From eyvaz_isaev at yahoo.com  Wed Jul  1 00:19:56 2009
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 30 Jun 2009 15:19:56 -0700 (PDT)
Subject: [Pw_forum] Error in dynmat.x calculation.
Message-ID: <841714.98509.qm@web65702.mail.ac4.yahoo.com>


Dear Mateus,

> ????? from readmat: error # 1 
> ????? mismatch in file reading 

Most likely your file is corrupted. If you send me your dyn-file 
I can  have a look at it to understand whether the suggestion is correct.

In my experience I have never met such kind message.

Bests,
Eyvaz. 

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


--- On Tue, 6/30/09, MATEUS JOS? FERNANDES MARTINS <mjfmartins at ice.ufjf.br> wrote:

> From: MATEUS JOS? FERNANDES MARTINS <mjfmartins at ice.ufjf.br>
> Subject: [Pw_forum] Error in dynmat.x calculation.
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Date: Tuesday, June 30, 2009, 2:52 PM
> Hello all 
> 
>  what is the error: 
> 
>  Reading Dynamical Matrix from file /
> home/mateus/FULL-2x1x1.mat 
> 
> ? %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%%%%%%%%%%% 
> ????? from readmat: error # 1 
> 
> ????? mismatch in file reading 
> ? %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%%%%%%%%%%% 
> 
> ????? stopping ... 
> 
>  Whenever the road dynmat.x this error appears. 
>  I can not find solution anywhere ... 
> 
> 
>  Thank you,
> 
> Mateus
> 
> 
> -----Inline Attachment Follows-----
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


      

From eyvaz_isaev at yahoo.com  Wed Jul  1 00:54:21 2009
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 30 Jun 2009 15:54:21 -0700 (PDT)
Subject: [Pw_forum] the sum of the born effective charge in phonon
	calculation
Message-ID: <139488.34761.qm@web65705.mail.ac4.yahoo.com>


Dear Cheng,

> ????conv_thr = 1.D-12,
You wast time with this threshold. Use less strong criteria.

> ????????? -2.01782??????
> ?????????  2.04775???????

I would say the Born charges are equivalent (by absolut values) with a numerical noise. Within this noise charges' sum is zero.

> ? tr2_ph=1.0d-12,
Try d-14, and more ecutwfc.

Bests,
Eyvaz.

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


--- On Mon, 6/29/09, ??? <yccheng.nju at gmail.com> wrote:

> From: ??? <yccheng.nju at gmail.com>
> Subject: [Pw_forum] the sum of the born effective charge in phonon calculation
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Date: Monday, June 29, 2009, 7:10 PM
> Dear pwscf users,
> ??? I calculated?the phonon?of ZnS at Gamma
> point.? I checked the output file, and found that the sum
> of the born effective charge is not zero.
> ================================
> ????????? Effective charges E-U in cartesian
> axis
> ?????????? atom???? 1
> ????????? (?????? -2.01782???????
> 0.00000??????? 0.00000 )
> ????????? (??????? 0.00000??????
> -2.01782??????? 0.00000 )
> ????????? (??????? 0.00000???????
> 0.00000?????? -2.01782 )
> ?????????? atom???? 2
> 
> ????????? (??????? 2.04775???????
> 0.00000??????? 0.00000 )
> ????????? (??????? 0.00000???????
> 2.04775??????? 0.00000 )
> ????????? (??????? 0.00000???????
> 0.00000??????? 2.04775 )
> ================================
> 
> My question?:
> 1.?why the sum of the effectvie charge is not
> zero?
> 2.how to improve the calculation of born effective
> charge?
> ?
> The following is my input files:
> scf.in
> ?&CONTROL
> ?????????????????????? title = fine,
> ????????????????????? prefix =
> 'zns'
> ???????????????? calculation =
> 'scf' ,
> ??????????????? restart_mode =
> 'from_scratch' ,
> ????????????????? wf_collect = .false. ,
> 
> ????????????????????? outdir =
> './' ,
> ????????????????? pseudo_dir =
> './' ,
> ???????????????????? tstress = .true.
> ,
> ???????????????????? tprnfor = .true.
> ,
> ?????????????????????? nstep = 100 ,
> 
> ?/
> ?&SYSTEM
> ?????????????????????? ibrav = 2,
> ?????????????????? celldm(1) =
> 10.204964632,
> ???????????????????????? nat = 2,
> ??????????????????????? ntyp = 2,
> ???????????????????? ecutwfc = 80,
> ?????????????????????? nosym =
> .false. ,
> 
> ?/
> ?&ELECTRONS
> ??????????? electron_maxstep = 100,
> ??????????????????? conv_thr = 1.D-12,
> ?/
> ATOMIC_SPECIES
> ??? S?? 32.066?? 16-S.GGA.fhi.UPF
> ??? Zn? 65.409?? 30-Zn.GGA.fhi.UPF
> ATOMIC_POSITIONS crystal
> 
> S??????? 0.250000000?? 0.250000000??
> 0.250000000
> Zn?????? 0.000000000?? 0.000000000?? 0.000000000
> K_POINTS automatic
> ? 16 16 16 0 0 0
> 
> ph.in
> phonon calculation for ZnS
> &inputph
> ? tr2_ph=1.0d-12,
> ? prefix='zns',
> ? epsil=.true.,
> ? trans=.true.,
> ? lraman=.true.,
> ? elop=.true.,
> ? amass(1)=32.066,
> ? amass(2)=65.409,
> ? outdir='./',
> 
> ? fildyn='ZnS_IR.dynG',
> ? fildrho='ZnS_IR.drho',
> ?/
> 0.0 0.0 0.0
> 
> 
> -- 
> Y. C. Cheng
> Department of Physics
> Nanjing University
> Nanjing 210093
> P. R. China
> Tel: 86-25-83592907
> Email: yccheng.nju at gmail.com
> 
> 
> -----Inline Attachment Follows-----
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


      

From yccheng.nju at gmail.com  Wed Jul  1 04:31:44 2009
From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=)
Date: Wed, 1 Jul 2009 10:31:44 +0800
Subject: [Pw_forum] the sum of the born effective charge in phonon
	calculation
In-Reply-To: <139488.34761.qm@web65705.mail.ac4.yahoo.com>
References: <139488.34761.qm@web65705.mail.ac4.yahoo.com>
Message-ID: <da7526cb0906301931s339315fay6c2a2fc2af193822@mail.gmail.com>

Dear Prof. Eyvaz lsaev,
        Thank you for your suggestion.  I have another problem concerning
this question.  The keyword "conv_thr" is the convergence threshold for scf,
and the "th2_ph" is the threshold for selfconsistency in phonon
calculation.  What is the difference between the two keywords?   Previously
I thought that the two keywords are both for wavefunction optimization and
they should have the same meaning.



2009/7/1 Eyvaz Isaev <eyvaz_isaev at yahoo.com>

>
> Dear Cheng,
>
> >     conv_thr = 1.D-12,
> You wast time with this threshold. Use less strong criteria.
>
> >           -2.01782
> >            2.04775
>
> I would say the Born charges are equivalent (by absolut values) with a
> numerical noise. Within this noise charges' sum is zero.
>
> >   tr2_ph=1.0d-12,
> Try d-14, and more ecutwfc.
>
>
>

 --
Y. C. Cheng
Department of Physics
Nanjing University
Nanjing 210093
P. R. China
Tel: 86-25-83592907
Email: yccheng.nju at gmail.com
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From marzari at MIT.EDU  Wed Jul  1 09:59:10 2009
From: marzari at MIT.EDU (Nicola Marzari)
Date: Wed, 01 Jul 2009 03:59:10 -0400
Subject: [Pw_forum] the sum of the born effective charge in
	phonon	calculation
In-Reply-To: <da7526cb0906301931s339315fay6c2a2fc2af193822@mail.gmail.com>
References: <139488.34761.qm@web65705.mail.ac4.yahoo.com>
	<da7526cb0906301931s339315fay6c2a2fc2af193822@mail.gmail.com>
Message-ID: <4A4B174E.5070809@mit.edu>



Dear Cheng,


your question provides again a chance for you (and everyone else)
to try out a few things, as exercise - these will, I assure you,
allow you to understand better what is going on.

My understanding is that the greatest error in Born effective charges
comes from BZ sampling - so a good exercise would be to plot
the effective charge on either atom as a function of k-point sampling -
say for a 2,2,2, then 3,3,3, then 4,4,4, ... k-point mesh. You could
plot two curves, one for an unshifted Monkhorst-Pack mesh (i.e. n n n 0 
0 0) and one for a shifted one (i.e. n n n 1 1 1).

See how these value converge; also, since you know that the sum of the
effective charges must be zero, see how the semidifference of the two 
converges (this is equivalent, for 2 atoms, to applying the acoustic sum 
rule, i.e. forcing the sum of the eff charges to be zero by subtracting
to each of the N charges 1/N of the their sum).

Then try to see if increasing or decreasing the cutoff changes the 
values you have. See also if changing the thresholds changes the results
(I tend to be overzealous on thresholds, since it doesn't cost that
much to increase accuracy with a few more iterations. For phonon 
calculations it is typically very useful to converge really well the 
ground state and the phonons themselves).

I'm not sure on the definition of the thresholds - would also be good if 
someone (e.g. from my group ?) could comment on typical safe thresholds 
for ground-state calculations, or for phonon calculations. Especially 
the latter, almost a FAQ, and requiring great care.


				nicola



??? wrote:
> Dear Prof. Eyvaz lsaev,
>         Thank you for your suggestion.  I have another problem 
> concerning this question.  The keyword "conv_thr" is the convergence 
> threshold for scf, and the "th2_ph" is the threshold for selfconsistency 
> in phonon calculation.  What is the difference between the two 
> keywords?   Previously I thought that the two keywords are both for 
> wavefunction optimization and they should have the same meaning. 
> 

-- 
---------------------------------------------------------------------
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 larikamonu at gmail.com  Wed Jul  1 11:58:31 2009
From: larikamonu at gmail.com (mousumi uk)
Date: Wed, 1 Jul 2009 11:58:31 +0200
Subject: [Pw_forum] Ni LDA relativistic potential
Message-ID: <42e352dc0907010258q51813b6fhd420c86fc1c78a8d@mail.gmail.com>

Dear All,

Am searching for a good LDA relativistic pseudopotentials for Ni.

Can any of you please help?

Thanks and best regards,
Mousumi Upadhyay Kahaly
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From paulatto at sissa.it  Wed Jul  1 16:49:05 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 01 Jul 2009 16:49:05 +0200
Subject: [Pw_forum] Stress calculation in quantum espresso
In-Reply-To: <470CF86F503347CD8E0764219C135304@solarflare>
References: <D4A761F73683694BBD69D634FF2980153AEA88@MAIL.tyndall.ie>
	<4A48DBC2.1060306@na.infn.it>
	<411F972BFE0A4FD1BAC4F3BF4A099242@solarflare>
	<54950.78.12.162.45.1246342671.squirrel@webmail.sissa.it>
	<470CF86F503347CD8E0764219C135304@solarflare>
Message-ID: <op.uwd8r3coa8x26q@paulax>

In data 30 giugno 2009 alle ore 13:27:20, Huiqun Zhou <hqzhou at nju.edu.cn>  
ha scritto:
> BTW, there are other items need to check:
> (1) ion_dynamics
>  add 'bfgs' for the case of calculation = 'vc-relax'

This is already fixed in cvs, actually BFGS is the default case now, even  
for vc-relax.

> (2) pot | wfc_extrapolation
>  please clarify if 'first_order', 'second_order' can be used in  
> calculations  other than 'md' or 'vc-md'. I used these options in  
> 'relax' and 'vc-relax'  without any errors, too. Of course, I don't know  
> if these were really in
>  effect.

Both can be used for non-dynamical optimization (such as BFGS), although  
they don't striclty make very much sense. Nevertheless, they can help  
speeding up convergence, especially when the minimization steps get  
smaller. I would need to consult Paolo Giannozzi (who implemented the  
extrapolation) to be 100% sure.

> (3) ecfixed, qcutz and q2sigma
>  in the original paper, the framework is an extension of PR dynamics to
>  CP. Please clarify if these are effective in other dynamics (damp-w,  
> bfgs).  If possible, suggest a guide line how to set these options  
> (there is only  one example of carbon in the paper), say, qcutz should  
> be at least N (2?)  times of ecfixed, ecfixed should be ecutwfc plus  
> alpha (5 Ry or so?),
>  q2sigma should be one N-th of qcutz ...

They are used to compute a correction to the stress tensor, hence the  
apply to all kind of variable-cell processes (if it makes sense or not, I  
really cannot say).

regards

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

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

From r.golesorkhtabar at gmail.com  Wed Jul  1 16:56:12 2009
From: r.golesorkhtabar at gmail.com (rostam golesorkhtabar)
Date: Wed, 1 Jul 2009 16:56:12 +0200
Subject: [Pw_forum] Elastic Constant Calculation Problem
Message-ID: <8622a7010907010756m701e0c64t664e1d363c1c3f0a@mail.gmail.com>

Dear Users
  I want to calculate elastic constant by espresso. I wrote my program for
calculation:
process of my program :
1- finding the optimized structure
2- making the different distortion for different component of elastic
tensor.
3- relaxing structures and finding the energy of them.
4- finally, analyzing the energy and derive elastic constant.
I have applied this process and WIEN2k code for NiTi B2 structure the result
is very good;
but i don't know why the results are not good by espresso?
 thank you in advance
Rostam golesorkhtabar
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From giannozz at democritos.it  Wed Jul  1 19:15:22 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 1 Jul 2009 19:15:22 +0200
Subject: [Pw_forum] WIEN2k interface
In-Reply-To: <b10315cd0906301154w48e3ee5dm4fda7ab14a636001@mail.gmail.com>
References: <4A4A50CF.9070404@phys.ufl.edu>
	<b10315cd0906301154w48e3ee5dm4fda7ab14a636001@mail.gmail.com>
Message-ID: <96189A93-DCC3-4075-A493-21F7BDCF3D6E@democritos.it>


On Jun 30, 2009, at 20:54 , samad zare wrote:

> is differed figures in pwscf and win2k?

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




From giannozz at democritos.it  Wed Jul  1 19:25:56 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 1 Jul 2009 19:25:56 +0200
Subject: [Pw_forum] Stress calculation in quantum espresso
In-Reply-To: <op.uwd8r3coa8x26q@paulax>
References: <D4A761F73683694BBD69D634FF2980153AEA88@MAIL.tyndall.ie>
	<4A48DBC2.1060306@na.infn.it>
	<411F972BFE0A4FD1BAC4F3BF4A099242@solarflare>
	<54950.78.12.162.45.1246342671.squirrel@webmail.sissa.it>
	<470CF86F503347CD8E0764219C135304@solarflare>
	<op.uwd8r3coa8x26q@paulax>
Message-ID: <42CA18A7-8158-4908-88CA-89EC1B4C3E0A@democritos.it>

On Jul 1, 2009, at 16:49 , Lorenzo Paulatto wrote:

>> (2) pot | wfc_extrapolation
>>  please clarify if 'first_order', 'second_order' can be used in
>> calculations  other than 'md' or 'vc-md'. I used these options in
>> 'relax' and 'vc-relax'  without any errors, too. Of course, I  
>> don't know
>> if these were really in effect.
>
> Both can be used for non-dynamical optimization (such as BFGS),  
> although
> they don't strictly make very much sense. Nevertheless, they can help
> speeding up convergence, especially when the minimization steps get
> smaller. I would need to consult Paolo Giannozzi (who implemented the
> extrapolation) to be 100% sure.

I didn't implemented the extrapolation, I just tried to clean up the  
mess that
it used to be. First- and second-order extrapolation are devised to  
work in
conjunction with a MD sequence of time steps. There is no point in using
them for structural optimization, in my opinion.

>> (3) ecfixed, qcutz and q2sigma
>>  in the original paper, the framework is an extension of PR  
>> dynamics to
>>  CP. Please clarify [...]

please experiment a little bit and report what you found

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




From giannozz at democritos.it  Wed Jul  1 19:28:38 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 1 Jul 2009 19:28:38 +0200
Subject: [Pw_forum] Elastic Constant Calculation Problem
In-Reply-To: <8622a7010907010756m701e0c64t664e1d363c1c3f0a@mail.gmail.com>
References: <8622a7010907010756m701e0c64t664e1d363c1c3f0a@mail.gmail.com>
Message-ID: <EEF6C154-FBC8-43B2-96AD-D97F57B97C60@democritos.it>


On Jul 1, 2009, at 16:56 , rostam golesorkhtabar wrote:

> I have applied this process and WIEN2k code for NiTi B2 structure
> the result is very good; but i don't know why the results are not good
> by espresso?

maybe you didn't use a good brand of coffee?

Seriously: put yourself in the place of people reading
this mailing list. How can you think that there is anybody
out there that can answer such a generic question?

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




From sumanta.bhandary at fysik.uu.se  Thu Jul  2 13:31:37 2009
From: sumanta.bhandary at fysik.uu.se (Sumanta Bhandary)
Date: Thu, 02 Jul 2009 13:31:37 +0200
Subject: [Pw_forum] DOS Calculation in W90
Message-ID: <20090702133137.u5xm8jueskwowks4@webmail5.uu.se>

Dear Users,
           I want to know how density of states calculated after  
wannierisation in W90 and how should I compare with that calculated  
with pwscf ?


thanks and with regards
Sumanta Bhandary
PhD student
Uppsala University
Uppsala,Sweden


From lex at phys.ufl.edu  Fri Jul  3 20:06:16 2009
From: lex at phys.ufl.edu (Lex Kemper)
Date: Fri, 03 Jul 2009 14:06:16 -0400
Subject: [Pw_forum] Projwfc and NaN's
Message-ID: <4A4E4898.5000906@phys.ufl.edu>

Hey everyone,

I'm using projwfc to look at the contribution of certain orbitals to the 
band structure. I am running into a strange result though for one of my 
systems -- for some kpoints, the |psi|^2 is NaN for all energies. This 
is of course not correct, unless all the projections are 0 identically 
which I highly doubt is right (the kpoints just next to the one that 
gives NaN look fine).

Any ideas where this originates?

Thanks,

Lex Kemper
Department of Physics
University of Florida

P.S. My apologies if this ends up on the listserv twice, I believe I 
sent it from the wrong e-mail address before.

From ferretti at MIT.EDU  Fri Jul  3 21:18:08 2009
From: ferretti at MIT.EDU (Andrea Ferretti)
Date: Fri, 3 Jul 2009 15:18:08 -0400 (EDT)
Subject: [Pw_forum] Projwfc and NaN's
In-Reply-To: <4A4E4898.5000906@phys.ufl.edu>
Message-ID: <Pine.GSO.4.30L.0907031419270.2464-100000@home-on-the-dome.mit.edu>



Hi Lex,

which version of Q-E are you using ??
running serial or parallel ??
is the problem reproducible ??

in order to figure out where the problem is, it would be of much help if
you could provide the make.sys file obtained during the configuration of
Q-E, and a working example showing the problem.

all the best
andrea

>
> I'm using projwfc to look at the contribution of certain orbitals to the
> band structure. I am running into a strange result though for one of my
> systems -- for some kpoints, the |psi|^2 is NaN for all energies. This
> is of course not correct, unless all the projections are 0 identically
> which I highly doubt is right (the kpoints just next to the one that
> gives NaN look fine).
>
> Any ideas where this originates?
>
> Thanks,
>
> Lex Kemper
> Department of Physics
> University of Florida
>
> P.S. My apologies if this ends up on the listserv twice, I believe I
> sent it from the wrong e-mail address before.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

-- 
Andrea Ferretti
MIT, Dept Material Science & Engineering
bldg 13-4078, 77, Massachusetts Ave, Cambridge, MA
Tel: +1 617-452-2455;  Skype: andrea_ferretti
URL: http://quasiamore.mit.edu

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



From positronium at gmail.com  Fri Jul  3 22:10:37 2009
From: positronium at gmail.com (Lex Kemper)
Date: Fri, 03 Jul 2009 16:10:37 -0400
Subject: [Pw_forum] Projwfc and NaN's
In-Reply-To: <Pine.GSO.4.30L.0907031419270.2464-100000@home-on-the-dome.mit.edu>
References: <Pine.GSO.4.30L.0907031419270.2464-100000@home-on-the-dome.mit.edu>
Message-ID: <4A4E65BD.2090207@phys.ufl.edu>

Hi Andrea,

I'm using Q-E 4.0.4, compiled parallel. I haven't reproduced it anywhere 
else, this is the first time I've seen it. The make.sys file is at the 
bottom of this e-mail, as is my input for profwfc.x. This input works 
fine for a different system.

Thanks,

Lex

------------- pdos.in  --------------------------
&inputpp
    prefix='SFAr'
    filpdos='bandCB122'
    filproj='bandprojections.dat'
    outdir='./tmp_bands'
    DeltaE=0.01
    ngauss = -99
    degauss = 0.002
/


------------- make.sys --------------------------
# 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:
         $(CPP) $(CPPFLAGS) $< -o $*.F90
         $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o

# .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__PGI -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA
FDFLAGS        = $(DFLAGS)

# IFLAGS = how to locate directories where files to be included are
# In most cases, IFLAGS = -I../include
# 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 need modules in ../PW and ../PH

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

# 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         = ftn
#F90           = pgf90
CC             = cc
#F77            = pgf77
F77            = ftn

# 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)
CFLAGS         = $(DFLAGS) $(IFLAGS) -v -V -O4 -fastsse 
-Mipa=fast,inline -Minfo=all -Minform=inform -Mneginfo
FFLAGS         = -r8 -v -V -O4 -fastsse -Mipa=fast,inline -Minfo=all 
-Minform=inform -Mneginfo
F90FLAGS       = $(FFLAGS) $(FDFLAGS) $(IFLAGS) $(MODFLAGS)

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

FFLAGS_NOOPT   = -O0

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

LD             = ftn
LDFLAGS        = #-v -V -O4 -fastsse -Mipa=fast,inline -Minfo=all 
-Minform=inform -Mneginfo
LD_LIBS        =

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

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

BLAS_LIBS      = -lsci_quadcore

# 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    = -lsci_quadcore

# 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_DYNAMIC is used in iotk to produce a dynamical library,
# for Mac OS-X with PowerPC and xlf compiler. In all other cases
# ARFLAGS_DYNAMIC = $(ARFLAGS)

AR             = ar
ARFLAGS        = ruv
ARFLAGS_DYNAMIC= ruv

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

RANLIB         = ranlib

# all internal and external libraries - do not modify

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


Andrea Ferretti wrote:
> 
> Hi Lex,
> 
> which version of Q-E are you using ??
> running serial or parallel ??
> is the problem reproducible ??
> 
> in order to figure out where the problem is, it would be of much help if
> you could provide the make.sys file obtained during the configuration of
> Q-E, and a working example showing the problem.
> 
> all the best
> andrea
> 
>> I'm using projwfc to look at the contribution of certain orbitals to the
>> band structure. I am running into a strange result though for one of my
>> systems -- for some kpoints, the |psi|^2 is NaN for all energies. This
>> is of course not correct, unless all the projections are 0 identically
>> which I highly doubt is right (the kpoints just next to the one that
>> gives NaN look fine).
>>
>> Any ideas where this originates?
>>
>> Thanks,
>>
>> Lex Kemper
>> Department of Physics
>> University of Florida
>>
>> P.S. My apologies if this ends up on the listserv twice, I believe I
>> sent it from the wrong e-mail address before.
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
> 

From hushujun at mail.sdu.edu.cn  Mon Jul  6 08:11:15 2009
From: hushujun at mail.sdu.edu.cn (Dr. Shu-jun Hu)
Date: Mon, 06 Jul 2009 14:11:15 +0800
Subject: [Pw_forum] qustions about the initio magnetization of ion
Message-ID: <ZDGTXYQQCCHURFLJETJWODDTPFPT.hushujun@mail.sdu.edu.cn>

Dear all,
I have some qustions about the initio magnetization of ion for LSDA calculation.
In the input file the "starting_magnetization" is used to break the spin symmetry of magnetic system. By specifying such parameters, how does pw.x initio the magnetic moment of certain ions?
Taking transition metal ion Fe for example, if the starting_magnetizaton(Fe)=0.4, how many electrons occupy the spin-up and spin-down channels respectively for the initio wfc? Only the symmetry breaking of 3d electrons are considered in LSDA calculation, or all the valence electrons (both 3d and 4s)?

Such a question concerns about the output information of calculation with constrained magnetization.
During the calculation, I got the output information as:
     atom number   14 relative position :    1.4040   4.1784   3.2357
     charge :     7.082847
     magnetization :          0.239576
     magnetization/charge:    0.033825
     constrained moment :     0.200000
Does the value of "magnetization" (0.239576) represent the magnetic moment of ion, or the polarization? If the latter case, how to derive the magnetic moment in unit of Bohr? 
-------
Another question is about the total energy given by constrained calculations.
I want to compare the total energy of a system with different magnetic moment for certain ions, and find the ground state.
In order to fix magnetic moment at the starting value, lambda = 1000 is setup. That's a large value.
As described in INPUT_PW.html, the penalty energy is introduced at this time. I wonder if the comparison make any sense?
Any reply to any question is appreciated. If you can also guide me to the position of source code refering to the question, that's great!
Best regards
Shujun Hu
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From degironc at sissa.it  Mon Jul  6 09:33:07 2009
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Mon, 06 Jul 2009 09:33:07 +0200
Subject: [Pw_forum] qustions about the initio magnetization of ion
In-Reply-To: <ZDGTXYQQCCHURFLJETJWODDTPFPT.hushujun@mail.sdu.edu.cn>
References: <ZDGTXYQQCCHURFLJETJWODDTPFPT.hushujun@mail.sdu.edu.cn>
Message-ID: <4A51A8B3.6050806@sissa.it>

Dr. Shu-jun Hu wrote:
>
> Dear all,
>
> I have some qustions about the initio magnetization of ion for LSDA
> calculation.
>
> In the input file the "starting_magnetization" is used to break the
> spin symmetry of magnetic system. By specifying such parameters, how
> does pw.x initio the magnetic moment of certain ions?
> Taking transition metal ion Fe for example, if the
> starting_magnetizaton(Fe)=0.4, how many electrons occupy the spin-up
> and spin-down channels respectively for the initio wfc? Only the
> symmetry breaking of 3d electrons are considered in LSDA calculation,
> or all the valence electrons (both 3d and 4s)?
>
the starting magnetization variables define the way the initial initial
charge density, that is used to generate the initial potential, is
built. The initial density is obtained from the superposition of atomic
charges, read from the pseudopotential file, and in the case of a spin
polarized calculation the initial charge density is defined as
rho(r,sigma) = sum_s=1,Nat rho_at_type(r-Rs) * (1 + sigma*
starting_magnetization_type)/2
where sigma is +/- 1 for up/down spin components

the atomic charge density is the total one (including the 4s in case of Fe).

occupation of the initial wfs is NOT imposed and is the result of the
first diagomalization + smearing + fermi energy...

> Such a question concerns about the output information of calculation
> with constrained magnetization.
>
> During the calculation, I got the output information as:
>
> atom number 14 relative position : 1.4040 4.1784 3.2357
> charge : 7.082847
> magnetization : 0.239576
> magnetization/charge: 0.033825
> constrained moment : 0.200000
>
> Does the value of "magnetization" (0.239576) represent the magnetic
> moment of ion, or the polarization? If the latter case, how to derive
> the magnetic moment in unit of Bohr?
>
I may be wrong (I'm not usign this feature often) but inspecting the
code the meaning of the following output is:
there are 7.08... electrons in the chosen sphere around the atom # 14
there are 0.2395... more up electrons than down ones in the sphere...
this is more the local moment than the local magnetization
0.033 is the ratio of the two numbers above
0.20 is the target value of the magnetic moment (the actual value is as
said 0.2395...). the fact that the actual moment does not agree with the
target one is due to the fact that the constraint is impose via a
penalty function. the larger the value of lambda the closer should be
the computed value to its target.

> -------
>
> Another question is about the total energy given by constrained
> calculations.
> I want to compare the total energy of a system with different magnetic
> moment for certain ions, and find the ground state.
> In order to fix magnetic moment at the starting value, lambda = 1000
> is setup. That's a large value.
> As described in INPUT_PW.html, the penalty energy is introduced at
> this time. I wonder if the comparison make any sense?
>
what the code minimizes is the energy including the penalty cost... This
penalty cost is reported in the output.... I'm not sure however whether
the printed value of the total energy includes or not this term...
I hope someone else can comment on that...

stefano de Gironcoli


> Any reply to any question is appreciated. If you can also guide me to
> the position of source code refering to the question, that's great!
>
> Best regards
>
> Shujun Hu
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From kazempoor2000 at yahoo.com  Mon Jul  6 10:06:13 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Mon, 6 Jul 2009 01:06:13 -0700 (PDT)
Subject: [Pw_forum] U
Message-ID: <307694.76468.qm@web112512.mail.gq1.yahoo.com>


Dear all
I want to study the effect of U(habburd parameter on band gap). According to method described in coccocini phd thesis , we are able to obtain U by setting alpha to different values and ? the difference in the slope of ns Vs. alpha and ns0 Vs. alpha0? is U parameter.
My question is : Do I Optimize the lattice constant After obtaining U from above procedure or not?
Does above method works for any bulk material that have d orbital? 
Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


      
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From sclauzer at sissa.it  Mon Jul  6 11:48:03 2009
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Mon, 6 Jul 2009 11:48:03 +0200
Subject: [Pw_forum] U
In-Reply-To: <307694.76468.qm@web112512.mail.gq1.yahoo.com>
References: <307694.76468.qm@web112512.mail.gq1.yahoo.com>
Message-ID: <862C76DC-8AEA-48AE-9F97-8847ADDB1C79@sissa.it>


Il giorno 06/lug/09, alle ore 10:06, ali kazempour ha scritto:
>
> Dear all
> I want to study the effect of U(habburd parameter on band gap).  
> According to method described in coccocini phd thesis , we are able  
> to obtain U by setting alpha to different values and   the  
> difference in the slope of ns Vs. alpha and ns0 Vs. alpha0  is U  
> parameter.
> My question is : Do I Optimize the lattice constant After obtaining  
> U from above procedure or not?
> Does above method works for any bulk material that have d orbital?

I think that in principle the correct procedure should be to recompute  
U for every lattice parameter value you will use to get the total  
energy and then fit to the equation of state. This is because of the  
internally consistent definition of U, which depends on the local  
environment surrounding the Hubbard atoms. At each value of the  
lattice parameter this environment changes, and the hybridization of  
the Hubbard orbitals is influenced by it. Anyway I guess that if you  
computed the U at a value of the lattice parameter not distant from  
the optimal one (theoretical), maybe you can use that value of U to  
get the total energy in the neighborhood of the optimal value. On the  
contrary, the estimation of the bulk modulus may be much more  
sensitive of the value of U which you employ.


GS


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




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From giuseppe.mattioli at mlib.ism.cnr.it  Mon Jul  6 12:33:33 2009
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Mon, 6 Jul 2009 12:33:33 +0200
Subject: [Pw_forum] U
In-Reply-To: <307694.76468.qm@web112512.mail.gq1.yahoo.com>
References: <307694.76468.qm@web112512.mail.gq1.yahoo.com>
Message-ID: <200907061233.34021.giuseppe.mattioli@mlib.ism.cnr.it>

I suggest you to reoptimize the lattice parameters. You could find quite 
different results with respect to the LDA or GGA results.

Giuseppe


On Monday 06 July 2009 10:06:13 ali kazempour wrote:
> Dear all
> I want to study the effect of U(habburd parameter on band gap). According
> to method described in coccocini phd thesis , we are able to obtain U by
> setting alpha to different values and ? the difference in the slope of ns
> Vs. alpha and ns0 Vs. alpha0? is U parameter. My question is : Do I
> Optimize the lattice constant After obtaining U from above procedure or
> not? Does above method works for any bulk material that have d orbital? Ali
> Kazempour
>
> Physics department, Isfahan University of Technology
>
> 84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733
>
> Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375

-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

   Giuseppe Mattioli                            
   CNR - ISTITUTO DI STRUTTURA DELLA MATERIA   
   v. Salaria Km 29,300 - C.P. 10                
   I 00016 - Monterotondo Stazione (RM)          
   Tel + 39 06 90672836 - Fax +39 06 90672316    
   E-mail: <giuseppe.mattioli at ism.cnr.it>
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From marzari at MIT.EDU  Mon Jul  6 12:39:58 2009
From: marzari at MIT.EDU (Nicola Marzari)
Date: Mon, 06 Jul 2009 06:39:58 -0400
Subject: [Pw_forum] U
In-Reply-To: <200907061233.34021.giuseppe.mattioli@mlib.ism.cnr.it>
References: <307694.76468.qm@web112512.mail.gq1.yahoo.com>
	<200907061233.34021.giuseppe.mattioli@mlib.ism.cnr.it>
Message-ID: <4A51D47E.9070507@mit.edu>

Giuseppe Mattioli wrote:
> I suggest you to reoptimize the lattice parameters. You could find quite 
> different results with respect to the LDA or GGA results.


Also, as a matter of caution - do use a single U value in your
equation of state - ideally what you'd get from Cococcioni procedure
close to the minimum of the DFT+U equation of state.

			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  Mon Jul  6 17:16:48 2009
From: matteo at umn.edu (Matteo Cococcioni)
Date: Mon, 06 Jul 2009 10:16:48 -0500
Subject: [Pw_forum] U
In-Reply-To: <4A51D47E.9070507@mit.edu>
References: <307694.76468.qm@web112512.mail.gq1.yahoo.com>	<200907061233.34021.giuseppe.mattioli@mlib.ism.cnr.it>
	<4A51D47E.9070507@mit.edu>
Message-ID: <4A521560.6080305@umn.edu>


Dear Ali

I just want to add something what Nicola, Giuseppe and Gabriele wrote.
it is a good idea to reoptimize the structure after computing U. If you 
only need to optimize the lattice parameter
(the atomic positions are fixed) this is easy: you just need to compute 
U for a series of different
lattice parameter and then fit E vs V on a Murnaghan eq of state for 
example.
If the relaxation of internal degrees of freedom is relevant there is a 
further level of consistency between U and
the structure. In principle for each volume (or each pressure) you need 
to iterate the calculation of U with the internal relaxation.
Hopefully U won't change much and an (average) U will work for all 
lattice parameters (as Nicola suggests) in your case. However
we have recently found that a structurally consistent U has a finite 
effect, if not on energies, on their derivative wrt to V, i.e. pressure.
see the paper PRB 79, 125124 (2009) for details.

regards,

Matteo



Nicola Marzari wrote:
> Giuseppe Mattioli wrote:
>   
>> I suggest you to reoptimize the lattice parameters. You could find quite 
>> different results with respect to the LDA or GGA results.
>>     
>
>
> Also, as a matter of caution - do use a single U value in your
> equation of state - ideally what you'd get from Cococcioni procedure
> close to the minimum of the DFT+U equation of state.
>
> 			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
>   


-- 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Matteo Cococcioni
Department of Chemical Engineering and Materials Science,
University of Minnesota
421 Washington Av. SE
Minneapolis, MN 55455
Tel. +1 612 624 9056    Fax +1 612 626 7246
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


From jdai3 at mail.ustc.edu.cn  Mon Jul  6 18:41:33 2009
From: jdai3 at mail.ustc.edu.cn (Jun Dai)
Date: Tue, 07 Jul 2009 00:41:33 +0800
Subject: [Pw_forum] V pseudopotential
Message-ID: <446898493.21790@ustc.edu.cn>

Dear all,
I want to have a try of the hybrid functional implemented in Q-E for a vanadium
oxide system, since the LDA+U failed to give reasonable results, and the ultrasoft
pp seems not supported yet, so can someone share a copy of norm-conserving V
pseudopotential with me? Thanks in advance.




------------------------------
Best regards,
Jun Dai

=============================================================
 J. Dai
 Ph.D. Candidate,
 Hefei National Laboratory For Physical Sciences at the Microscale,
 University of Science and Technology of China,
 Hefei, Anhui, 230026,
 People's Republic of China
 Tel.: 86-551-3606428
 Fax.: 86-551-3602969
 E-mail: jdai3 at mail.ustc.edu.cn
=============================================================

From dimpy.sharma at tyndall.ie  Mon Jul  6 19:45:22 2009
From: dimpy.sharma at tyndall.ie (Dimpy Sharma)
Date: Mon, 6 Jul 2009 18:45:22 +0100
Subject: [Pw_forum] Stress calculation in SCF
Message-ID: <D4A761F73683694BBD69D634FF2980153AEAA1@MAIL.tyndall.ie>


Hi Quantum  espresso user,

I want to calculate stress and my calculation is a scf calculation,howevr it is not converged, in the output it is showing that problme in cholesky decomposition. can anybody please help me in giving an explanation to this? as in the manual it is written  that stress can only be calculated if calculation is either vc-md or vc-relax.

Thanks

Dimpy
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From paulatto at sissa.it  Mon Jul  6 22:22:08 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Mon, 6 Jul 2009 22:22:08 +0200 (CEST)
Subject: [Pw_forum] Stress calculation in SCF
In-Reply-To: <D4A761F73683694BBD69D634FF2980153AEAA1@MAIL.tyndall.ie>
References: <D4A761F73683694BBD69D634FF2980153AEAA1@MAIL.tyndall.ie>
Message-ID: <46021.78.12.162.98.1246911728.squirrel@webmail.sissa.it>


On Mon, July 6, 2009 19:45, Dimpy Sharma wrote:
>  I want to calculate stress and my calculation is a scf calculation,howevr
>  it is not converged, in the output it is showing that problme in cholesky
>  decomposition.

It means that your pseudopotentials are bad, your lattice parameter is
massively off-shot, or you have used a smearing far too high, or possibley
some other reason. This is one of the most frequently asked question,
please have a look at the mailing list archives:
<http://www.google.com/search?&q=site%3Ademocritos.it+cholesky>



>  as in the manual it is written  that stress can only be calculated
>  if calculation is either vc-md or vc-relax.

Although the wording choice in the manual is a bit ambiguous, this is not
true: you can compute the stress also in a scf calculation, by setting
tstress=.true.

best regards


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



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From hushujun at mail.sdu.edu.cn  Tue Jul  7 04:39:57 2009
From: hushujun at mail.sdu.edu.cn (Dr. Shu-jun Hu)
Date: Tue, 07 Jul 2009 10:39:57 +0800
Subject: [Pw_forum] questions about the initio magnetization of ion
Message-ID: <TRNKRKJCLGNLLWXGONMRXOOMNAVT.hushujun@mail.sdu.edu.cn>

Dear Prof. Stefano de Gironcoli,
Thank you for your detailed reply.
After posting my question, I perform the projwfc calculation.
I found a puzzling relation between the starting magnetization and the resulting polarization (magnetic moment).
I setup the input file as: starting_magnetization(3) = -0.8, and a large value for lambda. In the last iteration pw.x output the following information:
 ==============================================================================
     atom number   20 relative position :    1.4040   4.1784   9.7071
     charge :     7.067449
     magnetization :         -0.801893
     magnetization/charge:   -0.113463
     constrained moment :    -0.800000
 ==============================================================================

Now, it was noted that the magnetization is constrained at -0.801893. However, the projwfc calculation gave the results:
     Atom #  20: total charge =  16.3788, s =  2.3540, p =  7.1679, d =  6.8569, 
                 spin up      =   7.2902, s =  1.1726, p =  3.5766, d =  2.5410, 
                 spin down    =   9.0886, s =  1.1814, p =  3.5913, d =  4.3159, 
                 polarization =  -1.7983, s = -0.0088, p = -0.0147, d = -1.7748, 
                                  ______________

Actually the magnetic moment is -1.7983 (muB?).
I tried the different value of starting_magnetization, and found that the polarization is always about the double of starting_magnetization. So I think the output "magnetization" duing the pw calculation is not the magnetic moment. If the polarized rho is defined as: rho(r)*(1/2+sigma*starting_magnetization), rather than rho(r)*(1+sigma*starting_magnetization)/2, the above relation is reasonable.Am I right?

Best regards
Shujun Hu


>Dr. Shu-jun Hu wrote:
>>
>> Dear all,
>>
>> I have some qustions about the initio magnetization of ion for LSDA
>> calculation.
>>
>> In the input file the "starting_magnetization" is used to break the
>> spin symmetry of magnetic system. By specifying such parameters, how
>> does pw.x initio the magnetic moment of certain ions?
>> Taking transition metal ion Fe for example, if the
>> starting_magnetizaton(Fe)=0.4, how many electrons occupy the spin-up
>> and spin-down channels respectively for the initio wfc? Only the
>> symmetry breaking of 3d electrons are considered in LSDA calculation,
>> or all the valence electrons (both 3d and 4s)?
>>
>the starting magnetization variables define the way the initial initial
>charge density, that is used to generate the initial potential, is
>built. The initial density is obtained from the superposition of atomic
>charges, read from the pseudopotential file, and in the case of a spin
>polarized calculation the initial charge density is defined as
>rho(r,sigma) = sum_s=1,Nat rho_at_type(r-Rs) * (1 + sigma*
>starting_magnetization_type)/2
>where sigma is +/- 1 for up/down spin components
>
>the atomic charge density is the total one (including the 4s in case of Fe).
>
>occupation of the initial wfs is NOT imposed and is the result of the
>first diagomalization + smearing + fermi energy...
>
>> Such a question concerns about the output information of calculation
>> with constrained magnetization.
>>
>> During the calculation, I got the output information as:
>>
>> atom number 14 relative position : 1.4040 4.1784 3.2357
>> charge : 7.082847
>> magnetization : 0.239576
>> magnetization/charge: 0.033825
>> constrained moment : 0.200000
>>
>> Does the value of "magnetization" (0.239576) represent the magnetic
>> moment of ion, or the polarization? If the latter case, how to derive
>> the magnetic moment in unit of Bohr?
>>
>I may be wrong (I'm not usign this feature often) but inspecting the
>code the meaning of the following output is:
>there are 7.08... electrons in the chosen sphere around the atom # 14
>there are 0.2395... more up electrons than down ones in the sphere...
>this is more the local moment than the local magnetization
>0.033 is the ratio of the two numbers above
>0.20 is the target value of the magnetic moment (the actual value is as
>said 0.2395...). the fact that the actual moment does not agree with the
>target one is due to the fact that the constraint is impose via a
>penalty function. the larger the value of lambda the closer should be
>the computed value to its target.
>
>> -------
>>
>> Another question is about the total energy given by constrained
>> calculations.
>> I want to compare the total energy of a system with different magnetic
>> moment for certain ions, and find the ground state.
>> In order to fix magnetic moment at the starting value, lambda = 1000
>> is setup. That's a large value.
>> As described in INPUT_PW.html, the penalty energy is introduced at
>> this time. I wonder if the comparison make any sense?
>>
>what the code minimizes is the energy including the penalty cost... This
>penalty cost is reported in the output.... I'm not sure however whether
>the printed value of the total energy includes or not this term...
>I hope someone else can comment on that...
>
>stefano de Gironcoli
>
>
>> Any reply to any question is appreciated. If you can also guide me to
>> the position of source code refering to the question, that's great!
>>
>> Best regards
>>
>> Shujun Hu
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>   
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From oulihui666 at 126.com  Tue Jul  7 08:27:43 2009
From: oulihui666 at 126.com (oulihui666)
Date: Tue, 7 Jul 2009 14:27:43 +0800 (CST)
Subject: [Pw_forum] About background charge
Message-ID: <15590744.261701246948063594.JavaMail.coremail@bj126app27.126.com>

Dear All,
In my calculated systems, which carry a positive charge, at the same time, background charges with same amount is added to all unit
cell include vacuum layer automatically, but in my systems, I don't want to let vacuum layer fill backgroun charges when calculated. 
Thus, I'd like to ask if PWSCF can do calculations that vacuum layer do not fill backgrount charges ?  
I have checked the manual and original pipemails, but didn't find many topics on background charges.
However,I found many discussions on EXTERNAL POTENTIAL which makes it possible to add an external 
electrostatic field.  
If possible, how ? 
 
Many thanks.
Best regards,
Lihui Ou


--

======================================
Lihui Ou
PH.D Candidate in Electrochemistry                      
College of Chemistry and Molecular Science            
Wuhan University,430072,Hubei Province,China 
E-mail:oulihui666 at 126.com
======================================
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From paulatto at sissa.it  Tue Jul  7 09:18:31 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 7 Jul 2009 09:18:31 +0200 (CEST)
Subject: [Pw_forum] About background charge
In-Reply-To: <15590744.261701246948063594.JavaMail.coremail@bj126app27.126.com>
References: <15590744.261701246948063594.JavaMail.coremail@bj126app27.126.com>
Message-ID: <35268.78.12.162.98.1246951111.squirrel@webmail.sissa.it>


On Tue, July 7, 2009 08:27, oulihui666 wrote:
>  Thus, I'd like to ask if PWSCF can do calculations that vacuum layer do
>  not fill backgrount charges ?

The system is not really filled with background charges, what is really
done is actively set the G=0 component of V to zero. In this way the
average value of the potential over the unit cell is zero, and everything
works fine (if you can afford a cell big enough to suppress periodic image
interaction)

>  I have checked the manual and original pipemails, but didn't find many
>  topics on background charges.

There are a few, e.g.
<http://www.democritos.it/pipermail/pw_forum/2005-April/002379.html>

>  However,I found many discussions on EXTERNAL POTENTIAL which makes it
>  possible to add an external electrostatic field.
>  If possible, how ?

Have a look at the documentation, Doc/INPUT_PW.html; there are two ways to
do it: using a sawtootk potential or using the modern theory of
polarization (Berry phase); the latter is only implemented for insulators.

>
>  Many thanks.

best regards



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



----------------------------------------------------------------
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From mastermik at gmail.com  Tue Jul  7 09:41:34 2009
From: mastermik at gmail.com (Mikiyas Tsegaye)
Date: Tue, 7 Jul 2009 03:41:34 -0400
Subject: [Pw_forum] force constant output
Message-ID: <8A26E43F-EF5F-40FE-B345-E67CCF27B857@gmail.com>

hello all,

I have performed a phonon calculation and have the output file  
"prefix.fc" which I understand is the file containing the real-space  
force constants F(r). Its a long list of numbers - Is there any guide  
for how to interpret the formatting of this file, so I know exactly  
what these numbers represent?

- Mikiyas Tsegaye
University of Virginia
Dept of Electrical and Computer Engineering
Charlottesville, VA, USA

From giannozz at democritos.it  Tue Jul  7 10:03:06 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 7 Jul 2009 10:03:06 +0200
Subject: [Pw_forum] force constant output
In-Reply-To: <8A26E43F-EF5F-40FE-B345-E67CCF27B857@gmail.com>
References: <8A26E43F-EF5F-40FE-B345-E67CCF27B857@gmail.com>
Message-ID: <BAC753F0-55D8-475A-BDD8-C034B8FA9965@democritos.it>


On Jul 7, 2009, at 9:41 , Mikiyas Tsegaye wrote:

> I have performed a phonon calculation and have the output file
> "prefix.fc" which I understand is the file containing the real-space
> force constants F(r). Its a long list of numbers - Is there any guide
> for how to interpret the formatting of this file, so I know exactly
> what these numbers represent?

it was explained in one (or more than one) message on this same
mailing list. Search "force constants file" and you will find this as
first item:
http://www.democritos.it/pipermail/pw_forum/2005-April/002408.html

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




From giuseppe.mattioli at mlib.ism.cnr.it  Tue Jul  7 12:07:16 2009
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Tue, 7 Jul 2009 12:07:16 +0200
Subject: [Pw_forum] V pseudopotential
In-Reply-To: <446898493.21790@ustc.edu.cn>
References: <446898493.21790@ustc.edu.cn>
Message-ID: <200907071207.17437.giuseppe.mattioli@mlib.ism.cnr.it>

I don't have any V normcons pseudo for you, but I still would share some 
results. I'm trying to study a 6 atom rutile TiO2 cell with the pbe0 hybrid 
functional (48 electrons, convergence achieved by using a k444 grid in the 
case of the pbe xc). Honestly, I didn't understand how to deal with the q grid 
in the case of periodic systems (the nqx variables. In the case of molecules I 
managed to have fine results by using the gamma point and a 111 q grid), then 
I tried different grids (q111, q222, q444). The q111 case requires reasonable 
resources but doesn't provide reliable results. The q222 case is already very 
expensive and the achieved results are still not very good. I regard a lattice 
parameter optimization in this case as a "bath of blood" (dunno if you say 
something similar...:-)). The q444 case... don't do it, please. I suspect that 
V oxide cells are larger, so work harder on the DFT+U calculations...

However, look (more than two seconds) at the /yourespresso/atomic_doc/ 
directory. It should be really easy to generate a norm conserving V 
pseudopotential. Then, make several tests in order to say if your 
pseudopotential is a good one (and this is a little more difficult). It is 
indeed one of the more instructive tasks if you want understand (on a 
practical basis) how to perform reliable calculations.

Yours
Giuseppe


On Monday 06 July 2009 18:41:33 Jun Dai wrote:
> Dear all,
> I want to have a try of the hybrid functional implemented in Q-E for a
> vanadium oxide system, since the LDA+U failed to give reasonable results,
> and the ultrasoft pp seems not supported yet, so can someone share a copy
> of norm-conserving V pseudopotential with me? Thanks in advance.
>
>
>
>
> ------------------------------
> Best regards,
> Jun Dai
>
> =============================================================
>  J. Dai
>  Ph.D. Candidate,
>  Hefei National Laboratory For Physical Sciences at the Microscale,
>  University of Science and Technology of China,
>  Hefei, Anhui, 230026,
>  People's Republic of China
>  Tel.: 86-551-3606428
>  Fax.: 86-551-3602969
>  E-mail: jdai3 at mail.ustc.edu.cn
> =============================================================
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

   Giuseppe Mattioli                            
   CNR - ISTITUTO DI STRUTTURA DELLA MATERIA   
   v. Salaria Km 29,300 - C.P. 10                
   I 00016 - Monterotondo Stazione (RM)          
   Tel + 39 06 90672836 - Fax +39 06 90672316    
   E-mail: <giuseppe.mattioli at ism.cnr.it>
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From dimpy.sharma at tyndall.ie  Tue Jul  7 13:06:54 2009
From: dimpy.sharma at tyndall.ie (Dimpy Sharma)
Date: Tue, 7 Jul 2009 12:06:54 +0100
Subject: [Pw_forum] Error in output in calculating stress
Message-ID: <D4A761F73683694BBD69D634FF2980153AEAA8@MAIL.tyndall.ie>


Hi Quantum espresso users,

I tried to calculate stress for a sytem by performing a scf calculation, presently I am running two diffrenet calculations by varying the lattice paarmeter of the system, howvever, I have found that at cell dimension either smaller or greater than the optimum lattice parameter, I cannot find the output, instead it is showing 
rm_l_6_1007: (61.828125) net_send: could not write to fd=5, errno = 32

can any body please give me a possible reason for the error,

also I want to ask one more thing, will there be any difference in my output result, if instead of atomic coordinates, I use fractional coordinates?

Thanks 

Dimpy
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From jdai3 at mail.ustc.edu.cn  Tue Jul  7 14:24:42 2009
From: jdai3 at mail.ustc.edu.cn (Jun Dai)
Date: Tue, 07 Jul 2009 20:24:42 +0800
Subject: [Pw_forum] V pseudopotential
Message-ID: <446969482.27212@ustc.edu.cn>

Giuseppe, thanks very much for the experience you shared, it's really valuable,
^_^. 


????????????????????:
>From: Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>
>Reply-To: PWSCF Forum <pw_forum at pwscf.org>
>To: Jun Dai <jdai3 at mail.ustc.edu.cn>,
PWSCF Forum <pw_forum at pwscf.org>
>Subject: Re: [Pw_forum] V pseudopotential
>Date:Tue, 7 Jul 2009 12:07:16 +0200
>
>I don't have any V normcons pseudo for you, but I still would share some 
>results. I'm trying to study a 6 atom rutile TiO2 cell with the pbe0 hybrid 
>functional (48 electrons, convergence achieved by using a k444 grid in the 
>case of the pbe xc). Honestly, I didn't understand how to deal with the q grid 
>in the case of periodic systems (the nqx variables. In the case of molecules I 
>managed to have fine results by using the gamma point and a 111 q grid), then 
>I tried different grids (q111, q222, q444). The q111 case requires reasonable 
>resources but doesn't provide reliable results. The q222 case is already very 
>expensive and the achieved results are still not very good. I regard a lattice 
>parameter optimization in this case as a "bath of blood" (dunno if you say 
>something similar...:-)). The q444 case... don't do it, please. I suspect that 
>V oxide cells are larger, so work harder on the DFT+U calculations...
>
>However, look (more than two seconds) at the /yourespresso/atomic_doc/ 
>directory. It should be really easy to generate a norm conserving V 
>pseudopotential. Then, make several tests in order to say if your 
>pseudopotential is a good one (and this is a little more difficult). It is 
>indeed one of the more instructive tasks if you want understand (on a 
>practical basis) how to perform reliable calculations.
>
>Yours
>Giuseppe
>
>
>On Monday 06 July 2009 18:41:33 Jun Dai wrote:
>> Dear all,
>> I want to have a try of the hybrid functional implemented in Q-E for a
>> vanadium oxide system, since the LDA+U failed to give reasonable results,
>> and the ultrasoft pp seems not supported yet, so can someone share a copy
>> of norm-conserving V pseudopotential with me? Thanks in advance.
>>
>>
>>
>>
>> ------------------------------
>> Best regards,
>> Jun Dai
>>
>> =============================================================
>>  J. Dai
>>  Ph.D. Candidate,
>>  Hefei National Laboratory For Physical Sciences at the Microscale,
>>  University of Science and Technology of China,
>>  Hefei, Anhui, 230026,
>>  People's Republic of China
>>  Tel.: 86-551-3606428
>>  Fax.: 86-551-3602969
>>  E-mail: jdai3 at mail.ustc.edu.cn
>> =============================================================
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>-- 
>********************************************************
>- Article premier - Les hommes naissent et demeurent
>libres et ?gaux en droits. Les distinctions sociales
>ne peuvent ?tre fond?es que sur l'utilit? commune
>- Article 2 - Le but de toute association politique
>est la conservation des droits naturels et 
>imprescriptibles de l'homme. Ces droits sont la libert?,
>la propri?t?, la s?ret? et la r?sistance ? l'oppression.
>********************************************************
>
>   Giuseppe Mattioli                            
>   CNR - ISTITUTO DI STRUTTURA DELLA MATERIA   
>   v. Salaria Km 29,300 - C.P. 10                
>   I 00016 - Monterotondo Stazione (RM)          
>   Tel + 39 06 90672836 - Fax +39 06 90672316    
>   E-mail: <giuseppe.mattioli at ism.cnr.it>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum




From akohlmey at cmm.chem.upenn.edu  Tue Jul  7 14:23:03 2009
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 07 Jul 2009 08:23:03 -0400
Subject: [Pw_forum] Error in output in calculating stress
In-Reply-To: <D4A761F73683694BBD69D634FF2980153AEAA8@MAIL.tyndall.ie>
References: <D4A761F73683694BBD69D634FF2980153AEAA8@MAIL.tyndall.ie>
Message-ID: <1246969383.22802.1540.camel@zero>

On Tue, 2009-07-07 at 12:06 +0100, Dimpy Sharma wrote:
> 
> Hi Quantum espresso users,
> 
> I tried to calculate stress for a sytem by performing a scf
> calculation, presently I am running two diffrenet calculations by
> varying the lattice paarmeter of the system, howvever, I have found
> that at cell dimension either smaller or greater than the optimum
> lattice parameter, I cannot find the output, instead it is showing
> rm_l_6_1007: (61.828125) net_send: could not write to fd=5, errno = 32

looks like an error from your MPI library. 
something must have gone wrong.

axel.

> can any body please give me a possible reason for the error,
> 
> also I want to ask one more thing, will there be any difference in my
> output result, if instead of atomic coordinates, I use fractional
> coordinates?
> 
> Thanks
> 
> Dimpy
> 
> _______________________________________________
> 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 giannozz at democritos.it  Tue Jul  7 14:26:31 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 7 Jul 2009 14:26:31 +0200
Subject: [Pw_forum] Error in output in calculating stress
In-Reply-To: <D4A761F73683694BBD69D634FF2980153AEAA8@MAIL.tyndall.ie>
References: <D4A761F73683694BBD69D634FF2980153AEAA8@MAIL.tyndall.ie>
Message-ID: <7A1E2292-8A80-4A9E-87CA-1FACDB238A2B@democritos.it>


On Jul 7, 2009, at 13:06 , Dimpy Sharma wrote:

> also I want to ask one more thing, will there be any
> difference in my output result, if instead of atomic
> coordinates, I use fractional coordinates?

you mean: atomic coordinates in crystal axis?
there is no difference, as long as they correspond
to the same system

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




From dimpy.sharma at tyndall.ie  Tue Jul  7 17:40:55 2009
From: dimpy.sharma at tyndall.ie (Dimpy Sharma)
Date: Tue, 7 Jul 2009 16:40:55 +0100
Subject: [Pw_forum] cholesky decomposition
Message-ID: <D4A761F73683694BBD69D634FF2980153AEAAA@MAIL.tyndall.ie>


Hi Quantum espresso user,

I have tried to run a calculation on a sytem using fractional coordinates of the system, however I ahve found that while suing fractioanl coordinates the itreations are not finished and in the erro it is showing problem in computing in cholesky decomposition. However while using atomic coordiantes, I can successfullt get my output, can anybody please help me .

Thanks 

Dimpy
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From akohlmey at cmm.chem.upenn.edu  Tue Jul  7 17:48:16 2009
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 07 Jul 2009 11:48:16 -0400
Subject: [Pw_forum] cholesky decomposition
In-Reply-To: <D4A761F73683694BBD69D634FF2980153AEAAA@MAIL.tyndall.ie>
References: <D4A761F73683694BBD69D634FF2980153AEAAA@MAIL.tyndall.ie>
Message-ID: <1246981696.22802.1588.camel@zero>

On Tue, 2009-07-07 at 16:40 +0100, Dimpy Sharma wrote:
> 
> Hi Quantum espresso user,
> 
> I have tried to run a calculation on a sytem using fractional
> coordinates of the system, however I ahve found that while suing
> fractioanl coordinates the itreations are not finished and in the erro
> it is showing problem in computing in cholesky decomposition. However
> while using atomic coordiantes, I can successfullt get my output, can
> anybody please help me .

dimpy,

please remember that Q-E - like most computational software -
strictly follows the GI-GO paradigm. internally, there is no 
difference between alat, angstrom, bohr, or fractional coordinates. 
so if an input works in one case, but not in another, _you_
must have made an error in your input.

cheers,
   axel.

p.s.: before you ask: GI-GO = garbage in, garbage out.

> 
> Thanks
> 
> Dimpy
> 
> _______________________________________________
> 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 kazempoor2000 at yahoo.com  Wed Jul  8 11:03:55 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Wed, 8 Jul 2009 02:03:55 -0700 (PDT)
Subject: [Pw_forum] vc-relax
Message-ID: <511270.21408.qm@web112502.mail.gq1.yahoo.com>

Can I use vc-relax to optimize the value of lattice constant in ZnO wurtzite structure?Because the lattice constant change and also atomic positions either. After finishing the run, Which atomic position shoud be used in next calculation(relaxed position or initial positions)? How can I optimize the value of u that is ideally equal to 3/8?
thanks a lot

Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


      
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From paulatto at sissa.it  Wed Jul  8 11:33:29 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 8 Jul 2009 11:33:29 +0200 (CEST)
Subject: [Pw_forum] vc-relax
In-Reply-To: <511270.21408.qm@web112502.mail.gq1.yahoo.com>
References: <511270.21408.qm@web112502.mail.gq1.yahoo.com>
Message-ID: <42848.78.12.162.251.1247045609.squirrel@webmail.sissa.it>


On Wed, July 8, 2009 11:03, ali kazempour wrote:
>  Can I use vc-relax to optimize the value of lattice constant in ZnO
>  wurtzite structure?

Dear ali,
of course you can!


> Because the lattice constant change and also atomic
>  positions either.

You can nail the atoms to their position by adding " 0 0 0" after the
atomic coordinates (see manual for detail), although it only make sense
for crystal and possibly alat coordinates, when you are doing vc-relax.

> After finishing the run, Which atomic position shoud be
>  used in next calculation(relaxed position or initial positions)?

The optimized ones, if not, why would you do the optimization?

>  How can I
>  optimize the value of u that is ideally equal to 3/8?

Doing vc-relax, I don't see the problem )I asume you are using this
notation: http://cst-www.nrl.navy.mil/lattice/struk/b4.html). If you want
the Zn atoms to stay in z=0 you can fix their position as explained above;
nevertheless "u" is just the difference in the z coordinate of Zn and O
atoms.

>  thanks a lot

you are welcome, best regards


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



----------------------------------------------------------------
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From l.salimi at ph.iut.ac.ir  Wed Jul  8 12:59:38 2009
From: l.salimi at ph.iut.ac.ir (leila salimi)
Date: Wed, 8 Jul 2009 14:29:38 +0330 (IRST)
Subject: [Pw_forum] Errors in examples of QuantumEspresso
Message-ID: <2112806.51091247050778893.JavaMail.root@mta.iut.ac.ir>

Hi every body,
I have been trying to install the code "espresso-4.0.5" on IBM pSeries 575, a clustered SMP (Symmetric Multiprocessing) system.
and I used the special make.sys which is matched with our system and then ?make pwall? was successful but now I'm getting the following error trying to run the examples.
I will attach "make.sys" and "environment_variables" to this mail.
Do you have any idea what is going wrong?

Best Regards,
Leila Salimi.
Isfahan University of Technology, Isfahan, Iran.


?from ewald : error # ? ? ? ? 1
> ? ? ?optimal alpha not found 

running the scf calculation...STOP 2
Error condition encountered during test: exit status = 2
Aborting
??running the geometry relaxation for CO...STOP 2
Error condition encountered during test: exit status = 2
Aborting
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From l.salimi at ph.iut.ac.ir  Wed Jul  8 13:15:02 2009
From: l.salimi at ph.iut.ac.ir (leila salimi)
Date: Wed, 8 Jul 2009 14:45:02 +0330 (IRST)
Subject: [Pw_forum] Errors in examples of QuantumEspresso
Message-ID: <13809261.51301247051702751.JavaMail.root@mta.iut.ac.ir>

Hi every body,
I have been trying to install the code "espresso-4.0.5" on IBM pSeries 575, a clustered SMP (Symmetric Multiprocessing) system.
and I used the special make.sys which is matched with our system and then ?make pwall? was successful but now I'm getting the following error trying to run the examples.
Do you have any idea what is going wrong?

