals
In-Reply-To: <aca2feb20705220028q35416ee3g15fdd014f48afc8c@mail.gmail.com>
References: <aca2feb20705220004m42e6a8e2w79b1db09b0c9f590@mail.gmail.com>	 <4652987F.200@mit.edu> <aca2feb20705220028q35416ee3g15fdd014f48afc8c@mail.gmail.com>
Message-ID: <4652B574.1070504@mit.edu>

xu yuehua wrote:
> yes,before pho calculation ,i have computed "scf" .the water. in is this
>  &system
> ibrav     = 0,
>   nat       = 15,
>   ntyp      = 2,
>   ecutwfc   = 29.98744D0,
>   ecutrho   =200
>   occupations = "smearing",
>   smearing    = "gauss",
>   degauss     = 0.003D0,
> if it is unsuitable ,i have no idea to use what occupations and so on 
> .please help me .thanks



> my name is xu yuehua
> affilation: physics depatment
>  nanjing university china.

Dear Xu,

welcome to the gang.

There are two comments to make here - if you want your calculation to 
work, start by droppping the keywords for occupations, smearing, and
degauss. Those three are used for systems with fractional occupations -
these are typically metals, and that's why phonon stopped. By the
way, "Phonon" calculation for the water molecule and the water dimer
are available in a 2005 JCP by Sit and Marzari - you could compare your
results and parameters with those.

The second comment is that even completing your calculations 
successfully won't be very helpful, if you do not first become
experienced in this kind of calculations.

Now, I'm not sure what to suggest - there is a book on "Electronic
Structure" by Richard Martin that is outstanding, but a bit advanced.
A more introductory one has recently come out, by Jorge Kohanoff
("Electronic Structure Calculations for Solids and Molecules).

I might sound self-serving, but our graduate class on atomistic
modeling of materials (including video lectures, and pwscf homework),
is fully on the web, linked from
http://quasiamore.mit.edu/pmwiki/index.php?n=Main.Teaching ).
This class takes MIT students of different backgrounds, and that
have never seen computational modeling, through a basic knowledge
of the fundamentals.

				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 baroni at sissa.it  Tue May 22 11:51:42 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Tue, 22 May 2007 10:51:42 +0100
Subject: [Pw_forum] phonon at G error : from phq_readin : error # 1 no elec. field with metals
In-Reply-To: <4652987F.200@mit.edu>
References: <aca2feb20705220004m42e6a8e2w79b1db09b0c9f590@mail.gmail.com> <4652987F.200@mit.edu>
Message-ID: <FC9D04BE-1576-4D8C-ACBF-8F7D4DEE89C9@sissa.it>


On May 22, 2007, at 8:15 AM, Nicola Marzari wrote:

>
> As I've mentioned before, I'll stop answering to anyone
> that doesn't sign their emails in full, with name and
> affiliation.

I think the point raised by Nicola should be considered seriously. I  
think it a sign of politeness to sign one's correspondence, as well  
as it is much more pleasant to answer a question raised by somebody  
with a name, rather than by Mr/Ms Nobody. So, it should be in  
everyone's interest to sign one's correspondence in this forum.

May I suggest that everyone in this forum makes an effort to use a  
signature file such as the one appended below? It really takes no  
effort. Almost every mail client allows for a signature file to be  
automatically appended to every outgoing e-mail.

Cheers - 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 njuxuyuehua at gmail.com  Tue May 22 15:46:10 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Tue, 22 May 2007 21:46:10 +0800
Subject: [Pw_forum] phonon at G error : from phq_readin : error # 1 no elec. field with metals
In-Reply-To: <4652B574.1070504@mit.edu>
References: <aca2feb20705220004m42e6a8e2w79b1db09b0c9f590@mail.gmail.com>
	 <4652987F.200@mit.edu>
	 <aca2feb20705220028q35416ee3g15fdd014f48afc8c@mail.gmail.com>
	 <4652B574.1070504@mit.edu>
Message-ID: <aca2feb20705220646x76ff7020y9e3f1a0515c3b6b0@mail.gmail.com>

Dear Prof Nicola Marzari:
thank you for your help  , i am really grateful  i will read the paper and
book  you have recommended to me.
if there is some question about the paper i would like to consult with you
.Hope get your help .

Xu Yuehua

07.05.22


2007/5/22, Nicola Marzari <marzari at mit.edu>:
>
> xu yuehua wrote:
> > yes,before pho calculation ,i have computed "scf" .the water. in is this
> >  &system
> > ibrav     = 0,
> >   nat       = 15,
> >   ntyp      = 2,
> >   ecutwfc   = 29.98744D0,
> >   ecutrho   =200
> >   occupations = "smearing",
> >   smearing    = "gauss",
> >   degauss     = 0.003D0,
> > if it is unsuitable ,i have no idea to use what occupations and so on
> > .please help me .thanks
>
>
>
> > my name is xu yuehua
> > affilation: physics depatment
> >  nanjing university china.
>
> Dear Xu,
>
> welcome to the gang.
>
> There are two comments to make here - if you want your calculation to
> work, start by droppping the keywords for occupations, smearing, and
> degauss. Those three are used for systems with fractional occupations -
> these are typically metals, and that's why phonon stopped. By the
> way, "Phonon" calculation for the water molecule and the water dimer
> are available in a 2005 JCP by Sit and Marzari - you could compare your
> results and parameters with those.
>
> The second comment is that even completing your calculations
> successfully won't be very helpful, if you do not first become
> experienced in this kind of calculations.
>
> Now, I'm not sure what to suggest - there is a book on "Electronic
> Structure" by Richard Martin that is outstanding, but a bit advanced.
> A more introductory one has recently come out, by Jorge Kohanoff
> ("Electronic Structure Calculations for Solids and Molecules).
>
> I might sound self-serving, but our graduate class on atomistic
> modeling of materials (including video lectures, and pwscf homework),
> is fully on the web, linked from
> http://quasiamore.mit.edu/pmwiki/index.php?n=Main.Teaching ).
> This class takes MIT students of different backgrounds, and that
> have never seen computational modeling, through a basic knowledge
> of the fundamentals.
>
>                                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
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
-------------- next part --------------
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From cao at qtp.ufl.edu  Tue May 22 16:44:34 2007
From: cao at qtp.ufl.edu (Chao Cao)
Date: Tue, 22 May 2007 10:44:34 -0400
Subject: [Pw_forum] A question about electron phonon coupling calculation
Message-ID: <465301D2.6030003@qtp.ufl.edu>

I noticed that the manual pointed out el-ph coupling calculation is 
limited to metal systems only. I am curious about where this restriction 
comes from? Is it related with screening?

Thanks

Chao Cao

-- 
Chao Cao

Quantum Theory Project and Department of Physics
University of Florida, Gainesville, FL 32611
U.S.A.



From degironc at sissa.it  Tue May 22 18:00:55 2007
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Tue, 22 May 2007 18:00:55 +0200 (CEST)
Subject: [Pw_forum] A question about electron phonon coupling calculation
In-Reply-To: <465301D2.6030003@qtp.ufl.edu>
References: <465301D2.6030003@qtp.ufl.edu>
Message-ID: <Pine.LNX.4.64.0705221758520.29824@shannon-01.sissa.it>

because the code calculates the integral of the el-ph strength averaged 
on the Fermi surface.
stefano

On Tue, 22 May 2007, Chao Cao wrote:

> I noticed that the manual pointed out el-ph coupling calculation is limited 
> to metal systems only. I am curious about where this restriction comes from? 
> Is it related with screening?
>
> Thanks
>
> Chao Cao
>
>


From amos at errno.com  Tue May 22 18:30:26 2007
From: amos at errno.com (Amos Leffler)
Date: Tue, 22 May 2007 10:30:26 -0600
Subject: [Pw_forum] CPU  times
Message-ID: <46531AA2.1080700@errno.com>

Dear Forum,
       I am using SuSE Linux 10.2 and have found that it configures and 
compiles espresso-3.2 using the simple commands in the users' manual.  
The program appears to run properly with one curious exception. The CPU 
times that are listed during the calculations are incorrect and are 
always barely larger than zero.  The Wall times seem reasonable.  Where 
is the CPU time calculated and can this be changed?
                                                                         
            Amos Leffler


From w2agz at pacbell.net  Tue May 22 19:48:34 2007
From: w2agz at pacbell.net (Paul M. Grant)
Date: Tue, 22 May 2007 10:48:34 -0700
Subject: [Pw_forum] CPU  times
In-Reply-To: <46531AA2.1080700@errno.com>
References: <46531AA2.1080700@errno.com>
Message-ID: <00a601c79c99$6be81650$0301a8c0@w2agz>

Amos, I had the same problem with SUSE 10.1 and I got a fix from Paolo
Gianozzi.  I'm in the middle of a conference call right now and will send it
to you later...if Paolo doesn't beat me to it.  In the meantime, you might
try searching the forum 'cause it's posted there as well.

BTW, I hope all will follow Nicola Marzari's and Stefano Baroni's request to
add their affiliation to their forum traffic...something other than just
"gmail" and "yahoo."

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford University
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com
?
?


-----Original Message-----
From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] On Behalf
Of Amos Leffler
Sent: Tuesday, May 22, 2007 9:30 AM
To: pw_forum at pwscf.org
Subject: [Pw_forum] CPU times

Dear Forum,
       I am using SuSE Linux 10.2 and have found that it configures and 
compiles espresso-3.2 using the simple commands in the users' manual.  
The program appears to run properly with one curious exception. The CPU 
times that are listed during the calculations are incorrect and are 
always barely larger than zero.  The Wall times seem reasonable.  Where 
is the CPU time calculated and can this be changed?
                                                                         
            Amos Leffler
_______________________________________________
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 May 22 19:49:45 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 22 May 2007 13:49:45 -0400 (EDT)
Subject: [Pw_forum] CPU  times
In-Reply-To: <46531AA2.1080700@errno.com>
Message-ID: <Pine.LNX.4.44.0705221346210.6382-200000@localhost.localdomain>

On Tue, 22 May 2007, Amos Leffler wrote:

amos,

AL> Dear Forum,
AL>        I am using SuSE Linux 10.2 and have found that it configures and 
AL> compiles espresso-3.2 using the simple commands in the users' manual.  
AL> The program appears to run properly with one curious exception. The CPU 
AL> times that are listed during the calculations are incorrect and are 
AL> always barely larger than zero.  The Wall times seem reasonable.  Where 
AL> is the CPU time calculated and can this be changed?

it should be fixed in the cvs version (at least it was fixed for me
on several machines after i sent in the patch last november). the 
code is in clib/cptimer.c see attachement.

cheers,
  axel.

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

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
-------------- next part --------------
/*
  Copyright (C) 2002-2006 Quantum-Espresso group
  This file is distributed under the terms of the
  GNU General Public License. See the file `License'
  in the root directory of the present distribution,
  or http://www.gnu.org/copyleft/gpl.txt .
*/

#include <sys/time.h>
#include <sys/resource.h>
#include <unistd.h>

#include "c_defs.h"

double F77_FUNC(cclock,CCLOCK)()

/* Return the second elapsed since Epoch (00:00:00 UTC, January 1, 1970)
*/

{

    struct timeval tmp;
    double sec;
    gettimeofday( &tmp, (struct timezone *)0 );
    sec = tmp.tv_sec + ((double)tmp.tv_usec)/1000000.0;
    return sec;

}

double F77_FUNC(scnds,SCNDS) ( )

/* Return the cpu time associated to the current process 
*/

{
        static struct rusage T;

        getrusage(RUSAGE_SELF, &T);

        return ((double)T.ru_utime.tv_sec + ((double)T.ru_utime.tv_usec)/1000000.0);
}


From eyvaz_isaev at yahoo.com  Tue May 22 23:14:58 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 22 May 2007 14:14:58 -0700 (PDT)
Subject: [Pw_forum] Re: [Pw_forum]Papers
In-Reply-To: <FC9D04BE-1576-4D8C-ACBF-8F7D4DEE89C9@sissa.it>
Message-ID: <591861.24816.qm@web60315.mail.yahoo.com>

Hi,

I am pleased to inform you that I have 2 excellent
papers in PNAS (available online), and Journal of
Applied Physics (sheduled on June, 15) where all
calculations have been done by means of the
Quantum-Espresso code. 
My personal thanks to developers, and hopefully these
publications will rise interest in the code.

Here are publicaltions mentioned above:

1. Eyvaz I. Isaev, Natalia V. Skorodumova, Rajeev
Ahuja, Yuri K. Vekilov, and B?rje Johansson 
Dynamical stability of Fe-H in the Earth's mantle and
core regions, PNAS published May 4, 2007,
10.1073/pnas.0609701104 ( Geophysics , Special Feature
)

2. E.I. Isaev, S.I. Simak, I.A. Abrikosov, R. Ahuja,
A.I. Lichtenstein, Yu.Kh. Vekilov, M.I. Katsnelson, B.
Johansson, Phonon related properties of transition
metals, their carbides and nitrides: a
first-principles study, Journal of Applied Physics, in
press, 2007

Bests,
Eyvaz.

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


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


From marzari at MIT.EDU  Tue May 22 23:22:22 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Tue, 22 May 2007 17:22:22 -0400
Subject: [Pw_forum] Re: [Pw_forum]Papers
In-Reply-To: <591861.24816.qm@web60315.mail.yahoo.com>
References: <591861.24816.qm@web60315.mail.yahoo.com>
Message-ID: <46535F0E.70401@mit.edu>

Eyvaz Isaev wrote:
> Hi,
> 
> I am pleased to inform you that I have 2 excellent
> papers in PNAS (available online), and Journal of
> Applied Physics (sheduled on June, 15) where all
> calculations have been done by means of the
> Quantum-Espresso code. 


Dear Eyvaz,

congratulations ! This is an excellent opportunity to remind everyone
that one of the ways that users can give back to the community is
by keeping an updated list of papers published using espresso.

To do this, you need to request a wiki password to bonini at mit.edu , and
then add your papers to

http://www.quantum-espresso.org/wiki/index.php/Bibliography

following carefully e.g. the examples given in

http://www.quantum-espresso.org/wiki/index.php/2005

Again, it's not compulsory, but it's a way of giving back.

				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 eyvaz_isaev at yahoo.com  Wed May 23 00:23:46 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 22 May 2007 15:23:46 -0700 (PDT)
Subject: [Pw_forum] Re: [Pw_forum]Papers
In-Reply-To: <46535F0E.70401@mit.edu>
Message-ID: <432386.55691.qm@web60314.mail.yahoo.com>

Hi Nicola,

Thanks! I have just sent a request for a wiki
password.

Bests
Eyvaz.

--- Nicola Marzari <marzari at MIT.EDU> wrote:

> Eyvaz Isaev wrote:
> > Hi,
> > 
> > I am pleased to inform you that I have 2 excellent
> > papers in PNAS (available online), and Journal of
> > Applied Physics (sheduled on June, 15) where all
> > calculations have been done by means of the
> > Quantum-Espresso code. 
> 
> 
> Dear Eyvaz,
> 
> congratulations ! This is an excellent opportunity
> to remind everyone
> that one of the ways that users can give back to the
> community is
> by keeping an updated list of papers published using
> espresso.
> 
> To do this, you need to request a wiki password to
> bonini at mit.edu , and
> then add your papers to
> 
>
http://www.quantum-espresso.org/wiki/index.php/Bibliography
> 
> following carefully e.g. the examples given in
> 
> http://www.quantum-espresso.org/wiki/index.php/2005
> 
> Again, it's not compulsory, but it's a way of giving
> back.
> 
> 				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
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


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


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


From hashem.yamani at gmail.com  Wed May 23 08:45:13 2007
From: hashem.yamani at gmail.com (Hashem Al-Yamani)
Date: Wed, 23 May 2007 09:45:13 +0300
Subject: [Pw_forum] plotband variables meaning
Message-ID: <82a593400705222345m519f52c4gce23bf487448af7e@mail.gmail.com>

Dear All ;

In the example05 line number 236 - 241 it says to plot the band structure
for the Si :

sibands.dat
-6.0 10
sibands.xmgr
sibands.ps
6.255
1.0 6.255



What does these numbers and variables means ? Any one knows please and I
would be very thankful ....



Regards ;
Hashem
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From wmbmacam at lg.ehu.es  Wed May 23 09:14:40 2007
From: wmbmacam at lg.ehu.es (=?ISO-8859-1?Q?Miguel_Mart=EDnez_Canales?=)
Date: Wed, 23 May 2007 09:14:40 +0200
Subject: [Pw_forum] plotband variables meaning
In-Reply-To: <82a593400705222345m519f52c4gce23bf487448af7e@mail.gmail.com>
References: <82a593400705222345m519f52c4gce23bf487448af7e@mail.gmail.com>
Message-ID: <4653E9E0.3040109@lg.ehu.es>

Dear Hashem,

Hashem Al-Yamani escribi?:
> to plot the band structure for the Si :
> 
> sibands.dat
> -6.0 10
> sibands.xmgr
> sibands.ps 
> 6.255
> 1.0 6.255

First line is the output from running pp.x, that is, filband.

The second line defines the range of energies in which the energies will be 
plotted.

The third line specifies, if I'm not wrong, a file to write a simple ASCII 
output, easily visualized using programs such as xmgrace. The output, 
though, specifies it's just xmgrace format.

The fourth line is the filename for the PostScript output.

The fifth line is the Fermi energy.

The sixth line defines the delta E (i.e. the ticks in the graph) and the 
reference energy (E=0 in the graph).

This info is mostly available on the output, at results/si.plotband.out. 
You might also play with the values, to see what they affect. Also, the 
ticks and the fermi energy lines probably only affect the postscript file.

In short,

filband
Emin   Emax
xmgrace.output
output.ps
Efermi
deltaE E0

By the way, the forum would be grateful if you also included your current 
affiliation. I hope this helps,

Miguel



-- 
----------------------------------------
Miguel Mart?nez Canales
Dto. F?sica de la Materia Condensada
UPV/EHU
Facultad de Ciencia y Tecnolog?a
Apdo. 644
48080 Bilbao (Spain)
Fax:  +34 94 601 3500
Tlf:  +34 94 601 5437
----------------------------------------

  "If you have an apple and I have an apple and
  we exchange these apples then you and I will
  still each have one apple. But if you have an
  idea and I have an idea and we exchange these
  ideas, then each of us will have two ideas."

    George Bernard Shaw



From paulatto at sissa.it  Wed May 23 09:54:08 2007
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 23 May 2007 09:54:08 +0200 (CEST)
Subject: [Pw_forum] plotband variables meaning
In-Reply-To: <82a593400705222345m519f52c4gce23bf487448af7e@mail.gmail.com>
References: <82a593400705222345m519f52c4gce23bf487448af7e@mail.gmail.com>
Message-ID: <16736.80.183.42.64.1179906848.squirrel@webmail.sissa.it>

On Wed, May 23, 2007 08:45, Hashem Al-Yamani wrote:
> What does these numbers and variables means ? Any one knows please and I
> would be very thankful ....

The input is feed to the program plotband.x (which is part of QE). Run it
by hand and you will see what those numbers mean.

Bye

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


----------------------------------------------------------------
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From giannozz at nest.sns.it  Wed May 23 14:01:38 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 23 May 2007 14:01:38 +0200
Subject: [Pw_forum] CPU  times
In-Reply-To: <Pine.LNX.4.44.0705221346210.6382-200000@localhost.localdomain>
References: <Pine.LNX.4.44.0705221346210.6382-200000@localhost.localdomain>
Message-ID: <5FE3AF84-0DF1-4071-BBBE-77806A0E9D2D@nest.sns.it>

On May 22, 2007, at 19:49 , Axel Kohlmeyer wrote:

> it should be fixed in the cvs version (at least it was fixed for me
> on several machines after i sent in the patch last november). the
> code is in clib/cptimer.c see attachement.

also in the 3.2.1 patch, available from www.pwscf.org, in the
download page. From the espresso root directory, one should
execute: patch -p1 < espresso-3.2.1.diff (assuming that the
diff file is in the same directory). There is a 3.2.2 patch as well
(to be installed aftre the 3.2.1 patch)

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




From niuli1978 at yahoo.com.cn  Wed May 23 15:51:45 2007
From: niuli1978 at yahoo.com.cn (li niu)
Date: Wed, 23 May 2007 21:51:45 +0800 (CST)
Subject: [Pw_forum] from ibrav=0 to 1
Message-ID: <87733.83450.qm@web15002.mail.cnb.yahoo.com>

Dear all,
  After many vc-relax calculations(first ibrav=1,then using ibrav=0, new cell_parameters,  new positions), I obtained 
the following results. It is obvious the cell angle parameters have been changed and the structure isn't the cubic structure.
  
 1. If I still set ibrav=1 in the next scf calculation, how to read the new lattice constant? 
I have attempted to use celldm(1)*(a11+a22+a33)/3 as the new celldm(1),
(axx is the diagonal element of cell_parameters) ,the output atomic_positions(alat) as the new atomic_positions,and neglect all of the nondiagonal elements.
After the first self-consistent,I gain stresses with very large value. How can I adapt the input parameters to avoid this condition and get smaller elements?
  
2.Must the k-points are same in the vc-relax and scf?
   
  any help will be appreciated!
  
Best!
   
  Niu Li
Harbin Institute of Technology
China
  ==================================================
!    total energy              =  -729.30084995 Ry
     Harris-Foulkes estimate   =  -729.30084995 Ry
     estimated scf accuracy    <        8.1E-10 Ry
       convergence has been achieved
       Forces acting on atoms (Ry/au):
       atom   1 type  1   force =     0.00000028   -0.00000032   -0.00000017
          ...
     atom  62 type  1   force =    -0.00000135    0.00000206    0.00000190
     atom  63 type  1   force =    -0.00000012   -0.00000115    0.00000144
     atom  64 type  1   force =    -0.00000077   -0.00000041   -0.00000140
       Total force =     0.000024     Total SCF correction =     0.000091
  
     entering subroutine stress ...
            total   stress  (Ry/bohr**3)                   (kbar)     P=    0.06
   0.00000025   0.00000101   0.00000074          0.04      0.15      0.11
   0.00000101   0.00000338  -0.00000180          0.15      0.50     -0.27
   0.00000074  -0.00000180  -0.00000237          0.11     -0.27     -0.35
  
 Wentzcovitch Damped Dynamics: convergence achieved, Efinal=  -729.30084995
  ------------------------------------------------------------------------
       Final estimate of lattice vectors (input alat units)
   0.988103212   0.021498496  -0.002655708
   0.021493430   1.013103454  -0.000556700
  -0.002655491  -0.000556401   0.983829644
  final unit-cell volume =   2649.6086 (a.u.)^3
  input alat =      13.9103 (a.u.)
  CELL_PARAMETERS (alat)
   0.988103212   0.021498496  -0.002655708
   0.021493430   1.013103454  -0.000556700
  -0.002655491  -0.000556401   0.983829644
  ATOMIC_POSITIONS (angstrom)
C        0.292559767  -0.288781798  -0.891844186
C        1.355532741  -0.743068572   3.628414295
...
C        3.388679954   3.539286798   4.255326154
  =========================================

 		
---------------------------------
????????-3.5G???20M??? 
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From niuli1978 at yahoo.com.cn  Wed May 23 16:23:40 2007
From: niuli1978 at yahoo.com.cn (li niu)
Date: Wed, 23 May 2007 22:23:40 +0800 (CST)
Subject: [Pw_forum] finite electric field method
Message-ID: <629613.21974.qm@web15008.mail.cnb.yahoo.com>

 Dear PaoloU,
  
Thanks for your help. I still have several questions to consult you.
1.Is it suitable to calculate Raman spectrum of tetrahedral amorphous carbon using the finite electric method?
2.You said that atomic forces and electric fields are implemented for the US 
pseudopotentials only in the cp code ,but I found they may be implemented for NC pseudopotentials for tetrahedral amorphous carbon. Why is it?
3.Using ph.x to calculate the phonon frequencies and eigenmodes and cp.x to calculate Raman susceptibilities by finite electric method, is it feasible?
 