Best Regards,
Leila Salimi.
Isfahan University of Technology, Isfahan, Iran.


 from ewald : error #         1
>      optimal alpha not found

running the scf calculation...STOP 2
Error condition encountered during test: exit status = 2
Aborting
  running the geometry relaxation for CO...STOP 2
Error condition encountered during test: exit status = 2
Aborting

As the following "make.sys"   :
# 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__XLF -D__MASS -D__ESSL -D__LINUX_ESSL
FDFLAGS        = -D__XLF,-D__MASS,-D__ESSL,-D__LINUX_ESSL

# 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 need modules in ../PW and ../PH

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

# 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         = mpfort
#F90           = xlf90_r
CC             = mpcc
F77            = xlf_r

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

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

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

CFLAGS         = -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS       = $(FFLAGS) -qfree=f90 -WF,$(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS         = -O4 -qsuffix=cpp=f90 -qdpc -qalias=nointptr -Q

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

FFLAGS_NOOPT   = -O0

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

LD             = mpfort
LDFLAGS        =
LD_LIBS        =

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

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

BLAS_LIBS      = /sara/sw/blas/1.0/lib/libblas.a

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

LAPACK_LIBS    = /sara/sw/lapack/3.1.1/lib/liblapack.a

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

FFT_LIBS       = /sara/sw/fftw3/3.1.2/lib/libfftw3f.a

# 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      =  -lmassvp6_64 -lmass_64
# ESSL added by Arieh tal 25-6-09
ESSL_LIBS      =  -lessl


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

PGPLOT_LIBS    =

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

AR             = ar
ARFLAGS        = ruv
ARFLAGS_DYNAMIC= ruv

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

RANLIB         = ranlib

# all internal and external libraries - do not modify
LIBOBJS        = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a
# Added ESSL
LIBS           = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(ESSL_LIBS) $(PGPLOT_LIBS) $(LD_LIBS)



From dimpy.sharma at tyndall.ie  Wed Jul  8 12:20:52 2009
From: dimpy.sharma at tyndall.ie (Dimpy Sharma)
Date: Wed, 8 Jul 2009 11:20:52 +0100
Subject: [Pw_forum] Strain calculation through quantum espresso
Message-ID: <D4A761F73683694BBD69D634FF2980153AEAAB@MAIL.tyndall.ie>


Hi Quantum espresso users,

Could anyone please tell me how to calculate strain of a supercell through quantum espresso, as in the manual it has not been mentioned properly.

Thanks

Dimpy

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From giannozz at democritos.it  Wed Jul  8 12:34:13 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 8 Jul 2009 12:34:13 +0200
Subject: [Pw_forum] Strain calculation through quantum espresso
In-Reply-To: <D4A761F73683694BBD69D634FF2980153AEAAB@MAIL.tyndall.ie>
References: <D4A761F73683694BBD69D634FF2980153AEAAB@MAIL.tyndall.ie>
Message-ID: <5662B04F-FC35-4CBE-8EE2-D83D29EEE658@democritos.it>


On Jul 8, 2009, at 12:20 , Dimpy Sharma wrote:
> Could anyone please tell me how to calculate strain of a supercell  
> through quantum espresso, as in the manual it has not been  
> mentioned properly.
>
could you please explain why you think that there should be anything  
special
in stress calculations for supercells?

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




From giannozz at democritos.it  Wed Jul  8 12:37:52 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 8 Jul 2009 12:37:52 +0200
Subject: [Pw_forum] Errors in examples of QuantumEspresso
In-Reply-To: <13809261.51301247051702751.JavaMail.root@mta.iut.ac.ir>
References: <13809261.51301247051702751.JavaMail.root@mta.iut.ac.ir>
Message-ID: <A2700779-F6D5-4EF9-854D-939C36894326@democritos.it>


On Jul 8, 2009, at 13:15 , leila salimi wrote:

>  from ewald : error #         1
>      optimal alpha not found

wasn't it explained a few days ago by LP? newer IBM
compilers have made a mess with the error function
(erf, erfc)

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




From dimpy.sharma at tyndall.ie  Wed Jul  8 12:56:13 2009
From: dimpy.sharma at tyndall.ie (Dimpy Sharma)
Date: Wed, 8 Jul 2009 11:56:13 +0100
Subject: [Pw_forum] Pw_forum Digest, Vol 25, Issue 10
References: <mailman.1408.1247049485.1425.pw_forum@pwscf.org>
Message-ID: <D4A761F73683694BBD69D634FF2980153AEAAD@MAIL.tyndall.ie>


Hi Paolo,

 I want to know about calculating strain from Q.E , howver from stress also we can calculate stress,as we can relate stress and strain .

DS
-----Original Message-----
From: pw_forum-bounces at pwscf.org on behalf of pw_forum-request at pwscf.org
Sent: Wed 7/8/2009 11:38 AM
To: pw_forum at pwscf.org
Subject: Pw_forum Digest, Vol 25, Issue 10
 
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Today's Topics:

   1. vc-relax (ali kazempour)
   2. Re: vc-relax (Lorenzo Paulatto)
   3. Errors in examples of QuantumEspresso (leila salimi)
   4. Errors in examples of QuantumEspresso (leila salimi)
   5. Strain calculation through quantum espresso (Dimpy Sharma)
   6. Re: Strain calculation through quantum espresso (Paolo Giannozzi)
   7. Re: Errors in examples of QuantumEspresso (Paolo Giannozzi)


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

Message: 1
Date: Wed, 8 Jul 2009 02:03:55 -0700 (PDT)
From: ali kazempour <kazempoor2000 at yahoo.com>
Subject: [Pw_forum] vc-relax
To: pw <pw_forum at pwscf.org>
Message-ID: <511270.21408.qm at web112502.mail.gq1.yahoo.com>
Content-Type: text/plain; charset="us-ascii"

Can I use vc-relax to optimize the value of lattice constant in ZnO wurtzite structure?Because the lattice constant change and also atomic positions either. After finishing the run, Which atomic position shoud be used in next calculation(relaxed position or initial positions)? How can I optimize the value of u that is ideally equal to 3/8?
thanks a lot

Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


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

Message: 2
Date: Wed, 8 Jul 2009 11:33:29 +0200 (CEST)
From: "Lorenzo Paulatto" <paulatto at sissa.it>
Subject: Re: [Pw_forum] vc-relax
To: "PWSCF Forum" <pw_forum at pwscf.org>
Message-ID: <42848.78.12.162.251.1247045609.squirrel at webmail.sissa.it>
Content-Type: text/plain;charset=iso-8859-1


On Wed, July 8, 2009 11:03, ali kazempour wrote:
>  Can I use vc-relax to optimize the value of lattice constant in ZnO
>  wurtzite structure?

Dear ali,
of course you can!


> Because the lattice constant change and also atomic
>  positions either.

You can nail the atoms to their position by adding " 0 0 0" after the
atomic coordinates (see manual for detail), although it only make sense
for crystal and possibly alat coordinates, when you are doing vc-relax.

> After finishing the run, Which atomic position shoud be
>  used in next calculation(relaxed position or initial positions)?

The optimized ones, if not, why would you do the optimization?

>  How can I
>  optimize the value of u that is ideally equal to 3/8?

Doing vc-relax, I don't see the problem )I asume you are using this
notation: http://cst-www.nrl.navy.mil/lattice/struk/b4.html). If you want
the Zn atoms to stay in z=0 you can fix their position as explained above;
nevertheless "u" is just the difference in the z coordinate of Zn and O
atoms.

>  thanks a lot

you are welcome, best regards


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



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



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

Message: 3
Date: Wed, 8 Jul 2009 14:29:38 +0330 (IRST)
From: leila salimi <l.salimi at ph.iut.ac.ir>
Subject: [Pw_forum] Errors in examples of QuantumEspresso
To: pw forum <pw_forum at pwscf.org>
Message-ID: <2112806.51091247050778893.JavaMail.root at mta.iut.ac.ir>
Content-Type: text/plain; charset="utf-8"

Hi every body,
I have been trying to install the code "espresso-4.0.5" on IBM pSeries 575, a clustered SMP (Symmetric Multiprocessing) system.
and I used the special make.sys which is matched with our system and then ?make pwall? was successful but now I'm getting the following error trying to run the examples.
I will attach "make.sys" and "environment_variables" to this mail.
Do you have any idea what is going wrong?

Best Regards,
Leila Salimi.
Isfahan University of Technology, Isfahan, Iran.


?from ewald : error # ? ? ? ? 1
> ? ? ?optimal alpha not found 

running the scf calculation...STOP 2
Error condition encountered during test: exit status = 2
Aborting
??running the geometry relaxation for CO...STOP 2
Error condition encountered during test: exit status = 2
Aborting
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------------------------------

Message: 4
Date: Wed, 8 Jul 2009 14:45:02 +0330 (IRST)
From: leila salimi <l.salimi at ph.iut.ac.ir>
Subject: [Pw_forum] Errors in examples of QuantumEspresso
To: pw forum <pw_forum at pwscf.org>, pw <pw_forum-request at pwscf.org>
Message-ID: <13809261.51301247051702751.JavaMail.root at mta.iut.ac.ir>
Content-Type: text/plain; charset=utf-8

Hi every body,
I have been trying to install the code "espresso-4.0.5" on IBM pSeries 575, a clustered SMP (Symmetric Multiprocessing) system.
and I used the special make.sys which is matched with our system and then ?make pwall? was successful but now I'm getting the following error trying to run the examples.
Do you have any idea what is going wrong?

Best Regards,
Leila Salimi.
Isfahan University of Technology, Isfahan, Iran.


 from ewald : error #         1
>      optimal alpha not found

running the scf calculation...STOP 2
Error condition encountered during test: exit status = 2
Aborting
  running the geometry relaxation for CO...STOP 2
Error condition encountered during test: exit status = 2
Aborting

As the following "make.sys"   :
# 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__XLF -D__MASS -D__ESSL -D__LINUX_ESSL
FDFLAGS        = -D__XLF,-D__MASS,-D__ESSL,-D__LINUX_ESSL

# 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 need modules in ../PW and ../PH

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

# 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         = mpfort
#F90           = xlf90_r
CC             = mpcc
F77            = xlf_r

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

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

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

CFLAGS         = -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS       = $(FFLAGS) -qfree=f90 -WF,$(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS         = -O4 -qsuffix=cpp=f90 -qdpc -qalias=nointptr -Q

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

FFLAGS_NOOPT   = -O0

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

LD             = mpfort
LDFLAGS        =
LD_LIBS        =

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

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

BLAS_LIBS      = /sara/sw/blas/1.0/lib/libblas.a

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

LAPACK_LIBS    = /sara/sw/lapack/3.1.1/lib/liblapack.a

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

FFT_LIBS       = /sara/sw/fftw3/3.1.2/lib/libfftw3f.a

# 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      =  -lmassvp6_64 -lmass_64
# ESSL added by Arieh tal 25-6-09
ESSL_LIBS      =  -lessl


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

PGPLOT_LIBS    =

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

AR             = ar
ARFLAGS        = ruv
ARFLAGS_DYNAMIC= ruv

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

RANLIB         = ranlib

# all internal and external libraries - do not modify
LIBOBJS        = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a
# Added ESSL
LIBS           = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(ESSL_LIBS) $(PGPLOT_LIBS) $(LD_LIBS)




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

Message: 5
Date: Wed, 8 Jul 2009 11:20:52 +0100
From: "Dimpy Sharma" <dimpy.sharma at tyndall.ie>
Subject: [Pw_forum] Strain calculation through quantum espresso
To: <pw_forum at pwscf.org>
Message-ID: <D4A761F73683694BBD69D634FF2980153AEAAB at MAIL.tyndall.ie>
Content-Type: text/plain; charset="iso-8859-1"


Hi Quantum espresso users,

Could anyone please tell me how to calculate strain of a supercell through quantum espresso, as in the manual it has not been mentioned properly.

Thanks

Dimpy

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

Message: 6
Date: Wed, 8 Jul 2009 12:34:13 +0200
From: Paolo Giannozzi <giannozz at democritos.it>
Subject: Re: [Pw_forum] Strain calculation through quantum espresso
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <5662B04F-FC35-4CBE-8EE2-D83D29EEE658 at democritos.it>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed


On Jul 8, 2009, at 12:20 , Dimpy Sharma wrote:
> Could anyone please tell me how to calculate strain of a supercell  
> through quantum espresso, as in the manual it has not been  
> mentioned properly.
>
could you please explain why you think that there should be anything  
special
in stress calculations for supercells?

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





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

Message: 7
Date: Wed, 8 Jul 2009 12:37:52 +0200
From: Paolo Giannozzi <giannozz at democritos.it>
Subject: Re: [Pw_forum] Errors in examples of QuantumEspresso
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <A2700779-F6D5-4EF9-854D-939C36894326 at democritos.it>
Content-Type: text/plain; charset=US-ASCII; format=flowed


On Jul 8, 2009, at 13:15 , leila salimi wrote:

>  from ewald : error #         1
>      optimal alpha not found

wasn't it explained a few days ago by LP? newer IBM
compilers have made a mess with the error function
(erf, erfc)

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





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

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From Giovanni.Cantele at na.infn.it  Wed Jul  8 13:20:59 2009
From: Giovanni.Cantele at na.infn.it (Giovanni Cantele)
Date: Wed, 08 Jul 2009 13:20:59 +0200
Subject: [Pw_forum] Strain calculation through quantum espresso
In-Reply-To: <D4A761F73683694BBD69D634FF2980153AEAAD@MAIL.tyndall.ie>
References: <mailman.1408.1247049485.1425.pw_forum@pwscf.org>
	<D4A761F73683694BBD69D634FF2980153AEAAD@MAIL.tyndall.ie>
Message-ID: <4A54811B.8010607@na.infn.it>

Dimpy Sharma wrote:
> Hi Paolo,
>
>  I want to know about calculating strain from Q.E , 
I cannot well understand your question. If I'm not wrong, strain is a 
measure of the deformation of a material,
the stress is the corresponding "load" applied to the material and 
producing the strain. So, if you apply a deformation ("strain") to your 
material,
let's say a cubic material with lattice constant A0 with strain along 
the x direction, you are changing the lattice constant
along x from the equilibrium value A0 to some value A. The strain will 
be measured as (A - A0) / A0.

> howver from stress also we can calculate stress,
?????

> as we can relate stress and strain .
>
>   
The QE calc. will give you the corresponding stress tensor if you set 
tstress=.true., *even though* you are using
calculation='scf', 'relax', ....

stress in QE:
http://www.quantum-espresso.org/wiki/index.php/Methodological_Background#Stress



Giovanni

 

-- 



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


From eariel99 at gmail.com  Wed Jul  8 14:03:51 2009
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Wed, 8 Jul 2009 08:03:51 -0400
Subject: [Pw_forum] Strain calculation through quantum espresso
	(Giovanni Cantele)
Message-ID: <be564dcb0907080503p67f3fc3ev5f94242999902a1b@mail.gmail.com>

Hi DS

Strain is a geometrical property. If you want a fast calculation, just use
the Bilbao Crystallographic Server.
http://www.cryst.ehu.es/cryst/strain.html
there you may input two sets of lattice parameters and get the strain
relating both lattices.

Take a look at Fast et al, PRB 51, 17431 (1995). In equations (1) and (2)
are explained the relation between lattice vectors and strain. In  Kittel's
textbook it is explained too, but I am not sure if in all the editions. In
the article of Fast it explains what you can do with Q-E and similar codes.

In Q-E you input the lattice parameters or the lattice vectors, and all the
other stuff, and get the stress tensor as explained in previous posts.

Maybe what you need is to find the strain of a crystal under an specified
stress tensor. As far as I know, with Q-E you cand do it only in the case of
hydrostatic stress (when the stress tensor is the pressure times the
identity matrix), using calculation='vc-relax'  and setting the variable
press. E.g.
 &control
    calculation = 'vc-relax'
..........
&CELL
        cell_dynamics='damp-pr',
        press = 35.0, (the value of pressure in kbars)
        cell_dofree='all',


For a non-hydrostatic stress, you may need to find the elastic constants (as
in Fasts's paper) first and then solve the equations of elasticity. If the
stress is big, you may need an iterative process.

If you need the strain under a fully specified stress tensor, i.e., the six
independent components of the tensor, you may device a minimization
algorithm implemented in a shell or python script, that run pw.x  to get the
energies and stress.
An alternative is  to find the elastic constants (as in Fasts's paper) first
and then solve the equations of elasticity. If the stress is big, you may
need an iterative process to find the elastic constants under a stress that
is close to your derired stress.

In simple cases, such as uniaxial stress and orthorombic lattices, you do
cell relaxations with constraints (cell_dofree='xxxxx' ) keeping one lattice
vector fixed, and by trial and error you can obtain the lattice that produce
the desired component of the stress.




-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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From cristian.degliesposti at unibo.it  Wed Jul  8 16:26:58 2009
From: cristian.degliesposti at unibo.it (Cristian Degli Esposti Boschi)
Date: Wed, 08 Jul 2009 16:26:58 +0200
Subject: [Pw_forum] Units in dynamical matrix files
Message-ID: <4A54ACB2.5070807@unibo.it>

Dear all,

I would like to have some clarifications on the units used in dynamical 
matrix files produced by the ph.x program in the QE suite.

At the beginning of dynamical matrix file the masses are not expressed 
in the same units as in the input files used for pw.x, that is [amu].

It seems to me that in the dynamical matrix file the masses could be in
atomic units, which I would say correspond to electron masses.

So there should be a conversion factor

1 amu = (1.660538782 ? 10^-27 kg / 9.1093826 ? 10^-31 kg) me
       = 1822.8884 me

However there is still a factor 1/2 to include to pass from
the amu values to those reported at the beginning of the dynamical
matrix file.

Am I right? Why the 1/2 factor?

And what are the typical units used for force constants?

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



From nakhmanson at anl.gov  Wed Jul  8 16:55:12 2009
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Wed, 08 Jul 2009 09:55:12 -0500
Subject: [Pw_forum] Units in dynamical matrix files
In-Reply-To: <4A54ACB2.5070807@unibo.it>
References: <4A54ACB2.5070807@unibo.it>
Message-ID: <4A54B350.8080809@anl.gov>

I had to ponder this question some time ago.

I think the difference here is the same as
between Ry and Ha energy units, so that in
the "convention" that QE uses an extra 1/2
proliferates into the mass units as well.

But this is my guess, which may not be the
ultimate truth. Actually, considering how
many times I get my butt handed back to me
in this forum, I could be totally wrong
about it.

Cheers,

S.

Cristian Degli Esposti Boschi wrote:
> 
> Am I right? Why the 1/2 factor?
> 
> And what are the typical units used for force constants?


-- 
*********************************************************
  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 paulatto at sissa.it  Wed Jul  8 17:23:35 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 08 Jul 2009 17:23:35 +0200
Subject: [Pw_forum] Units in dynamical matrix files
In-Reply-To: <4A54B350.8080809@anl.gov>
References: <4A54ACB2.5070807@unibo.it> <4A54B350.8080809@anl.gov>
Message-ID: <op.uwq81lima8x26q@paulax>

In data 08 luglio 2009 alle ore 16:55:12, Serge Nakhmanson  
<nakhmanson at anl.gov> ha scritto:
> I think the difference here is the same as
> between Ry and Ha energy units, so that in
> the "convention" that QE uses an extra 1/2
> proliferates into the mass units as well.

I does indeed, Rydberg atomic units have a few quirks. The other important  
one in electron_charge = sqrt(2)

If you are interested in more details, have a look at this table I found  
on google where everything is explained clearly:  
<http://ilan.schnell-web.net/physics/rydberg.pdf>

best regards


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

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

From giannozz at democritos.it  Wed Jul  8 18:09:15 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 8 Jul 2009 18:09:15 +0200
Subject: [Pw_forum] Units in dynamical matrix files
In-Reply-To: <4A54ACB2.5070807@unibo.it>
References: <4A54ACB2.5070807@unibo.it>
Message-ID: <B2C854BC-732C-4733-94A1-23814E859C70@democritos.it>


On Jul 8, 2009, at 16:26 , Cristian Degli Esposti Boschi wrote:

> And what are the typical units used for force constants?

I don't think there are "typical" units for force constants:
one chooses a system of units and uses those. All Q-E
codes use atomic Rydberg units, with the exception of
CP that uses atomic Hartree units

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




From giannozz at democritos.it  Wed Jul  8 18:12:25 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 8 Jul 2009 18:12:25 +0200
Subject: [Pw_forum] Units in dynamical matrix files
In-Reply-To: <B2C854BC-732C-4733-94A1-23814E859C70@democritos.it>
References: <4A54ACB2.5070807@unibo.it>
	<B2C854BC-732C-4733-94A1-23814E859C70@democritos.it>
Message-ID: <11EDED09-C869-48EF-B51D-ACC731480249@democritos.it>


On Jul 8, 2009, at 18:09 , Paolo Giannozzi wrote:

> All Q-E codes use atomic Rydberg units

i.e. energy in Ry, lengths in Bohr radii
(or \hbar=1, e^2=2, electron mass m=1/2)

> with the exception of CP that uses atomic Hartree units

i.e. energy in Ha, lengths in Bohr radii
(or \hbar=1, e=1, electron mass m=1)

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




From miguel.martinez at ehu.es  Thu Jul  9 18:39:58 2009
From: miguel.martinez at ehu.es (Miguel =?UTF-8?B?TWFydMOtbmV6?=)
Date: Thu, 9 Jul 2009 18:39:58 +0200
Subject: [Pw_forum] Questions regarding max_irr_dim
Message-ID: <20090709183958.0b96c3dc@lcpybm>

Dear espreso lovers,

I've been lately wondering why max_irr_dim is set to 4 in
espresso/PH/phcom.f90. Space group no 223 (Pm-3n) for example can have
6-fold degeneracy in R, and I'm pretty sure other space groups also may
display high degeneracy. I know it's just a swift change and a quick
recompile away, but maybe there's an additional reason why this
parameter is set to 4. Memory usage? Lost NaNs? Warning sign to the
interested ones?

Another side question is how espresso determines the system symmetry.
Performing calculation on AlH3 at ~110 GPa (2 formula units per cell,
space grop Pm-3n) it just happens that with some magic parametres the
phonon degeneracy at R splits in half, even after fixing nq(i). Maybe
this is related to the line 26 comment in PH/find_mode_sym.f90:

 "It does NOT work at zone border in non symmorphic space groups"

Finally, the REPRES tool at www.cryst.ehu.es states that the Pm-3n
group at R (0.5 0.5 0.5) can have three dim2 irreps and one dim6 irrep,
while ph.x finds one 4-fold degenerate mode. I've consulted one of the
mantainers and he checked those values. Is there any reason why
espresso would get a false degeneracy?

Regards,

Miguel

PS: In case one is interested in the input files...

============  alh3.scf.in ===============
&control
	calculation	=	'scf'
	restart_mode	=	'from_scratch'
	pseudo_dir 	=	'./'
	outdir		=	'/tmp/espresso-miguel/'
	prefix		=	'alh3'
 /
&system
        ibrav           =       1
        celldm(1)       =       5.8204  
        nat             =       8
        ntyp            =       2
        ecutwfc         =       30. 
        ecutrho         =       200.    
        nbnd            =       20
        occupations     =       'smearing'
        smearing        =       'marzari-vanderbilt'
        degauss         =       0.02
 /
&electrons
	diagonalization	=	'david'
	conv_thr        =       1.D-8
        mixing_beta     =       0.7D0
 /
ATOMIC_SPECIES
Al 26.981538    Al.pbe-n-van.UPF
H  1.00794      H.pbe-van_ak.UPF
ATOMIC_POSITIONS crystal
Al      0.000000000   0.000000000   0.000000000
Al      0.500000000   0.500000000   0.500000000
H       0.250000000   0.000000000   0.500000000
H       0.750000000   0.000000000   0.500000000
H       0.500000000   0.250000000   0.000000000
H       0.500000000   0.750000000   0.000000000
H       0.000000000   0.500000000   0.250000000
H       0.000000000   0.500000000   0.750000000
K_POINTS automatic
12 12 12  1 1 1


============= alh3.ph.in ==============
phonons of AlH3
&inputph
        tr2_ph  =       1.0d-14
        prefix  =       'alh3'
        fildyn  =       'mat.dyn'
        outdir  =       '/tmp/espresso-miguel'
        amass(1)=       26.981538
        amass(2)=       1.00794
	lnscf	=	.true.
/
-0.5 -0.5 -0.5





-- 
----------------------------------------
Miguel Mart?nez Canales
   Condensed Matter Physics Dpt.
   UPV/EHU
   Faculty of Science and Technology
   Apdo. 644
   48080 Bilbao (Spain)
Fax:  +34 94 601 3500
Tlf:  +34 94 601 5326
----------------------------------------

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

 George Bernard Shaw 


From giannozz at democritos.it  Thu Jul  9 21:27:04 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 9 Jul 2009 21:27:04 +0200
Subject: [Pw_forum] Questions regarding max_irr_dim
In-Reply-To: <20090709183958.0b96c3dc@lcpybm>
References: <20090709183958.0b96c3dc@lcpybm>
Message-ID: <98E4329F-C8D4-40CB-8116-5110DAC4F0D8@democritos.it>


On Jul 9, 2009, at 18:39 , Miguel Mart?nez wrote:

> I've been lately wondering why max_irr_dim is set to 4 in
> espresso/PH/phcom.f90 [...] I know it's just a swift change and a  
> quick
> recompile away, but maybe there's an additional reason why this
> parameter is set to 4.

I think memory usage is the only reason why it is set to 4

> Another side question is how espresso determines the system symmetry.

it may find a lower sysmmetry than in reality, but never a higher or  
different
symmetry, as far as I know

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




From spmmal at gmail.com  Thu Jul  9 21:56:48 2009
From: spmmal at gmail.com (Mail List)
Date: Thu, 9 Jul 2009 14:56:48 -0500
Subject: [Pw_forum] How can I set 'tot_magnetization' in advance
Message-ID: <d1bf85990907091256h54994bbdh350d76af06f97219@mail.gmail.com>

Dear all,

I would like to calculate '3-atom Oxygen trimer' in a vaccuum cell. It is
known that one Oxygen atom has '2' unpaired electrons. Does it mean that I
have to set
tot_magnetization=6 (from 3*2) in advance to do a scf calculation and get
the correct total energy in the end.Thanks.
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From kazempoor2000 at yahoo.com  Fri Jul 10 14:42:31 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Fri, 10 Jul 2009 05:42:31 -0700 (PDT)
Subject: [Pw_forum] GW
Message-ID: <953083.31653.qm@web112510.mail.gq1.yahoo.com>

Dear all
?I want to use GW approximation . Which code is compatible with espresso?
thanks

Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


      
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From stenuit at sissa.it  Fri Jul 10 14:57:28 2009
From: stenuit at sissa.it (Geoffrey Stenuit)
Date: Fri, 10 Jul 2009 14:57:28 +0200
Subject: [Pw_forum] GW
In-Reply-To: <953083.31653.qm@web112510.mail.gq1.yahoo.com>
References: <953083.31653.qm@web112510.mail.gq1.yahoo.com>
Message-ID: <4A573AB8.30807@sissa.it>

Dear Ali,

Actually, it depends on what you would like to study within the GW 
approximation (GWA) framework.

Roughly speaking, if you have to deal with calculations in big 
supercells (+/- 100 atoms), or you would like to study the QPE in 
molecules, then... please wait !
The GW method based on the used of Wannier-like orbitals [ GWW, see PRB 
79, 201104(R) (2009) ] for evaluating the polarization propagator should 
be released soon (this summer anyway).

Otherwise, the Sax code ( https://qe-forge.org/projects/sax-project/ ) 
should help you...
This package allows you to compute the GWA electronic AND optical 
properties.

Hope it helps,

Joe


ali kazempour wrote:
> Dear all
>  I want to use GW approximation . Which code is compatible with espresso?
> thanks
>
> Ali Kazempour
> Physics department, Isfahan University of Technology
> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733
> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
--------------------------------------------------------------------
Geoffrey Stenuit
Theory at Elettra Group
CNR-INFM DEMOCRITOS National Simulation Center
c/o Sincrotrone Trieste - SS14, Km 163,5 Basovizza, I-34012 TRIESTE
email: stenuit at sissa.it    tel: +39 040 375-8713    fax: -8776


From iori at theory.polytechnique.fr  Fri Jul 10 15:12:29 2009
From: iori at theory.polytechnique.fr (Federico Iori)
Date: Fri, 10 Jul 2009 15:12:29 +0200
Subject: [Pw_forum] GW
In-Reply-To: <953083.31653.qm@web112510.mail.gq1.yahoo.com>
References: <953083.31653.qm@web112510.mail.gq1.yahoo.com>
Message-ID: <4A573E3D.1090706@theory.polytechnique.fr>

hi!
you can also have a look at the Yambo code developed in Rome.
http://www.yambo-code.org/

Ciao
Federico.

ali kazempour wrote:
> Dear all
>  I want to use GW approximation . Which code is compatible with espresso?
> thanks
>
> Ali Kazempour
> Physics department, Isfahan University of Technology
> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733
> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
Dr. Federico Iori, PhD!

Laboratoire des Solides Irradi?s,
Ecole Polytechnique - CEA/DSM, CNRS 
91128 Palaiseau, France

www.etsf.polytechnique.fr

phone: +33 (0) 1 69 33 44 85
emails: federico.iori @ polytechnique.edu 
        iori.federico @ unimore.it
http://www.pdmodena.it/
http://www.comune.mo.it


From Adriano.Mosca.Conte at roma2.infn.it  Fri Jul 10 15:03:34 2009
From: Adriano.Mosca.Conte at roma2.infn.it (Adriano Mosca Conte)
Date: Fri, 10 Jul 2009 15:03:34 +0200 (CEST)
Subject: [Pw_forum] GW
In-Reply-To: <953083.31653.qm@web112510.mail.gq1.yahoo.com>
References: <953083.31653.qm@web112510.mail.gq1.yahoo.com>
Message-ID: <37454.141.108.253.47.1247231014.squirrel@141.108.253.47>

YAMBO
see link:
http://www.fisica.uniroma2.it/~self/

> Dear all
> ?I want to use GW approximation . Which code is compatible with espresso?
> thanks
>
> Ali Kazempour
>
> Physics department, Isfahan University of Technology
>
> 84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733
>
> Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375
>
>
>       _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


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00133 Roma, Italia
Tel. +39 06 7259 4741
Fax  +39 06 2023507

From yccheng.nju at gmail.com  Sun Jul 12 04:54:12 2009
From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=)
Date: Sun, 12 Jul 2009 10:54:12 +0800
Subject: [Pw_forum] relativistic pseudopotential for Zn
Message-ID: <da7526cb0907111954v36efad5hf883d140033d512a@mail.gmail.com>

Dear pwscf users,
     I am using pwscf to study the semiconductor ZnS with the spin-orbital
interaction.  In the directory /atomic_doc/pseudo_library/LDA/REL, there is
no relativistic pseudopotential for Zn.  I am failed to generate such PP for
Zn.  Does anybody have the pseudopotential for Zn?  Thank you in advance.

-- 
Y. C. Cheng
Department of Physics
Nanjing University
Nanjing 210093
P. R. China
Tel: 86-25-83592907
Email: yccheng.nju at gmail.com
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From giannozz at democritos.it  Mon Jul 13 09:48:26 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 13 Jul 2009 09:48:26 +0200
Subject: [Pw_forum] How can I set 'tot_magnetization' in advance
In-Reply-To: <d1bf85990907091256h54994bbdh350d76af06f97219@mail.gmail.com>
References: <d1bf85990907091256h54994bbdh350d76af06f97219@mail.gmail.com>
Message-ID: <4A5AE6CA.4070901@democritos.it>

Dear unknown

> I would like to calculate '3-atom Oxygen trimer' in a vaccuum cell. It 
> is known that one Oxygen atom has '2' unpaired electrons. Does it mean 
> that I have to set tot_magnetization=6 (from 3*2) in advance to do a  
> scf calculation and get the correct total energy in the end.

tot_magnetization (or else multiplicity) fixes the spin state
of the molecule. The energy will depend upon the spin state.
As an alternative you can break the initial symmetry (using 
starting_magnetization) and leave the code find the
magnetization of the ground state.
Please provide your name and affiliation whan you post.

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

From kazempoor2000 at yahoo.com  Mon Jul 13 12:25:58 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Mon, 13 Jul 2009 03:25:58 -0700 (PDT)
Subject: [Pw_forum] tetragonal
Message-ID: <468912.24780.qm@web112511.mail.gq1.yahoo.com>


Dear all
I want to optimize the lattice constant for tetragonal cell. I first start with volume=constant and change the value of c/a ,then at next step for optimized c/a I changed the value of volume in (-4,-2,0,2,4) percent to obtain E(v). Here I want to use murnaghan equation of state by ev.x . Which option do I use in first question :Sc or hex?
Thanks? a lot 
Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


      
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From hashemifar at cc.iut.ac.ir  Mon Jul 13 12:35:23 2009
From: hashemifar at cc.iut.ac.ir (Seyed Javad Hashemifar)
Date: Mon, 13 Jul 2009 12:35:23 +0200
Subject: [Pw_forum] tetragonal
In-Reply-To: <468912.24780.qm@web112511.mail.gq1.yahoo.com>
References: <468912.24780.qm@web112511.mail.gq1.yahoo.com>
Message-ID: <2fb18d9f0907130335l313c8f99q23a584101b9c7170@mail.gmail.com>

Dear Ali

Most likely you have to use option hex because you are listing the obtained
energies as a function of volume not as a function of lattice parameter in
your ev.x input file. As far as I know the option hex is not used only for
hexagonal structures but it is the appropriate option for any structure the
has more than one lattice parameter.

Regards
Javad Hashemifar


On Mon, Jul 13, 2009 at 12:25 PM, ali kazempour <kazempoor2000 at yahoo.com>wrote:

>
> Dear all
> I want to optimize the lattice constant for tetragonal cell. I first start
> with volume=constant and change the value of c/a ,then at next step for
> optimized c/a I changed the value of volume in (-4,-2,0,2,4) percent to
> obtain E(v). Here I want to use murnaghan equation of state by ev.x . Which
> option do I use in first question :Sc or hex?
> Thanks  a lot
> Ali Kazempour
> Physics department, Isfahan University of Technology
> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733
> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
======================================
Seyed Javad  Hashemifar
Physics Department, Isfahan University of Technology
84156-83111 Isfahan, Iran
Tel: +98 311 391 2375     Fax:+98 311 3912376
Email:  hashemifar at cc.iut.ac.ir
Homepage:  http://hashemifar.iut.ac.ir
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From kazempoor2000 at yahoo.com  Mon Jul 13 15:49:12 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Mon, 13 Jul 2009 06:49:12 -0700 (PDT)
Subject: [Pw_forum] binding energy
Message-ID: <635991.67295.qm@web112517.mail.gq1.yahoo.com>


Dear all
?I have one question :
I don,t know how LDA underestimate the binding energy of 3d state in ZnO that give rise to overestimation of hybridization with p orbitals. Does it means that? (like most cases) LDA? gives stronger bond between Zn and O atom.
Thanks? alot
Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


      
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From bipulrr at gmail.com  Mon Jul 13 17:27:04 2009
From: bipulrr at gmail.com (Bipul Rakshit)
Date: Mon, 13 Jul 2009 20:57:04 +0530
Subject: [Pw_forum] About LDA and GGA
Message-ID: <3a749910907130827hd2d8824y6a6684f071cb41bd@mail.gmail.com>

Dear PWSCF users,
Generally LDA underestimate the lattice constant and GGA overestimate
it. But is it possible that for some materials, LDA also overestimate
the lattice constants, when compared with experimental value?

regards

-- 
Bipul Rakshit
Research Fellow,
Barkatullah University,
Bhopal 462026,
MP, India

From hashemifar at cc.iut.ac.ir  Mon Jul 13 17:58:16 2009
From: hashemifar at cc.iut.ac.ir (Seyed Javad Hashemifar)
Date: Mon, 13 Jul 2009 17:58:16 +0200
Subject: [Pw_forum] About LDA and GGA
In-Reply-To: <3a749910907130827hd2d8824y6a6684f071cb41bd@mail.gmail.com>
References: <3a749910907130827hd2d8824y6a6684f071cb41bd@mail.gmail.com>
Message-ID: <2fb18d9f0907130858r7a0157f9sadaa0d728e9e7331@mail.gmail.com>

If I remember correctly, for Si, LDA gives a larger lattice constant than
experiment (I am not sure). As far as I know, it is not guaranteed that LDA
should always underestimates lattice parameters.

Javad Hashemifar

On Mon, Jul 13, 2009 at 5:27 PM, Bipul Rakshit <bipulrr at gmail.com> wrote:

> Dear PWSCF users,
> Generally LDA underestimate the lattice constant and GGA overestimate
> it. But is it possible that for some materials, LDA also overestimate
> the lattice constants, when compared with experimental value?
>
> regards
>
> --
> Bipul Rakshit
> Research Fellow,
> Barkatullah University,
> Bhopal 462026,
> MP, India
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
======================================
Seyed Javad  Hashemifar
Physics Department, Isfahan University of Technology
84156-83111 Isfahan, Iran
Tel: +98 311 391 2375     Fax:+98 311 3912376
Email:  hashemifar at cc.iut.ac.ir
Homepage:  http://hashemifar.iut.ac.ir
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From pushpajnc at gmail.com  Mon Jul 13 21:53:39 2009
From: pushpajnc at gmail.com (pushpa raghani)
Date: Mon, 13 Jul 2009 12:53:39 -0700
Subject: [Pw_forum] Errors in PS-KS equation
Message-ID: <f40d6a250907131253p2e4f1137m2624a85c80544101@mail.gmail.com>

Dear all,
I have to generate a fully relativistic pseudopotential for Ti. Since it is
the first time I do this job, I thought of first generating a SR pp and
match it with the available Ti.pbe-sp-van_ak.UPF.

I am getting an error "phi has nodes before r_c". Following is my input
file. When I increase the value of rcut from 1.0 to 1.2, above error goes
away and I get different error of "Errors in PS-KS equation". Any
suggestions?

&input
    title='Ti',
    zed=22.,
    rel=1,
    config='[Ne] 3s2.0 3p6 3d2.0 4s2.0',
    iswitch=3,
    dft='PBE'
 /
 &inputp
   lloc=0,
   pseudotype=3,
   file_pseudopw='Ti.pbe-rrkjus.UPF',
   nlcc=.f.,
   rcore=0.9,
 /
5
3P  3  1  6.00  0.00  1.00  1.80  1
3P  3  1  0.00 -0.30  1.00  1.80  1
3D  3  2  2.00  0.00  1.00  1.80  1
3S  3  0  2.00  0.00  1.00  1.80  1
4S  4  0  2.00  0.00  1.00  1.80  1

 Many Thanks,
Pushpa
(Stanford University)
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From giannozz at democritos.it  Mon Jul 13 22:39:20 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 13 Jul 2009 22:39:20 +0200
Subject: [Pw_forum] Errors in PS-KS equation
In-Reply-To: <f40d6a250907131253p2e4f1137m2624a85c80544101@mail.gmail.com>
References: <f40d6a250907131253p2e4f1137m2624a85c80544101@mail.gmail.com>
Message-ID: <AE0F8C49-DD8D-4AB1-840C-A04CCBB6FB14@democritos.it>


On Jul 13, 2009, at 21:53 , pushpa raghani wrote:

>  I am getting an error "phi has nodes before r_c".

if this happens for l=0 states, try to assign a small value,
0.01 or so, to variable "rho0" (i.e. rho(r=0)). This will
force the usage of 4 Bessel functions instead of 3.

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




From positronium at gmail.com  Tue Jul 14 01:22:09 2009
From: positronium at gmail.com (Lex Kemper)
Date: Mon, 13 Jul 2009 19:22:09 -0400
Subject: [Pw_forum] About LDA and GGA
In-Reply-To: <3a749910907130827hd2d8824y6a6684f071cb41bd@mail.gmail.com>
References: <3a749910907130827hd2d8824y6a6684f071cb41bd@mail.gmail.com>
Message-ID: <4A5BC1A1.3070305@phys.ufl.edu>

Hi Bipul,

This sort of question is hard to answer without more specifics. People 
who have worked on certain materials will be able to tell you what 
LDA/GGA think about the lattice constants, but AFAIK the 
over/underestimation by LDA/GGA are trends, not certainties.

Lex Kemper
Department of Physics
University of Florida

Bipul Rakshit wrote:
> Dear PWSCF users,
> Generally LDA underestimate the lattice constant and GGA overestimate
> it. But is it possible that for some materials, LDA also overestimate
> the lattice constants, when compared with experimental value?
> 
> regards
> 

From decboy9 at gmail.com  Tue Jul 14 08:29:00 2009
From: decboy9 at gmail.com (dev sharma)
Date: Tue, 14 Jul 2009 11:59:00 +0530
Subject: [Pw_forum] Error : from cdiaghg : error #363, info =/= 0
Message-ID: <a591fe200907132329uf1f386cj6e158a3404840952@mail.gmail.com>

hi,
I am new to PwScf and trying some calculation for Co3O4 which has a cubic
spinel structure. My input file for SCF is below. I am getting --- from
cdiaghg : error #363, info =/= 0 ...... stopping...... in the output and
simulation stops. Please  help.

with regards,
Sumit


&control
    calculation='scf',
    restart_mode='from_scratch',
    prefix='co3o4'
    pseudo_dir = '/home/physics/pseudo/',
    outdir='/home/physics/work/project/temp'
 /
 &system
    ibrav = 2, celldm(1) =15.285, nat=71, ntyp= 2,
    ecutwfc = 40.0,ecutrho=200,
    occupations='smearing', smearing    = "methfessel-paxton",degauss=0.05,
nspin=2,

 /
 &electrons
    mixing_beta = 0.50
    conv_thr =  1.0e-6

/
 &ions
 /

ATOMIC_SPECIES
  Co     58.933  Co.pbe-nd-rrkjus.UPF
   O     15.9994   O.pbe-van_ak.UPF

ATOMIC_POSITIONS    {angstrom}
Co      4.03750000      .00000000      .00000000
Co      8.07500000     4.03750000      .00000000
Co     6.05625000     2.01875000      .00000000
Co     8.07500000      .00000000     4.03750000
Co      6.05625000      .00000000     2.01875000
Co      .00000000     4.03750000      .00000000
Co      4.03750000     8.07500000      .00000000
Co     2.01875000     6.05625000      .00000000
Co       .00000000      .00000000     4.03750000
Co      1.00937500     1.00937500     1.00937500
Co      4.03750000     4.03750000     4.03750000
Co     4.03750000     2.01875000     2.01875000
Co      2.01875000     4.03750000     2.01875000
Co     2.01875000     2.01875000     4.03750000
O      1.90570000     1.90570000     1.90570000
O      1.90570000      .11305000      .11305000
O       .11305000     1.90570000      .11305000
O       .11305000      .11305000     1.90570000
Co      5.04687500     5.04687500     1.00937500
Co     8.07500000     8.07500000     4.03750000
Co     8.07500000     6.05625000     2.01875000
Co     6.05625000     8.07500000     2.01875000
Co     6.05625000     6.05625000     4.03750000
O      5.94320000     5.94320000     1.90570000
O      5.94320000     4.15055000      .11305000
O      4.15055000     5.94320000      .11305000
O      4.15055000     4.15055000     1.90570000
Co     4.03750000      .00000000     8.07500000
Co     2.01875000      .00000000     6.05625000
Co      5.04687500     1.00937500     5.04687500
Co     8.07500000     4.03750000     8.07500000
Co     8.07500000     2.01875000     6.05625000
Co     6.05625000     4.03750000     6.05625000
Co      6.05625000     2.01875000     8.07500000
O      5.94320000     1.90570000     5.94320000
O      5.94320000      .11305000     4.15055000
O      4.15055000     1.90570000     4.15055000
O      4.15055000      .11305000     5.94320000
Co     7.06562500     3.02812500     3.02812500
O      6.16930000     2.13180000     2.13180000
O      6.16930000     3.92445000     3.92445000
O      7.96195000     2.13180000     3.92445000
O      7.96195000     3.92445000     2.13180000
Co      .00000000     8.07500000     4.03750000
Co      .00000000     6.05625000     2.01875000
Co      .00000000     4.03750000     8.07500000
Co    .00000000     2.01875000     6.05625000
Co     1.00937500     5.04687500     5.04687500
Co    4.03750000     8.07500000     8.07500000
Co     4.03750000     6.05625000     6.05625000
Co      2.01875000     8.07500000     6.05625000
Co     2.01875000     6.05625000     8.07500000
O      1.90570000     5.94320000     5.94320000
O      1.90570000     4.15055000     4.15055000
O       .11305000     5.94320000     4.15055000
O       .11305000     4.15055000     5.94320000
Co     3.02812500     7.06562500     3.02812500
O      2.13180000     6.16930000     2.13180000
O      2.13180000     7.96195000     3.92445000
O      3.92445000     6.16930000     3.92445000
O      3.92445000     7.96195000     2.13180000
Co      3.02812500     3.02812500     7.06562500
O      2.13180000     2.13180000     6.16930000
O      2.13180000     3.92445000     7.96195000
O      3.92445000     2.13180000     7.96195000
O      3.92445000     3.92445000     6.16930000
Co      7.06562500     7.06562500     7.06562500
O      6.16930000     6.16930000     6.16930000
O      6.16930000     7.96195000     7.96195000
O      7.96195000     6.16930000     7.96195000
O      7.96195000     7.96195000     6.16930000

K_POINTS {automatic}
  2 2 2 0 0 0
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From paulatto at sissa.it  Tue Jul 14 09:06:35 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 14 Jul 2009 09:06:35 +0200 (CEST)
Subject: [Pw_forum] Error : from cdiaghg : error #363, info =/= 0
In-Reply-To: <a591fe200907132329uf1f386cj6e158a3404840952@mail.gmail.com>
References: <a591fe200907132329uf1f386cj6e158a3404840952@mail.gmail.com>
Message-ID: <39304.78.12.162.155.1247555195.squirrel@webmail.sissa.it>


On Tue, July 14, 2009 08:29, dev sharma wrote:
>      occupations='smearing', smearing    =
>  "methfessel-paxton",degauss=0.05,

Dear Dev,
your value of degauss is quite high, and (if I remember correctly) the M-P
recipe for the smearing can produce some small negative occupancies, which
the diagonalizing algorithm does not like. Try to reduce the smearing
(which is in Ry units!), or use gaussian smearing; I would suggest the
first solution, as it is more likely to produce meaningful results.

cheers

P.S. please provide your full affiliation when writing to this mailing list



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



----------------------------------------------------------------
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From neelphysics at yahoo.in  Tue Jul 14 09:07:48 2009
From: neelphysics at yahoo.in (Neel Singh)
Date: Tue, 14 Jul 2009 12:37:48 +0530 (IST)
Subject: [Pw_forum] Problem In Creating Proper Structure in Xcrysden
Message-ID: <200329.34376.qm@web95012.mail.in2.yahoo.com>

I am new to PWscf and working on bismuth titanate. I have made the following input file and visualized the structure in xcrysden. But it is not the same as given in M.-Q. Cai et al? Chemical Physics Letters 399 (2004) 89-93 though I have used the same coordinates as that given in the above paper. Please help or give some suggestions.
Neel

?&control
??? calculation='scf',
??? restart_mode='from_scratch',
??? prefix='bit'
??? pseudo_dir = '/home/physics/pseudo/',
??? outdir='/home/physics/work/bit/temp'
?/
?&system
??? ibrav = 7, celldm(1) =7.733,celldm(3)=8.611,? nat=? 9, ntyp= 3,
??? ecutwfc = 20.0,ecutrho=100,
??? occupations='smearing', smearing??? = "methfessel-paxton",degauss=0.05,
? 
?/
?&electrons
??? mixing_beta = 0.50
??? conv_thr =? 1.0e-6
/
?&ions
?/

ATOMIC_SPECIES
? Bi???? 208.327? Bi.pbe-d-mt.UPF
? Ti??? 47.867??? Ti.pbe-sp-van_ak.UPF
? O???? 15.9994?? O.pbe-van_ak.UPF
ATOMIC_POSITIONS {crystal}
? Bi??? 0.500??? 0.500??? 0.06752
? Bi??? 0.500??? 0.500??? 0.21147
? Ti??? 0.500??? 0.500??? 0.500
? Ti??? 0.500??? 0.500??? 0.37074
? O???? 0.500??? 0.000??? 0.000
? O???? 0.500??? 0.000??? 0.250
? O???? 0.500??? 0.500??? 0.4411
? O???? 0.500??? 0.500??? 0.31830
? O???? 0.500??? 0.000?? 0.11768
K_POINTS {automatic}
2 2 1 0 0 0



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From giannozz at democritos.it  Tue Jul 14 09:22:56 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 14 Jul 2009 09:22:56 +0200
Subject: [Pw_forum] Problem In Creating Proper Structure in Xcrysden
In-Reply-To: <200329.34376.qm@web95012.mail.in2.yahoo.com>
References: <200329.34376.qm@web95012.mail.in2.yahoo.com>
Message-ID: <572D7866-6EA0-4E65-852F-9CBD925DD63C@democritos.it>


On Jul 14, 2009, at 9:07 , Neel Singh wrote:

> [..] it is not the same as given in M.-Q.. Cai et al  [...]
>  though I have used the same coordinates as that
> given in the above paper.

this may mean that the conventions for crystal axis used
by PWscf are not the same as those used in that paper.
The former are described in detail in the documentation
and printed on output. The latter I don't know.

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




From sakuma.h.aa at m.titech.ac.jp  Tue Jul 14 09:48:40 2009
From: sakuma.h.aa at m.titech.ac.jp (SAKUMA Hiroshi)
Date: Tue, 14 Jul 2009 16:48:40 +0900
Subject: [Pw_forum] Problem in energy conservation in NVE MD using cp.x
Message-ID: <4A5C3858.5010100@m.titech.ac.jp>

Dear all,

I was running the cp.x using the example input files in
a folder of "examples_cp/water-cp" provided by Summer School 2006, Quantum Espresso Lab.
After the wavefunction optimization, I tried a MD run of NVE ensemble using the h2o_mol.in.03.
The total energy (econt) was almost constant until 0.2 ps, 
however it exponentially increased after 0.2 ps.
This is not affected by the choice of time step and fictious mass.

I used the Quantum-espresso 4.0.5 and 4.0.3.

Do you have any idea about this problem?

Thanks,

Hiroshi Sakuma

- 
Department of Earth & Planetary Sciences
Graduate School of Science & Engineering
Tokyo Institute of Technology
2-12-1 Ookayama Meguro-ku Tokyo 1528551
Kawamura Lab.
Tel: +81-3-5734-2617


# h2o_mol.in.03
# Electronic + Ionic Dynamic
# quenching electrons and ions.

&CONTROL
title = ' Water Molecule ',
calculation = 'cp',
restart_mode = 'reset_counters',
ndr = 51,
ndw = 52,
nstep = 5000,
iprint = 5,
isave = 100,
tstress = .FALSE.,
tprnfor = .TRUE.,
dt = 4.0d0,
etot_conv_thr = 1.d-9,
ekin_conv_thr = 1.d-4,
prefix = 'h2o_mol'
/

&SYSTEM
ibrav = 14,
celldm(1) = 10.0, celldm(2) = 1.0, celldm(3) = 1.0,
celldm(4) = 0.0, celldm(5) = 0.0, celldm(6) = 0.0,
nat = 3,
ntyp = 2,
ecutwfc = 70.0,
nr1b = 16, nr2b = 16, nr3b = 16
/

&ELECTRONS
emass = 300.d0,
emass_cutoff = 2.5d0,
orthogonalization = 'ortho',
electron_dynamics = 'verlet',
electron_velocities = 'zero',
electron_temperature = 'not_controlled',
/

&IONS
ion_dynamics = 'verlet',
ion_velocities = 'zero',
ion_temperature = 'not_controlled',
/

ATOMIC_SPECIES
O 16.0d0 O.BLYP.UPF
H 1.00d0 H.fpmd.UPF

ATOMIC_POSITIONS (bohr)
O 5.0099 5.0099 5.0000 0 0 0
H 6.8325 4.7757 4.9999 1 1 1
H 4.7757 6.8325 4.9998 1 1 1




From sylvian.cadars at cnrs-orleans.fr  Tue Jul 14 10:58:15 2009
From: sylvian.cadars at cnrs-orleans.fr (Sylvian Cadars)
Date: Tue, 14 Jul 2009 10:58:15 +0200
Subject: [Pw_forum] Chosing outpu file using the -in/input option
Message-ID: <4A5C48A7.6070208@cnrs-orleans.fr>

Hi,
I recently installed quantum espresso on a cluster machine equipped with 
openmpi and the OAR job submission system.  Using the standard syntax:
mpirun -np [n.o.cpus] /path/to/pw.x < inputfile.in > outputfile.out
I found that the job would only use processors within a single node, 
such that there are several pw.x processes running on each CPU if the 
number of specified CPUs is larger than the number of CPUs per node, 
while other remain unused.

This problem is partially solved using the "-in/input" syntax:
mpirun -np [n.o.cpus] /path/to/pw.x -in inputfile.in > outputfile.out
(as in 
http://www.quantum-espresso.org/wiki/index.php/Running_on_parallel_machines#Trouble_with_input_files)

That is: the job actually uses the number of requested CPUs, including 
when the number of requested CPUs is greater than the number of CPUs per 
node.  However, a problem remains with the redirection of the output.  
Instead of writing the output in "ouputfile.out " pw.x writes it in the 
OAR output (OAR.jobID.stdout).

In summary, the question is: how can I chose my output file when using 
the -in/input option ?

Thanks for your help.
Best regards.

Sylvian

-- 
------------------------------------------------------------------------
*Dr. Sylvian CADARS*
CEMHTI-CNRS
1D, Av. de la Recherche Scientifique
45071 Orl?ans Cedex 2, France
------------------------------------------------------------------------


From mahasinalam at yahoo.co.uk  Tue Jul 14 11:21:45 2009
From: mahasinalam at yahoo.co.uk (MAHASIN ALAM)
Date: Tue, 14 Jul 2009 09:21:45 +0000 (GMT)
Subject: [Pw_forum] XCrysDen
Message-ID: <958591.36079.qm@web24102.mail.ird.yahoo.com>

Dear All,
?
I am trying to install the "XCrysDen" software in MS-Windows, I have downloaded the specified file from the "Quantum Espresso" site. But when I unzipped the file, the error message showing is that the "xcConfigure" file is not created. Can any one please help me how to install the software.
?
Warm regards
?
Sk Mahasin Alam


      
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From paulatto at sissa.it  Tue Jul 14 11:34:21 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 14 Jul 2009 11:34:21 +0200
Subject: [Pw_forum] Chosing outpu file using the -in/input option
In-Reply-To: <4A5C48A7.6070208@cnrs-orleans.fr>
References: <4A5C48A7.6070208@cnrs-orleans.fr>
Message-ID: <op.uw1wvjyya8x26q@paulax>

In data 14 luglio 2009 alle ore 10:58:15, Sylvian Cadars  
<sylvian.cadars at cnrs-orleans.fr> ha scritto:
> In summary, the question is: how can I chose my output file when using
> the -in/input option ?

You cannot, the output (comprising standard output and standard error)  
cannot be redirected to a file in QE. If you cannot find ouputfile.out it  
is likely that the work directory used by OAR to start your job is not the  
one you expect, please check its documentation. Otherwise, you can  
configure mpi and/or OAR to put the output where you wish it to do.

> Sylvian

regards

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

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

From paulatto at sissa.it  Tue Jul 14 11:36:49 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 14 Jul 2009 11:36:49 +0200
Subject: [Pw_forum] XCrysDen
In-Reply-To: <958591.36079.qm@web24102.mail.ird.yahoo.com>
References: <958591.36079.qm@web24102.mail.ird.yahoo.com>
Message-ID: <op.uw1wzndsa8x26q@paulax>

In data 14 luglio 2009 alle ore 11:21:45, MAHASIN ALAM  
<mahasinalam at yahoo.co.uk> ha scritto:
> I am trying to install the "XCrysDen" software in MS-Windows, I have  
> downloaded the specified file from the "Quantum Espresso" site. But when  
> I unzipped the file, the error message showing is that the "xcConfigure"  
> file is not created. Can any one please help me how to install the  
> software.

Dear Mahasin,
you should really just read xcrysden documentation, where the installation  
procedure is explained in details.
Nevertheless, I would advice you to use the 1.6 pre-release version of  
xcrysden, instead, which does not involve any installation procedure and  
is more compatible with the newer versions of QE:  
<http://www.xcrysden.org/Download.html#__toc__1>

cheers


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

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

From decboy9 at gmail.com  Tue Jul 14 11:54:05 2009
From: decboy9 at gmail.com (dev sharma)
Date: Tue, 14 Jul 2009 15:24:05 +0530
Subject: [Pw_forum] Error : from cdiaghg : error #363, info =/= 0
In-Reply-To: <39304.78.12.162.155.1247555195.squirrel@webmail.sissa.it>
References: <a591fe200907132329uf1f386cj6e158a3404840952@mail.gmail.com>
	<39304.78.12.162.155.1247555195.squirrel@webmail.sissa.it>
Message-ID: <a591fe200907140254q3eeace14ve668f6859729cbc2@mail.gmail.com>

Dear SIr,

 I have tried both the option as suggested by you by changing degauss or
smearing but the problem is same. is the problem is because of the spinel
structure as it has two types of Co i.e Co2+ and Co3+  but we are treating
them same. We have given ntyp=2 in & system . so is the same error is due to
that fact ???? please help


 Dev Sharma,
JRF, University of Delhi, India


On Tue, Jul 14, 2009 at 12:36 PM, Lorenzo Paulatto <paulatto at sissa.it>wrote:

>
> On Tue, July 14, 2009 08:29, dev sharma wrote:
> >      occupations='smearing', smearing    =
> >  "methfessel-paxton",degauss=0.05,
>
> Dear Dev,
> your value of degauss is quite high, and (if I remember correctly) the M-P
> recipe for the smearing can produce some small negative occupancies, which
> the diagonalizing algorithm does not like. Try to reduce the smearing
> (which is in Ry units!), or use gaussian smearing; I would suggest the
> first solution, as it is more likely to produce meaningful results.
>
> cheers
>
> P.S. please provide your full affiliation when writing to this mailing list
>
>
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/<http://people.sissa.it/%7Epaulatto/>
>
>
>
> ----------------------------------------------------------------
>  SISSA Webmail https://webmail.sissa.it/
>  Powered by SquirrelMail http://www.squirrelmail.org/
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From paulatto at sissa.it  Tue Jul 14 12:13:47 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 14 Jul 2009 12:13:47 +0200
Subject: [Pw_forum] Error : from cdiaghg : error #363, info =/= 0
In-Reply-To: <a591fe200907140254q3eeace14ve668f6859729cbc2@mail.gmail.com>
References: <a591fe200907132329uf1f386cj6e158a3404840952@mail.gmail.com>
	<39304.78.12.162.155.1247555195.squirrel@webmail.sissa.it>
	<a591fe200907140254q3eeace14ve668f6859729cbc2@mail.gmail.com>
Message-ID: <op.uw1yo9r8a8x26q@paulax>

In data 14 luglio 2009 alle ore 11:54:05, dev sharma <decboy9 at gmail.com>  
ha scritto:
> so is the same error is  due to that fact ????

No, I can exclude this possibility.

On the other hand, I've had a look at your structure with xcrysden and,  
although I've had some problem displaying it, I think you may have made  
some mistake in setting the atoms positions; if some core regions overlap  
too much it is likely to cause those kind of diagonalization errors.  
Please have a second look at your structure, be expecially careful to NOT  
include both and atom and one of its periodic replicas!

best regards

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

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

From marzari at MIT.EDU  Tue Jul 14 12:18:05 2009
From: marzari at MIT.EDU (Nicola Marzari)
Date: Tue, 14 Jul 2009 06:18:05 -0400
Subject: [Pw_forum] Error : from cdiaghg : error #363, info =/= 0
In-Reply-To: <a591fe200907140254q3eeace14ve668f6859729cbc2@mail.gmail.com>
References: <a591fe200907132329uf1f386cj6e158a3404840952@mail.gmail.com>	<39304.78.12.162.155.1247555195.squirrel@webmail.sissa.it>
	<a591fe200907140254q3eeace14ve668f6859729cbc2@mail.gmail.com>
Message-ID: <4A5C5B5D.9020008@mit.edu>

dev sharma wrote:
> Dear SIr,
> 
>  I have tried both the option as suggested by you by changing degauss or 
> smearing but the problem is same. is the problem is because of the 
> spinel structure as it has two types of Co i.e Co2+ and Co3+  but we are 
> treating them same. We have given ntyp=2 in & system . so is the same 
> error is due to that fact ???? please help


Also, unlikely standard lda/gga will give you good results - lda+u
might help, but those are difficult cases, to be studied carefully.
And use 'm-v' smearing -).

			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 mahasinalam at yahoo.co.uk  Tue Jul 14 13:38:53 2009
From: mahasinalam at yahoo.co.uk (MAHASIN ALAM)
Date: Tue, 14 Jul 2009 11:38:53 +0000 (GMT)
Subject: [Pw_forum] XCrysDen
Message-ID: <189263.74548.qm@web24106.mail.ird.yahoo.com>

Dear Lorenzo Paulatto,
?
Thank you very much for your help.
?
Regards
?
Mahasin

--- On Tue, 14/7/09, Lorenzo Paulatto <paulatto at sissa.it> wrote:


From: Lorenzo Paulatto <paulatto at sissa.it>
Subject: Re: [Pw_forum] XCrysDen
To: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Tuesday, 14 July, 2009, 3:06 PM


In data 14 luglio 2009 alle ore 11:21:45, MAHASIN ALAM? 
<mahasinalam at yahoo.co.uk> ha scritto:
> I am trying to install the "XCrysDen" software in MS-Windows, I have? 
> downloaded the specified file from the "Quantum Espresso" site. But when? 
> I unzipped the file, the error message showing is that the "xcConfigure"? 
> file is not created. Can any one please help me how to install the? 
> software.