Best wishes,
   
  Niu Li
Harbin Institute of Technology
China


       
---------------------------------
????????3.5G???20M??? 
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From kondor.jess at gmail.com  Wed May 23 17:16:59 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Wed, 23 May 2007 10:16:59 -0500
Subject: [Pw_forum] projwfc analysis
Message-ID: <1d9d5d9d0705230816s56d40a54odf98122f380f659b@mail.gmail.com>

Hello, everybody,

  I have a question. I would like to analyze a magnetic structure (to define
magnetic moments on each atom) using projwfc postprocessing code. In the
example08 from espresso distribution (nickel in that case), the next steps
were performed : 'scf', 'nscf', then DOS was calculated and after that
projwfc was used. I  am wondering, is it really needed (and correct) to use
'projwfc' code after non-scf calculation? The number of k-points will be
huge with respect to scf calculation, and thus the computer time for
analysis will be increased.

cheers,
  jess
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From giannozz at nest.sns.it  Wed May 23 17:43:11 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 23 May 2007 17:43:11 +0200
Subject: [Pw_forum] Na phonon issues
In-Reply-To: <464C6701.7040501@lg.ehu.es>
References: <464C6701.7040501@lg.ehu.es>
Message-ID: <541B963C-8560-4D8B-A688-493E1B3A1FF9@nest.sns.it>

On May 17, 2007, at 16:30 , Miguel Mart?nez Canales wrote:

> I've been doing some phonon calculations on Na lately, and I've got
> an issue with the Na.pw91-n-mt.UPF pseudopotential [...]
>      omega( 1) =      -0.102259 [THz] =      -3.411026 [cm-1]
>      omega( 2) =       0.766410 [THz] =      25.564857 [cm-1]
>      omega( 3) =       1.171147 [THz] =      39.065511 [cm-1]
> [...]
> If I use the LDA pseudo Na.pz-n-vbc.UPF near equilibrium  
> (a=7.738a_0) with ecut=30 Ry and 18 18 18 shifted M-P grid, I get  
> the following omegas:
>      omega( 1) =       0.273215 [THz] =       9.113532 [cm-1]
>      omega( 2) =       0.835358 [THz] =      27.864728 [cm-1]
>      omega( 3) =       1.264994 [THz] =      42.195940 [cm-1]
>
> While the Na.pbe-sp-van_ak.UPF pseudo, with the same grid as the  
> enclosed input (20 20 20 shifted M-P), ecut=35 and ecutrho=300 Ry,  
> I get also sensible results (with 7.932 a_0 as lattice parametre):
>      omega( 1) =       0.390200 [THz] =      13.015753 [cm-1]
>      omega( 2) =       0.857166 [THz] =      28.592182 [cm-1]
>      omega( 3) =       1.238921 [THz] =      41.326237 [cm-1]
>
> So I have the following question: Is the mechanical instability I  
> see a product of my input or a product of the pseudopotential?

it might be the usual problem of the loss of translational invariance
at q=0, whose influence extends to small q as well; or it might be
related to the rather nasty numerical behaviour of the PW91 functional.
I would try the pw91 pseudopotential with lda (the pp file must be  
edited),
then the lda pp with pw91 functional, just to see what happens...

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




From giannozz at nest.sns.it  Wed May 23 17:44:33 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 23 May 2007 17:44:33 +0200
Subject: [Pw_forum] projwfc analysis
In-Reply-To: <1d9d5d9d0705230816s56d40a54odf98122f380f659b@mail.gmail.com>
References: <1d9d5d9d0705230816s56d40a54odf98122f380f659b@mail.gmail.com>
Message-ID: <76D685D8-CD1C-46AB-85B3-247CE7CE6D9A@nest.sns.it>

On May 23, 2007, at 17:16 , Jess Kondor wrote:

>  is it really needed (and correct) to use 'projwfc' code after non-scf
> calculation? The number of k-points will be huge with respect to scf
> calculation, and thus the computer time for analysis will be  
> increased.

if you want a nice-looking and accurate DOS, you need a sizable
number of k-points (typically larger than what you need for a good scf).
Also, if you want your DOS to cover the energy range of conduction
bands, you typically need more bands for the DOS than for a scf  
calculation.
You can run the projwfc analysis after the scf step, though

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




From wmbmacam at lg.ehu.es  Wed May 23 17:50:15 2007
From: wmbmacam at lg.ehu.es (=?ISO-8859-1?Q?Miguel_Mart=EDnez_Canales?=)
Date: Wed, 23 May 2007 17:50:15 +0200
Subject: [Pw_forum] Na phonon issues
In-Reply-To: <541B963C-8560-4D8B-A688-493E1B3A1FF9@nest.sns.it>
References: <464C6701.7040501@lg.ehu.es> <541B963C-8560-4D8B-A688-493E1B3A1FF9@nest.sns.it>
Message-ID: <465462B7.2060503@lg.ehu.es>


Paolo Giannozzi escribi?:
> it might be the usual problem of the loss of translational invariance
> at q=0, whose influence extends to small q as well; or it might be
> related to the rather nasty numerical behaviour of the PW91 functional.
> I would try the pw91 pseudopotential with lda (the pp file must be edited),
> then the lda pp with pw91 functional, just to see what happens...

Thank you very much for your suggestions, Paolo. Especially for the PW91 
Exc comment. I will try again with the hacked pseudopotentials and report 
the results. Even though I don't have good memories with exchanging pw91 
and lda Exc's inside a pseudopotential...

Good afternoon,

Miguel


-- 
----------------------------------------
Miguel Mart?nez Canales
Dto. F?sica de la Materia Condensada
UPV/EHU
Facultad de Ciencia y Tecnolog?a
Apdo. 644
48080 Bilbao (Spain)
Fax:  +34 94 601 3500
Tlf:  +34 94 601 5437
----------------------------------------

  "If you have an apple and I have an apple and
  we exchange these apples then you and I will
  still each have one apple. But if you have an
  idea and I have an idea and we exchange these
  ideas, then each of us will have two ideas."

    George Bernard Shaw



From chaohao.mse at gmail.com  Wed May 23 17:57:03 2007
From: chaohao.mse at gmail.com (Chaohao Hu)
Date: Wed, 23 May 2007 17:57:03 +0200
Subject: [Pw_forum] some questions about compiling espresso3.2
Message-ID: <6502ee650705230857m69320a05l899e2c8ec978aef4@mail.gmail.com>

Dear Pwscf users,


I want to compile epsresso3.2 on my system using the intel90 compiler mkl80
lib, I run into some problems. Some error informations as following always
appear. But I can compile it in my notepad using the intel90 compiler. Why?

If I use the make.sys configured automatically by machine, in which the g95
fortran compiler is used and the option "-ftrace=frame" is only added, I can
compile it successfully. But When running some examples involving in the
phonon calculations like example02, the Traceback information appears!!! How
to solve these problems? Here, I attach my make.sys files.

In addition, When can the the module of the noncollinear + GGA (not LDA) be
implemented in the espresso packages?

=================intel90+mkl80==============================

: undefined reference to `create_plan_1d_'

../Modules/fft_scalar.o(.text+0xf3a): more undefined references to
`create_plan_1d_' follow

../Modules/fft_scalar.o(.text+0x10b4): In function `fft_scalar_mp_cft_b_':

: undefined reference to `fftw_inplace_drv_1d_'

../Modules/fft_scalar.o(.text+0x10ef): In function `fft_scalar_mp_cft_b_':

: undefined reference to `fftw_inplace_drv_2d_'

../Modules/fft_scalar.o(.text+0x1127): In function `fft_scalar_mp_cft_b_':

: undefined reference to `destroy_plan_1d_'

../Modules/fft_scalar.o(.text+0x113e): In function `fft_scalar_mp_cft_b_':

: undefined reference to `create_plan_1d_'

../Modules/fft_scalar.o(.text+0x1153): In function `fft_scalar_mp_cft_b_':

: undefined reference to `destroy_plan_2d_'

../Modules/fft_scalar.o(.text+0x1169): In function `fft_scalar_mp_cft_b_':

: undefined reference to `create_plan_2d_'

../Modules/xml_io_base.o(.text+0x1309): In function
`xml_io_base_mp_create_directory_.':

: undefined reference to `c_mkdir_'

libpw.a(input.o)(.text+0x6550): In function `verify_tmpdir_.':

: undefined reference to `c_mkdir_'

make[1]: *** [pw.x] Error 1

=======================g95==================================

cleaning *******************/tmp... done

running the scf calculation... done

running the phonon calculation at Gamma... done

running the nscf calculation at X... done

running the phonon calculation at X... done

running the nscf calculation at X for a single mode... done

running the phonon calculation at X for a single mode...At line 47 of file
stop_ph.f90

Traceback: (Innermost first)

Called from line 0 of file ./run_example: line 245: 32630 Segmentation fault
$PH_COMMAND <si.phXsingle.in >si.phXsingle.out

done

cleaning *****************/tmp... done

running the scf calculation for C... done

running the phonon calculation at Gamma... done

running the scf calculation for Ni... done

running the non-scf calculation for phonon at X of Ni... done

running the phonon calculation at X... done
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# make.sys.  Generated from make.sys.in by configure.

# compilation rules

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

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

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

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

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

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


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

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

# IFLAGS = how to locate directories where files to be included are
# In most cases, IFLAGS = -I../include
# If loading an external FFTW library, add the location of FFTW include files

IFLAGS         = -I../include

# MODFLAGS = flag used by f90 compiler to locate modules
# You need to search for modules in ./, in ../iotk/src, in ../Modules
# Some applications also neeed modules in ../PW, ../PH, ../CPV

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

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

MPIF90         = ifort
#F90           = ifort
CC             = icc
F77            = ifort

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

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

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

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

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

FFLAGS_NOOPT   = -O0 -assume byterecl

# Linker and linker-specific flags (if any)
# Typically LD coincides with F90 or MPIF90 - not actually used

# LD             = mpif90
LDFLAGS        = 

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

# If you have nothing better, use the local copy : ../flib/blas.a

BLAS_LIBS      = -L/**************/Intel_9.0/mkl/8.0/lib/32 -lmkl_ia32 -lguide -lpthread

# The following lapack libraries will be available in flib/ :
# ../flib/lapack.a : contains all needed routines
# ../flib/lapack_atlas.a: only routines not present in the Atlas library
# For IBM machines with essl: load essl BEFORE lapack !
# remember that LAPACK_LIBS precedes BLAS_LIBS in loading order

LAPACK_LIBS    = -L/**************/Intel_9.0/mkl/8.0/lib/32 -lmkl_lapack

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

FFT_LIBS       =

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

MPI_LIBS       =

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

MASS_LIBS      = 

# pgplot libraries (used by some post-processing tools)

PGPLOT_LIBS    = 

# ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv
# ARFLAGS_DYNAMICS is used in iotk to produce a dynamical library,
# for Mac OS-X with PowerPC and xlf compiler. In all other cases
# ARFLAGS_DYNAMICS = $(ARFLAGS)

AR             = ar
ARFLAGS        = ruv
ARFLAGS_DYNAMIC= ruv

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

RANLIB         = ranlib

# all internal and external libraries - do not modify

LIBOBJS        = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a
LIBS           = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS)
-------------- next part --------------
# make.sys.  Generated from make.sys.in by configure.

# compilation rules

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

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

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

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

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

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


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

DFLAGS         =  -D__FFTW -D__USE_INTERNAL_FFTW
FDFLAGS        = $(DFLAGS)

# IFLAGS = how to locate directories where files to be included are
# In most cases, IFLAGS = -I../include
# If loading an external FFTW library, add the location of FFTW include files

IFLAGS         = -I../include 

# MODFLAGS = flag used by f90 compiler to locate modules
# You need to search for modules in ./, in ../iotk/src, in ../Modules
# Some applications also neeed modules in ../PW, ../PH, ../CPV

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

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

MPIF90         = g95
#F90           = g95
CC             = cc
F77            = g95

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

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

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

CFLAGS         = -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS       = $(FFLAGS) $(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS         = -O3 -cpp -ftrace=frame

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

FFLAGS_NOOPT   = -O0 -cpp

# Linker and linker-specific flags (if any)
# Typically LD coincides with F90 or MPIF90 - not actually used

# LD             = g95
LDFLAGS        = 

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

# If you have nothing better, use the local copy : ../flib/blas.a

BLAS_LIBS      = ../flib/blas.a

# The following lapack libraries will be available in flib/ :
# ../flib/lapack.a : contains all needed routines
# ../flib/lapack_atlas.a: only routines not present in the Atlas library
# For IBM machines with essl: load essl BEFORE lapack !
# remember that LAPACK_LIBS precedes BLAS_LIBS in loading order

LAPACK_LIBS    = ../flib/lapack.a

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

FFT_LIBS       = 

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

MPI_LIBS       = 

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

MASS_LIBS      = 

# pgplot libraries (used by some post-processing tools)

PGPLOT_LIBS    = 

# ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv
# ARFLAGS_DYNAMICS is used in iotk to produce a dynamical library,
# for Mac OS-X with PowerPC and xlf compiler. In all other cases
# ARFLAGS_DYNAMICS = $(ARFLAGS)

AR             = ar
ARFLAGS        = ruv
ARFLAGS_DYNAMIC= ruv

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

RANLIB         = ranlib

# all internal and external libraries - do not modify

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

From baroni at sissa.it  Wed May 23 19:01:10 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 23 May 2007 18:01:10 +0100
Subject: [Pw_forum] some questions about compiling espresso3.2
In-Reply-To: <6502ee650705230857m69320a05l899e2c8ec978aef4@mail.gmail.com>
References: <6502ee650705230857m69320a05l899e2c8ec978aef4@mail.gmail.com>
Message-ID: <61366880-974F-4A08-804D-796EAABC844F@sissa.it>

signature? affiliation? thanks - Stefano

On May 23, 2007, at 4:57 PM, Chaohao Hu wrote:

> Dear Pwscf users,
>
> I want to compile epsresso3.2 on my system using the intel90  
> compiler mkl80 lib, I run into some problems. Some error  
> informations as following always appear. But I can compile it in my  
> notepad using the intel90 compiler. Why?
>
> If I use the make.sys configured automatically by machine, in which  
> the g95 fortran compiler is used and the option "-ftrace=frame" is  
> only added, I can compile it successfully. But When running some  
> examples involving in the phonon calculations like example02, the  
> Traceback information appears!!! How to solve these problems? Here,  
> I attach my make.sys files.
>
> In addition, When can the the module of the noncollinear + GGA (not  
> LDA) be implemented in the espresso packages?
>
> =================intel90+mkl80==============================
>
> : undefined reference to `create_plan_1d_'
>
> ../Modules/fft_scalar.o(.text+0xf3a): more undefined references to  
> `create_plan_1d_' follow
>
> ../Modules/fft_scalar.o(.text+0x10b4): In function  
> `fft_scalar_mp_cft_b_':
>
> : undefined reference to `fftw_inplace_drv_1d_'
>
> ../Modules/fft_scalar.o(.text+0x10ef): In function  
> `fft_scalar_mp_cft_b_':
>
> : undefined reference to `fftw_inplace_drv_2d_'
>
> ../Modules/fft_scalar.o(.text+0x1127): In function  
> `fft_scalar_mp_cft_b_':
>
> : undefined reference to `destroy_plan_1d_'
>
> ../Modules/fft_scalar.o(.text+0x113e): In function  
> `fft_scalar_mp_cft_b_':
>
> : undefined reference to `create_plan_1d_'
>
> ../Modules/fft_scalar.o(.text+0x1153): In function  
> `fft_scalar_mp_cft_b_':
>
> : undefined reference to `destroy_plan_2d_'
>
> ../Modules/fft_scalar.o(.text+0x1169): In function  
> `fft_scalar_mp_cft_b_':
>
> : undefined reference to `create_plan_2d_'
>
> ../Modules/xml_io_base.o(.text+0x1309): In function  
> `xml_io_base_mp_create_directory_.':
>
> : undefined reference to `c_mkdir_'
>
> libpw.a(input.o)(.text+0x6550): In function `verify_tmpdir_.':
>
> : undefined reference to `c_mkdir_'
>
> make[1]: *** [pw.x] Error 1
>
> =======================g95==================================
>
> cleaning *******************/tmp... done
>
> running the scf calculation... done
>
> running the phonon calculation at Gamma... done
>
> running the nscf calculation at X... done
>
> running the phonon calculation at X... done
>
> running the nscf calculation at X for a single mode... done
>
> running the phonon calculation at X for a single mode...At line 47  
> of file stop_ph.f90
>
> Traceback: (Innermost first)
>
> Called from line 0 of file ./run_example: line 245: 32630  
> Segmentation fault $PH_COMMAND <si.phXsingle.in >si.phXsingle.out
>
> done
>
> cleaning *****************/tmp... done
>
> running the scf calculation for C... done
>
> running the phonon calculation at Gamma... done
>
> running the scf calculation for Ni... done
>
> running the non-scf calculation for phonon at X of Ni... done
>
> running the phonon calculation at X... done
>
>
>
>
> <make.sys_intel90>
> <make.sys_g95>

---
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 umari at democritos.it  Wed May 23 19:14:11 2007
From: umari at democritos.it (umari at democritos.it)
Date: Wed, 23 May 2007 19:14:11 +0200
Subject: [Pw_forum] Re: finite electric field method (li niu)
Message-ID: <20070523191411.4uyl1g5ut35kw8ww@mail.democritos.it>


> Dear PaoloU,

> Thanks for your help. I still have several questions to consult you.
> 1.Is it suitable to calculate Raman spectrum of tetrahedral amorphous 
> carbon >using the finite electric method?

Yes, it is (in the nonresonant limit)  and should be not particularly 
demanding in terms of
computational resources. You can follow the methods described in
Diamond and related materials, 14, 1255 (2005).


> 2.You said that atomic forces and electric fields are implemented for the US
> pseudopotentials only in the cp code ,but I found they may be 
> implemented for >NC pseudopotentials for tetrahedral amorphous 
> carbon. Why is it?

forces for NC pseudopotential plus electric field do not require additional
terms and are correctly calculated both in cp and pw

> 3.Using ph.x to calculate the phonon frequencies and eigenmodes and 
> cp.x to >calculate Raman susceptibilities by finite electric method, 
> is it feasible?

Yes it is but you could also calculate directly the Raman spectrum 
using the 2n+1 theorem which is implemented with pw and phonon

PaoloU

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.



From kondor.jess at gmail.com  Wed May 23 19:31:06 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Wed, 23 May 2007 12:31:06 -0500
Subject: [Pw_forum] projwfc analysis
In-Reply-To: <76D685D8-CD1C-46AB-85B3-247CE7CE6D9A@nest.sns.it>
References: <1d9d5d9d0705230816s56d40a54odf98122f380f659b@mail.gmail.com>
	 <76D685D8-CD1C-46AB-85B3-247CE7CE6D9A@nest.sns.it>
Message-ID: <1d9d5d9d0705231031ib1cea83o9c1331dd5af2406e@mail.gmail.com>

Paolo,

 Thank you for explanation.

 Usually for DOS I use tetrahedra method (which cannot be used for projwfc).
What I need to know - only magnetic moments. So, I wonder if  their values
obtaining from scf calculations (few k-points) will be the same after
non-scf calculation (more k-points).

jess

On 5/23/07, Paolo Giannozzi <giannozz at nest.sns.it> wrote:
>
>
> On May 23, 2007, at 17:16 , Jess Kondor wrote:
>
> >  is it really needed (and correct) to use 'projwfc' code after non-scf
> > calculation? The number of k-points will be huge with respect to scf
> > calculation, and thus the computer time for analysis will be
> > increased.
>
> if you want a nice-looking and accurate DOS, you need a sizable
> number of k-points (typically larger than what you need for a good scf).
> Also, if you want your DOS to cover the energy range of conduction
> bands, you typically need more bands for the DOS than for a scf
> calculation.
> You can run the projwfc analysis after the scf step, though
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
-----------------
Regards,
   JFK
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From chaohao.mse at gmail.com  Thu May 24 08:55:31 2007
From: chaohao.mse at gmail.com (Chaohao Hu)
Date: Thu, 24 May 2007 08:55:31 +0200
Subject: [Pw_forum] some questions about compiling espresso3.2
In-Reply-To: <61366880-974F-4A08-804D-796EAABC844F@sissa.it>
References: <6502ee650705230857m69320a05l899e2c8ec978aef4@mail.gmail.com>
	 <61366880-974F-4A08-804D-796EAABC844F@sissa.it>
Message-ID: <6502ee650705232355h1b93b3aeq50e0bf0b76c5bbc0@mail.gmail.com>

Dear Prof. Stefano,

Thank you for your suggestion. I have updated my signature. But I still hope
some experienced users can give me some hints to my problem. Thanks in
advance;

Best regards,
C.H. Hu


On 5/23/07, Stefano Baroni <baroni at sissa.it> wrote:
>
> signature? affiliation? thanks - Stefano
>  On May 23, 2007, at 4:57 PM, Chaohao Hu wrote:
>
>  Dear Pwscf users,
>
>
> I want to compile epsresso3.2 on my system using the intel90 compiler
> mkl80 lib, I run into some problems. Some error informations as following
> always appear. But I can compile it in my notepad using the intel90
> compiler. Why?
>
> If I use the make.sys configured automatically by machine, in which the
> g95 fortran compiler is used and the option "-ftrace=frame" is only added, I
> can compile it successfully. But When running some examples involving in the
> phonon calculations like example02, the Traceback information appears!!! How
> to solve these problems? Here, I attach my make.sys files.
>
> In addition, When can the the module of the noncollinear + GGA (not LDA)
> be implemented in the espresso packages?
>
> =================intel90+mkl80==============================
>
> : undefined reference to `create_plan_1d_'
>
> ../Modules/fft_scalar.o(.text+0xf3a): more undefined references to
> `create_plan_1d_' follow
>
> ../Modules/fft_scalar.o(.text+0x10b4): In function `fft_scalar_mp_cft_b_':
>
> : undefined reference to `fftw_inplace_drv_1d_'
>
> ../Modules/fft_scalar.o(.text+0x10ef): In function `fft_scalar_mp_cft_b_':
>
> : undefined reference to `fftw_inplace_drv_2d_'
>
> ../Modules/fft_scalar.o(.text+0x1127): In function `fft_scalar_mp_cft_b_':
>
> : undefined reference to `destroy_plan_1d_'
>
> ../Modules/fft_scalar.o(.text+0x113e): In function `fft_scalar_mp_cft_b_':
>
> : undefined reference to `create_plan_1d_'
>
> ../Modules/fft_scalar.o(.text+0x1153): In function `fft_scalar_mp_cft_b_':
>
> : undefined reference to `destroy_plan_2d_'
>
> ../Modules/fft_scalar.o(.text+0x1169): In function `fft_scalar_mp_cft_b_':
>
> : undefined reference to `create_plan_2d_'
>
> ../Modules/xml_io_base.o(.text+0x1309): In function
> `xml_io_base_mp_create_directory_.':
>
> : undefined reference to `c_mkdir_'
>
> libpw.a(input.o)(.text+0x6550): In function `verify_tmpdir_.':
>
> : undefined reference to `c_mkdir_'
>
> make[1]: *** [pw.x] Error 1
>
> =======================g95==================================
>
> cleaning *******************/tmp... done
>
> running the scf calculation... done
>
> running the phonon calculation at Gamma... done
>
> running the nscf calculation at X... done
>
> running the phonon calculation at X... done
>
> running the nscf calculation at X for a single mode... done
>
> running the phonon calculation at X for a single mode...At line 47 of file
> stop_ph.f90
>
> Traceback: (Innermost first)
>
> Called from line 0 of file ./run_example: line 245: 32630 Segmentation
> fault $PH_COMMAND <si.phXsingle.in <http://si.phxsingle.in/> >
> si.phXsingle.out
>
> done
>
> cleaning *****************/tmp... done
>
> running the scf calculation for C... done
>
> running the phonon calculation at Gamma... done
>
> running the scf calculation for Ni... done
>
> running the non-scf calculation for phonon at X of Ni... done
>
> running the phonon calculation at X... done
>
>
>
>
>
>
> <make.sys_intel90>
> <make.sys_g95>
>
>
>  ---
> 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
>
>
>
>
>
>



-- 
============================
C.H. Hu
Postdoctoral fellow
Chimie et Physico-Chimie appliquees
Institut Francais du Petrole (IFP)
Rueil-Malmaison, France
E_mail: chaohao.mse at gmail.com
============================
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From giannozz at nest.sns.it  Thu May 24 09:20:49 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 24 May 2007 09:20:49 +0200
Subject: [Pw_forum] some questions about compiling espresso3.2
In-Reply-To: <6502ee650705232355h1b93b3aeq50e0bf0b76c5bbc0@mail.gmail.com>
References: <6502ee650705230857m69320a05l899e2c8ec978aef4@mail.gmail.com> <61366880-974F-4A08-804D-796EAABC844F@sissa.it> <6502ee650705232355h1b93b3aeq50e0bf0b76c5bbc0@mail.gmail.com>
Message-ID: <9828FE73-A49B-4F75-8CFD-1D13B9F93C69@nest.sns.it>

On May 24, 2007, at 8:55 , Chaohao Hu wrote:

> But I still hope some experienced users can give me some hints
> to my problem.

with the description of the problem you gave, you need a magician
to get some hints. "make clean" first; "./configure", then "make all".
Compare what you get in the two machines for "make.sys" and for
"include/c_defs.h" and "include/fft_defs.h" (they are generated by
"configure"). Look into "config.log" if there are unexplained  
differences
between the two machines.

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




From giannozz at nest.sns.it  Thu May 24 09:33:28 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 24 May 2007 09:33:28 +0200
Subject: [Pw_forum] Compilation Problem
In-Reply-To: <257234.96962.qm@web50604.mail.re2.yahoo.com>
References: <257234.96962.qm@web50604.mail.re2.yahoo.com>
Message-ID: <1C3407C3-D8EB-4AD2-8A6B-8B68CB5E9B56@nest.sns.it>

On May 18, 2007, at 10:14 , vu ongphuong wrote:

> During install PWSCF, I encounter the following error message:
>
> cpp -P -traditional -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA  
> -I../include  wannier.f90 -o wannier.F90
>
> wannier.f90:8: #include expects "fname" or <fname>

check if the wannier.f90 is corrupted
---
Paolo Giannozzi, Democritos and University of Udine, Italy




From chaohao.mse at gmail.com  Thu May 24 12:01:50 2007
From: chaohao.mse at gmail.com (Chaohao Hu)
Date: Thu, 24 May 2007 12:01:50 +0200
Subject: [Pw_forum] some questions about compiling espresso3.2
In-Reply-To: <9828FE73-A49B-4F75-8CFD-1D13B9F93C69@nest.sns.it>
References: <6502ee650705230857m69320a05l899e2c8ec978aef4@mail.gmail.com>
	 <61366880-974F-4A08-804D-796EAABC844F@sissa.it>
	 <6502ee650705232355h1b93b3aeq50e0bf0b76c5bbc0@mail.gmail.com>
	 <9828FE73-A49B-4F75-8CFD-1D13B9F93C69@nest.sns.it>
Message-ID: <6502ee650705240301l399c872am1d1c569f40bf63e9@mail.gmail.com>

Dear Dr. Paolo,

Thank you for your help. I have solved this problem. In my present system,
the default compiler is g95. while in my notepad, the default compiler is
intel90. According to the manual of Pwscf, I just configured it again using
"./configure --disable-parallel F77=ifort FFLAGS="-O2 -assume byterecl"
CC=icc CFLAGS=-O3 LDFLAGS=-i-static". Now it's OK.

Best regards,
C.H. Hu

On 5/24/07, Paolo Giannozzi <giannozz at nest.sns.it> wrote:
>
>
> On May 24, 2007, at 8:55 , Chaohao Hu wrote:
>
> > But I still hope some experienced users can give me some hints
> > to my problem.
>
> with the description of the problem you gave, you need a magician
> to get some hints. "make clean" first; "./configure", then "make all".
> Compare what you get in the two machines for "make.sys" and for
> "include/c_defs.h" and "include/fft_defs.h" (they are generated by
> "configure"). Look into "config.log" if there are unexplained
> differences
> between the two machines.
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
============================
C.H. Hu
Postdoctoral fellow
Chimie et Physico-Chimie appliquees
Institut Francais du Petrole (IFP)
Rueil-Malmaison, France
E_mail: chaohao.mse at gmail.com
============================
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From degironc at sissa.it  Thu May 24 12:21:40 2007
From: degironc at sissa.it (degironc)
Date: Thu, 24 May 2007 12:21:40 +0200
Subject: [Pw_forum] from ibrav=0 to 1
In-Reply-To: <87733.83450.qm@web15002.mail.cnb.yahoo.com>
References: <87733.83450.qm@web15002.mail.cnb.yahoo.com>
Message-ID: <46556734.7050909@sissa.it>

If vc-relaxation produces a non-cubic solution then the system is likely
to be non-cubic.
In any event if you insist in using a cubic set-up it could be more
convenient to give the
atomic coordinates in crystal format so that they are automatically
scaled according to the
modified cell-edge dimensions
regards,
stefano

li niu wrote:
> Dear all,
> After many vc-relax calculations(first ibrav=1,then using ibrav=0, new
> cell_parameters, new positions), I obtained
> the following results. It is obvious the cell angle parameters have
> been changed and the structure isn't the cubic structure.
>
> 1. If I still set ibrav=1 in the next scf calculation, how to read the
> new lattice constant?
> I have attempted to use celldm(1)*(a11+a22+a33)/3 as the new celldm(1),
> (axx is the diagonal element of cell_parameters) ,the output
> atomic_positions(alat) as the new atomic_positions,and neglect all of
> the nondiagonal elements.
> After the first self-consistent,I gain stresses with very large value.
> How can I adapt the input parameters to avoid this condition and get
> smaller elements?
>
> 2.Must the k-points are same in the vc-relax and scf?
> any help will be appreciated!
>
> Best!
> Niu Li
> Harbin Institute of Technology
> China
> ==================================================
> ! total energy = -729.30084995 Ry
> Harris-Foulkes estimate = -729.30084995 Ry
> estimated scf accuracy < 8.1E-10 Ry
> convergence has been achieved
> Forces acting on atoms (Ry/au):
> atom 1 type 1 force = 0.00000028 -0.00000032 -0.00000017
> ...
> atom 62 type 1 force = -0.00000135 0.00000206 0.00000190
> atom 63 type 1 force = -0.00000012 -0.00000115 0.00000144
> atom 64 type 1 force = -0.00000077 -0.00000041 -0.00000140
> Total force = 0.000024 Total SCF correction = 0.000091
>
> entering subroutine stress ...
> total stress (Ry/bohr**3) (kbar) P= 0.06
> 0.00000025 0.00000101 0.00000074 0.04 0.15 0.11
> 0.00000101 0.00000338 -0.00000180 0.15 0.50 -0.27
> 0.00000074 -0.00000180 -0.00000237 0.11 -0.27 -0.35
>
> Wentzcovitch Damped Dynamics: convergence achieved, Efinal= -729.30084995
> ------------------------------------------------------------------------
> Final estimate of lattice vectors (input alat units)
> 0.988103212 0.021498496 -0.002655708
> 0.021493430 1.013103454 -0.000556700
> -0.002655491 -0.000556401 0.983829644
> final unit-cell volume = 2649.6086 (a.u.)^3
> input alat = 13.9103 (a.u.)
> CELL_PARAMETERS (alat)
> 0.988103212 0.021498496 -0.002655708
> 0.021493430 1.013103454 -0.000556700
> -0.002655491 -0.000556401 0.983829644
> ATOMIC_POSITIONS (angstrom)
> C 0.292559767 -0.288781798 -0.891844186
> C 1.355532741 -0.743068572 3.628414295
> ...
> C 3.388679954 3.539286798 4.255326154
> =========================================
>
> ------------------------------------------------------------------------
> ????????-3.5G???20M??? <http://cn.mail.yahoo.com> 



From hashem.yamani at gmail.com  Thu May 24 12:18:48 2007
From: hashem.yamani at gmail.com (Hashem Al-Yamani)
Date: Thu, 24 May 2007 13:18:48 +0300
Subject: [Pw_forum] Parallel installation error???
Message-ID: <82a593400705240318led4aa9cl15d6fd3a0074f236@mail.gmail.com>

Dear All ;

While trying to install espresso-3.2 on a machine with parallel connection
using mpich2 it didn't recognize that its parallel and gave the following
error :


Parallel environment not detected (is this a parallel machine?).
Configured for compilation of serial executables.

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

The following libraries have been found:
  BLAS_LIBS=../flib/blas.a
  LAPACK_LIBS=../flib/lapack.a
  FFT_LIBS=
Please check if this is what you expect.

If any libraries are missing, you may specify a list of directories
to search and retry, as follows:
  ./configure LIBDIRS="list of directories, separated by spaces"

Parallel environment not detected (is this a parallel machine?).
Configured for compilation of serial executables.

For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex).
--------------------------------------------------------------------
configure: success

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


it gave the same error when I put the "--enable-shared" option .......
please tell me if I am wrong ..... I've installed the fortran compiler and
in the same terminal I exported the path of the mpich2 installation
directory bin and thin gave the configure command from the espresso
directory .....    is there a specific way to install espresso on parallell
or is it another problem ......  Any help would be very appreciaple ...
thanks alot ....


Regards ;

Hashem
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From paulatto at sissa.it  Thu May 24 14:07:36 2007
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 24 May 2007 14:07:36 +0200 (CEST)
Subject: [Pw_forum] Parallel installation error???
In-Reply-To: <82a593400705240318led4aa9cl15d6fd3a0074f236@mail.gmail.com>
References: <82a593400705240318led4aa9cl15d6fd3a0074f236@mail.gmail.com>
Message-ID: <25210.82.50.170.169.1180008456.squirrel@webmail.sissa.it>

On Thu, May 24, 2007 12:18, Hashem Al-Yamani wrote:
> or is it another problem ......  Any help would be very appreciaple ...
> thanks alot ....

Have you used the same compiler to compile mpi and espresso? Different
compilers may not produce compatible binaries.

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


----------------------------------------------------------------
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From giannozz at nest.sns.it  Thu May 24 14:17:32 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 24 May 2007 14:17:32 +0200
Subject: [Pw_forum] Parallel installation error???
In-Reply-To: <82a593400705240318led4aa9cl15d6fd3a0074f236@mail.gmail.com>
References: <82a593400705240318led4aa9cl15d6fd3a0074f236@mail.gmail.com>
Message-ID: <C5F5BA66-2E01-42BC-8296-603DDEA7BA6F@nest.sns.it>

On May 24, 2007, at 12:18 , Hashem Al-Yamani wrote:

> While trying to install espresso-3.2 on a machine with parallel  
> connection
> using mpich2 it didn't recognize that its parallel

see at the beginning of the FAQ:
http://www.quantum-espresso.org/wiki/index.php/ 
Frequently_Asked_Questions
You need
1) a working mpif90 script for parallel compilation, and
2) working mpi libraries located in a place that configure can find

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




From marzari at MIT.EDU  Thu May 24 14:35:42 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 24 May 2007 08:35:42 -0400
Subject: [Pw_forum] some questions about compiling espresso3.2
In-Reply-To: <9828FE73-A49B-4F75-8CFD-1D13B9F93C69@nest.sns.it>
References: <6502ee650705230857m69320a05l899e2c8ec978aef4@mail.gmail.com> <61366880-974F-4A08-804D-796EAABC844F@sissa.it> <6502ee650705232355h1b93b3aeq50e0bf0b76c5bbc0@mail.gmail.com> <9828FE73-A49B-4F75-8CFD-1D13B9F93C69@nest.sns.it>
Message-ID: <4655869E.3010702@mit.edu>

Paolo Giannozzi wrote:
> 
> On May 24, 2007, at 8:55 , Chaohao Hu wrote:
> 
>> But I still hope some experienced users can give me some hints
>> to my problem.
> 
> with the description of the problem you gave, you need a magician
> to get some hints.


But Paolo, you *are* a magician, among us all Muggles.

				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 baroni at sissa.it  Thu May 24 16:06:33 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 24 May 2007 15:06:33 +0100
Subject: [Pw_forum] Parallel installation error???
In-Reply-To: <C5F5BA66-2E01-42BC-8296-603DDEA7BA6F@nest.sns.it>
References: <82a593400705240318led4aa9cl15d6fd3a0074f236@mail.gmail.com> <C5F5BA66-2E01-42BC-8296-603DDEA7BA6F@nest.sns.it>
Message-ID: <6E25B5BF-A651-4E84-890E-5AC21BAC1A80@sissa.it>

Also, would you mind indicating your affiliation? Thanks - Stefano

On May 24, 2007, at 1:17 PM, Paolo Giannozzi wrote:

>
> On May 24, 2007, at 12:18 , Hashem Al-Yamani wrote:
>
>> While trying to install espresso-3.2 on a machine with parallel  
>> connection
>> using mpich2 it didn't recognize that its parallel
>
> see at the beginning of the FAQ:
> http://www.quantum-espresso.org/wiki/index.php/ 
> Frequently_Asked_Questions
> You need
> 1) a working mpif90 script for parallel compilation, and
> 2) working mpi libraries located in a place that configure can find
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
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 njuxuyuehua at gmail.com  Thu May 24 17:15:18 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Thu, 24 May 2007 23:15:18 +0800
Subject: [Pw_forum] dynamt.x error
Message-ID: <aca2feb20705240815j41331480rd5233e090271f4af@mail.gmail.com>

 Reading Dynamical Matrix from file /raid/xyh/pwscf/pho_scf_relax/fXXX.dynG
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
hi all
when i am about to compute dynamt.x ,there is a error(see below)
i know someone has met the same problem ,but his solution is :go back to scf
,and specify the ibra ,and  then  compute form the  scratch.
i want to know why i must to specify the ibra ,once i use a very strange
cell,especially iwheni use supercell.and not  belong to any of the bra ? how
to slove the error?
i wish get your help .




Reading Dynamical Matrix from file /raid/xyh/pwscf/pho_scf_relax/ww.dynG

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from latgen : error #         1
     wrong at for ibrav=0
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
Fatal error; unknown error handler
May be MPI call before MPI_INIT.  Error message is MPI_COMM_RANK and code is
197
Fatal error; unknown error handler
May be MPI call before MPI_INIT.  Error message is MPI_ABORT and code is 197
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
dynmat.x           0000000000823740  Unknown               Unknown  Unknown
dynmat.x           0000000000777F69  Unknown               Unknown  Unknown
dynmat.x           0000000000455679  Unknown               Unknown  Unknown
dynmat.x           000000000045602B  Unknown               Unknown  Unknown
dynmat.x           0000000000403350  Unknown               Unknown  Unknown
dynmat.x           0000000000400834  Unknown               Unknown  Unknown
dynmat.x           0000000000400296  Unknown               Unknown  Unknown
dynmat.x           000000000081D391  Unknown               Unknown  Unknown
dynmat.x           00000000004001AA  Unknown               Unknown  Unknown
Thu May 24 22:55:50 CST 2007

 --
Xu Yuehua
physics Department of Nanjing university
China
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From niuli1978 at yahoo.com.cn  Fri May 25 00:48:45 2007
From: niuli1978 at yahoo.com.cn (li niu)
Date: Fri, 25 May 2007 06:48:45 +0800 (CST)
Subject: [Pw_forum] atomic coordinates from angstrom to crystal format
In-Reply-To: <20070524102201.8212.86370.Mailman@democritos.sissa.it>
Message-ID: <727554.602.qm@web15006.mail.cnb.yahoo.com>

Dear stefano,
Thanks for your help.
I obtained the atomic coordinates in angstrom format using the CPMD method. How to change the atomic coordinates to crystal format?
  Bests!
  Niu Li
Harbin Institute of Technology
China


       
---------------------------------
????????3.5G???20M??? 
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From njuxuyuehua at gmail.com  Fri May 25 04:28:28 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 25 May 2007 10:28:28 +0800
Subject: [Pw_forum] uncertainty about the *.dynG file :what is "cubic" mean ? and what is the difference between *.dyn and *. matdyn file ?
Message-ID: <aca2feb20705241928o59a1e53r142c0e397208928d@mail.gmail.com>

hi all :
In the *.dynG file ,there is "cubic" ,i don know what is meaning ,because my
cell is not the type as you can see my scf file



-------------------------------------dynG.FILE------------------------------

Dynamical matrix file

  2   15  0 38.1852405  0.0000000  0.0000000  0.0000000  0.0000000
0.0000000
cubic
      0.866025710    0.499999470    0.000000000
      0.000000000    0.999998940    0.000000000
      0.000000000    0.000000000    0.143563323

------------------------------------------------------------------------scf
file -----------------------------------
this is the scf output :

bravais-lattice index     =            0
     lattice parameter (a_0)   =      38.1852  a.u.
     unit-cell volume          =    6922.4594 (a.u.)^3
     number of atoms/cell      =           15
     number of atomic types    =            2
     kinetic-energy cutoff     =      29.9874  Ry
     charge density cutoff     =     200.0000  Ry
     convergence threshold     =      1.0E-09
     beta                      =       0.2000
     number of iterations used =            8  plain     mixing
     Exchange-correlation      =  SLA  PW   PBE  PBE (1434)
     celldm(1)=  38.185240  celldm(2)=   0.000000  celldm(3)=   0.000000
     celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=   0.000000

     crystal axes: (cart. coord. in units of a_0)
               a(1) = (  0.866026  0.499999  0.000000 )
               a(2) = (  0.000000  0.999999  0.000000 )
               a(3) = (  0.000000  0.000000  0.143563 )











-- 
Xu Yuehua
physics Department of Nanjing university
China
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From eyvaz_isaev at yahoo.com  Fri May 25 06:57:23 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 24 May 2007 21:57:23 -0700 (PDT)
Subject: [Pw_forum] atomic coordinates from angstrom to crystal format
In-Reply-To: <727554.602.qm@web15006.mail.cnb.yahoo.com>
Message-ID: <542286.78413.qm@web60317.mail.yahoo.com>

Der Li

--- li niu <niuli1978 at yahoo.com.cn> wrote:

> Dear stefano,
> Thanks for your help.
> I obtained the atomic coordinates in angstrom format
> using the CPMD method. How to change the atomic
> coordinates to crystal format?

I do not think you need to convert these to crystal
format (of course, it is a useful teaching problem),
but you can just specify "angstrom" instead of
"crystal" in ATOMIC_POSITIONS.

Bests,
Eyvaz.


>   Bests!
>   Niu Li
> Harbin Institute of Technology
> China
> 
> 
>        
> ---------------------------------
> ????????????????3.5G??????20M?????? 


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


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


From ding at sissa.it  Fri May 25 10:41:55 2007
From: ding at sissa.it (Xunlei Ding)
Date: Fri, 25 May 2007 10:41:55 +0200
Subject: [Pw_forum] atomic coordinates from angstrom to crystal format
In-Reply-To: <727554.602.qm@web15006.mail.cnb.yahoo.com>
References: <727554.602.qm@web15006.mail.cnb.yahoo.com>
Message-ID: <4656A153.2000001@sissa.it>

Hi Niu,

In angstrom format, the coordinate of an atom is like (x,y,z).
Supposing the crystal vectors are e1, e2, e3, and the new coordinate in
crystal format is (x',y',z'),
then (x,y,z)= x'*e1+y'*e2+z'*e3.
So we can get (x',y',z').
Suggestion: always to use xcrysden to check the input geometry.

Best wishs,
Ding


li niu wrote:

> Dear stefano,
> Thanks for your help.
> I obtained the atomic coordinates in angstrom format using the CPMD
> method. How to change the atomic coordinates to crystal format?
> Bests!
> Niu Li
> Harbin Institute of Technology
> China
>
> ------------------------------------------------------------------------
> ????????3.5G???20M??? <http://cn.mail.yahoo.com> 



From ding at sissa.it  Fri May 25 10:46:09 2007
From: ding at sissa.it (Xunlei Ding)
Date: Fri, 25 May 2007 10:46:09 +0200
Subject: [Pw_forum] uncertainty about the *.dynG file :what is "cubic"
 mean ? and what is the difference between *.dyn and *. matdyn file ?
In-Reply-To: <aca2feb20705241928o59a1e53r142c0e397208928d@mail.gmail.com>
References: <aca2feb20705241928o59a1e53r142c0e397208928d@mail.gmail.com>
Message-ID: <4656A251.9030206@sissa.it>

Hi Xu,

You can find the same numbers in your scf output files:
     crystal axes: (cart. coord. in units of a_0)
               a(1) = (  0.866026  0.499999  0.000000 )
               a(2) = (  0.000000  0.999999  0.000000 )
               a(3) = (  0.000000  0.000000  0.143563 )

So I think "cubic" means a cubic cell, not  hexagonal .