Dear Mahasin,
you should really just read xcrysden documentation, where the installation? 
procedure is explained in details.
Nevertheless, I would advice you to use the 1.6 pre-release version of? 
xcrysden, instead, which does not involve any installation procedure and? 
is more compatible with the newer versions of QE:? 
<http://www.xcrysden.org/Download.html#__toc__1>

cheers


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

? ???*** save italian brains ***
? http://saveitalianbrains.wordpress.com/
_______________________________________________
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 Jul 14 14:01:37 2009
From: marzari at MIT.EDU (Nicola Marzari)
Date: Tue, 14 Jul 2009 08:01:37 -0400
Subject: [Pw_forum] Problem in energy conservation in NVE MD using cp.x
In-Reply-To: <4A5C3858.5010100@m.titech.ac.jp>
References: <4A5C3858.5010100@m.titech.ac.jp>
Message-ID: <4A5C73A1.1060504@mit.edu>


CC: Paolo Giannozzi, Carlo Cavazzoni, Roberto Car. Notes below
also relevant for BO dynamics with pwscf. Please focus on
the bottom part of the email.


Dear Hiroshi,


well spotted. To summarize, for all - this is a single water molecule,
almost relaxed at equilibrium. The oxygen atom is clamped (allowing it 
to move does not change the problem). When the microcanonical cp
dynamics starts, the ionic temperature oscillates around 1 or 2 degrees
Kelvin, but after 0.2-0.4 ps it picks up.

Hiroshi: I do not believe it's an exponential increase - if you continue 
the simulations for longer, it starts oscillating between 0 and 50 
Kelvin, instead of between 0 and 2 Kelvin, although after 1ps or so
I believe the molecule has started to move so fast that the integration
breaks down, and things start getting worse.

I believe the problem is this: you are seeing a transfer of quantity of
motion between the subset of the ions, and the electronic fictitious
degrees of freedom. Remember this: the cp lagrangian, when integrated
correctly (i.e. with a small time step) evolves correctly the full
dynamical system with all degrees of freedom (physical ionic masses,
fictitious electronic masses). If there is an electronic gap in your
system (like here) the two subsets of ions and electrons evolve without
exchanging energy between each other, and conserving the momentum
(linear and angular) of the mixed system (ionic + fictitious
electronic). The center of mass of the physical subset (e.g. ions) can
pick up momentum (both linear and angular momentum), provided this is
cancelled out by the fictitious momentum of the electrons (and it will 
cancel out, if the equation of motions are integrated properly).

So, I think (also due to your use of normconserving psp, leading to a 
lot of plane waves) that you are seeing transfer of momentum from the
fictitious electrons to the ions. Also, your ions have almost no kinetic
energy, so instead of giving it to the fictioous electronic degrees of
freedom (as would usually happen, say, in a simulation with a small gap)
they are slowly picking up kinetic energy from the electrons.

On top of this, the routine that calculates the temperature removes
the contribution from the motion of the center of mass - it is in 
Modules, so I believe this is also used for pwscf. I believe this
is never the right thing to do, and maybe this is a good time to
sort this out.

So, these would be my recommendations, starting from the easy ones:

1) for BO dynamics in CP and PWSCF: I believe the right procedure is
to force the sum of the hellmann-fenyman forces to be zero (it will 
never be exactly zero to imperfect convergence), and never remove the
motion of the center of mass from the temperature. This will assure that
the system does not start moving. For an isolated system, the same 
should also be done for the angular momentum. For an extended system,
not sure - a solid will never pick up angular momentum, a liquid could,
in principle.

2) for CP dynamics in CP: I'm not sure what would be the best strategy.
I believe again we should calculate the temperature without removing
the center of mass, and I believe we should fix, in the move_ions, the
center of mass. This is what used to happen in previous version of the
codes (like - 10 years ago).

			nicola



SAKUMA Hiroshi wrote:
> Dear all,
> 
> I was running the cp.x using the example input files in
> a folder of "examples_cp/water-cp" provided by Summer School 2006, Quantum Espresso Lab.
> After the wavefunction optimization, I tried a MD run of NVE ensemble using the h2o_mol.in.03.
> The total energy (econt) was almost constant until 0.2 ps, 
> however it exponentially increased after 0.2 ps.
> This is not affected by the choice of time step and fictious mass.
> 
> I used the Quantum-espresso 4.0.5 and 4.0.3.
> 
> Do you have any idea about this problem?

-- 
---------------------------------------------------------------------
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 positronium at gmail.com  Tue Jul 14 15:24:39 2009
From: positronium at gmail.com (Lex Kemper)
Date: Tue, 14 Jul 2009 09:24:39 -0400
Subject: [Pw_forum] Chosing outpu file using the -in/input option
In-Reply-To: <4A5C48A7.6070208@cnrs-orleans.fr>
References: <4A5C48A7.6070208@cnrs-orleans.fr>
Message-ID: <4A5C8717.4080709@phys.ufl.edu>

Hi Sylvian,

This sounds more like an MPI/compilation problem to me than an inputfile 
issue. Are you sure that the cluster is set up right (I don't know if 
you maintain it), and that Q-E is compiled correctly?

Lex Kemper
Department of Physics
University of Florida

Sylvian Cadars wrote:
> Hi,
> I recently installed quantum espresso on a cluster machine equipped with 
> openmpi and the OAR job submission system.  Using the standard syntax:
> mpirun -np [n.o.cpus] /path/to/pw.x < inputfile.in > outputfile.out
> I found that the job would only use processors within a single node, 
> such that there are several pw.x processes running on each CPU if the 
> number of specified CPUs is larger than the number of CPUs per node, 
> while other remain unused.
> 
> This problem is partially solved using the "-in/input" syntax:
> mpirun -np [n.o.cpus] /path/to/pw.x -in inputfile.in > outputfile.out
> (as in 
> http://www.quantum-espresso.org/wiki/index.php/Running_on_parallel_machines#Trouble_with_input_files)
> 
> That is: the job actually uses the number of requested CPUs, including 
> when the number of requested CPUs is greater than the number of CPUs per 
> node.  However, a problem remains with the redirection of the output.  
> Instead of writing the output in "ouputfile.out " pw.x writes it in the 
> OAR output (OAR.jobID.stdout).
> 
> In summary, the question is: how can I chose my output file when using 
> the -in/input option ?
> 
> Thanks for your help.
> Best regards.
> 
> Sylvian
> 

From positronium at gmail.com  Tue Jul 14 15:25:45 2009
From: positronium at gmail.com (Lex Kemper)
Date: Tue, 14 Jul 2009 09:25:45 -0400
Subject: [Pw_forum] Problem In Creating Proper Structure in Xcrysden
In-Reply-To: <200329.34376.qm@web95012.mail.in2.yahoo.com>
References: <200329.34376.qm@web95012.mail.in2.yahoo.com>
Message-ID: <4A5C8759.90206@phys.ufl.edu>

Hi Neel,

Make sure you're using the newest version of XCrysDen. I had issues with 
ibrav=7 as well, it was fixed in the newest version.

Lex Kemper
Department of Physics
University of Florida

Neel Singh wrote:
> I am new to PWscf and working on bismuth titanate. I have made the 
> following input file and visualized the structure in xcrysden. But it is 
> not the same as given in M.-Q.. Cai et al  Chemical Physics Letters 399 
> (2004) 89-93 though I have used the same coordinates as that given in 
> the above paper. Please help or give some suggestions.
> Neel
> 
>  &control
>     calculation='scf',
>     restart_mode='from_scratch',
>     prefix='bit'
>     pseudo_dir = '/home/physics/pseudo/',
>     outdir='/home/physics/work/bit/temp'
>  /
>  &system
>     ibrav = 7, celldm(1) =7.733,celldm(3)=8.611,  nat=  9, ntyp= 3,
>     ecutwfc = 20.0,ecutrho=100,
>     occupations='smearing', smearing    = "methfessel-paxton",degauss=0.05,
>  
>  /
>  &electrons
>     mixing_beta = 0.50
>     conv_thr =  1.0e-6
> /
>  &ions
>  /
> 
> ATOMIC_SPECIES
>   Bi     208.327  Bi.pbe-d-mt.UPF
>   Ti    47.867    Ti.pbe-sp-van_ak.UPF
>   O     15.9994   O.pbe-van_ak.UPF
> ATOMIC_POSITIONS {crystal}
>   Bi    0.500    0.500    0.06752
>   Bi    0.500    0.500    0.21147
>   Ti    0.500    0.500    0.500
>   Ti    0.500    0.500    0.37074
>   O     0.500    0.000    0.000
>   O     0.500    0.000    0.250
>   O     0.500    0.500    0.4411
>   O     0.500    0.500    0.31830
>   O     0.500    0.000   0.11768
> K_POINTS {automatic}
> 2 2 1 0 0 0
> 
> 
> ------------------------------------------------------------------------
> Love Cricket? Check out live scores, photos, video highlights and more. 
> Click here 
> <http://in.rd.yahoo.com/tagline_cricket_2/*http://cricket.yahoo.com>.
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

From jtmullen at ncsu.edu  Tue Jul 14 23:21:40 2009
From: jtmullen at ncsu.edu (jtmullen at ncsu.edu)
Date: Tue, 14 Jul 2009 17:21:40 -0400 (EDT)
Subject: [Pw_forum] Generating k points for the full first brillouin zone
Message-ID: <60890.152.14.74.99.1247606500.squirrel@webmail.ncsu.edu>

Greetings all,

I have a need to generate k points which cover the complete first BZ, not
just the irreducible BZ. I notice a subroutine in PW/kpoint_grid.f90 which
returns k points in the IBZ given grid dimensions (nk1, nk2, nk3), but
before I set about modifying this routine or writing my own, I thought it
prudent to find if a routine to generate k points in the entire BZ (given
the same grid dimensions) already exists in the codebase. If it does, can
someone let me know the proper subroutine?

Thanks
Jeff Mullen
NCSU Physics



From positronium at gmail.com  Wed Jul 15 01:20:07 2009
From: positronium at gmail.com (Lex Kemper)
Date: Tue, 14 Jul 2009 19:20:07 -0400
Subject: [Pw_forum] Generating k points for the full first brillouin zone
In-Reply-To: <60890.152.14.74.99.1247606500.squirrel@webmail.ncsu.edu>
References: <60890.152.14.74.99.1247606500.squirrel@webmail.ncsu.edu>
Message-ID: <4A5D12A7.7000607@phys.ufl.edu>

Hi Jeff,

Wannier90 (which comes with QE) comes with a utility that does it, I 
believe.

Lex Kemper
Department of Physics
University of Florida

jtmullen at ncsu.edu wrote:
> Greetings all,
> 
> I have a need to generate k points which cover the complete first BZ, not
> just the irreducible BZ. I notice a subroutine in PW/kpoint_grid.f90 which
> returns k points in the IBZ given grid dimensions (nk1, nk2, nk3), but
> before I set about modifying this routine or writing my own, I thought it
> prudent to find if a routine to generate k points in the entire BZ (given
> the same grid dimensions) already exists in the codebase. If it does, can
> someone let me know the proper subroutine?
> 
> Thanks
> Jeff Mullen
> NCSU Physics
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

From padmaja_patnaik at yahoo.co.uk  Wed Jul 15 07:56:53 2009
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Wed, 15 Jul 2009 05:56:53 +0000 (GMT)
Subject: [Pw_forum] Problem in compilation
Message-ID: <19957.94643.qm@web26103.mail.ukl.yahoo.com>

Dear all
While trying to compile espresso-4.0.5 in Linux x86_64 machine, it gets configuresd succespully and also finds the libraries. But the make all command gives the following error.? Can ayone please suggest what has to be done?

make[1]: Entering directory `/home/padmaja/espresso-4.0.5/clib'
cc -O3 -D__GFORTRAN -D__FFTW -I../include??? -c stack.c
cc -O3 -D__GFORTRAN -D__FFTW -I../include??? -c c_mkdir.c
cc -O3 -D__GFORTRAN -D__FFTW -I../include??? -c cptimer.c
cc -O3 -D__GFORTRAN -D__FFTW -I../include??? -c fft_stick.c
cc -O3 -D__GFORTRAN -D__FFTW -I../include??? -c indici.c
cc -O3 -D__GFORTRAN -D__FFTW -I../include??? -c memstat.c
In file included from /usr/include/stdio.h:910,
???????????????? from /usr/include/malloc.h:27,
???????????????? from memstat.c:21:
/usr/include/bits/stdio.h: In function 'memstat_':
/usr/include/bits/stdio.h:38: error: nested function 'vprintf' declared 'extern'
/usr/include/bits/stdio.h:37: error: static declaration of 'vprintf' follows non-static declaration
/usr/include/bits/stdio.h:46: error: nested function 'getchar' declared 'extern'
/usr/include/bits/stdio.h:45: error: static declaration of 'getchar' follows non-static declaration
/usr/include/stdio.h:522: note: previous declaration of 'getchar' was here
/usr/include/bits/stdio.h:55: error: nested function 'fgetc_unlocked' declared 'extern'
/usr/include/bits/stdio.h:54: error: static declaration of 'fgetc_unlocked' follows non-static declaration
/usr/include/stdio.h:545: note: previous declaration of 'fgetc_unlocked' was here
In file included from /usr/include/stdio.h:910,
???????????????? from /usr/include/malloc.h:27,
???????????????? from memstat.c:21:
/usr/include/bits/stdio.h:65: error: nested function 'getc_unlocked' declared 'extern'
/usr/include/bits/stdio.h:64: error: static declaration of 'getc_unlocked' follows non-static declaration
/usr/include/stdio.h:534: note: previous declaration of 'getc_unlocked' was here
/usr/include/bits/stdio.h:72: error: nested function 'getchar_unlocked' declared 'extern'
/usr/include/bits/stdio.h:71: error: static declaration of 'getchar_unlocked' follows non-static declaration
/usr/include/stdio.h:535: note: previous declaration of 'getchar_unlocked' was here
/usr/include/bits/stdio.h:81: error: nested function 'putchar' declared 'extern'
/usr/include/bits/stdio.h:80: error: static declaration of 'putchar' follows non-static declaration
/usr/include/bits/stdio.h:90: error: nested function 'fputc_unlocked' declared 'extern'
/usr/include/bits/stdio.h:89: error: static declaration of 'fputc_unlocked' follows non-static declaration
/usr/include/bits/stdio.h:100: error: nested function 'putc_unlocked' declared 'extern'
/usr/include/bits/stdio.h:99: error: static declaration of 'putc_unlocked' follows non-static declaration
/usr/include/bits/stdio.h:107: error: nested function 'putchar_unlocked' declared 'extern'
/usr/include/bits/stdio.h:106: error: static declaration of 'putchar_unlocked' follows non-static declaration
In file included from /usr/include/stdio.h:910,
???????????????? from /usr/include/malloc.h:27,
???????????????? from memstat.c:21:
/usr/include/bits/stdio.h:127: error: nested function 'feof_unlocked' declared 'extern'
/usr/include/bits/stdio.h:126: error: static declaration of 'feof_unlocked' follows non-static declaration
/usr/include/stdio.h:811: note: previous declaration of 'feof_unlocked' was here
/usr/include/bits/stdio.h:134: error: nested function 'ferror_unlocked' declared 'extern'
/usr/include/bits/stdio.h:133: error: static declaration of 'ferror_unlocked' follows non-static declaration
/usr/include/stdio.h:812: note: previous declaration of 'ferror_unlocked' was here
make[1]: *** [memstat.o] Error 1
make[1]: Leaving directory `/home/padmaja/espresso-4.0.5/clib'
make: *** [libs] Error 2

Thanks in advance.
regards
Padmaja Patnaik

Research Scholar

Dept of Physics

IIT Bombay

Mumbai, India


      
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From giannozz at democritos.it  Wed Jul 15 08:24:22 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 15 Jul 2009 08:24:22 +0200
Subject: [Pw_forum] Problem in compilation
In-Reply-To: <19957.94643.qm@web26103.mail.ukl.yahoo.com>
References: <19957.94643.qm@web26103.mail.ukl.yahoo.com>
Message-ID: <36631485-F144-40DD-B672-82DC5EAFA3CC@democritos.it>


On Jul 15, 2009, at 7:56 , Padmaja Patnaik wrote:

> cc -O3 -D__GFORTRAN -D__FFTW -I../include    -c memstat.c
> In file included from /usr/include/stdio.h:910,
>                  from /usr/include/malloc.h:27,
>                  from memstat.c:21:
> /usr/include/bits/stdio.h: In function 'memstat_':
> /usr/include/bits/stdio.h:38: error: nested function 'vprintf'  
> declared 'extern' [...]

>

in include/c_defs.h, comment the line
#define HAVE_MALLINFO 1
or change it to
#undef HAVE_MALLINFO

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




From giannozz at democritos.it  Wed Jul 15 08:26:25 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 15 Jul 2009 08:26:25 +0200
Subject: [Pw_forum] Generating k points for the full first brillouin zone
In-Reply-To: <60890.152.14.74.99.1247606500.squirrel@webmail.ncsu.edu>
References: <60890.152.14.74.99.1247606500.squirrel@webmail.ncsu.edu>
Message-ID: <4E04980B-E33B-4678-B0A6-CA6F0B66F3DD@democritos.it>


On Jul 14, 2009, at 23:21 , jtmullen at ncsu.edu wrote:

> I have a need to generate k points which cover the complete first  
> BZ, not
> just the irreducible BZ. I notice a subroutine in PW/ 
> kpoint_grid.f90 which
> returns k points in the IBZ given grid dimensions (nk1, nk2, nk3)

and in the complete BZ if you answer "t" to the question "write all k"

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




From sclauzer at sissa.it  Wed Jul 15 08:37:37 2009
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Wed, 15 Jul 2009 08:37:37 +0200
Subject: [Pw_forum] Generating k points for the full first brillouin zone
In-Reply-To: <4E04980B-E33B-4678-B0A6-CA6F0B66F3DD@democritos.it>
References: <60890.152.14.74.99.1247606500.squirrel@webmail.ncsu.edu>
	<4E04980B-E33B-4678-B0A6-CA6F0B66F3DD@democritos.it>
Message-ID: <4A5D7931.8050104@sissa.it>

Paolo Giannozzi wrote:
> On Jul 14, 2009, at 23:21 , jtmullen at ncsu.edu wrote:
> 
>> I have a need to generate k points which cover the complete first  
>> BZ, not
>> just the irreducible BZ. I notice a subroutine in PW/ 
>> kpoint_grid.f90 which
>> returns k points in the IBZ given grid dimensions (nk1, nk2, nk3)
> 
> and in the complete BZ if you answer "t" to the question "write all k"

I think this applies for the kpoints.x program in pwtools/, not to the kpoint_grid 
subroutine. Anyway I agree that kpoints.x can be used exactly for this purpose (answering 
't', of course).

GS


> 
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

-- 


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

From padmaja_patnaik at yahoo.co.uk  Wed Jul 15 09:17:34 2009
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Wed, 15 Jul 2009 07:17:34 +0000 (GMT)
Subject: [Pw_forum] Problem in compilation
Message-ID: <134995.6870.qm@web26102.mail.ukl.yahoo.com>

Thanks a lot.
It solved my problem.

On Jul 15, 2009, at 7:56 , Padmaja Patnaik wrote:

> cc -O3 -D__GFORTRAN -D__FFTW -I../include? ? -c memstat.c
> In file included from /usr/include/stdio.h:910,
>? ? ? ? ? ? ? ? ? from /usr/include/malloc.h:27,
>? ? ? ? ? ? ? ? ? from memstat.c:21:
> /usr/include/bits/stdio.h: In function 'memstat_':
> /usr/include/bits/stdio.h:38: error: nested function 'vprintf'? 
> declared 'extern' [...]

>

in include/c_defs.h, comment the line
#define HAVE_MALLINFO 1
or change it to
#undef HAVE_MALLINFO

P.

Padmaja Patnaik

Research Scholar

Dept of Physics

IIT Bombay

Mumbai, India


      
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From padmaja_patnaik at yahoo.co.uk  Wed Jul 15 09:28:30 2009
From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik)
Date: Wed, 15 Jul 2009 07:28:30 +0000 (GMT)
Subject: [Pw_forum] Error: insufficient virtual memory
Message-ID: <455784.997.qm@web26107.mail.ukl.yahoo.com>

Dear All

I am running espresso-4.0.5. I am doing scf and dos calculations for a super cell. Its Linux machine. Scf part is done and then for the dos calculations it says, insufficient virtual memory and the job stops automatically. I have given Gamma point calculation for scf and minimum possible k-points and number of bands are taken. This calculation i have done many times in different machine. I wonder whats wrong in this machine. 
Can anybody suggest how can i increase the virtual memory? Or else is there any toher wat to deal with this problem?

Thanks in advance.
Regards

Padmaja Patnaik

Research Scholar

Dept of Physics

IIT Bombay

Mumbai, India


      
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From sagarambavale at yahoo.co.in  Wed Jul 15 10:45:12 2009
From: sagarambavale at yahoo.co.in (ambavale sagar)
Date: Wed, 15 Jul 2009 14:15:12 +0530 (IST)
Subject: [Pw_forum] ncpp for Ag
Message-ID: <43670.95962.qm@web94616.mail.in2.yahoo.com>

Dear all,
I am working on the system made of Ag, S, C, H atoms. I could found on the PWscf website, the normconserving pseudopotentials (ncpp) with PZ xc function for S, C, H atoms but not for Ag . Ultrasoft pseudo potential with PZ xc function is available there. Can anybody provide me ncpp with PZ exannge-correlation function for Ag. 
If I use uspp along with ncpp in the calculations, which would be changes in the values of ecut and ecutrho? {I read in wiki that hardest atom ecut should be used but what if the hardest atom is of uspp type? what about ecutrho?}

Thank you.
Sagar Ambavale
PhD student
M.S. University of Baroda
India



      See the Web&#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/
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From kazempoor2000 at yahoo.com  Wed Jul 15 11:25:36 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Wed, 15 Jul 2009 02:25:36 -0700 (PDT)
Subject: [Pw_forum] semicore
Message-ID: <336926.76144.qm@web112512.mail.gq1.yahoo.com>

Dear All
I want to make ncpp for Ti by fhi2upf and I make enter semicore electron . How can I do this?
thanks

Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


      
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From paulatto at sissa.it  Wed Jul 15 11:51:23 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 15 Jul 2009 11:51:23 +0200
Subject: [Pw_forum] semicore
In-Reply-To: <336926.76144.qm@web112512.mail.gq1.yahoo.com>
References: <336926.76144.qm@web112512.mail.gq1.yahoo.com>
Message-ID: <op.uw3sbxz9a8x26q@paulax>

In data 15 luglio 2009 alle ore 11:25:36, ali kazempour  
<kazempoor2000 at yahoo.com> ha scritto:
> I want to make ncpp for Ti by fhi2upf

Dear Ali,
fhi2upf is not a pseudopotential generation code, but only a tool to  
convert pseudopotential from the abinit format to the quantum-espresso  
format.

> and I make enter semicore electron . How can I do this?

If the semicore electrons are included in the original abinit  
pseudopotential they will be in included in the resulting UPF file, at  
least they should. Are you having some specific problem? Which  
pseudopotential file are you trying to convert?

best regards

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

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

From sylvian.cadars at cnrs-orleans.fr  Wed Jul 15 11:54:24 2009
From: sylvian.cadars at cnrs-orleans.fr (Sylvian Cadars)
Date: Wed, 15 Jul 2009 11:54:24 +0200
Subject: [Pw_forum] Sujet : Re: Chosing output file using the -in/input
	option
Message-ID: <4A5DA750.7060602@cnrs-orleans.fr>

Hi,
Thanks Lex and Lorentzo for your answers.  I cannot tell for sure that 
the cluster is set up right.  It is a recent cluster that is still in 
testing phase, and which I do not maintain.  I would be grateful if you 
could please give me some indication on how to help the cluster manager 
locate the problem and solve it...  Please just let me know if you need 
information from me.
I used the quick Q-E compilation, which seemed to occur normally.  Maybe 
I could find an installation logfile to help (just don't know where to 
find it).

What makes me think the problem comes more form Q-E is that the job is 
well distributed on the processors of all nodes as soon as the Q-E 
(right?) option "-in inputfile.in" is used (as explained in Q-E user 
guide, see link below) instead of the standard "pw.x <inputfile.in> 
outputfile.out" syntax.
http://www.quantum-espresso.org/wiki/index.php/Running_on_parallel_machines#Trouble_with_input_files

If as Lorentzo wrote it is not possible to redirect the output, then it 
is sad, since I found it particularly convenient to be able to run 
series of  calculations using a single script, as is typically done in 
the example files.  This is particularly convenient when looking for the 
best cutoff energy, for example.

Best regards.

Sylvian.

-- 
------------------------------------------------------------------------
*Sylvian CADARS*
CEMHTI-CNRS
1D, Av. de la Recherche Scientifique
45071 Orl?ans Cedex 2, France
------------------------------------------------------------------------


From kazempoor2000 at yahoo.com  Wed Jul 15 11:56:58 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Wed, 15 Jul 2009 02:56:58 -0700 (PDT)
Subject: [Pw_forum] semicore
In-Reply-To: <op.uw3sbxz9a8x26q@paulax>
Message-ID: <278746.84809.qm@web112509.mail.gq1.yahoo.com>

Dear Lorenzo
I want normconserving pseudopotential for Zn, Ti, (including semicore) and O , since i want to perform GW approximation by sax code that need norm conserving pseudopotentials? in FHI format or espresso ?
thanks a lot

Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375

--- On Wed, 7/15/09, Lorenzo Paulatto <paulatto at sissa.it> wrote:

From: Lorenzo Paulatto <paulatto at sissa.it>
Subject: Re: [Pw_forum] semicore
To: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Wednesday, July 15, 2009, 2:51 AM

In data 15 luglio 2009 alle ore 11:25:36, ali kazempour? 
<kazempoor2000 at yahoo.com> ha scritto:
> I want to make ncpp for Ti by fhi2upf

Dear Ali,
fhi2upf is not a pseudopotential generation code, but only a tool to? 
convert pseudopotential from the abinit format to the quantum-espresso? 
format.

> and I make enter semicore electron . How can I do this?

If the semicore electrons are included in the original abinit? 
pseudopotential they will be in included in the resulting UPF file, at? 
least they should. Are you having some specific problem? Which? 
pseudopotential file are you trying to convert?

best regards

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

? ???*** save italian brains ***
? http://saveitalianbrains.wordpress.com/
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum



      
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From paulatto at sissa.it  Wed Jul 15 12:04:53 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 15 Jul 2009 12:04:53 +0200
Subject: [Pw_forum] Sujet : Re: Chosing output file using the -in/input
 option
In-Reply-To: <4A5DA750.7060602@cnrs-orleans.fr>
References: <4A5DA750.7060602@cnrs-orleans.fr>
Message-ID: <op.uw3syf0ha8x26q@paulax>

In data 15 luglio 2009 alle ore 11:54:24, Sylvian Cadars  
<sylvian.cadars at cnrs-orleans.fr> ha scritto:
> If as Lorentzo wrote it is not possible to redirect the output, then it
> is sad, since I found it particularly convenient to be able to run
> series of  calculations using a single script, as is typically done in
> the example files.  This is particularly convenient when looking for the
> best cutoff energy, for example.

Is is not impossible, but normally the standard redirection ">" works with  
(open)mpi out-of-the-box. If you cannot find the output file it may  
indicate that the working directory used by mpirun is not the directory in  
which you are looking for the output file; see the "Current Working  
Directory" section of mpirun manual for details. You can set the working  
directory explicitly using the option -wd "/path/to/directory" to settle  
this issue.

Another issue I've had sometime, that could cause problems similar to the  
one you've had, is related to two conflicting version of mpi. The mpirun  
instance on the master node tries to start the wrong mpirun on the other  
nodes. Use the --prefix option to be sure this is not your case (syntax  
example: "mpirun --prefix /opt/openmpi-1.3.1" without "/bin/")

Best regards.


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

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

From giannozz at democritos.it  Wed Jul 15 12:08:37 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 15 Jul 2009 12:08:37 +0200
Subject: [Pw_forum] Sujet : Re: Chosing output file using the -in/input
 option
In-Reply-To: <4A5DA750.7060602@cnrs-orleans.fr>
References: <4A5DA750.7060602@cnrs-orleans.fr>
Message-ID: <4A5DAAA5.7020307@democritos.it>

Sylvian Cadars wrote:

> What makes me think the problem comes more from Q-E is that the job is 
> well distributed on the processors of all nodes as soon as the Q-E 
> (right?) option "-in inputfile.in" is used (as explained in Q-E user 
> guide, see link below) instead of the standard "pw.x <inputfile.in> 
> outputfile.out" syntax.

the problem does not come from q-e. It is your cluster that is set up
in a strange way. Anyway, if it works with "-in input_file", it is
irrelevant where the problem is.

> If as Lorenzo wrote it is not possible to redirect the output

it is: just use " > ". If redirection doesn't work on your system,
that's another story. You can go to PW/startup.f90 and change

   IF ( me_image /= root_image ) &
      OPEN( UNIT = stdout, FILE = '/dev/null', STATUS = 'UNKNOWN' )

into

   IF ( me_image /= root_image ) THEN
      OPEN( UNIT = stdout, FILE = '/dev/null', STATUS = 'UNKNOWN' )
   ELSE
      OPEN( UNIT = stdout, FILE = 'some_file_name', STATUS = 'UNKNOWN' )
   END IF

For CP, edit CPV/environment.f90 in a similar way

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

From paulatto at sissa.it  Wed Jul 15 12:10:46 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 15 Jul 2009 12:10:46 +0200
Subject: [Pw_forum] ncpp for Ag
In-Reply-To: <43670.95962.qm@web94616.mail.in2.yahoo.com>
References: <43670.95962.qm@web94616.mail.in2.yahoo.com>
Message-ID: <op.uw3s780na8x26q@paulax>

In data 15 luglio 2009 alle ore 10:45:12, ambavale sagar  
<sagarambavale at yahoo.co.in> ha scritto:
> If I use uspp along with ncpp in the calculations, which would be  
> changes in the values of ecut and ecutrho?

It depends on the details of the various pseudopotentials, it is likely  
that one of the norm-conserving will require the higher ecutwfc (and that  
values will have to be used for all the calculations). Under this  
assumption, you have to test the ultrasoft pseudopotential with this high  
values of ecutwfc and test if it is well converged with respect to ecutrho.

Let's make an example, "->" means "is well converged at":
S -> ecutwfc = 50Ry
C -> ecutwfc = 60Ry
H -> ecutwfc = 45Ry

=> you'll have to take ecutwfc=60, which imply ecutrho >= 60*4 = 240

case 1:
Ag -> ecutwfc = 25, ecutrho = 200
==> you just take ecutwfc=60, and ecutrho will be large enough for the Ag  
pseudopotential too

case 2:
Ag -> ecutwfc = 36, ecutrho = 360
==> you have to take ecutwfc=60 (as required by the C pseudopotential) and  
ecutrho=360 (as required by the Ag ultrasoft-pseudopotential)

best regards


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

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

From alex.mazheika at gmail.com  Wed Jul 15 12:18:51 2009
From: alex.mazheika at gmail.com (Alexej Mazheika)
Date: Wed, 15 Jul 2009 13:18:51 +0300
Subject: [Pw_forum] a problem with 64-bit OS by multiprocess calculation
Message-ID: <ec86c07d0907150318g609ae307y82cd93539d67c5be@mail.gmail.com>

Hi

I apply Espresso-package under Linux with mpich2 applying it for parallel
processes calculations. The Espresso I compiled from source-files with
mpich2-compilers. I noticed a strange phenomenon. The CPU of my PC is Intel
Core Quad (64-bit). When I make my calculations under 64-bit linux-system
(openSUSE 11.0) it lasts longer than under 32-bit one (openSUSE-11.0). For
example, the average time of SCF procedure of my task is 8 min under 64-bit
OS vs 7 min under 32-bit OS. Can this problem be binded with installation or
work of Espresso? If yes, then how to solve it? I asked the developers of
mpich2 about it, and they couldn't help me.

regards,

Alex Mazheika, Research institut for Physical Chemical Problems of BSU,
Leningradskayastr. 14, 220050 Minsk, Belarus
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From paulatto at sissa.it  Wed Jul 15 12:37:36 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 15 Jul 2009 12:37:36 +0200
Subject: [Pw_forum] semicore
In-Reply-To: <278746.84809.qm@web112509.mail.gq1.yahoo.com>
References: <278746.84809.qm@web112509.mail.gq1.yahoo.com>
Message-ID: <op.uw3ugypka8x26q@paulax>

In data 15 luglio 2009 alle ore 11:56:58, ali kazempour  
<kazempoor2000 at yahoo.com> ha scritto:
> I want normconserving pseudopotential for Zn, Ti, (including semicore)  
> and O , since i want to perform GW approximation by sax code that need  
> norm conserving pseudopotentials? in FHI format or espresso ?
> thanks a lot

I don't know anything about SaX, from what I can see in the documentation  
it supports (at least) UPF pseudopotential, athough only version 1.

best regards


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

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

From giannozz at democritos.it  Wed Jul 15 12:32:47 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 15 Jul 2009 12:32:47 +0200
Subject: [Pw_forum] a problem with 64-bit OS by multiprocess calculation
In-Reply-To: <ec86c07d0907150318g609ae307y82cd93539d67c5be@mail.gmail.com>
References: <ec86c07d0907150318g609ae307y82cd93539d67c5be@mail.gmail.com>
Message-ID: <4A5DB04F.50006@democritos.it>

Alexej Mazheika wrote:

> When I make my calculations under 64-bit linux-system (openSUSE 11.0) 
> it lasts longer than under 32-bit one (openSUSE-11.0)

also in serial execution? if so, that's it

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

From lanhaiping at gmail.com  Wed Jul 15 14:15:28 2009
From: lanhaiping at gmail.com (lan haiping)
Date: Wed, 15 Jul 2009 20:15:28 +0800
Subject: [Pw_forum] semicore
In-Reply-To: <op.uw3ugypka8x26q@paulax>
References: <278746.84809.qm@web112509.mail.gq1.yahoo.com>
	<op.uw3ugypka8x26q@paulax>
Message-ID: <c92002fa0907150515w48406135o9c40a451417f308@mail.gmail.com>

I once learned that Sax package only support NCPP  right now .  But I donot
know whether this situation has changed or not .


Regards,
Hai-Ping



On Wed, Jul 15, 2009 at 6:37 PM, Lorenzo Paulatto <paulatto at sissa.it> wrote:

> In data 15 luglio 2009 alle ore 11:56:58, ali kazempour
> <kazempoor2000 at yahoo.com> ha scritto:
> > I want normconserving pseudopotential for Zn, Ti, (including semicore)
> > and O , since i want to perform GW approximation by sax code that need
> > norm conserving pseudopotentials? in FHI format or espresso ?
> > thanks a lot
>
> I don't know anything about SaX, from what I can see in the documentation
> it supports (at least) UPF pseudopotential, athough only version 1.
>
> best regards
>
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/<http://people.sissa.it/%7Epaulatto/>
>
>     *** save italian brains ***
>  http://saveitalianbrains.wordpress.com/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From akohlmey at cmm.chem.upenn.edu  Wed Jul 15 15:07:25 2009
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 15 Jul 2009 09:07:25 -0400
Subject: [Pw_forum] a problem with 64-bit OS by multiprocess calculation
In-Reply-To: <ec86c07d0907150318g609ae307y82cd93539d67c5be@mail.gmail.com>
References: <ec86c07d0907150318g609ae307y82cd93539d67c5be@mail.gmail.com>
Message-ID: <1247663245.2840.2996.camel@zero>

On Wed, 2009-07-15 at 13:18 +0300, Alexej Mazheika wrote:
> Hi
> 
> I apply Espresso-package under Linux with mpich2 applying it for
> parallel processes calculations. The Espresso I compiled from
> source-files with mpich2-compilers. I noticed a strange phenomenon.
> The CPU of my PC is Intel Core Quad (64-bit). When I make my
> calculations under 64-bit linux-system (openSUSE 11.0) it lasts longer
> than under 32-bit one (openSUSE-11.0). For example, the average time
> of SCF procedure of my task is 8 min under 64-bit OS vs 7 min under
> 32-bit OS. Can this problem be binded with installation or work of
> Espresso? If yes, then how to solve it? I asked the developers of
> mpich2 about it, and they couldn't help me. 

i don't think that this is a strange phenomenon at all.
in general, a 64-bit compilation of a code should be expected
to be slower than a 32-bit compilation. all memory pointers
are twice the size and thus require more memory bandwidth and 
incur a reduced cache efficiency.

only, it usually doesn't show so much on x86_64 since the 32-bit 
x86 cpu design is to horribly register starved and AMD doubled 
the number of registers to make up for it. however, if your job
runs only for a few minutes then you may still see the additional
overhead from the larger pointers. for a larger problem, that 
should be reduced. if not, there may be different compilers or
compiler settings.

on non-x86 CPUs a 64-bit mode compilation on codes like Q-E 
is typically about 10-20% slower than a 32-bit compile.

cheers,
   axel.
> 
> regards,
> 
> Alex Mazheika, Research institut for Physical Chemical Problems of
> BSU, Leningradskayastr. 14, 220050 Minsk, Belarus
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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


From marzari at MIT.EDU  Wed Jul 15 16:21:32 2009
From: marzari at MIT.EDU (Nicola Marzari)
Date: Wed, 15 Jul 2009 10:21:32 -0400
Subject: [Pw_forum] Problem in energy conservation in NVE MD using cp.x
In-Reply-To: <60FBF58F-8404-4B7C-A275-EC1286CEFEAF@Princeton.EDU>
References: <4A5C3858.5010100@m.titech.ac.jp> <4A5C73A1.1060504@mit.edu>
	<4A5C774D.9090002@mit.edu>
	<60FBF58F-8404-4B7C-A275-EC1286CEFEAF@Princeton.EDU>
Message-ID: <4A5DE5EC.4090503@mit.edu>




Dear Hiroshi,


thanks again for your observations - it turns out that in recent times 
(years) a small modification had arisen in the way the center of mass
is treated that gave rise (in the very exotic case that you have been
looking at) to the observed behavior. Roberto Car and his group 
(Federico Zipoli and Zhaofeng Li) has also noticed this a few months
ago, but it has percolated back into the code just now.

You can download the working version from the cvs, with these two commands:

cvs -d :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e login
cvs -d :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e checkout espresso

or wait for a few days for the new release of the code, coinciding
with the Santa Barbara school.

If you apply it to your example, you'll notice that the constant
of motion of the CP lagrangian is perfectly conserved, the physical
constant of motion is very well conserved (as it should be), and also
that after a fraction of a ps the water molecule will take up some 
kinetic energy (average around 10K, i.e. osciallting between 0 and 20K)
due to the transfer of momentum between the fictitious system and the
physical one. This is normal, and the relatively large amount is due to
this very unusual case, using on top a lot of plane waves. It would be 
negligible in any large system.

All the best,

			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 sylvian.cadars at cnrs-orleans.fr  Wed Jul 15 16:59:08 2009
From: sylvian.cadars at cnrs-orleans.fr (Sylvian Cadars)
Date: Wed, 15 Jul 2009 16:59:08 +0200
Subject: [Pw_forum] Chosing output file name using the -in/input option
In-Reply-To: <mailman.1592.1247652522.1425.pw_forum@pwscf.org>
References: <mailman.1592.1247652522.1425.pw_forum@pwscf.org>
Message-ID: <4A5DEEBC.50901@cnrs-orleans.fr>

Hi,
Thanks for the solutions you proposed.  I tried most of them, and the 
results are summarized below:
> Is is not impossible, but normally the standard redirection ">" works 
> with (open)mpi out-of-the-box. If you cannot find the output file it 
> may indicate that the working directory used by mpirun is not the 
> directory in which you are looking for the output file; see the 
> "Current Working Directory" section of mpirun manual for details. You 
> can set the working directory explicitly using the option -wd 
> "/path/to/directory" to settle this issue.
I tried, and it does not change anything.  Just to let you know, when I 
do a ssh on each node, I get the same files and directories as on the 
master node (don't know if this helps...).
> Another issue I've had sometime, that could cause problems similar to 
> the one you've had, is related to two conflicting version of mpi. The 
> mpirun instance on the master node tries to start the wrong mpirun on 
> the other nodes. Use the --prefix option to be sure this is not your 
> case (syntax example: "mpirun --prefix /opt/openmpi-1.3.1" without 
> "/bin/")
I have not tried this yet.  I tried to change a few things that I 
believe are related to similar issues and explained on the user guide, 
but I am not sure I did this well (besides, reading it again, it does 
not seem to apply for openMPI, does it?).
http://www.quantum-espresso.org/wiki/index.php/Running_on_parallel_machines#Trouble_with_MKL_and_OpenMP_parallelization
Where are the typical locations where environmental variables are 
changed: my .bashrc file (I am using the bash environment)?  What is the 
correct syntax to do this?
 
> just use " > ". If redirection doesn't work on your system,
> that's another story.
Redirection does not seem to work.

> You can go to PW/startup.f90 and change
>
>   IF ( me_image /= root_image ) &
>      OPEN( UNIT = stdout, FILE = '/dev/null', STATUS = 'UNKNOWN' )
>
> into
>
>   IF ( me_image /= root_image ) THEN
>      OPEN( UNIT = stdout, FILE = '/dev/null', STATUS = 'UNKNOWN' )
>   ELSE
>      OPEN( UNIT = stdout, FILE = 'some_file_name', STATUS = 'UNKNOWN' )
>   END IF
I tried and it seems to work.  PWscf now does write the output in the 
file 'some_file_name'.  So I guess that the idea is then to use the 
command 'mv' in my script to change this file (thus used as a temporary 
file fir each job) to the file name I want.  Am I correct?
Am I then supposed to apply these changes to all the programs I want to 
use (e.g. gipaw.x, band.x, and maybe others) ?

Thanks.

Sylvian.


-- 
------------------------------------------------------------------------
*Dr. Sylvian CADARS*
CEMHTI-CNRS
1D, Av. de la Recherche Scientifique
45071 Orl?ans Cedex 2, France
Fax: +33 (0) 2 38 63 81 03
Tel: +33 (0) 2 38 25 55 04
email: sylvian.cadars at cnrs-orleans.fr
http://www.cemhti.cnrs-orleans.fr/?nom=cadars
------------------------------------------------------------------------
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From pastore at democritos.it  Wed Jul 15 17:13:00 2009
From: pastore at democritos.it (pastore at democritos.it)
Date: Wed, 15 Jul 2009 17:13:00 +0200
Subject: [Pw_forum] Problem in energy conservation in NVE MD using cp.x
In-Reply-To: <4A5C73A1.1060504@mit.edu>
References: <4A5C3858.5010100@m.titech.ac.jp> <4A5C73A1.1060504@mit.edu>
Message-ID: <20090715171300.ubuf3f44w0ogow8g@mail.democritos.it>

Maybe just a few additional comments about this issue may be useful.

Quoting Nicola Marzari <marzari at MIT.EDU>:

>
> CC: Paolo Giannozzi, Carlo Cavazzoni, Roberto Car. Notes below
> also relevant for BO dynamics with pwscf. Please focus on
> the bottom part of the email.
> ...
> I believe the problem is this: you are seeing a transfer of quantity of
> motion between the subset of the ions, and the electronic fictitious
> degrees of freedom. Remember this: the cp lagrangian, when integrated
> correctly (i.e. with a small time step) evolves correctly the full
> dynamical system with all degrees of freedom (physical ionic masses,
> fictitious electronic masses). If there is an electronic gap in your
> system (like here) the two subsets of ions and electrons evolve without
> exchanging energy between each other, and conserving the momentum
> (linear and angular) of the mixed system (ionic + fictitious
> electronic).

Well, the existence of a gap alone is not sufficient to prevent 
transfer of energy from one set of degrees of freedom to another. It is 
also necessary that the gap does not change too much  during the ionic 
evolution (the adiabatic invariant is not the energy of normal modes 
but the ratio energy/frequency,  cfr. formula 28 of the old PRA 28, 
6334 (1991)). I do not think this should be the case for a water 
molecule, if the pseudopotential and the electronic structure are 
reasonable , but it is useful to have in mind such a difference when 
discussing energy transfer issues.

The conserved linear momentum can be evaluated exactly (beware: to the 
electronic term in formula 22 of the above cited PRA,  one  should add 
its complex conjugate, as remarked in Morishita T, Nose S, PRB 59, 
15126 (1999), this last paper was centered on the problem of the 
momentum conservation in CP dynamics.

Periodic boundary conditions prevent angular momentum to be a conserved 
quantity, even for classical simulations, so there is no good reason to 
put constraints on that quantity.

...
> On top of this, the routine that calculates the temperature removes
> the contribution from the motion of the center of mass - it is in
> Modules, so I believe this is also used for pwscf. I believe this
> is never the right thing to do, and maybe this is a good time to
> sort this out.
>

I would not agree with this last point. The physical meaning of 
temperature does not include the center of mass kinetic energy. I can 
remember the very old times  when people using the very first versions 
of CP  code were thinking to have high temperature systems whereas they 
had only  very fast flying clusters!

I would agree with some monitoring of the center of mass motion, but 
without including such a contribution in the ionic physical temperature.

Giorgio

--
Giorgio Pastore - Dipartimento di Fisica Teorica dell' Universita'
                  and CNR-INFM Democritos
                  Strada Costiera 11, 34151 Trieste, Italy
  phone :         + 39 040 2240247   fax: + 39 040 224601
  e-mail:         pastore at ts.infn.it




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


From giannozz at democritos.it  Wed Jul 15 17:31:32 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 15 Jul 2009 17:31:32 +0200
Subject: [Pw_forum] Chosing output file name using the -in/input option
In-Reply-To: <4A5DEEBC.50901@cnrs-orleans.fr>
References: <mailman.1592.1247652522.1425.pw_forum@pwscf.org>
	<4A5DEEBC.50901@cnrs-orleans.fr>
Message-ID: <4A5DF654.20904@democritos.it>

Sylvian Cadars wrote:

> I tried and it seems to work.  PWscf now does write the output in the 
> file 'some_file_name'.  So I guess that the idea is then to use the 
> command 'mv' in my script to change this file (thus used as a temporary 
> file fir each job) to the file name I want.  Am I correct?

I htink so. It would be possible and not too difficult to add
a "-out some_file" option tot pw.x : see flib/inpfile.f90.
Some MPI implementations may have a problem with command line
options, though!

> Am I then supposed to apply these changes to all the programs I want to 
> use (e.g. gipaw.x, band.x, and maybe others) ?

IIRC PW/startup.f90 is called by almost all quantum-espresso
codes

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

From marzari at MIT.EDU  Wed Jul 15 17:45:46 2009
From: marzari at MIT.EDU (Nicola Marzari)
Date: Wed, 15 Jul 2009 11:45:46 -0400
Subject: [Pw_forum] Problem in energy conservation in NVE MD using cp.x
In-Reply-To: <20090715171300.ubuf3f44w0ogow8g@mail.democritos.it>
References: <4A5C3858.5010100@m.titech.ac.jp> <4A5C73A1.1060504@mit.edu>
	<20090715171300.ubuf3f44w0ogow8g@mail.democritos.it>
Message-ID: <4A5DF9AA.8010209@mit.edu>



Hi Giorgio,


thanks for reminding us of the two key papers on this topic - would
be very useful reading for everyone interested in ab-initio md ! Two
quick comments:

pastore at democritos.it wrote:
> Periodic boundary conditions prevent angular momentum to be a conserved 
> quantity, even for classical simulations, so there is no good reason to 
> put constraints on that quantity.

I was thinking at an isolated system - the water molecule of Hiroshi
could start spinning, on top of moving. On the other hand, Roberto et al
pointed out that one should not put constraints in the trajectories
of the CP dynamics - and that is what we just fixed in the cvs today.

I presume the right thing to do would be to clean a posteriori a
trajectory from any cdm linear motion if bulk, and maybe even for
angular momentum if isolated. I believe this is what we were doing in 
the past (with Brandon Wood or Matteo Cococcioni, respectively).

>> On top of this, the routine that calculates the temperature removes
>> the contribution from the motion of the center of mass - it is in
>> Modules, so I believe this is also used for pwscf. I believe this
>> is never the right thing to do, and maybe this is a good time to
>> sort this out.
>>
> 
> I would not agree with this last point. The physical meaning of 
> temperature does not include the center of mass kinetic energy. I can 
> remember the very old times  when people using the very first versions 
> of CP  code were thinking to have high temperature systems whereas they 
> had only  very fast flying clusters!
> 
> I would agree with some monitoring of the center of mass motion, but 
> without including such a contribution in the ionic physical temperature.

I think that the ionic kinetic energy that goes into the Lagrangian,
and into the constant of motion, should include the center of mass
kinetic  energy - and it looks to me that this is what the code is doing
(by calculating ekinp). This is what I had in mind when I wrote the line
above, although I should have used kinetic energy instead of
temperature.

The code prints out the "physical" temperature, with the cdm motion
removed (ekinpr). These are the two aide-by-side subroutines ions_kinene
and ions_temp in ions_base.f90 .

		nic

---------------------------------------------------------------------
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 kazempoor2000 at yahoo.com  Wed Jul 15 17:51:58 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Wed, 15 Jul 2009 08:51:58 -0700 (PDT)
Subject: [Pw_forum] norm conserving
Message-ID: <623289.50100.qm@web112502.mail.gq1.yahoo.com>


Dear all
For first step calculation, we know that the optimization of ecut and kpoint is necessary . But I use norm conserving pseudopotential? that the check of convergency with respect to total energy is time consuming. Is any parameter except total energy that can i put treshold on its convergency or not?
thanks? a lot? 
Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


      
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From kazempoor2000 at yahoo.com  Wed Jul 15 18:58:33 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Wed, 15 Jul 2009 09:58:33 -0700 (PDT)
Subject: [Pw_forum] norm conserving
Message-ID: <612734.4064.qm@web112509.mail.gq1.yahoo.com>


Dear all
For first step calculation, we know that the optimization of ecut and kpoint is necessary . But I use norm conserving pseudopotential? that the check of convergency with respect to total energy is time consuming. Is any parameter except total energy that can i put treshold on its convergency or not?
thanks? a lot? 
Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


      
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From hashemifar at cc.iut.ac.ir  Wed Jul 15 18:53:48 2009
From: hashemifar at cc.iut.ac.ir (Seyed Javad Hashemifar)
Date: Wed, 15 Jul 2009 18:53:48 +0200
Subject: [Pw_forum] norm conserving
In-Reply-To: <623289.50100.qm@web112502.mail.gq1.yahoo.com>
References: <623289.50100.qm@web112502.mail.gq1.yahoo.com>
Message-ID: <2fb18d9f0907150953i341a201dl1e80b2e1bd666404@mail.gmail.com>

Hi Ali
In order to speed up the optimization procedure, it might be possible to
optimize ecut and kpoint in a smaller system. For example if you want to do
any surface or interface supercell calculations, I think it is enough to
optimize ecut in the corresponding bulk materials. About kpoint you have to
be more careful. The bulk optimized kpoint should be transferred to
supercell calculation by taking into account the ratio of lattice
parameters. I mean if a supercell lattice parameter is twice the bulk
lattice parameter, then half of the number of bulk kpoint in the
corresponding direction should be used in the supercell calculation. I think
it is still better to verify the accuracy of kpoint by doing some supercell
calculations in a denser kmesh.
Kind regards
Javad Hashemifar

On Wed, Jul 15, 2009 at 5:51 PM, ali kazempour <kazempoor2000 at yahoo.com>wrote:

>
> Dear all
> For first step calculation, we know that the optimization of ecut and
> kpoint is necessary . But I use norm conserving pseudopotential  that the
> check of convergency with respect to total energy is time consuming. Is any
> parameter except total energy that can i put treshold on its convergency or
> not?
> thanks  a lot
> Ali Kazempour
> Physics department, Isfahan University of Technology
> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733
> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
======================================
Seyed Javad  Hashemifar
Physics Department, Isfahan University of Technology
84156-83111 Isfahan, Iran
Tel: +98 311 391 2375     Fax:+98 311 3912376
Email:  hashemifar at cc.iut.ac.ir
Homepage:  http://hashemifar.iut.ac.ir
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From arvifis at gmail.com  Wed Jul 15 20:32:32 2009
From: arvifis at gmail.com (Arles V. Gil Rebaza)
Date: Wed, 15 Jul 2009 14:32:32 -0400
Subject: [Pw_forum] confirm cdd51d2a6ef538cf2ebd310ab745f2bb27b14e43
In-Reply-To: <mailman.0.1247682298.12678.pw_forum@pwscf.org>
References: <mailman.0.1247682298.12678.pw_forum@pwscf.org>
Message-ID: <de70fddd0907151132t4fabbdc1tfdc3d551993d740a@mail.gmail.com>

Dear pwscf users,
Has anybody got fully relativistic pseudopoential for Fe and N?
I've many due for th generations of PP. Please anyboby can send me this PP
with fully relativistic...!!

I will be grateful for any help.


-- 
###--------->   Arles V.   <---------###
La Plata - Argentina
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From arvifis at gmail.com  Wed Jul 15 20:35:55 2009
From: arvifis at gmail.com (Arles V. Gil Rebaza)
Date: Wed, 15 Jul 2009 14:35:55 -0400
Subject: [Pw_forum] Full Relativistic PP for Fe and N...!!!
Message-ID: <de70fddd0907151135r28ebd2a4ida1db324eb3cb09f@mail.gmail.com>

---------- Forwarded message ----------
From: Arles V. Gil Rebaza <arvifis at gmail.com>
Date: 2009/7/15
Subject: Re: confirm cdd51d2a6ef538cf2ebd310ab745f2bb27b14e43
To: pw_forum at pwscf.org


Dear pwscf users,
Has anybody got fully relativistic pseudopoential for Fe and N?
I've many due for th generations of PP. Please anyboby can send me this PP
with fully relativistic (norm converving)...!!

I will be grateful for any help.


-- 
###--------->   Arles V.   <---------###
La Plata - Argentina



-- 
###--------->   Arles V.   <---------###
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From wshen02 at gmail.com  Wed Jul 15 21:27:41 2009
From: wshen02 at gmail.com (=?UTF-8?B?5paH5rKI?=)
Date: Wed, 15 Jul 2009 12:27:41 -0700
Subject: [Pw_forum] Dear All, question about the wannier90 use
Message-ID: <2c9df8a80907151227k6e337df0u5ad4d08d9dfacc8c@mail.gmail.com>

Dear All,
Currently I am trying to use Wannier 90 code under Quantum espresso folder
to calculate the overlaps between different orbitals  for different atoms.
What I find in the W90 tutorial is that it produce a .mmn file to give the
overlap matrix in k space. But what I need is the overlaps for different
orbitals rather than the total overlaps.
Anybody has  the experience to use Wannier 90 code to calculate the overlaps
for different orbitals in real space? Please help


Wen Shen
Ph.D candidate
Gerogetown University
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From sakuma.h.aa at m.titech.ac.jp  Thu Jul 16 00:47:29 2009
From: sakuma.h.aa at m.titech.ac.jp (SAKUMA Hiroshi)
Date: Thu, 16 Jul 2009 07:47:29 +0900
Subject: [Pw_forum] Problem in energy conservation in NVE MD using cp.x
Message-ID: <4A5E5C81.2060209@m.titech.ac.jp>

Dear Nicola,

Thanks for your kind explanation.
I will use the working version from the cvs and the new release of the code.

Best regards,

hiroshi

- 
Department of Earth & Planetary Sciences
Graduate School of Science & Engineering
Tokyo Institute of Technology
2-12-1 Ookayama Meguro-ku Tokyo 1528551
Kawamura Lab.
Tel: +81-3-5734-2617



Nicola wrote:

>Dear Hiroshi,


>thanks again for your observations - it turns out that in recent times 
>(years) a small modification had arisen in the way the center of mass
>is treated that gave rise (in the very exotic case that you have been
>looking at) to the observed behavior. Roberto Car and his group 
>(Federico Zipoli and Zhaofeng Li) has also noticed this a few months
>ago, but it has percolated back into the code just now.

>You can download the working version from the cvs, with these two >commands:

>cvs -d :pserver:anonymous at scm.qe-forge.org <http://www.democritos.it/mailman/listinfo/pw_forum>:/cvsroot/q-e login
>cvs -d :pserver:anonymous at scm.qe-forge.org <http://www.democritos.it/mailman/listinfo/pw_forum>:/cvsroot/q-e checkout >espresso

>or wait for a few days for the new release of the code, coinciding
>with the Santa Barbara school.

>If you apply it to your example, you'll notice that the constant
>of motion of the CP lagrangian is perfectly conserved, the physical
>constant of motion is very well conserved (as it should be), and also
>that after a fraction of a ps the water molecule will take up some 

>kinetic energy (average around 10K, i.e. osciallting between 0 and 20K)
>due to the transfer of momentum between the fictitious system and the
>physical one. This is normal, and the relatively large amount is due to
>this very unusual case, using on top a lot of plane waves. It would be 
>negligible in any large system.

>All the best,

>			nicola




From pushpajnc at gmail.com  Thu Jul 16 02:19:36 2009
From: pushpajnc at gmail.com (pushpa raghani)
Date: Wed, 15 Jul 2009 17:19:36 -0700
Subject: [Pw_forum] Errors in PS-KS equation
In-Reply-To: <f40d6a250907131253p2e4f1137m2624a85c80544101@mail.gmail.com>
References: <f40d6a250907131253p2e4f1137m2624a85c80544101@mail.gmail.com>
Message-ID: <f40d6a250907151719r5ea0e789v81ab5d12e58a292a@mail.gmail.com>

Dear Paolo,
I did try with rho0 as 0.01 and also 0.02 but still it gives the error
"Errors in PS-KS equation". I also tried the Troullier-Martins pseudization
instead of RRKJ but that also gives the same problem. Any ideas?

Thanks,
Pushpa

On Mon, Jul 13, 2009 at 12:53 PM, pushpa raghani <pushpajnc at gmail.com>wrote:

> Dear all,
> I have to generate a fully relativistic pseudopotential for Ti. Since it is
> the first time I do this job, I thought of first generating a SR pp and
> match it with the available Ti.pbe-sp-van_ak.UPF.
>
> I am getting an error "phi has nodes before r_c". Following is my input
> file. When I increase the value of rcut from 1.0 to 1.2, above error goes
> away and I get different error of "Errors in PS-KS equation". Any
> suggestions?
>
> &input
>     title='Ti',
>     zed=22.,
>     rel=1,
>     config='[Ne] 3s2.0 3p6 3d2.0 4s2.0',
>     iswitch=3,
>     dft='PBE'
>  /
>  &inputp
>    lloc=0,
>    pseudotype=3,
>    file_pseudopw='Ti.pbe-rrkjus.UPF',
>    nlcc=.f.,
>    rcore=0.9,
>  /
> 5
> 3P  3  1  6.00  0.00  1.00  1.80  1
> 3P  3  1  0.00 -0.30  1.00  1.80  1
> 3D  3  2  2.00  0.00  1.00  1.80  1
> 3S  3  0  2.00  0.00  1.00  1.80  1
> 4S  4  0  2.00  0.00  1.00  1.80  1
>
>  Many Thanks,
> Pushpa
> (Stanford University)
>
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From marzari at MIT.EDU  Thu Jul 16 07:43:09 2009
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 16 Jul 2009 01:43:09 -0400
Subject: [Pw_forum] Dear All, question about the wannier90 use
In-Reply-To: <2c9df8a80907151227k6e337df0u5ad4d08d9dfacc8c@mail.gmail.com>
References: <2c9df8a80907151227k6e337df0u5ad4d08d9dfacc8c@mail.gmail.com>
Message-ID: <4A5EBDED.4080402@mit.edu>

?? wrote:
> Dear All,
> Currently I am trying to use Wannier 90 code under Quantum espresso 
> folder to calculate the overlaps between different orbitals  for 
> different atoms.
> What I find in the W90 tutorial is that it produce a .mmn file to give 
> the overlap matrix in k space. But what I need is the overlaps for 
> different orbitals rather than the total overlaps.
> Anybody has  the experience to use Wannier 90 code to calculate the 
> overlaps for different orbitals in real space? Please help


Dear Wen,


can you detail better with orbitals are you referring to ?

Mmn are <u_mk|u_nk'>, where u_mk is the periodic part of the Bloch 
eigenstate for band m, k-point k. Localized orbitals such as Wannier 
functions are orthogonal - zero overlap.

				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 alex.mazheika at gmail.com  Thu Jul 16 11:21:20 2009
From: alex.mazheika at gmail.com (Alexej Mazheika)
Date: Thu, 16 Jul 2009 12:21:20 +0300
Subject: [Pw_forum] a problem with 64-bit OS by multiprocess calculation
In-Reply-To: <ec86c07d0907150318g609ae307y82cd93539d67c5be@mail.gmail.com>
References: <ec86c07d0907150318g609ae307y82cd93539d67c5be@mail.gmail.com>
Message-ID: <ec86c07d0907160221y173a314cm74d5c9dc5e698648@mail.gmail.com>

>
> i don't think that this is a strange phenomenon at all.
> in general, a 64-bit compilation of a code should be expected
> to be slower than a 32-bit compilation. all memory pointers
> are twice the size and thus require more memory bandwidth and
> incur a reduced cache efficiency.
>
> only, it usually doesn't show so much on x86_64 since the 32-bit
> x86 cpu design is to horribly register starved and AMD doubled
> the number of registers to make up for it. however, if your job
> runs only for a few minutes then you may still see the additional
> overhead from the larger pointers. for a larger problem, that
> should be reduced. if not, there may be different compilers or
> compiler settings.
>
> on non-x86 CPUs a 64-bit mode compilation on codes like Q-E
> is typically about 10-20% slower than a 32-bit compile.
>
> cheers,
> axel.
>

Thank you for explaination of the reason of my problem. The time-difference
is not so much, so I think I won't undertake anything. With various compiler
settings I experimented by compilation but it didn't bring any considerable
results.

regards,
Alex
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From kazempoor2000 at yahoo.com  Thu Jul 16 11:24:36 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Thu, 16 Jul 2009 02:24:36 -0700 (PDT)
Subject: [Pw_forum] opium
Message-ID: <12557.8877.qm@web112512.mail.gq1.yahoo.com>

Dear all
Is it possible to convert the opium pseudopotential ti UPF?
thanks a lot

Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


      
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From giannozz at democritos.it  Thu Jul 16 11:30:07 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 16 Jul 2009 11:30:07 +0200
Subject: [Pw_forum] opium
In-Reply-To: <12557.8877.qm@web112512.mail.gq1.yahoo.com>
References: <12557.8877.qm@web112512.mail.gq1.yahoo.com>
Message-ID: <4A5EF31F.7020104@democritos.it>

ali kazempour wrote:

> Is it possible to convert the opium pseudopotential ti UPF?

opium can write PPs in the "old" file format used by PWscf.
This format is still supported, or else it can be converted
using ncpp2upf

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

From kazempoor2000 at yahoo.com  Thu Jul 16 12:59:06 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Thu, 16 Jul 2009 03:59:06 -0700 (PDT)
Subject: [Pw_forum] opiu
Message-ID: <940905.37147.qm@web112517.mail.gq1.yahoo.com>


Dear Paolo
I use ncpp2upf in espresso-4.0.5 but this is the error :
#################################
from read_ncpp:error # 1
pseudo file is empty or wrong
#################################

Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


      
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From giannozz at democritos.it  Thu Jul 16 13:04:54 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 16 Jul 2009 13:04:54 +0200
Subject: [Pw_forum] opiu
In-Reply-To: <940905.37147.qm@web112517.mail.gq1.yahoo.com>
References: <940905.37147.qm@web112517.mail.gq1.yahoo.com>
Message-ID: <4A5F0956.5000401@democritos.it>

ali kazempour wrote:

> I use ncpp2upf in espresso-4.0.5 but this is the error :
> #################################
> from read_ncpp:error # 1
> pseudo file is empty or wrong

you have the error, try to figure out what is the reason.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From bipulrr at gmail.com  Thu Jul 16 15:16:56 2009
From: bipulrr at gmail.com (Bipul Rakshit)
Date: Thu, 16 Jul 2009 18:46:56 +0530
Subject: [Pw_forum] about elastic constant
Message-ID: <3a749910907160616m3874bc03taa942263b0c291c2@mail.gmail.com>

Dear PWSCF users,
In the paper of S Q Wang et al. J Phys. Cond. Matter 15 (2003) 5307,
(attached with this mail)
He uses three types of strains

1. Tri-axial shear strain to calculate C44
2. volume conservative orthorombic strain to calculate shear modulus C`
and
3. Hydrostatic pressure to calculate Bulk modulus.