Best wishes,
Ding

xu yuehua wrote:

> hi all :
> In the *.dynG file ,there is "cubic" ,i don know what is meaning 
> ,because my cell is not the type as you can see my scf file
>  
>  
>  
> -------------------------------------dynG.FILE 
> ------------------------------
>
> Dynamical matrix file
>
>   2   15  0 38.1852405  0.0000000  0.0000000  0.0000000  0.0000000  
> 0.0000000
> cubic
>       0.866025710    0.499999470    0.000000000
>       0.000000000    0.999998940    0.000000000
>       0.000000000    0.000000000     0.143563323
>
> ------------------------------------------------------------------------scf 
> file -----------------------------------
> this is the scf output :
>
> bravais-lattice index     =            0
>      lattice parameter (a_0)   =      38.1852  a.u.
>      unit-cell volume          =    6922.4594 (a.u.)^3
>      number of atoms/cell      =           15
>      number of atomic types    =            2
>      kinetic-energy cutoff     =      29.9874  Ry
>      charge density cutoff     =     200.0000  Ry
>      convergence threshold     =      1.0E-09
>      beta                      =       0.2000
>      number of iterations used =            8  plain     mixing
>      Exchange-correlation      =  SLA  PW   PBE  PBE (1434)
>      celldm(1)=  38.185240  celldm(2)=   0.000000  celldm(3)=   0.000000
>      celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=   0.000000
>
>      crystal axes: (cart. coord. in units of a_0)
>                a(1) = (  0.866026  0.499999  0.000000 )
>                a(2) = (  0.000000  0.999999  0.000000 )
>                a(3) = (  0.000000  0.000000  0.143563 )
>
>  
>  
>  
>  
>  
>  
>  
>  
>  
>
>
> -- 
> Xu Yuehua
> physics Department of Nanjing university
> China



From degironc at sissa.it  Fri May 25 13:53:33 2007
From: degironc at sissa.it (degironc)
Date: Fri, 25 May 2007 13:53:33 +0200
Subject: [Pw_forum] atomic coordinates from angstrom to crystal format
In-Reply-To: <727554.602.qm@web15006.mail.cnb.yahoo.com>
References: <727554.602.qm@web15006.mail.cnb.yahoo.com>
Message-ID: <4656CE3D.4040405@sissa.it>

if you run your calculation with verbosity='high' specified in the
control namelist
the atomic positions in crystal coordinates will be written on output.
stefano

li niu wrote:
> Dear stefano,
> Thanks for your help.
> I obtained the atomic coordinates in angstrom format using the CPMD
> method. How to change the atomic coordinates to crystal format?
> Bests!
> Niu Li
> Harbin Institute of Technology
> China
>
> ------------------------------------------------------------------------
> ????????3.5G???20M??? <http://cn.mail.yahoo.com> 



From degironc at sissa.it  Fri May 25 13:59:50 2007
From: degironc at sissa.it (degironc)
Date: Fri, 25 May 2007 13:59:50 +0200
Subject: [Pw_forum] uncertainty about the *.dynG file :what is "cubic"
 mean ? and what is the difference between *.dyn and *. matdyn file ?
In-Reply-To: <aca2feb20705241928o59a1e53r142c0e397208928d@mail.gmail.com>
References: <aca2feb20705241928o59a1e53r142c0e397208928d@mail.gmail.com>
Message-ID: <4656CFB6.10206@sissa.it>

the word "cubic" is a reminder for the code that the symmetry group of 
the crystal in a subset of the cubic one (the other option would be 
"hexagonal"). this does not means that the system is actually cubic but 
just that the symmetry operations that it satisfies should be searched 
among those of the cubic group.
.. is "cubic" the right symmetry system for your crystal ? the 
fundamental lattice vectors you get look like belonging to some 
triangular lattice...
stefano

xu yuehua wrote:
> hi all :
> In the *.dynG file ,there is "cubic" ,i don know what is meaning 
> ,because my cell is not the type as you can see my scf file
>  
> -------------------------------------dynG.FILE 
> ------------------------------
>
> Dynamical matrix file
>
>   2   15  0 38.1852405  0.0000000  0.0000000  0.0000000  0.0000000  
> 0.0000000
> cubic
>       0.866025710    0.499999470    0.000000000
>       0.000000000    0.999998940    0.000000000
>       0.000000000    0.000000000     0.143563323
>
> ------------------------------------------------------------------------scf 
> file -----------------------------------
> this is the scf output :
>
> bravais-lattice index     =            0
>      lattice parameter (a_0)   =      38.1852  a.u.
>      unit-cell volume          =    6922.4594 (a.u.)^3
>      number of atoms/cell      =           15
>      number of atomic types    =            2
>      kinetic-energy cutoff     =      29.9874  Ry
>      charge density cutoff     =     200.0000  Ry
>      convergence threshold     =      1.0E-09
>      beta                      =       0.2000
>      number of iterations used =            8  plain     mixing
>      Exchange-correlation      =  SLA  PW   PBE  PBE (1434)
>      celldm(1)=  38.185240  celldm(2)=   0.000000  celldm(3)=   0.000000
>      celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=   0.000000
>
>      crystal axes: (cart. coord. in units of a_0)
>                a(1) = (  0.866026  0.499999  0.000000 )
>                a(2) = (  0.000000  0.999999  0.000000 )
>                a(3) = (  0.000000  0.000000  0.143563 )
>
>  
>  
>  
>  
>  
>  
>  
>  
>  
>
>
> -- 
> Xu Yuehua
> physics Department of Nanjing university
> China



From njuxuyuehua at gmail.com  Fri May 25 14:51:04 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 25 May 2007 20:51:04 +0800
Subject: [Pw_forum] uncertainty about the *.dynG file :what is "cubic" mean ? and what is the difference between *.dyn and *. matdyn file ?
In-Reply-To: <4656CFB6.10206@sissa.it>
References: <aca2feb20705241928o59a1e53r142c0e397208928d@mail.gmail.com>
	 <4656CFB6.10206@sissa.it>
Message-ID: <aca2feb20705250551w26265e3dsfee1ab5bd92a0338@mail.gmail.com>

Dear Ding and Degiron

i  think about my problem again ,i think my lattice not belongs cubic
neither triangular lattice .it is unuall lattice .a=b, the angle of a and b
is 30 degree.a,b plumb c.it is supercell. thank your hints. i have to
redesign it .


2007/5/25, degironc <degironc at sissa.it>:
>
> the word "cubic" is a reminder for the code that the symmetry group of
> the crystal in a subset of the cubic one (the other option would be
> "hexagonal"). this does not means that the system is actually cubic but
> just that the symmetry operations that it satisfies should be searched
> among those of the cubic group.
> .. is "cubic" the right symmetry system for your crystal ? the
> fundamental lattice vectors you get look like belonging to some
> triangular lattice...
> stefa
>
> xu yuehua wrote:
> > hi all :
> > In the *.dynG file ,there is "cubic" ,i don know what is meaning
> > ,because my cell is not the type as you can see my scf file
> >
> > -------------------------------------dynG.FILE
> > ------------------------------
> >
> > Dynamical matrix file
> >
> >   2   15  0 38.1852405  0.0000000  0.0000000  0.0000000  0.0000000
> > 0.0000000
> > cubic
> >       0.866025710    0.499999470    0.000000000
> >       0.000000000    0.999998940    0.000000000
> >       0.000000000    0.000000000     0.143563323
> >
> >
> ------------------------------------------------------------------------scf
> > file -----------------------------------
> > this is the scf output :
> >
> > bravais-lattice index     =            0
> >      lattice parameter (a_0)   =      38.1852  a.u.
> >      unit-cell volume          =    6922.4594 (a.u.)^3
> >      number of atoms/cell      =           15
> >      number of atomic types    =            2
> >      kinetic-energy cutoff     =      29.9874  Ry
> >      charge density cutoff     =     200.0000  Ry
> >      convergence threshold     =      1.0E-09
> >      beta                      =       0.2000
> >      number of iterations used =            8  plain     mixing
> >      Exchange-correlation      =  SLA  PW   PBE  PBE (1434)
> >      celldm(1)=  38.185240  celldm(2)=   0.000000  celldm(3)=   0.000000
> >      celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=   0.000000
> >
> >      crystal axes: (cart. coord. in units of a_0)
> >                a(1) = (  0.866026  0.499999  0.000000 )
> >                a(2) = (  0.000000  0.999999  0.000000 )
> >                a(3) = (  0.000000  0.000000  0.143563 )
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > --
> > Xu Yuehua
> > physics Department of Nanjing university
> > China
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From njuxuyuehua at gmail.com  Sat May 26 05:43:37 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Sat, 26 May 2007 11:43:37 +0800
Subject: [Pw_forum] in ralax out file :what the tau( 1) stand for ?
Message-ID: <aca2feb20705252043q67d98275pd08f61d33c7d8914@mail.gmail.com>

 hi all
i want to check the the position of atoms generateing from my input ,but i
do not know the "tau "stands for

outfile:

 Cartesian axes

     site n.     atom                  positions (a_0 units)

         tau(  1) = (   0.0955000  -0.0222921   0.0877964  )
           tau(  2) = (   0.1203713   0.0259950   0.1476673  )
         tau(  3) = (  -0.0913367  -0.0311881   0.0864053  )
         tau(  4) = (  -0.0933862  -0.0952227   0.0371086  )
         tau(  5) = (  -0.1146783   0.0578960   0.1453950  )
          tau(  6) = (  -0.0622673   0.0735890   0.0858806  )
          tau(  7) = (   0.0005149  -0.0944603   0.1013409  )
         tau(  8) = (   0.0589802  -0.1140741   0.1536128  )
wish your assist
-- 
Xu Yuehua
physics Department of Nanjing university
China
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From hongyi.zhao at gmail.com  Sat May 26 05:57:42 2007
From: hongyi.zhao at gmail.com (Hongyi Zhao)
Date: Sat, 26 May 2007 11:57:42 +0800
Subject: [Pw_forum] How can I generate the USPP of hafnium used by PWSCF?
Message-ID: <20070526035742.GA25645@debianhy.localdomain>

Hi all,

Now, I want to do some computations on HfO_2 under the vanderbilt's 
scheme of USPP, but I cann't find any available USPP of hafnium.  What 
should I do, will you anyone give me some hints?

Thanks in advance.
---
Honyi Zhao <hongyi.zhao at gmail.com>
Xinjiang Technical Institute of Physics and Chemistry 
Chinese Academy of Sciences
gpg DSA: 0xD108493B



From marzari at MIT.EDU  Sat May 26 07:19:07 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Sat, 26 May 2007 01:19:07 -0400
Subject: [Pw_forum] How can I generate the USPP of hafnium used by PWSCF?
In-Reply-To: <20070526035742.GA25645@debianhy.localdomain>
References: <20070526035742.GA25645@debianhy.localdomain>
Message-ID: <4657C34B.1040104@mit.edu>

Hongyi Zhao wrote:
> Hi all,
> 
> Now, I want to do some computations on HfO_2 under the vanderbilt's 
> scheme of USPP, but I cann't find any available USPP of hafnium.  What 
> should I do, will you anyone give me some hints?
> 
> Thanks in advance.
> ---
> Honyi Zhao <hongyi.zhao at gmail.com>
> Xinjiang Technical Institute of Physics and Chemistry 
> Chinese Academy of Sciences
> gpg DSA: 0xD108493B


Dear Honyi,

have a look at this:
Davide Ceresoli and David Vanderbilt, "Structural and dielectric 
properties of amorphous ZrO2 and HfO2, Physical Review B 74, 125108 (2006).

Maybe they report the parameters used to generate the pseudo,
or you could ask directly, politely, to Davide or to David if
they could send you a copy.

If they do, send the pseudo also to Paolo Giannozzi,
Paolo Giannozzi <p.giannozzi at fisica.uniud.it>, so he can
update the web site, and mention that it was used for the paper
above.

				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 eyvaz_isaev at yahoo.com  Sat May 26 11:13:31 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sat, 26 May 2007 02:13:31 -0700 (PDT)
Subject: [Pw_forum] in ralax out file :what the tau( 1) stand for ?
In-Reply-To: <aca2feb20705252043q67d98275pd08f61d33c7d8914@mail.gmail.com>
Message-ID: <438997.96880.qm@web60316.mail.yahoo.com>

--- xu yuehua <njuxuyuehua at gmail.com> wrote:

>  hi all
> i want to check the the position of atoms
> generateing from my input ,but i
> do not know the "tau "stands for
> 
> outfile:
> 
>  Cartesian axes
> 
>      site n.     atom                  positions
> (a_0 units)
> 
>          tau(  1) = (   0.0955000  -0.0222921  
> 0.0877964  )
>            tau(  2) = (   0.1203713   0.0259950  
> 0.1476673  )
>          tau(  3) = (  -0.0913367  -0.0311881  
> 0.0864053  )
>          tau(  4) = (  -0.0933862  -0.0952227  
> 0.0371086  )
>          tau(  5) = (  -0.1146783   0.0578960  
> 0.1453950  )
>           tau(  6) = (  -0.0622673   0.0735890  
> 0.0858806  )
>           tau(  7) = (   0.0005149  -0.0944603  
> 0.1013409  )
>          tau(  8) = (   0.0589802  -0.1140741  
> 0.1536128  )
> wish your assist

Dear, Xu, 

The answer is given right after "Cartesian axes":
atomic position of atom j of type i and atomic
position is in cartesian coordinates which are scaled
by lattice parameter a_0. 
If you have troubles reading such a kind information,
you  should first read any solid state physics
textbook by, as example, Kittel, Aschkroft-Mermin,
Ziman, Harrison etc.

Bests,
Eyvaz.

> -- 
> Xu Yuehua
> physics Department of Nanjing university
> China
> 


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


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


From kazempoor2000 at yahoo.com  Sat May 26 11:37:25 2007
From: kazempoor2000 at yahoo.com (ali kazempoor)
Date: Sat, 26 May 2007 02:37:25 -0700 (PDT)
Subject: [Pw_forum] Mn pseudopotentials
Message-ID: <867941.5372.qm@web33109.mail.mud.yahoo.com>

hi all
has anyone ultrasoft pseudopotential for Mn that has
large rcut and need to less plan wave for convergence.
.thanks


       
____________________________________________________________________________________Yahoo! oneSearch: Finally, mobile search 
that gives answers, not web links. 
http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC


From hashem.yamani at gmail.com  Sat May 26 17:16:13 2007
From: hashem.yamani at gmail.com (Hashem Al-Yamani)
Date: Sat, 26 May 2007 18:16:13 +0300
Subject: [Pw_forum] parallel installation usinf mpich2 & intel fortran ??
Message-ID: <82a593400705260816y7c8d8423ia50aa181ee713f26@mail.gmail.com>

Dear All ;

     Am trying to install espresso 3.2 on two parallel connected machines
using mpich2 and Intel fortran which I gave the command "source" to indicate
to the espresso about its libraries ... but when doing so it doesn't
recognise the parallel environment .... any one knows the properiate
configurations for such a case ??? ... or is there another way without using
intel fortran ????


Thanks alot .



Regards ;
Hashem
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From hashem.yamani at gmail.com  Sat May 26 20:28:10 2007
From: hashem.yamani at gmail.com (Hashem Al-Yamani)
Date: Sat, 26 May 2007 21:28:10 +0300
Subject: [Pw_forum] Done successfully ... but .... !!!
Message-ID: <82a593400705261128we5b1169y331cb24f320efbdd@mail.gmail.com>

Dear All ;


I 've made my first cluster using mpich2 and PWSCF ..... I put the espresso
folder and psedue and tmp folders on /home directory which is shared by NFS
via the machines ...... now when I tryed a file it gave the following error
:



     from outdir:  : error #         1
     /home/espresso-3.2/tmp/ non existent or non writable
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
   Program PWSCF     v.3.2    starts ...
     Today is 26May2007 at 15:10:47

     Parallel version (MPI)

     Number of processors in use:       2
     R & G space division:  proc/pool =    2

     Ultrasoft (Vanderbilt) Pseudopotentials

     Current dimensions of program pwscf are:

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

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from outdir:  : error #         1
     /home/espresso-3.2/tmp/ non existent or non writable
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
rank 1 in job 9  server2_1074   caused collective abort of all ranks
  exit status of rank 1: return code 47
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------


Now does this means that the other machine (i.e : not the server that am
running the job from) is not able to write in the tmp folder ... or is it
something else .......... and if so what could be a reasonable solution
....................   any ideas would be very appreciaple ... and thanks
all


Regards ;
Hashem
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From jin.zhang.pku at gmail.com  Sun May 27 07:07:32 2007
From: jin.zhang.pku at gmail.com (Jin Zhang)
Date: Sun, 27 May 2007 13:07:32 +0800
Subject: [Pw_forum] Problems with phonon calculation in one-dimensional chains
Message-ID: <5d233b6a0705262207q3e009ee1n53b63678328339e8@mail.gmail.com>

Dear all,

I have encountered several issues related to Gamma point phonon calculation
in simple 1d chains(including aluminum, gold and platinum). The symptom is
*sometimes* there are one or more eigen-*optical*-modes having
negative(usually large) frequencies. The system I considered are all
2-atom/cell 1d chains(to produce optical branches), with large vacuum region
around them(usually 16-20Bohrs). For example, the aluminum input are listed
below,
---------------------------------------------------------
pw.x----------------------------------------------------------
Infinite Al Chain NCPP
   &CONTROL
      calculation = 'scf',
      prefix='al',
      nstep=100,
      tstress = .TRUE.,
      tprnfor = .TRUE.,
      outdir='./tmp/',
      pseudo_dir = '/home/i/opt/espresso- 3.2/pseudo',
      wf_collect=.true.,
   /
   &SYSTEM
      ibrav=8,
      celldm(1)=20.0,
      celldm(2)=1.0,
      celldm(3)=0.9,
      nat=2,
      ntyp=1,
      ecutwfc=30.0,
      occupations='smearing',
      smearing='cold',
      degauss=0.05,
      !nbnd=40,
      la2F=.true.,
   /
   &ELECTRONS
      electron_maxstep = 100,
      mixing_beta = 0.5,
      conv_thr =  1.0d-8,
   /
   &IONS
   /
ATOMIC_SPECIES
Al  26.98154  Al.pz-vbc.UPF
ATOMIC_POSITIONS {crystal}
Al    0.000    0.0   0.0
Al    0.000    0.0   0.5
K_POINTS (automatic)
  1 1 40  0 0 1
------------------------------------------------------------
ph.x---------------------------------------------------------------
 &inputph
  tr2_ph=1.0d-14,
  recover = .false.
  prefix='al',
  fildvscf='dvscf',
  alpha_mix=0.5,
  amass(1)=26.98154,
  outdir='./tmp',
  fildyn='dyn',
  elph=.false.,
  trans=.true.,
  ldisp=.true.,
  nq1 =1, nq2 =1, nq3 = 1,
/
-------------------------------------------------------------------------------------------------------------------------------

The obtained frequency is

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


     omega( 1) =      -3.982548 [THz] =    -132.844370 [cm-1]
 (  0.000000  0.000000  0.000000  0.000000  0.711951  0.000000 )
 (  0.000000  0.000000  0.000000  0.000000 -0.702229  0.000000 )
     omega( 2) =       0.377569 [THz] =      12.594436 [cm-1]
 ( -0.762581  0.000000  0.000000  0.000000  0.000000  0.000000 )
 ( -0.646893  0.000000  0.000000  0.000000  0.000000  0.000000 )
     omega( 3) =       0.377569 [THz] =      12.594436 [cm-1]
 (  0.000000  0.000000 -0.762581  0.000000  0.000000  0.000000 )
 (  0.000000  0.000000 -0.646893  0.000000  0.000000  0.000000 )
     omega( 4) =       0.525357 [THz] =      17.524138 [cm-1]
 (  0.000000  0.000000  0.000000  0.000000 -0.702229  0.000000 )
 (  0.000000  0.000000  0.000000  0.000000 -0.711951  0.000000 )
     omega( 5) =       1.396045 [THz] =      46.567374 [cm-1]
 (  0.000000  0.000000 -0.646893  0.000000  0.000000  0.000000 )
 (  0.000000  0.000000  0.762581  0.000000  0.000000  0.000000 )
     omega( 6) =       1.396045 [THz] =      46.567374 [cm-1]
 ( -0.646893  0.000000  0.000000  0.000000   0.000000  0.000000 )
 (  0.762581  0.000000  0.000000  0.000000  0.000000  0.000000 )
-----------------------------------------------------------------------------------------------------------------------------

As you can see, the LO mode is largely negative while other modes(including
acoustic ones) seem fine. I have made convergence test to k-points,  ecut
and degauss. In other cases like the gold and platinum chains, the negative
modes are usually TO ones. So my question is: Why does this happen? Is there
any physics I missed in the above calculation, or just some naive settings
make the result weird?

Looking forward to your help. Thanks in advance!

Best wishes,
Jin Zhang
-- 
MPhil
Dept. of Physics, Peking University
Beijing, 100871, P.R.China
Phone: 86-10-62768590
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From marzari at MIT.EDU  Sun May 27 07:42:59 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Sun, 27 May 2007 01:42:59 -0400
Subject: [Pw_forum] Problems with phonon calculation in one-dimensional
 chains
In-Reply-To: <5d233b6a0705262207q3e009ee1n53b63678328339e8@mail.gmail.com>
References: <5d233b6a0705262207q3e009ee1n53b63678328339e8@mail.gmail.com>
Message-ID: <46591A63.7000406@mit.edu>


Dear Jin,

One possibility is that the chain wants to dimerize - i.e.
have an alternation of short or long bonds. With your current
input, the symmetry of the system is such that the forces are all
zero (and pwscf actually symmetrizes charge densities and forces
so that they satisfy all the symmetry operations that were found
by the code, so that the forces will actually be 0.0000000 with no 
numerical noise). In this way, you are permanently stuck at a
maximum or saddle point of the potential energy surface, instead of
a minimum.

Try breaking the symmetry by hand (e.g. put the first atom in
0.0 0.0 0.1) and relax the structure first.