In my calculations, on applying the 3rd strain, I am getting different
volumes for different set of strained lattice vectors (Volume non-conserve)
and 1st & 2nd type volume remain same (volume conserved)


Because in order to calculate 3 elastic constants (C11, C12 and C44) we
require 3 equations, so do I have to use the above three equations, both
type (volume conservative and non-conservative) to calculate a single set of
elastic constants?

please guide me for the same.

-- 
Bipul Rakshit
PhD Student,
Barkatullah University,
Bhopal 462026,
MP, India
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From ejwalt at wm.edu  Thu Jul 16 16:42:20 2009
From: ejwalt at wm.edu (Eric J. Walter)
Date: Thu, 16 Jul 2009 10:42:20 -0400
Subject: [Pw_forum] opium
In-Reply-To: <4A5EF31F.7020104@democritos.it>
References: <12557.8877.qm@web112512.mail.gq1.yahoo.com>
	<4A5EF31F.7020104@democritos.it>
Message-ID: <4A5F3C4C.6050701@wm.edu>


Hi,

I have found that the fhi format converts to UPF much more easily using 
fhi2upf.x. 
But, you must remove the footer part of the fhi file before trying to 
convert it.  By footer,
I mean the copy of the param file at the end.

Just a suggestion.

Eric




Paolo Giannozzi wrote:
> ali kazempour wrote:
>
>   
>> Is it possible to convert the opium pseudopotential ti UPF?
>>     
>
> opium can write PPs in the "old" file format used by PWscf.
> This format is still supported, or else it can be converted
> using ncpp2upf
>
> P.
>   


From rcjhawk at gmail.com  Thu Jul 16 18:57:56 2009
From: rcjhawk at gmail.com (Michael Mehl)
Date: Thu, 16 Jul 2009 12:57:56 -0400
Subject: [Pw_forum] about elastic constant
In-Reply-To: <3a749910907160616m3874bc03taa942263b0c291c2@mail.gmail.com>
References: <3a749910907160616m3874bc03taa942263b0c291c2@mail.gmail.com>
Message-ID: <4A5F5C14.5090009@gmail.com>

Bipul Rakshit wrote:

> Because in order to calculate 3 elastic constants (C11, C12 and C44) we 
> require 3 equations, so do I have to use the above three equations, both 
> type (volume conservative and non-conservative) to calculate a single 
> set of elastic constants?

Yes.

> 
> please guide me for the same.

You'll have to compute the bulk modulus at same volume that you use to 
compute C44 and C11-C12.  In a cubic system B = (C11+2 C12)/3, giving 
you enough information to get all three elastic constants at that volume.

There are many, many programs that will compute B(V), see this list's 
archives for details.

My favorite reviews of the subject are:

http://cst-www.nrl.navy.mil/users/mehl/papers/cij453.pdf

and

Phys. Rev. B 47, 2493 (1993)

but I may be somewhat biased.

-- 
Michael J. Mehl, Naval Research Laboratory, Washington DC
On Sabbatical at Duke University until 31 July 2009

From bipulrr at gmail.com  Thu Jul 16 20:25:57 2009
From: bipulrr at gmail.com (Bipul Rakshit)
Date: Thu, 16 Jul 2009 23:55:57 +0530
Subject: [Pw_forum] about elastic constant
In-Reply-To: <4A5F5C14.5090009@gmail.com>
References: <3a749910907160616m3874bc03taa942263b0c291c2@mail.gmail.com>
	<4A5F5C14.5090009@gmail.com>
Message-ID: <3a749910907161125g110b968bv516d9ad2d06665c4@mail.gmail.com>

Dear Michael Mehl,
I have read the two papers
http://cst-www.nrl.navy.mil/users/mehl/papers/cij453.pdf

and

Phys. Rev. B 47, 2493 (1993)
,
But my question is, they have given only two equation, and our unknown
quantity are 3 (C11, C12, and C44). So can we find three unknown quantity
from two equations acuratelly.



On Thu, Jul 16, 2009 at 10:27 PM, Michael Mehl <rcjhawk at gmail.com> wrote:

> Bipul Rakshit wrote:
>
> > Because in order to calculate 3 elastic constants (C11, C12 and C44) we
> > require 3 equations, so do I have to use the above three equations, both
> > type (volume conservative and non-conservative) to calculate a single
> > set of elastic constants?
>
> Yes.
>
> >
> > please guide me for the same.
>
> You'll have to compute the bulk modulus at same volume that you use to
> compute C44 and C11-C12.  In a cubic system B = (C11+2 C12)/3, giving
> you enough information to get all three elastic constants at that volume.
>
> There are many, many programs that will compute B(V), see this list's
> archives for details.
>
> My favorite reviews of the subject are:
>
> http://cst-www.nrl.navy.mil/users/mehl/papers/cij453.pdf
>
> and
>
> Phys. Rev. B 47, 2493 (1993)
>
> but I may be somewhat biased.
>
> --
> Michael J. Mehl, Naval Research Laboratory, Washington DC
> On Sabbatical at Duke University until 31 July 2009
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Bipul Rakshit
PhD Student,
Barkatullah University,
Bhopal 462026,
MP, India
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From rcjhawk at gmail.com  Thu Jul 16 22:57:38 2009
From: rcjhawk at gmail.com (Michael Mehl)
Date: Thu, 16 Jul 2009 16:57:38 -0400
Subject: [Pw_forum] about elastic constant
In-Reply-To: <3a749910907161125g110b968bv516d9ad2d06665c4@mail.gmail.com>
References: <3a749910907160616m3874bc03taa942263b0c291c2@mail.gmail.com>	<4A5F5C14.5090009@gmail.com>
	<3a749910907161125g110b968bv516d9ad2d06665c4@mail.gmail.com>
Message-ID: <4A5F9442.8060008@gmail.com>

Bipul Rakshit wrote:

> Dear Michael Mehl,
> I have read the two papers
> http://cst-www.nrl.navy.mil/users/mehl/papers/cij453.pdf
> 
> and
> 
> Phys. Rev. B 47, 2493 (1993)
> ,
> But my question is, they have given only two equation, and our unknown 
> quantity are 3 (C11, C12, and C44). So can we find three unknown 
> quantity from two equations acuratelly.

C44 is computed directly.

C' = C11-C12, or maybe 1/2 (C11-C12).

For a cubic crystal, B = (C11 + 2 C12)/3.

That's three equations for three unknowns.

C44 and C' are computed as outlined in Wang's paper, my papers, and 
elsewhere.  The bulk modulus is obtained from

B = V E''(V),

and you can compute the second derivative of the energy by finding the 
energy at several volumes and either using one of the many 
equation-of-state fitting codes available, or via numerical differentiation.

--
Michael J. Mehl, Naval Research Laboratory, Washington DC
On Sabbatical at Duke University until 31 July 2009

From wshen02 at gmail.com  Fri Jul 17 00:43:34 2009
From: wshen02 at gmail.com (=?UTF-8?B?5paH5rKI?=)
Date: Thu, 16 Jul 2009 15:43:34 -0700
Subject: [Pw_forum] Dear All, question about the wannier90 use
In-Reply-To: <4A5EBDED.4080402@mit.edu>
References: <2c9df8a80907151227k6e337df0u5ad4d08d9dfacc8c@mail.gmail.com>
	<4A5EBDED.4080402@mit.edu>
Message-ID: <2c9df8a80907161543waae16f6pc5b9b132242c7e68@mail.gmail.com>

Dear Nicola,
Thanks for your reply.
What I want to do is the calculate the different orbital overlap. I mean for
example for Ti atom, I want to know how to calculate the Wannier function
for dz2 orbital and dxy orbital and then to calculate the overlap between
these orbitals, not only the total d orbitals.

besides,
I read through the output file for wannier90, I find that inside it there
are a number of wavefunctions which is stated with WF centre and spread. If
you know what is these WFs, please explain this to me.


A lot of Thanks!

Wen

On Wed, Jul 15, 2009 at 10:43 PM, Nicola Marzari <marzari at mit.edu> wrote:

> ?? wrote:
> > Dear All,
> > Currently I am trying to use Wannier 90 code under Quantum espresso
> > folder to calculate the overlaps between different orbitals  for
> > different atoms.
> > What I find in the W90 tutorial is that it produce a .mmn file to give
> > the overlap matrix in k space. But what I need is the overlaps for
> > different orbitals rather than the total overlaps.
> > Anybody has  the experience to use Wannier 90 code to calculate the
> > overlaps for different orbitals in real space? Please help
>
>
> Dear Wen,
>
>
> can you detail better with orbitals are you referring to ?
>
> Mmn are <u_mk|u_nk'>, where u_mk is the periodic part of the Bloch
> eigenstate for band m, k-point k. Localized orbitals such as Wannier
> functions are orthogonal - zero overlap.
>
>                                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 trinh.vo at jpl.nasa.gov  Fri Jul 17 02:47:25 2009
From: trinh.vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Thu, 16 Jul 2009 17:47:25 -0700
Subject: [Pw_forum] nsfd
Message-ID: <63E24D720DCE7246ABAA722B52D23CDF0153D2B3CEEE@ALTPHYEMBEVSP10.RES.AD.JPL>

Dear PWSCF Users,

I am using QE-ver 4.0.3 on my cluster.  I submitted one job from the the 2nd node (I call the head node as the 1st node).  This job used 40CPUs, with the distribution being 5 nodes (nodes #3 to #9, and 6CPUs/node) and 1 node (node #10, and 4CPUs/node).  When I used 'top' command on node#2 to see the jobs listing, memory uses,...I usually saw lines of 'nsfd' appear on the 'Command' column.  What 'nsfd' means?

The reason I have this question is that the machine is usually slower (i.e. hangs up for 20 seconds or more) if I submit a 2nd job from node#2, but use other nodes (say nodes #11 to 17).  Having this 2nd job running at the same time with the 1st job, I saw more 'nsfd' lines appear, and the machine is slower.  I appreciate if you could explain to me what "nsfd" means.

Thank you,

Trinh Vo

HCCP Group
Jet Propulsion Laboratory/CalTech
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From bipulrr at gmail.com  Fri Jul 17 09:16:11 2009
From: bipulrr at gmail.com (Bipul Rakshit)
Date: Fri, 17 Jul 2009 12:46:11 +0530
Subject: [Pw_forum] about elastic constant
In-Reply-To: <4A5F9442.8060008@gmail.com>
References: <3a749910907160616m3874bc03taa942263b0c291c2@mail.gmail.com>
	<4A5F5C14.5090009@gmail.com>
	<3a749910907161125g110b968bv516d9ad2d06665c4@mail.gmail.com>
	<4A5F9442.8060008@gmail.com>
Message-ID: <3a749910907170016ib389bbck10b06cebe4d71a24@mail.gmail.com>

Dear Michael Mehl,
I am calculating elastic constant of Mg2Si (C11=126, C12=26, C44=48)
experimental.
Now using the formula by S. Q. Wang, H. Q. Ye, J. Phys. condense matter.
using all the three equation, i am getting, 109, 25, 47 (C11,  C12, C44)
respectively.

But using only Eq. (6) and (7) only, I am getting 121, 20, 47 GPa,
So can you please elaborate, whether, by using two equations, and by fitting
the graphs, is it correct to find all the three elastic constants?

On Fri, Jul 17, 2009 at 2:27 AM, Michael Mehl <rcjhawk at gmail.com> wrote:

> Bipul Rakshit wrote:
>
> > Dear Michael Mehl,
> > I have read the two papers
> > http://cst-www.nrl.navy.mil/users/mehl/papers/cij453.pdf
> >
> > and
> >
> > Phys. Rev. B 47, 2493 (1993)
> > ,
> > But my question is, they have given only two equation, and our unknown
> > quantity are 3 (C11, C12, and C44). So can we find three unknown
> > quantity from two equations acuratelly.
>
> C44 is computed directly.
>
> C' = C11-C12, or maybe 1/2 (C11-C12).
>
> For a cubic crystal, B = (C11 + 2 C12)/3.
>
> That's three equations for three unknowns.
>
> C44 and C' are computed as outlined in Wang's paper, my papers, and
> elsewhere.  The bulk modulus is obtained from
>
> B = V E''(V),
>
> and you can compute the second derivative of the energy by finding the
> energy at several volumes and either using one of the many
> equation-of-state fitting codes available, or via numerical
> differentiation.
>
> --
> Michael J. Mehl, Naval Research Laboratory, Washington DC
> On Sabbatical at Duke University until 31 July 2009
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Bipul Rakshit
PhD Student,
Barkatullah University,
Bhopal 462026,
MP, India
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From decboy9 at gmail.com  Fri Jul 17 10:58:18 2009
From: decboy9 at gmail.com (dev sharma)
Date: Fri, 17 Jul 2009 14:28:18 +0530
Subject: [Pw_forum] B2cb Space Group
Message-ID: <a591fe200907170158kcb1be6bg35bbc2437a5f62db@mail.gmail.com>

Hi all,
 Can any body tell ibrav for B2cb and B1a1 space group.
Thanks


Dev Sharma,
JRF
University of Delhi
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From giannozz at democritos.it  Fri Jul 17 11:32:39 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 17 Jul 2009 11:32:39 +0200
Subject: [Pw_forum] nsfd
In-Reply-To: <63E24D720DCE7246ABAA722B52D23CDF0153D2B3CEEE@ALTPHYEMBEVSP10.RES.AD.JPL>
References: <63E24D720DCE7246ABAA722B52D23CDF0153D2B3CEEE@ALTPHYEMBEVSP10.RES.AD.JPL>
Message-ID: <B5CCD636-02FB-4A86-A61D-612A3E076ABF@democritos.it>

On Jul 17, 2009, at 2:47 , Vo, Trinh (388C) wrote:
> I usually saw lines of ?nsfd? appear on the ?Command? column.  What  
> ?nsfd? means?
>
"National Science Foundation daemon". It checks how you are spending the
taxpayer's money, terminates your NSF grant if you are wasting it :-)

Seriously: it is "nfsd", it stands for "network file system daemon",  
it means that
you are performing heavy I/O via the network, using the nfs software.
This is something you should avoid as much as possible.

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




From decboy9 at gmail.com  Fri Jul 17 12:36:55 2009
From: decboy9 at gmail.com (dev sharma)
Date: Fri, 17 Jul 2009 16:06:55 +0530
Subject: [Pw_forum] Bismuth Titanate Structure
In-Reply-To: <a591fe200907170037g3cf6dd09iff69ef5dce91a947@mail.gmail.com>
References: <a591fe200907170037g3cf6dd09iff69ef5dce91a947@mail.gmail.com>
Message-ID: <a591fe200907170336q12a08248med7967c111a5870a@mail.gmail.com>

Hi all,

I am new to PWscf and XCrysden. My Input file for Bismuth Titanate is below.
The output structure in XCRYSden window is seemed to be right but it is
giving mssg ......... typed below. Please help or give suggestion.

Number of Atoms:  133
Number of Frames: 12
WARNING: Atom 1 and atom 12 are very close !!!
         Atom 12 deleted !!!
WARNING: Atom 2 and atom 122 are very close !!!
         Atom 122 deleted !!!
WARNING: Atom 3 and atom 14 are very close !!!
         Atom 14 deleted !!!
WARNING: Atom 4 and atom 123 are very close !!!
         Atom 123 deleted !!!
WARNING: Atom 5 and atom 16 are very close !!!
         Atom 16 deleted !!!
WARNING: Atom 6 and atom 124 are very close !!!
         Atom 124 deleted !!!......
.........................................................
......

 and because of this PWScf  SCF run stops and gives the mssg wrong atomic
co-ordinates.


 &control
    calculation='scf',
    restart_mode='from_scratch',
    prefix='bit'
    pseudo_dir = '/home/physics/pseudo/',
    outdir='/home/physics/work/bit/temp'
 /
 &system
    ibrav = 7, a=3.86334, b= 3.86334, c=33.2942
, nat =38, ntyp= 3,
    ecutwfc = 60.0,ecutrho=200,
   occupations='smearing', smearing    = "methfessel-paxton", degauss=0.01,

 /
 &electrons
    mixing_beta = 0.50
    conv_thr =  1.0e-6
/
 &ions
 /

ATOMIC_SPECIES
  Bi     208.980     Bi.pbe-d-mt.UPF
  Ti      47.867       Ti.pbe-sp-van_ak.UPF
  O     15.9994      O.pbe-van_ak.UPF
ATOMIC_POSITIONS {bohr}
Bi             3.65032726386637    3.65032726386637    4.24815040995715
Bi             3.65032726386637    3.65032726386637   13.30504053709336
Ti             3.65032726386637    3.65032726386637   23.32581852937194
O             3.65032726386637    3.65032726386637   27.75265329698888
O             3.65032726386637    3.65032726386637   19.74332980289407
Bi             0.00000000000000    0.00000000000000   35.70661018533794
Bi             0.00000000000000    0.00000000000000   44.76350031247415
Ti             0.00000000000000    0.00000000000000   54.78427830475272
O             0.00000000000000    0.00000000000000   -3.70580647839191
O             0.00000000000000    0.00000000000000   51.20178957827486
Bi             3.65032726386637    3.65032726386637      58.66876914080443
Bi             3.65032726386637    3.65032726386637      49.61187901366822
Ti              3.65032726386637    3.65032726386637     39.59110102138964
O             3.65032726386637    3.65032726386637      35.16426625377269
O             3.65032726386637    3.65032726386637      43.17358974786750
Bi             0.00000000000000    0.00000000000000   27.21030936542364
Bi             0.00000000000000    0.00000000000000   18.15341923828743
Ti              0.00000000000000    0.00000000000000    8.13264124600885
O             0.00000000000000    0.00000000000000    3.70580647839191
O              0.00000000000000    0.00000000000000   11.71512997248671
Ti              3.65032726386637    3.65032726386637   31.45845977538078
Ti              0.00000000000000    0.00000000000000    0.00000000000000
O             3.65032726386637    0.00000000000000    0.00000000000000
O             0.00000000000000    3.65032726386637   31.45845977538078
O             0.00000000000000    3.65032726386637    0.00000000000000
O             3.65032726386637    0.00000000000000   31.45845977538078
O             3.65032726386637    0.00000000000000   15.72922988769039
O             0.00000000000000    3.65032726386637   15.72922988769039
O             3.65032726386637    0.00000000000000   47.18768966307118
O             0.00000000000000    3.65032726386637   47.18768966307118
O             3.65032726386637    0.00000000000000    7.40406298501923
O             0.00000000000000    3.65032726386637   38.86252276040002
O             0.00000000000000    3.65032726386637    7.40406298501923
O             3.65032726386637    0.00000000000000   38.86252276040002
O             3.65032726386637    0.00000000000000   55.51285656574235
O             0.00000000000000    3.65032726386637   24.05439679036155
O             0.00000000000000    3.65032726386637   55.51285656574235
O             3.65032726386637    0.00000000000000   24.05439679036155

K_POINTS {automatic}
  4 4 1 0 0 0
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From giannozz at democritos.it  Fri Jul 17 12:56:19 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 17 Jul 2009 12:56:19 +0200
Subject: [Pw_forum] Bismuth Titanate Structure
In-Reply-To: <a591fe200907170336q12a08248med7967c111a5870a@mail.gmail.com>
References: <a591fe200907170037g3cf6dd09iff69ef5dce91a947@mail.gmail.com>
	<a591fe200907170336q12a08248med7967c111a5870a@mail.gmail.com>
Message-ID: <17FBEB29-7F12-4140-8DAB-A175F3E3A84D@democritos.it>


On Jul 17, 2009, at 12:36 , dev sharma wrote:

> The output structure in XCRYSden window is seemed to be right

but it isn't. The messages below mean one thing: your data is
wrong. Remember that a,b,c are in ANGSTROM, and that the
lattice vectors are those described in the documentation and
reprinted on output (i.e. not necessarily the axis you like)

> WARNING: Atom 1 and atom 12 are very close !!!
>          Atom 12 deleted !!!
> WARNING: Atom 2 and atom 122 are very close !!!
>          Atom 122 deleted !!!
> WARNING: Atom 3 and atom 14 are very close !!!
>          Atom 14 deleted !!!
> WARNING: Atom 4 and atom 123 are very close !!!
>          Atom 123 deleted !!!
> WARNING: Atom 5 and atom 16 are very close !!!
>          Atom 16 deleted !!!
> WARNING: Atom 6 and atom 124 are very close !!!
>          Atom 124 deleted !!!......


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




From decboy9 at gmail.com  Fri Jul 17 13:16:22 2009
From: decboy9 at gmail.com (dev sharma)
Date: Fri, 17 Jul 2009 16:46:22 +0530
Subject: [Pw_forum] Bismuth Titanate Structure
In-Reply-To: <17FBEB29-7F12-4140-8DAB-A175F3E3A84D@democritos.it>
References: <a591fe200907170037g3cf6dd09iff69ef5dce91a947@mail.gmail.com>
	<a591fe200907170336q12a08248med7967c111a5870a@mail.gmail.com>
	<17FBEB29-7F12-4140-8DAB-A175F3E3A84D@democritos.it>
Message-ID: <a591fe200907170416k38aa5879wcf7d11bb387a1ee6@mail.gmail.com>

Dear Sir,
 Please tell how to resolve this problems as i am sure about the position of
atoms.. My a, b, c are also in Angstrom. Secondly, when i am running the
same file through PWGui, it is giving error---- wrong number of columns.How
to proceed further.

Thanks

On Fri, Jul 17, 2009 at 4:26 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Jul 17, 2009, at 12:36 , dev sharma wrote:
>
> > The output structure in XCRYSden window is seemed to be right
>
> but it isn't. The messages below mean one thing: your data is
> wrong. Remember that a,b,c are in ANGSTROM, and that the
> lattice vectors are those described in the documentation and
> reprinted on output (i.e. not necessarily the axis you like)
>
> > WARNING: Atom 1 and atom 12 are very close !!!
> >          Atom 12 deleted !!!
> > WARNING: Atom 2 and atom 122 are very close !!!
> >          Atom 122 deleted !!!
> > WARNING: Atom 3 and atom 14 are very close !!!
> >          Atom 14 deleted !!!
> > WARNING: Atom 4 and atom 123 are very close !!!
> >          Atom 123 deleted !!!
> > WARNING: Atom 5 and atom 16 are very close !!!
> >          Atom 16 deleted !!!
> > WARNING: Atom 6 and atom 124 are very close !!!
> >          Atom 124 deleted !!!......
>
>
> Paolo
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From Giovanni.Cantele at na.infn.it  Fri Jul 17 14:52:31 2009
From: Giovanni.Cantele at na.infn.it (Giovanni Cantele)
Date: Fri, 17 Jul 2009 14:52:31 +0200
Subject: [Pw_forum] Bismuth Titanate Structure
In-Reply-To: <a591fe200907170416k38aa5879wcf7d11bb387a1ee6@mail.gmail.com>
References: <a591fe200907170037g3cf6dd09iff69ef5dce91a947@mail.gmail.com>	<a591fe200907170336q12a08248med7967c111a5870a@mail.gmail.com>	<17FBEB29-7F12-4140-8DAB-A175F3E3A84D@democritos.it>
	<a591fe200907170416k38aa5879wcf7d11bb387a1ee6@mail.gmail.com>
Message-ID: <4A60740F.6010105@na.infn.it>

Let' consider the Bi atoms:
Bi             3.65032726386637    3.65032726386637    4.24815040995715
Bi             3.65032726386637    3.65032726386637   13.30504053709336
Bi             0.00000000000000    0.00000000000000   18.15341923828743
Bi             0.00000000000000    0.00000000000000   27.21030936542364
Bi             0.00000000000000    0.00000000000000   35.70661018533794
Bi             0.00000000000000    0.00000000000000   44.76350031247415
Bi             3.65032726386637    3.65032726386637      49.61187901366822
Bi             3.65032726386637    3.65032726386637      58.66876914080443

which I label from 1 to 8.

Now, you chose ibrav=7 which corresponds to a Tetragonal I (bct) whose 
lattice vectors are chosen, within QE,
as ( see Doc/INPUT_PW* ):

body centered tetragonal (i)
                   ================================
                      v1 = (a/2)(1,-1,c/a),  v2 = (a/2)(1,1,c/a),  v3 = 
(a/2)(-1,-1,c/a)

If we do explicitly write these vectors in bohr we get:
v1=  (  3.6503, -3.6503, 31.458 )
v2 = (  3.6503,  3.6503, 31.458 )
v3 = ( -3.6503, -3.6503, 31.458 )

Now, let's consider the
Bi             0.00000000000000    0.00000000000000   35.70661018533794
and add to it a crystal translation, in particular -v3. We get the new 
(equivalent) position
( 3.6503, 3.6503, 35.7066-31.458) = ( 3.6503, 3.6503, 4.2486)
which is exactly the same as the position of the first atom.

Therefore, (unless I did something wrong!) either you chose a wrong 
ibrav, or you specified wrong units, or you gave in input wrong atomic 
coordinates.

Also consider that your input file setting:
ecutwfc = 60.0,ecutrho=200,
is wrong because ecutrho = N * ecutwfc where N=4 if you use only norm 
conserving PPs, while N>4 if your calc. included US
PPs (as in your case).

Hope this helps,

    Giovanni

dev sharma wrote:
> Dear Sir,
>  Please tell how to resolve this problems as i am sure about the 
> position of atoms.. My a, b, c are also in Angstrom. Secondly, when i 
> am running the same file through PWGui, it is giving error---- wrong 
> number of columns.How to proceed further.
>
> Thanks
>
> On Fri, Jul 17, 2009 at 4:26 PM, Paolo Giannozzi 
> <giannozz at democritos.it <mailto:giannozz at democritos.it>> wrote:
>
>
>     On Jul 17, 2009, at 12:36 , dev sharma wrote:
>
>     > The output structure in XCRYSden window is seemed to be right
>
>     but it isn't. The messages below mean one thing: your data is
>     wrong. Remember that a,b,c are in ANGSTROM, and that the
>     lattice vectors are those described in the documentation and
>     reprinted on output (i.e. not necessarily the axis you like)
>
>     > WARNING: Atom 1 and atom 12 are very close !!!
>     >          Atom 12 deleted !!!
>     > WARNING: Atom 2 and atom 122 are very close !!!
>     >          Atom 122 deleted !!!
>     > WARNING: Atom 3 and atom 14 are very close !!!
>     >          Atom 14 deleted !!!
>     > WARNING: Atom 4 and atom 123 are very close !!!
>     >          Atom 123 deleted !!!
>     > WARNING: Atom 5 and atom 16 are very close !!!
>     >          Atom 16 deleted !!!
>     > WARNING: Atom 6 and atom 124 are very close !!!
>     >          Atom 124 deleted !!!......
>
>
>     Paolo
>     ---
>     Paolo Giannozzi, Dept of Physics, University of Udine
>     via delle Scienze 208, 33100 Udine, Italy
>     Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 



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


From marzari at MIT.EDU  Fri Jul 17 17:18:51 2009
From: marzari at MIT.EDU (Nicola Marzari)
Date: Fri, 17 Jul 2009 11:18:51 -0400
Subject: [Pw_forum] Dear All, question about the wannier90 use
In-Reply-To: <2c9df8a80907161543waae16f6pc5b9b132242c7e68@mail.gmail.com>
References: <2c9df8a80907151227k6e337df0u5ad4d08d9dfacc8c@mail.gmail.com>	<4A5EBDED.4080402@mit.edu>
	<2c9df8a80907161543waae16f6pc5b9b132242c7e68@mail.gmail.com>
Message-ID: <4A60965B.5090109@mit.edu>

?? wrote:
> Dear Nicola,
> Thanks for your reply.
> What I want to do is the calculate the different orbital overlap. I mean 
> for example for Ti atom, I want to know how to calculate the Wannier 
> function for dz2 orbital and dxy orbital and then to calculate the 
> overlap between these orbitals, not only the total d orbitals.


They are orthogonal - zero overlap.

> besides,
> I read through the output file for wannier90, I find that inside it 
> there are a number of wavefunctions which is stated with WF centre and 
> spread. If you know what is these WFs, please explain this to me.

you need to read the manual, or the 1997 prb. those are the spreads
and centers of the wannier functions.

			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 wshen02 at gmail.com  Fri Jul 17 19:19:39 2009
From: wshen02 at gmail.com (=?UTF-8?B?5paH5rKI?=)
Date: Fri, 17 Jul 2009 10:19:39 -0700
Subject: [Pw_forum] Dear All, question about the wannier90 use
In-Reply-To: <4A60965B.5090109@mit.edu>
References: <2c9df8a80907151227k6e337df0u5ad4d08d9dfacc8c@mail.gmail.com>
	<4A5EBDED.4080402@mit.edu>
	<2c9df8a80907161543waae16f6pc5b9b132242c7e68@mail.gmail.com>
	<4A60965B.5090109@mit.edu>
Message-ID: <2c9df8a80907171019x771c2047qd9977bfd705ad087@mail.gmail.com>

Thanks Nicola,
So you mean in the real space, if we use wannier function instead of plane
wave, there will be no overlap in real space? This will mean no exchange
coupling when using wannier function, is this correct?

best

Wen
On Fri, Jul 17, 2009 at 8:18 AM, Nicola Marzari <marzari at mit.edu> wrote:

> ?? wrote:
> > Dear Nicola,
> > Thanks for your reply.
> > What I want to do is the calculate the different orbital overlap. I mean
> > for example for Ti atom, I want to know how to calculate the Wannier
> > function for dz2 orbital and dxy orbital and then to calculate the
> > overlap between these orbitals, not only the total d orbitals.
>
>
> They are orthogonal - zero overlap.
>
> > besides,
> > I read through the output file for wannier90, I find that inside it
> > there are a number of wavefunctions which is stated with WF centre and
> > spread. If you know what is these WFs, please explain this to me.
>
> you need to read the manual, or the 1997 prb. those are the spreads
> and centers of the wannier functions.
>
>                        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 giannozz at democritos.it  Fri Jul 17 20:53:57 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 17 Jul 2009 20:53:57 +0200
Subject: [Pw_forum] Errors in PS-KS equation
In-Reply-To: <f40d6a250907151719r5ea0e789v81ab5d12e58a292a@mail.gmail.com>
References: <f40d6a250907131253p2e4f1137m2624a85c80544101@mail.gmail.com>
	<f40d6a250907151719r5ea0e789v81ab5d12e58a292a@mail.gmail.com>
Message-ID: <00600DBC-C249-4E7B-8E6E-05098AD21CFE@democritos.it>


On Jul 16, 2009, at 2:19 , pushpa raghani wrote:

> I did try with rho0 as 0.01 and also 0.02 but still it gives
> the error "Errors in PS-KS equation". [....] Any ideas?

"Errors in PS-KS equation" is a polite way to say "your
pseudopotential is bad". Generating a pseudopotential,
especially a nonstandard one like yours (ultrasoft and
with semicore states) may be tricky (do you really need
3s and 3p semicore states?) You should start from the
simpler configuration and the simpler generation
method and move step by step and one thing at the
time towards the most complicated object you manage
to generate.

See the attached sequence of files:
ti0 = norm-conserving, s local, single projector (simple,
you have to experiment a bit with core radii)
ti1 = norm-conserving, s local, two projectors for p and d
(you have to experiment a little bit with energies of the
second atomic wave)
ti2 = ultrasoft, one s, two p and two d projectors (this is
trickier, you have to experiment a little bit with US core
radii, local potential, etc; no warranty the pseudopotential
you get bear any resemblance with real Ti)
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--
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From sunyang198498 at gmail.com  Sat Jul 18 01:20:22 2009
From: sunyang198498 at gmail.com (=?GB2312?B?y+/R9A==?=)
Date: Fri, 17 Jul 2009 18:20:22 -0500
Subject: [Pw_forum] Stoner parameter estimation
Message-ID: <98e7a0810907171620g2ffef341oc0d3bcff678f9f3@mail.gmail.com>

Hi, Has anybody used pwscf to estimate the Stoner parameter.
I want do this simple test for my system. I start with the Palladium
bulk, using the fixing moment calculation, and then get the difference
of the total energy and the single particle energy as a function of the
fixed moment, which is supposed to be magnetic energy, 0.25*I*M^2.
So, we could get the Stoner parameter. The result I got is quite not
reasonable. I would ask if this way is reasonable?

Thank you,


Yang

-- 
University of Nebraska at Lincoln
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From trinh.vo at jpl.nasa.gov  Sat Jul 18 04:00:54 2009
From: trinh.vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Fri, 17 Jul 2009 19:00:54 -0700
Subject: [Pw_forum] nsfd
In-Reply-To: <B5CCD636-02FB-4A86-A61D-612A3E076ABF@democritos.it>
Message-ID: <C6867AE6.20F7%Trinh.Vo@jpl.nasa.gov>

Hi Paolo,

Thank you for your message.

I understand now (hope it is correct).   Since we do not have Parallel File system on our cluster, all I/O via the network are used.  One  option now is probably to write directly on local scratch disk to avoid NSF.  (I do not like this option very much).  In your opinion, is it possible to add the Parallel File System to an existing cluster?

Trinh


On 7/17/09 2:32 AM, "Paolo Giannozzi" <giannozz at democritos.it> wrote:

On Jul 17, 2009, at 2:47 , Vo, Trinh (388C) wrote:
> I usually saw lines of 'nsfd' appear on the 'Command' column.  What
> 'nsfd' means?
>
"National Science Foundation daemon". It checks how you are spending the
taxpayer's money, terminates your NSF grant if you are wasting it :-)

Seriously: it is "nfsd", it stands for "network file system daemon",
it means that
you are performing heavy I/O via the network, using the nfs software.
This is something you should avoid as much as possible.

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



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

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From akohlmey at cmm.chem.upenn.edu  Sat Jul 18 04:49:28 2009
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Fri, 17 Jul 2009 22:49:28 -0400
Subject: [Pw_forum] nsfd
In-Reply-To: <C6867AE6.20F7%Trinh.Vo@jpl.nasa.gov>
References: <C6867AE6.20F7%Trinh.Vo@jpl.nasa.gov>
Message-ID: <1247885368.2840.6985.camel@zero>

On Fri, 2009-07-17 at 19:00 -0700, Vo, Trinh (388C) wrote:
> Hi Paolo,
> 
> Thank you for your message.  
> 
> I understand now (hope it is correct).   Since we do not have Parallel
> File system on our cluster, all I/O via the network are used.  One
> option now is probably to write directly on local scratch disk to
> avoid NSF.  (I do not like this option very much).  In your opinion,
> is it possible to add the Parallel File System to an existing cluster?

yes. but it is an administrative nightmare. if you still 
confuse NFS with NSF, then you should not get into it.
regardless, using a local scratch is _much_ better and
needs to additional configuration.

cheers,
   axel.

>   
> 
> Trinh   
> 
> 
> On 7/17/09 2:32 AM, "Paolo Giannozzi" <giannozz at democritos.it> wrote:
> 
>         On Jul 17, 2009, at 2:47 , Vo, Trinh (388C) wrote:
>         > I usually saw lines of ?nsfd? appear on the ?Command?
>         column.  What 
>         > ?nsfd? means?
>         >
>         "National Science Foundation daemon". It checks how you are
>         spending the
>         taxpayer's money, terminates your NSF grant if you are wasting
>         it :-)
>         
>         Seriously: it is "nfsd", it stands for "network file system
>         daemon", 
>         it means that
>         you are performing heavy I/O via the network, using the nfs
>         software.
>         This is something you should avoid as much as possible.
>         
>         Paolo
>         ---
>         Paolo Giannozzi, Dept of Physics, University of Udine
>         via delle Scienze 208, 33100 Udine, Italy
>         Phone +39-0432-558216, fax +39-0432-558222
>         
>         
>         
>         _______________________________________________
>         Pw_forum mailing list
>         Pw_forum at pwscf.org
>         http://www.democritos.it/mailman/listinfo/pw_forum
>         
> _______________________________________________
> 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 trinh.vo at jpl.nasa.gov  Sat Jul 18 05:42:29 2009
From: trinh.vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Fri, 17 Jul 2009 20:42:29 -0700
Subject: [Pw_forum] nsfd
In-Reply-To: <1247885368.2840.6985.camel@zero>
Message-ID: <C68692B5.20FB%Trinh.Vo@jpl.nasa.gov>

Hi Axel,

Thank you!
Honestly, I am ignorant in this area, and I am trying to pick up little by little.

Trinh

P.S.  I am sorry, I don't know why I was haunted by the word "NSF".  :-).   Paolo pointed out, but I kept repeating it.




On 7/17/09 7:49 PM, "Axel Kohlmeyer" <akohlmey at cmm.chem.upenn.edu> wrote:

On Fri, 2009-07-17 at 19:00 -0700, Vo, Trinh (388C) wrote:
> Hi Paolo,
>
> Thank you for your message.
>
> I understand now (hope it is correct).   Since we do not have Parallel
> File system on our cluster, all I/O via the network are used.  One
> option now is probably to write directly on local scratch disk to
> avoid NSF.  (I do not like this option very much).  In your opinion,
> is it possible to add the Parallel File System to an existing cluster?

yes. but it is an administrative nightmare. if you still
confuse NFS with NSF, then you should not get into it.
regardless, using a local scratch is _much_ better and
needs to additional configuration.

cheers,
   axel.

>
>
> Trinh
>
>
> On 7/17/09 2:32 AM, "Paolo Giannozzi" <giannozz at democritos.it> wrote:
>
>         On Jul 17, 2009, at 2:47 , Vo, Trinh (388C) wrote:
>         > I usually saw lines of 'nsfd' appear on the 'Command'
>         column.  What
>         > 'nsfd' means?
>         >
>         "National Science Foundation daemon". It checks how you are
>         spending the
>         taxpayer's money, terminates your NSF grant if you are wasting
>         it :-)
>
>         Seriously: it is "nfsd", it stands for "network file system
>         daemon",
>         it means that
>         you are performing heavy I/O via the network, using the nfs
>         software.
>         This is something you should avoid as much as possible.
>
>         Paolo
>         ---
>         Paolo Giannozzi, Dept of Physics, University of Udine
>         via delle Scienze 208, 33100 Udine, Italy
>         Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>         _______________________________________________
>         Pw_forum mailing list
>         Pw_forum at pwscf.org
>         http://www.democritos.it/mailman/listinfo/pw_forum
>
> _______________________________________________
> 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.

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

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From physolde at yahoo.fr  Sun Jul 19 00:51:46 2009
From: physolde at yahoo.fr (kada galami)
Date: Sat, 18 Jul 2009 22:51:46 +0000 (GMT)
Subject: [Pw_forum] run_example
Message-ID: <968902.62295.qm@web26604.mail.ukl.yahoo.com>

dear users

when i try to run_examples i found this 

physolde at linux-0jjw:~/espresso-4.0.5/examples/example06> ./run_example

/home/physolde/espresso-4.0.5/examples/example06 : starting

This example shows how to calculate interatomic force constants in
real space for AlAs in zincblende structure.

? executables directory: /home/physolde/espresso-4.0.5/bin
? pseudo directory:????? /home/physolde/espresso-4.0.5/pseudo
? temporary directory:?? /home/physolde/tmp
? checking that needed directories and files exist...
ERROR: /home/physolde/espresso-4.0.5/bin/pw.x not existent or not executable
Aborting
i use oppensuse 11






      
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From rdmeneze at yahoo.com.br  Sun Jul 19 01:00:38 2009
From: rdmeneze at yahoo.com.br (Rafael Dias Menezes)
Date: Sat, 18 Jul 2009 16:00:38 -0700 (PDT)
Subject: [Pw_forum] run_example
Message-ID: <427990.32114.qm@web65710.mail.ac4.yahoo.com>

Dear Kada,

You must verify id the directory  /home/physolde/espresso-4.0.5/bin/pw.x? exist.



--- Em s?b, 18/7/09, kada galami <physolde at yahoo.fr> escreveu:

De: kada galami <physolde at yahoo.fr>
Assunto: [Pw_forum] run_example
Para: pw_forum at pwscf.org
Data: S?bado, 18 de Julho de 2009, 19:51

dear users

when i try to run_examples i found this 

physolde at linux-0jjw:~/espresso-4.0.5/examples/example06> ./run_example

/home/physolde/espresso-4.0.5/examples/example06 : starting

This example shows how to calculate interatomic force constants in
real space for AlAs in zincblende structure.

? executables directory: /home/physolde/espresso-4.0.5/bin
? pseudo directory:????? /home/physolde/espresso-4.0.5/pseudo
? temporary directory:?? /home/physolde/tmp
? checking that needed directories and files exist...
ERROR: /home/physolde/espresso-4.0.5/bin/pw.x not existent or not executable
Aborting
i use oppensuse 11








      
-----Anexo incorporado-----

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



      ____________________________________________________________________________________
Veja quais s?o os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com
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From yccheng.nju at gmail.com  Sun Jul 19 03:29:35 2009
From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=)
Date: Sun, 19 Jul 2009 09:29:35 +0800
Subject: [Pw_forum] run_example
In-Reply-To: <968902.62295.qm@web26604.mail.ukl.yahoo.com>
References: <968902.62295.qm@web26604.mail.ukl.yahoo.com>
Message-ID: <da7526cb0907181829j10cb7cd0u24c7ae19ace601d8@mail.gmail.com>

You should compile pw.x first.

2009/7/19 kada galami <physolde at yahoo.fr>

>   dear users
>
> when i try to run_examples i found this
>
> physolde at linux-0jjw:~/espresso-4.0.5/examples/example06> ./run_example
>
> /home/physolde/espresso-4.0.5/examples/example06 : starting
>
> This example shows how to calculate interatomic force constants in
> real space for AlAs in zincblende structure.
>
>   executables directory: /home/physolde/espresso-4.0.5/bin
>   pseudo directory:      /home/physolde/espresso-4.0.5/pseudo
>   temporary directory:   /home/physolde/tmp
>   checking that needed directories and files exist...
> ERROR: /home/physolde/espresso-4.0.5/bin/pw.x not existent or not
> executable
> Aborting
> i use oppensuse 11
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Y. C. Cheng
Department of Physics
Nanjing University
Nanjing 210093
P. R. China
Tel: 86-25-83592907
Email: yccheng.nju at gmail.com
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From nedward at MIT.EDU  Sun Jul 19 15:59:04 2009
From: nedward at MIT.EDU (Nicholas E. Singh-Miller)
Date: Sun, 19 Jul 2009 09:59:04 -0400 (EDT)
Subject: [Pw_forum] Stoner parameter estimation
In-Reply-To: <98e7a0810907171620g2ffef341oc0d3bcff678f9f3@mail.gmail.com>
References: <98e7a0810907171620g2ffef341oc0d3bcff678f9f3@mail.gmail.com>
Message-ID: <Pine.GSO.4.64L.0907190954520.19317@department-of-alchemy.mit.edu>

Hi Yang,

Never did any Stoner parameter calculations.  But just a heads up, if you 
are using GGA(PBE) the ground state of bulk Pd is found to be magnetic.

A few references to this end are:

S. S. Alexandre, M. Mattesini, J. M. Soler, and F. Yndurain, Phys. Rev. 
Lett. 96, 079701 (2006).

D. A. Stewart, J. Appl. Phys. 101, 09D503 (2007).

-Nick



On Fri, 17 Jul 2009, ???? wrote:

> Hi, Has anybody used pwscf to estimate the Stoner parameter.
> I want do this simple test for my system. I start with the Palladium
> bulk, using the fixing moment calculation, and then get the difference
> of the total energy and the single particle energy as a function of the
> fixed moment, which is supposed to be magnetic energy, 0.25*I*M^2.
> So, we could get the Stoner parameter. The result I got is quite not
> reasonable. I would ask if this way is reasonable?
>
> Thank you,
>
>
> Yang
>
>

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

From sunyang198498 at gmail.com  Sun Jul 19 16:55:03 2009
From: sunyang198498 at gmail.com (=?GB2312?B?y+/R9A==?=)
Date: Sun, 19 Jul 2009 09:55:03 -0500
Subject: [Pw_forum] Stoner parameter estimation
In-Reply-To: <Pine.GSO.4.64L.0907190954520.19317@department-of-alchemy.mit.edu>
References: <98e7a0810907171620g2ffef341oc0d3bcff678f9f3@mail.gmail.com>
	<Pine.GSO.4.64L.0907190954520.19317@department-of-alchemy.mit.edu>
Message-ID: <98e7a0810907190755x4da0da83k6b2ec4f76dfe2bfa@mail.gmail.com>

Thanks, Nicholas, It seems that our goal is to expore the technique
for estimating the Stoner parameter for some specific atom in any
structure, not only for the bulk. Your help is great!

Yang

2009/7/19 Nicholas E. Singh-Miller <nedward at mit.edu>

> Hi Yang,
>
> Never did any Stoner parameter calculations.  But just a heads up, if you
> are using GGA(PBE) the ground state of bulk Pd is found to be magnetic.
>
> A few references to this end are:
>
> S. S. Alexandre, M. Mattesini, J. M. Soler, and F. Yndurain, Phys. Rev.
> Lett. 96, 079701 (2006).
>
> D. A. Stewart, J. Appl. Phys. 101, 09D503 (2007).
>
> -Nick
>
>
>
>
> On Fri, 17 Jul 2009, ?? wrote:
>
> Hi, Has anybody used pwscf to estimate the Stoner parameter.
>> I want do this simple test for my system. I start with the Palladium
>> bulk, using the fixing moment calculation, and then get the difference
>> of the total energy and the single particle energy as a function of the
>> fixed moment, which is supposed to be magnetic energy, 0.25*I*M^2.
>> So, we could get the Stoner parameter. The result I got is quite not
>> reasonable. I would ask if this way is reasonable?
>>
>> Thank you,
>>
>>
>> Yang
>>
>>
>>
> *****************************************
> Nicholas E. Singh-Miller
> Prof. Marzari Group (quasiamore.mit.edu)
> Materials Science and Engineering
> Massachusetts Institute of Technology
> 13-4066
> (617)324-0372
> *****************************************
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
University of Nebraska at Lincoln
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From cyrille.barreteau at cea.fr  Sun Jul 19 18:27:37 2009
From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille)
Date: Sun, 19 Jul 2009 18:27:37 +0200
Subject: [Pw_forum] =?iso-8859-1?q?RE=A0=3A__Stoner_parameter_estimation?=
References: <98e7a0810907171620g2ffef341oc0d3bcff678f9f3@mail.gmail.com>
Message-ID: <18E4AC9C2FAC504E994A6759DE5ABE8D949B04@DIODON.extra.cea.fr>

Dear Yang,

A way to estimate the Stoner parameter is to do a series of scf calculations at several
lattice parameters (without any constraint). For the value of the lattice parameter at which the magnetsim just appears the Stoner criterion is exactly fulfilled, i.e. In(Ef)=1.
Where n(Ef) is the density of states at the Fermi level (and per spin).
In this way you can evaluate I from n(Ef).

best wishes

  cyrille


==================================================================
Cyrille Barreteau  | phone : +33 (0)1 69 08 29 51
CEA Saclay         | fax   : +33 (0)1 69 08 84 46
DSM/IRAMIS/SPCSI   | email cyrille.barreteau at cea.fr
Batiment 462       |
91191 Gif sur Yvette Cedex  FRANCE
           ~~~~~~~~~~~~~~~~~~~~~~~~
http://iramis.cea.fr/Images/Pisp/cbarreteau/cbarreteau_fr.html
==================================================================



-------- Message d'origine--------
De: pw_forum-bounces at pwscf.org de la part de ??
Date: sam. 7/18/2009 01:20
?: PWSCF Forum
Objet : [Pw_forum] Stoner parameter estimation
 
Hi, Has anybody used pwscf to estimate the Stoner parameter.
I want do this simple test for my system. I start with the Palladium
bulk, using the fixing moment calculation, and then get the difference
of the total energy and the single particle energy as a function of the
fixed moment, which is supposed to be magnetic energy, 0.25*I*M^2.
So, we could get the Stoner parameter. The result I got is quite not
reasonable. I would ask if this way is reasonable?

Thank you,


Yang

-- 
University of Nebraska at Lincoln

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From lanhaiping at gmail.com  Mon Jul 20 05:49:51 2009
From: lanhaiping at gmail.com (lan haiping)
Date: Mon, 20 Jul 2009 11:49:51 +0800
Subject: [Pw_forum] failure with NCPP
Message-ID: <c92002fa0907192049g7f3ddc07pa131cb3902539cbe@mail.gmail.com>

Dear All,

  I tried to examine ZnO's properties with norm-conserving pseudopotetials,
but the calculation was crashed with
"
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from read_ncpp : error #         1
     order of wavefunctions
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

"

My pseudopotentials were generated by opium package 3.0.3 with Professor
Rappe's input settings, and  QE is 4.0.4 version.
I wonder  whether QE still support NCPP format or other special
consideration needs to take into for opium's pp ?

regards

Hai-Ping
-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From xomiakk at gmail.com  Mon Jul 20 10:11:03 2009
From: xomiakk at gmail.com (Olga Sedelnikova)
Date: Mon, 20 Jul 2009 15:11:03 +0700
Subject: [Pw_forum] epsilon calculation
Message-ID: <ff62e3f0907200111o375fcb02j778a71a17e287ca6@mail.gmail.com>

Dear PWScf Users,
I try to do the dielectric tensor calculations. At first I did the
scf-calculation after that I used the code epsilon.x. This code didn't find
files created by the scf calculation (*.save in outdir).
Why such a problem occurs?

My input files is as following:

: scf

  &CONTROL
    calculation='scf'
    restart_mode='from_scratch',
    prefix='gr'
    pseudo_dir = '/home/olya/espresso-4.0.3/pseudo/',
    outdir='/home/olya/espresso-4.0.3/work/eps/tmp/'
  /
   &SYSTEM
     ibrav = 0,
     celldm(1)= 1.0
     nat = 4,
     ntyp = 1,
     ecutwfc = 16.0,
     nbnd = 16,
   /
   &ELECTRONS
     conv_thr =  1.0d-8
     mixing_beta = 0.7
   /
   ATOMIC_SPECIES
   C 12.011000  C.pz-vbc.UPF
   CELL_PARAMETERS
   4.0279528  2.325539  0.000000
   4.0269528 -2.325539  0.000000
   0.000000   0.000000 12.62333
   ATOMIC_POSITIONS angstrom
   C     0      0.00000  0.000000
   C  0.333333   0.3333333  0.000000
   C  0.000000     0.000000   0.5000000
   C     0.6666666666    -0.3333333  0.5000000
K_POINTS {automatic}
18 18 18 0 0 0

: epsilon

&inputpp
    outdir='home/olya/espresso-4.0.3/work/eps/tmp/'
    prefix='gr'
    calculation='eps'
/
&energy_grid
    smeartype='gauss'
    intersmear=0.1360d0
    intrasmear=0.0d0
    wmax=30.0d0
    wmin=0.0d0
    nw=600
    shift=0.0d0
/

error:

     from pp_check_file : error #         2
     file home/olya/espresso-4.0.3/work/eps/tmp/gr.save not found



Thank you.

Best wishes,
Olga
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From giannozz at democritos.it  Mon Jul 20 10:20:26 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 20 Jul 2009 10:20:26 +0200
Subject: [Pw_forum] epsilon calculation
In-Reply-To: <ff62e3f0907200111o375fcb02j778a71a17e287ca6@mail.gmail.com>
References: <ff62e3f0907200111o375fcb02j778a71a17e287ca6@mail.gmail.com>
Message-ID: <4A6428CA.7020703@democritos.it>

Olga Sedelnikova wrote:

>     outdir='/home/olya/espresso-4.0.3/work/eps/tmp/'

>     outdir='home/olya/espresso-4.0.3/work/eps/tmp/'

"the devil is in the details"
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Mon Jul 20 10:49:12 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 20 Jul 2009 10:49:12 +0200
Subject: [Pw_forum] failure with NCPP
In-Reply-To: <c92002fa0907192049g7f3ddc07pa131cb3902539cbe@mail.gmail.com>
References: <c92002fa0907192049g7f3ddc07pa131cb3902539cbe@mail.gmail.com>
Message-ID: <4A642F88.5000401@democritos.it>

lan haiping wrote:

> I wonder  whether QE still support NCPP format

it does, otherwise it would have issued a different message

> or other special consideration needs to take into for opium's pp ?

atomic wavefunctions should be in order of increasing l.
Not sure why this is needed and whethere it is really needed.

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

From lanhaiping at gmail.com  Mon Jul 20 14:28:57 2009
From: lanhaiping at gmail.com (lan haiping)
Date: Mon, 20 Jul 2009 20:28:57 +0800
Subject: [Pw_forum] failure with NCPP
In-Reply-To: <4A642F88.5000401@democritos.it>
References: <c92002fa0907192049g7f3ddc07pa131cb3902539cbe@mail.gmail.com>
	<4A642F88.5000401@democritos.it>
Message-ID: <c92002fa0907200528t15c1dd8er9437468c24ea76d6@mail.gmail.com>

Dear Paolo,
Thanks .
I then check input settings for opium ,  and find the wavefunctions are
already arranged by increasing 'l'.
 The setting for Zn  pseudopotential  is following:
"
[Atom]
Zn
8                   # norb: number of orbitals
100  2.00  -        # nlm occ eigen(- means auto-generate)
200  2.00  -
210  6.00  -
300  2.00  -
310  6.00  -
400  1.50  -
410  0.00  -
320  10.00  -

[Pseudo]
3  1.87 1.85 1.97
opt

[Optinfo]
7.07 10
7.07 10
7.07 10
[XC]
gga               # lda[PZ] or gga[PBE]

[KBdesign]
0                 # local orb
1                # number of aug. operators
au 0.1 1.60 -3.05  # unit(gp or au)  left  right  height(Ry)
[Loginfo]
0
2.0 -4.0 4.0
"
and for O is
"
[Atom]
O
3
100   2.00   -
200   2.00   -
210   4.00   -
[Pseudo]
2  1.34 1.53
opt
[Optinfo]
7.07  10
7.07  10
conmax
[XC]
gga
"

I donot know why these PP cannot be read by pw.x .
By the way, is there any simple method to use  opium's settings  in
ld1.x   ?


Regards,

Hai-Ping


On Mon, Jul 20, 2009 at 4:49 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

> lan haiping wrote:
>
> > I wonder  whether QE still support NCPP format
>
> it does, otherwise it would have issued a different message
>
> > or other special consideration needs to take into for opium's pp ?
>
> atomic wavefunctions should be in order of increasing l.
> Not sure why this is needed and whethere it is really needed.
>
> P.
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From lshulenburger at ciw.edu  Mon Jul 20 16:38:49 2009
From: lshulenburger at ciw.edu (Luke Shulenburger)
Date: Mon, 20 Jul 2009 10:38:49 -0400
Subject: [Pw_forum] failure with NCPP
In-Reply-To: <c92002fa0907200528t15c1dd8er9437468c24ea76d6@mail.gmail.com>
References: <c92002fa0907192049g7f3ddc07pa131cb3902539cbe@mail.gmail.com>
	<4A642F88.5000401@democritos.it>
	<c92002fa0907200528t15c1dd8er9437468c24ea76d6@mail.gmail.com>
Message-ID: <b74576e70907200738n146ba4aes46dd7c1d0d986120@mail.gmail.com>

Hello,

I took a quick look at these pseudopotentials.  The first thing I
found is that the problem seems to be related to  the augmentation
functions.  I removed the second and third line after KBdesign in the
Zn input and the potential loads into pwscf without issue.  I haven't
used augmentation functions much, so I'm not sure quite what the
problem is.  I know Eric Walter looks at this list from time to time,
perhaps he could comment on the reason for this.  The other thing is
that the the output from opium for the Zn pseudopotential looks
somewhat strange.  As an example, the plots of the ionic potential are
not very smooth at all and there are large kinks near the origin which
will likely result an a very high plane wave cutoff being necessary to
get converged results.  Has this potential been tested?

Sincerely,
Luke Shulenburger
(lshulenburger at ciw.edu)
Geophysical Laboratory
Carnegie Institution of Washington
5251 Broad Branch Rd. NW
Washington, DC 20015


On Mon, Jul 20, 2009 at 8:28 AM, lan haiping<lanhaiping at gmail.com> wrote:
> Dear Paolo,
> Thanks .
> I then check input settings for opium ,? and find the wavefunctions are
> already arranged by increasing 'l'.
> ?The setting for Zn? pseudopotential? is following:
> "
> [Atom]
> Zn
> 8?????????????????? # norb: number of orbitals
> 100? 2.00? -??????? # nlm occ eigen(- means auto-generate)
> 200? 2.00? -
> 210? 6.00? -
> 300? 2.00? -
> 310? 6.00? -
> 400? 1.50? -
> 410? 0.00? -
> 320? 10.00? -
>
> [Pseudo]
> 3? 1.87 1.85 1.97
> opt
>
> [Optinfo]
> 7.07 10
> 7.07 10
> 7.07 10
> [XC]
> gga?????????????? # lda[PZ] or gga[PBE]
>
> [KBdesign]
> 0???????????????? # local orb
> 1??????????????? # number of aug. operators
> au 0.1 1.60 -3.05? # unit(gp or au)? left? right? height(Ry)
> [Loginfo]
> 0
> 2.0 -4.0 4.0
> "
> and for O is
> "
> [Atom]
> O
> 3
> 100?? 2.00?? -
> 200?? 2.00?? -
> 210?? 4.00?? -
> [Pseudo]
> 2? 1.34 1.53
> opt
> [Optinfo]
> 7.07? 10
> 7.07? 10
> conmax
> [XC]
> gga
> "
>
> I donot know why these PP cannot be read by pw.x .
> By the way, is there any simple method to use? opium's settings? in
> ld1.x?? ?
>
>
> Regards,
>
> Hai-Ping
>
>
> On Mon, Jul 20, 2009 at 4:49 PM, Paolo Giannozzi <giannozz at democritos.it>
> wrote:
>>
>> lan haiping wrote:
>>
>> > I wonder ?whether QE still support NCPP format
>>
>> it does, otherwise it would have issued a different message
>>
>> > or other special consideration needs to take into for opium's pp ?
>>
>> atomic wavefunctions should be in order of increasing l.
>> Not sure why this is needed and whethere it is really needed.
>>
>> P.
>> --
>> Paolo Giannozzi, Democritos and University of Udine, Italy
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> --
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871
> lanhaiping at gmail.com, hplan at pku.edu.cn
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

From ejwalt at wm.edu  Mon Jul 20 16:44:26 2009
From: ejwalt at wm.edu (Eric J. Walter)
Date: Mon, 20 Jul 2009 10:44:26 -0400
Subject: [Pw_forum] failure with NCPP
In-Reply-To: <c92002fa0907200528t15c1dd8er9437468c24ea76d6@mail.gmail.com>
References: <c92002fa0907192049g7f3ddc07pa131cb3902539cbe@mail.gmail.com>	<4A642F88.5000401@democritos.it>
	<c92002fa0907200528t15c1dd8er9437468c24ea76d6@mail.gmail.com>
Message-ID: <4A6482CA.407@wm.edu>


Ian,

Does fhi2upf work if you start with the fhi output and strip off the 
param file at the end?

I can try this myself later.

Eric






lan haiping wrote:
> Dear Paolo,
> Thanks .
> I then check input settings for opium ,  and find the wavefunctions 
> are already arranged by increasing 'l'.
>  The setting for Zn  pseudopotential  is following:
> "
> [Atom]
> Zn
> 8                   # norb: number of orbitals
> 100  2.00  -        # nlm occ eigen(- means auto-generate)
> 200  2.00  -
> 210  6.00  -
> 300  2.00  -
> 310  6.00  -
> 400  1.50  -
> 410  0.00  -
> 320  10.00  -
>
> [Pseudo]
> 3  1.87 1.85 1.97
> opt
>
> [Optinfo]
> 7.07 10
> 7.07 10
> 7.07 10
> [XC]
> gga               # lda[PZ] or gga[PBE]
>
> [KBdesign]
> 0                 # local orb
> 1                # number of aug. operators
> au 0.1 1.60 -3.05  # unit(gp or au)  left  right  height(Ry)
> [Loginfo]
> 0
> 2.0 -4.0 4.0
> "
> and for O is
> "
> [Atom]
> O 
> 3
> 100   2.00   -
> 200   2.00   -
> 210   4.00   -
> [Pseudo]
> 2  1.34 1.53
> opt
> [Optinfo]
> 7.07  10
> 7.07  10
> conmax
> [XC]
> gga
> "
>
> I donot know why these PP cannot be read by pw.x . 
> By the way, is there any simple method to use  opium's settings  in   
> ld1.x   ?
>
>
> Regards,
>
> Hai-Ping
>
>
> On Mon, Jul 20, 2009 at 4:49 PM, Paolo Giannozzi 
> <giannozz at democritos.it <mailto:giannozz at democritos.it>> wrote:
>
>     lan haiping wrote:
>
>     > I wonder  whether QE still support NCPP format
>
>     it does, otherwise it would have issued a different message
>
>     > or other special consideration needs to take into for opium's pp ?
>
>     atomic wavefunctions should be in order of increasing l.
>     Not sure why this is needed and whethere it is really needed.
>
>     P.
>     --
>     Paolo Giannozzi, Democritos and University of Udine, Italy
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> -- 
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871
> lanhaiping at gmail.com <mailto:lanhaiping at gmail.com>, hplan at pku.edu.cn 
> <mailto:hplan at pku.edu.cn>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From lanhaiping at gmail.com  Mon Jul 20 17:11:36 2009
From: lanhaiping at gmail.com (lan haiping)
Date: Mon, 20 Jul 2009 23:11:36 +0800
Subject: [Pw_forum] failure with NCPP
In-Reply-To: <b74576e70907200738n146ba4aes46dd7c1d0d986120@mail.gmail.com>
References: <c92002fa0907192049g7f3ddc07pa131cb3902539cbe@mail.gmail.com>
	<4A642F88.5000401@democritos.it>
	<c92002fa0907200528t15c1dd8er9437468c24ea76d6@mail.gmail.com>
	<b74576e70907200738n146ba4aes46dd7c1d0d986120@mail.gmail.com>
Message-ID: <c92002fa0907200811s45475a0eib7b82e7ad1bfb63b@mail.gmail.com>

Dear Luke,

I tested this pseudopotential for Zinc  bulk (Hex), and got   well
comparable lattice constants 2.65 , 4.97 \AA,  and the bulk module is 74.2
KBar by fitting Murnaghan Equation (Energy cutoff was set to 50 Hartree) .
Opium's test also gives small differences for eigenvalues from different
configurations.