If that is the case, this is probably something to be added to
http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions 
. You could write to bonini at mit.edu, and ask a password for the wiki,
and add it yourself !

				nicola
Jin Zhang wrote:
> Dear all,
> 
> I have encountered several issues related to Gamma point phonon 
> calculation in simple 1d chains(including aluminum, gold and platinum). 
> The symptom is *sometimes* there are one or more eigen-*optical*-modes 
> having negative(usually large) frequencies. The system I considered are 
> all 2-atom/cell 1d chains(to produce optical branches), with large 
> vacuum region around them(usually 16-20Bohrs). For example, the aluminum 
> input are listed below,
> ---------------------------------------------------------pw.x----------------------------------------------------------
> Infinite Al Chain NCPP
>    &CONTROL
>       calculation = 'scf',
>       prefix='al',
>       nstep=100,
>       tstress = .TRUE.,
>       tprnfor = .TRUE.,
>       outdir='./tmp/',
>       pseudo_dir = '/home/i/opt/espresso- 3.2/pseudo',
>       wf_collect=.true.,
>    /
>    &SYSTEM
>       ibrav=8,
>       celldm(1)=20.0,
>       celldm(2)=1.0,
>       celldm(3)=0.9,
>       nat=2,
>       ntyp=1,
>       ecutwfc=30.0,
>       occupations='smearing',
>       smearing='cold',
>       degauss=0.05,
>       !nbnd=40,
>       la2F=.true.,
>    /
>    &ELECTRONS
>       electron_maxstep = 100,
>       mixing_beta = 0.5,
>       conv_thr =  1.0d-8,
>    /
>    &IONS
>    /
> ATOMIC_SPECIES
> Al  26.98154  Al.pz-vbc.UPF
> ATOMIC_POSITIONS {crystal}
> Al    0.000    0.0   0.0
> Al    0.000    0.0   0.5
> K_POINTS (automatic)
>   1 1 40  0 0 1
> ------------------------------------------------------------ph.x---------------------------------------------------------------
>  &inputph
>   tr2_ph=1.0d-14,
>   recover = .false.
>   prefix='al',
>   fildvscf='dvscf',
>   alpha_mix=0.5,
>   amass(1)=26.98154,
>   outdir='./tmp',
>   fildyn='dyn',
>   elph=.false.,
>   trans=.true.,
>   ldisp=.true.,
>   nq1 =1, nq2 =1, nq3 = 1,
> /
> -------------------------------------------------------------------------------------------------------------------------------
> 
> The obtained frequency is
> 
> ------------------------------------------------------------------------------------------------------------------------------- 
> 
> 
>      omega( 1) =      -3.982548 [THz] =    -132.844370 [cm-1]
>  (  0.000000  0.000000  0.000000  0.000000  0.711951  0.000000 )
>  (  0.000000  0.000000  0.000000  0.000000 -0.702229  0.000000 )
>      omega( 2) =       0.377569 [THz] =      12.594436 [cm-1]
>  ( -0.762581  0.000000  0.000000  0.000000  0.000000  0.000000 )
>  ( -0.646893  0.000000  0.000000  0.000000  0.000000  0.000000 )
>      omega( 3) =       0.377569 [THz] =      12.594436 [cm-1]
>  (  0.000000  0.000000 -0.762581  0.000000  0.000000  0.000000 )
>  (  0.000000  0.000000 -0.646893  0.000000  0.000000  0.000000 )
>      omega( 4) =       0.525357 [THz] =      17.524138 [cm-1]
>  (  0.000000  0.000000  0.000000  0.000000 -0.702229  0.000000 )
>  (  0.000000  0.000000  0.000000  0.000000 -0.711951  0.000000 )
>      omega( 5) =       1.396045 [THz] =      46.567374 [cm-1]
>  (  0.000000  0.000000 -0.646893  0.000000  0.000000  0.000000 )
>  (  0.000000  0.000000  0.762581  0.000000  0.000000  0.000000 )
>      omega( 6) =       1.396045 [THz] =      46.567374 [cm-1]
>  ( -0.646893  0.000000  0.000000  0.000000   0.000000  0.000000 )
>  (  0.762581  0.000000  0.000000  0.000000  0.000000  0.000000 )
> ----------------------------------------------------------------------------------------------------------------------------- 
> 
> As you can see, the LO mode is largely negative while other 
> modes(including acoustic ones) seem fine. I have made convergence test 
> to k-points,  ecut and degauss. In other cases like the gold and 
> platinum chains, the negative modes are usually TO ones. So my question 
> is: Why does this happen? Is there any physics I missed in the above 
> calculation, or just some naive settings make the result weird?
> 
> Looking forward to your help. Thanks in advance!
> 
> Best wishes,
> Jin Zhang
> -- 
> MPhil
> Dept. of Physics, Peking University
> Beijing, 100871, P.R.China
> Phone: 86-10-62768590


-- 
---------------------------------------------------------------------
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 hqzhou at nju.edu.cn  Sun May 27 06:22:38 2007
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Sun, 27 May 2007 12:22:38 +0800
Subject: [Pw_forum] Done successfully ... but .... !!!
References: <82a593400705261128we5b1169y331cb24f320efbdd@mail.gmail.com>
Message-ID: <006d01c7a01d$97fe0010$1d00a8c0@solarflare>

Hashem,

The error message is very clear. You'd better check whether your tmp directory
is under /home or /home/espresso-3.2, and you have given "write" permission
to the folder for all users.


Huiqun Zhou at Nanjing University, China

  ----- Original Message ----- 
  From: Hashem Al-Yamani 
  To: pw_forum 
  Sent: Sunday, May 27, 2007 2:28 AM
  Subject: [Pw_forum] Done successfully ... but .... !!!


  Dear All ;


  I 've made my first cluster using mpich2 and PWSCF ..... I put the espresso folder and psedue and tmp folders on /home directory which is shared by NFS via the machines ...... now when I tryed a file it gave the following error : 



       from outdir:  : error #         1
       /home/espresso-3.2/tmp/ non existent or non writable
  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 
     Program PWSCF     v.3.2    starts ...
       Today is 26May2007 at 15:10:47 

       Parallel version (MPI)

       Number of processors in use:       2
       R & G space division:  proc/pool =    2

       Ultrasoft (Vanderbilt) Pseudopotentials

       Current dimensions of program pwscf are:

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

   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
       from outdir:  : error #         1
       /home/espresso-3.2/tmp/ non existent or non writable
   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

       stopping ...
  rank 1 in job 9  server2_1074   caused collective abort of all ranks
    exit status of rank 1: return code 47 
  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 


  Now does this means that the other machine (i.e : not the server that am running the job from) is not able to write in the tmp folder ... or is it something else .......... and if so what could be a reasonable solution ....................   any ideas would be very appreciaple ... and thanks all 


  Regards ;
  Hashem
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From mbaris at metu.edu.tr  Sun May 27 13:33:55 2007
From: mbaris at metu.edu.tr (mbaris at metu.edu.tr)
Date: Sun, 27 May 2007 14:33:55 +0300
Subject: [Pw_forum] pwscf tests/examples question
Message-ID: <20070527143355.885zl5k08e0wk40w@webmail2.metu.edu.tr>

Hello to all,
   First of all, I must mention that I am completely a newbie, and some 
of my questions may be too trivial, but I will be glad if you answer 
them.

    I recently compiled espresso 3.2.2 on an Intel box (details at the 
end), the compilation went smoothly, but I am encountering some errors 
in tests/examples.

First things first, when I edit the environment_variables file to use 
mpich2 (PARA_PREFIX="mpiexec -n 4") and run run_all_examples, the batch 
halts at   example05 in running pp.x. On a single cpu (i.e. with 
PARA_PREFIX empty) upto example34 can be run, which fails stating vdw.x 
can not be found. Is this a bug, or something related to my computer? 
(I failed to see the error in example05 script)

Secondly, (and this is the most important problem I encounter)
In some of the examples, there are deviations from the reference data, 
most of them are not worth mentioning, as they are not in the final 
structure, however there is one puzzling me and my colleague greatly. 
Looking at c.scf.out in example02 (>:reference <:my computer) :
<      estimated scf accuracy    <        4.3E-10 Ry
---
>      estimated scf accuracy    <        4.4E-10 Ry
207,209c193,195
<      one-electron contribution =     7.88010983 Ry
<      hartree contribution      =     1.91301246 Ry
<      xc contribution           =    -7.07049550 Ry
---
>      one-electron contribution =     7.88010934 Ry
>      hartree contribution      =     1.91301318 Ry
>      xc contribution           =    -7.07049573 Ry
As you can see, the contribution weights are different, however the 
resulting energy is the same!!! check_example seems to ignore this. I 
have tried running the example using version 3.2 and 3.2.1 to no avail, 
always the same. What might be the problem, or is it a problem I need 
to dig further?

Lastly, with the encouragement of the manual I have installed intel 
MKL, but instead of seeing a performance leap, the code runs slightly 
slower now (order of 0.01 sec). I guess more fine tuning is required on 
my side.

This box is a test bed for a highly parallel blade server array in my 
school, I am using it to prepare mpich2 integrated gridengine scripts 
and such (which I am happy to share if demanded) along with the 
projects I am assigned.

Thank you for your time,
O. Baris Malcioglu  METU Physics Dep. Ankara

Intel box details:
Hardware:
  Intel D975xbx2
  Intel core 2 quad 6600
  2 gb ddr2 667 4-4-4-15 ram
  Raid 5 sata disk array.
Software:
  OpenSuse 10.2 64 bit (Stock Kernel 2.6.18.8-0.3, stock glibc 2.5-25)
  Intel fortran compiler 64bit 9.1.045
  Intel c compiler 64 bit 9.1.049
  Intel mkl 9.0
  mpich2 with smpd daemon (for tight integration with sge)
  Sun grid engine 6.1




From mbaris at metu.edu.tr  Sun May 27 14:57:27 2007
From: mbaris at metu.edu.tr (mbaris at metu.edu.tr)
Date: Sun, 27 May 2007 15:57:27 +0300
Subject: [Pw_forum] vc-relax newbie question
Message-ID: <20070527155727.r4y8kp89468wg8s4@webmail2.metu.edu.tr>

Hello to all,
  This is my second post to this list today, sorry about that, but I 
think this requires another thread.  As I have mentioned before, I am a 
newbie, and some of the questions may not make sense, however I would 
be glad if you answer them.  In the project I am assigned, I am 
required to find lattice constant of the Pd crystal several times. As 
suggested, due to simplicity, this can be done by interpolating a 
volume vs. E curve, but my previous experience with other programs 
suggest that this is rather inefficient if not inaccurate. At this 
point vc-relax comes to help. This is the input (please notice &cell 
card):

--------begin input card --------------

&control
    calculation = 'vc-relax'
    verbosity = 'minimal'
    restart_mode='from_scratch',
    pseudo_dir = 'somewhere'
    outdir='somewhere',
    prefix='bla-bla'
/
&system
    ibrav = 2,
    celldm(1) = 7.353,
    nat = 1,
    ntyp = 1,
        ecutwfc = 25,
        ecutrho = 250,
    occupations = 'smearing',
        smearing = 'mp',
        degauss = 0.001,
/
&Electrons
/
&ions
/
&CELL
        wmass=425.68   <- I am ok with the defaults mostly, however 
running the #pw.x it complains about missing wmass, bug? /
ATOMIC_SPECIES
Pd 106.42 Pd.pbe-nd-rrkjus.UPF
ATOMIC_POSITIONS {crystal}
Pd 0 0 0
K_POINTS {automatic}
6 6 6 0 0 0

--------end input card --------------
If I understand correctly, this (the defaults) should be sufficient for 
the calculation of ideal (theoretical) lattice constant (any 
help/comments is appreciated here).

The problem is, I can not locate the resulting lattice parameters in 
the output file!

in reporting the stress on the system, there is an output like

----- begin output -------
     entering subroutine stress ...

          total   stress  (Ry/bohr**3)                   (kbar)     P=  107.95
   0.00073383   0.00000000   0.00000000        107.95      0.00      0.00
   0.00000000   0.00073383   0.00000000          0.00    107.95      0.00
   0.00000000   0.00000000   0.00073383          0.00      0.00    107.95


     Damped Dynamics: convergence achieved, Efinal=   -76.06544689
------ end output ----------

The stress seems to be minimized but high

in the previous non-converged step, there was volume reported, but in 
the last step it is missing and volume information may not be relevant 
for i.e. oblique cells in finding angles etc.


the other output is pretty useless to me as I don't expect anything 
other than fcc:

----- begin output -------

CELL_PARAMETERS (alat)
  -0.500000000   0.000000000   0.500000000
   0.000000000   0.500000000   0.500000000
  -0.500000000   0.500000000   0.000000000

ATOMIC_POSITIONS (crystal)
Pd       0.000000000   0.000000000   0.000000000
------ end output ----------

but where is a(1)?

I looked through the documentation and could not found anything (is 
there something like OUTPUT_PW? If not, it should be greatly 
appreciated)

and digging thorough various xml files in tmp directory yielded nothing 
up to now.

The most interesting thing is, when I change the lattice dimension to 
8, the stress increase and the system converge immediately in the first 
step. The error seems to be most fundamental but being new to the 
topic, I can not locate it.

P.S. increasing verbosity does not help.


any help is appreciated. O. Baris Malcioglu




From giannozz at nest.sns.it  Mon May 28 09:24:56 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 28 May 2007 09:24:56 +0200
Subject: [Pw_forum] Done successfully ... but .... !!!
In-Reply-To: <006d01c7a01d$97fe0010$1d00a8c0@solarflare>
References: <82a593400705261128we5b1169y331cb24f320efbdd@mail.gmail.com> <006d01c7a01d$97fe0010$1d00a8c0@solarflare>
Message-ID: <665EBCB5-0FE6-4529-87D3-17A8D2F10CA7@nest.sns.it>

On May 27, 2007, at 6:22 , Huiqun Zhou wrote:

> The error message is very clear. You'd better check whether
> your tmp directory is under /home or /home/espresso-3.2, and
> you have given "write" permission to the folder for all users.

not necessarily so: the scratch directory used by QE has to
exist, and to be writable by the user who runs the code.
There is no need to make it writable to all users

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




From hashem.yamani at gmail.com  Mon May 28 10:18:48 2007
From: hashem.yamani at gmail.com (Hashem Al-Yamani)
Date: Mon, 28 May 2007 11:18:48 +0300
Subject: [Pw_forum] Parallel PWSCF
Message-ID: <82a593400705280118q61957659hf41897669e3b03f0@mail.gmail.com>

Dear All ;

Is it neccessary that jobs be faster while using parallel environment thatn
in serial ?

and if not so what is the use of parallel environment ??


Thanks .



Regards ;

Hashem
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From cesards at msi.umn.edu  Mon May 28 10:42:02 2007
From: cesards at msi.umn.edu (cesards at msi.umn.edu)
Date: Mon, 28 May 2007 03:42:02 -0500 (CDT)
Subject: [Pw_forum] vc-relax newbie question
Message-ID: <50388.209.162.9.168.1180341722.squirrel@www.msi.umn.edu>

Hi Baris,

there are somethings necessary in your input:

1-use default verbosity
2-wmass is way too high. Use something like 0.002
3-In Electrons namelist use conv_thr at least as small as conv_thr=1.0d-8.
4-in Cell namelist, you have to set the target pressure (like   press=0.0).
5-dt has to be set in Control namelist. dt=80 will probably do OK.


Yours,

Cesar R.S. da Silva



From Giovanni.Cantele at na.infn.it  Mon May 28 11:06:48 2007
From: Giovanni.Cantele at na.infn.it (Giovanni Cantele)
Date: Mon, 28 May 2007 11:06:48 +0200
Subject: [Pw_forum] Parallel PWSCF
In-Reply-To: <82a593400705280118q61957659hf41897669e3b03f0@mail.gmail.com>
References: <82a593400705280118q61957659hf41897669e3b03f0@mail.gmail.com>
Message-ID: <465A9BA8.70206@na.infn.it>

Hashem Al-Yamani wrote:
> Dear All ;
>  
> Is it neccessary that jobs be faster while using parallel environment 
> thatn in serial ?
It is not! It depends on the code, how many CPUs are used, their 
interconnection....

Of course, if you properly use parallelism, it can significantly improve 
the performances
of a given code and Quantum-Espresso is quite a good example!!!!   :-)
>  
> and if not so what is the use of parallel environment ??
If your question concerns parallel computing in general, you can search, 
for example "parallel programming" on google.
Among the results, from: http://en.wikipedia.org/wiki/Parallel_computing

*Parallel computing* is the simultaneous execution of the /same task/ 
(split up and specially adapted) on multiple processors 
<http://en.wikipedia.org/wiki/Central_processing_unit> in order to 
obtain results faster. The idea is based on the fact that the process of 
solving a problem usually can be divided into smaller tasks, which may 
be carried out simultaneously with some coordination.

Lot of manuals and handbooks, including examples, can also be found.


Instead, if you question concerns, more specifically parallelism 
performances in Quantum-Espresso, you could start from
answers already given in this forum, that you can easily browse using 
the Search option.
For example:
http://www.democritos.it/pipermail/pw_forum/2005-September/002993.html


Also, you could have a look to the user guide:

http://www.quantum-espresso.org/wiki/index.php/User_Guide

Here, you'll find a section "Performance issues (PWscf) 
<http://www.quantum-espresso.org/wiki/index.php/Performance_issues_%28PWscf%29>" 
that could give answers to your questions.


Hope this helps,
Giovanni


-- 



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



From giannozz at nest.sns.it  Mon May 28 11:14:45 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 28 May 2007 11:14:45 +0200
Subject: [Pw_forum] vc-relax newbie question
In-Reply-To: <20070527155727.r4y8kp89468wg8s4@webmail2.metu.edu.tr>
References: <20070527155727.r4y8kp89468wg8s4@webmail2.metu.edu.tr>
Message-ID: <4EEB6AC8-66B1-4789-AB26-F1E03F97C5FF@nest.sns.it>

On May 27, 2007, at 14:57 , mbaris at metu.edu.tr wrote:

> I am required to find lattice constant of the Pd crystal several  
> times.
> As suggested, due to simplicity, this can be done by interpolating a
> volume vs. E curve, but my previous experience with other programs
> suggest that this is rather inefficient if not inaccurate.

my previous experience suggests the opposite, at least for a simple
system

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




From lanhaiping at gmail.com  Mon May 28 15:21:49 2007
From: lanhaiping at gmail.com (lan haiping)
Date: Mon, 28 May 2007 21:21:49 +0800
Subject: [Pw_forum] About xcrysden display
Message-ID: <c92002fa0705280621p5d62130dga210ace1023274d7@mail.gmail.com>

Dear All :

 I am sorry for  sending this problem to pw forum , since i thought there
should be  a few experienced people here.
I do want to display several xsf maps in the same crystal structure with
XCRYSDEN, but i donot find any solution.
I just find script of  multiscript for displaying several results
successively, e.g. displaying results with the same setting parameters.
Is there any way to display several xsf files in  single screen ? If so,
Would you  please share the script with me ?

Regards,
H.P

-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From paulatto at sissa.it  Mon May 28 16:06:08 2007
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Mon, 28 May 2007 16:06:08 +0200 (CEST)
Subject: [Pw_forum] About xcrysden display
In-Reply-To: <c92002fa0705280621p5d62130dga210ace1023274d7@mail.gmail.com>
References: <c92002fa0705280621p5d62130dga210ace1023274d7@mail.gmail.com>
Message-ID: <14082.147.122.5.194.1180361168.squirrel@webmail.sissa.it>

On Mon, May 28, 2007 15:21, lan haiping wrote:
> Is there any way to display several xsf files in  single screen ? If so,
> Would you  please share the script with me ?

As far as I know you cannot do what you wish. You can merge together
several xsf files (it's very easy if they use the same mesh), but xcd will
only display one mesh (isosurface), or the (weighted) sum of more meshes, 
at a time.

gOpenMol can plot different meshes, but only works for cubic SC lattices.

bye

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


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



From giannozz at nest.sns.it  Mon May 28 16:07:54 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 28 May 2007 16:07:54 +0200
Subject: [Pw_forum] pwscf tests/examples question
In-Reply-To: <20070527143355.885zl5k08e0wk40w@webmail2.metu.edu.tr>
References: <20070527143355.885zl5k08e0wk40w@webmail2.metu.edu.tr>
Message-ID: <B824BB5E-8A52-4613-B149-1D78CBD6869E@nest.sns.it>

On May 27, 2007, at 13:33 , mbaris at metu.edu.tr wrote:

> when I edit the environment_variables file to use mpich2
> (PARA_PREFIX="mpiexec -n 4") and run run_all_examples,
> the batch halts at example05 in running pp.x

there are a few things that you cannot do in parallel using pp.x

> On a single cpu (i.e. with PARA_PREFIX empty) upto example34
> can be run, which fails stating vdw.x can not be found.

it is not there, it has to be separately downloaded. If you do not
need it, just ignore it

> <      one-electron contribution =     7.88010983 Ry
> <      hartree contribution      =     1.91301246 Ry
> <      xc contribution           =    -7.07049550 Ry
> ---
>>      one-electron contribution =     7.88010934 Ry
>>      hartree contribution      =     1.91301318 Ry
>>      xc contribution           =    -7.07049573 Ry
> As you can see, the contribution weights are different, however the  
> resulting energy is the same!!!

these are minor numerical differences that it is hard to avoid. Since  
the
total energy is variational (i.e. the first-order error wrt the error  
in the
charge density vanishes), it is less sensitive to minor differences  
in the
calculated rho than the various contributions

> check_example seems to ignore this.

check_example was written exactly to ignore such small numerical  
differences

> Lastly, with the encouragement of the manual I have installed intel  
> MKL, but instead of seeing a performance leap, the code runs  
> slightly slower now (order
> of 0.01 sec). I guess more fine tuning is required on my side.

it is unlikely to see much gain in small calculations, but in serious  
calculations
the advantage of using MKL will be visible

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




From mbaris at metu.edu.tr  Mon May 28 16:16:57 2007
From: mbaris at metu.edu.tr (obm)
Date: Mon, 28 May 2007 17:16:57 +0300
Subject: [Pw_forum] vc-relax newbie question
In-Reply-To: <4EEB6AC8-66B1-4789-AB26-F1E03F97C5FF@nest.sns.it>
References: <20070527155727.r4y8kp89468wg8s4@webmail2.metu.edu.tr> <4EEB6AC8-66B1-4789-AB26-F1E03F97C5FF@nest.sns.it>
Message-ID: <465AE459.1060608@metu.edu.tr>

Hi,

First of all, thank you very much for the quick reply,

at this point I will no longer try using vc-relax for this problem, as
Paolo suggests (let the scripting begin).

However, I wish to comment the suggestions Cesar R.S. da Silva made, at
least for reference purposes


1-use default verbosity
I tried all verbosity levels, all to no avail (looking down, possibly
the problem was different)
2-wmass is way too high. Use something like 0.002
I am completely puzzled at this. Looking at the help document INPUT_PW
wmass          REAL ( default = sum of atomic masses in the cell )
               fictitious cell mass [amu] for variable-cell simulations
               (both 'vc-md' and 'vc-relax')
being a fcc crystal, there are 4 atoms in the cell with mass 106.42 amu
each summing to indicated value. I can only imagine your suggestion is
based on a deeper understanding of the relaxation procedure which I
failed to find a reference to in the manuals. I would be grateful if you
suggest one.
3-In Electrons namelist use conv_thr at least as small as conv_thr=1.0d-8.
You are absolutely right.
4-in Cell namelist, you have to set the target pressure (like   press=0.0).
Again in the manual INPUT_PW it states 0.0 is the default value.

press          REAL ( default = 0.D0 )
               target pressure [KBar] in a variable-cell md or
relaxation run.

Do I have to include cards, even I will use the default values?

5-dt has to be set in Control namelist. dt=80 will probably do OK.
So, does vc-relax rely on some molecular dynamics? I thought it was
similar to implementation in gaussian03, where the program does the
volume to energy fitting for you (in a rather efficient manner) and
returns the final cell parameters. Well, if this is the case, it really
does not fit my purposes.



Thank you again,

Yours,
O Baris Malcioglu.


From giannozz at nest.sns.it  Mon May 28 16:27:05 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 28 May 2007 16:27:05 +0200
Subject: [Pw_forum] a question about a calculation on a relatively large system
In-Reply-To: <dac27ff50701311349r61c0842ew5a749ccd75ba727c@mail.gmail.com>
References: <dac27ff50701151127k638aede7qd7e2e50663159c7b@mail.gmail.com> <421493EA-D152-4912-8B08-705AB755EEEC@nest.sns.it> <dac27ff50701160819j9987059j9eaeb8db16f372e8@mail.gmail.com> <484321DC-4E72-449C-953A-0D74635C06C1@nest.sns.it> <dac27ff50701311349r61c0842ew5a749ccd75ba727c@mail.gmail.com>
Message-ID: <B8DB46C5-1C46-424F-ABD1-316B0D4EAABA@nest.sns.it>

On Jan 15, 2007, at 14:27 , Peter Winey wrote:

> I am trying to do a structural relaxation on a relatively large  
> system,
> which has 240 atoms in one unit cell
> [...]
> The run stopped without giving any information expect saying that "mpi
> stopped without calling mpi_finalize" or sth like that.
>
> I repeated the calculation and it always stopped at the same place.
> It is wierd since I had no problem before when running smaller systems
> (say, 150 atoms).

I recently encountered a similar problem (with 200 atoms; no problem
in a smaller cell). Apparently the code crashes in the three following
lines of update_inverse_hessian, in Modules/bfgs_modules.f90 :

       inv_hess = inv_hess + 1.D0 / sdoty * &
                  ( ( 1.D0 + ( y .dot. Hy ) / sdoty ) * matrix( s,  
s ) - &
                   ( matrix( s, yH ) +  matrix( Hy, s ) ) )

If you replace the three lines above with old-style fortran:

       ydotHy = ( y .dot. Hy )
       do j=1,n
          do i=1,n
             inv_hess(i,j) = inv_hess(i,j) + 1.D0 / sdoty * &
                       ( ( 1.D0 + ydotHy / sdoty ) * s(i) * s(j) - &
                          ( s(i)*yH(j) + Hy(i)*s(j) ) )
          end do
       end do

it works (ifort on a PC cluster). I cannot see any good reason
for such a behavior.

By the way: in case of trouble with bfgs, one can always
try damped dynamics.

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




From akohlmey at cmm.chem.upenn.edu  Mon May 28 17:28:55 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 28 May 2007 11:28:55 -0400 (EDT)
Subject: [Pw_forum] About xcrysden display
In-Reply-To: <c92002fa0705280621p5d62130dga210ace1023274d7@mail.gmail.com>
Message-ID: <Pine.LNX.4.44.0705281127100.6382-100000@localhost.localdomain>

On Mon, 28 May 2007, lan haiping wrote:

HP> Dear All :
HP> 
HP>  I am sorry for  sending this problem to pw forum , since i thought there
HP> should be  a few experienced people here.
HP> I do want to display several xsf maps in the same crystal structure with
HP> XCRYSDEN, but i donot find any solution.
HP> I just find script of  multiscript for displaying several results
HP> successively, e.g. displaying results with the same setting parameters.
HP> Is there any way to display several xsf files in  single screen ? If so,
HP> Would you  please share the script with me ?

you could try VMD ( http://www.ks.uiuc.edu/Research/vmd ).
since it is primarily written for biomolecules, the support
for crystal structure specific features is limited, but it
can handle displaying multiple gridded (3-d) datasets at
the same time.
cheers,
   axel.


HP> 
HP> Regards,
HP> H.P
HP> 
HP> 

-- 
=======================================================================
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 hongyi.zhao at gmail.com  Tue May 29 11:02:23 2007
From: hongyi.zhao at gmail.com (Hongyi Zhao)
Date: Tue, 29 May 2007 17:02:23 +0800
Subject: [Pw_forum] How can I generate the USPP of hafnium used by PWSCF?
In-Reply-To: <895f446b0705280247h5f704447ta78ef7974b943087@mail.gmail.com>
References: <20070526035742.GA25645@debianhy.localdomain> <4657C34B.1040104@mit.edu> <895f446b0705280247h5f704447ta78ef7974b943087@mail.gmail.com>
Message-ID: <20070529090223.GA10697@debianhy.localdomain>

 2007/5/26, Nicola Marzari <marzari at mit.edu>:
 
     Hongyi Zhao wrote:
     > Hi all,
     >
     > Now, I want to do some computations on HfO_2 under the vanderbilt's
     > scheme of USPP, but I cann't find any available USPP of hafnium.  What
     > should I do, will you anyone give me some hints?
     >
     > Thanks in advance.
     > ---
     > Honyi Zhao <hongyi.zhao at gmail.com>
     > Xinjiang Technical Institute of Physics and Chemistry
     > Chinese Academy of Sciences
     > gpg DSA: 0xD108493B
 
 
     Dear Honyi,
 
     have a look at this:
     Davide Ceresoli and David Vanderbilt, "Structural and dielectric
     properties of amorphous ZrO2 and HfO2, Physical Review B 74, 125108 (2006).
 
     Maybe they report the parameters used to generate the pseudo,
     or you could ask directly, politely, to Davide or to David if
     they could send you a copy.
 
     If they do, send the pseudo also to Paolo Giannozzi,
     Paolo Giannozzi <p.giannozzi at fisica.uniud.it>, so he can
     update the web site, and mention that it was used for the paper
     above.
 
                                     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
     _______________________________________________
     Pw_forum mailing list
     Pw_forum at pwscf.org
     http://www.democritos.it/mailman/listinfo/pw_forum
 
Dear Nicola and Paolo,

I've send a mail to David Vanderbilt according to the suggestions above,?
and David has send me a reply mail.  Now, I post all the contents of the?
mail here verbatim for further helps:


---------------------------------------------
The original mails between David and me begins here:
 
Dear Hongyi,

Please try this and see if it works:

------------------------------------------------------------------------
     0    2    1    1    3             ifae,ifpsp,ifprt,ifplw,ilogd (5i5)
    2.5      -2.4       1.6       80   rlogd,emin,emax,nnt (3f10.5,i5)
    1.0d-10   1.0d-09   0.5        0   thresh,tol.damp,maxit (2e10.1,f10.5,i5)
hf                                    title (a20)
    12    2    3                       ncores,nvales,nang (3i5)
  10.0      10.0       40.0        5.0   besrmax, besemin,besemax,besde(4f10.5)
     3    0   1.2                      keyps,ifpcor,rinner (2i5)
     4   2.4                           nbeta,rcloc (i5,f10.5)
    2.4       2.4       2.4            rc (4f10.5)
     0    2   0.0        2             lll,keyee,eeread,iptype (2i5,f10.5,i5)
     0    0   3.5        2             lll,keyee,eeread,iptype (2i5,f10.5,i5)
     2    1   0.0        2
     2    0   0.0        2
     8  10.0                           npf,ptryc (i5,f10.5)
     1    0  -0.5        1             lloc,keyee,eloc,iploctype (2i5,f10.5,i5)
     3    8  10.00000                  ifqopt,nqf,qtryc (2i5,f10.5
------------------------------------------------------------------------

I cannot publish this online because it was developed as part of a
commercial project, ie, it is NOT open-source.  (Ever since, I have
tried to avoid such problems by working only in open-source
environments.)

David Vanderbilt


On Mon, 28 May 2007, Hongyi Zhao wrote:

> Dear Prof. David,
>
> Now, I want to do some computations on HfO_2 under your
> scheme of USPP by using the PWSCF code, but I cann't find any available
> USPP of hafnium on the website of PWSCF.  Furthmore, I also look
> through the Ultra-Soft Pseudopotential Site of yours, that is, the URL:
>
> http://www.physics.rutgers.edu/~dhv/uspp/
>
> but unfortunately, I find that the pseudo of hafnium haven't been generated
> by members of your group or contributed by members of the
> wider user community yet.
>
> I know the PWSCF itself has a  utility called ld1.x which can generate
> both Norm-Conserving (NC) and Ultrasoft (US) PP's.  But I'm a novice in
> doing this thing and the pseudo-generating ifself is a very tricky thing
> in my mind.
>
> As a last resort, I take the liberty to write to you this mail for your
> help.  Would you be so kindly give me some hints or the parameters used
> to generate the pseudo which has been used by you or your group in some
> paper(s) for hafnium?  BTW, it will be most fortunate for me if you just
> has the pseudo at hand and would like to give me a copy of it.
>
> If I can get a copy of the pseudo, I'll
> send it to Paolo Giannozzi,<p.giannozzi at fisica.uniud.it>, so that he can
> update the PWSCF's website, and at the meantime, I'll  mention
> that it was used for the *corresponding* paper of yours.
>
> ---
> Hongyi Zhao <hongyi.zhao at gmail.com>
> Xinjiang Technical Institute of Physics and Chemistry
> Chinese Academy of Sciences
> GnuPG DSA: 0xD108493B
>

The original mails between David and me begins end here.
--------------------------------------------------
  






From mbaris at metu.edu.tr  Tue May 29 12:31:56 2007
From: mbaris at metu.edu.tr (obm)
Date: Tue, 29 May 2007 13:31:56 +0300
Subject: [Pw_forum] Effect of kernel parameters to calculation of larger systems
Message-ID: <465C011C.1080007@metu.edu.tr>

Hi to all,
	Does configurable kernel variables like shmmax have any impact on the
size of the system that can be calculated?




From akohlmey at cmm.chem.upenn.edu  Tue May 29 14:44:52 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 29 May 2007 08:44:52 -0400 (EDT)
Subject: [Pw_forum] Effect of kernel parameters to calculation of larger
 systems
In-Reply-To: <465C011C.1080007@metu.edu.tr>
Message-ID: <Pine.LNX.4.44.0705290840531.31278-100000@localhost.localdomain>

On Tue, 29 May 2007, obm wrote:

> Hi to all,

hi to <unknown>!

> 	Does configurable kernel variables like shmmax have any impact on the
> size of the system that can be calculated?

not directly, however some compilers, e.g. the intel fortran
compilers require a larger stack segment, than what is the
default, and some MPI libraries or interconnects, e.g. infiniband
with OpenMPI needs the maximum locked memory area to be much
enlarged, can required changes in the default settings, either
in the kernel or in ulimit/pam settings. however, those are
not specific to the quantum espresso software (unlike, e.g., 
gaussian, that needs a large shared memory segment for its
_internal_ shared memory parallelization).

cheers,
   axel.

> _______________________________________________
> 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 kondor.jess at gmail.com  Tue May 29 16:10:45 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Tue, 29 May 2007 09:10:45 -0500
Subject: [Pw_forum] relaxation
Message-ID: <1d9d5d9d0705290710o2d876813t5c6817c4253b3288@mail.gmail.com>

Hi, everyone,

 I have a question. Sometimes (at least, I found several times in the papers
for ferroelectrics), we need to relax a system with very tight criteria for
forces - up to 1 meV/Ang ( ~4.0d-5 in `pw (a.u.)` units). However, I found
that it is hard to achieve this criteria. If I use 'bfgs' with   conv_thr =
1.d-6 (or better) and upscale = 10.d0 , calculations often crashes with
message ''bfgs history was reset on the previous step...' and number of bfgs
steps = 15, number of scf steps = 2 . If I switch a relaxation method to
'damp' with dt=70.0, after one (or two) ionic steps forces are small, but
then 'Total force' increases rapidly (from 0.001 to 0.4 or something) and
remains almost constant. So, are there any other parameters which can help
in geometry relaxation?

cheers,
   Jess
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From akohlmey at cmm.chem.upenn.edu  Tue May 29 15:50:38 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 29 May 2007 09:50:38 -0400 (EDT)
Subject: [Pw_forum] relaxation
In-Reply-To: <1d9d5d9d0705290710o2d876813t5c6817c4253b3288@mail.gmail.com>
Message-ID: <Pine.LNX.4.44.0705290947480.31278-100000@localhost.localdomain>

On Tue, 29 May 2007, Jess Kondor wrote:

JK> Hi, everyone,

hi jess,

JK>  I have a question. Sometimes (at least, I found several times in the papers
JK> for ferroelectrics), we need to relax a system with very tight criteria for
JK> forces - up to 1 meV/Ang ( ~4.0d-5 in `pw (a.u.)` units). However, I found
JK> that it is hard to achieve this criteria. If I use 'bfgs' with   conv_thr =
JK> 1.d-6 (or better) and upscale = 10.d0 , calculations often crashes with

if you want to converge the geometry tightly, you have to converge 
the wavefunction even more tightly. also, you may run into 'ripples', 
particularly when using ultra-soft pseudopotentials.
in that case, you may also need to crank up the density cutoff.

cheers,
   axel.

JK> message ''bfgs history was reset on the previous step...' and number of bfgs
JK> steps = 15, number of scf steps = 2 . If I switch a relaxation method to
JK> 'damp' with dt=70.0, after one (or two) ionic steps forces are small, but
JK> then 'Total force' increases rapidly (from 0.001 to 0.4 or something) and
JK> remains almost constant. So, are there any other parameters which can help
JK> in geometry relaxation?
JK> 
JK> cheers,
JK>    Jess
JK> 

-- 
=======================================================================
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 kondor.jess at gmail.com  Tue May 29 17:06:06 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Tue, 29 May 2007 10:06:06 -0500
Subject: [Pw_forum] relaxation
In-Reply-To: <Pine.LNX.4.44.0705290947480.31278-100000@localhost.localdomain>
References: <1d9d5d9d0705290710o2d876813t5c6817c4253b3288@mail.gmail.com>
	 <Pine.LNX.4.44.0705290947480.31278-100000@localhost.localdomain>
Message-ID: <1d9d5d9d0705290806w199bb64do40f34acd27a084ac@mail.gmail.com>

Hi Axel,

>
> if you want to converge the geometry tightly, you have to converge
> the wavefunction even more tightly. also, you may run into 'ripples',
> particularly when using ultra-soft pseudopotentials.
> in that case, you may also need to crank up the density cutoff.
>
>
Thank you for suggestions, I'll try it. By the way, I use ecutwfc=35 Ry, and
ecutrho=350 Ry, I think it was enough for ultrasoft PP.

cheers,
  jess
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From akohlmey at cmm.chem.upenn.edu  Tue May 29 16:19:36 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 29 May 2007 10:19:36 -0400 (EDT)
Subject: [Pw_forum] relaxation
In-Reply-To: <1d9d5d9d0705290806w199bb64do40f34acd27a084ac@mail.gmail.com>
Message-ID: <Pine.LNX.4.44.0705291013500.31278-100000@localhost.localdomain>

On Tue, 29 May 2007, Jess Kondor wrote:

JK> Hi Axel,
JK> 
JK> >
JK> > if you want to converge the geometry tightly, you have to converge
JK> > the wavefunction even more tightly. also, you may run into 'ripples',
JK> > particularly when using ultra-soft pseudopotentials.
JK> > in that case, you may also need to crank up the density cutoff.
JK> >
JK> >
JK> Thank you for suggestions, I'll try it. By the way, I use ecutwfc=35 Ry, and
JK> ecutrho=350 Ry, I think it was enough for ultrasoft PP.

it should be. it might depend on the pseudization parameters a little 
bit. and if you need high accuracy, you may need to crank up the 
wavefunction cutoff, too. 

cheers,
  axel.

JK> 
JK> cheers,
JK>   jess
JK> 

-- 
=======================================================================
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 peterwiney at gmail.com  Tue May 29 19:22:30 2007
From: peterwiney at gmail.com (Peter Winey)
Date: Tue, 29 May 2007 13:22:30 -0400
Subject: [Pw_forum] a question about a calculation on a relatively large system
In-Reply-To: <B8DB46C5-1C46-424F-ABD1-316B0D4EAABA@nest.sns.it>
References: <dac27ff50701151127k638aede7qd7e2e50663159c7b@mail.gmail.com>
	 <421493EA-D152-4912-8B08-705AB755EEEC@nest.sns.it>
	 <dac27ff50701160819j9987059j9eaeb8db16f372e8@mail.gmail.com>
	 <484321DC-4E72-449C-953A-0D74635C06C1@nest.sns.it>
	 <dac27ff50701311349r61c0842ew5a749ccd75ba727c@mail.gmail.com>
	 <B8DB46C5-1C46-424F-ABD1-316B0D4EAABA@nest.sns.it>
Message-ID: <dac27ff50705291022w5d23a8f9p80fd9d67deb545a3@mail.gmail.com>

Dear Paolo, Thanks for sharing the information!

I followed your way and recompiled the code. However, the code still crashed
after the second scf iteration, same as before.

When I used damped dynamics, the code crashed after the first scf iteration.
This behavior is also same as before.

I'll sent my pwscf input file to your email address for a test (it is a
bit long to be
posted here).

I was using cp.x these days for relatively large system with no problem. But
still, it would be nice if I could run pw.x and compare the cp.x result with
the
pw.x result.

Thanks!

On 5/28/07, Paolo Giannozzi <giannozz at nest.sns.it> wrote:


> I recently encountered a similar problem (with 200 atoms; no problem
> in a smaller cell). Apparently the code crashes in the three following
> lines of update_inverse_hessian, in Modules/bfgs_modules.f90 :
>
>       inv_hess = inv_hess + 1.D0 / sdoty * &
>                  ( ( 1.D0 + ( y .dot. Hy ) / sdoty ) * matrix( s,
> s ) - &
>                   ( matrix( s, yH ) +  matrix( Hy, s ) ) )
>
> If you replace the three lines above with old-style fortran:
>
>       ydotHy = ( y .dot. Hy )
>       do j=1,n
>          do i=1,n
>             inv_hess(i,j) = inv_hess(i,j) + 1.D0 / sdoty * &
>                       ( ( 1.D0 + ydotHy / sdoty ) * s(i) * s(j) - &
>                          ( s(i)*yH(j) + Hy(i)*s(j) ) )
>          end do
>       end do
>
> it works (ifort on a PC cluster). I cannot see any good reason
> for such a behavior.
>
> By the way: in case of trouble with bfgs, one can always
> try damped dynamics.
>
> Paolo
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From ghaderyan at gmail.com  Tue May 29 23:38:21 2007
From: ghaderyan at gmail.com (saman ghaderyan)
Date: Wed, 30 May 2007 01:08:21 +0330
Subject: [Pw_forum] pseudo potential
Message-ID: <aa36e8060705291438g7e23ba27q64abea5c73d938a5@mail.gmail.com>

hi
i have a question about format

 Perdew-Zunger (LDA) exch-corr
when i attention to this file
nl pn  l   occ               Rcut            Rcut US             E pseu
4S  0  0  2.00      0.00000000000      0.00000000000      0.00000000000
4P  0  1  1.00      0.00000000000      0.00000000000      0.00000000000
why pn ,Rcut and RCut US are zero!,
and i would like product (NC-LDA)for Zn what format is better.
(i exam it but when i test the result aren't true)
tanx alot.
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From akohlmey at cmm.chem.upenn.edu  Wed May 30 01:44:16 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 29 May 2007 19:44:16 -0400 (EDT)
Subject: [Pw_forum] pseudo potential
In-Reply-To: <aa36e8060705291438g7e23ba27q64abea5c73d938a5@mail.gmail.com>
Message-ID: <Pine.LNX.4.44.0705291940440.31278-100000@localhost.localdomain>

On Wed, 30 May 2007, saman ghaderyan wrote:

SG> hi
SG> i have a question about format
SG> 
SG>  Perdew-Zunger (LDA) exch-corr
SG> when i attention to this file
SG> nl pn  l   occ               Rcut            Rcut US             E pseu
SG> 4S  0  0  2.00      0.00000000000      0.00000000000      0.00000000000
SG> 4P  0  1  1.00      0.00000000000      0.00000000000      0.00000000000
SG> why pn ,Rcut and RCut US are zero!,

this is from the the <PP_INFO> section of the UPF file and 
the values are for (dis)informational purposes only.
see the file upftools/UPF for more details on the UPF format.

SG> and i would like product (NC-LDA)for Zn what format is better.
SG> (i exam it but when i test the result aren't true)

the format of the pseudopotential should not matter (if it 
is supported by the code, that is).

cheers,
   axel.

SG> tanx alot.
SG> 

-- 
=======================================================================
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 helen at fh.huji.ac.il  Wed May 30 13:48:07 2007
From: helen at fh.huji.ac.il (Helen)
Date: Wed, 30 May 2007 14:48:07 +0300
Subject: [Pw_forum] example01 errors;conjugate-gradient algorithm;changing code functionals
References: <Pine.LNX.4.44.0705281108180.6382-100000@localhost.localdomain>
Message-ID: <019401c7a2b0$6412dc90$cd604084@fh.huji.ac.il>

Hi,
I've been working a few days on the problem and have found that it occurs 
when ZGEMM is called in the ccalbec.f90 routine in the PW directory. The 
routine is called while calculating force_us_k. When the routine is called I 
get the error message:
forrtl: severe (174): SIGSEGV, segmentation fault occurred

Stack trace terminated abnormally.

I've checked all the input variables and they all seem to be the correct 
size and type, apart from perhaps npw which I thought should equal npwx? 
However I also tried running with npwx instead of npw in ZGEMM, whcih 
doesn't solve the problem. I've also checked that ZGEMM works on a little 
test routine I created so the ZGEMM is present and in principle works.

Any ideas what is causing this segmentation fault, maybe a memory leak?



A different question: the program is compiling and running on one computer, 
I tried running on a different computer and I get the error message

error while loading shared libraries: libguide.so: cannot open shared object 
file: No such file or directory

I tried to stop (unsuccessfully) dynamic linking by writing

./configure FFLAGS='-i-static'


or by writing

./configure FFLAGS='-static'



Any ideas of how to fix this problem?