Is there any way to improve the quality or remove the kink you mentioned ?
I forgot to check ionic potential, and just found it indeed has a large kink
.

thanks.

regards,
On Mon, Jul 20, 2009 at 10:38 PM, Luke Shulenburger
<lshulenburger at ciw.edu>wrote:

> Hello,
>
> I took a quick look at these pseudopotentials.  The first thing I
> found is that the problem seems to be related to  the augmentation
> functions.  I removed the second and third line after KBdesign in the
> Zn input and the potential loads into pwscf without issue.  I haven't
> used augmentation functions much, so I'm not sure quite what the
> problem is.  I know Eric Walter looks at this list from time to time,
> perhaps he could comment on the reason for this.  The other thing is
> that the the output from opium for the Zn pseudopotential looks
> somewhat strange.  As an example, the plots of the ionic potential are
> not very smooth at all and there are large kinks near the origin which
> will likely result an a very high plane wave cutoff being necessary to
> get converged results.  Has this potential been tested?
>
> Sincerely,
> Luke Shulenburger
> (lshulenburger at ciw.edu)
> Geophysical Laboratory
> Carnegie Institution of Washington
> 5251 Broad Branch Rd. NW
> Washington, DC 20015
>
>
> On Mon, Jul 20, 2009 at 8:28 AM, lan haiping<lanhaiping at gmail.com> wrote:
> > Dear Paolo,
> > Thanks .
> > I then check input settings for opium ,  and find the wavefunctions are
> > already arranged by increasing 'l'.
> >  The setting for Zn  pseudopotential  is following:
> > "
> > [Atom]
> > Zn
> > 8                   # norb: number of orbitals
> > 100  2.00  -        # nlm occ eigen(- means auto-generate)
> > 200  2.00  -
> > 210  6.00  -
> > 300  2.00  -
> > 310  6.00  -
> > 400  1.50  -
> > 410  0.00  -
> > 320  10.00  -
> >
> > [Pseudo]
> > 3  1.87 1.85 1.97
> > opt
> >
> > [Optinfo]
> > 7.07 10
> > 7.07 10
> > 7.07 10
> > [XC]
> > gga               # lda[PZ] or gga[PBE]
> >
> > [KBdesign]
> > 0                 # local orb
> > 1                # number of aug. operators
> > au 0.1 1.60 -3.05  # unit(gp or au)  left  right  height(Ry)
> > [Loginfo]
> > 0
> > 2.0 -4.0 4.0
> > "
> > and for O is
> > "
> > [Atom]
> > O
> > 3
> > 100   2.00   -
> > 200   2.00   -
> > 210   4.00   -
> > [Pseudo]
> > 2  1.34 1.53
> > opt
> > [Optinfo]
> > 7.07  10
> > 7.07  10
> > conmax
> > [XC]
> > gga
> > "
> >
> > I donot know why these PP cannot be read by pw.x .
> > By the way, is there any simple method to use  opium's settings  in
> > ld1.x   ?
> >
> >
> > Regards,
> >
> > Hai-Ping
> >
> >
> > On Mon, Jul 20, 2009 at 4:49 PM, Paolo Giannozzi <giannozz at democritos.it
> >
> > wrote:
> >>
> >> lan haiping wrote:
> >>
> >> > I wonder  whether QE still support NCPP format
> >>
> >> it does, otherwise it would have issued a different message
> >>
> >> > or other special consideration needs to take into for opium's pp ?
> >>
> >> atomic wavefunctions should be in order of increasing l.
> >> Not sure why this is needed and whethere it is really needed.
> >>
> >> P.
> >> --
> >> Paolo Giannozzi, Democritos and University of Udine, Italy
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> > --
> > Hai-Ping Lan
> > Department of Electronics ,
> > Peking University , Bejing, 100871
> > lanhaiping at gmail.com, hplan at pku.edu.cn
> >
> > _______________________________________________
> > 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
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From lanhaiping at gmail.com  Mon Jul 20 17:22:35 2009
From: lanhaiping at gmail.com (lan haiping)
Date: Mon, 20 Jul 2009 23:22:35 +0800
Subject: [Pw_forum] failure with NCPP
In-Reply-To: <4A6482CA.407@wm.edu>
References: <c92002fa0907192049g7f3ddc07pa131cb3902539cbe@mail.gmail.com>
	<4A642F88.5000401@democritos.it>
	<c92002fa0907200528t15c1dd8er9437468c24ea76d6@mail.gmail.com>
	<4A6482CA.407@wm.edu>
Message-ID: <c92002fa0907200822l3a7472abg47759505d871170e@mail.gmail.com>

Dear Eric,
I tried  fhi2upf, it works fine after i stripped off the param file at the
end.
I still a  problem . In opium, the configuration for PP generation only
pseudos 3  shells , i.e. , 4s/4p/3d, while fhi2upf inquire me to set 4
shells .   What  should i deal with this situation ?


Best wishes,
Hai-Ping
On Mon, Jul 20, 2009 at 10:44 PM, Eric J. Walter <ejwalt at wm.edu> wrote:

>
> Ian,
>
> Does fhi2upf work if you start with the fhi output and strip off the
> param file at the end?
>
> I can try this myself later.
>
> Eric
>
>
>
>
>
>
> lan haiping wrote:
> > Dear Paolo,
> > Thanks .
> > I then check input settings for opium ,  and find the wavefunctions
> > are already arranged by increasing 'l'.
> >  The setting for Zn  pseudopotential  is following:
> > "
> > [Atom]
> > Zn
> > 8                   # norb: number of orbitals
> > 100  2.00  -        # nlm occ eigen(- means auto-generate)
> > 200  2.00  -
> > 210  6.00  -
> > 300  2.00  -
> > 310  6.00  -
> > 400  1.50  -
> > 410  0.00  -
> > 320  10.00  -
> >
> > [Pseudo]
> > 3  1.87 1.85 1.97
> > opt
> >
> > [Optinfo]
> > 7.07 10
> > 7.07 10
> > 7.07 10
> > [XC]
> > gga               # lda[PZ] or gga[PBE]
> >
> > [KBdesign]
> > 0                 # local orb
> > 1                # number of aug. operators
> > au 0.1 1.60 -3.05  # unit(gp or au)  left  right  height(Ry)
> > [Loginfo]
> > 0
> > 2.0 -4.0 4.0
> > "
> > and for O is
> > "
> > [Atom]
> > O
> > 3
> > 100   2.00   -
> > 200   2.00   -
> > 210   4.00   -
> > [Pseudo]
> > 2  1.34 1.53
> > opt
> > [Optinfo]
> > 7.07  10
> > 7.07  10
> > conmax
> > [XC]
> > gga
> > "
> >
> > I donot know why these PP cannot be read by pw.x .
> > By the way, is there any simple method to use  opium's settings  in
> > ld1.x   ?
> >
> >
> > Regards,
> >
> > Hai-Ping
> >
> >
> > On Mon, Jul 20, 2009 at 4:49 PM, Paolo Giannozzi
> > <giannozz at democritos.it <mailto:giannozz at democritos.it>> wrote:
> >
> >     lan haiping wrote:
> >
> >     > I wonder  whether QE still support NCPP format
> >
> >     it does, otherwise it would have issued a different message
> >
> >     > or other special consideration needs to take into for opium's pp ?
> >
> >     atomic wavefunctions should be in order of increasing l.
> >     Not sure why this is needed and whethere it is really needed.
> >
> >     P.
> >     --
> >     Paolo Giannozzi, Democritos and University of Udine, Italy
> >     _______________________________________________
> >     Pw_forum mailing list
> >     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> >     http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> >
> > --
> > Hai-Ping Lan
> > Department of Electronics ,
> > Peking University , Bejing, 100871
> > lanhaiping at gmail.com <mailto:lanhaiping at gmail.com>, hplan at pku.edu.cn
> > <mailto:hplan at pku.edu.cn>
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > 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
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From ejwalt at wm.edu  Mon Jul 20 17:33:05 2009
From: ejwalt at wm.edu (Eric J. Walter)
Date: Mon, 20 Jul 2009 11:33:05 -0400
Subject: [Pw_forum] failure with NCPP
In-Reply-To: <c92002fa0907200822l3a7472abg47759505d871170e@mail.gmail.com>
References: <c92002fa0907192049g7f3ddc07pa131cb3902539cbe@mail.gmail.com>	<4A642F88.5000401@democritos.it>	<c92002fa0907200528t15c1dd8er9437468c24ea76d6@mail.gmail.com>	<4A6482CA.407@wm.edu>
	<c92002fa0907200822l3a7472abg47759505d871170e@mail.gmail.com>
Message-ID: <4A648E31.7070700@wm.edu>



Hai-Ping,

Yes, it looks to me that fhi2upf works fine.  The ncpp2upf works for 
most psps but seems to be broken for the case of having
an augmentation function (like you do).

The 4th occupation # should be zero.  It is just a potential for lmax+1 
which is the local potential and requires no wavefunction to be present.

Hope this helps,

Eric



lan haiping wrote:
> Dear Eric,
> I tried  fhi2upf, it works fine after i stripped off the param file at 
> the end.
> I still a  problem . In opium, the configuration for PP generation 
> only pseudos 3  shells , i.e. , 4s/4p/3d, while fhi2upf inquire me to 
> set 4 shells .   What  should i deal with this situation ?
>
>
> Best wishes,
> Hai-Ping
> On Mon, Jul 20, 2009 at 10:44 PM, Eric J. Walter <ejwalt at wm.edu 
> <mailto:ejwalt at wm.edu>> wrote:
>
>
>     Ian,
>
>     Does fhi2upf work if you start with the fhi output and strip off the
>     param file at the end?
>
>     I can try this myself later.
>
>     Eric
>
>
>
>
>
>
>     lan haiping wrote:
>     > Dear Paolo,
>     > Thanks .
>     > I then check input settings for opium ,  and find the wavefunctions
>     > are already arranged by increasing 'l'.
>     >  The setting for Zn  pseudopotential  is following:
>     > "
>     > [Atom]
>     > Zn
>     > 8                   # norb: number of orbitals
>     > 100  2.00  -        # nlm occ eigen(- means auto-generate)
>     > 200  2.00  -
>     > 210  6.00  -
>     > 300  2.00  -
>     > 310  6.00  -
>     > 400  1.50  -
>     > 410  0.00  -
>     > 320  10.00  -
>     >
>     > [Pseudo]
>     > 3  1.87 1.85 1.97
>     > opt
>     >
>     > [Optinfo]
>     > 7.07 10
>     > 7.07 10
>     > 7.07 10
>     > [XC]
>     > gga               # lda[PZ] or gga[PBE]
>     >
>     > [KBdesign]
>     > 0                 # local orb
>     > 1                # number of aug. operators
>     > au 0.1 1.60 -3.05  # unit(gp or au)  left  right  height(Ry)
>     > [Loginfo]
>     > 0
>     > 2.0 -4.0 4.0
>     > "
>     > and for O is
>     > "
>     > [Atom]
>     > O
>     > 3
>     > 100   2.00   -
>     > 200   2.00   -
>     > 210   4.00   -
>     > [Pseudo]
>     > 2  1.34 1.53
>     > opt
>     > [Optinfo]
>     > 7.07  10
>     > 7.07  10
>     > conmax
>     > [XC]
>     > gga
>     > "
>     >
>     > I donot know why these PP cannot be read by pw.x .
>     > By the way, is there any simple method to use  opium's settings  in
>     > ld1.x   ?
>     >
>     >
>     > Regards,
>     >
>     > Hai-Ping
>     >
>     >
>     > On Mon, Jul 20, 2009 at 4:49 PM, Paolo Giannozzi
>     > <giannozz at democritos.it <mailto:giannozz at democritos.it>
>     <mailto:giannozz at democritos.it <mailto:giannozz at democritos.it>>>
>     wrote:
>     >
>     >     lan haiping wrote:
>     >
>     >     > I wonder  whether QE still support NCPP format
>     >
>     >     it does, otherwise it would have issued a different message
>     >
>     >     > or other special consideration needs to take into for
>     opium's pp ?
>     >
>     >     atomic wavefunctions should be in order of increasing l.
>     >     Not sure why this is needed and whethere it is really needed.
>     >
>     >     P.
>     >     --
>     >     Paolo Giannozzi, Democritos and University of Udine, Italy
>     >     _______________________________________________
>     >     Pw_forum mailing list
>     >     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     <mailto:Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>>
>     >     http://www.democritos.it/mailman/listinfo/pw_forum
>     >
>     >
>     >
>     >
>     > --
>     > Hai-Ping Lan
>     > Department of Electronics ,
>     > Peking University , Bejing, 100871
>     > lanhaiping at gmail.com <mailto:lanhaiping at gmail.com>
>     <mailto:lanhaiping at gmail.com <mailto:lanhaiping at gmail.com>>,
>     hplan at pku.edu.cn <mailto:hplan at pku.edu.cn>
>     > <mailto:hplan at pku.edu.cn <mailto:hplan at pku.edu.cn>>
>     >
>     ------------------------------------------------------------------------
>     >
>     > _______________________________________________
>     > Pw_forum mailing list
>     > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     > http://www.democritos.it/mailman/listinfo/pw_forum
>     >
>
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> -- 
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871
> lanhaiping at gmail.com <mailto:lanhaiping at gmail.com>, hplan at pku.edu.cn 
> <mailto:hplan at pku.edu.cn>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From lshulenburger at gmail.com  Mon Jul 20 18:36:51 2009
From: lshulenburger at gmail.com (Luke Shulenburger)
Date: Mon, 20 Jul 2009 12:36:51 -0400
Subject: [Pw_forum] failure with NCPP
In-Reply-To: <c92002fa0907200811s45475a0eib7b82e7ad1bfb63b@mail.gmail.com>
References: <c92002fa0907192049g7f3ddc07pa131cb3902539cbe@mail.gmail.com>
	<4A642F88.5000401@democritos.it>
	<c92002fa0907200528t15c1dd8er9437468c24ea76d6@mail.gmail.com>
	<b74576e70907200738n146ba4aes46dd7c1d0d986120@mail.gmail.com>
	<c92002fa0907200811s45475a0eib7b82e7ad1bfb63b@mail.gmail.com>
Message-ID: <b74576e70907200936p315c812we8d8d58d89e1c57@mail.gmail.com>

Dear Ian,

In regards to the kink in the ionic potential near the origin, this is
often caused because the GGA functionals can be ill behaved in regions
of small charge density.  Opium has two options for handling this
problem.  The first is to switch to LDA inside of some radius and the
second is to extrapolate the potential from outside of some radius
into the core.  These two options are controlled by adding a line
after the functional name in the [XC] section of your input.  If a
positive number is given, this is the radius at which the code
switches to LDA.  If a negative number, this gives the radius at which
the extrapolation begins.

About your tests, it appears you have everything under control.  I
would just make sure that your results are well converged with respect
to the plane wave cutoff.  When I ran opium with your input file, it
suggested that very high cutoffs (>400Ry) would be necessary to get
energy convergence within 1mRy (or even 10mRy).  This may not be
entirely accurate (and indeed, I have made changes to this part of my
version of opium so it may not even be correct), but it is always a
good idea to test this.

Luke
(lshulenburger at ciw.edu)
Geophysical Laboratory
Carnegie Institution of Washington
5251 Broad Branch Rd NW
Washington, DC 20015

On Mon, Jul 20, 2009 at 11:11 AM, lan haiping<lanhaiping at gmail.com> wrote:
> Dear Luke,
>
> I tested this pseudopotential for Zinc? bulk (Hex), and got?? well
> comparable lattice constants 2.65 , 4.97 \AA,? and the bulk module is 74.2
> KBar by fitting Murnaghan Equation (Energy cutoff was set to 50 Hartree) .
> Opium's test also gives small differences for eigenvalues from different
> configurations.
>
> Is there any way to improve the quality or remove the kink you mentioned ?
> I forgot to check ionic potential, and just found it indeed has a large kink
> .
>
> thanks.
>
> regards,
> On Mon, Jul 20, 2009 at 10:38 PM, Luke Shulenburger <lshulenburger at ciw.edu>
> wrote:
>>
>> Hello,
>>
>> I took a quick look at these pseudopotentials. ?The first thing I
>> found is that the problem seems to be related to ?the augmentation
>> functions. ?I removed the second and third line after KBdesign in the
>> Zn input and the potential loads into pwscf without issue. ?I haven't
>> used augmentation functions much, so I'm not sure quite what the
>> problem is. ?I know Eric Walter looks at this list from time to time,
>> perhaps he could comment on the reason for this. ?The other thing is
>> that the the output from opium for the Zn pseudopotential looks
>> somewhat strange. ?As an example, the plots of the ionic potential are
>> not very smooth at all and there are large kinks near the origin which
>> will likely result an a very high plane wave cutoff being necessary to
>> get converged results. ?Has this potential been tested?
>>
>> Sincerely,
>> Luke Shulenburger
>> (lshulenburger at ciw.edu)
>> Geophysical Laboratory
>> Carnegie Institution of Washington
>> 5251 Broad Branch Rd. NW
>> Washington, DC 20015
>>
>>
>> On Mon, Jul 20, 2009 at 8:28 AM, lan haiping<lanhaiping at gmail.com> wrote:
>> > Dear Paolo,
>> > Thanks .
>> > I then check input settings for opium ,? and find the wavefunctions are
>> > already arranged by increasing 'l'.
>> > ?The setting for Zn? pseudopotential? is following:
>> > "
>> > [Atom]
>> > Zn
>> > 8?????????????????? # norb: number of orbitals
>> > 100? 2.00? -??????? # nlm occ eigen(- means auto-generate)
>> > 200? 2.00? -
>> > 210? 6.00? -
>> > 300? 2.00? -
>> > 310? 6.00? -
>> > 400? 1.50? -
>> > 410? 0.00? -
>> > 320? 10.00? -
>> >
>> > [Pseudo]
>> > 3? 1.87 1.85 1.97
>> > opt
>> >
>> > [Optinfo]
>> > 7.07 10
>> > 7.07 10
>> > 7.07 10
>> > [XC]
>> > gga?????????????? # lda[PZ] or gga[PBE]
>> >
>> > [KBdesign]
>> > 0???????????????? # local orb
>> > 1??????????????? # number of aug. operators
>> > au 0.1 1.60 -3.05? # unit(gp or au)? left? right? height(Ry)
>> > [Loginfo]
>> > 0
>> > 2.0 -4.0 4.0
>> > "
>> > and for O is
>> > "
>> > [Atom]
>> > O
>> > 3
>> > 100?? 2.00?? -
>> > 200?? 2.00?? -
>> > 210?? 4.00?? -
>> > [Pseudo]
>> > 2? 1.34 1.53
>> > opt
>> > [Optinfo]
>> > 7.07? 10
>> > 7.07? 10
>> > conmax
>> > [XC]
>> > gga
>> > "
>> >
>> > I donot know why these PP cannot be read by pw.x .
>> > By the way, is there any simple method to use? opium's settings? in
>> > ld1.x?? ?
>> >
>> >
>> > Regards,
>> >
>> > Hai-Ping
>> >
>> >
>> > On Mon, Jul 20, 2009 at 4:49 PM, Paolo Giannozzi
>> > <giannozz at democritos.it>
>> > wrote:
>> >>
>> >> lan haiping wrote:
>> >>
>> >> > I wonder ?whether QE still support NCPP format
>> >>
>> >> it does, otherwise it would have issued a different message
>> >>
>> >> > or other special consideration needs to take into for opium's pp ?
>> >>
>> >> atomic wavefunctions should be in order of increasing l.
>> >> Not sure why this is needed and whethere it is really needed.
>> >>
>> >> P.
>> >> --
>> >> Paolo Giannozzi, Democritos and University of Udine, Italy
>> >> _______________________________________________
>> >> Pw_forum mailing list
>> >> Pw_forum at pwscf.org
>> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>> >
>> >
>> > --
>> > Hai-Ping Lan
>> > Department of Electronics ,
>> > Peking University , Bejing, 100871
>> > lanhaiping at gmail.com, hplan at pku.edu.cn
>> >
>> > _______________________________________________
>> > 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
>
>
>
> --
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871
> lanhaiping at gmail.com, hplan at pku.edu.cn
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

From ejwalt at wm.edu  Mon Jul 20 18:45:00 2009
From: ejwalt at wm.edu (Eric J. Walter)
Date: Mon, 20 Jul 2009 12:45:00 -0400
Subject: [Pw_forum] failure with NCPP
In-Reply-To: <c92002fa0907200811s45475a0eib7b82e7ad1bfb63b@mail.gmail.com>
References: <c92002fa0907192049g7f3ddc07pa131cb3902539cbe@mail.gmail.com>	<4A642F88.5000401@democritos.it>	<c92002fa0907200528t15c1dd8er9437468c24ea76d6@mail.gmail.com>	<b74576e70907200738n146ba4aes46dd7c1d0d986120@mail.gmail.com>
	<c92002fa0907200811s45475a0eib7b82e7ad1bfb63b@mail.gmail.com>
Message-ID: <4A649F0C.6070005@wm.edu>


Dear Haiping and Luke,

The kink is due to the GGA functional and it occurs in both TM and Opt 
forms of the psp (and in other psp generation codes as well using similar
parameters).  This does not result in a large cut-off energy, which  
Haiping may have known since he probably checked the energy
convergence w.r.t. cut-off energy. (?)

The psp can be regenerated with the directive to smooth the XC potential 
before a certain radius.  This is done by adding either a positive or
negative (for two different smoothing methods) after "gga" in the XC 
block.  If I add -0.02, I get a very nice looking potential.

I think that any further opium questions/discussions should be sent to 
the opium mailing list:  opium-talk at sourceforge.net

Hope this helps,

Eric



lan haiping wrote:
> Dear Luke,
>
> I tested this pseudopotential for Zinc  bulk (Hex), and got   well 
> comparable lattice constants 2.65 , 4.97 \AA,  and the bulk module is 
> 74.2 KBar by fitting Murnaghan Equation (Energy cutoff was set to 50 
> Hartree) .   Opium's test also gives small differences for eigenvalues 
> from different configurations.  
>
> Is there any way to improve the quality or remove the kink you 
> mentioned ?  I forgot to check ionic potential, and just found it 
> indeed has a large kink .
>
> thanks.
>
> regards,
> On Mon, Jul 20, 2009 at 10:38 PM, Luke Shulenburger 
> <lshulenburger at ciw.edu <mailto:lshulenburger at ciw.edu>> wrote:
>
>     Hello,
>
>     I took a quick look at these pseudopotentials.  The first thing I
>     found is that the problem seems to be related to  the augmentation
>     functions.  I removed the second and third line after KBdesign in the
>     Zn input and the potential loads into pwscf without issue.  I haven't
>     used augmentation functions much, so I'm not sure quite what the
>     problem is.  I know Eric Walter looks at this list from time to time,
>     perhaps he could comment on the reason for this.  The other thing is
>     that the the output from opium for the Zn pseudopotential looks
>     somewhat strange.  As an example, the plots of the ionic potential are
>     not very smooth at all and there are large kinks near the origin which
>     will likely result an a very high plane wave cutoff being necessary to
>     get converged results.  Has this potential been tested?
>
>     Sincerely,
>     Luke Shulenburger
>     (lshulenburger at ciw.edu <mailto:lshulenburger at ciw.edu>)
>     Geophysical Laboratory
>     Carnegie Institution of Washington
>     5251 Broad Branch Rd. NW
>     Washington, DC 20015
>
>
>     On Mon, Jul 20, 2009 at 8:28 AM, lan haiping<lanhaiping at gmail.com
>     <mailto:lanhaiping at gmail.com>> wrote:
>     > Dear Paolo,
>     > Thanks .
>     > I then check input settings for opium ,  and find the
>     wavefunctions are
>     > already arranged by increasing 'l'.
>     >  The setting for Zn  pseudopotential  is following:
>     > "
>     > [Atom]
>     > Zn
>     > 8                   # norb: number of orbitals
>     > 100  2.00  -        # nlm occ eigen(- means auto-generate)
>     > 200  2.00  -
>     > 210  6.00  -
>     > 300  2.00  -
>     > 310  6.00  -
>     > 400  1.50  -
>     > 410  0.00  -
>     > 320  10.00  -
>     >
>     > [Pseudo]
>     > 3  1.87 1.85 1.97
>     > opt
>     >
>     > [Optinfo]
>     > 7.07 10
>     > 7.07 10
>     > 7.07 10
>     > [XC]
>     > gga               # lda[PZ] or gga[PBE]
>     >
>     > [KBdesign]
>     > 0                 # local orb
>     > 1                # number of aug. operators
>     > au 0.1 1.60 -3.05  # unit(gp or au)  left  right  height(Ry)
>     > [Loginfo]
>     > 0
>     > 2.0 -4.0 4.0
>     > "
>     > and for O is
>     > "
>     > [Atom]
>     > O
>     > 3
>     > 100   2.00   -
>     > 200   2.00   -
>     > 210   4.00   -
>     > [Pseudo]
>     > 2  1.34 1.53
>     > opt
>     > [Optinfo]
>     > 7.07  10
>     > 7.07  10
>     > conmax
>     > [XC]
>     > gga
>     > "
>     >
>     > I donot know why these PP cannot be read by pw.x .
>     > By the way, is there any simple method to use  opium's settings  in
>     > ld1.x   ?
>     >
>     >
>     > Regards,
>     >
>     > Hai-Ping
>     >
>     >
>     > On Mon, Jul 20, 2009 at 4:49 PM, Paolo Giannozzi
>     <giannozz at democritos.it <mailto:giannozz at democritos.it>>
>     > wrote:
>     >>
>     >> lan haiping wrote:
>     >>
>     >> > I wonder  whether QE still support NCPP format
>     >>
>     >> it does, otherwise it would have issued a different message
>     >>
>     >> > or other special consideration needs to take into for opium's
>     pp ?
>     >>
>     >> atomic wavefunctions should be in order of increasing l.
>     >> Not sure why this is needed and whethere it is really needed.
>     >>
>     >> P.
>     >> --
>     >> Paolo Giannozzi, Democritos and University of Udine, Italy
>     >> _______________________________________________
>     >> Pw_forum mailing list
>     >> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     >> http://www.democritos.it/mailman/listinfo/pw_forum
>     >
>     >
>     >
>     > --
>     > Hai-Ping Lan
>     > Department of Electronics ,
>     > Peking University , Bejing, 100871
>     > lanhaiping at gmail.com <mailto:lanhaiping at gmail.com>,
>     hplan at pku.edu.cn <mailto:hplan at pku.edu.cn>
>     >
>     > _______________________________________________
>     > Pw_forum mailing list
>     > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     > http://www.democritos.it/mailman/listinfo/pw_forum
>     >
>     >
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> -- 
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871
> lanhaiping at gmail.com <mailto:lanhaiping at gmail.com>, hplan at pku.edu.cn 
> <mailto:hplan at pku.edu.cn>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From lanhaiping at gmail.com  Tue Jul 21 03:30:18 2009
From: lanhaiping at gmail.com (lan haiping)
Date: Tue, 21 Jul 2009 09:30:18 +0800
Subject: [Pw_forum] failure with NCPP
In-Reply-To: <4A649F0C.6070005@wm.edu>
References: <c92002fa0907192049g7f3ddc07pa131cb3902539cbe@mail.gmail.com>
	<4A642F88.5000401@democritos.it>
	<c92002fa0907200528t15c1dd8er9437468c24ea76d6@mail.gmail.com>
	<b74576e70907200738n146ba4aes46dd7c1d0d986120@mail.gmail.com>
	<c92002fa0907200811s45475a0eib7b82e7ad1bfb63b@mail.gmail.com>
	<4A649F0C.6070005@wm.edu>
Message-ID: <c92002fa0907201830i63e7594bpa78168ab5fc2f98c@mail.gmail.com>

Dear Eric and Luke:

I have  tested the total energy over cutoff , it gives me a 60 Hatree for
ZnO to get 0.003 Hatree convergence.
It seems a bit large for this configuration , and  i will take your
suggestion to get a smooth one .
Best wishes,

Hai-Ping
On Tue, Jul 21, 2009 at 12:45 AM, Eric J. Walter <ejwalt at wm.edu> wrote:

>
> Dear Haiping and Luke,
>
> The kink is due to the GGA functional and it occurs in both TM and Opt
> forms of the psp (and in other psp generation codes as well using similar
> parameters).  This does not result in a large cut-off energy, which
> Haiping may have known since he probably checked the energy
> convergence w.r.t. cut-off energy. (?)
>
> The psp can be regenerated with the directive to smooth the XC potential
> before a certain radius.  This is done by adding either a positive or
> negative (for two different smoothing methods) after "gga" in the XC
> block.  If I add -0.02, I get a very nice looking potential.
>
> I think that any further opium questions/discussions should be sent to
> the opium mailing list:  opium-talk at sourceforge.net
>
> Hope this helps,
>
> Eric
>
>
>
> lan haiping wrote:
> > Dear Luke,
> >
> > I tested this pseudopotential for Zinc  bulk (Hex), and got   well
> > comparable lattice constants 2.65 , 4.97 \AA,  and the bulk module is
> > 74.2 KBar by fitting Murnaghan Equation (Energy cutoff was set to 50
> > Hartree) .   Opium's test also gives small differences for eigenvalues
> > from different configurations.
> >
> > Is there any way to improve the quality or remove the kink you
> > mentioned ?  I forgot to check ionic potential, and just found it
> > indeed has a large kink .
> >
> > thanks.
> >
> > regards,
> > On Mon, Jul 20, 2009 at 10:38 PM, Luke Shulenburger
> > <lshulenburger at ciw.edu <mailto:lshulenburger at ciw.edu>> wrote:
> >
> >     Hello,
> >
> >     I took a quick look at these pseudopotentials.  The first thing I
> >     found is that the problem seems to be related to  the augmentation
> >     functions.  I removed the second and third line after KBdesign in the
> >     Zn input and the potential loads into pwscf without issue.  I haven't
> >     used augmentation functions much, so I'm not sure quite what the
> >     problem is.  I know Eric Walter looks at this list from time to time,
> >     perhaps he could comment on the reason for this.  The other thing is
> >     that the the output from opium for the Zn pseudopotential looks
> >     somewhat strange.  As an example, the plots of the ionic potential
> are
> >     not very smooth at all and there are large kinks near the origin
> which
> >     will likely result an a very high plane wave cutoff being necessary
> to
> >     get converged results.  Has this potential been tested?
> >
> >     Sincerely,
> >     Luke Shulenburger
> >     (lshulenburger at ciw.edu <mailto:lshulenburger at ciw.edu>)
> >     Geophysical Laboratory
> >     Carnegie Institution of Washington
> >     5251 Broad Branch Rd. NW
> >     Washington, DC 20015
> >
> >
> >     On Mon, Jul 20, 2009 at 8:28 AM, lan haiping<lanhaiping at gmail.com
> >     <mailto:lanhaiping at gmail.com>> wrote:
> >     > Dear Paolo,
> >     > Thanks .
> >     > I then check input settings for opium ,  and find the
> >     wavefunctions are
> >     > already arranged by increasing 'l'.
> >     >  The setting for Zn  pseudopotential  is following:
> >     > "
> >     > [Atom]
> >     > Zn
> >     > 8                   # norb: number of orbitals
> >     > 100  2.00  -        # nlm occ eigen(- means auto-generate)
> >     > 200  2.00  -
> >     > 210  6.00  -
> >     > 300  2.00  -
> >     > 310  6.00  -
> >     > 400  1.50  -
> >     > 410  0.00  -
> >     > 320  10.00  -
> >     >
> >     > [Pseudo]
> >     > 3  1.87 1.85 1.97
> >     > opt
> >     >
> >     > [Optinfo]
> >     > 7.07 10
> >     > 7.07 10
> >     > 7.07 10
> >     > [XC]
> >     > gga               # lda[PZ] or gga[PBE]
> >     >
> >     > [KBdesign]
> >     > 0                 # local orb
> >     > 1                # number of aug. operators
> >     > au 0.1 1.60 -3.05  # unit(gp or au)  left  right  height(Ry)
> >     > [Loginfo]
> >     > 0
> >     > 2.0 -4.0 4.0
> >     > "
> >     > and for O is
> >     > "
> >     > [Atom]
> >     > O
> >     > 3
> >     > 100   2.00   -
> >     > 200   2.00   -
> >     > 210   4.00   -
> >     > [Pseudo]
> >     > 2  1.34 1.53
> >     > opt
> >     > [Optinfo]
> >     > 7.07  10
> >     > 7.07  10
> >     > conmax
> >     > [XC]
> >     > gga
> >     > "
> >     >
> >     > I donot know why these PP cannot be read by pw.x .
> >     > By the way, is there any simple method to use  opium's settings  in
> >     > ld1.x   ?
> >     >
> >     >
> >     > Regards,
> >     >
> >     > Hai-Ping
> >     >
> >     >
> >     > On Mon, Jul 20, 2009 at 4:49 PM, Paolo Giannozzi
> >     <giannozz at democritos.it <mailto:giannozz at democritos.it>>
> >     > wrote:
> >     >>
> >     >> lan haiping wrote:
> >     >>
> >     >> > I wonder  whether QE still support NCPP format
> >     >>
> >     >> it does, otherwise it would have issued a different message
> >     >>
> >     >> > or other special consideration needs to take into for opium's
> >     pp ?
> >     >>
> >     >> atomic wavefunctions should be in order of increasing l.
> >     >> Not sure why this is needed and whethere it is really needed.
> >     >>
> >     >> P.
> >     >> --
> >     >> Paolo Giannozzi, Democritos and University of Udine, Italy
> >     >> _______________________________________________
> >     >> Pw_forum mailing list
> >     >> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> >     >> http://www.democritos.it/mailman/listinfo/pw_forum
> >     >
> >     >
> >     >
> >     > --
> >     > Hai-Ping Lan
> >     > Department of Electronics ,
> >     > Peking University , Bejing, 100871
> >     > lanhaiping at gmail.com <mailto:lanhaiping at gmail.com>,
> >     hplan at pku.edu.cn <mailto:hplan at pku.edu.cn>
> >     >
> >     > _______________________________________________
> >     > Pw_forum mailing list
> >     > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> >     > http://www.democritos.it/mailman/listinfo/pw_forum
> >     >
> >     >
> >     _______________________________________________
> >     Pw_forum mailing list
> >     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> >     http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> >
> > --
> > Hai-Ping Lan
> > Department of Electronics ,
> > Peking University , Bejing, 100871
> > lanhaiping at gmail.com <mailto:lanhaiping at gmail.com>, hplan at pku.edu.cn
> > <mailto:hplan at pku.edu.cn>
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > 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
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From anavat_ila at yahoo.com  Tue Jul 21 14:26:31 2009
From: anavat_ila at yahoo.com (Ali Tavana)
Date: Tue, 21 Jul 2009 05:26:31 -0700 (PDT)
Subject: [Pw_forum] sum over lambda(q)
Message-ID: <539897.60289.qm@web51810.mail.re2.yahoo.com>


Dear all,

I want to sum lambda(q,mode) (e-ph coefficient) over BZ for each mode. From the number of the starts of each q-point I calculate the weights for each q point (number of stars of that q point/total number of starts of all q points). Then I do a summation over q points in IBZ (lambda(q,mode)w(q)). But when I calculate the total lambda from the summation over all the modes I get a different value from what QE itself calculates by matdyn program (matdyn calculates it from the integration of Eliashberg's function). So do you think I haven't do it correctly or what has caused this difference (about 20-30%)?

Should I also take into account the electronic part by some means? I asked it because I've change one electronic structure parameter but the trends of total lambda of main and QE are different.

Thank you in advanced.
Ali


      

From wangqj1 at 126.com  Wed Jul 22 06:42:56 2009
From: wangqj1 at 126.com (wangqj1)
Date: Wed, 22 Jul 2009 12:42:56 +0800 (CST)
Subject: [Pw_forum] about U
Message-ID: <19741619.690911248237776631.JavaMail.coremail@bj126app82.126.com>


Dear matteo
     I want to compute the value of U,in the paper PRB 71, 035105 (2005),the Eq.(18),(19),but I don't know how to built the matrices \chi and \chi_0,I want to built the matrices manually instead of programe pack like your example. And how do I extract the the date from the out file of unperturbed self-consistent calculation and the files of perturbed calculations(like pert-0.1.out ,pert-0.2.out and so on ) to construct the matrices of \chi and \chi_0 as in Eq.(18) ?
Beat regards
Q J Wang
XiangTan University
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From sagarambavale at yahoo.co.in  Wed Jul 22 15:24:15 2009
From: sagarambavale at yahoo.co.in (ambavale sagar)
Date: Wed, 22 Jul 2009 18:54:15 +0530 (IST)
Subject: [Pw_forum] pwcond-problem with linear system
Message-ID: <369699.29800.qm@web94602.mail.in2.yahoo.com>

Dear all,
I am running a pwcond program for system made of Al electrodes and vaccum (> 10 angstrom) in between. Even for such a large vaccum I get nonzero values (10e-1 to 10e-4) of transmission coefficient (T) at higher energies (> 2 eV +Ef). for energies < 2 eV, T become almost zero. After 0.8 eV +Ef energy the program got terminated giving error:
 error # 5411
problems with the linear system. 
What might be a source of error in my case? Can I substract this contribution of leads from the T values I got for electrode-molecule-electrode system to get accurate T in case of molecule attached to electrodes?
The other question is little sidelined. Why Al is not used as electrode in most of the studies? In other words, what are the drawbacks of using Al as an electrode?

regards
Sagar Ambavale
PhD student
M.S. University of Baroda
India



      See the Web&#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/
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From snd2mra at yahoo.com  Wed Jul 22 16:02:48 2009
From: snd2mra at yahoo.com (snd2mra at yahoo.com)
Date: Wed, 22 Jul 2009 07:02:48 -0700 (PDT)
Subject: [Pw_forum] Compilation using -DEXX
Message-ID: <46022.51739.qm@web53305.mail.re2.yahoo.com>


Hello,
       I am compiling the recent version of pwscf 4.1 to perform calculations using the PBE0 functional. I have this doubt. Do I have to include the '-DEXX' both in DFLAGS and CPPFLAGS ? The details given in the examples folder suggest us to add this to just DFLAGS.

Thank you.

- Madan Mithra

                         ----------------------------------------
                         Madan Mithra .L.M
                         Senior Research Fellow
                         Dept.of Physics
                         Indian Institute of Science
                         Bangalore - 560 012
                         INDIA
                         .........................................
                         e-mail : mit at physics.iisc.ernet.in
                                : snd2mra at yahoo.com
                         Phone  : 91-80-22932313    (Lab)
                         FAX    : (080) 360 2602
                         -----------------------------------------



      

From Giovanni.Cantele at na.infn.it  Wed Jul 22 16:10:03 2009
From: Giovanni.Cantele at na.infn.it (Giovanni Cantele)
Date: Wed, 22 Jul 2009 16:10:03 +0200
Subject: [Pw_forum] Compilation using -DEXX
In-Reply-To: <46022.51739.qm@web53305.mail.re2.yahoo.com>
References: <46022.51739.qm@web53305.mail.re2.yahoo.com>
Message-ID: <4A671DBB.90305@na.infn.it>

snd2mra at yahoo.com wrote:
> Hello,
>        I am compiling the recent version of pwscf 4.1 to perform calculations using the PBE0 functional. I have this doubt. Do I have to include the '-DEXX' both in DFLAGS and CPPFLAGS ? The details given in the examples folder suggest us to add this to just DFLAGS.
>
> Thank you.
>
> - Madan Mithra
>
>
>   
as you may see from this line in the make.sys you find in your QE top 
directory
CPPFLAGS       = -P -traditional $(DFLAGS) $(IFLAGS)
DFLAGS are included in the preproceccing flags CPPFLAGS

Giovanni                                     

-- 



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


From Max.Lawson at unige.ch  Wed Jul 22 18:40:03 2009
From: Max.Lawson at unige.ch (=?ISO-8859-1?Q?Lat=E9vi_Max_LAWSON_DAKU?=)
Date: Wed, 22 Jul 2009 18:40:03 +0200
Subject: [Pw_forum] correction to functional.f90 (4.1): optx identified as a
 meta-GGA functional
Message-ID: <4A6740E3.5020904@unige.ch>

Hi,

Line 399 of functional.f90:

    ismeta     =  (igcx == 7) .or. (igcx == 6 )

should be changed to

    ismeta     =  (igcx == 7)

That is, the OPTX functional was flagged as a meta-GGA.


I noticed this while trying to generate a pseudopotential
with ld1.x  using the OLYP functional (input key "olyp").

By the way, the following comment is written in functional.90.

  !              "olyp"  = "nox+lyp+optx+blyp"!!! UNTESTED !!!

Does this mean, simply, that the olyp shortname is not well tested?
or something else?


By the way, I noticed that the keyword "blyp" is used for designating
both the blyp XC functional and the lyp gradient correction to
correlation. This perhaps explains that the following error message

     from set_dft_value : error #         1
     two conflicting matching values

was issued when I tried to specify the olyp functional as follows:

    'nox-lyp-optx-blyp'

This is a guess based on the presence of Line 261:

    if (matches ('BLYP', dftout) ) call set_dft_value (igcx, 1)



Finally, I've inserted the following lines in the subroutine dft_name(),
Line 609:

  else if (iexch_==0.and.icorr_==3.and.igcx_==6.and.igcc_==3) then
     shortname_ = 'OLYP'


Best regards,
Max


-- 
***********************************************
Latevi Max LAWSON DAKU
Departement de chimie physique 
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 

Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103
***********************************************


From manoj at phys.ufl.edu  Wed Jul 22 19:15:36 2009
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Wed, 22 Jul 2009 13:15:36 -0400 (EDT)
Subject: [Pw_forum] pwcond-problem with linear system
In-Reply-To: <369699.29800.qm@web94602.mail.in2.yahoo.com>
Message-ID: <Pine.GSO.4.21.0907221311080.1407-100000@neptune.phys.ufl.edu>

Dear Sagar, 
 The error 'Problems with the linear system' generally gets
removed if you change 'ecut2d' parameter, which is the 2D energy cutoff
and determines how many plane waves would you have in your calculation. I
am guessing that the other problem is also coming from energy convergence.
I suggest to check that.

-Manoj 

On Wed, 22 Jul 2009, ambavale sagar wrote:

> Dear all,
I am running a pwcond program for system made of Al electrodes and vaccum (> 10 angstrom) in between. Even for such a large vaccum I get nonzero values (10e-1 to 10e-4) of transmission coefficient (T) at higher energies (> 2 eV +Ef). for energies < 2 eV, T become almost zero. After 0.8 eV +Ef energy the program got terminated giving error: error # 5411
problems with the linear system. 
What might be a source of error in my case? Can I substract this contribution of leads from the T values I got for electrode-molecule-electrode system to get accurate T in case of molecule attached to electrodes?
The other question is little sidelined. Why Al is not used as electrode in most of the studies? In other words, what are the drawbacks of using Al as an electrode?

regards
Sagar Ambavale
PhD student
M.S. University of Baroda
India



      See the Web&#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/


From anavat_ila at yahoo.com  Thu Jul 23 10:52:58 2009
From: anavat_ila at yahoo.com (Ali Tavana)
Date: Thu, 23 Jul 2009 01:52:58 -0700 (PDT)
Subject: [Pw_forum] e-ph methode
Message-ID: <748361.5893.qm@web51803.mail.re2.yahoo.com>


Dear all,

Is there any reference for e-ph coefficient calculation method in QE?

thanks


      

From giannozz at democritos.it  Thu Jul 23 10:56:05 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 23 Jul 2009 10:56:05 +0200
Subject: [Pw_forum] correction to functional.f90 (4.1): optx identified
 as a meta-GGA functional
In-Reply-To: <4A6740E3.5020904@unige.ch>
References: <4A6740E3.5020904@unige.ch>
Message-ID: <4A6825A5.8090102@democritos.it>

Lat?vi Max LAWSON DAKU wrote:

> the OPTX functional was flagged as a meta-GGA.

thank you for reporting this

> By the way, the following comment is written in functional.90.
> 
>   !              "olyp"  = "nox+lyp+optx+blyp"!!! UNTESTED !!!
> 
> Does this mean, simply, that the olyp shortname is not well tested?

exactly. It should work, because it has been working in some version
in the past, but if you have the possibility to verify it, please do
it, report if that comment can be removed

> By the way, I noticed that the keyword "blyp" is used for designating
> both the blyp XC functional and the lyp gradient correction to
> correlation. 

the logic used to label XC functionals, based on four keywords,
seemed a smart method years ago, but it has been outsmarted by
the ever-increasing number of XC functionals, and by a choice
for the meaning of "blyp" that turned out not to be a good one.
Changing the way XC functionals are labelled (in particular,
fixing the "blyp" inconsistency you mention) might break old
pseudopotentials (the XC functional is read from pseudopotential
files).

> Finally, I've inserted the following lines in the subroutine dft_name(),
> Line 609:
> 
>   else if (iexch_==0.and.icorr_==3.and.igcx_==6.and.igcc_==3) then
>      shortname_ = 'OLYP'

that's a good solution...your changes will go in the next version

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

From eyvaz_isaev at yahoo.com  Thu Jul 23 11:35:51 2009
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 23 Jul 2009 02:35:51 -0700 (PDT)
Subject: [Pw_forum] e-ph methode
Message-ID: <663493.96141.qm@web65707.mail.ac4.yahoo.com>


Dear Ali, 

I think  Savrasov's paper is a good starting point:

PHYSICAL REVIEW B 54 (23), 1996, Electron-phonon interactions and related physical properties of metals from linear-response theory, S. Y. Savrasov, D. Y. Savrasov

And see References, of course.

Happy reading,
Eyvaz.

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


--- On Thu, 7/23/09, Ali Tavana <anavat_ila at yahoo.com> wrote:

> From: Ali Tavana <anavat_ila at yahoo.com>
> Subject: [Pw_forum] e-ph methode
> To: pw_forum at pwscf.org
> Date: Thursday, July 23, 2009, 12:52 PM
> 
> Dear all,
> 
> Is there any reference for e-ph coefficient calculation
> method in QE?
> 
> thanks
> 
> 
> ? ? ? 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


      

From kazempoor2000 at yahoo.com  Thu Jul 23 11:36:05 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Thu, 23 Jul 2009 02:36:05 -0700 (PDT)
Subject: [Pw_forum] xmgrace
Message-ID: <351091.76930.qm@web112520.mail.gq1.yahoo.com>

Dear users
I calculate the band structure for wurtzite ZnO. Then I plot by plotbands.x , but the ps format has good shape and the bands that were plot by xmgrace have some inapprprate vertical line and is not similar to the ps format.
I attach related file
Thanks 

Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


      
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From pw_users-bounces at pwscf.org  Thu Jul 23 11:37:36 2009
From: pw_users-bounces at pwscf.org (pw_users-bounces at pwscf.org)
Date: Thu, 23 Jul 2009 11:37:36 +0200
Subject: [Pw_forum] Forward of moderated message
Message-ID: <mailman.1.1248341856.23773.pw_users@pwscf.org>

An embedded message was scrubbed...
From: Wei Li <weili747 at gmail.com>
Subject: Performance of Quantum Express
Date: Thu, 23 Jul 2009 16:10:11 +0800
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From paulatto at sissa.it  Thu Jul 23 12:16:58 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 23 Jul 2009 12:16:58 +0200
Subject: [Pw_forum] xmgrace
In-Reply-To: <351091.76930.qm@web112520.mail.gq1.yahoo.com>
References: <351091.76930.qm@web112520.mail.gq1.yahoo.com>
Message-ID: <op.uximukf3a8x26q@paulax>

In data 23 luglio 2009 alle ore 11:36:05, ali kazempour  
<kazempoor2000 at yahoo.com> ha scritto:
> plot by xmgrace have some inapprprate vertical line and is not similar  
> to the ps format.

Dear Ali,
if I understand your problem correctly, I think those line are just  
markers for the high-symmetry points, and were put there on purpose.  
Nevertheless, I'm no expert with xmgrace, hence I cannot suggest a way to  
remove them if you so wish.

regards


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

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

From ggokoglu at hacettepe.edu.tr  Thu Jul 23 11:46:33 2009
From: ggokoglu at hacettepe.edu.tr (Gokhan GOKOGLU)
Date: Thu, 23 Jul 2009 12:46:33 +0300
Subject: [Pw_forum] inconsistent bands and DOS...
Message-ID: <7380ff7c324.4a685ba9@hacettepe.edu.tr>

Dear PWSCF users,
I am trying to calculate the electronic band structure of a system. There is a small gap 
in DOS, but the band structure seems to be metallic. I am using exactly same parameters for 
both band and DOS calculation. I would be very grateful, if someone could give an idea. Thanks..
 
Dr. Gokhan Gokoglu
Department of Physics
Karabuk University
Turkey 
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From giuseppe.mattioli at mlib.ism.cnr.it  Thu Jul 23 14:06:16 2009
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Thu, 23 Jul 2009 14:06:16 +0200
Subject: [Pw_forum] inconsistent bands and DOS...
In-Reply-To: <7380ff7c324.4a685ba9@hacettepe.edu.tr>
References: <7380ff7c324.4a685ba9@hacettepe.edu.tr>
Message-ID: <200907231406.17391.giuseppe.mattioli@mlib.ism.cnr.it>

Dear Gokhan
How do you think we can help you if you don't provide any detail of your 
calculations?

Giuseppe

On Thursday 23 July 2009 11:46:33 Gokhan GOKOGLU wrote:
> Dear PWSCF users,
> I am trying to calculate the electronic band structure of a system. There
> is a small gap in DOS, but the band structure seems to be metallic. I am
> using exactly same parameters for both band and DOS calculation. I would be
> very grateful, if someone could give an idea. Thanks..
>
> Dr. Gokhan Gokoglu
> Department of Physics
> Karabuk University
> Turkey

-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

   Giuseppe Mattioli                            
   CNR - ISTITUTO DI STRUTTURA DELLA MATERIA   
   v. Salaria Km 29,300 - C.P. 10                
   I 00016 - Monterotondo Stazione (RM)          
   Tel + 39 06 90672836 - Fax +39 06 90672316    
   E-mail: <giuseppe.mattioli at ism.cnr.it>
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From kazempoor2000 at yahoo.com  Thu Jul 23 14:47:30 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Thu, 23 Jul 2009 05:47:30 -0700 (PDT)
Subject: [Pw_forum] ZnO
Message-ID: <1404.42295.qm@web112510.mail.gq1.yahoo.com>


Dear all
I obtain U from linear response that implemented in espresso for ZnO? bulk. But the differences?? between 
d(alpha)/d(n) - d(alpha)/d(n0)
is very large. For d(alpha)/d(n)=463.43 and for 
d(alpha)/d(n0) = 69.05.
Is it because that the d orbital for Zn is full or has another reason/
Thanks a lot
 Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


      
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From ggokoglu at hacettepe.edu.tr  Thu Jul 23 15:40:13 2009
From: ggokoglu at hacettepe.edu.tr (Gokhan GOKOGLU)
Date: Thu, 23 Jul 2009 16:40:13 +0300
Subject: [Pw_forum] inconsistent bands and DOS...
In-Reply-To: <200907231406.17391.giuseppe.mattioli@mlib.ism.cnr.it>
References: <7380ff7c324.4a685ba9@hacettepe.edu.tr>
	<200907231406.17391.giuseppe.mattioli@mlib.ism.cnr.it>
Message-ID: <7360bde65811.4a68926d@hacettepe.edu.tr>

Hello,
The details of band and DOS calculations are attached below. Thanks....
 
DOS calculation:
 
 
&control
    calculation = 'scf'
    restart_mode='from_scratch',
    prefix='co2crbi',
    tstress = .true.
    tprnfor = .true.
    pseudo_dir = '$ESPRESSO_HOME/pseudo/',
    outdir='/home_palamut2/ggokoglu/co2crbi/dos/tmp'
 /
&system
   ibrav=  2, celldm(1) =11.731316, nat=4,ntyp=3, nspin=2,starting_magnetization(1)=0.7,
   starting_magnetization(2)=0.7, ecutwfc =85, ecutrho = 300.0,nbnd=28,
    occupations='smearing', smearing='methfessel-paxton', degauss=0.02
/
 &electrons
    diagonalization='david'
    mixing_mode = 'plain'
    mixing_beta = 0.7
    conv_thr =  1.0d-8
 /
ATOMIC_SPECIES
 Co  58.933     Co.pbe-nd-rrkjus.UPF
 Cr  51.9961    Cr.pbe-sp-van.UPF 
 Bi  208.98038  Bi.pbe-d-mt.UPF 
ATOMIC_POSITIONS
 Co 0.00 0.00 0.00
 Co 0.50 0.50 0.50
 Cr 0.25 0.25 0.25
 Bi 0.75 0.75 0.75
K_POINTS {automatic}
12 12 12 0 0 0
EOF
/usr/bin/time mpirun -np $CPU_NEEDED -machinefile $HOST_NODEFILE $ESPRESSO_HOME/bin/pw.x -procs 2 < co2crbi.scf.in > /home_palamut2/ggokoglu/c
o2crbi/dos/co2crbi.scf.out

# DOS calculation for co2crbi
cat > co2crbi.dos.in << EOF
&control
    calculation = 'nscf'
    restart_mode='from_scratch',
    prefix='co2crbi',
    tstress = .true.
    tprnfor = .true.
    pseudo_dir = '$ESPRESSO_HOME/pseudo/',
    outdir='/home_palamut2/ggokoglu/co2crbi/dos/tmp'
 /
&system
   ibrav=  2, celldm(1) =11.731316, nat=4,ntyp=3, nspin=2,starting_magnetization(1)=0.7,
   starting_magnetization(2)=0.7, ecutwfc =85, ecutrho = 300.0,nbnd=28,
    occupations='smearing', smearing='methfessel-paxton', degauss=0.02
/
 &electrons
    diagonalization='david'
    mixing_mode = 'plain'
mixing_beta = 0.7
    conv_thr =  1.0d-8
 /
ATOMIC_SPECIES
 Co  58.933     Co.pbe-nd-rrkjus.UPF
 Cr  51.9961    Cr.pbe-sp-van.UPF
 Bi  208.98038  Bi.pbe-d-mt.UPF
ATOMIC_POSITIONS
 Co 0.00 0.00 0.00
 Co 0.50 0.50 0.50
 Cr 0.25 0.25 0.25
 Bi 0.75 0.75 0.75
K_POINTS {automatic}
12 12 12 0 0 0
EOF
cat > co2crbi.dos2.in << EOF
 &inputpp
    outdir='/home_palamut2/ggokoglu/co2crbi/dos/tmp' 
    prefix='co2crbi'
    fildos='co2cr.dos',
    DeltaE=0.1
 /
EOF
/usr/bin/time mpirun -np $CPU_NEEDED -machinefile $HOST_NODEFILE $ESPRESSO_HOME/bin/pw.x -procs 2 < co2crbi.dos.in > /home_palamut2/ggokoglu/c
o2crbi/dos/co2crbi.dos.out
 
/usr/bin/time mpirun -np $CPU_NEEDED -machinefile $HOST_NODEFILE $ESPRESSO_HOME/bin/dos.x -procs 2 < co2crbi.dos2.in > /home_palamut2/ggokoglu
/cocrbi/dos/co2crbi.dos2.out

cat > co2crbi.pdos.in << EOF
 &inputpp
    outdir='/home_palamut2/ggokoglu/co2crbi/dos/tmp' 
    prefix='co2crbi'
    DeltaE=0.1
    ngauss=1, degauss=0.02
 /
EOF
/usr/bin/time mpirun -np $CPU_NEEDED -machinefile $HOST_NODEFILE $ESPRESSO_HOME/bin/projwfc.x  -procs 2 < co2crbi.pdos.in > /home_palamut2/ggo
koglu/co2crbi/dos/co2crbi.pdos.out
###################################################################
####################################################################
 
BAND Calculation:
 
# self-consistent calculation
cat > co2crbi.scf.in << EOF
&control
    calculation = 'scf'
    restart_mode='from_scratch',
    prefix='co2crbi',
    tstress = .true.
    tprnfor = .true.
    pseudo_dir = '$ESPRESSO_HOME/pseudo/',
    outdir='/home_palamut2/ggokoglu/co2crbi/band/tmp'
 /
&system
   ibrav=  2, celldm(1) =11.731316, nat=4,ntyp=3, nspin=2,starting_magnetization(1)=0.7,
   starting_magnetization(2)=0.7, ecutwfc =85, ecutrho = 300.0,nbnd=28,
    occupations='smearing', smearing='methfessel-paxton', degauss=0.02
/
 &electrons
    diagonalization='david'
    mixing_mode = 'plain'
    mixing_beta = 0.7
    conv_thr =  1.0d-8
 /
ATOMIC_SPECIES
 Co  58.933     Co.pbe-nd-rrkjus.UPF
 Cr  51.9961    Cr.pbe-sp-van.UPF 
 Bi  208.98038  Bi.pbe-d-mt.UPF 
ATOMIC_POSITIONS
 Co 0.00 0.00 0.00
 Co 0.50 0.50 0.50
 Cr 0.25 0.25 0.25
 Bi 0.75 0.75 0.75
K_POINTS {automatic}
12 12 12 0 0 0
EOF
/usr/bin/time mpirun -np $CPU_NEEDED -machinefile $HOST_NODEFILE $ESPRESSO_HOME/bin/pw.x -procs 2 < co2crbi.scf.in > /home_palamut2/ggokoglu/c
o2crbi/band/co2crbi.scf.out

# band structure calculation along delta, sigma and lambda lines
    cat > co2crbi.band.in << EOF
 &control
    calculation='bands'
     prefix='co2crbi',
    pseudo_dir = '$ESPRESSO_HOME/pseudo/',
    outdir='/home_palamut2/ggokoglu/co2crbi/band/tmp' 
/
&system
   ibrav=  2, celldm(1) =11.731316, nat=4,ntyp=3, nspin=2,starting_magnetization(1)=0.7,
   starting_magnetization(2)=0.7, ecutwfc =85, ecutrho = 300.0,nbnd=28,
    occupations='smearing', smearing='methfessel-paxton', degauss=0.02
/
 &electrons
    diagonalization='david'
 /
ATOMIC_SPECIES
Co  58.933     Co.pbe-nd-rrkjus.UPF
 Cr  51.9961    Cr.pbe-sp-van.UPF
 Bi  208.98038  Bi.pbe-d-mt.UPF
ATOMIC_POSITIONS
 Co 0.00 0.00 0.00
 Co 0.50 0.50 0.50
 Cr 0.25 0.25 0.25
 Bi 0.75 0.75 0.75
K_POINTS 
101
  1.00 0.00 0.00 1.00
  0.975 0.00 0.00 1.00
  0.95 0.00 0.00 1.00 
  0.925 0.00 0.00 1.00
  0.90 0.00 0.00 1.00 
  0.875 0.00 0.00 1.00
  0.85 0.00 0.00 1.00
  0.825 0.00 0.00 1.00
  0.80 0.00 0.00 1.00
  0.775 0.00 0.00 1.00
  0.75 0.00 0.00 1.00
  0.725 0.00 0.00 1.00
  0.70 0.00 0.00 1.00
  0.675 0.00 0.00 1.00
  0.65 0.00 0.00 1.00
  0.625 0.00 0.00 1.00
  0.60 0.00 0.00 1.00
  0.575 0.00 0.00 1.00
0.55 0.00 0.00 1.00
  0.525 0.00 0.00 1.00
  0.50 0.00 0.00 1.00
  0.475 0.00 0.00 1.00
  0.45 0.00 0.00 1.00
  0.425 0.00 0.00 1.00
  0.40 0.00 0.00 1.00
  0.375 0.00 0.00 1.00
  0.35 0.00 0.00 1.00
  0.325 0.00 0.00 1.00
  0.30 0.00 0.00 1.00
  0.275 0.00 0.00 1.00
  0.25 0.00 0.00 1.00
  0.225 0.00 0.00 1.00
  0.20 0.00 0.00 1.00
  0.175 0.00 0.00 1.00
  0.15 0.00 0.00 1.00
  0.125 0.00 0.00 1.00
  0.10 0.00 0.00 1.00
  0.075 0.00 0.00 1.00
  0.05 0.00 0.00 1.00
  0.025 0.00 0.00 1.00
  0.00 0.00 0.00 1.00
  0.025 0.025 0.025 1.00
  0.05 0.05 0.05 1.00
  0.075 0.075 0.075 1.00
  0.10 0.10 0.10 1.00
  0.125 0.125 0.125 1.00
  0.15 0.15 0.15 1.00
  0.175 0.175 0.175 1.00
  0.20 0.20 0.20 1.00
  0.225 0.225 0.225 1.00
  0.25 0.25 0.25 1.00
  0.275 0.275 0.275 1.00
  0.30 0.30 0.30 1.00
  0.325 0.325 0.325 1.00
  0.35 0.35 0.35 1.00
  0.375 0.375 0.375 1.00
  0.40 0.40 0.40 1.00
  0.425 0.425 0.425 1.00
  0.45 0.45 0.45 1.00
  0.475 0.475 0.475 1.00
  0.50 0.50 0.50 1.00
  0.525 0.525 0.45 1.00
  0.55 0.55 0.40 1.00
  0.575 0.575 0.35 1.00
  0.60 0.60 0.30 1.00
  0.625 0.625 0.25 1.00
  0.65 0.65 0.20 1.00
  0.675 0.675 0.15 1.00
  0.70 0.70 0.10 1.00
  0.725 0.725 0.05 1.00
  0.75 0.75 0.00 1.00
  0.725 0.725 0.00 1.00
  0.70 0.70 0.00 1.00
  0.675 0.675 0.00 1.00
0.65 0.65 0.00 1.00
  0.625 0.625 0.00 1.00
  0.60 0.60 0.00 1.00
  0.575 0.575 0.00 1.00
  0.55 0.55 0.00 1.00
  0.525 0.525 0.00 1.00
  0.50 0.50 0.00 1.00
  0.475 0.475 0.00 1.00
  0.45 0.45 0.00 1.00
  0.425 0.425 0.00 1.00
  0.40 0.40 0.00 1.00
  0.375 0.375 0.00 1.00
  0.35 0.35 0.00 1.00
  0.325 0.325 0.00 1.00
  0.30 0.30 0.00 1.00
  0.275 0.275 0.00 1.00
  0.25 0.25 0.00 1.00
  0.225 0.225 0.00 1.00
  0.20 0.20 0.00 1.00
  0.175 0.175 0.00 1.00
  0.15 0.15 0.00 1.00
  0.125 0.125 0.00 1.00
  0.10 0.10 0.00 1.00
  0.075 0.075 0.00 1.00
  0.05 0.05 0.00 1.00
  0.025 0.025 0.00 1.00
  0.00 0.00 0.00 1.00
EOF
 
 

----- Orjinal Mesaj -----
Kimden: Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>
Tarih: Thursday, July 23, 2009 3:03 pm
Konu: Re: [Pw_forum] inconsistent bands and DOS...
Kime: PWSCF Forum <pw_forum at pwscf.org>



> Dear Gokhan
> How do you think we can help you if you don't provide any detail of your calculations?
> Giuseppe
> On Thursday 23 July 2009 11:46:33 Gokhan GOKOGLU wrote:
> > Dear PWSCF users,
> > I am trying to calculate the electronic band structure of a system. There
> > is a small gap in DOS, but the band structure seems to be metallic. I am
> > using exactly same parameters for both band and DOS calculation. I would be
> > very grateful, if someone could give an idea. Thanks..
>
> > Dr. Gokhan Gokoglu
> > Department of Physics
> > Karabuk University
> > Turkey
> -- 
> ********************************************************
> - Article premier - Les hommes naissent et demeurent
> libres et ?gaux en droits. Les distinctions sociales
> ne peuvent ?tre fond?es que sur l'utilit? commune
> - Article 2 - Le but de toute association politique
> est la conservation des droits naturels et 
> imprescriptibles de l'homme. Ces droits sont la libert?,
> la propri?t?, la s?ret? et la r?sistance ? l'oppression.
> ********************************************************
> Giuseppe Mattioli 
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA 
> v. Salaria Km 29,300 - C.P. 10 
> I 00016 - Monterotondo Stazione (RM) 
> Tel + 39 06 90672836 - Fax +39 06 90672316 
> E-mail: <giuseppe.mattioli at ism.cnr.it>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
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From sanjeev0302 at rediffmail.com  Thu Jul 23 16:05:13 2009
From: sanjeev0302 at rediffmail.com (SanjeevKGupta)
Date: 23 Jul 2009 14:05:13 -0000
Subject: [Pw_forum] e-ph methode
Message-ID: <1248341647.S.3961.17270.f4mail-235-216.rediffmail.com.old.1248357913.21836@webmail.rediffmail.com>

correct reference is:
Phys. Rev. B 54, 16487 - 16501 (1996)
cheers
SKG

On Thu, 23 Jul 2009 15:04:07 +0530  wrote
>
>Dear Ali, 
>
>I think ?Savrasov's paper is a good starting point:
>
>PHYSICAL REVIEW B 54 (23), 1996, Electron-phonon interactions and related physical properties of metals from linear-response theory, S. Y. Savrasov, D. Y. Savrasov
>
>And see References, of course.
>
>Happy reading,
>Eyvaz.
>
>-------------------------------------------------------------------
>Prof. Eyvaz Isaev, 
>Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
>Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
>Condensed Matter Theory Group, Uppsala University, Sweden 
>Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
>--- On Thu, 7/23/09, Ali Tavana  wrote:
>
>> From: Ali Tavana 
>> Subject: [Pw_forum] e-ph methode
>> To: pw_forum at pwscf.org
>> Date: Thursday, July 23, 2009, 12:52 PM
>> 
>> Dear all,
>> 
>> Is there any reference for e-ph coefficient calculation
>> method in QE?
>> 
>> thanks
>> 
>> 
>> ? ? ? 
>> _______________________________________________
>> 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
>

S. K. Gupta
PhD Candidate,
Dept. of Physics,
Bhavnagar University.
Bhavnagar, 364 002., Gujarat.
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From giannozz at democritos.it  Thu Jul 23 17:59:41 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 23 Jul 2009 17:59:41 +0200
Subject: [Pw_forum] inconsistent bands and DOS...
In-Reply-To: <7360bde65811.4a68926d@hacettepe.edu.tr>
References: <7380ff7c324.4a685ba9@hacettepe.edu.tr>	<200907231406.17391.giuseppe.mattioli@mlib.ism.cnr.it>
	<7360bde65811.4a68926d@hacettepe.edu.tr>
Message-ID: <4A6888ED.3050207@democritos.it>

Gokhan GOKOGLU wrote:

> There is a small gap in DOS, but the band structure seems to be metallic.