Thnks for your help,

Helen


----- Original Message ----- 
From: "Axel Kohlmeyer" <akohlmey at cmm.chem.upenn.edu>
To: "Helen" <helen at fh.huji.ac.il>
Sent: Monday, May 28, 2007 6:14 PM
Subject: Re: [Pw_forum] example01 errors;conjugate-gradient 
algorithm;changing code functionals


> On Sun, 27 May 2007, Helen wrote:
>
> hello helen,
>
> HE> Thank you so much for your help
> HE> The output file si.scf.cg.out is indeed different from the reference 
> output
> HE> file. The output is identical up to the line
> HE>
> HE> convergence has been achieved
> HE>
> HE> Forces acting on atoms (Ry/au):
> HE>
> HE> and then the output of forces,stresses and writing to output data file 
> are
> HE> missing.
>
> which would mean, that your calculation was stopped and did not write
> the restart file, that is required for postprocessing.
>
> there are a number of possible reasons, most likely, the directory
> that you specified in the outdir parameter does not exist or is
> full.
>
> HE> I tried running other examples with the same problems.
>
> HE> My operating system is Linux i386
> HE> My cpu is Intel 3.2 GHz
> HE> My compiler is Intel (R) Fortran Compiler for 32-bit applications, 
> Version
> HE> 9.0, Intel (R) C Compiler for 32-bit applications, Version 9.0
>
> with the intel compilers, it is advisable to keep them updated to the
> latest patchlevel. however, your problem is not very likely related
> to a compiler problem. i wold investigate that when the more obvious
> explanations have been exhausted.
>
> HE> My libraries are
> HE> blas_libs='-L/opt/intel/mkl/8.0.1/lib/32 -lmkl_ia32 -lguide -lpthread'
> HE> lapack_libs='-lmkl_lapack'
> HE> fft_libs=' -lfftw '
>
> that looks reasonable. thanks for providing complete information
> on the compile. this is much appreciated.
>
> [...]
>
> HE> Is there anyway that when I run it will write where the code is 
> failing in
> HE> the error message?
>
> have a look at the Doc/INPUT_PW file for a list of common flags
> and their meaning. i would suggest setting verbosity='high' to
> narrow it down, but also, please check the validity of the entry
> for 'outdir' in your input.
>
> HE> Thank you again for your help,
> HE> Helen Eisenberg
> HE>
>
> cheers,
>   axel.
>
> -- 
> =======================================================================
> Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>   Center for Molecular Modeling   --   University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> 



From shruba at gmail.com  Wed May 30 18:30:43 2007
From: shruba at gmail.com (shruba at gmail.com)
Date: Wed, 30 May 2007 12:30:43 -0400
Subject: [Pw_forum] error # list
Message-ID: <822f4ec80705300930p66c83c3fp95b4abe042b25d72@mail.gmail.com>

Hi all
  I am a new user of espresso package, I am using espresso-3.2. My question
is, Is there any file/directory where I can check the description of error
number I am getting at the end of the file?
 Thanks in advance.
                       shruba



-- 
'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
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From degironc at sissa.it  Wed May 30 18:36:34 2007
From: degironc at sissa.it (degironc)
Date: Wed, 30 May 2007 18:36:34 +0200
Subject: [Pw_forum] error # list
In-Reply-To: <822f4ec80705300930p66c83c3fp95b4abe042b25d72@mail.gmail.com>
References: <822f4ec80705300930p66c83c3fp95b4abe042b25d72@mail.gmail.com>
Message-ID: <465DA812.6050305@sissa.it>

the errors in the espresso package usually indicate the routine where it 
occurred and a description of the problem.
If  the error originates in called libraries one should make reference 
to them.
hope this help.
stefano


shruba at gmail.com wrote:
> Hi all
>   I am a new user of espresso package, I am using espresso-3.2. My 
> question is, Is there any file/directory where I can check the 
> description of error number I am getting at the end of the file?
>  Thanks in advance.
>                        shruba
>                                    
>  
>
> -- 
> 'friendship doubles joys and reduces sorrows by half' (Francis Bacon).



From giannozz at nest.sns.it  Wed May 30 18:42:35 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 30 May 2007 18:42:35 +0200
Subject: [Pw_forum] error # list
In-Reply-To: <822f4ec80705300930p66c83c3fp95b4abe042b25d72@mail.gmail.com>
References: <822f4ec80705300930p66c83c3fp95b4abe042b25d72@mail.gmail.com>
Message-ID: <79B987DB-19AD-41C6-93BC-FA816B2934EA@nest.sns.it>

On May 30, 2007, at 18:30 , shruba at gmail.com wrote:

> I am a new user of espresso package, I am using espresso-3.2.
> My question is, Is there any file/directory where I can check the
> description of error number I am getting at the end of the file?

short answer: no.

In some cases, the printed numbers have a relationship with the text
printed in the error message, but you have to look inside the source
code to understand which relationship. In other cases, the error numbers
are those returned by fortran, whose exact meaning (assuming they have
one) is hidden somewhere in some obscure reference manual.
In conclusion: ignore them.

And before somebody else tells you :-): please sign with a real name
and an affiliation

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




From giannozz at nest.sns.it  Wed May 30 19:07:54 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 30 May 2007 19:07:54 +0200
Subject: [Pw_forum] example01 errors;conjugate-gradient algorithm;changing code functionals
In-Reply-To: <019401c7a2b0$6412dc90$cd604084@fh.huji.ac.il>
References: <Pine.LNX.4.44.0705281108180.6382-100000@localhost.localdomain> <019401c7a2b0$6412dc90$cd604084@fh.huji.ac.il>
Message-ID: <3AA57E0D-5B83-486D-95CC-4D3A094A85E5@nest.sns.it>

On May 30, 2007, at 13:48 , Helen wrote:

> I've been working a few days on the problem and have found that it  
> occurs when ZGEMM is called in the ccalbec.f90 routine in the PW  
> directory. The routine is called while calculating force_us_k.

notice to everybody: THIS is an error report! what goes wrong and
where, NOT "it doesn't work" ! :-)

Unfortunately this is as useful as "it doesn't work" :-( , because this
kind of error is either
1) a compiler bug, or
2) a library bug, or
3) a well-hidden bug in the fortran code, causing the code to crash in
some part that is completely unrelated to where the error occurs
(the routine "ccalbec" is called in many different places in the code,
even before the place where it crashes, so the problem cannot be there).

While it is hard to rule out 3), it seems to me exceedingly unlikely  
that
there is a bug in the simple selfconsistent and force calculation, that
shows up only on one specific executable and cannot be reproduced
on any of the many existing installations of Q-E on many different
machines. My opinion is that it is either 1) or 2). A first simple  
test is
to use internal LAPACK instead of MKL.

> error while loading shared libraries: libguide.so: cannot open  
> shared object file: No such file or directory

this is the first item in the Troubleshooting section:
http://www.quantum-espresso.org/wiki/index.php/Troubleshooting_% 
28PWscf%29
The surest (but not smartest) way to prevent such problems is to
have a copy of MKL on all processors.

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




From akohlmey at cmm.chem.upenn.edu  Wed May 30 18:26:23 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 30 May 2007 12:26:23 -0400 (EDT)
Subject: [Pw_forum] example01 errors;conjugate-gradient algorithm;changing
 code functionals
In-Reply-To: <019401c7a2b0$6412dc90$cd604084@fh.huji.ac.il>
Message-ID: <Pine.LNX.4.44.0705301206240.31278-100000@localhost.localdomain>

On Wed, 30 May 2007, Helen wrote:

helen,

HE> Hi,
HE> I've been working a few days on the problem and have found that it occurs 
HE> when ZGEMM is called in the ccalbec.f90 routine in the PW directory. The 
HE> routine is called while calculating force_us_k. When the routine is called I 
HE> get the error message:
HE> forrtl: severe (174): SIGSEGV, segmentation fault occurred
HE> 
HE> Stack trace terminated abnormally.

HE> I've checked all the input variables and they all seem to be the correct 
HE> size and type, apart from perhaps npw which I thought should equal npwx? 
HE> However I also tried running with npwx instead of npw in ZGEMM, whcih 
HE> doesn't solve the problem. I've also checked that ZGEMM works on a little 
HE> test routine I created so the ZGEMM is present and in principle works.
HE> 
HE> Any ideas what is causing this segmentation fault, maybe a memory leak?

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


HE> A different question: the program is compiling and running on one computer, 
HE> I tried running on a different computer and I get the error message
HE> 
HE> error while loading shared libraries: libguide.so: cannot open shared object 
HE> file: No such file or directory

this is due to dynamicsally linking libguide (which is
provided by both your compiler and mkl).

HE> I tried to stop (unsuccessfully) dynamic linking by writing
HE> 
HE> ./configure FFLAGS='-i-static'

FFLAGS is not a good place for that as it may also disable
optimization, LDFLAGS would be. it is probably easier to
edit your make.sys file manually. linux machines are so
unpredictably installed, that configure has a really hard
time to get it perfect. to trick the intel compiler into
linking libguide statically, i use:
LDFLAGS="-i-static -openmp"

here are my settings to compile QE with intel and intel MKL
(on x86_64, for i386 just replace lib/em64t with lib/32 and
-lmkl_em64t with -lmkl_ia32 ).

DFLAGS         =  -D__INTEL -D__FFTW -D__MPI -D__PARA
MPIF90         = mpif90
#F90           = ifort
CC             = icc
F77            = ifort
CPP            = cpp
CPPFLAGS       = -P -traditional $(DFLAGS) $(IFLAGS)
CFLAGS         = -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS       = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) 
$(MODFLAGS)
FFLAGS         = -O2 -assume byterecl -tpp6 -pc64 -unroll
FFLAGS_NOOPT   = -O0 -assume byterecl
LD             = mpif90
LDFLAGS        = -i-static -openmp
BLAS_LIBS      = -L/opt/intel/mkl/9.0/lib/em64t -lmkl_em64t 
LAPACK_LIBS    = -L/opt/intel/mkl/9.0/lib/em64t -lmkl_lapack
FFT_LIBS       =  -lfftw 

n.b. this is for parallel. in serial, you have to drop -D__PARA -D__MPI
and use ifort instead of mpif90.

HE> 
HE> 
HE> or by writing
HE> 
HE> ./configure FFLAGS='-static'

using fully static linking is no longer a good idea,
particularly not on linux machines, since the resulting
executables are usually _less_ portable than semi-statically
linked executables.

hope that helps,

  axel.

HE> 
HE> Any ideas of how to fix this problem?
HE> 
HE> Thnks for your help,
HE> 
HE> Helen
HE> 
HE> 

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




From eyvaz_isaev at yahoo.com  Wed May 30 19:29:35 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Wed, 30 May 2007 10:29:35 -0700 (PDT)
Subject: [Pw_forum] error # list
In-Reply-To: <822f4ec80705300930p66c83c3fp95b4abe042b25d72@mail.gmail.com>
Message-ID: <38669.14998.qm@web60315.mail.yahoo.com>

Dear Sharuba,

First of all, please provide your affiliation. 

As concerns your question, NO, there is no such a kind
of file. A message you get just tells you in which
program the program has troubles. Have a look at a
program mentioned to inspect why it happens.

Bests,
Eyvaz. 

 
--- shruba at gmail.com wrote:

> Hi all
>   I am a new user of espresso package, I am using
> espresso-3.2. My question
> is, Is there any file/directory where I can check
> the description of error
> number I am getting at the end of the file?
>  Thanks in advance.
>                        shruba
> 
> 
> 
> -- 
> 'friendship doubles joys and reduces sorrows by
> half' (Francis Bacon).
> 


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


       
____________________________________________________________________________________You snooze, you lose. Get messages ASAP with AutoCheck
in the all-new Yahoo! Mail Beta.
http://advision.webevents.yahoo.com/mailbeta/newmail_html.html


From shruba at gmail.com  Wed May 30 19:53:41 2007
From: shruba at gmail.com (shruba at gmail.com)
Date: Wed, 30 May 2007 13:53:41 -0400
Subject: [Pw_forum] error in "vc-relax" calculation
Message-ID: <822f4ec80705301053t49ab2569t9decddd727d4f8f0@mail.gmail.com>

Thanks for the help
and I am sorry about not writing my complete name and designation,
 I am running an optimization for SrFeO3 ( a mettalic perovskite system )"
the input structure is

calculation = 'vc-relax',

restart_mode = 'from_scratch',

tstress = .TRUE.,

tprnfor = .TRUE.,

prefix = 'vcanti',

pseudo_dir =

outdir=

/

&SYSTEM

ibrav = 1,

celldm(1) = 7.66,

nbnd=188,

nat =40,

nelec = 288,

ntyp =3,

ecutwfc = 100,

ecutrho = 395,

occupations = 'ensemble',

smearing='fd',

degauss=6000,

nspin=2,

nelup=160,

neldw=128,

/

&ELECTRONS

diagonalization = 'cg',

emass = 1000.d0,

emass_cutoff = 4.d0,

orthogonalization = 'Gram-Schmidt',

startingwfc = 'random',

n_inner = 8,

tcg = .true.,

passop=0.3,

maxiter = 250,

conv_thr=1.d-6

/

&IONS

ion_dynamics = 'sd',

ion_damping = 0.,

ion_positions = 'from_input',

greasp=1.0,

ion_temperature = 'not_controlled',

/

&CELL

cell_dynamics = 'sd'

/

ATOMIC_SPECIES

Sr 87.62 Sr.pbe-nsp-van.UPF

Fe 55.85 Fe.pbe-nd-rrkjus.UPF

O 16.00 O.pbe-van-bm.UPF

ATOMIC_POSITIONS

Sr 0.250000 0.250000 0.250000

Sr 0.750000 0.250000 0.250000

Sr 0.250000 0.750000 0.250000

Sr 0.750000 0.750000 0.250000

Sr 0.250000 0.250000 0.750000

Sr 0.750000 0.250000 0.750000

Sr 0.250000 0.750000 0.750000

Sr 0.750000 0.750000 0.750000

Fe 0.000000 0.000000 0.000000

Fe 0.500000 0.000000 0.000000

Fe 0.000000 0.500000 0.000000

Fe 0.500000 0.500000 0.000000

Fe 0.000000 0.000000 0.500000

Fe 0.500000 0.000000 0.500000

Fe 0.000000 0.500000 0.500000

Fe 0.500000 0.500000 0.500000

O 0.250000 0.250000 0.000000

O 0.250000 0.000000 0.250000

O 0.000000 0.250000 0.250000

O 0.750000 0.250000 0.000000

O 0.750000 0.000000 0.250000

O 0.500000 0.250000 0.250000

O 0.250000 0.750000 0.000000

O 0.250000 0.500000 0.250000

O 0.000000 0.750000 0.250000

O 0.750000 0.750000 0.000000

O 0.750000 0.500000 0.250000

O 0.500000 0.750000 0.250000

O 0.250000 0.250000 0.500000

O 0.250000 0.000000 0.750000

O 0.000000 0.250000 0.750000

O 0.750000 0.250000 0.500000

O 0.750000 0.000000 0.750000

O 0.500000 0.250000 0.750000

O 0.250000 0.750000 0.500000

O 0.250000 0.500000 0.750000

O 0.000000 0.750000 0.750000

O 0.750000 0.750000 0.500000

O 0.750000 0.500000 0.750000

O 0.500000 0.750000 0.750000

K_POINTS {automatic}

2 2 2 0 0 0

 and the error I am getting is

PERFORMING CONJUGATE GRADIENT MINIMIZATION OF EL. STATES

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

from dspev_drv : error # 287

diagonalization failed

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

stopping ...



If please help me in this matter that will be really great.

Thanks in advance.

                        shruba gangopadhyay

                       Graduate student

                      Department of chemistry,

                      University of Central Florida

                      FL - 32826


-- 
'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
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From hande at newton.physics.metu.edu.tr  Thu May 31 00:11:15 2007
From: hande at newton.physics.metu.edu.tr (Hande Ustunel)
Date: Thu, 31 May 2007 01:11:15 +0300 (EEST)
Subject: [Pw_forum] Li pseudo
In-Reply-To: <465AE459.1060608@metu.edu.tr>
Message-ID: <Pine.LNX.4.44.0705310103430.20041-100000@newton.physics.metu.edu.tr>

Dear PWSCF users,

Does anyone have a us pbe Li pseudopotential lying around with 1s
state in valence? I see that the one already in the library has been
removed.

Related to this issue, has anyone else noticed a ~2% decrease in the
lattice constant of bcc Li when s states are included? Is this perhaps
a well-known thing?

Thank you very much in advance.

-- 
Hande Ustunel
Department of Physics
Office 439
Middle East Technical University
Ankara 06531, Turkey
Tel : +90 312 210 3264
http://www.physics.metu.edu.tr/~hande



From akohlmey at cmm.chem.upenn.edu  Wed May 30 23:54:16 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 30 May 2007 17:54:16 -0400 (EDT)
Subject: [Pw_forum] Li pseudo
In-Reply-To: <Pine.LNX.4.44.0705310103430.20041-100000@newton.physics.metu.edu.tr>
Message-ID: <Pine.LNX.4.44.0705301746561.3290-100000@localhost.localdomain>

On Thu, 31 May 2007, Hande Ustunel wrote:

HU> Dear PWSCF users,
HU> 
HU> Does anyone have a us pbe Li pseudopotential lying around with 1s
HU> state in valence? I see that the one already in the library has been
HU> removed.

yes. i have the one(s) that was/were removed and it/they 
was/were working very well for some systems, but horribly
bad for others. so far i have not been able to either 
improve the potential(s) or find an error in the calculations
that show bad results.

if you want to give it a try, i can forward you the required
info and parameters that i was using. it took a bit of tweaking
to get a usable potential at all, since i was working under
the constraints of making it compatible to CPMD, limits the
choices for the number of projectors you can use (for mostly
historical reasons).

cheers,
  axel.


HU> 
HU> Related to this issue, has anyone else noticed a ~2% decrease in the
HU> lattice constant of bcc Li when s states are included? Is this perhaps
HU> a well-known thing?
HU> 
HU> Thank you very much in advance.
HU> 
HU> 

-- 
=======================================================================
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 hande at newton.physics.metu.edu.tr  Thu May 31 00:56:56 2007
From: hande at newton.physics.metu.edu.tr (Hande Ustunel)
Date: Thu, 31 May 2007 01:56:56 +0300 (EEST)
Subject: [Pw_forum] Li pseudo
In-Reply-To: <Pine.LNX.4.44.0705301746561.3290-100000@localhost.localdomain>
Message-ID: <Pine.LNX.4.44.0705310156060.20041-100000@newton.physics.metu.edu.tr>

Dear Axel,

Yes, I would very much appreciate the parameters that you used to
create the pseudo.

Many thanks,
Hande


-- 
Hande Ustunel
Department of Physics
Office 439
Middle East Technical University
Ankara 06531, Turkey
Tel : +90 312 210 3264
http://www.physics.metu.edu.tr/~hande



From ackollias at gmail.com  Thu May 31 04:50:15 2007
From: ackollias at gmail.com (sasha)
Date: Wed, 30 May 2007 22:50:15 -0400
Subject: [Pw_forum] occupations
Message-ID: <1180579816.3020.8.camel@cryptonomicon>

Greetings,
	For LDA+U pwscf, for system such a FeO, prints out the occupations as,

  occupations
 0.200  0.000  0.000  0.000  0.000
 0.000  0.200  0.000  0.000  0.000
 0.000  0.000  0.200  0.000  0.000
 0.000  0.000  0.000  0.200  0.000
 0.000  0.000  0.000  0.000  0.200

These are obviously the orbital occupations of the Hubbard matrix.  I'm
interested in using the final occupations obtained in a PWSCF
calculation as initial guess occupations in a full potential code. What
convention is used for these printed occupations i.e. cubic or spherical
harmonic and are what is the exact ordering of the occupations? i.e.,

yz          zx          xy        x2-y2       3z2-1

Thanks in advance of the any information

Sasha



From clie at aphy.iphy.ac.cn  Thu May 31 07:57:28 2007
From: clie at aphy.iphy.ac.cn (clie)
Date: Thu, 31 May 2007 05:57:28 GMT
Subject: [Pw_forum] (no subject)
Message-ID: <20070531055728.19664.eqmail@aphy.iphy.ac.cn>

Dear profssors, 
  i come across some troubles when i calculate the electron-phonon coupling usin
g pwscf , could you give me some suggestions , tkanks in advance.
  
#!/bin/sh
# run from directory where this script is
cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname
EXAMPLE_DIR=`pwd`

# check whether echo has the -e option
if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi

$ECHO
$ECHO "$EXAMPLE_DIR : starting"
$ECHO
$ECHO "This example shows how to calculate electron-phonon interaction"
$ECHO "coefficients for fcc GeH4."

# set the needed environment variables 
. ../environment_variables
# required executables and pseudopotentials
BIN_LIST="pw.x ph.x q2r.x matdyn.x"
PSEUDO_LIST="Ge.pz-bhs.UPF H.pz-van_ak.UPF"

$ECHO
$ECHO "  executables directory: $BIN_DIR"
$ECHO "  pseudo directory:      $PSEUDO_DIR"
$ECHO "  temporary directory:   $TMP_DIR"
$ECHO "  checking that needed directories and files exist...\c"

# check for directories
for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do
    if test ! -d $DIR ; then
        $ECHO
        $ECHO "ERROR: $DIR not existent or not a directory"
        $ECHO "Aborting"
        exit 1
    fi
done
for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do
    if test ! -d $DIR ; then
        mkdir $DIR
    fi
done
for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do
    if test ! -d $DIR ; then
        mkdir $DIR
    fi
done
cd $EXAMPLE_DIR/results

# check for executables
for FILE in $BIN_LIST ; do
    if test ! -x $BIN_DIR/$FILE ; then
        $ECHO
        $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable"
        $ECHO "Aborting"
        exit 1
    fi
done
 
# check for pseudopotentials
for FILE in $PSEUDO_LIST ; do
    if test ! -r $PSEUDO_DIR/$FILE ; then
        $ECHO
        $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable"
        $ECHO "Aborting"
        exit 1
    fi
done
$ECHO " done"

# how to run executables
PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
PH_COMMAND="$PARA_PREFIX $BIN_DIR/ph.x $PARA_POSTFIX"
Q2R_COMMAND="$PARA_PREFIX $BIN_DIR/q2r.x $PARA_POSTFIX"
MATDYN_COMMAND="$PARA_PREFIX $BIN_DIR/matdyn.x $PARA_POSTFIX"
$ECHO
$ECHO "  running pw.x as: $PW_COMMAND"
$ECHO "  running ph.x as: $PH_COMMAND"
$ECHO "  running q2r.x as: $Q2R_COMMAND"
$ECHO "  running matdyn.x as: $MATDYN_COMMAND"
$ECHO