I repeated your calculations at ecutwfc=35 Ry, which should be
sufficient, and both bands and the dos are metallic

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

From ggokoglu at hacettepe.edu.tr  Fri Jul 24 09:36:14 2009
From: ggokoglu at hacettepe.edu.tr (Gokhan GOKOGLU)
Date: Fri, 24 Jul 2009 10:36:14 +0300
Subject: [Pw_forum] inconsistent bands and DOS...
In-Reply-To: <4A6888ED.3050207@democritos.it>
References: <7380ff7c324.4a685ba9@hacettepe.edu.tr>
	<200907231406.17391.giuseppe.mattioli@mlib.ism.cnr.it>
	<7360bde65811.4a68926d@hacettepe.edu.tr>
	<4A6888ED.3050207@democritos.it>
Message-ID: <73e09bc04c1f.4a698e9e@hacettepe.edu.tr>

Dear Paolo,
Did you get the metallic structure for both up and down spin states? Spin-up 
bands and dos are both metallic, this is evident. But the problem is down-spin states. Did you see
the metallic character for down spins at bands and DOS? Thank you very much for your effort. 
 
Dr. Gokhan Gokoglu
Dept. Physics
Karabuk Univ, TR 

----- Orjinal Mesaj -----
Kimden: Paolo Giannozzi <giannozz at democritos.it>
Tarih: Thursday, July 23, 2009 7:00 pm
Konu: Re: [Pw_forum] inconsistent bands and DOS...
Kime: PWSCF Forum <pw_forum at pwscf.org>

> Gokhan GOKOGLU wrote:
> 
> > There is a small gap in DOS, but the band structure seems to 
> be metallic.
> 
> I repeated your calculations at ecutwfc=35 Ry, which should be
> sufficient, and both bands and the dos are metallic
> 
> Paolo
> -- 
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
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From neelphysics at yahoo.in  Fri Jul 24 13:36:10 2009
From: neelphysics at yahoo.in (Neel Singh)
Date: Fri, 24 Jul 2009 17:06:10 +0530 (IST)
Subject: [Pw_forum] parallel execution of PWscf
Message-ID: <885881.42290.qm@web95002.mail.in2.yahoo.com>

Hi 
I am using LG Quad core processor machine with PWscf running on linux. I want to know whether there is any command to run it parallely on the four processors or by default with simple installation (i.e.,? ./configure and make all) it uses all the four processors?
?
Neel
University of Delhi


      See the Web&#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/
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From paulatto at sissa.it  Fri Jul 24 13:51:38 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Fri, 24 Jul 2009 13:51:38 +0200
Subject: [Pw_forum] parallel execution of PWscf
In-Reply-To: <885881.42290.qm@web95002.mail.in2.yahoo.com>
References: <885881.42290.qm@web95002.mail.in2.yahoo.com>
Message-ID: <op.uxklwciaa8x26q@paulax>

In data 24 luglio 2009 alle ore 13:36:10, Neel Singh  
<neelphysics at yahoo.in> ha scritto:
> I am using LG Quad core processor machine with PWscf running on linux. I  
> want to know whether there is any command to run it parallely on the  
> four processors or by default with simple installation (i.e.,   
> ./configure and make all) it uses all the four processors?

Dear Neel,
QE uses mpi for parallelization. Which means, you have to compile it with  
mpi libraries in order to produce a parallel executable. If the configure  
script can detect any mpi implementation (such as the popular opnmpi) it  
will use them, and print this message:
   Parallel environment detected successfully.
   Configured for compilation of parallel executables.
How to run a code parallelized with mpi depends on its implementation,  
usually something like
   mpirun -np 4 pw.x ...
is required.

Very recently openmp (which is totally different from mpi/openmpi) has  
also been implemented in QE. Although it is  still experimental it does  
not require any specific library (but a openmp-capable compiler) and may  
be more appropriate for a multi-core single-node configuration.

best regards

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

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

From Max.Lawson at unige.ch  Fri Jul 24 14:22:26 2009
From: Max.Lawson at unige.ch (=?ISO-8859-1?Q?Lat=E9vi_Max_LAWSON_DAKU?=)
Date: Fri, 24 Jul 2009 14:22:26 +0200
Subject: [Pw_forum] correction to functional.f90 (4.1): optx identified
 as a meta-GGA functional
In-Reply-To: <4A6825A5.8090102@democritos.it>
References: <4A6740E3.5020904@unige.ch> <4A6825A5.8090102@democritos.it>
Message-ID: <4A69A782.9010109@unige.ch>

Dear Paolo,

Thanks a lot for your answer and explanations.

Please find attached the changes I made to the file 
"Modules/functionals.f90".
With these changes, the olyp functional can be input using either its
shortname or its raw definition "nox+lyp+optx+blyp".


Regards,
Max

On 23. 07. 09 10:56, Paolo Giannozzi wrote:
> Lat?vi Max LAWSON DAKU wrote:
>
>   
>> the OPTX functional was flagged as a meta-GGA.
>>     
>
> thank you for reporting this
>
>   
>> By the way, the following comment is written in functional.90.
>>
>>   !              "olyp"  = "nox+lyp+optx+blyp"!!! UNTESTED !!!
>>
>> Does this mean, simply, that the olyp shortname is not well tested?
>>     
>
> exactly. It should work, because it has been working in some version
> in the past, but if you have the possibility to verify it, please do
> it, report if that comment can be removed
>
>   
>> By the way, I noticed that the keyword "blyp" is used for designating
>> both the blyp XC functional and the lyp gradient correction to
>> correlation. 
>>     
>
> the logic used to label XC functionals, based on four keywords,
> seemed a smart method years ago, but it has been outsmarted by
> the ever-increasing number of XC functionals, and by a choice
> for the meaning of "blyp" that turned out not to be a good one.
> Changing the way XC functionals are labelled (in particular,
> fixing the "blyp" inconsistency you mention) might break old
> pseudopotentials (the XC functional is read from pseudopotential
> files).
>
>   
>> Finally, I've inserted the following lines in the subroutine dft_name(),
>> Line 609:
>>
>>   else if (iexch_==0.and.icorr_==3.and.igcx_==6.and.igcc_==3) then
>>      shortname_ = 'OLYP'
>>     
>
> that's a good solution...your changes will go in the next version
>
> Paolo
>   

-- 
***********************************************
Latevi Max LAWSON DAKU
Departement de chimie physique 
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 

Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103
***********************************************

-------------- next part --------------
--- BAK_functionals.f90	2009-07-23 16:35:14.000000000 +0200
+++ functionals.f90	2009-07-23 18:39:16.000000000 +0200
@@ -258,7 +258,12 @@
     enddo
 
     ! special case : BLYP => B88 for gradient correction on exchange
-    if (matches ('BLYP', dftout) ) call set_dft_value (igcx, 1)
+    ! warning: the keyword BLYP is used for both the XC functional 
+    !          "BLYP" and the Lee-Yang-Parr gradient correction to 
+    !          correlation => in the former case, iexch and igcx 
+    !          shouldn't have been set
+    if (matches('BLYP', dftout) .and. (iexch == notset .and. igcx == notset)) &
+         call set_dft_value (igcx, 1)
 
     ! special case : revPBE
     if (matches ('REVPBE', dftout) ) then
@@ -396,7 +401,7 @@
     logical, external :: matches
 
     isgradient =  (igcx > 0) .or. (igcc > 0) 
-    ismeta     =  (igcx == 7) .or. (igcx == 6 )
+    ismeta     =  (igcx == 7)
 
     ! PBE0
     IF ( iexch==6 .or. igcx ==8 ) exx_fraction = 0.25_DP
@@ -606,6 +611,8 @@
   else if (iexch_==7.and.(icorr_==10.or.icorr_==2).and.igcx_==9.and. &
            igcc_==7) then
      shortname_ = 'B3LYP'
+  else if (iexch_==0.and.icorr_==3.and.igcx_==6.and.igcc_==3) then
+     shortname_ = 'OLYP'
   else
      shortname_ = ' '
   end if

From kazempoor2000 at yahoo.com  Fri Jul 24 16:27:51 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Fri, 24 Jul 2009 07:27:51 -0700 (PDT)
Subject: [Pw_forum] LDA+U
Message-ID: <693737.33137.qm@web112513.mail.gq1.yahoo.com>

Dear all
My results after doing LDA+U is very strange for isolated Ti atoms. For d(alpha)/d(n) I see discontinuities .is our result true? And is any way to correct that?
Another question:If our calculation for U instead in the bulk,? would be done in big supercell, Do I get different value for U or both are same?
thanks? a lot

Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


      
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From giannozz at democritos.it  Fri Jul 24 18:25:14 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 24 Jul 2009 18:25:14 +0200
Subject: [Pw_forum] inconsistent bands and DOS...
In-Reply-To: <73e09bc04c1f.4a698e9e@hacettepe.edu.tr>
References: <7380ff7c324.4a685ba9@hacettepe.edu.tr>	<200907231406.17391.giuseppe.mattioli@mlib.ism.cnr.it>	<7360bde65811.4a68926d@hacettepe.edu.tr>	<4A6888ED.3050207@democritos.it>
	<73e09bc04c1f.4a698e9e@hacettepe.edu.tr>
Message-ID: <4A69E06A.9020600@democritos.it>

Gokhan GOKOGLU wrote:

> Did you get the metallic structure for both up and down spin states? 
> Spin-up bands and dos are both metallic, this is evident. But the
> problem is down-spin states. Did you see the metallic character for
> down spins at bands and DOS?

I see for both bands and DOS at both spins a metallic character,
but I had to look quite carefully! the DOS at Ef for spin down
is not zero, but it is VERY small (look at the data produced
by code dos.x). If you look at the output of the non-scf
calculation used to produce the DOS, you will notice that
the only points of your uniform grid that give a contribution
to the DOS are very close to k=0. So the DOS and the bands are
perfectly consistent

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

From eariel99 at gmail.com  Fri Jul 24 18:28:54 2009
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Fri, 24 Jul 2009 12:28:54 -0400
Subject: [Pw_forum] Fwd: Mixed MPI-OpenMP
In-Reply-To: <be564dcb0907240906l486f8bd4kd132dea85e4fb3e8@mail.gmail.com>
References: <be564dcb0907240906l486f8bd4kd132dea85e4fb3e8@mail.gmail.com>
Message-ID: <be564dcb0907240928p7dd23197nf7afbed73cff121a@mail.gmail.com>

Hi,
I read the following in Paolo's announcement of version 4.1

 * mixed openMP-MPI parallelization: both CP and PWscf have been
   demonstrated to run on 65536 processors

1) How should one compile and run? I could not find it on the manual.

2)  Could someone, please, suggest a strategy to mix OpenMP and MPI
efficiently? How many OpenMP threads per node, how many MPI processes per
node? Just not to begin experimenting from the ground. For a test case, I
have a cluster infiniband-connected, where each node have two Quadcore
Xeons, i.e., 8 cores per node.

Thanks,





-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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From giannozz at democritos.it  Fri Jul 24 18:57:08 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 24 Jul 2009 18:57:08 +0200
Subject: [Pw_forum] Fwd: Mixed MPI-OpenMP
In-Reply-To: <be564dcb0907240928p7dd23197nf7afbed73cff121a@mail.gmail.com>
References: <be564dcb0907240906l486f8bd4kd132dea85e4fb3e8@mail.gmail.com>
	<be564dcb0907240928p7dd23197nf7afbed73cff121a@mail.gmail.com>
Message-ID: <4A69E7E4.7050009@democritos.it>

Eduardo Ariel Menendez Proupin wrote:

> 1) How should one compile and run? I could not find it on the manual.

because it is not (yet) there: the mixed mpi-openmp parallelization
is still for the brave. If you feel brave:

   DFLAGS=...-D__OPENMP _D__FFTW (or -D__ESSL if you have an IBM
   machine with ESSL and AIX, -D__ESSL_LINUX with ESSL and Linux)

   compilation flags for openmp (-openmp for ifort)

   openMP-aware libraries (essl, mkl, acml I think)

   OMP_NUM_THREADS set to the number of desired processes in the
   script that submits the job

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

From giannozz at democritos.it  Fri Jul 24 19:49:01 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 24 Jul 2009 19:49:01 +0200
Subject: [Pw_forum] Fwd: Mixed MPI-OpenMP
In-Reply-To: <4A69E7E4.7050009@democritos.it>
References: <be564dcb0907240906l486f8bd4kd132dea85e4fb3e8@mail.gmail.com>
	<be564dcb0907240928p7dd23197nf7afbed73cff121a@mail.gmail.com>
	<4A69E7E4.7050009@democritos.it>
Message-ID: <73A34A48-AD14-4DA8-BC61-DEE3895A802A@democritos.it>


On Jul 24, 2009, at 18:57 , Paolo Giannozzi wrote:

>    DFLAGS=...-D__OPENMP _D__FFTW (or -D__ESSL if you have an IBM
>    machine with ESSL and AIX, -D__ESSL_LINUX with ESSL and Linux)
>
>    compilation flags for openmp (-openmp for ifort)
>
>    openMP-aware libraries (essl, mkl, acml I think)
>
>    OMP_NUM_THREADS set to the number of desired processes in the
>    script that submits the job


correction:
    DFLAGS=...-D__OPENMP _D__FFTW + ifort -openmp + mkl
is tested and safe; other combinations may still run into trouble
due to conflicts between "internal" OpenMP and autothreading
libraries.

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




From haoweipeng at gmail.com  Fri Jul 24 23:06:12 2009
From: haoweipeng at gmail.com (Haowei Peng)
Date: Fri, 24 Jul 2009 16:06:12 -0500
Subject: [Pw_forum] Pw_forum Digest, Vol 25, Issue 39
In-Reply-To: <mailman.12.1248457767.24402.pw_forum@pwscf.org>
References: <mailman.12.1248457767.24402.pw_forum@pwscf.org>
Message-ID: <7559eb240907241406n5ebbbd84seeb1d5a609c7ac8d@mail.gmail.com>

can I use a parallel compiled version as serial one..
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From lanhaiping at gmail.com  Sat Jul 25 00:57:58 2009
From: lanhaiping at gmail.com (lan haiping)
Date: Sat, 25 Jul 2009 06:57:58 +0800
Subject: [Pw_forum] Pw_forum Digest, Vol 25, Issue 39
In-Reply-To: <7559eb240907241406n5ebbbd84seeb1d5a609c7ac8d@mail.gmail.com>
References: <mailman.12.1248457767.24402.pw_forum@pwscf.org>
	<7559eb240907241406n5ebbbd84seeb1d5a609c7ac8d@mail.gmail.com>
Message-ID: <c92002fa0907241557x36710240m4c2aac0eea71d74@mail.gmail.com>

Of coz, you can .
Just try to  run  pw.x like
" pw.x <pw.in >pw.out "

Regards

On Sat, Jul 25, 2009 at 5:06 AM, Haowei Peng <haoweipeng at gmail.com> wrote:

> can I use a parallel compiled version as serial one..
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From trinh.vo at jpl.nasa.gov  Sat Jul 25 02:00:02 2009
From: trinh.vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Fri, 24 Jul 2009 17:00:02 -0700
Subject: [Pw_forum] (no subject)
Message-ID: <63E24D720DCE7246ABAA722B52D23CDF0153D2B3D777@ALTPHYEMBEVSP10.RES.AD.JPL>

Dear PWSCF Users,

I am looking for part of the code that computes the vacuum level.  Could any of you  tell me where it is in the QE package.  I see in  the subroutine " makov_payne.f90", there is a subroutine called "vacuum_level( x0, zion )".   I briefly looked at it, the result would be printed out as  "corrected vacuum level", so I am not sure if it is the right one.

Thank you,

Trinh Vo

JPL/CalTech
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From lanhaiping at gmail.com  Sat Jul 25 02:15:02 2009
From: lanhaiping at gmail.com (lan haiping)
Date: Sat, 25 Jul 2009 08:15:02 +0800
Subject: [Pw_forum] (no subject)
In-Reply-To: <63E24D720DCE7246ABAA722B52D23CDF0153D2B3D777@ALTPHYEMBEVSP10.RES.AD.JPL>
References: <63E24D720DCE7246ABAA722B52D23CDF0153D2B3D777@ALTPHYEMBEVSP10.RES.AD.JPL>
Message-ID: <c92002fa0907241715hd976750qaeb21d3d55f1e35c@mail.gmail.com>

Hi, Trinh :

I think you should use  the postprocessing code of QE, pp.x . Just looking
through its document,  you can set plot_num =11 to get the potential
distribution of your system.   While, to further obtain the vacuum level,
you need perform  macroscopic average over the static potential, which can
be achieved by average.x routine. And You will find a constant value at
certain vacuum region for this quantity, which is the so-called vacuum
level.

A simple way to get through this issue,  i think , is to play with the
example  supplied  in $QE/examples/WorkFct_example.


Regards,

On Sat, Jul 25, 2009 at 8:00 AM, Vo, Trinh (388C) <trinh.vo at jpl.nasa.gov>wrote:

>  Dear PWSCF Users,
>
>
>
> I am looking for part of the code that computes the vacuum level.  Could
> any of you  tell me where it is in the QE package.  I see in  the subroutine
> ? makov_payne.f90?, there is a subroutine called ?vacuum_level( x0, zion
> )?.   I briefly looked at it, the result would be printed out as  ?corrected
> vacuum level?, so I am not sure if it is the right one.
>
>
>
> Thank you,
>
>
>
> Trinh Vo
>
>
>
> JPL/CalTech
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From trinh.vo at jpl.nasa.gov  Sat Jul 25 03:27:22 2009
From: trinh.vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Fri, 24 Jul 2009 18:27:22 -0700
Subject: [Pw_forum] (no subject)
In-Reply-To: <c92002fa0907241715hd976750qaeb21d3d55f1e35c@mail.gmail.com>
References: <63E24D720DCE7246ABAA722B52D23CDF0153D2B3D777@ALTPHYEMBEVSP10.RES.AD.JPL>
	<c92002fa0907241715hd976750qaeb21d3d55f1e35c@mail.gmail.com>
Message-ID: <63E24D720DCE7246ABAA722B52D23CDF0153D2B3D78B@ALTPHYEMBEVSP10.RES.AD.JPL>

Hi Lan,

Thanks for your message.  I actually like to read the code to see how it is calculated.  However, from what you said, I can trace back where it is.  Also, I am still curious what the subroutine vacuum_level( x0, zion ) in the " makov_payne.f90" is used for ?

Thanks,

Trinh

From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of lan haiping
Sent: Friday, July 24, 2009 5:15 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] (no subject)

Hi, Trinh :

I think you should use  the postprocessing code of QE, pp.x . Just looking through its document,  you can set plot_num =11 to get the potential distribution of your system.   While, to further obtain the vacuum level, you need perform  macroscopic average over the static potential, which can be achieved by average.x routine. And You will find a constant value at certain vacuum region for this quantity, which is the so-called vacuum level.

A simple way to get through this issue,  i think , is to play with the example  supplied  in $QE/examples/WorkFct_example.


Regards,
On Sat, Jul 25, 2009 at 8:00 AM, Vo, Trinh (388C) <trinh.vo at jpl.nasa.gov<mailto:trinh.vo at jpl.nasa.gov>> wrote:

Dear PWSCF Users,



I am looking for part of the code that computes the vacuum level.  Could any of you  tell me where it is in the QE package.  I see in  the subroutine " makov_payne.f90", there is a subroutine called "vacuum_level( x0, zion )".   I briefly looked at it, the result would be printed out as  "corrected vacuum level", so I am not sure if it is the right one.



Thank you,



Trinh Vo



JPL/CalTech

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



--
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com<mailto:lanhaiping at gmail.com>, hplan at pku.edu.cn<mailto:hplan at pku.edu.cn>
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From giannozz at democritos.it  Sat Jul 25 09:26:00 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 25 Jul 2009 09:26:00 +0200
Subject: [Pw_forum] Pw_forum Digest, Vol 25, Issue 39
In-Reply-To: <7559eb240907241406n5ebbbd84seeb1d5a609c7ac8d@mail.gmail.com>
References: <mailman.12.1248457767.24402.pw_forum@pwscf.org>
	<7559eb240907241406n5ebbbd84seeb1d5a609c7ac8d@mail.gmail.com>
Message-ID: <EF5131DA-9F31-454B-B407-0845A8395AF4@democritos.it>


On Jul 24, 2009, at 23:06 , Haowei Peng wrote:

> can I use a parallel compiled version as serial one..

you can. It will be only a little bit slower than the serial version

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




From giannozz at democritos.it  Sat Jul 25 16:41:25 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 25 Jul 2009 16:41:25 +0200
Subject: [Pw_forum] (no subject)
In-Reply-To: <63E24D720DCE7246ABAA722B52D23CDF0153D2B3D777@ALTPHYEMBEVSP10.RES.AD.JPL>
References: <63E24D720DCE7246ABAA722B52D23CDF0153D2B3D777@ALTPHYEMBEVSP10.RES.AD.JPL>
Message-ID: <C53E3141-FFD8-4021-BA9F-EC598BB77D74@democritos.it>


On Jul 25, 2009, at 2:00 , Vo, Trinh (388C) wrote:
> I am looking for part of the code that computes the vacuum level.
>
please read this thread:
http://www.democritos.it/pipermail/pw_forum/2009-June/013228.html

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




From bobjohn.lzu at gmail.com  Sun Jul 26 07:17:46 2009
From: bobjohn.lzu at gmail.com (john Bob)
Date: Sun, 26 Jul 2009 13:17:46 +0800
Subject: [Pw_forum] About fhi2upf.x
Message-ID: <401230aa0907252217h7ad47643r5049c00b5d627ff7@mail.gmail.com>

Dear Pwscf users:

       I meet a problem while using fhi2upf. "Segment fault" occures after
typing in the file name, while converting 22-Ti.LDA.fhi to upf.
22-Ti.LDA.fhi was downloaded from ABINIT website. I don't know whether it is
compilation problem. Converting 01-H.GGA.fhi successed. Convert
56-Ba.GGA.fhi (mentioned in this Forum) also successed. pwscf 405 and 41
seem have the same problem.

   Compiler : intel fortran 9.1 (10.1 tried)
   Mathlib:  mkl8.1

Eager for your answers.



Zhou  Bo
2009.7.26
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From eariel99 at gmail.com  Sun Jul 26 16:05:04 2009
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Sun, 26 Jul 2009 10:05:04 -0400
Subject: [Pw_forum] parallel execution of PWscf
Message-ID: <be564dcb0907260705j464be779t32b618b1ce69dd82@mail.gmail.com>

>I am using LG Quad core processor machine with PWscf running on linux. I
want to know >whether there is any command to run it parallely on the four
processors or by default with >simple installation (i.e.,  ./configure and
make all) it uses all the four processors?

It depends. configure detects your environment and set the options for an
optimal "compilation".

If you have MPI well installed, then configure detects it , and you run it
as Lorenzo explained (mpirun -np path-to-executables/pw.x )

There is another paralellism that you can exploit, although it is not from
espresso, but from the Intel MKL implementation of the BLAS/LAPACK
libraries. With ifort compiler (or other OpenMP capable compiler) and the
Intel MKL libraries well installed, configure detects the MKL and sets the
compilation options automatically to use the MKL. The MKL have OpenMP
parallelism implemented, and you run pw.x like a serial program, but the
matrix operations made by MKL libraries will run parallel. If it works, with
the command top you will see
CPU use higher than 100%, near 400 % if you have a QuadCore.

Take it into account if you compare performance of mpi vs "serial". When I
was unaware of the MKL built-in parallelism got unhappy because mpirun -np 2
pw.x (in a Dual Xeon) was only 30 % faster than just pw.x

Generally, this is slower than paralellization with MPI, but there is at
least one example where OpenMP runs faster.
http://www.democritos.it/pipermail/pw_forum/2008-May/008870.html
and
http://www.democritos.it/pipermail/pw_forum/2008-May/008884.html


If you have Intel or AMD CPU, try to compile espresso with the MKL. For
large calculations, the one for which speed is really important, using the
MKL can provide a factor of 5 in speed.

In summary,
If you just want to do fast calculations for small systems, do not care of
installing the parallel environment.
If you want to calculate large systems, take your time to study the manual.
After some training one can set the system to run efficiently in half a day,
i.e., install Fortran compiler, MKL libraries, MPI, ESPRESSO an do some
tests. Note that the latests distributions of Intel Fortran Compiler include
the MKl, then it is one step less.

Regards
Eduardo

---------- Mensaje reenviado ----------
> From: Neel Singh <neelphysics at yahoo.in>
> To: pw_forum at pwscf.org
> Date: Fri, 24 Jul 2009 17:06:10 +0530 (IST)
> Subject: [Pw_forum] parallel execution of PWscf
> Hi
> I am using LG Quad core processor machine with PWscf running on linux. I
> want to know whether there is any command to run it parallely on the four
> processors or by default with simple installation (i.e.,  ./configure and
> make all) it uses all the four processors?
>
> Neel
> University of Delhi
>
> ------------------------------
>
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From giannozz at democritos.it  Sun Jul 26 22:38:09 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 26 Jul 2009 22:38:09 +0200
Subject: [Pw_forum] About fhi2upf.x
In-Reply-To: <401230aa0907252217h7ad47643r5049c00b5d627ff7@mail.gmail.com>
References: <401230aa0907252217h7ad47643r5049c00b5d627ff7@mail.gmail.com>
Message-ID: <78F37F3A-879F-4FFB-87F5-BFED33F9ACC4@democritos.it>


On Jul 26, 2009, at 7:17 , john Bob wrote:

>        I meet a problem while using fhi2upf.
> "Segment fault" occures after typing in the
> file name, while converting 22-Ti.LDA.fhi to upf.

it works for me

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




From trinh.vo at jpl.nasa.gov  Mon Jul 27 00:04:04 2009
From: trinh.vo at jpl.nasa.gov (Vo, Trinh (388C))
Date: Sun, 26 Jul 2009 15:04:04 -0700
Subject: [Pw_forum] (no subject)
In-Reply-To: <C53E3141-FFD8-4021-BA9F-EC598BB77D74@democritos.it>
References: <63E24D720DCE7246ABAA722B52D23CDF0153D2B3D777@ALTPHYEMBEVSP10.RES.AD.JPL>
	<C53E3141-FFD8-4021-BA9F-EC598BB77D74@democritos.it>
Message-ID: <63E24D720DCE7246ABAA722B52D23CDF0153D2B3D7D6@ALTPHYEMBEVSP10.RES.AD.JPL>

Thanks, Paolo.

Trinh 

-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi
Sent: Saturday, July 25, 2009 7:41 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] (no subject)


On Jul 25, 2009, at 2:00 , Vo, Trinh (388C) wrote:
> I am looking for part of the code that computes the vacuum level.
>
please read this thread:
http://www.democritos.it/pipermail/pw_forum/2009-June/013228.html

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



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

From ismotochi at gmail.com  Mon Jul 27 08:24:16 2009
From: ismotochi at gmail.com (isaac motochi)
Date: Sun, 26 Jul 2009 18:24:16 -1200
Subject: [Pw_forum] surface band structure and dos
Message-ID: <9d6ea92e0907262324x7374a0b3o4579c84803a589fb@mail.gmail.com>

Hi forum friends,
Could anyone please assist me with information on how one can calculate band
structure and density of states on say a 5 bilayer surface

Motochi Isaac
Moi University-Kenya
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From nkxirainbow at gmail.com  Mon Jul 27 08:33:03 2009
From: nkxirainbow at gmail.com (xirainbow)
Date: Mon, 27 Jul 2009 14:33:03 +0800
Subject: [Pw_forum] surface band structure and dos
In-Reply-To: <9d6ea92e0907262324x7374a0b3o4579c84803a589fb@mail.gmail.com>
References: <9d6ea92e0907262324x7374a0b3o4579c84803a589fb@mail.gmail.com>
Message-ID: <21fbc4790907262333u777c7e16hf7f0c5f004850879@mail.gmail.com>

Dear Motochi Isaac:
                The PWcond code provides the complex band structures of the
leads, that is the Bloch states with complex kz in the direction of
transport, describing wave functions exponentially growing or decaying in
the z direction.
Maybe you can get what you want by using PWcond code.

Yours sincerely.

??????????????????????????????????
Hui Wang
Nankai University, Tianjin, China


On 7/27/09, isaac motochi <ismotochi at gmail.com> wrote:
>
> Hi forum friends,
> Could anyone please assist me with information on how one can calculate
> band structure and density of states on say a 5 bilayer surface
>
> Motochi Isaac
> Moi University-Kenya
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From bobjohn.lzu at gmail.com  Mon Jul 27 09:31:44 2009
From: bobjohn.lzu at gmail.com (john Bob)
Date: Mon, 27 Jul 2009 15:31:44 +0800
Subject: [Pw_forum] About fhi2upf.x
In-Reply-To: <78F37F3A-879F-4FFB-87F5-BFED33F9ACC4@democritos.it>
References: <401230aa0907252217h7ad47643r5049c00b5d627ff7@mail.gmail.com>
	<78F37F3A-879F-4FFB-87F5-BFED33F9ACC4@democritos.it>
Message-ID: <401230aa0907270031k7b80ca05o7d94dde60728a5f0@mail.gmail.com>

dear Paolo:

       Thank you for your reply. The tests results are attached.


Checking atom...passed
Checking atom-lsda...passed
Checking atom-pbe...discrepancy in number of scf iterations detected
Reference: 7, You got: 5
discrepancy in pressure detected
Reference: -14.44, You got: -14.46
Checking atom-sigmapbe...discrepancy in pressure detected
Reference: -15.02, You got: -14.98
Checking berry...passed
Checking berry, step 2 ...passed
Checking dipole...passed
Checking electric0...passed
Checking electric1...passed
Checking electric2...passed
Checking eval_infix...passed
Checking eval_infix, step 2 ...discrepancy in HOMO detected
Reference: -8.4542, You got: -8.4544
discrepancy in LUMO detected
Reference: -0.4297, You got: -0.4298
Checking lattice-ibrav0-abc...passed
Checking lattice-ibrav0-cell_parameters+a...passed
Checking lattice-ibrav0-cell_parameters+celldm...passed
Checking lattice-ibrav0-cell_parameters...passed
Checking lattice-ibrav10...passed
Checking lattice-ibrav10-kauto...passed
Checking lattice-ibrav11...passed
Checking lattice-ibrav11-kauto...passed
Checking lattice-ibrav12...passed
Checking lattice-ibrav12-kauto...passed
Checking lattice-ibrav13...passed
Checking lattice-ibrav13-kauto...passed
Checking lattice-ibrav14...passed
Checking lattice-ibrav14-kauto...passed
Checking lattice-ibrav1...passed
Checking lattice-ibrav1-kauto...passed
Checking lattice-ibrav2...passed
Checking lattice-ibrav2-kauto...passed
Checking lattice-ibrav3...passed
Checking lattice-ibrav3-kauto...passed
Checking lattice-ibrav4...passed
Checking lattice-ibrav4-kauto...passed
Checking lattice-ibrav5...passed
Checking lattice-ibrav5-kauto...passed
Checking lattice-ibrav6...passed
Checking lattice-ibrav6-kauto...passed
Checking lattice-ibrav7...passed
Checking lattice-ibrav7-kauto...passed
Checking lattice-ibrav8...passed
Checking lattice-ibrav8-kauto...passed
Checking lattice-ibrav9...passed
Checking lattice-ibrav9-kauto...passed
Checking lda+U_force...discrepancy in force detected
Reference:   0.5445, You got:   0.5447
discrepancy in pressure detected
Reference: 362.42, You got: 361.99
Checking lda+U_gamma...discrepancy in number of scf iterations detected
Reference: 46, You got: 41
discrepancy in force detected
Reference:   0.4682, You got:   0.4681
discrepancy in pressure detected
Reference: 549.51, You got: 546.89
Checking lda+U...passed
Checking lda+U-noU...passed
Checking lda+U-user_ns...passed
Checking lsda-cg...passed
Checking lsda...discrepancy in pressure detected
Reference: -14.96, You got: -14.97
Checking lsda, step 2 ...passed
Checking lsda-mixing_localTF...passed
Checking lsda-mixing_ndim...passed
Checking lsda-mixing_TF...passed
Checking lsda-nelup+neldw...passed
Checking lsda-tot_magnetization...passed
Checking md...passed
Checking md-pot_extrap1...passed
Checking md-pot_extrap2...passed
Checking md-wfc_extrap1...passed
Checking md-wfc_extrap2...passed
Checking metadyn...passed
Checking metaGGA...passed
Checking metal-fermi_dirac...passed
Checking metal-gaussian...passed
Checking metal...passed
Checking metal, step 2 ...passed
Checking metal-tetrahedra...passed
Checking metal-tetrahedra, step 2 ...passed
Checking neb1-H2+H...passed
Checking neb2-H2+H-symm...passed
Checking neb3-H2+H-asym...passed
Checking noncolin-cg...discrepancy in total energy detected
Reference:   -55.699684, You got:   -55.699683
Checking noncolin-constrain_angle...passed
Checking noncolin-constrain_atomic...discrepancy in total energy detected
Reference:   -55.690284, You got:   -55.690268
discrepancy in number of scf iterations detected
Reference: 12, You got: 13
Checking noncolin-constrain_total...discrepancy in total energy detected
Reference:   -55.544783, You got:   -55.544782
discrepancy in number of scf iterations detected
Reference: 32, You got: 33
Checking noncolin...discrepancy in pressure detected
Reference: 193.22, You got: 193.31
Checking noncolin, step 2 ...passed
Checking paw-atom...passed
Checking paw-atom_l=2...passed
Checking paw-atom_lda...passed
Checking paw-atom_spin...discrepancy in total energy detected
Reference:   -41.264991, You got:   -41.264994
discrepancy in number of scf iterations detected
Reference: 6, You got: 12
Checking paw-atom_spin_lda...discrepancy in total energy detected
Reference:   -40.244090, You got:   -40.244093
Checking paw-atom_tqr...passed
Checking paw-bfgs...discrepancy in number of scf iterations detected
Reference: 7, You got: 8
Checking paw-vcbfgs...passed
Checking relax2-bfgs_ndim3...passed
Checking relax2...passed
Checking relax-damped...passed
Checking relax-el...passed
Checking relax...passed
Checking scf-cg...passed
Checking scf-disk_io...passed
Checking scf-gamma...passed
Checking scf...passed
Checking scf, step 2 ...passed
Checking scf-k0...passed
Checking scf-kauto...passed
Checking scf-mixing_beta...passed
Checking scf-mixing_localTF...passed
Checking scf-mixing_ndim...passed
Checking scf-mixing_TF...passed
Checking scf-ncpp...passed
Checking scf-wf_collect...passed
Checking spinorbit...passed
Checking spinorbit, step 2 ...passed
Checking uspp1-coulomb...passed
Checking uspp1...passed
Checking uspp2...discrepancy in pressure detected
Reference: -30.68, You got: -30.67
Checking uspp-cg...passed
Checking uspp...discrepancy in pressure detected
Reference: 0.61, You got: 0.60
Checking uspp, step 2 ...passed
Checking uspp-mixing_localTF...passed
Checking uspp-mixing_ndim...passed
Checking uspp-mixing_TF...passed
Checking uspp-singlegrid...passed
Checking vc-relax1...passed
Checking vc-relax2...passed
Checking vc-relax3...passed
Checking vc-relax4...passed
Checking vdw...passed
================================
pwscf 4.0  compiled with ifort 9.1 cmkl9.0 mpich-1.2.7p , run on 4 nodes.

Are these results OK? I am going to do some phonon concerned
calculation. Are these divergence acceptable?

Thanks

Zhou bo
2009.7.27
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From giannozz at democritos.it  Mon Jul 27 10:05:56 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 27 Jul 2009 10:05:56 +0200
Subject: [Pw_forum] About fhi2upf.x
In-Reply-To: <78F37F3A-879F-4FFB-87F5-BFED33F9ACC4@democritos.it>
References: <401230aa0907252217h7ad47643r5049c00b5d627ff7@mail.gmail.com>
	<78F37F3A-879F-4FFB-87F5-BFED33F9ACC4@democritos.it>
Message-ID: <4A6D5FE4.3070600@democritos.it>

Paolo Giannozzi wrote:

> it works for me

well, no, it doesn't with ifort ...

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

From giannozz at democritos.it  Mon Jul 27 10:33:37 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 27 Jul 2009 10:33:37 +0200
Subject: [Pw_forum] About fhi2upf.x
In-Reply-To: <401230aa0907270031k7b80ca05o7d94dde60728a5f0@mail.gmail.com>
References: <401230aa0907252217h7ad47643r5049c00b5d627ff7@mail.gmail.com>	<78F37F3A-879F-4FFB-87F5-BFED33F9ACC4@democritos.it>
	<401230aa0907270031k7b80ca05o7d94dde60728a5f0@mail.gmail.com>
Message-ID: <4A6D6661.1040201@democritos.it>

In upftools/fhi2upf.f90, replace line 98
   if ( i /= 0 ) then
with
   if ( i /= 0 .or. zval <= 0.0 .or. zval > 100.0 ) then
and recompile. This is a check on the contents of the
first line that should return an error code (i) for
pseudopotentials from abinit web site, but for some
obscure reason it returns i=0 (i.e. no error) in this
specific cases. Thank you for remarking this

> Are these results OK?

they are

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

From eariel99 at gmail.com  Mon Jul 27 17:44:43 2009
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Mon, 27 Jul 2009 11:44:43 -0400
Subject: [Pw_forum] failure with npool
Message-ID: <be564dcb0907270844o342c6370v2bb2845793734974@mail.gmail.com>

Hi,
I have found a problem with a benchmark calculation with pw.x . It aborts
when running with the -npool option.

However, it runs normally without the npool option. The calculation uses 34
k-points.


I have tried with
mpirun -np 32 pw.x -npool 2
mpirun -np 32 pw.x -npool 4
mpirun -np 4 pw.x -npool 2
mpirun -np 4 pw.x -npool 2

in two machines, using OpenMPI and HPMPI, single nodes and multiples nodes.
All the times it fails.

Looking at the output I see the following messages

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from addusdens_r : error #         1
     from addusdens_r : error #         1
     expected  360.00000000, found  101.25021916: wrong charge, increase
ecutrho
     from addusdens_r : error #         1
     expected  360.00000000, found  101.25021916: wrong charge, increase
ecutrho
     expected  360.00000000, found  101.25021916: wrong charge, increase
ecutrho
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...


     stopping ...
     stopping ...
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from addusdens_r : error #         1
     expected  360.00000000, found  101.25021916: wrong charge, increase
ecutrho
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

the previous output was with -npool 4. Using -npool 2 I get outpits like
this

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from addusdens_r : error #         1
     expected  360.00000000, found  180.00040683: wrong charge, increase
ecutrho
     from addusdens_r : error #         1
     expected  360.00000000, found  180.00040683: wrong charge, increase
ecutrho

It looks like hving problems to sum the charge densities of the pools.

Here is the input (the pseudos are from the web site)

 &CONTROL
                 calculation = 'scf' ,
                restart_mode = 'from_scratch' ,
                       outdir = '.' ,
                   pseudo_dir = '.'
                      prefix = 'cdsebench' ,
                      wfcdir = '/tmp',
 /
 &SYSTEM
                       ibrav = 0,
                   celldm(1) = 1.8897261,
                         nat = 40,
                        ntyp = 2,
                     ecutwfc = 30.0 ,
                     ecutrho = 180.0 ,
                 occupations = 'smearing' ,
                     degauss = 0.02 ,
                    smearing = 'gaussian' ,
!                   qcutz=150., q2sigma=2.0, ecfixed=24.0
 /
 &ELECTRONS
            electron_maxstep = 60,
                    conv_thr = 1.0D-6 ,
                 startingpot = 'atomic' ,
                 startingwfc = 'random' ,
!                 mixing_mode = 'TF' ,
                 mixing_beta = 0.7D0,
                 mixing_beta = 0.7D0,
              diagonalization = 'david' ,
                        tqr = .true.
 /

CELL_PARAMETERS hexagonal
     4.373836756  0.000000000  0.000000000
    -2.187115631  3.787739854  0.000000000
     0.000000000  0.000000000 71.411016248

ATOMIC_SPECIES
   Cd  112.41000  Cd.pbe-van.UPF
   Se  78.960000  Se.pbe-van.UPF

ATOMIC_POSITIONS (crystal)
Cd    0.000000000    0.000000000    0.000000000
Cd    0.000000000    0.000000000    0.100000000
Cd    0.000000000    0.000000000    0.200000000
Cd    0.000000000    0.000000000    0.300000000
Cd    0.000000000    0.000000000    0.400000000
Cd    0.000000000    0.000000000    0.500000000
Cd    0.000000000    0.000000000    0.600000000
Cd    0.000000000    0.000000000    0.700000000
Cd    0.000000000    0.000000000    0.800000000
Cd    0.000000000    0.000000000    0.900000000
Cd    0.666663821    0.333312908    0.050000151
Cd    0.666663821    0.333312908    0.150000151
Cd    0.666663821    0.333312908    0.250000151
Cd    0.666663821    0.333312908    0.350000151
Cd    0.666663821    0.333312908    0.450000151
Cd    0.666663821    0.333312908    0.550000151
Cd    0.666663821    0.333312908    0.650000151
Cd    0.666663821    0.333312908    0.750000151
Cd    0.666663821    0.333312908    0.850000151
Cd    0.666663821    0.333312908    0.950000151
Se    0.000000000    0.000000000    0.037565413
Se    0.000000000    0.000000000    0.137565413
Se    0.000000000    0.000000000    0.237565413
Se    0.000000000    0.000000000    0.337565413
Se    0.000000000    0.000000000    0.437565413
Se    0.000000000    0.000000000    0.537565413
Se    0.000000000    0.000000000    0.637565413
Se    0.000000000    0.000000000    0.737565413
Se    0.000000000    0.000000000    0.837565413
Se    0.000000000    0.000000000    0.937565413
Se    0.666665290    0.333319516    0.087565394
Se    0.666665290    0.333319516    0.187565394
Se    0.666665290    0.333319516    0.287565394
Se    0.666665290    0.333319516    0.387565394
Se    0.666665290    0.333319516    0.487565394
Se    0.666665290    0.333319516    0.587565394
Se    0.666665290    0.333319516    0.687565394
Se    0.666665290    0.333319516    0.787565394
Se    0.666665290    0.333319516    0.887565394
Se    0.666665290    0.333319516    0.987565394
K_POINTS automatic
8 8 1 0 0 0


Testing the speed, version 4.1 is a bit slower than 4.0.4 (about 9% more
time in this benchmark: 39.5 vs 36 minutes, using 32 cpus). I guess this is
irrelevant in face of Moore's law.



Thank you,
Best regards

-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez<http://fisica.ciencias.uchile.cl/%7Eemenendez>
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From paulatto at sissa.it  Mon Jul 27 17:48:37 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Mon, 27 Jul 2009 17:48:37 +0200
Subject: [Pw_forum] failure with npool
In-Reply-To: <be564dcb0907270844o342c6370v2bb2845793734974@mail.gmail.com>
References: <be564dcb0907270844o342c6370v2bb2845793734974@mail.gmail.com>
Message-ID: <op.uxqgvbpja8x26q@paulax>

In data 27 luglio 2009 alle ore 17:44:43, Eduardo Ariel Menendez Proupin  
<eariel99 at gmail.com> ha scritto:
>                         tqr = .true.

Dear Eduardo,
I knew real-space augmentation + pools had some problem, I thought I had  
fixed it though. I'll have a look at it as soon as possible, although it  
may take more than a while.

best regards

P.S. If someone who knows both pool parallelization and real space  
augmentation could have a look it would be helpful




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

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

From giannozz at democritos.it  Mon Jul 27 17:53:26 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 27 Jul 2009 17:53:26 +0200
Subject: [Pw_forum] failure with npool
In-Reply-To: <be564dcb0907270844o342c6370v2bb2845793734974@mail.gmail.com>
References: <be564dcb0907270844o342c6370v2bb2845793734974@mail.gmail.com>
Message-ID: <4A6DCD76.2040000@democritos.it>

Eduardo Ariel Menendez Proupin wrote:

> Testing the speed, version 4.1 is a bit slower than 4.0.4 (about 9%
> more time in this benchmark: 39.5 vs 36 minutes, using 32 cpus).

I don't see any good reason why this should happen. Not that I trust
timings. Not since I saw one job running 15% slower after removal of
a variable THAT WASN'T EVEN USED.

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

From akohlmey at cmm.chem.upenn.edu  Mon Jul 27 18:06:18 2009
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 27 Jul 2009 12:06:18 -0400
Subject: [Pw_forum] failure with npool
In-Reply-To: <4A6DCD76.2040000@democritos.it>
References: <be564dcb0907270844o342c6370v2bb2845793734974@mail.gmail.com>
	<4A6DCD76.2040000@democritos.it>
Message-ID: <1248710778.12990.11987.camel@zero>

On Mon, 2009-07-27 at 17:53 +0200, Paolo Giannozzi wrote:
> Eduardo Ariel Menendez Proupin wrote:
> 
> > Testing the speed, version 4.1 is a bit slower than 4.0.4 (about 9%
> > more time in this benchmark: 39.5 vs 36 minutes, using 32 cpus).
> 
> I don't see any good reason why this should happen. Not that I trust

memory alignment of data structures and arrays.

particularly with intel fortran, the compiler will automatically
try to use SSE instructions instead of regular FP math, as those
can process two double precision numbers at the same time. however,
SSE requires 16-byte aligned data or you take a performance hit, 
but the standard malloc usually only returns 8-byte aligned data.


> timings. Not since I saw one job running 15% slower after removal of
> a variable THAT WASN'T EVEN USED.

depends on where the variable was placed. if it was in a place, where
the compiler was not allowed to optimize it away, than you can run
into exactly the alignment issue that i was mentioning.

cheers,
   axel.

> 
> P.

-- 
=======================================================================
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 democritos.it  Mon Jul 27 18:45:53 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 27 Jul 2009 18:45:53 +0200
Subject: [Pw_forum] failure with npool
In-Reply-To: <be564dcb0907270844o342c6370v2bb2845793734974@mail.gmail.com>
References: <be564dcb0907270844o342c6370v2bb2845793734974@mail.gmail.com>
Message-ID: <4A6DD9C1.4070803@democritos.it>

Eduardo Ariel Menendez Proupin wrote:
    1
>      from addusdens_r : error #         1
>      expected  360.00000000, found  101.25021916: wrong charge

actually it looks like the charge is good: it is the test that is
wrong! quick fix:

diff -w -i -b -r1.37 PW/realus.f90
1472c1472
<       USE mp_global,        ONLY : intra_pool_comm
---
 >       USE mp_global,        ONLY : intra_pool_comm, inter_pool_comm
1526a1527
 >       CALL mp_sum(  charge , inter_pool_comm )

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

From kazempoor2000 at yahoo.com  Mon Jul 27 18:51:26 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Mon, 27 Jul 2009 09:51:26 -0700 (PDT)
Subject: [Pw_forum] LDA+U isolated atom
Message-ID: <428325.51466.qm@web112520.mail.gq1.yahoo.com>

Dear all
By using script in wiki I obtain U for isolated Ti atom. but the value of? 
#!/bin/bash
PSEUDO_DIR=/home/kazempou/WORK_FHI/TiO2/u-linear-response-atom
PW_ROOT=/home/akazem/espresso-4.0.2/
TMP_DIR=/home/kazempou/tmp/Ucalc
TMP_DIR1=/home/kazempou/tmp/Ucalc1
mkdir -p $TMP_DIR
mkdir -p $TMP_DIR1

WORK=$( pwd )

rm -rf $TMP_DIR/*
rm -rf $TMP_DIR1/*

mkdir $WORK/results_Mn_ucalc
cd $WORK/results_Mn_ucalc
# unperturbed self-consistent calculation
cat > Ti.scf.in << EOF
?&control
??? calculation = 'scf'
??? restart_mode='from_scratch',
??? prefix='Ti',
??? pseudo_dir = '$PSEUDO_DIR',
??? outdir='$TMP_DIR'
?/
?&system
??? ibrav=? 0, celldm(1)=20, nat=? 1, ntyp= 1,
??? ecutwfc = 45 , ecutrho=400 , 
??? lda_plus_u = .true.
??? hubbard_u(1) = 1.D-20, 
??? starting_magnetization(1)= 1.0,
??? occupations='smearing', smearing='gauss', degauss=0.01,
??? nspin=2,
?/
?&electrons
??? mixing_beta = 0.7
??? conv_thr =? 1.0d-6
?/
CELL_PARAMETERS
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
ATOMIC_SPECIES
Ti?? 47 ti.optgga2.fhi.UPF
ATOMIC_POSITIONS {crystal}
Ti 0.5 0.5 0.5
K_POINTS {gamma}
EOF

/home/kazempou/Desktop/espresso-4.0.5/bin/pw.x < Ti.scf.in > Ti.scf.out 


for a in 0.0 -0.1 0.1? -0.2 0.2?? ; do
rm -rf $TMP_DIR/*

# perturbed calculations (finite alpha)
rm -f Ti.scf.in
cat > Ti.scf.in << EOF
?&control
??? calculation = 'scf'
??? restart_mode='from_scratch',
??? prefix='Ti',
??? pseudo_dir = '$PSEUDO_DIR',
??? outdir='$TMP_DIR'
?/
?&system
??? ibrav=? 0, celldm(1)=20, nat=? 1,? ntyp= 1,
??? ecutwfc = 45.0 , ecutrho=400 , 
??? lda_plus_u = .true.
??? hubbard_u(1) = 1.D-20, 
??? starting_magnetization(1)= 1.0,
??? occupations='smearing', smearing='gauss', degauss=0.01,
??? nspin=2,
??? hubbard_alpha(1)=$a
?/
?&electrons
??? diagonalization = 'cg'
??? mixing_beta = 0.7
??? conv_thr =? 1.0d-6
??? startingpot = 'file'
??? startingwfc = 'file'
??? diago_thr_init = 1.d-12
?/
CELL_PARAMETERS
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
ATOMIC_SPECIES
Ti?? 47? ti.optgga2.fhi.UPF
ATOMIC_POSITIONS {crystal}
Ti 0.5 0.5 0.5
K_POINTS {gamma}
EOF

/home/kazempou/Desktop/espresso-4.0.5/bin/pw.x < Ti.scf.in > Ti.pert_$a.out

done



thanks? a lot



Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


      
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From wshen02 at gmail.com  Tue Jul 28 01:12:10 2009
From: wshen02 at gmail.com (=?UTF-8?B?5paH5rKI?=)
Date: Mon, 27 Jul 2009 16:12:10 -0700
Subject: [Pw_forum] Dear all,
	anybody knows what is the unit for the spin polarzation and charge
	density for the plotting file provided by pp.x?
Message-ID: <2c9df8a80907271612h514b9d84o75a2637156c4dff6@mail.gmail.com>

Hi, Dear all,
currently I am trying to use the output file from pp.x for the spin
polarization and charge density to calculate the spin polarization and
charge sit on each atom.

Does anybody know what is the unit for the densities in the output file of
pp.x both for spin polarization and charge density?


A lot of Thanks


Best

Wen Shen

Ph.D Candidate

Georgetown University
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From wshen02 at gmail.com  Tue Jul 28 01:23:36 2009
From: wshen02 at gmail.com (=?UTF-8?B?5paH5rKI?=)
Date: Mon, 27 Jul 2009 16:23:36 -0700
Subject: [Pw_forum] Dear all,
	can someone tell me why my force for the relax calculation get to
	NAN?
Message-ID: <2c9df8a80907271623u292a36d0md6d3a24d685f101b@mail.gmail.com>

when I do a relaxation calculation for the Cr atom sit on the CuN surface.
the calculation always get the Total force as NAN
I grep the Total force from my out put file
 Total force =          NAN     Total SCF correction =     0.000851
     Total force =          NAN     Total SCF correction =     0.001184
     Total force =          NAN     Total SCF correction =     0.000620
     Total force =          NAN     Total SCF correction =     0.000731
     Total force =          NAN     Total SCF correction =     0.000699
     Total force =          NAN     Total SCF correction =     0.001291
     Total force =          NAN     Total SCF correction =     0.000744
     Total force =          NAN     Total SCF correction =     0.001344
     Total force =          NAN     Total SCF correction =     0.001741
     Total force =          NAN     Total SCF correction =     0.000733
     Total force =          NAN     Total SCF correction =     0.001029
     Total force =          NAN     Total SCF correction =     0.000619
     Total force =          NAN     Total SCF correction =     0.001437
     Total force =          NAN     Total SCF correction =     0.000516
     Total force =          NAN     Total SCF correction =     0.000703
And finally the calculation comes to an end as the error
 from bfgs : error #         1
bfgs history already reset at previous step
I read the discussion on bfgs errors, people at least get the Total force,
can anybody tell me what is the problem.
My input file is as follows

 &CONTROL
    calculation   = 'relax',
    restart_mode  = 'from_scratch',
    outdir        = './scratch1',
    PSEUDO_DIR    = './',
    verbosity     = 'high',
    wf_collect    = .t.,
    tprnfor       = .t.,
 /
 &SYSTEM
    ibrav         =  0,
    celldm(1)     =  6.95,
    nat           =  50,
    ntyp          =  3,
    ecutwfc       =  30.0d0,
    ecutrho       =  240.0d0,
    nbnd          =  280,
    occupations   =  'smearing',
    degauss       =  0.01d0,
    smearing      =  'mp',
    nspin = 2
  starting_magnetization(3)= 0.01,
    lda_plus_u=.true.  Hubbard_U(3)=4.7,
 /
 &ELECTRONS
    conv_thr     =  1.0d-7,
    mixing_mode  =  'local-TF',
    Mixing_beta  =  0.3d0,
    diagonalization = 'cg',
 /
&IONS
    upscale = 10.0d0,
/
ATOMIC_SPECIES
 Cu   63.55    Cu.pbe-d-rrkjus.UPF
 N    14.007   N.pbe-rrkjus.UPF
 Cr   51.9961   Cr.pbe-sp-van.UPF
ATOMIC_POSITIONS
Cr       0.000000000   0.500000000   1.617097960
N        0.000000000   0.033485659   1.300651193
Cu       0.000000000   0.500000000   0.914604714
Cu       0.479729230   0.010025581   1.092991536
Cu       0.509849811   0.500000000   0.484981840
Cu       0.000000000  -0.012342787   0.487244546
Cu       0.000000000   0.500000000   0.000000000
Cu       0.499999748  -0.000000018   0.000000000
Cu       0.000000000  -0.012342787  -0.487244546
Cu       0.509849811   0.500000000  -0.484981840
Cu       0.479729230   0.010025581  -1.092991536
Cu       0.000000000   0.500000000  -0.914604714
N        0.000000000   0.033485659  -1.300651193
Cr       0.000000000   0.500000000  -1.617097960
N        1.000000000  -0.001186178   1.063754946
N        0.000000000   0.966514341   1.300651193
N        1.000000000   1.001186178   1.063754946
Cu       1.000000000   0.500000000   1.032716156
Cu       0.000000000   1.500000000   1.243320618
Cu       1.000000000   1.500000000   1.039781621
Cu       1.520270770   0.010025581   1.092991536
Cu       0.479729230   0.989974419   1.092991536
Cu       1.520270770   0.989974419   1.092991536
Cu       1.490150189   0.500000000   0.484981840
Cu       0.485102831   1.500000000   0.513536013
Cu       1.514897169   1.500000000   0.513536013
Cu       1.000000000  -0.010730065   0.508502844
Cu       0.000000000   1.012342787   0.487244546
Cu       1.000000000   1.010730065   0.508502844
Cu       1.000000000   0.500000000   0.000000000
Cu       0.000000000   1.500000000   0.000000000
Cu       1.000000000   1.500000000   0.000000000
Cu       1.500000252  -0.000000018   0.000000000
Cu       0.499999748   1.000000018   0.000000000
Cu       1.500000252   1.000000018   0.000000000
Cu       1.000000000  -0.010730065  -0.508502844
Cu       0.000000000   1.012342787  -0.487244546
Cu       1.000000000   1.010730065  -0.508502844
Cu       1.490150189   0.500000000  -0.484981840
Cu       0.485102831   1.500000000  -0.513536013
Cu       1.514897169   1.500000000  -0.513536013
Cu       1.520270770   0.010025581  -1.092991536
Cu       0.479729230   0.989974419  -1.092991536
Cu       1.520270770   0.989974419  -1.092991536
Cu       1.000000000   0.500000000  -1.032716156
Cu       0.000000000   1.500000000  -1.243320618
Cu       1.000000000   1.500000000  -1.039781621
N        1.000000000  -0.001186178  -1.063754946
N        0.000000000   0.966514341  -1.300651193
N        1.000000000   1.001186178  -1.063754946
CELL_PARAMETERS
2.0 0.0 0.0
0.0 2.0 0.0
0.0 0.0 7.0
K_POINTS {automatic}
6 6 1 0 0 0Cu       1.000000000  -0.010730065  -0.508502844
Cu       0.000000000   1.012342787  -0.487244546
Cu       1.000000000   1.010730065  -0.508502844
Cu       1.490150189   0.500000000  -0.484981840
Cu       0.485102831   1.500000000  -0.513536013
Cu       1.514897169   1.500000000  -0.513536013
Cu       1.520270770   0.010025581  -1.092991536
Cu       0.479729230   0.989974419  -1.092991536
Cu       1.520270770   0.989974419  -1.092991536
Cu       1.000000000   0.500000000  -1.032716156
Cu       0.000000000   1.500000000  -1.243320618
Cu       1.000000000   1.500000000  -1.039781621
N        1.000000000  -0.001186178  -1.063754946
N        0.000000000   0.966514341  -1.300651193
N        1.000000000   1.001186178  -1.063754946
CELL_PARAMETERS
2.0 0.0 0.0
0.0 2.0 0.0
0.0 0.0 7.0
K_POINTS {automatic}
12 12 1 0 0 0
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From matteo at umn.edu  Tue Jul 28 01:25:56 2009
From: matteo at umn.edu (Matteo Cococcioni)
Date: Mon, 27 Jul 2009 18:25:56 -0500
Subject: [Pw_forum] LDA+U
In-Reply-To: <693737.33137.qm@web112513.mail.gq1.yahoo.com>
References: <693737.33137.qm@web112513.mail.gq1.yahoo.com>
Message-ID: <4A6E3784.5000104@umn.edu>


Dear Ali,

your email is confusing so I don't know if I will be able to answer.

calculations of U on isolated atoms are problematic (why do you want to 
do that?) because the system has a discrete set of
energy levels and so linear response based on the continuum variation of 
on-site occupations have little meaning. Also there is no
way the electrons can move on other energy levels when you perturb 
entire l multiplets unless the pertubation is of the same order
of the energy difference.

yes if you compute the U in the bulk (a supercell is a bulk calculation) 
you obtain a different value. you actually need to
study the convergence of U with the size of the supercell used in its 
calculation.

hope this helps.

regards,

Matteo



ali kazempour wrote:
> Dear all
> My results after doing LDA+U is very strange for isolated Ti atoms. 
> For d(alpha)/d(n) I see discontinuities .is our result true? And is 
> any way to correct that?
> Another question:If our calculation for U instead in the bulk,  would 
> be done in big supercell, Do I get different value for U or both are same?
> thanks  a lot
>
> Ali Kazempour
> Physics department, Isfahan University of Technology
> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733
> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Matteo Cococcioni
Department of Chemical Engineering and Materials Science,
University of Minnesota
421 Washington Av. SE
Minneapolis, MN 55455
Tel. +1 612 624 9056    Fax +1 612 626 7246
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 


From giannozz at democritos.it  Tue Jul 28 08:52:08 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 28 Jul 2009 08:52:08 +0200
Subject: [Pw_forum] Dear all,
	can someone tell me why my force for the relax calculation get to
	NAN?
In-Reply-To: <2c9df8a80907271623u292a36d0md6d3a24d685f101b@mail.gmail.com>
References: <2c9df8a80907271623u292a36d0md6d3a24d685f101b@mail.gmail.com>
Message-ID: <F743094E-6FB8-4490-B872-748487809592@democritos.it>


On Jul 28, 2009, at 1:23 , ?? wrote:

> the calculation always get the Total force as NAN

please provide a complete output file

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




From neelphysics at yahoo.in  Tue Jul 28 11:54:14 2009
From: neelphysics at yahoo.in (Neel Singh)
Date: Tue, 28 Jul 2009 15:24:14 +0530 (IST)
Subject: [Pw_forum] Not getting right Band structure
Message-ID: <529503.37396.qm@web95013.mail.in2.yahoo.com>



--- On Tue, 28/7/09, Neel Singh <neelphysics at yahoo.in> wrote:



Hi all,

?I am new to PWSCF and trying to calculate Band structure of YVO4 but facing two problems ?

1.)No band is plotted in grpah above 0.0 value. The band structure is very large? , as in the? band? Output file? it is calculated like 

?End of band structure calculation

????????? k = 0.0000 0.0000 0.0000???? band energies (ev):

-12.5188 -12.0378 -11.9977 -11.5969 -11.2203 -11.0959 -10.5816 -10.5411
?? -10.4664 -10.4588 -10.0894 -10.0558? -9.6071? -9.5783? -9.0182? -8.9833
???? 0.3058?? 0.6382?? 0.7747?? 0.9726?? 1.3117?? 1.4323?? 1.4740?? 1.5240
means band gap at gamma = 0.3058-(-8.9833)=
 8.2891
?which is very large ??

2) In the output of SCF and Bands , the output file has 4 warnings 

?warning: symmetry operation #? 3 not allowed.?? fractional translation:
?????? 0.0000000 -0.5000000? 0.1164604? in crystal coordinates
???? warning: symmetry operation #? 4 not allowed.?? fractional translation:
?????? 0.0000000? 0.0000000? 0.1164604? in crystal coordinates
???? warning: symmetry operation # 25 not allowed.?? fractional translation:
?????? 0.0000000? 0.0000000? 0.1164604? in crystal coordinates
???? warning: symmetry operation # 26 not allowed.?? fractional translation:
?????? 0.0000000 -0.5000000? 0.1164604? in
 crystal coordinates

for this I have already increase the following quantities? in the? increments
kinetic-energy cutoff???? =????? 40.0000? Ry to 60
???? charge density cutoff???? =???? 250.0000? Ry to 400
But still the warnings are there.

Please help me. I will be very thankful. My Inputs for the calculations are following: 

SCF INPUTS

&control
??? calculation='scf',
??? restart_mode='from_scratch',
??? prefix='yvo'
??? pseudo_dir = '/home/physics/pseudo/',
??? outdir='/home/physics/work/yvo/temp'
?/
?&system
??? ibrav =1, a=7.118300514, b= 7.118300514, c=6.289300454
, nat =24, ntyp= 3,? ecutwfc = 40.0,ecutrho=250,
?occupations='smearing',
 smearing='mp', degauss=0.01, 


?/
?&electrons
??? mixing_beta = 0.7
??? diagonalization = 'david'
??? conv_thr =? 1.0e-4
/
?&ions
?/

ATOMIC_SPECIES
? Y???? 88.90585???? Y.pbe-nsp-van.UPF
? V???? 50.9415????? V.pbe-sp-van.UPF
? O???? 15.9994????? O.pbe-van_ak.UPF
ATOMIC_POSITIONS {angstrom}
Y???????????? 0.000000000?? 5.338725356??? 0.786162553
Y???????????? 3.559150238?? 1.779575118??? 3.930812762
Y???????????? 3.559150238??
 5.338725356??? 2.358487657
Y???????????? 0.000000000?? 1.779575118??? 5.503137866
V???????????? 0.000000000?? 1.779575118??? 2.358487657
V???????????? 3.559150238?? 5.338725356??? 5.503137866
V???????????? 0.000000000?? 5.338725356??? 3.930812762
V???????????? 3.559150238?? 1.779575118??? 0.786162553
O???????????? 0.000000000?? 3.090765987???
 1.262891534
O???????????? 3.559150238?? 6.649916224??? 4.407541744
O???????????? 3.559150238?? 4.027534488??? 4.407541744
O???????????? 0.000000000?? 0.468384251??? 1.262891534
O???????????? 5.807109607?? 5.338725356??? 2.835216639
O???????????? 4.870341106?? 1.779575118??? 5.979866849
O???????????? 3.559150238?? 3.090765987??? 1.881758675
O????????????
 0.000000000?? 6.649916224??? 5.026408885
O???????????? 0.000000000?? 4.027534488??? 5.026408885
O???????????? 3.559150238?? 0.468384251??? 1.881758675
O???????????? 4.870341106?? 5.338725356??? 0.30943357
O???????????? 5.807109607?? 1.779575118??? 3.45408378
O???????????? 1.311190868?? 1.779575118??? 3.45408378
O???????????? 2.247959369?? 5.338725356???
 0.30943357
O???????????? 2.247959369?? 1.779575118??? 5.979866849
O???????????? 1.311190868?? 5.338725356??? 2.835216639

K_POINTS {automatic}
? 2 2 2 0 0 0

------------------------------------------------------------------------------------------------
???????????????????????????????????? BANDS INPUT
---------------------------------------------------------------------------------------------------

&control
??? calculation='bands'
??? pseudo_dir = '/home/physics/pseudo/',
???
 outdir='/home/physics/work/yvo/temp',
??? prefix='yvo',
? 
?/
?&system
??? ibrav =1, a=7.118300514, b= 7.118300514, c=6.289300454, nat=24, ntyp=3, 
ecutwfc = 40.0,ecutrho=250, occupations='smearing', smearing='mp', degauss=0.01, nbnd= 98, 
??? 
?/
?&electrons
?? mixing_beta=0.7
?? conv_thr=1.0e-4
?diagonalization = 'david'
/
&ions
?/

ATOMIC_SPECIES
?Y?????? 88.90585???? Y.pbe-nsp-van.UPF
? V????? 50.9415????? V.pbe-sp-van.UPF
? O???? 15.9994????? O.pbe-van_ak.UPF
ATOMIC_POSITIONS {angstrom}
Y???????????? 0.000000000?? 5.338725356???
 0.786162553
..
..
..
O? ............ ?????  

K_POINTS
?26
0.000 0.000 0.000? 1
0.000 0.000 0.125? 1
0.000 0.000 0.250? 1
0.000 0.000 0.375? 1
0.000 0.000 0.500? 1???????????????????????????? 
0.125 0.125 0.500? 1???????????????????????????? 
0.250 0.250 0.500? 1???????????????????????????? 
0.375 0.375 0.500?
 1??????????????????????????? 
0.500 0.500 0.500? 1???????????????????????????? 
0.500 0.500 0.333? 1???????????????????????????? 
0.500 0.500 0.166? 1???????????????????????????? 
0.500 0.500 0.000? 1???????????????????????????? 
0.375
 0.375 0.000? 1???????????????????????????? 
0.250 0.250 0.000? 1???????????????????????????? 
0.125 0.125 0.000? 1???????????????????????????? 
0.000 0.000 0.000? 1???????????????????????????? 
0.000 0.000 0.166?
 1??????????????????????????? 
0.000 0.000 0.333? 1???????????????????????????? 
0.000 0.166 0.500? 1?????????????????????????? 
0.000 0.333 0.500? 1??????????????????????????? 
0.000 0.500 0.500? 1???????????????????????????? 
0.000 0.500 0.333?
 1???????????????????????????? 
0.000 0.500 0.166? 1???????????????????????????? 
0.000 0.500 0.000? 1???????????????????????????? 
0.000 0.333 0.000? 1???????????????????????????? 
0.000 0.166 0.000? 1
 

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

&inputpp
??? prefix? = 'yvo'
??? outdir = '/home/physics/work/yvo/temp'
??? filband = 'yvobands.dat'
/

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

yvobands.dat
-15? 10
yvobands.xmgr
yvobands.ps
6.1088
1.0? 6.1088

--------------------------------------------------------
-------------------------------------------------- please help . Thanks in Advance



With Regards.
Neel Singh 
University of Delhi
India,







       Looking for local information? Find it on  Yahoo! Local


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From paulatto at sissa.it  Tue Jul 28 12:07:01 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 28 Jul 2009 12:07:01 +0200
Subject: [Pw_forum] Not getting right Band structure
In-Reply-To: <529503.37396.qm@web95013.mail.in2.yahoo.com>
References: <529503.37396.qm@web95013.mail.in2.yahoo.com>
Message-ID: <op.uxrvpz0ba8x26q@paulax>

In data 28 luglio 2009 alle ore 11:54:14, Neel Singh  
<neelphysics at yahoo.in> ha scritto:
> means band gap at gamma = 0.3058-(-8.9833)=  8.2891
>  which is very large ??

Not necessarily, the offset of band in a periodic system is arbitrary. You  
need to know where you Fermi energy is, or which are the HOMO and LUMO of  
your system to find the gap.


> 2) In the output of SCF and Bands , the output file has 4 warnings

This a very frequently asked question, please see the corresponing entry  
in the manual:
http://www.pwscf.org/guide/2.1.2/html-node/node56.html
http://www.pwscf.org/guide/2.1.2/html-node/node57.html


> for this I have already increase the following quantities  in the   
> increments
> kinetic-energy cutoff     =      40.0000  Ry to 60
>      charge density cutoff     =     250.0000  Ry to 400
> But still the warnings are there.

It is not a big increment of the cutoff that will solve this problem, but  
a small increment or nr1, nr2 nr3

cheers, and good work

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

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

From neelphysics at yahoo.in  Tue Jul 28 13:32:01 2009
From: neelphysics at yahoo.in (Neel Singh)
Date: Tue, 28 Jul 2009 17:02:01 +0530 (IST)
Subject: [Pw_forum] Intallation on Itanium Processor
Message-ID: <706615.23763.qm@web95006.mail.in2.yahoo.com>

Hi to All,

?I want to Know , weather PWSCF is compatible on Itanium I7920 processor (64? Bit Processor) or not ?? 
Thanks for your suggestions.

With regards,
Neel Singh
Univeristy of Delhi



      Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com
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From giannozz at democritos.it  Tue Jul 28 14:45:52 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 28 Jul 2009 14:45:52 +0200
Subject: [Pw_forum] Intallation on Itanium Processor
In-Reply-To: <706615.23763.qm@web95006.mail.in2.yahoo.com>
References: <706615.23763.qm@web95006.mail.in2.yahoo.com>
Message-ID: <4D9843D2-28B4-4D9D-9E93-8C587C78DF91@democritos.it>


On Jul 28, 2009, at 13:32 , Neel Singh wrote:

> I want to Know , weather PWSCF is compatible on
> Itanium I7920 processor (64  Bit Processor) or not ??

the correct question is whether your Itanium I7920
64-bit processor is compatible with PWscf. Has
your system working, non-buggy f95 compiler and
libraries? if so, it is compatible.

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




From mastermik at gmail.com  Tue Jul 28 15:26:29 2009
From: mastermik at gmail.com (Mikiyas Tsegaye)
Date: Tue, 28 Jul 2009 09:26:29 -0400
Subject: [Pw_forum] graphene phonon dispersion problem
Message-ID: <4772D337-0891-46AC-8A78-B51A623E0BE5@gmail.com>

Dear all,

I get the following message after running a phonon dispersion  
calculation for graphite.

****************************************************************************************************
message from matdyn routine


Z* not found in file graphite.fc, TO-LO splitting at q=0 will be absent
A direction for q was not specified: TO-LO splitting will be absent

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

I thought the solution would be to include epsil = .true. in the ph  
input file, but that makes the calculation crash at that step. Also,  
I'm not quite sure what it means by "direction of q not specified". my  
q inputs in the matdyn.in file look fine (gamma-K-M-gamma) and they  
actually do produce a dispersion plot, but it has more branches than  
are physically allowed, and they are quite jagged.

I would appreciate some help. thanks in advance.

- Mikiyas Tsegaye
   University of Virginia, Dept of ECE
   Carlottesville, VA, USA 
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From giannozz at democritos.it  Tue Jul 28 15:55:00 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 28 Jul 2009 15:55:00 +0200
Subject: [Pw_forum] Dear all,
 anybody knows what is the unit for the spin polarzation and
 charge	density for the plotting file provided by pp.x?
In-Reply-To: <2c9df8a80907271612h514b9d84o75a2637156c4dff6@mail.gmail.com>
References: <2c9df8a80907271612h514b9d84o75a2637156c4dff6@mail.gmail.com>
Message-ID: <4A6F0334.7090702@democritos.it>

?? wrote:.

> Does anybody know what is the unit for the densities in the output file 
> of pp.x both for spin polarization and charge density?

please read this and messages in the same thread:
http://www.democritos.it/pipermail/pw_forum/2008-September/010079.html

You could have found it and many other messages by searching
"units" and "charge" in the pw_forum archives

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

From eariel99 at gmail.com  Tue Jul 28 16:19:15 2009
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Tue, 28 Jul 2009 10:19:15 -0400
Subject: [Pw_forum] failure with npool
In-Reply-To: <be564dcb0907271239m1276eb1cn8f84317b310618a6@mail.gmail.com>
References: <be564dcb0907271239m1276eb1cn8f84317b310618a6@mail.gmail.com>
Message-ID: <be564dcb0907280719n5a7305b7wa0c096958f69b0b3@mail.gmail.com>

Dear Paolo,
I made the correction and recompiled. Regretfully, it fails with the same
error.
Commenting the tqr input  keyword it works, however much slower.

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from addusdens_r : error #         1
     expected  360.00000000, found  180.00057894: wrong charge, increase
ecutrho
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Best regards
Eduardo


> ---------- Mensaje reenviado ----------
> From: Paolo Giannozzi <giannozz at democritos.it>
> To: PWSCF Forum <pw_forum at pwscf.org>
> Date: Mon, 27 Jul 2009 18:45:53 +0200
> Subject: Re: [Pw_forum] failure with npool
> Eduardo Ariel Menendez Proupin wrote:
>   1
>
>>     from addusdens_r : error #         1
>>     expected  360.00000000, found  101.25021916: wrong charge
>>
>
> actually it looks like the charge is good: it is the test that is
> wrong! quick fix:
>
> diff -w -i -b -r1.37 PW/realus.f90
> 1472c1472
> <       USE mp_global,        ONLY : intra_pool_comm
> ---
> >       USE mp_global,        ONLY : intra_pool_comm, inter_pool_comm
> 1526a1527
> >       CALL mp_sum(  charge , inter_pool_comm )
>
> P.
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
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From eariel99 at gmail.com  Tue Jul 28 16:24:50 2009
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Tue, 28 Jul 2009 10:24:50 -0400
Subject: [Pw_forum] failure with npool
In-Reply-To: <be564dcb0907280719n5a7305b7wa0c096958f69b0b3@mail.gmail.com>
References: <be564dcb0907271239m1276eb1cn8f84317b310618a6@mail.gmail.com>
	<be564dcb0907280719n5a7305b7wa0c096958f69b0b3@mail.gmail.com>
Message-ID: <be564dcb0907280724v3a907d43g6c972a4cd9624d3e@mail.gmail.com>

Dear Paolo, Axel, and every one,

Regarding the timings of 4.1 and 4.0.4, I sent yesterday the outputs
produced by both codes.
Due to the size of the attachements, the message is awaiting for moderation.
I am not sure if I can send attachments to the forum :-(. In any case, find
below a summary of the differences of the outputs.I see 4.1 mades 8 SCF
iterations, while, 4.0.4 made 9, but in shorter time. Here is a collection
of most noticeable differences. I hope it helps
tuning.

< Program PWSCF v.4.0.4 starts ...
< Today is 25Jul2009 at 11:19:38
---
> Program PWSCF v.4.1 starts ...
> Today is 26Jul2009 at 12:15:35
16,26c16
< Found additional translation: 0.0000 0.0000 0.1000
< Found additional translation: 0.0000 0.0000 0.2000
< Found additional translation: 0.0000 0.0000 0.3000
< Found additional translation: 0.0000 0.0000 0.4000
< Found additional translation: 0.0000 0.0000 -0.5000
< Found additional translation: 0.0000 0.0000 -0.4000
< Found additional translation: 0.0000 0.0000 -0.3000
< Found additional translation: 0.0000 0.0000 -0.2000
< Found additional translation: 0.0000 0.0000 -0.1000
<
< Iterative solution of the eigenvalue problem
---
> Waiting for input...
27a18
> Subspace diagonalization in iterative solution of the eigenvalue problem:
31a23,24
> Found symmetry operation: I + ( 0.0000 0.0000 0.1000)
> This is a supercell, fractional translation are disabled


1389c1370
< convergence has been achieved in 9 iterations
---
> convergence has been achieved in 8 iterations
1393c1374
< PWSCF : 30m58.57s CPU time, 36m 1.09s wall time
---
> PWSCF : 34m36.46s CPU time, 39m42.87s wall time
1395,1396c1376,1377
< init_run : 37.43s CPU
< electrons : 1818.18s CPU
---
> init_run : 38.88s CPU
> electrons : 2034.45s CPU
1399,1401c1380,1382
< wfcinit : 36.15s CPU
< potinit : 0.36s CPU
< realus : 0.20s CPU
---
> wfcinit : 37.84s CPU
> potinit : 0.37s CPU
> realus : 0.18s CPU
1404,1408c1385,1389
< c_bands : 1690.30s CPU ( 10 calls, 169.030 s avg)
< sum_band : 126.80s CPU ( 10 calls, 12.680 s avg)
< v_of_rho : 0.35s CPU ( 10 calls, 0.035 s avg)
< newd : 0.07s CPU ( 10 calls, 0.007 s avg)
< mix_rho : 0.06s CPU ( 10 calls, 0.006 s avg)
---
> c_bands : 1920.64s CPU ( 9 calls, 213.404 s avg)
> sum_band : 112.93s CPU ( 9 calls, 12.547 s avg)
> v_of_rho : 0.30s CPU ( 9 calls, 0.033 s avg)
> newd : 0.06s CPU ( 9 calls, 0.007 s avg)
> mix_rho : 0.04s CPU ( 9 calls, 0.005 s avg)
1411,1412c1392,1393
< init_us_2 : 3.62s CPU ( 714 calls, 0.005 s avg)
< cegterg : 1677.69s CPU ( 340 calls, 4.934 s avg)
---
> init_us_2 : 3.22s CPU ( 646 calls, 0.005 s avg)
> cegterg : 1909.07s CPU ( 306 calls, 6.239 s avg)
415,1418c1396,1399
< h_psi : 736.21s CPU ( 1487 calls, 0.495 s avg)
< s_psi : 79.33s CPU ( 1487 calls, 0.053 s avg)
< g_psi : 2.70s CPU ( 1113 calls, 0.002 s avg)
< cdiaghg : 605.99s CPU ( 1419 calls, 0.427 s avg)
---
> h_psi : 695.24s CPU ( 1661 calls, 0.419 s avg)
> s_psi : 72.59s CPU ( 1661 calls, 0.044 s avg)
> g_psi : 2.17s CPU ( 1321 calls, 0.002 s avg)
> cdiaghg : 893.34s CPU ( 1593 calls, 0.561 s avg)
1421c1402
< add_vuspsi : 78.47s CPU ( 1487 calls, 0.053 s avg)
---
> add_vuspsi : 73.58s CPU ( 1661 calls, 0.044 s avg)
1424,1427c1405,1408
< calbec : 126.54s CPU ( 1827 calls, 0.069 s avg)
< cft3s : 633.97s CPU ( 505734 calls, 0.001 s avg)
< interpolate : 0.09s CPU ( 20 calls, 0.005 s avg)
< davcio : 0.02s CPU ( 1054 calls, 0.000 s avg)
---
> calbec : 127.38s CPU ( 1967 calls, 0.065 s avg)
> cft3s : 583.31s CPU ( 468124 calls, 0.001 s avg)
> interpolate : 0.08s CPU ( 18 calls, 0.005 s avg)
> davcio : 0.02s CPU ( 952 calls, 0.000 s avg)
430c1411
< fft_scatter : 411.50s CPU ( 505734 calls, 0.001 s avg)
---
> fft_scatter : 396.13s CPU ( 468124 calls, 0.001 s avg)


Note that I repeated the tests and the timings changes less than 10 seconds
in 35 min.
Best regards,


-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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From giannozz at democritos.it  Tue Jul 28 16:56:18 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 28 Jul 2009 16:56:18 +0200
Subject: [Pw_forum] failure with npool
In-Reply-To: <be564dcb0907280724v3a907d43g6c972a4cd9624d3e@mail.gmail.com>
References: <be564dcb0907271239m1276eb1cn8f84317b310618a6@mail.gmail.com>	<be564dcb0907280719n5a7305b7wa0c096958f69b0b3@mail.gmail.com>
	<be564dcb0907280724v3a907d43g6c972a4cd9624d3e@mail.gmail.com>
Message-ID: <4A6F1192.6000501@democritos.it>

Eduardo Ariel Menendez Proupin wrote:

> Due to the size of the attachements, the message is awaiting for 
> moderation. I am not sure if I can send attachments to the forum :-(.

My advice is to send a URL pointing to a web page. You just need a
place, accessible by a web server, where you can put a file

< cdiaghg : 605.99s CPU ( 1419 calls, 0.427 s avg)

> cdiaghg : 893.34s CPU ( 1593 calls, 0.561 s avg)

here it is: subspace diagonalization. Are you sure that the two
codes were compiled in the same way? and that you are running
under the same conditions? If so, please get the previous version
of Modules/zhpev_drv.f90:
http://qe-forge.org/cgi-bin/cvstrac/q-e/fileview?f=espresso/Modules/zhpev_drv.f90&v=1.4
then 1.3 and 1.2, and please let us know if and when you notice a
difference.  If you get errors related to nonexistent routines
'numroc' and 'indxl2g', just remove the line
      INTEGER     :: numroc, INDXL2G
Some changes that were needed to ensure statibility on weird
machines may have slowed down the general performances. If
you have scalapack, it mighy be interesting to try it.

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

From giannozz at democritos.it  Tue Jul 28 17:09:55 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 28 Jul 2009 17:09:55 +0200
Subject: [Pw_forum] failure with npool
In-Reply-To: <be564dcb0907280719n5a7305b7wa0c096958f69b0b3@mail.gmail.com>
References: <be564dcb0907271239m1276eb1cn8f84317b310618a6@mail.gmail.com>
	<be564dcb0907280719n5a7305b7wa0c096958f69b0b3@mail.gmail.com>
Message-ID: <4A6F14C3.8040502@democritos.it>

Eduardo Ariel Menendez Proupin wrote:

> I made the correction and recompiled. Regretfully, it fails with the 
> same error.

are you REALLY sure that you made the correct correction? this is the
correct file:
http://qe-forge.org/cgi-bin/cvstrac/q-e/getfile?f=espresso/PW/realus.f90&v=1.38
(by the way, in my previous message, replace "fileview" with "getfile")

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

From giannozz at democritos.it  Tue Jul 28 17:12:21 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 28 Jul 2009 17:12:21 +0200
Subject: [Pw_forum] graphene phonon dispersion problem
In-Reply-To: <4772D337-0891-46AC-8A78-B51A623E0BE5@gmail.com>
References: <4772D337-0891-46AC-8A78-B51A623E0BE5@gmail.com>
Message-ID: <4A6F1555.20300@democritos.it>

Mikiyas Tsegaye wrote:

> I thought the solution would be to include epsil = .true. in the ph 
> input file, but that makes the calculation crash at that step.

no, it makes the calculation "stop", not "crash", because you
cannot calculate effective charges in a metal

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

From eariel99 at gmail.com  Tue Jul 28 18:00:53 2009
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Tue, 28 Jul 2009 12:00:53 -0400
Subject: [Pw_forum] how to keep mails in the same thread
Message-ID: <be564dcb0907280900q1423bf70g5e2c54d742af827a@mail.gmail.com>

Hi,
I made a question yesterday. There are replies in the same thread, but after
my reply, there are two threads in the Forum archive. Then it will be hard
to trace this issue in the future.
It has happened to me before and I do not discover the correct way yet :-((.


If the original message that I sent to pw_forum at pwscf.org had the Subject
"failure with npool", what is the subject for the replies?
Any one of the followings

failure with npool
[Pw_forum] failure with npool
Re: [Pw_forum] failure with npool
Re: Re: [Pw_forum] failure with npool

I apologize
-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez<http://fisica.ciencias.uchile.cl/%7Eemenendez>
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From paulatto at sissa.it  Tue Jul 28 18:05:36 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 28 Jul 2009 18:05:36 +0200
Subject: [Pw_forum] how to keep mails in the same thread
In-Reply-To: <be564dcb0907280900q1423bf70g5e2c54d742af827a@mail.gmail.com>
References: <be564dcb0907280900q1423bf70g5e2c54d742af827a@mail.gmail.com>
Message-ID: <op.uxscbmvca8x26q@paulax>

In data 28 luglio 2009 alle ore 18:00:53, Eduardo Ariel Menendez Proupin  
<eariel99 at gmail.com> ha scritto:
> I made a question yesterday. There are replies in the same thread, but  
> after my reply, there are two threads in the Forum archive. Then it will  
> be hard to trace this issue in the future.

If a mail is a reply or not does not depend on the subject, but on the  
"In-Reply-To" header, which lists the full message id (for your first  
message: <be564dcb0907270844o342c6370v2bb2845793734974 at mail.gmail.com>).

> It has happened to me before and I do not discover the correct way yet  
> :-((.

It is a problem with your email client or your webmail. If you are using  
gmail webmail, it may be easily google that has misconfigured it (they do  
the same for usenet groups groups.google.com...), but I have never tested  
it myself.

cheers

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

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

From eariel99 at gmail.com  Tue Jul 28 19:35:22 2009
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Tue, 28 Jul 2009 13:35:22 -0400
Subject: [Pw_forum] failure with npool
In-Reply-To: <be564dcb0907280724v3a907d43g6c972a4cd9624d3e@mail.gmail.com>
References: <be564dcb0907271239m1276eb1cn8f84317b310618a6@mail.gmail.com>
	<be564dcb0907280719n5a7305b7wa0c096958f69b0b3@mail.gmail.com>
	<be564dcb0907280724v3a907d43g6c972a4cd9624d3e@mail.gmail.com>
Message-ID: <be564dcb0907281035k56cc4709i249a95d618f4759a@mail.gmail.com>

>are you REALLY sure that you made the correct correction? this is the
>correct file:
>http://qe-forge.org/cgi-bin/cvstrac/q-e/getfile?f=espresso/PW/realus.f90&v=1.38 <http://qe-forge.org/cgi-bin/cvstrac/q-e/getfile?f=espresso/PW/realus.f90&v=1.38>

>(by the way, in my previous message, replace "fileview" with "getfile")

>P.

Not REALLY sure. I had changed the line 1526, instead of adding it. Now it
works fine. Thank you.

The tests runs for zhpev_drv.f90 are queued.



-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez<http://fisica.ciencias.uchile.cl/%7Eemenendez>
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From aryjunior at gmail.com  Tue Jul 28 22:57:06 2009
From: aryjunior at gmail.com (Ary Junior)
Date: Tue, 28 Jul 2009 17:57:06 -0300
Subject: [Pw_forum] wrong record length
Message-ID: <4c9c61c20907281357v15e52ef9t185ff6a07c3ad0f5@mail.gmail.com>

Please, recently I posted a question about an error returned when I run
ph.x... I use ph.x with many other structures but with one in particular
ph.x stop and return:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     task #         0
     from diropn : error #         3
     wrong record length
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

By PW/diropn.f90 code inspection, the error occours because the unf_recl
variable value is negative... I wrote the value of the variables responsible
for this negative value like this:

...
  write(stdout,*)'the extension value is ',extension
...
  !
  !      the unit for record length is unfortunately machine-dependent
  !
  unf_recl = DIRECT_IO_FACTOR * recl
  write(stdout,*)'the DIRECT_IO_FACTOR value is ',DIRECT_IO_FACTOR
  write(stdout,*)'the recl value is ',recl
  write(stdout,*)'the unf_recl value is ',unf_recl
  if (unf_recl <= 0) call errore ('diropn', 'wrong record length', 3)
...

After this change the last lines of my ph.out file is:

...
     Representation   292      1 modes - To be done

     Representation   293      1 modes - To be done

     Representation   294      1 modes - To be done
the extension value is wfc
the DIRECT_IO_FACTOR value is            8
the recl value is     41634666
the unf_recl value is    333077328
the extension value is bar
the DIRECT_IO_FACTOR value is            8
the recl value is     41634666
the unf_recl value is    333077328
the extension value is dwf
the DIRECT_IO_FACTOR value is            8
the recl value is     41634666
the unf_recl value is    333077328
the extension value is prd
the DIRECT_IO_FACTOR value is            8
the recl value is      5184000
the unf_recl value is     41472000
the extension value is com
the DIRECT_IO_FACTOR value is            8
the recl value is     41634666
the unf_recl value is    333077328
the extension value is dvkb3
the DIRECT_IO_FACTOR value is            8
the recl value is    355119210
the unf_recl value is  -1454013616

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from diropn : error #         3
     wrong record length
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

Well, as already discussed in this list, the problem can be related to the
default 32 bits integer size when I compile PWscf with ifort... then I'm
compiling PWscf with MPI support and if I set FFLAGS in my make.sys like
this:

FFLAGS         = -i8 -integer-size 64 -O2 -assume byterecl -xHost

I get the error when I run any calculation with ph.x or pw.x:

*** error in Message Passing (mp) module ***
*** error msg:
*** error code:  8066
[xeonquad02:24463] MPI_ABORT invoked on rank 0 in communicator
MPI_COMM_WORLD with errorcode 8066

Please, anybody can help me? If I compile with FFLAGS without "-i8
-integer-size 64" pw.x and ph.x run ok.

Thank you very much!!!

-- 
http://lattes.cnpq.br/8221674673413336
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From wshen02 at gmail.com  Tue Jul 28 23:37:55 2009
From: wshen02 at gmail.com (=?UTF-8?B?5paH5rKI?=)
Date: Tue, 28 Jul 2009 14:37:55 -0700
Subject: [Pw_forum] Does anybody have the same problem for the relax
	calculation about the atom force
Message-ID: <2c9df8a80907281437j48077c4dif65dd73e75304af3@mail.gmail.com>

Dear all can anybody tell me why my relax calculation doesn't provide the
force output correctly?

As follows, in the output file, it gives the force and 0.000000000 or
*******.  I don't know why it doesn't give any correct force value.my input
file is in the attachment


  atom   1 type  3   force =     0.00000000    0.00000000**************
     atom   2 type  2   force =     0.00000000****************************
     atom   3 type  1   force =     0.00000000    0.00000000**************
     atom   4 type  1   force = ******************************************
     atom   5 type  1   force = **************    0.00000000**************
     atom   6 type  1   force =     0.00000000****************************
     atom   7 type  1   force =     0.00000000    0.00000000    0.00000000
     atom   8 type  1   force = ****************************    0.00000000
     atom   9 type  1   force =     0.00000000****************************
     atom  10 type  1   force = **************    0.00000000**************
     atom  11 type  1   force = ******************************************
     atom  12 type  1   force =     0.00000000    0.00000000**************
     atom  13 type  2   force =     0.00000000****************************
     atom  14 type  3   force =     0.00000000    0.00000000**************
     atom  15 type  2   force =     0.00000000****************************
     atom  16 type  2   force =     0.00000000****************************
     atom  17 type  2   force =     0.00000000****************************
     atom  18 type  1   force =     0.00000000    0.00000000**************
     atom  19 type  1   force =     0.00000000    0.00000000**************
     atom  20 type  1   force =     0.00000000    0.00000000**************
     atom  21 type  1   force = ******************************************
     atom  22 type  1   force = ******************************************
     atom  23 type  1   force = ******************************************
     atom  24 type  1   force = **************    0.00000000**************
     atom  25 type  1   force = **************    0.00000000**************
     atom  26 type  1   force = **************    0.00000000**************
     atom  27 type  1   force =     0.00000000****************************
     atom  28 type  1   force =     0.00000000****************************
     atom  29 type  1   force =     0.00000000****************************
     atom  30 type  1   force =     0.00000000    0.00000000    0.00000000
     atom  31 type  1   force =     0.00000000    0.00000000    0.00000000
     atom  32 type  1   force =     0.00000000    0.00000000    0.00000000
     atom  33 type  1   force = ******************************************
     atom  34 type  1   force = ****************************    0.00000000
     atom  35 type  1   force = ****************************    0.00000000
     atom  36 type  1   force =     0.00000000****************************
     atom  37 type  1   force =     0.00000000****************************
     atom  38 type  1   force =     0.00000000****************************
     atom  39 type  1   force = **************    0.00000000**************
     atom  40 type  1   force = **************    0.00000000**************
     atom  41 type  1   force = **************    0.00000000**************
     atom  42 type  1   force = ******************************************
     atom  43 type  1   force = ******************************************
     atom  44 type  1   force = ******************************************
     atom  45 type  1   force =     0.00000000    0.00000000**************
     atom  46 type  1   force =     0.00000000    0.00000000**************
     atom  47 type  1   force =     0.00000000    0.00000000**************
     atom  48 type  2   force =     0.00000000****************************
     atom  49 type  2   force =     0.00000000****************************
     atom  50 type  2   force =     0.00000000****************************
     Total force =          NAN     Total SCF correction =     0.000703
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From giannozz at democritos.it  Wed Jul 29 08:35:38 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 29 Jul 2009 08:35:38 +0200
Subject: [Pw_forum] wrong record length
In-Reply-To: <4c9c61c20907281357v15e52ef9t185ff6a07c3ad0f5@mail.gmail.com>
References: <4c9c61c20907281357v15e52ef9t185ff6a07c3ad0f5@mail.gmail.com>
Message-ID: <AE2DF120-F64F-4F03-8A5E-C64A6F87D62E@democritos.it>


On Jul 28, 2009, at 22:57 , Ary Junior wrote:

> the extension value is dvkb3
> the DIRECT_IO_FACTOR value is            8
> the recl value is    355119210
> the unf_recl value is  -1454013616

Since only unf_recl=DIRECT_IO_FACTOR*recl is overflowing
(8*355119210 = 2840953680 > 2147483648 =2**31) you may
try first one of the two following workarounds: in PW/diropn.f90
- define only unf_recl as integer(8), or
-  define DIRECT_IO_FACTOR=2, remove "-assume byterecl"
from compiler flags

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




From ismotochi at gmail.com  Wed Jul 29 09:27:22 2009
From: ismotochi at gmail.com (isaac motochi)
Date: Wed, 29 Jul 2009 00:27:22 -0700
Subject: [Pw_forum] surface band structure and dos
In-Reply-To: <21fbc4790907262333u777c7e16hf7f0c5f004850879@mail.gmail.com>
References: <9d6ea92e0907262324x7374a0b3o4579c84803a589fb@mail.gmail.com>
	<21fbc4790907262333u777c7e16hf7f0c5f004850879@mail.gmail.com>
Message-ID: <9d6ea92e0907290027q28bd9c75w4a828c47234d4df9@mail.gmail.com>

Thanks Hui Wang for your swift response, i ll try it then keep you posted


Motochi
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From paulatto at sissa.it  Wed Jul 29 09:54:37 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 29 Jul 2009 09:54:37 +0200
Subject: [Pw_forum] Does anybody have the same problem for the relax
 calculation about the atom force
In-Reply-To: <2c9df8a80907281437j48077c4dif65dd73e75304af3@mail.gmail.com>
References: <2c9df8a80907281437j48077c4dif65dd73e75304af3@mail.gmail.com>
Message-ID: <op.uxtj9bg0a8x26q@paulax>

In data 28 luglio 2009 alle ore 23:37:55, ?? <wshen02 at gmail.com> ha  
scritto:
> As follows, in the output file, it gives the force and 0.000000000 or
> *******.  I don't know why it doesn't give any correct force value.my  
> input

The **** are just a problem with the fortran format, it means that the  
forces are too large and won't fit in their respective fields.

>      Total force =          NAN     Total SCF correction =     0.000703

I'm more concerned about the NAN as total force, there may be several  
explanations for this (bug in QE, bugs in libraries)
The only advice I can give you at the moment is to increase the number of  
bands: you are using 280 bands for 508 electrons, which means you only  
have ~10% more bands than the bare minimum to fit all the electrons. This  
may not be enough to insure band occupations become negligible before the  
code runs out of bands (your smearing is 10mRy).
Also, you've not defined Hubbard_U for types 1 and 2, although I'm quite  
sure the code sets them automatically to zero.

best regards

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

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

From giannozz at democritos.it  Wed Jul 29 09:57:11 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 29 Jul 2009 09:57:11 +0200
Subject: [Pw_forum] Does anybody have the same problem for the
 relax	calculation about the atom force
In-Reply-To: <2c9df8a80907281437j48077c4dif65dd73e75304af3@mail.gmail.com>
References: <2c9df8a80907281437j48077c4dif65dd73e75304af3@mail.gmail.com>
Message-ID: <4A7000D7.7090706@democritos.it>

?? wrote:

> Dear all can anybody tell me why my relax calculation doesn't provide 
> the force output correctly?

it is not that simple to provide the answer you keep requiring.
Your job is not small and running it requires a nonnegligible
amount of computer and human time. You didn't specify the
conditions under which you observe this problem: which version
of the code, hoe compiled, how executed, and most inmportant:
if it is reproducible on other machines or with another compiler;
if it is triggered by some specific option(s) or execution mode.
With the right piece of information, problems can be localized
and fixed in less then no time. Without, it is not fun to invest
hours just to discover that the problem is irreproducibile (i.e.
nonexistent for scientists)

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

From neelphysics at yahoo.in  Wed Jul 29 10:35:54 2009
From: neelphysics at yahoo.in (Neel Singh)
Date: Wed, 29 Jul 2009 14:05:54 +0530 (IST)
Subject: [Pw_forum] Not getting right Band structure
In-Reply-To: <op.uxrvpz0ba8x26q@paulax>
Message-ID: <580605.23553.qm@web95004.mail.in2.yahoo.com>

Hi sir,

?Sir i have calculated the band structure of YVO4? and it is coming as near about 0.5 ev .. sir as suggested by you in earlier reply that 

>means band gap at gamma = 0.3058-(-8.9833)=? 8.2891
>? which is very large ??

Not necessarily, the offset of band in a periodic system is arbitrary. You? 
need to know where you Fermi energy is, or which are the HOMO and LUMO of? 
your system to find the gap.

I have calculated Fermi energy and it is coming as 6.108. The band gap of YVO4 is 3.9 eV experimental and DFT calculates the band gap as nearly half i..e. it should come as 1.8 eV approx. Please help.. Thanks In advance.My Input files are listed below...

SCF INPUT
===============================================

?&control
??? calculation='scf',
??? restart_mode='from_scratch',
??? prefix='yvo'
??? pseudo_dir = '/home/physics/pseudo/',
??? outdir='/home/physics/work/yvo/temp'
?/
?&system
??? ibrav =1, a=7.118300514, b= 7.118300514, c=6.289300454
, nat =24, ntyp= 3,? ecutwfc = 40.0,ecutrho=300,
?occupations='smearing', smearing='mp', degauss=0.01, 


?/
?&electrons
??? mixing_beta = 0.7
??? diagonalization = 'david'
??? conv_thr =? 1.0e-6
/
?&ions
?/

ATOMIC_SPECIES
? Y???? 88.90585???? Y.pbe-nsp-van.UPF
? V???? 50.9415????? V.pbe-sp-van.UPF
? O???? 15.9994????? O.pbe-van_ak.UPF
ATOMIC_POSITIONS {angstrom}
Y???????????? 0.000000000?? 5.338725356??? 0.786162553
/
/

K_POINTS {automatic}
? 4 4 4 0 0 0
=======================================================
?????????????????????????????? Bands Input
======================================================


?&control
??? calculation='bands'
??? pseudo_dir = '/home/physics/pseudo/',
??? outdir='/home/physics/work/yvo/temp',
??? prefix='yvo',
? 
?/
?&system
??? ibrav =1, a=7.118300514, b= 7.118300514, c=6.289300454, nat=24, ntyp=3, 
ecutwfc = 40.0,ecutrho=300, occupations='smearing', smearing='mp', degauss=0.01, nbnd= 115, 
??? 
?/
?&electrons
?? mixing_beta=0.7
?? conv_thr=1.0e-6
?diagonalization = 'david'
/
&ions
?/

ATOMIC_SPECIES
?Y?????? 88.90585???? Y.pbe-nsp-van.UPF
? V????? 50.9415????? V.pbe-sp-van.UPF
? O???? 15.9994????? O.pbe-van_ak.UPF
ATOMIC_POSITIONS {angstrom}
Y???????????? 0.000000000?? 5.338725356??? 0.786162553
\
\
K_POINTS
?26
0.000 0.000 0.000? 1
0.000 0.000 0.125? 1
0.000 0.000 0.250? 1
0.000 0.000 0.375? 1
0.000 0.000 0.500? 1???????????????????????????? 
0.125 0.125 0.500? 1???????????????????????????? 
0.250 0.250 0.500? 1???????????????????????????? 
0.375 0.375 0.500? 1??????????????????????????? 
0.500 0.500 0.500? 1???????????????????????????? 
0.500 0.500 0.333? 1???????????????????????????? 
0.500 0.500 0.166? 1???????????????????????????? 
0.500 0.500 0.000? 1???????????????????????????? 
0.375 0.375 0.000? 1???????????????????????????? 
0.250 0.250 0.000? 1???????????????????????????? 
0.125 0.125 0.000? 1???????????????????????????? 
0.000 0.000 0.000? 1???????????????????????????? 
0.000 0.000 0.166? 1??????????????????????????? 
0.000 0.000 0.333? 1???????????????????????????? 
0.000 0.166 0.500? 1?????????????????????????? 
0.000 0.333 0.500? 1??????????????????????????? 
0.000 0.500 0.500? 1???????????????????????????? 
0.000 0.500 0.333? 1???????????????????????????? 
0.000 0.500 0.166? 1???????????????????????????? 
0.000 0.500 0.000? 1???????????????????????????? 
0.000 0.333 0.000? 1???????????????????????????? 
0.000 0.166 0.000? 1 
============================================================
===========================================================
?&inputpp
??? prefix? = 'yvo'
??? outdir = '/home/physics/work/yvo/temp'
??? filband = 'yvobands.dat'
/
========================================
Plotband INPUTS
=======================================
yvobands.dat
-10? 12
yvobands.xmgr
yvobands.ps
6.1088
1.0? 0.00
================================================
============================================

With regards,
Neel Singh
Univeristy of Delhi
--- On Tue, 28/7/09, Lorenzo Paulatto <paulatto at sissa.it> wrote:

From: Lorenzo Paulatto <paulatto at sissa.it>
Subject: Re: [Pw_forum] Not getting right Band structure
To: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Tuesday, 28 July, 2009, 10:07 AM

In data 28 luglio 2009 alle ore 11:54:14, Neel Singh? 
<neelphysics at yahoo.in> ha scritto:
> means band gap at gamma = 0.3058-(-8.9833)=? 8.2891
>? which is very large ??

Not necessarily, the offset of band in a periodic system is arbitrary. You? 
need to know where you Fermi energy is, or which are the HOMO and LUMO of? 
your system to find the gap.


> 2) In the output of SCF and Bands , the output file has 4 warnings

This a very frequently asked question, please see the corresponing entry? 
in the manual:
http://www.pwscf.org/guide/2.1.2/html-node/node56.html
http://www.pwscf.org/guide/2.1.2/html-node/node57.html


> for this I have already increase the following quantities? in the???
> increments
> kinetic-energy cutoff? ???=? ? ? 40.0000? Ry to 60
>? ? ? charge density cutoff? ???=? ???250.0000? Ry to 400
> But still the warnings are there.

It is not a big increment of the cutoff that will solve this problem, but? 
a small increment or nr1, nr2 nr3

cheers, and good work

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

? ???*** save italian brains ***
? http://saveitalianbrains.wordpress.com/
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From paulatto at sissa.it  Wed Jul 29 10:41:25 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 29 Jul 2009 10:41:25 +0200
Subject: [Pw_forum] Not getting right Band structure
In-Reply-To: <580605.23553.qm@web95004.mail.in2.yahoo.com>
References: <580605.23553.qm@web95004.mail.in2.yahoo.com>
Message-ID: <op.uxtmfbzha8x26q@paulax>

In data 29 luglio 2009 alle ore 10:35:54, Neel Singh  
<neelphysics at yahoo.in> ha scritto:
> I have calculated Fermi energy and it is coming as 6.108. The band gap  
> of YVO4 is 3.9 eV experimental and DFT calculates the band gap as nearly  
> half i..e. it should come as 1.8 eV approx.

This is not necessarily, some specific choice of functional tend to  
underestimate the gap, but it is not a theorem.

I cannot understand what your problem is exactly; I could be more helpful  
if you provided a complete output file, as I don't have the time nor the  
resources to reproduce your calculations.

best regards

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

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

From degironc at sissa.it  Wed Jul 29 13:05:45 2009
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 29 Jul 2009 13:05:45 +0200
Subject: [Pw_forum] Not getting right Band structure
In-Reply-To: <580605.23553.qm@web95004.mail.in2.yahoo.com>
References: <580605.23553.qm@web95004.mail.in2.yahoo.com>
Message-ID: <20090729130545.xjtytr5ts0k4g444@webmail.sissa.it>

Dear Neel Singh,

   your input specifies ibrav=1 (that is Simple Cubic): only the value of a is
taken in consideration while b and c are discarded. If you want an orthorombic
structure the proper ibrav is another one. (ibrav=6 if I remember  
correctly, but please check).
   have you tried to visualize your structure by xcrysdens to check it is ok?
   is the system magnetic ? if so you need to specify some starting  
magnetization.

   best regrads,
  stefano de Gironcoli - SISSA and DEMOCRITOS

Quoting Neel Singh <neelphysics at yahoo.in>:

> Hi sir,
>
> ?Sir i have calculated the band structure of YVO4? and it is coming   
> as near about 0.5 ev .. sir as suggested by you in earlier reply that
>
>> means band gap at gamma = 0.3058-(-8.9833)=? 8.2891
>> ? which is very large ??
>
> Not necessarily, the offset of band in a periodic system is arbitrary. You?
> need to know where you Fermi energy is, or which are the HOMO and LUMO of?
> your system to find the gap.
>
> I have calculated Fermi energy and it is coming as 6.108. The band   
> gap of YVO4 is 3.9 eV experimental and DFT calculates the band gap   
> as nearly half i..e. it should come as 1.8 eV approx. Please help..   
> Thanks In advance.My Input files are listed below...
>
> SCF INPUT
> ===============================================
>
> ?&control
> ??? calculation='scf',
> ??? restart_mode='from_scratch',
> ??? prefix='yvo'
> ??? pseudo_dir = '/home/physics/pseudo/',
> ??? outdir='/home/physics/work/yvo/temp'
> ?/
> ?&system
> ??? ibrav =1, a=7.118300514, b= 7.118300514, c=6.289300454
> , nat =24, ntyp= 3,? ecutwfc = 40.0,ecutrho=300,
> ?occupations='smearing', smearing='mp', degauss=0.01,
>
>
> ?/
> ?&electrons
> ??? mixing_beta = 0.7
> ??? diagonalization = 'david'
> ??? conv_thr =? 1.0e-6
> /
> ?&ions
> ?/
>
> ATOMIC_SPECIES
> ? Y???? 88.90585???? Y.pbe-nsp-van.UPF
> ? V???? 50.9415????? V.pbe-sp-van.UPF
> ? O???? 15.9994????? O.pbe-van_ak.UPF
> ATOMIC_POSITIONS {angstrom}
> Y???????????? 0.000000000?? 5.338725356??? 0.786162553
> /
> /
>
> K_POINTS {automatic}
> ? 4 4 4 0 0 0
> =======================================================
> ?????????????????????????????? Bands Input
> ======================================================
>
>
> ?&control
> ??? calculation='bands'
> ??? pseudo_dir = '/home/physics/pseudo/',
> ??? outdir='/home/physics/work/yvo/temp',
> ??? prefix='yvo',
> ?
> ?/
> ?&system
> ??? ibrav =1, a=7.118300514, b= 7.118300514, c=6.289300454, nat=24, ntyp=3,
> ecutwfc = 40.0,ecutrho=300, occupations='smearing', smearing='mp',   
> degauss=0.01, nbnd= 115,
> ???
> ?/
> ?&electrons
> ?? mixing_beta=0.7
> ?? conv_thr=1.0e-6
> ?diagonalization = 'david'
> /
> &ions
> ?/
>
> ATOMIC_SPECIES
> ?Y?????? 88.90585???? Y.pbe-nsp-van.UPF
> ? V????? 50.9415????? V.pbe-sp-van.UPF
> ? O???? 15.9994????? O.pbe-van_ak.UPF
> ATOMIC_POSITIONS {angstrom}
> Y???????????? 0.000000000?? 5.338725356??? 0.786162553
> \
> \
> K_POINTS
> ?26
> 0.000 0.000 0.000? 1
> 0.000 0.000 0.125? 1
> 0.000 0.000 0.250? 1
> 0.000 0.000 0.375? 1
> 0.000 0.000 0.500? 1????????????????????????????
> 0.125 0.125 0.500? 1????????????????????????????
> 0.250 0.250 0.500? 1????????????????????????????
> 0.375 0.375 0.500? 1???????????????????????????
> 0.500 0.500 0.500? 1????????????????????????????
> 0.500 0.500 0.333? 1????????????????????????????
> 0.500 0.500 0.166? 1????????????????????????????
> 0.500 0.500 0.000? 1????????????????????????????
> 0.375 0.375 0.000? 1????????????????????????????
> 0.250 0.250 0.000? 1????????????????????????????
> 0.125 0.125 0.000? 1????????????????????????????
> 0.000 0.000 0.000? 1????????????????????????????
> 0.000 0.000 0.166? 1???????????????????????????
> 0.000 0.000 0.333? 1????????????????????????????
> 0.000 0.166 0.500? 1??????????????????????????
> 0.000 0.333 0.500? 1???????????????????????????
> 0.000 0.500 0.500? 1????????????????????????????
> 0.000 0.500 0.333? 1????????????????????????????
> 0.000 0.500 0.166? 1????????????????????????????
> 0.000 0.500 0.000? 1????????????????????????????
> 0.000 0.333 0.000? 1????????????????????????????
> 0.000 0.166 0.000? 1
> ============================================================
> ===========================================================
> ?&inputpp
> ??? prefix? = 'yvo'
> ??? outdir = '/home/physics/work/yvo/temp'
> ??? filband = 'yvobands.dat'
> /
> ========================================
> Plotband INPUTS
> =======================================
> yvobands.dat
> -10? 12
> yvobands.xmgr
> yvobands.ps
> 6.1088
> 1.0? 0.00
> ================================================
> ============================================
>
> With regards,
> Neel Singh
> Univeristy of Delhi
> --- On Tue, 28/7/09, Lorenzo Paulatto <paulatto at sissa.it> wrote:
>
> From: Lorenzo Paulatto <paulatto at sissa.it>
> Subject: Re: [Pw_forum] Not getting right Band structure
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Date: Tuesday, 28 July, 2009, 10:07 AM
>
> In data 28 luglio 2009 alle ore 11:54:14, Neel Singh?
> <neelphysics at yahoo.in> ha scritto:
>> means band gap at gamma = 0.3058-(-8.9833)=? 8.2891
>> ? which is very large ??
>
> Not necessarily, the offset of band in a periodic system is arbitrary. You?
> need to know where you Fermi energy is, or which are the HOMO and LUMO of?
> your system to find the gap.
>
>
>> 2) In the output of SCF and Bands , the output file has 4 warnings
>
> This a very frequently asked question, please see the corresponing entry?
> in the manual:
> http://www.pwscf.org/guide/2.1.2/html-node/node56.html
> http://www.pwscf.org/guide/2.1.2/html-node/node57.html
>
>
>> for this I have already increase the following quantities? in the???
>> increments
>> kinetic-energy cutoff? ???=? ? ? 40.0000? Ry to 60
>> ? ? ? charge density cutoff? ???=? ???250.0000? Ry to 400
>> But still the warnings are there.
>
> It is not a big increment of the cutoff that will solve this problem, but?
> a small increment or nr1, nr2 nr3
>
> cheers, and good work
>
> --
> Lorenzo Paulatto
> SISSA? &? DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:???http://people.sissa.it/~paulatto/
>
> ? ???*** save italian brains ***
> ? http://saveitalianbrains.wordpress.com/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>       See the Web&#39;s breaking stories, chosen by people like you.  
>  Check out Yahoo! Buzz. http://in.buzz.yahoo.com/



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From giannozz at democritos.it  Wed Jul 29 13:11:09 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 29 Jul 2009 13:11:09 +0200
Subject: [Pw_forum] Does anybody have the same problem for the
 relax	calculation about the atom force
In-Reply-To: <2c9df8a80907281437j48077c4dif65dd73e75304af3@mail.gmail.com>
References: <2c9df8a80907281437j48077c4dif65dd73e75304af3@mail.gmail.com>
Message-ID: <4A702E4D.5020704@democritos.it>

A faster version of your input (with just 1 k-point)
works on my PC

P.

-- 
Paolo Giannozzi, Democritos and University of Udine, Italy
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From spmmal at gmail.com  Wed Jul 29 17:28:16 2009
From: spmmal at gmail.com (Caloma Trumica)
Date: Wed, 29 Jul 2009 11:28:16 -0400
Subject: [Pw_forum] Wavefunction file
Message-ID: <d1bf85990907290828k53c1b1b4wa77e34470a9511f2@mail.gmail.com>

Dear All,

I do not want to save down the wavefunction file after running PWSCF.

How can I set the input file to realize this, thanks.



Caloma Trumica

University of Washington
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From paulatto at sissa.it  Wed Jul 29 17:31:21 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 29 Jul 2009 17:31:21 +0200
Subject: [Pw_forum] Wavefunction file
In-Reply-To: <d1bf85990907290828k53c1b1b4wa77e34470a9511f2@mail.gmail.com>
References: <d1bf85990907290828k53c1b1b4wa77e34470a9511f2@mail.gmail.com>
Message-ID: <op.uxt5ej16a8x26q@paulax>

In data 29 luglio 2009 alle ore 17:28:16, Caloma Trumica  
<spmmal at gmail.com> ha scritto:
> I do not want to save down the wavefunction file after running PWSCF.

Dear Caloma,
I'm pasting an extract from Doc/INPUT_PW.txt:

    Variable:       disk_io

    Type:           CHARACTER
    Default:        'default'
    Description:    Specifies the amount of disk I/O activity
                    'high':    save all data at each SCF step

                    'default': save wavefunctions at each SCF step unless
                               there is a single k-point per process

                    'low' :    store wfc in memory, save only at the end

                    'none':    do not save wfc, not even at the end

                    If restarting from an interrupted calculation, the code
                    will try to figure out what is available on disk. The
                    more you write, the more complete the restart will be.

"wfc" stands for wavefunctions
best regards


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

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

From giannozz at democritos.it  Wed Jul 29 17:31:34 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 29 Jul 2009 17:31:34 +0200
Subject: [Pw_forum] Wavefunction file
In-Reply-To: <d1bf85990907290828k53c1b1b4wa77e34470a9511f2@mail.gmail.com>
References: <d1bf85990907290828k53c1b1b4wa77e34470a9511f2@mail.gmail.com>
Message-ID: <4A706B56.5050509@democritos.it>

Caloma Trumica wrote:

> I do not want to save down the wavefunction file after running PWSCF.

disk_io='none' in namelist &control

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

From kazempoor2000 at yahoo.com  Wed Jul 29 18:22:40 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Wed, 29 Jul 2009 09:22:40 -0700 (PDT)
Subject: [Pw_forum] GGA+U
Message-ID: <434054.51951.qm@web112503.mail.gq1.yahoo.com>


Dear all


From bogus@does.not.exist.com  Fri Jul 24 13:42:27 2009
From: bogus@does.not.exist.com ()
Date: Fri, 24 Jul 2009 11:42:27 -0000
Subject: No subject
Message-ID: <mailman.0.1248884567.24399.pw_forum@pwscf.org>

double the unit cell in z direction and again compute U ,I get three differ=
ent value for Ti atoms.(U=3D5.63,5.46,5.70).
Why these values are not same . what is the main reason? Does it in numeric=
al variation errors?
ANother question:
When we perturb D level by alpha, it give rise to change in d occupancy . I=
s it correct that if we impose negative alpha , the occupation becomes less=
 than initial state .?
for Ti isolated atom for apha=3D0.1=A0 tr[ns(na)] after first-iteration equ=
al to the 0.002 and at the end of calculation is 2.327 while we know that f=
or Ti,=A0 tr[ns(na)] =3D2.000. Does it seems to be correct.?