# clean TMP_DIR
$ECHO "  cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/*
$ECHO "  done"

#
# SCF at dense k-mesh, good enough for electronic DOS  
#
cat > GeH4.scf.fit.in << EOF
 &control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='GeH4',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
 /
 &system
    ibrav=  8, celldm(1) =7.478, celldm(2)=0.76, celldm(3)=0.72, nat=10, ntyp= 2
,
    ecutwfc =15.0,   
    occupations='smearing', smearing='methfessel-paxton', degauss=0.05,
    la2F = .true., 
 /
 &electrons
    conv_thr =  1.0d-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Ge   72.61     Ge.pz-bhs.UPF
 H    1.000794  H.pz-van_ak.UPF
ATOMIC_POSITIONS
 Ge  0.500000    0.000000   0.500000
 Ge  0.000000    0.000000   0.000000
 H   0.000000    0.388640   0.688119
 H   0.500000    0.611360   0.188119
 H   0.500000    0.388640   0.811881
 H   0.000000    0.611360   0.311881
 H   0.250000    0.357636   0.250000
 H   0.250000    0.642364   0.750000
 H   0.750000    0.642364   0.750000
 H   0.750000    0.357636   0.250000
K_POINTS {automatic}
 16 16 16  0.0  0.5  0.5
EOF
$ECHO "  running the scf calculation with dense k-point grid...\c"
$PW_COMMAND  < GeH4.scf.fit.in > GeH4.scf.fit.out
$ECHO "  done"
#
#  SCF at k-mesh good enough for phonons
#
cat > GeH4.scf.in << EOF
 &control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='GeH4',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
 /
 &system
    ibrav=  8, celldm(1) =7.478, celldm(2)=0.76, celldm(3)=0.72, nat=10, ntyp= 2

    ecutwfc =15.0, 
    occupations='smearing', smearing='methfessel-paxton', degauss=0.05
 /
 &electrons
    conv_thr =  1.0d-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Ge   72.61     Ge.pz-bhs.UPF
 H    1.000794  H.pz-van_ak.UPF
ATOMIC_POSITIONS
 Ge  0.500000    0.000000   0.500000
 Ge  0.000000    0.000000   0.000000
 H   0.000000    0.388640   0.688119
 H   0.500000    0.611360   0.188119
 H   0.500000    0.388640   0.811881
 H   0.000000    0.611360   0.311881
 H   0.250000    0.357636   0.250000
 H   0.250000    0.642364   0.750000
 H   0.750000    0.642364   0.750000
 H   0.750000    0.357636   0.250000
K_POINTS {automatic}
 8 8 8  0.0  0.5  0.5
EOF
$ECHO "  running the scf calculation...\c"
$PW_COMMAND < GeH4.scf.in > GeH4.scf.out
$ECHO "  done"
#
cat > GeH4.elph.in << EOF
Electron-phonon coefficients for GeH4
 &inputph
  tr2_ph=1.0d-10,
  prefix='GeH4',
  fildvscf='GeH4dv',
  amass(1)=72.61,
  amass(2)=1.00794,
  outdir='$TMP_DIR/',
  fildyn='GeH4.dyn',
  elph=.true.,
  trans=.true.,
  ldisp=.true.,
  nq1=2, nq2=2, nq3=2
 /
EOF
$ECHO "  running the el-ph calculation...\c"
$PH_COMMAND < GeH4.elph.in > GeH4.elph.out
$ECHO "  done"
#
#   q2r and matdyn
#
cat > q2r.in << EOF 
 &input
   fildyn='GeH4.dyn', flfrc='GeH4444.fc', la2F=.true.
 /
EOF
$ECHO "  running q2r...\c"
$Q2R_COMMAND < q2r.in > q2r.out
$ECHO "  done"
#
#
#
cat > matdyn.in.freq << EOF 
 &input
    asr='simple',   amass(1)=72.61, amass(2)=1.00794,
    flfrc='GeH4444.fc', flfrq='GeH4444.freq', la2F=.true., dos=.false. 
 /
  19
  0.000 0.0 0.0     0.0
  0.125 0.0 0.0     0.0
  0.250 0.0 0.0     0.0
  0.375 0.0 0.0     0.0
  0.500 0.0 0.0     0.0
  0.750 0.0 0.0     0.0
  1.000 0.0 0.0     0.0
  0.825 0.125 0.125 0.0
  0.750 0.250 0.250 0.0
  0.625 0.375 0.375 0.0
  0.500 0.500 0.500 0.0
  0.325 0.325 0.325 0.0
  0.250 0.250 0.250 0.0
  0.125 0.125 0.125 0.0
  0.000 0.000 0.000 0.0
  0.125 0.125 0.000 0.0
  0.250 0.250 0.000 0.0
  0.325 0.325 0.000 0.0
  0.500 0.500 0.000 0.0
EOF
$ECHO "  running matdyn for frequency calculation...\c"
$MATDYN_COMMAND < matdyn.in.freq > matdyn.out.freq
$ECHO "  done"
#
#
#
cat > matdyn.in.dos << EOF 
 &input
    asr='simple',   amass(1)=72.61, amass(2)=1.00794,
    flfrc='GeH4444.fc', flfrq='GeH4444.freq', la2F=.true., dos=.true. 
    fldos='phonon.dos', nk1=10, nk2=10, nk3=10, ndos=50
 /
EOF
$ECHO "  running matdyn for a2F(omega) calculation...\c"
$MATDYN_COMMAND < matdyn.in.dos > matdyn.out.dos
$ECHO "  done"

This is my input file , and part of elph.out file is below.
......... calculate the e-p coupling at q(0,0,0) no error.........
 q = (    0.000000000   0.438596491   0.000000000 ) 

 **************************************************************************
     omega( 1) =     -36.256771 [THz] =   -1209.403744 [cm-1]
     omega( 2) =     -33.905968 [THz] =   -1130.988878 [cm-1]
     omega( 3) =     -31.534608 [THz] =   -1051.888298 [cm-1]
     omega( 4) =     -29.936477 [THz] =    -998.580032 [cm-1]
     omega( 5) =     -28.175603 [THz] =    -939.843185 [cm-1]
     omega( 6) =     -21.533181 [THz] =    -718.274373 [cm-1]
     omega( 7) =     -20.483982 [THz] =    -683.276640 [cm-1]
     omega( 8) =     -16.937416 [THz] =    -564.975136 [cm-1]
     omega( 9) =     -15.854217 [THz] =    -528.843275 [cm-1]
     omega(10) =     -10.364352 [THz] =    -345.719856 [cm-1]
     omega(11) =      -9.156807 [THz] =    -305.440234 [cm-1]
     omega(12) =      -6.312172 [THz] =    -210.552797 [cm-1]
     omega(13) =      -5.744229 [THz] =    -191.608114 [cm-1]
     omega(14) =       1.611170 [THz] =      53.743192 [cm-1]
     omega(15) =       2.091266 [THz] =      69.757593 [cm-1]
     omega(16) =       4.095794 [THz] =     136.621875 [cm-1]
     omega(17) =       5.432707 [THz] =     181.216804 [cm-1]
     omega(18) =       8.428428 [THz] =     281.143952 [cm-1]
     omega(19) =      11.978931 [THz] =     399.576795 [cm-1]
     omega(20) =      13.995627 [THz] =     466.846959 [cm-1]
     omega(21) =      21.724606 [THz] =     724.659678 [cm-1]
     omega(22) =      22.544804 [THz] =     752.018713 [cm-1]
     omega(23) =      24.793624 [THz] =     827.031757 [cm-1]
     omega(24) =      26.424792 [THz] =     881.442025 [cm-1]
     omega(25) =      27.241010 [THz] =     908.668308 [cm-1]
     omega(26) =      37.560540 [THz] =    1252.893077 [cm-1]
     omega(27) =      58.547230 [THz] =    1952.938376 [cm-1]
     omega(28) =      65.537647 [THz] =    2186.115128 [cm-1]
     omega(29) =      80.880266 [THz] =    2697.893215 [cm-1]
     omega(30) =      83.409456 [THz] =    2782.258477 [cm-1]
 **************************************************************************

     Mode symmetry, C_s (m)     point group:

     omega(  1 -  1) =  -1209.40374  [cm-1]   --> A'             
     omega(  2 -  2) =  -1130.98888  [cm-1]   --> A'             
     omega(  3 -  3) =  -1051.88830  [cm-1]   --> A''            
     omega(  4 -  4) =   -998.58003  [cm-1]   --> A''            
     omega(  5 -  5) =   -939.84319  [cm-1]   --> A'             
     omega(  6 -  6) =   -718.27437  [cm-1]   --> A'             
     omega(  7 -  7) =   -683.27664  [cm-1]   --> A''            
     omega(  8 -  8) =   -564.97514  [cm-1]   --> A''            
     omega(  9 -  9) =   -528.84327  [cm-1]   --> A'             
     omega( 10 - 10) =   -345.71986  [cm-1]   --> A''            
     omega( 11 - 11) =   -305.44023  [cm-1]   --> A'             
     omega( 12 - 12) =   -210.55280  [cm-1]   --> A''            
     omega( 13 - 13) =   -191.60811  [cm-1]   --> A'             
     omega( 14 - 14) =     53.74319  [cm-1]   --> A'             
     omega( 15 - 15) =     69.75759  [cm-1]   --> A''            
     omega( 16 - 16) =    136.62187  [cm-1]   --> A'             
     omega( 17 - 17) =    181.21680  [cm-1]   --> A'             
     omega( 18 - 18) =    281.14395  [cm-1]   --> A'             
     omega( 19 - 19) =    399.57679  [cm-1]   --> A''            
     omega( 20 - 20) =    466.84696  [cm-1]   --> A'             
     omega( 21 - 21) =    724.65968  [cm-1]   --> A''            
     omega( 22 - 22) =    752.01871  [cm-1]   --> A'             
     omega( 23 - 23) =    827.03176  [cm-1]   --> A''            
     omega( 24 - 24) =    881.44203  [cm-1]   --> A'             
     omega( 25 - 25) =    908.66831  [cm-1]   --> A''            
     omega( 26 - 26) =   1252.89308  [cm-1]   --> A'             
     omega( 27 - 27) =   1952.93838  [cm-1]   --> A''            
     omega( 28 - 28) =   2186.11513  [cm-1]   --> A'             
     omega( 29 - 29) =   2697.89322  [cm-1]   --> A'             
     omega( 30 - 30) =   2782.25848  [cm-1]   --> A'             

 **************************************************************************
     electron-phonon interaction  ...


 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from lint : error #        73
     cannot remap grid on k-point list
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...



From degironc at sissa.it  Thu May 31 09:16:05 2007
From: degironc at sissa.it (degironc)
Date: Thu, 31 May 2007 09:16:05 +0200
Subject: [Pw_forum] occupations
In-Reply-To: <1180579816.3020.8.camel@cryptonomicon>
References: <1180579816.3020.8.camel@cryptonomicon>
Message-ID: <465E7635.10300@sissa.it>

the ordering is the same as used in the projected dos... it's the QE 
internal order for l=2 spherical harmonics
z2-1/3   zx    zy    x2-y2   xy
stefano
-
Stefano de Gironcoli - SISSA and DEMOCRITOS

sasha wrote:
> Greetings,
> 	For LDA+U pwscf, for system such a FeO, prints out the occupations as,
>
>   occupations
>  0.200  0.000  0.000  0.000  0.000
>  0.000  0.200  0.000  0.000  0.000
>  0.000  0.000  0.200  0.000  0.000
>  0.000  0.000  0.000  0.200  0.000
>  0.000  0.000  0.000  0.000  0.200
>
> These are obviously the orbital occupations of the Hubbard matrix.  I'm
> interested in using the final occupations obtained in a PWSCF
> calculation as initial guess occupations in a full potential code. What
> convention is used for these printed occupations i.e. cubic or spherical
> harmonic and are what is the exact ordering of the occupations? i.e.,
>
> yz          zx          xy        x2-y2       3z2-1
>
> Thanks in advance of the any information
>
> Sasha
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   



From wmbmacam at lg.ehu.es  Thu May 31 10:21:59 2007
From: wmbmacam at lg.ehu.es (=?GB2312?B?TWlndWVsIE1hcnSoqm5leiBDYW5hbGVz?=)
Date: Thu, 31 May 2007 10:21:59 +0200
Subject: [Pw_forum] GeH4 electron-phonon issues
In-Reply-To: <20070531055728.19664.eqmail@aphy.iphy.ac.cn>
References: <20070531055728.19664.eqmail@aphy.iphy.ac.cn>
Message-ID: <465E85A7.5060304@lg.ehu.es>

Dear clie,

First of all, you have more severe issues than your script not working.
Your structure isn't stable (at least ph.x doesn't think it is). See the
13!!! imaginary frequencies you get at (0 0.5 0). I haven't seen the gamma
frequencies, but if you have more thant three negative frequencies there,
you should relax your structure. If not, double your cell in the b axis and
relax. I'd also suggest increasing the cutoff, since 15 Ry seems a bit too
small for me.

Anyway, I'd guess your issues are related to the K_POINTS of each scf run.
I'd change it for

K_POINTS {automatic}
16 16 16  0 0 0

in the fine scf run. In a similar fashion, the less fine scf run should be

K_POINTS {automatic}
8 8 8  0 0 0

Finally, some of us would be grateful if you signed your messages with your
real name and affiliation. Especially because I am also working on hydrides
and would be glad to read your results once you publish them ;-)

Have a nice day,

Miguel

-- 
----------------------------------------
Miguel Mart?nez Canales
Dto. F?sica de la Materia Condensada
UPV/EHU
Facultad de Ciencia y Tecnolog?a
Apdo. 644
48080 Bilbao (Spain)
Fax:  +34 94 601 3500
Tlf:  +34 94 601 5437
----------------------------------------

 "If you have an apple and I have an apple and
 we exchange these apples then you and I will
 still each have one apple. But if you have an
 idea and I have an idea and we exchange these
 ideas, then each of us will have two ideas."

   George Bernard Shaw



From niuli1978 at yahoo.com.cn  Thu May 31 16:08:35 2007
From: niuli1978 at yahoo.com.cn (li niu)
Date: Thu, 31 May 2007 22:08:35 +0800 (CST)
Subject: [Pw_forum] the procedure of calculating the Raman tensor using the finite electric field method
In-Reply-To: <20070526053812.16009.48101.Mailman@democritos.sissa.it>
Message-ID: <98618.15996.qm@web15008.mail.cnb.yahoo.com>

Dear PaoloU,
   
  Thanks for your help. I now still have some puzzlements about the procedure of 
  calculating vibrationl spectrum by finite electric field method.
   
  1.I consider a model structure of tetrahedral amorphous carbon obtained by my schoolmate using a Car-Parrinello molecular dynamics approach.    
   
  2.When running a self-consistent calculation for this structure (using different exchange-crrelation energy and pseudopotential with in CPMD), I found the forces and stress are big.
In this case, I should use pw.x to compute the equilibrium geometry 
before running finite electric field method to calculate Raman tensor. Is it right?
 
   Total force =     0.633437     Total SCF correction =     0.000080
     total   stress  (Ry/bohr**3)                   (kbar)     P=  -69.10
  -0.00087420   0.00095392  -0.00017791       -128.60    140.33    -26.17
   0.00095392   0.00033110   0.00005680        140.33     48.71      8.35
  -0.00017791   0.00005680  -0.00086609        -26.17      8.35   -127.41
   
  3.I run a vc-relax calculation and input and output files are as follows.
It is obvious the cell angle parameters have been changed and the structure isn't the cubic structure. 
   
  (1)ATOMIC_POSITIONS (angstrom)
&CONTROL
  calculation  = "vc-relax",
  prefix       = "ta-c",
  pseudo_dir   = "/home/niuli/espresso-3.2/pseudo",
  outdir       = "/home/niuli/tmp",
  etot_conv_thr=1.0D-4,
  forc_conv_thr=1.0D-5
  tstress = .true. ,
  tprnfor = .true. ,
                       nstep = 65 ,
                       dt = 50 ,
/
&SYSTEM
    ibrav = 1, 
    celldm(1) = 13.9103, 
    nat= 64, ntyp= 1,
    ecutwfc =55    
/
&ELECTRONS
  conv_thr    = 1.D-9,
  mixing_beta = 0.7D0,
/
&IONS
  
/
&CELL
               cell_dynamics = 'damp-w' ,
                      press = 0.0 ,
/
ATOMIC_SPECIES
 C   12.0107  C.pz-mt.UPF
  ATOMIC_POSITIONS (angstrom)
 C      0.335930     -0.353760     -0.911160
 C      1.410315     -0.756669      3.705328
 C     -0.462432      3.049465     -0.168292
  ...
K_POINTS automatic
1 1 1 0 0 0
----------------------------------------------------------
final unit-cell volume =   2649.6086 (a.u.)^3
  input alat =      13.9103 (a.u.)
  CELL_PARAMETERS (alat)
   0.988103212   0.021498496  -0.002655708
   0.021493430   1.013103454  -0.000556700
  -0.002655491  -0.000556401   0.983829644
  ATOMIC_POSITIONS (angstrom)
C        0.292559767  -0.288781798  -0.891844186
C        1.355532741  -0.743068572   3.628414295
C       -0.355484435   3.081913445  -0.167170533
C        0.095087835   3.109571795   3.835737135
C        4.156057825   0.859970231  -0.191362362
...
-------------------------------------------------------------
(2)ATOMIC_POSITIONS (crystal)
  
CELL_PARAMETERS (alat)
   0.997839246   0.002690608  -0.000417664
   0.002690608   1.001016967   0.000136231
  -0.000417664   0.000136231   0.997967842
 
ATOMIC_POSITIONS (crystal)
C        0.040549747  -0.039126226  -0.123246079
C        0.194302645  -0.104600063   0.504317492
C       -0.056833511   0.414314558  -0.024646663
C        0.005446848   0.417400176   0.531096601
C        0.569734741   0.101952019  -0.026079258
C        0.849788292   0.163379218   0.703668015
C        0.572774545   0.583287732   0.029202254
...
------------------------------------------------------------
  4.If I set ibrav=0 and use the obtained new cell parameter and atomic positions in the next scf calculation, the results on forces and stress are the same with that in vc-relax.
But if I set ibrav=1 in the next scf calculation, how to read the new lattice constant?
 
5. Then run ph.x code to obtain the phonon frequencies and eigenmodes. The phonon density of states is also obtained by dynmat.x code.
In your papers,the dynamical matrix is calculated by taking finite differences of atomic forces for atomic displacements of a constant bohr.What is the difference between two methods?
 Why don't you use the linear response method(ph.x code) to calculate the vibrational properties? 
   
  6. Supposing I obtain the equilibrium geometry of ibrav= 1, I then can calculate Raman tensor by considering second derivatives of the atomic forces(cp.x code).
 
Is my thought right on the procedure of calculating?
 
Best wishes,
   
  Niu Li
Harbin Institute of Technology
China


       
---------------------------------
????????3.5G???20M??? 
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From giannozz at nest.sns.it  Thu May 31 18:46:54 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 31 May 2007 18:46:54 +0200
Subject: [Pw_forum] the procedure of calculating the Raman tensor using the finite electric field method
In-Reply-To: <98618.15996.qm@web15008.mail.cnb.yahoo.com>
References: <98618.15996.qm@web15008.mail.cnb.yahoo.com>
Message-ID: <AD91C0BA-56E6-4FF7-84F8-B32EAA0AD592@nest.sns.it>

On May 31, 2007, at 16:08 , li niu wrote:

> 2.When running a self-consistent calculation for this structure  
> (using different exchange-correlation energy and pseudopotential  
> with in CPMD), I found the forces and stress are big.

are you really sure that the positions from CPMD are correctly
passed to the scf code?
---
Paolo Giannozzi, Democritos and University of Udine, Italy




From ongphuongvu at yahoo.com  Thu May 31 19:55:20 2007
From: ongphuongvu at yahoo.com (vu ongphuong)
Date: Thu, 31 May 2007 10:55:20 -0700 (PDT)
Subject: [Pw_forum] About phonon frequency in .dynG out-put file
Message-ID: <974823.40097.qm@web50603.mail.re2.yahoo.com>

Dear users,
   
  My question is the  omega's  in the .dynG out-put file is the eigenvalues of dynamical matrix i.e the square of phonon frequencies or phonon frequencies themselves?
   
  Thank you very much for your help
   
  O. P. Vu

  
---------------------------------
Looking for earth-friendly autos? 
 Browse Top Cars by "Green Rating" at Yahoo! Autos' Green Center.  
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From nakhmanson at anl.gov  Thu May 31 19:56:18 2007
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Thu, 31 May 2007 12:56:18 -0500
Subject: [Pw_forum] the procedure of calculating the Raman tensor using the
 finite electric field method
In-Reply-To: <98618.15996.qm@web15008.mail.cnb.yahoo.com>
References: <98618.15996.qm@web15008.mail.cnb.yahoo.com>
Message-ID: <465F0C42.1060207@anl.gov>

Just a small comment. Irregardless of schoolmate connections,
a "quench-from-the-melt" approach is not a good way to create
models of tetrahedrally bonded CRNs (continuous random
networks), which, among other things, might explain why your
stress and forces are so large. There are better methods/models
available for Silicon and Carbon (I think, Normand Mousseau
has good models of various sizes):

*] F. Wooten, K. Winer, D. Weaire, PRL 54, 1392 (1985),
**] G.T. Barkema and N. Mousseau, PRB 62, 4985 (2000).

I would also suggest checking whether or not your model
is actually metallic. All the under/over-coordinated
defect states that you have in "quench-from-the-melt"
models tend to fill out their DFT band gaps. See,
e.g., Fig. 16 in Voyles et al, JAP 90, 4437 (2001)
and compare, e.g., to Fig. 4 in Nakhmanson et al, PRB 63,
235207 (2001). In a (relatively) small model that you
may be studying such states could have significant
overlap despite being localized.

If your model is indeed metallic, then you are in a
"crap in -- crap out" mode and whatever you might
compute for it cannot be fully trusted.

Of course, Car and Parrinello did a pioneering work in
1987, but the field of CRN modeling has evolved a bit
since then :))

Hope this helps (all of the above is IMHO),

Serge

li niu wrote:
>  
> 1.I consider a model structure of tetrahedral amorphous carbon obtained 
> by my schoolmate using a Car-Parrinello molecular dynamics approach.   
> 

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


From baroni at sissa.it  Thu May 31 22:32:43 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 31 May 2007 22:32:43 +0200
Subject: [Pw_forum] the procedure of calculating the Raman tensor using the finite electric field method
In-Reply-To: <465F0C42.1060207@anl.gov>
References: <98618.15996.qm@web15008.mail.cnb.yahoo.com> <465F0C42.1060207@anl.gov>
Message-ID: <80A77606-336D-4474-A527-9023A60C4726@sissa.it>

Just a brief comment on a recent note by

On May 31, 2007, at 7:56 PM, Serge Nakhmanson wrote:

> Just a small comment. Irregardless of schoolmate connections,
> a "quench-from-the-melt" approach is not a good way to create
> models of tetrahedrally bonded CRNs (continuous random
> networks), which, among other things, might explain why your
> stress and forces are so large.

I am afraid this is not correct. Whether or not a model for  
disordered system obtained from a simulated quench is correct (this  
will depend on the size of the model and the speed of the quench),  
the atomic forces and overall stress should vanish if the quench has  
been performed in a numerically accurate way.

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 nakhmanson at anl.gov  Thu May 31 23:17:00 2007
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Thu, 31 May 2007 16:17:00 -0500
Subject: [Pw_forum] the procedure of calculating the Raman tensor using the
 finite electric field method
In-Reply-To: <80A77606-336D-4474-A527-9023A60C4726@sissa.it>
References: <98618.15996.qm@web15008.mail.cnb.yahoo.com>
 <465F0C42.1060207@anl.gov> <80A77606-336D-4474-A527-9023A60C4726@sissa.it>
Message-ID: <465F3B4C.3010705@anl.gov>

Dear Stefano,

You are, of course, correct, but what you are saying is so
obvious that I simply omitted this moment in my comment.

With the "quench-from-the-melt" technique it usually takes forever
to converge to zero forces and stress for a decent-size model that
simultaneously has accurate RDF and bond/dihedral angle distribution
functions. Large residual forces and strain unequivocally point to
a problem with model's structural relaxation. However, if one does
not want to spend forever relaxing it properly, *my advice* is to
use a model made with the Wooten-Winer-Weaire algorithm as an
initial guess and dance from there.

Naturally, a really small model would be easier to relax but
at the same time it would be useless for the studies of disorder.

I'm sorry that my comment might have been vague.

S.

Stefano Baroni wrote:
> Just a brief comment on a recent note by
> 
> On May 31, 2007, at 7:56 PM, Serge Nakhmanson wrote:
> 
>> Just a small comment. Irregardless of schoolmate connections,
>> a "quench-from-the-melt" approach is not a good way to create
>> models of tetrahedrally bonded CRNs (continuous random
>> networks), which, among other things, might explain why your
>> stress and forces are so large. 
> 
> I am afraid this is not correct. Whether or not a model for disordered 
> system obtained from a simulated quench is correct (this will depend on 
> the size of the model and the speed of the quench), the atomic forces 
> and overall stress should vanish if the quench has been performed in a 
> numerically accurate way. 
> 
> 

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