=A0=A0=A0=A0 Number of iteration with fixed ns =3D=A0 0
=A0=A0=A0=A0 Starting ns and Hubbard U :
=A0enter write_ns
U( 1) =3D=A0 0.0000
alpha( 1) =3D=A0 0.1000
atom=A0 1=A0=A0 Tr[ns(na)]=3D=A0=A0 2.0000000
atom=A0 1=A0 spin=A0 1
eigenvalues:=A0 0.4000000 0.4000000 0.4000000 0.4000000 0.4000000
=A0eigenvectors
=A01=A0=A0 1.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000
=A02=A0=A0 0.0000000=A0 1.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000
=A03=A0=A0 0.0000000=A0 0.0000000=A0 1.0000000=A0 0.0000000=A0 0.0000000
=A04=A0=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 1.0000000=A0 0.0000000
=A05=A0=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 1.0000000
=A0occupations
=A00.400=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.400=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.400=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.400=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.400
atom=A0 1=A0 spin=A0 2
eigenvalues:=A0 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
=A0eigenvectors
=A01=A0=A0 1.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000
=A02=A0=A0 0.0000000=A0 1.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000
=A03=A0=A0 0.0000000=A0 0.0000000=A0 1.0000000=A0 0.0000000=A0 0.0000000
=A04=A0=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 1.0000000=A0 0.0000000
=A05=A0=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 1.0000000
=A0occupations
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.000
nsum =3D=A0=A0 2.0000000
=A0exit write_ns
=A0Atomic wfc used for LDA+U Projector are NOT orthogonalized
=A0=A0=A0=A0 Starting wfc are=A0=A0=A0 9 atomic +=A0=A0=A0 1 random wfc

=A0=A0=A0=A0 total cpu time spent up to now is=A0=A0=A0=A0 13.34 secs

=A0=A0=A0=A0 per-process dynamical memory:=A0=A0 326.3 Mb

=A0=A0=A0=A0 Self-consistent Calculation

=A0=A0=A0=A0 iteration #=A0 1=A0=A0=A0=A0 ecut=3D=A0=A0=A0 45.00 Ry=A0=A0=
=A0=A0 beta=3D0.70
=A0=A0=A0=A0 CG style diagonalization
=A0=A0=A0=A0 c_bands:=A0 3 eigenvalues not converged
=A0=A0=A0=A0 c_bands:=A0 2 eigenvalues not converged
=A0=A0=A0=A0 ethr =3D=A0 1.00E-12,=A0 avg # of iterations =3D 40.4
=A0enter write_ns
U( 1) =3D=A0 0.0000
alpha( 1) =3D=A0 0.1000
atom=A0 1=A0=A0 Tr[ns(na)]=3D=A0=A0 0.0021401
atom=A0 1=A0 spin=A0 1
eigenvalues:=A0 0.0000001 0.0000001 0.0000001 0.0009883 0.0009883
=A0eigenvectors
=A01=A0=A0 0.0000000 -0.8803392 -0.4743427=A0 0.0000000=A0 0.0013927
=A02=A0=A0 0.0000000 -0.4743432=A0 0.8803400=A0 0.0000000 -0.0000040
=A03=A0=A0 0.0000000=A0 0.0012242=A0 0.0006642=A0 0.0000000=A0 0.9999990
=A04=A0 -0.8886820=A0 0.0000000=A0 0.0000000 -0.4585240=A0 0.0000000
=A05=A0=A0 0.4585240=A0 0.0000000=A0 0.0000000 -0.8886820=A0 0.0000000
=A0occupations
=A00.001=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.001=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.000
---------------------------------- and end of the file is=20
:
=A0=A0=A0=A0 End of self-consistent calculation
=A0enter write_ns
U( 1) =3D=A0 0.0000
alpha( 1) =3D=A0 0.1000
atom=A0 1=A0=A0 Tr[ns(na)]=3D=A0=A0 2.3270531
atom=A0 1=A0 spin=A0 1
eigenvalues:=A0 0.1574294 0.1574294 0.1574294 0.9273825 0.9273825
=A0eigenvectors
=A01=A0=A0 0.0000000 -0.4359030 -0.7986559=A0 0.0000000=A0 0.4148945
=A02=A0=A0 0.0000000=A0 0.7269732 -0.0406891=A0 0.0000000=A0 0.6854592
=A03=A0=A0 0.0000000 -0.5305643=A0 0.6004109=A0 0.0000000=A0 0.5983379
=A04=A0 -0.9258933=A0 0.0000000=A0 0.0000000 -0.3777851=A0 0.0000000
=A05=A0=A0 0.3777851=A0 0.0000000=A0 0.0000000 -0.9258933=A0 0.0000000
=A0occupations
=A00.927=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.157=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.157=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.927=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.157


Thanks a lot
Ali Kazempour
=0APhysics department, Isfahan University of Technology
=0A84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733
=0AFax: +98 311 391 2376      Tel-2:  +98 311 391 2375=0A=0A=0A      
--0-576403044-1248884560=:51951
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable

<table cellspacing=3D"0" cellpadding=3D"0" border=3D"0" ><tr><td valign=3D"=
top" style=3D"font: inherit;"><br>Dear all<br><br>From Linear response calc=
ulation ,I get for TiO2 bulk U=3D5.73, But when I double the unit cell in z=
 direction and again compute U ,I get three different value for Ti atoms.(U=
=3D5.63,5.46,5.70).<br>Why these values are not same . what is the main rea=
son? Does it in numerical variation errors?<br>ANother question:<br>When we=
 perturb D level by alpha, it give rise to change in d occupancy . Is it co=
rrect that if we impose negative alpha , the occupation becomes less than i=
nitial state .?<br>for Ti isolated atom for apha=3D0.1&nbsp; tr[ns(na)] aft=
er first-iteration equal to the 0.002 and at the end of calculation is 2.32=
7 while we know that for Ti,&nbsp; tr[ns(na)] =3D2.000. Does it seems to be=
 correct.?<br><br>&nbsp;&nbsp;&nbsp;&nbsp; Number of iteration with fixed n=
s =3D&nbsp; 0<br>&nbsp;&nbsp;&nbsp;&nbsp; Starting ns and Hubbard U :<br>&n=
bsp;enter
 write_ns<br>U( 1) =3D&nbsp; 0.0000<br>alpha( 1) =3D&nbsp; 0.1000<br>atom&n=
bsp; 1&nbsp;&nbsp; Tr[ns(na)]=3D&nbsp;&nbsp; 2.0000000<br>atom&nbsp; 1&nbsp=
; spin&nbsp; 1<br>eigenvalues:&nbsp; 0.4000000 0.4000000 0.4000000 0.400000=
0 0.4000000<br>&nbsp;eigenvectors<br>&nbsp;1&nbsp;&nbsp; 1.0000000&nbsp; 0.=
0000000&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 0.0000000<br>&nbsp;2&nbsp;&nb=
sp; 0.0000000&nbsp; 1.0000000&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 0.00000=
00<br>&nbsp;3&nbsp;&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 1.0000000&nbsp; 0=
.0000000&nbsp; 0.0000000<br>&nbsp;4&nbsp;&nbsp; 0.0000000&nbsp; 0.0000000&n=
bsp; 0.0000000&nbsp; 1.0000000&nbsp; 0.0000000<br>&nbsp;5&nbsp;&nbsp; 0.000=
0000&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 1.0000000<br>&nb=
sp;occupations<br>&nbsp;0.400&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.0=
00<br>&nbsp;0.000&nbsp; 0.400&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000<br>&nbsp;=
0.000&nbsp; 0.000&nbsp; 0.400&nbsp; 0.000&nbsp; 0.000<br>&nbsp;0.000&nbsp;
 0.000&nbsp; 0.000&nbsp; 0.400&nbsp; 0.000<br>&nbsp;0.000&nbsp; 0.000&nbsp;=
 0.000&nbsp; 0.000&nbsp; 0.400<br>atom&nbsp; 1&nbsp; spin&nbsp; 2<br>eigenv=
alues:&nbsp; 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000<br>&nbsp;eig=
envectors<br>&nbsp;1&nbsp;&nbsp; 1.0000000&nbsp; 0.0000000&nbsp; 0.0000000&=
nbsp; 0.0000000&nbsp; 0.0000000<br>&nbsp;2&nbsp;&nbsp; 0.0000000&nbsp; 1.00=
00000&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 0.0000000<br>&nbsp;3&nbsp;&nbsp=
; 0.0000000&nbsp; 0.0000000&nbsp; 1.0000000&nbsp; 0.0000000&nbsp; 0.0000000=
<br>&nbsp;4&nbsp;&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 1.0=
000000&nbsp; 0.0000000<br>&nbsp;5&nbsp;&nbsp; 0.0000000&nbsp; 0.0000000&nbs=
p; 0.0000000&nbsp; 0.0000000&nbsp; 1.0000000<br>&nbsp;occupations<br>&nbsp;=
0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000<br>&nbsp;0.000&nbsp; =
0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000<br>&nbsp;0.000&nbsp; 0.000&nbsp; =
0.000&nbsp; 0.000&nbsp; 0.000<br>&nbsp;0.000&nbsp; 0.000&nbsp;
 0.000&nbsp; 0.000&nbsp; 0.000<br>&nbsp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp;=
 0.000&nbsp; 0.000<br>nsum =3D&nbsp;&nbsp; 2.0000000<br>&nbsp;exit write_ns=
<br>&nbsp;Atomic wfc used for LDA+U Projector are NOT orthogonalized<br>&nb=
sp;&nbsp;&nbsp;&nbsp; Starting wfc are&nbsp;&nbsp;&nbsp; 9 atomic +&nbsp;&n=
bsp;&nbsp; 1 random wfc<br><br>&nbsp;&nbsp;&nbsp;&nbsp; total cpu time spen=
t up to now is&nbsp;&nbsp;&nbsp;&nbsp; 13.34 secs<br><br>&nbsp;&nbsp;&nbsp;=
&nbsp; per-process dynamical memory:&nbsp;&nbsp; 326.3 Mb<br><br>&nbsp;&nbs=
p;&nbsp;&nbsp; Self-consistent Calculation<br><br>&nbsp;&nbsp;&nbsp;&nbsp; =
iteration #&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp; ecut=3D&nbsp;&nbsp;&nbsp; 45.00=
 Ry&nbsp;&nbsp;&nbsp;&nbsp; beta=3D0.70<br>&nbsp;&nbsp;&nbsp;&nbsp; CG styl=
e diagonalization<br>&nbsp;&nbsp;&nbsp;&nbsp; c_bands:&nbsp; 3 eigenvalues =
not converged<br>&nbsp;&nbsp;&nbsp;&nbsp; c_bands:&nbsp; 2 eigenvalues not =
converged<br>&nbsp;&nbsp;&nbsp;&nbsp; ethr =3D&nbsp; 1.00E-12,&nbsp; avg #
 of iterations =3D 40.4<br>&nbsp;enter write_ns<br>U( 1) =3D&nbsp; 0.0000<b=
r>alpha( 1) =3D&nbsp; 0.1000<br>atom&nbsp; 1&nbsp;&nbsp; Tr[ns(na)]=3D&nbsp=
;&nbsp; 0.0021401<br>atom&nbsp; 1&nbsp; spin&nbsp; 1<br>eigenvalues:&nbsp; =
0.0000001 0.0000001 0.0000001 0.0009883 0.0009883<br>&nbsp;eigenvectors<br>=
&nbsp;1&nbsp;&nbsp; 0.0000000 -0.8803392 -0.4743427&nbsp; 0.0000000&nbsp; 0=
.0013927<br>&nbsp;2&nbsp;&nbsp; 0.0000000 -0.4743432&nbsp; 0.8803400&nbsp; =
0.0000000 -0.0000040<br>&nbsp;3&nbsp;&nbsp; 0.0000000&nbsp; 0.0012242&nbsp;=
 0.0006642&nbsp; 0.0000000&nbsp; 0.9999990<br>&nbsp;4&nbsp; -0.8886820&nbsp=
; 0.0000000&nbsp; 0.0000000 -0.4585240&nbsp; 0.0000000<br>&nbsp;5&nbsp;&nbs=
p; 0.4585240&nbsp; 0.0000000&nbsp; 0.0000000 -0.8886820&nbsp; 0.0000000<br>=
&nbsp;occupations<br>&nbsp;0.001&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000&nbsp; =
0.000<br>&nbsp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000<br>&nb=
sp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000&nbsp;
 0.000<br>&nbsp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.001&nbsp; 0.000<br>&n=
bsp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000<br>--------------=
-------------------- and end of the file is <br>:<br>&nbsp;&nbsp;&nbsp;&nbs=
p; End of self-consistent calculation<br>&nbsp;enter write_ns<br>U( 1) =3D&=
nbsp; 0.0000<br>alpha( 1) =3D&nbsp; 0.1000<br>atom&nbsp; 1&nbsp;&nbsp; Tr[n=
s(na)]=3D&nbsp;&nbsp; 2.3270531<br>atom&nbsp; 1&nbsp; spin&nbsp; 1<br>eigen=
values:&nbsp; 0.1574294 0.1574294 0.1574294 0.9273825 0.9273825<br>&nbsp;ei=
genvectors<br>&nbsp;1&nbsp;&nbsp; 0.0000000 -0.4359030 -0.7986559&nbsp; 0.0=
000000&nbsp; 0.4148945<br>&nbsp;2&nbsp;&nbsp; 0.0000000&nbsp; 0.7269732 -0.=
0406891&nbsp; 0.0000000&nbsp; 0.6854592<br>&nbsp;3&nbsp;&nbsp; 0.0000000 -0=
.5305643&nbsp; 0.6004109&nbsp; 0.0000000&nbsp; 0.5983379<br>&nbsp;4&nbsp; -=
0.9258933&nbsp; 0.0000000&nbsp; 0.0000000 -0.3777851&nbsp; 0.0000000<br>&nb=
sp;5&nbsp;&nbsp; 0.3777851&nbsp; 0.0000000&nbsp; 0.0000000
 -0.9258933&nbsp; 0.0000000<br>&nbsp;occupations<br>&nbsp;0.927&nbsp; 0.000=
&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000<br>&nbsp;0.000&nbsp; 0.157&nbsp; 0.000=
&nbsp; 0.000&nbsp; 0.000<br>&nbsp;0.000&nbsp; 0.000&nbsp; 0.157&nbsp; 0.000=
&nbsp; 0.000<br>&nbsp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.927&nbsp; 0.000=
<br>&nbsp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.157<br><br><br>=
Thanks a lot<br>Ali Kazempour<br>=0APhysics department, Isfahan University =
of Technology<br>=0A84156 Isfahan, Iran.            Tel-1:  +98 311 391 373=
3<br>=0AFax: +98 311 391 2376      Tel-2:  +98 311 391 2375</td></tr></tabl=
e><br>=0A=0A=0A=0A      
--0-576403044-1248884560=:51951--

From baroni at sissa.it  Wed Jul 29 19:17:16 2009
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 29 Jul 2009 19:17:16 +0200
Subject: [Pw_forum] IMPORTANT ANNOUNCEMENT
Message-ID: <1C2A72F4-FAF9-428A-AA05-F85136800DD1@sissa.it>

Dear All,

it is my pleasure to announce the forthcoming appearance on Journal of  
Physics Condensed Matter of a paper reporting on the current status of  
the Quantum ESPRESSO project. The final draft of the paper is  
available on aXiv:

http://arxiv.org/abs/0906.2569v2

The provisional reference of the paper is:

P. Giannozzi et al., J. Phys.: Condens. Matt. (2009), in press; arXiv: 
0906.2569v2 [cond-mat.mtrl-sci].

Please, quote it whenever you publish results obtained using the  
Quantum ESPRESSO distribution. We will keep you updated as to when a  
final bibliographic reference will be available.

Thank you for being part of our community.

Stefano Baroni

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

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

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








From wshen02 at gmail.com  Wed Jul 29 20:03:30 2009
From: wshen02 at gmail.com (=?UTF-8?B?5paH5rKI?=)
Date: Wed, 29 Jul 2009 11:03:30 -0700
Subject: [Pw_forum] Does anybody have the same problem for the relax
	calculation about the atom force
In-Reply-To: <4A702E4D.5020704@democritos.it>
References: <2c9df8a80907281437j48077c4dif65dd73e75304af3@mail.gmail.com>
	<4A702E4D.5020704@democritos.it>
Message-ID: <2c9df8a80907291103k1e7393d1w46bcda14fa721f51@mail.gmail.com>

Thanks Paolo,
Can you tell me which pseudopotential are you using?
please send it to me.
Thanks

Wen

On Wed, Jul 29, 2009 at 4:11 AM, Paolo Giannozzi <giannozz at democritos.it>wrote:

> A faster version of your input (with just 1 k-point)
> works on my PC
>
> P.
>
>
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From giannozz at democritos.it  Wed Jul 29 20:20:12 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 29 Jul 2009 20:20:12 +0200
Subject: [Pw_forum] Does anybody have the same problem for the relax
	calculation about the atom force
In-Reply-To: <2c9df8a80907291103k1e7393d1w46bcda14fa721f51@mail.gmail.com>
References: <2c9df8a80907281437j48077c4dif65dd73e75304af3@mail.gmail.com>
	<4A702E4D.5020704@democritos.it>
	<2c9df8a80907291103k1e7393d1w46bcda14fa721f51@mail.gmail.com>
Message-ID: <22D52536-AB66-45E6-A445-8693C8981438@democritos.it>


On Jul 29, 2009, at 20:03 , ?? wrote:

> Can you tell me which pseudopotential are you using?

those on the quantum espresso web site

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




From jjr19 at uakron.edu  Wed Jul 29 20:32:38 2009
From: jjr19 at uakron.edu (J. J. Ramsey)
Date: Wed, 29 Jul 2009 11:32:38 -0700 (PDT)
Subject: [Pw_forum] Pseudopotentials with negative "Max angular momentum
	component"?
Message-ID: <488304.4541.qm@web50912.mail.re2.yahoo.com>

I noticed that some of the pseudopotentials on the QE website (e.g. http://www.quantum-espresso.org/pseudo/1.3/UPF/H.pz-vbc.UPF, http://www.quantum-espresso.org/pseudo/1.3/UPF/H.tpss-mt.UPF) have "-1" as the value of the max. angular momentum component in the PP_HEADER section. It's unclear from the page on the UPF format (http://www.quantum-espresso.org/wiki/index.php/Unified_pseudopotential_format) what this is supposed to mean. What is that negative value supposed to indicate?

University of Akron
Civil Engineering Department



      

From wshen02 at gmail.com  Wed Jul 29 21:02:38 2009
From: wshen02 at gmail.com (=?UTF-8?B?5paH5rKI?=)
Date: Wed, 29 Jul 2009 12:02:38 -0700
Subject: [Pw_forum] Does anybody have the same problem for the relax
	calculation about the atom force
In-Reply-To: <22D52536-AB66-45E6-A445-8693C8981438@democritos.it>
References: <2c9df8a80907281437j48077c4dif65dd73e75304af3@mail.gmail.com>
	<4A702E4D.5020704@democritos.it>
	<2c9df8a80907291103k1e7393d1w46bcda14fa721f51@mail.gmail.com>
	<22D52536-AB66-45E6-A445-8693C8981438@democritos.it>
Message-ID: <2c9df8a80907291202x615cc75vf182891512a9023a@mail.gmail.com>

I also runned the 1 1 1 kpoints here, still the same problem.

Can you tell me which type of Pseudopotential you were using?

I use all PBE pseudo

Thanks!

Wen

On Wed, Jul 29, 2009 at 11:20 AM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Jul 29, 2009, at 20:03 , ?? wrote:
>
> > Can you tell me which pseudopotential are you using?
>
> those on the quantum espresso web site
>
> P.
> --
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From giannozz at democritos.it  Wed Jul 29 22:54:07 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 29 Jul 2009 22:54:07 +0200
Subject: [Pw_forum] Does anybody have the same problem for the relax
	calculation about the atom force
In-Reply-To: <2c9df8a80907291202x615cc75vf182891512a9023a@mail.gmail.com>
References: <2c9df8a80907281437j48077c4dif65dd73e75304af3@mail.gmail.com>
	<4A702E4D.5020704@democritos.it>
	<2c9df8a80907291103k1e7393d1w46bcda14fa721f51@mail.gmail.com>
	<22D52536-AB66-45E6-A445-8693C8981438@democritos.it>
	<2c9df8a80907291202x615cc75vf182891512a9023a@mail.gmail.com>
Message-ID: <57CC674D-29AD-4F22-9773-64D8EE47CC0C@democritos.it>


On Jul 29, 2009, at 21:02 , ?? wrote:

> Can you tell me which type of Pseudopotential you were using?

can you read?

> > Can you tell me which pseudopotential are you using?
>
> those on the quantum espresso web site

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




From giannozz at democritos.it  Wed Jul 29 22:55:48 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 29 Jul 2009 22:55:48 +0200
Subject: [Pw_forum] Pseudopotentials with negative "Max angular momentum
	component"?
In-Reply-To: <488304.4541.qm@web50912.mail.re2.yahoo.com>
References: <488304.4541.qm@web50912.mail.re2.yahoo.com>
Message-ID: <17B99343-7DAF-4EDF-99F7-EAF8230EC2B8@democritos.it>


On Jul 29, 2009, at 20:32 , J. J. Ramsey wrote:

> I noticed that some of the pseudopotentials on the QE website
> [...] have "-1" as the value of the max. angular momentum
> component in the PP_HEADER section. It's unclear [...]
> what this is supposed to mean.

local pseudopotentials, i.e. no nonlocal part. Lmax = 0 means
s local part

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




From yukihiro_okuno at fujifilm.co.jp  Thu Jul 30 04:00:53 2009
From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp)
Date: Thu, 30 Jul 2009 11:00:53 +0900
Subject: [Pw_forum] Use of wannier90.x for the calculation of Born Effective
	Charge
Message-ID: <OFE1D0FCEE.6E83DF2C-ON49257603.00071D85-49257603.000B0FD5@mta.fujifilm.co.jp>


Dear PWSCF users.

I'm now using wannier90.x in PWSCF package (espresso-4.1) for

the calculation of Born Effective charge for each orbital like

N.Marzari and D. Vanderbilt  http:/arxiv.org/abs/cond-mat/9802210.

I employ the example of BaTiO3.

For cubic symmetry (centro symmetric atomic position),  the calculation

is done with reasonable results.   But, in order to calculate

the Ti's Born effective charge ,   I displacing the Ti atom, like ( 0.5 0.5
0.505) from

the centro-symmetric position (0.5,0.5,0.5),  the error occurred in the

calculation of pw2wannier.x  with the message below,

Something wrong

numk = 64    iknum=  130.


This is due to that the symmetry is lowered by the displacement of Ti atom

and the k-points are  added in the non-SCF calculation

in PWSCF (in the subroutine sgama).


If we set nosym in the input file of non-SCF calculation with k-points is
same as

BaTiO3.win file., the symmetry of the results of wannier center

broken, so the calculated Born Effective Charges are wrong.

How should treat the k-points inconsistent when we calculate the Born
effective

charge in displacing the atom.

Here is my input file for BaTiO3.win.


num_wann        =  9
num_iter        = 100

!here we exclude all bands except the O2p bands
exclude_bands : 1,2,3,4,5,6,7,8,9,10,11

write_xyz = T
guiding_centres = T

begin atoms_frac
Ba 0.0 0.0 0.0
Ti 0.5 0.5 0.502
O  0.0 0.5 0.5
O  0.5 0.5 0.0
O  0.5 0.0 0.5
end atoms_frac

begin kpoint_path
L 0.50000  0.50000 0.5000 G 0.00000  0.00000 0.0000
G 0.00000  0.00000 0.0000 X 0.50000  0.00000 0.5000
X 0.50000 -0.50000 0.0000 K 0.37500 -0.37500 0.0000
K 0.37500 -0.37500 0.0000 G 0.00000  0.00000 0.0000
end kpoint_path
bands_plot =T


!!To plot the WF
!restart = plot
!wannier_plot = true
!wannier_plot_supercell = 2
!wannier_plot_list = 3


begin projections
O:p
end projections


begin unit_cell_cart
bohr
7.44266 0.0 0.0
0.0 7.44266 0.0
0.0 0.0 7.44266
end unit_cell_cart

mp_grid : 4 4 4

begin kpoints
  0.00000000  0.00000000  0.00000000
  0.00000000  0.00000000  0.25000000
  0.00000000  0.00000000  0.50000000
  0.00000000  0.00000000  0.75000000
  0.00000000  0.25000000  0.00000000
  0.00000000  0.25000000  0.25000000
  0.00000000  0.25000000  0.50000000
  0.00000000  0.25000000  0.75000000
  0.00000000  0.50000000  0.00000000
  0.00000000  0.50000000  0.25000000
  0.00000000  0.50000000  0.50000000
  0.00000000  0.50000000  0.75000000
  0.00000000  0.75000000  0.00000000
  0.00000000  0.75000000  0.25000000
  0.00000000  0.75000000  0.50000000
  0.00000000  0.75000000  0.75000000
  0.25000000  0.00000000  0.00000000
  0.25000000  0.00000000  0.25000000
  0.25000000  0.00000000  0.50000000
  0.25000000  0.00000000  0.75000000
  0.25000000  0.25000000  0.00000000
  0.25000000  0.25000000  0.25000000
  0.25000000  0.25000000  0.50000000
  0.25000000  0.25000000  0.75000000
  0.25000000  0.50000000  0.00000000
  0.25000000  0.50000000  0.25000000
  0.25000000  0.50000000  0.50000000
  0.25000000  0.50000000  0.75000000
  0.25000000  0.75000000  0.00000000
  0.25000000  0.75000000  0.25000000
  0.25000000  0.75000000  0.50000000
  0.25000000  0.75000000  0.75000000
  0.50000000  0.00000000  0.00000000
  0.50000000  0.00000000  0.25000000
  0.50000000  0.00000000  0.50000000
  0.50000000  0.00000000  0.75000000
  0.50000000  0.25000000  0.00000000
  0.50000000  0.25000000  0.25000000
  0.50000000  0.25000000  0.50000000
  0.50000000  0.25000000  0.75000000
  0.50000000  0.50000000  0.00000000
  0.50000000  0.50000000  0.25000000
  0.50000000  0.50000000  0.50000000
  0.50000000  0.50000000  0.75000000
  0.50000000  0.75000000  0.00000000
  0.50000000  0.75000000  0.25000000
  0.50000000  0.75000000  0.50000000
  0.50000000  0.75000000  0.75000000
  0.75000000  0.00000000  0.00000000
  0.75000000  0.00000000  0.25000000
  0.75000000  0.00000000  0.50000000
  0.75000000  0.00000000  0.75000000
  0.75000000  0.25000000  0.00000000
  0.75000000  0.25000000  0.25000000
  0.75000000  0.25000000  0.50000000
  0.75000000  0.25000000  0.75000000
  0.75000000  0.50000000  0.00000000
  0.75000000  0.50000000  0.25000000
  0.75000000  0.50000000  0.50000000
  0.75000000  0.50000000  0.75000000
  0.75000000  0.75000000  0.00000000
  0.75000000  0.75000000  0.25000000
  0.75000000  0.75000000  0.50000000
  0.75000000  0.75000000  0.75000000
end kpoints



Sincerely.


From vamsi.iisc at gmail.com  Thu Jul 30 07:56:14 2009
From: vamsi.iisc at gmail.com (vamsi kv)
Date: Thu, 30 Jul 2009 11:26:14 +0530
Subject: [Pw_forum] plotting chargedensity
Message-ID: <84ff69170907292256o7756bf68n9bd14af0f0e4b2eb@mail.gmail.com>

Hi everyone,

I am using the quantum espresso for my thesis work for looking at
chargedensity difference plots. Now i want to see the difference between two
structures and i also want to see the chargedensity distribution in these
two structures to understand some of the basis concepts

so the thing i want to know is is there any way to pull the charge density
information and plot it using different software like MATLAB.


regards,
K V Vamsi
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From vamsi.iisc at gmail.com  Thu Jul 30 07:54:55 2009
From: vamsi.iisc at gmail.com (vamsi kv)
Date: Thu, 30 Jul 2009 11:24:55 +0530
Subject: [Pw_forum] plotting chargedensity
Message-ID: <84ff69170907292254j7f7d4d0fh9aca2f09039d6b7a@mail.gmail.com>

Hi everyone,

I am using the quantum espresso for my thesis work for looking at
chargedensity difference plots. Now i want to see the difference between two
structures and i also want to see the chargedensity distribution in these
two structures to understand some of the basis concepts

so the thing i want to know is is there any way to pull the charge density
information and plot it using different software like MATLAB.
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From paulatto at sissa.it  Thu Jul 30 10:58:56 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 30 Jul 2009 10:58:56 +0200
Subject: [Pw_forum] plotting chargedensity
In-Reply-To: <84ff69170907292254j7f7d4d0fh9aca2f09039d6b7a@mail.gmail.com>
References: <84ff69170907292254j7f7d4d0fh9aca2f09039d6b7a@mail.gmail.com>
Message-ID: <op.uxvhwiwxa8x26q@paulax>

In data 30 luglio 2009 alle ore 07:54:55, vamsi kv <vamsi.iisc at gmail.com>  
ha scritto:
> so the thing i want to know is is there any way to pull the charge  
> density information and plot it using different software like MATLAB.

The post-processing utility (pp.x) can extract the charge density and save  
it in several formats; it can also compute directly the charge density  
difference from two system sharing the same unit cell (actually, any  
linear combination of charge densities).

It can also output the density (or any other quantity you ask it to  
extract) in several formats. Some of these formats are quite  
self-explanatory or widely documented, like the XCrysDen format  
<http://www.xcrysden.org/doc/XSF.html> or the gaussian cube format  
<http://local.wasp.uwa.edu.au/~pbourke/dataformats/cube/>. Although it  
could be easily done, there is no option to save the output in matlab  
format.

What you can do is write a mini-program (can be done in matlab itself) to  
import one of the other formats, or write an output subroutine that saves  
in matlab format (you have to know a bit of fortran).


best regards

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

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

From somesh.kb at gmail.com  Thu Jul 30 17:09:14 2009
From: somesh.kb at gmail.com (Somesh Kumar Bhattacharya)
Date: Thu, 30 Jul 2009 17:09:14 +0200
Subject: [Pw_forum] Fwd: Help required
In-Reply-To: <e0e40e0d0907300614n2d2fc2c0qc1d4fef87e3d80e@mail.gmail.com>
References: <e0e40e0d0907300614n2d2fc2c0qc1d4fef87e3d80e@mail.gmail.com>
Message-ID: <e0e40e0d0907300809w186821a9x194a58b8ba2d333@mail.gmail.com>

Dear All,

I am doing a scf calculation of Ice surface with a Cl atom which is
negatively charged.

 The scf calculation for bare Ice surface was trivial. However,  for the Ice
surface+ Cl(-ve anion)

However, the scf is not moving at all in the sense that the calculation
crashes every time.

The input is  :
&CONTROL
  calculation = "scf",
  prefix = 'Cl-surface'
  restart_mode = 'from_scratch',
  tprnfor = .TRUE.,
  wf_collect = .TRUE.,
  max_seconds = 21000,
  pseudo_dir = '/scratch/userictp/ictpcm16/pseudo/'
  outdir = './'

/
&SYSTEM
    ibrav=  14,
    celldm(1) = 16.972000,
    celldm(2) = 1.,
    celldm(3) = 4.9733070,
    celldm(4) = 0.0,
    celldm(5) = 0.0,
    celldm(6) = -0.5,
    nat=  97,
    ntyp= 3,
    ecutwfc = 80.0,
    ecutrho = 400.0
    nbnd=160,
    nspin = 2,
    nelec=264,
    nelup = 132,
    neldw = 132,
    occupations = 'fixed',
/
&ELECTRONS
  diagonalization = 'david',
  conv_thr    = 1.D-7,
  mixing_beta = 0.2D0,
  mixing_mode = 'local-TF'
/

ATOMIC_SPECIES
Cl 35.4527  Cl.blyp-mt.UPF
O  15.9990  O.blyp-mt.UPF
H   1.0008  H.blyp-vbc.UPF

ATOMIC_POSITIONS (bohr)
   Cl   0.442065E+01  0.306161E+01 -0.266987E+02
   O    0.000000E+00  0.000000E+00  0.000000E+00
   O    0.424300E+01  0.734909E+01  0.000000E+00
   O    0.851569E+01  0.000000E+00  0.000000E+00
   O    0.126108E+02  0.734909E+01  0.000000E+00
   O    0.438891E+01  0.244970E+01 -0.173220E+01
   O    0.848600E+01  0.956439E+01 -0.173220E+01
   O    0.127290E+02  0.271183E+01 -0.173220E+01
   O    0.169720E+02  0.944817E+01 -0.173220E+01
   O    0.428030E+01  0.725274E+01 -0.840389E+01
   O    0.841685E+01 -0.436113E-01 -0.861498E+01
   O    0.124692E+02  0.715221E+01 -0.903980E+01
   O    0.165969E+02 -0.158654E+00 -0.830754E+01
   O   -0.183694E+00  0.969090E+01 -0.719695E+01
   O    0.397887E+01  0.232368E+01 -0.681051E+01
   O    0.858600E+01  0.965094E+01 -0.682273E+01
   O    0.125603E+02  0.238309E+01 -0.670488E+01
   O   -0.544601E+00 -0.420609E+00 -0.133708E+02
   O    0.440102E+01  0.742833E+01 -0.137164E+02
   O    0.842565E+01  0.144513E-01 -0.136329E+02
   O    0.121833E+02  0.713481E+01 -0.145496E+02
   O    0.382665E+01  0.235481E+01 -0.139532E+02
   O    0.827943E+01  0.101149E+02 -0.163476E+02
   O    0.125329E+02  0.218570E+01 -0.160069E+02
   O    0.168335E+02  0.944957E+01 -0.143380E+02
   O    0.383163E+01  0.784639E+01 -0.197508E+02
   O    0.793527E+01 -0.657036E-01 -0.230354E+02
   O    0.118885E+02  0.671256E+01 -0.227310E+02
   O    0.172021E+02  0.506853E+00 -0.231756E+02
   O   -0.369799E+00  0.930820E+01 -0.234342E+02
   O    0.412088E+01  0.246691E+01 -0.190829E+02
   O    0.816263E+01  0.100876E+02 -0.219343E+02
   O    0.126415E+02  0.165939E+01 -0.210947E+02
   H    0.158053E+01  0.777030E+00 -0.615741E+00
   H    0.101349E+01  0.609887E+00 -0.136132E+02
   H    0.295433E-02 -0.174804E+01 -0.635311E+00
   H   -0.320957E+00 -0.200415E+01 -0.143969E+02
   H    0.409538E+01  0.747239E+01  0.182080E+01
   H    0.449351E+01  0.762299E+01 -0.118706E+02
   H    0.263941E+01  0.814680E+01 -0.681465E+00
   H    0.274098E+01  0.817016E+01 -0.141897E+02
   H    0.100102E+02  0.916500E+00 -0.623627E+00
   H    0.982207E+01  0.832598E+00 -0.145990E+02
   H    0.703605E+01  0.919996E+00 -0.686878E+00
   H    0.685374E+01  0.100312E+01 -0.138837E+02
   H    0.126555E+02  0.722834E+01  0.182702E+01
   H    0.121280E+02  0.702454E+01 -0.126965E+02
   H    0.126852E+02  0.551011E+01 -0.665021E+00
   H    0.123271E+02  0.535587E+01 -0.151826E+02
   H    0.421851E+01  0.243526E+01 -0.362234E+01
   H    0.382764E+01  0.225861E+01 -0.158333E+02
   H    0.434800E+01  0.422513E+01 -0.119546E+01
   H    0.396446E+01  0.423069E+01 -0.136939E+02
   H    0.694714E+01  0.871016E+01 -0.113223E+01
   H    0.677200E+01  0.916570E+01 -0.157926E+02
   H    0.995458E+01  0.865760E+01 -0.102494E+01
   H    0.971274E+01  0.902918E+01 -0.158122E+02
   H    0.126648E+02  0.260576E+01 -0.365650E+01
   H    0.126353E+02  0.188395E+01 -0.178750E+02
   H    0.142630E+02  0.176495E+01 -0.119721E+01
   H    0.139745E+02  0.128942E+01 -0.152125E+02
   H    0.153671E+02  0.871276E+01 -0.111388E+01
   H    0.151700E+02  0.870562E+01 -0.147042E+02
   H    0.169513E+02  0.112617E+02 -0.120529E+01
   H    0.166825E+02  0.112966E+02 -0.143418E+02
   H   -0.186080E+00  0.967497E+01 -0.534322E+01
   H   -0.410716E+00  0.111769E+02 -0.235014E+02
   H   -0.170693E+00  0.115036E+02 -0.772370E+01
   H    0.606586E+00  0.869850E+01 -0.248594E+02
   H    0.241458E+01  0.149908E+01 -0.745774E+01
   H    0.278675E+01  0.175538E+01 -0.201536E+02
   H    0.400545E+01  0.408502E+01 -0.747655E+01
   H    0.410033E+01  0.431163E+01 -0.194638E+02
   H    0.869216E+01  0.953273E+01 -0.496001E+01
   H    0.839309E+01  0.103335E+02 -0.201056E+02
   H    0.100559E+02  0.872566E+01 -0.757565E+01
   H    0.944654E+01  0.876504E+01 -0.223573E+02
   H    0.110200E+02  0.152522E+01 -0.737847E+01
   H    0.112050E+02  0.835252E+00 -0.219509E+02
   H    0.140384E+02  0.135637E+01 -0.730830E+01
   H    0.142191E+02  0.119371E+01 -0.220024E+02
   H    0.578777E+01  0.817933E+01 -0.778715E+01
   H    0.517532E+01  0.854101E+01 -0.208405E+02
   H    0.275644E+01  0.826658E+01 -0.801262E+01
   H    0.224952E+01  0.825531E+01 -0.206219E+02
   H    0.851028E+01  0.801689E-02 -0.105254E+02
   H    0.704752E+01  0.853268E+00 -0.244147E+02
   H    0.681312E+01  0.785612E+00 -0.813077E+01
   H    0.700809E+01  0.491320E+00 -0.215355E+02
   H    0.140548E+02  0.803540E+01 -0.859465E+01
   H    0.135749E+02  0.747089E+01 -0.228574E+02
   H    0.126118E+02  0.543782E+01 -0.830772E+01
   H    0.120930E+02  0.495909E+01 -0.221546E+02
   H    0.164613E+02 -0.340182E+00 -0.101937E+02
   H    0.183449E+02  0.123088E+01 -0.244582E+02
   H    0.167906E+02 -0.192736E+01 -0.769333E+01
   H    0.173328E+02 -0.135460E+01 -0.231944E+02
K_POINTS {automatic}
2 2 1 0 0 0



For  diagonalization = 'david' the calculation is not proceeding at all
after

Self-consistent Calculation

     iteration #  1     ecut=    80.00 Ry     beta=0.20
     Davidson diagonalization with overlap
------------------------------------------------------------------------------------------------------------------------------------------------------


Even for diagonalization = 'cg', the 1st iteration goes fine ....... But
from second iteration onwards, it says certain eigenvalues not converged and
finally it crashes.

When I changed the occupations to smearing, then also am not overcoming the
problem.

Can you please take a look at this and let me know the reason ??

thanking you in anticipation,

Regards,

Somesh
-- 
Somesh Kr. Bhattacharya
Post Doctoral Fellow
Room No. 263,
Leonardo Building,
The Abdus Salam International Centre for Theoretical Physics
Strada Costiera, 11
I-34014 Trieste
Italy
Phone: +39-040-2240399
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From paulatto at sissa.it  Thu Jul 30 17:23:24 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 30 Jul 2009 17:23:24 +0200
Subject: [Pw_forum] Fwd: Help required
In-Reply-To: <e0e40e0d0907300809w186821a9x194a58b8ba2d333@mail.gmail.com>
References: <e0e40e0d0907300614n2d2fc2c0qc1d4fef87e3d80e@mail.gmail.com>
	<e0e40e0d0907300809w186821a9x194a58b8ba2d333@mail.gmail.com>
Message-ID: <op.uxvzpaa3a8x26q@paulax>

In data 30 luglio 2009 alle ore 17:09:14, Somesh Kumar Bhattacharya  
<somesh.kb at gmail.com> ha scritto:
> finally it crashes.

Dear Somesh,
your system is huge, can you please provide the full output (if possible  
for the different cases you've tried), up to the point where it crashes so  
we can take a look without wasting all that CPU time?

best regards


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

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

From kazempoor2000 at yahoo.com  Thu Jul 30 17:37:43 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Thu, 30 Jul 2009 08:37:43 -0700 (PDT)
Subject: [Pw_forum] occupation
Message-ID: <10309.19544.qm@web112513.mail.gq1.yahoo.com>


Dear all


From bogus@does.not.exist.com  Fri Jul 24 13:42:27 2009
From: bogus@does.not.exist.com ()
Date: Fri, 24 Jul 2009 11:42:27 -0000
Subject: No subject
Message-ID: <mailman.1.1248968280.24399.pw_forum@pwscf.org>

I double the unit cell in z direction and again=0Acompute U ,I get three di=
fferent value for Ti atoms.(U=3D5.63,5.46,5.70).
Why these values are not same . what is the main reason? Does it in numeric=
al variation errors?
ANother question:
When=0Awe perturb D level by alpha, it give rise to change in d occupancy .=
 Is=0Ait correct that if we impose negative alpha , the occupation becomes=
=0Aless than initial state .?
for Ti isolated atom for apha=3D0.1=A0=0Atr[ns(na)] after first-iteration e=
qual to the 0.002 and at the end of=0Acalculation is 2.327 while we know th=
at for Ti,=A0 tr[ns(na)] =3D2.000.=0ADoes it seems to be correct.?

=A0=A0=A0=A0 Number of iteration with fixed ns =3D=A0 0
=A0=A0=A0=A0 Starting ns and Hubbard U :
=A0enter=0A write_ns
U( 1) =3D=A0 0.0000
alpha( 1) =3D=A0 0.1000
atom=A0 1=A0=A0 Tr[ns(na)]=3D=A0=A0 2.0000000
atom=A0 1=A0 spin=A0 1
eigenvalues:=A0 0.4000000 0.4000000 0.4000000 0.4000000 0.4000000
=A0eigenvectors
=A01=A0=A0 1.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000
=A02=A0=A0 0.0000000=A0 1.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000
=A03=A0=A0 0.0000000=A0 0.0000000=A0 1.0000000=A0 0.0000000=A0 0.0000000
=A04=A0=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 1.0000000=A0 0.0000000
=A05=A0=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 1.0000000
=A0occupations
=A00.400=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.400=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.400=A0 0.000=A0 0.000
=A00.000=A0=0A 0.000=A0 0.000=A0 0.400=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.400
atom=A0 1=A0 spin=A0 2
eigenvalues:=A0 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
=A0eigenvectors
=A01=A0=A0 1.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000
=A02=A0=A0 0.0000000=A0 1.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000
=A03=A0=A0 0.0000000=A0 0.0000000=A0 1.0000000=A0 0.0000000=A0 0.0000000
=A04=A0=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 1.0000000=A0 0.0000000
=A05=A0=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 0.0000000=A0 1.0000000
=A0occupations
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0=0A 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.000
nsum =3D=A0=A0 2.0000000
=A0exit write_ns
=A0Atomic wfc used for LDA+U Projector are NOT orthogonalized
=A0=A0=A0=A0 Starting wfc are=A0=A0=A0 9 atomic +=A0=A0=A0 1 random wfc

=A0=A0=A0=A0 total cpu time spent up to now is=A0=A0=A0=A0 13.34 secs

=A0=A0=A0=A0 per-process dynamical memory:=A0=A0 326.3 Mb

=A0=A0=A0=A0 Self-consistent Calculation

=A0=A0=A0=A0 iteration #=A0 1=A0=A0=A0=A0 ecut=3D=A0=A0=A0 45.00 Ry=A0=A0=
=A0=A0 beta=3D0.70
=A0=A0=A0=A0 CG style diagonalization
=A0=A0=A0=A0 c_bands:=A0 3 eigenvalues not converged
=A0=A0=A0=A0 c_bands:=A0 2 eigenvalues not converged
=A0=A0=A0=A0 ethr =3D=A0 1.00E-12,=A0 avg #=0A of iterations =3D 40.4
=A0enter write_ns
U( 1) =3D=A0 0.0000
alpha( 1) =3D=A0 0.1000
atom=A0 1=A0=A0 Tr[ns(na)]=3D=A0=A0 0.0021401
atom=A0 1=A0 spin=A0 1
eigenvalues:=A0 0.0000001 0.0000001 0.0000001 0.0009883 0.0009883
=A0eigenvectors
=A01=A0=A0 0.0000000 -0.8803392 -0.4743427=A0 0.0000000=A0 0.0013927
=A02=A0=A0 0.0000000 -0.4743432=A0 0.8803400=A0 0.0000000 -0.0000040
=A03=A0=A0 0.0000000=A0 0.0012242=A0 0.0006642=A0 0.0000000=A0 0.9999990
=A04=A0 -0.8886820=A0 0.0000000=A0 0.0000000 -0.4585240=A0 0.0000000
=A05=A0=A0 0.4585240=A0 0.0000000=A0 0.0000000 -0.8886820=A0 0.0000000
=A0occupations
=A00.001=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0=0A 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.001=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.000
---------------------------------- and end of the file is=20
:
=A0=A0=A0=A0 End of self-consistent calculation
=A0enter write_ns
U( 1) =3D=A0 0.0000
alpha( 1) =3D=A0 0.1000
atom=A0 1=A0=A0 Tr[ns(na)]=3D=A0=A0 2.3270531
atom=A0 1=A0 spin=A0 1
eigenvalues:=A0 0.1574294 0.1574294 0.1574294 0.9273825 0.9273825
=A0eigenvectors
=A01=A0=A0 0.0000000 -0.4359030 -0.7986559=A0 0.0000000=A0 0.4148945
=A02=A0=A0 0.0000000=A0 0.7269732 -0.0406891=A0 0.0000000=A0 0.6854592
=A03=A0=A0 0.0000000 -0.5305643=A0 0.6004109=A0 0.0000000=A0 0.5983379
=A04=A0 -0.9258933=A0 0.0000000=A0 0.0000000 -0.3777851=A0 0.0000000
=A05=A0=A0 0.3777851=A0 0.0000000=A0 0.0000000=0A -0.9258933=A0 0.0000000
=A0occupations
=A00.927=A0 0.000=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.157=A0 0.000=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.157=A0 0.000=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.927=A0 0.000
=A00.000=A0 0.000=A0 0.000=A0 0.000=A0 0.157


Ali Kazempour
=0APhysics department, Isfahan University of Technology
=0A84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733
=0AFax: +98 311 391 2376      Tel-2:  +98 311 391 2375=0A=0A=0A      
--0-877763539-1248968263=:19544
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable

<table cellspacing=3D"0" cellpadding=3D"0" border=3D"0" ><tr><td valign=3D"=
top" style=3D"font: inherit;"><br>Dear all<br><br>From Linear response calc=
ulation ,I get for TiO2=0Abulk U=3D5.73, But when I double the unit cell in=
 z direction and again=0Acompute U ,I get three different value for Ti atom=
s.(U=3D5.63,5.46,5.70).<br>Why these values are not same . what is the main=
 reason? Does it in numerical variation errors?<br>ANother question:<br>Whe=
n=0Awe perturb D level by alpha, it give rise to change in d occupancy . Is=
=0Ait correct that if we impose negative alpha , the occupation becomes=0Al=
ess than initial state .?<br>for Ti isolated atom for apha=3D0.1&nbsp;=0Atr=
[ns(na)] after first-iteration equal to the 0.002 and at the end of=0Acalcu=
lation is 2.327 while we know that for Ti,&nbsp; tr[ns(na)] =3D2.000.=0ADoe=
s it seems to be correct.?<br><br>&nbsp;&nbsp;&nbsp;&nbsp; Number of iterat=
ion with fixed ns =3D&nbsp; 0<br>&nbsp;&nbsp;&nbsp;&nbsp; Starting ns and H=
ubbard U :<br>&nbsp;enter=0A write_ns<br>U( 1) =3D&nbsp; 0.0000<br>alpha( 1=
) =3D&nbsp; 0.1000<br>atom&nbsp; 1&nbsp;&nbsp; Tr[ns(na)]=3D&nbsp;&nbsp; 2.=
0000000<br>atom&nbsp; 1&nbsp; spin&nbsp; 1<br>eigenvalues:&nbsp; 0.4000000 =
0.4000000 0.4000000 0.4000000 0.4000000<br>&nbsp;eigenvectors<br>&nbsp;1&nb=
sp;&nbsp; 1.0000000&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 0=
.0000000<br>&nbsp;2&nbsp;&nbsp; 0.0000000&nbsp; 1.0000000&nbsp; 0.0000000&n=
bsp; 0.0000000&nbsp; 0.0000000<br>&nbsp;3&nbsp;&nbsp; 0.0000000&nbsp; 0.000=
0000&nbsp; 1.0000000&nbsp; 0.0000000&nbsp; 0.0000000<br>&nbsp;4&nbsp;&nbsp;=
 0.0000000&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 1.0000000&nbsp; 0.0000000<=
br>&nbsp;5&nbsp;&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 0.00=
00000&nbsp; 1.0000000<br>&nbsp;occupations<br>&nbsp;0.400&nbsp; 0.000&nbsp;=
 0.000&nbsp; 0.000&nbsp; 0.000<br>&nbsp;0.000&nbsp; 0.400&nbsp; 0.000&nbsp;=
 0.000&nbsp; 0.000<br>&nbsp;0.000&nbsp; 0.000&nbsp; 0.400&nbsp; 0.000&nbsp;=
 0.000<br>&nbsp;0.000&nbsp;=0A 0.000&nbsp; 0.000&nbsp; 0.400&nbsp; 0.000<br=
>&nbsp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.400<br>atom&nbsp; =
1&nbsp; spin&nbsp; 2<br>eigenvalues:&nbsp; 0.0000000 0.0000000 0.0000000 0.=
0000000 0.0000000<br>&nbsp;eigenvectors<br>&nbsp;1&nbsp;&nbsp; 1.0000000&nb=
sp; 0.0000000&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 0.0000000<br>&nbsp;2&nb=
sp;&nbsp; 0.0000000&nbsp; 1.0000000&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 0=
.0000000<br>&nbsp;3&nbsp;&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 1.0000000&n=
bsp; 0.0000000&nbsp; 0.0000000<br>&nbsp;4&nbsp;&nbsp; 0.0000000&nbsp; 0.000=
0000&nbsp; 0.0000000&nbsp; 1.0000000&nbsp; 0.0000000<br>&nbsp;5&nbsp;&nbsp;=
 0.0000000&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 0.0000000&nbsp; 1.0000000<=
br>&nbsp;occupations<br>&nbsp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000&nbs=
p; 0.000<br>&nbsp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000<br>=
&nbsp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000<br>&nbsp;0.000&=
nbsp; 0.000&nbsp;=0A 0.000&nbsp; 0.000&nbsp; 0.000<br>&nbsp;0.000&nbsp; 0.0=
00&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000<br>nsum =3D&nbsp;&nbsp; 2.0000000<br=
>&nbsp;exit write_ns<br>&nbsp;Atomic wfc used for LDA+U Projector are NOT o=
rthogonalized<br>&nbsp;&nbsp;&nbsp;&nbsp; Starting wfc are&nbsp;&nbsp;&nbsp=
; 9 atomic +&nbsp;&nbsp;&nbsp; 1 random wfc<br><br>&nbsp;&nbsp;&nbsp;&nbsp;=
 total cpu time spent up to now is&nbsp;&nbsp;&nbsp;&nbsp; 13.34 secs<br><b=
r>&nbsp;&nbsp;&nbsp;&nbsp; per-process dynamical memory:&nbsp;&nbsp; 326.3 =
Mb<br><br>&nbsp;&nbsp;&nbsp;&nbsp; Self-consistent Calculation<br><br>&nbsp=
;&nbsp;&nbsp;&nbsp; iteration #&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp; ecut=3D&nbs=
p;&nbsp;&nbsp; 45.00 Ry&nbsp;&nbsp;&nbsp;&nbsp; beta=3D0.70<br>&nbsp;&nbsp;=
&nbsp;&nbsp; CG style diagonalization<br>&nbsp;&nbsp;&nbsp;&nbsp; c_bands:&=
nbsp; 3 eigenvalues not converged<br>&nbsp;&nbsp;&nbsp;&nbsp; c_bands:&nbsp=
; 2 eigenvalues not converged<br>&nbsp;&nbsp;&nbsp;&nbsp; ethr =3D&nbsp; 1.=
00E-12,&nbsp; avg #=0A of iterations =3D 40.4<br>&nbsp;enter write_ns<br>U(=
 1) =3D&nbsp; 0.0000<br>alpha( 1) =3D&nbsp; 0.1000<br>atom&nbsp; 1&nbsp;&nb=
sp; Tr[ns(na)]=3D&nbsp;&nbsp; 0.0021401<br>atom&nbsp; 1&nbsp; spin&nbsp; 1<=
br>eigenvalues:&nbsp; 0.0000001 0.0000001 0.0000001 0.0009883 0.0009883<br>=
&nbsp;eigenvectors<br>&nbsp;1&nbsp;&nbsp; 0.0000000 -0.8803392 -0.4743427&n=
bsp; 0.0000000&nbsp; 0.0013927<br>&nbsp;2&nbsp;&nbsp; 0.0000000 -0.4743432&=
nbsp; 0.8803400&nbsp; 0.0000000 -0.0000040<br>&nbsp;3&nbsp;&nbsp; 0.0000000=
&nbsp; 0.0012242&nbsp; 0.0006642&nbsp; 0.0000000&nbsp; 0.9999990<br>&nbsp;4=
&nbsp; -0.8886820&nbsp; 0.0000000&nbsp; 0.0000000 -0.4585240&nbsp; 0.000000=
0<br>&nbsp;5&nbsp;&nbsp; 0.4585240&nbsp; 0.0000000&nbsp; 0.0000000 -0.88868=
20&nbsp; 0.0000000<br>&nbsp;occupations<br>&nbsp;0.001&nbsp; 0.000&nbsp; 0.=
000&nbsp; 0.000&nbsp; 0.000<br>&nbsp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.=
000&nbsp; 0.000<br>&nbsp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000&nbsp;=0A=
 0.000<br>&nbsp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.001&nbsp; 0.000<br>&n=
bsp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000<br>--------------=
-------------------- and end of the file is <br>:<br>&nbsp;&nbsp;&nbsp;&nbs=
p; End of self-consistent calculation<br>&nbsp;enter write_ns<br>U( 1) =3D&=
nbsp; 0.0000<br>alpha( 1) =3D&nbsp; 0.1000<br>atom&nbsp; 1&nbsp;&nbsp; Tr[n=
s(na)]=3D&nbsp;&nbsp; 2.3270531<br>atom&nbsp; 1&nbsp; spin&nbsp; 1<br>eigen=
values:&nbsp; 0.1574294 0.1574294 0.1574294 0.9273825 0.9273825<br>&nbsp;ei=
genvectors<br>&nbsp;1&nbsp;&nbsp; 0.0000000 -0.4359030 -0.7986559&nbsp; 0.0=
000000&nbsp; 0.4148945<br>&nbsp;2&nbsp;&nbsp; 0.0000000&nbsp; 0.7269732 -0.=
0406891&nbsp; 0.0000000&nbsp; 0.6854592<br>&nbsp;3&nbsp;&nbsp; 0.0000000 -0=
.5305643&nbsp; 0.6004109&nbsp; 0.0000000&nbsp; 0.5983379<br>&nbsp;4&nbsp; -=
0.9258933&nbsp; 0.0000000&nbsp; 0.0000000 -0.3777851&nbsp; 0.0000000<br>&nb=
sp;5&nbsp;&nbsp; 0.3777851&nbsp; 0.0000000&nbsp; 0.0000000=0A -0.9258933&nb=
sp; 0.0000000<br>&nbsp;occupations<br>&nbsp;0.927&nbsp; 0.000&nbsp; 0.000&n=
bsp; 0.000&nbsp; 0.000<br>&nbsp;0.000&nbsp; 0.157&nbsp; 0.000&nbsp; 0.000&n=
bsp; 0.000<br>&nbsp;0.000&nbsp; 0.000&nbsp; 0.157&nbsp; 0.000&nbsp; 0.000<b=
r>&nbsp;0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.927&nbsp; 0.000<br>&nbsp;0.00=
0&nbsp; 0.000&nbsp; 0.000&nbsp; 0.000&nbsp; 0.157<br><br><br>Ali Kazempour<=
br>=0APhysics department, Isfahan University of Technology<br>=0A84156 Isfa=
han, Iran.            Tel-1:  +98 311 391 3733<br>=0AFax: +98 311 391 2376 =
     Tel-2:  +98 311 391 2375</td></tr></table><br>=0A=0A=0A=0A      
--0-877763539-1248968263=:19544--

From kazempoor2000 at yahoo.com  Thu Jul 30 17:47:49 2009
From: kazempoor2000 at yahoo.com (ali kazempour)
Date: Thu, 30 Jul 2009 08:47:49 -0700 (PDT)
Subject: [Pw_forum] u-atom
Message-ID: <675514.19833.qm@web112512.mail.gq1.yahoo.com>

Dear all
Basically Is it possible to compute hubbard parameter for isolated transition metal atoms like Mn, Fe, .. by linear response? method?How ? 
Thanks a lot


Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.            Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376      Tel-2:  +98 311 391 2375


      
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From matteo at umn.edu  Thu Jul 30 17:57:47 2009
From: matteo at umn.edu (Matteo Cococcioni)
Date: Thu, 30 Jul 2009 10:57:47 -0500
Subject: [Pw_forum] occupation
In-Reply-To: <10309.19544.qm@web112513.mail.gq1.yahoo.com>
References: <10309.19544.qm@web112513.mail.gq1.yahoo.com>
Message-ID: <4A71C2FB.8040308@umn.edu>


Dear Ali,

on the wiki page of quantum-espresso you should be able to find a new 
tutorial on the calculation of U. Please download it
and run the scripts in there following the instructions.



ali kazempour wrote:
>
> Dear all
>
> From Linear response calculation ,I get for TiO2 bulk U=5.73, But when 
> I double the unit cell in z direction and again compute U ,I get three 
> different value for Ti atoms.(U=5.63,5.46,5.70).
>

what are these three values? I assume they are what you get with 
supercells of three different sizes. is this correct? if it is the only 
strange thing is that the intermediate value is lower than the other 
two. otherwise you got pretty nice convergence of U which is what you 
want to achieve. Is there any particular reason (apart computational 
cost) why you only enlarge the cell in z direction?

> Why these values are not same . what is the main reason? Does it in 
> numerical variation errors?
> ANother question:
> When we perturb D level by alpha, it give rise to change in d 
> occupancy . Is it correct that if we impose negative alpha , the 
> occupation becomes less than initial state .?
>

no. positive alpha -- > decrease in total n. but you need to look at the 
right n....

> for Ti isolated atom for apha=0.1  tr[ns(na)] after first-iteration 
> equal to the 0.002 and at the end of calculation is 2.327 while we 
> know that for Ti,  tr[ns(na)] =2.000. Does it seems to be correct.?
>
>      Number of iteration with fixed ns =  0
>      Starting ns and Hubbard U :
>  enter write_ns
> U( 1) =  0.0000
> alpha( 1) =  0.1000
> atom  1   Tr[ns(na)]=   2.0000000
> atom  1  spin  1
> eigenvalues:  0.4000000 0.4000000 0.4000000 0.4000000 0.4000000
>  eigenvectors
>  1   1.0000000  0.0000000  0.0000000  0.0000000  0.0000000
>  2   0.0000000  1.0000000  0.0000000  0.0000000  0.0000000
>  3   0.0000000  0.0000000  1.0000000  0.0000000  0.0000000
>  4   0.0000000  0.0000000  0.0000000  1.0000000  0.0000000
>  5   0.0000000  0.0000000  0.0000000  0.0000000  1.0000000
>  occupations
>  0.400  0.000  0.000  0.000  0.000
>  0.000  0.400  0.000  0.000  0.000
>  0.000  0.000  0.400  0.000  0.000
>  0.000  0.000  0.000  0.400  0.000
>  0.000  0.000  0.000  0.000  0.400
> atom  1  spin  2
> eigenvalues:  0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
>  eigenvectors
>  1   1.0000000  0.0000000  0.0000000  0.0000000  0.0000000
>  2   0.0000000  1.0000000  0.0000000  0.0000000  0.0000000
>  3   0.0000000  0.0000000  1.0000000  0.0000000  0.0000000
>  4   0.0000000  0.0000000  0.0000000  1.0000000  0.0000000
>  5   0.0000000  0.0000000  0.0000000  0.0000000  1.0000000
>  occupations
>  0.000  0.000  0.000  0.000  0.000
>  0.000  0.000  0.000  0.000  0.000
>  0.000  0.000  0.000  0.000  0.000
>  0.000  0.000  0.000  0.000  0.000
>  0.000  0.000  0.000  0.000  0.000
> nsum =   2.0000000
>  exit write_ns
>

this is not the first iteration. this is what the initial guess of the 
on-site occupations the code does to start the calculation


>  Atomic wfc used for LDA+U Projector are NOT orthogonalized
>      Starting wfc are    9 atomic +    1 random wfc
>
>      total cpu time spent up to now is     13.34 secs
>
>      per-process dynamical memory:   326.3 Mb
>
>      Self-consistent Calculation
>
>      iteration #  1     ecut=    45.00 Ry     beta=0.70
>      CG style diagonalization
>      c_bands:  3 eigenvalues not converged
>      c_bands:  2 eigenvalues not converged
>      ethr =  1.00E-12,  avg # of iterations = 40.4
>  enter write_ns
> U( 1) =  0.0000
> alpha( 1) =  0.1000
> atom  1   Tr[ns(na)]=   0.0021401
> atom  1  spin  1
> eigenvalues:  0.0000001 0.0000001 0.0000001 0.0009883 0.0009883
>  eigenvectors
>  1   0.0000000 -0.8803392 -0.4743427  0.0000000  0.0013927
>  2   0.0000000 -0.4743432  0.8803400  0.0000000 -0.0000040
>  3   0.0000000  0.0012242  0.0006642  0.0000000  0.9999990
>  4  -0.8886820  0.0000000  0.0000000 -0.4585240  0.0000000
>  5   0.4585240  0.0000000  0.0000000 -0.8886820  0.0000000
>  occupations
>  0.001  0.000  0.000  0.000  0.000
>  0.000  0.000  0.000  0.000  0.000
>  0.000  0.000  0.000  0.000  0.000
>  0.000  0.000  0.000  0.001  0.000
>  0.000  0.000  0.000  0.000  0.000
>

this is the first iteration! the problem is, in my opinion, that you 
didn't start this calculation from wfc and potential saved from the scf 
unperturbed run, but from scratch (that's why the code has to make the 
initial guess for the n).

regards,

Matteo
> ---------------------------------- and end of the file is
> :
>      End of self-consistent calculation
>  enter write_ns
> U( 1) =  0.0000
> alpha( 1) =  0.1000
> atom  1   Tr[ns(na)]=   2.3270531
> atom  1  spin  1
> eigenvalues:  0.1574294 0.1574294 0.1574294 0.9273825 0.9273825
>  eigenvectors
>  1   0.0000000 -0.4359030 -0.7986559  0.0000000  0.4148945
>  2   0.0000000  0.7269732 -0.0406891  0.0000000  0.6854592
>  3   0.0000000 -0.5305643  0.6004109  0.0000000  0.5983379
>  4  -0.9258933  0.0000000  0.0000000 -0.3777851  0.0000000
>  5   0.3777851  0.0000000  0.0000000 -0.9258933  0.0000000
>  occupations
>  0.927  0.000  0.000  0.000  0.000
>  0.000  0.157  0.000  0.000  0.000
>  0.000  0.000  0.157  0.000  0.000
>  0.000  0.000  0.000  0.927  0.000
>  0.000  0.000  0.000  0.000  0.157
>
>
> Ali Kazempour
> Physics department, Isfahan University of Technology
> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733
> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Matteo Cococcioni
Department of Chemical Engineering and Materials Science,
University of Minnesota
421 Washington Av. SE
Minneapolis, MN 55455
Tel. +1 612 624 9056    Fax +1 612 626 7246
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 


From cristian.degliesposti at unibo.it  Thu Jul 30 18:47:47 2009
From: cristian.degliesposti at unibo.it (Cristian Degli Esposti Boschi)
Date: Thu, 30 Jul 2009 18:47:47 +0200
Subject: [Pw_forum] Symmetry of the dynamical matrix
Message-ID: <4A71CEB3.5080209@unibo.it>

Dear all,

using the phonon code I noticed that, even
for simple molecular structures, the dynamical
matrix computed by ph.x is not symmetric.
(I limited myself to Gamma point calculations.)

In general, this does not guarantee real
eigenvalues. How are the eigenfrequencies
computed then?

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


From giannozz at democritos.it  Thu Jul 30 19:25:42 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 30 Jul 2009 19:25:42 +0200
Subject: [Pw_forum] Symmetry of the dynamical matrix
In-Reply-To: <4A71CEB3.5080209@unibo.it>
References: <4A71CEB3.5080209@unibo.it>
Message-ID: <4C8B09FA-50E7-4899-A06A-528CDB28CCC7@democritos.it>


On Jul 30, 2009, at 18:47 , Cristian Degli Esposti Boschi wrote:

> using the phonon code I noticed that, even
> for simple molecular structures, the dynamical
> matrix computed by ph.x is not symmetric [...]
> In general, this does not guarantee real
> eigenvalues. How are the eigenfrequencies
> computed then?

the dynamical matrix is symmetrized before diagonalization.
There is a check that the unsymmetric part (coming from
inexact self-consistency) is small. If not, a message is issued

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




From arvifis at gmail.com  Thu Jul 30 19:59:23 2009
From: arvifis at gmail.com (Arles V. Gil Rebaza)
Date: Thu, 30 Jul 2009 14:59:23 -0300
Subject: [Pw_forum] Full Relativistic PP for Fe and N...!!!
In-Reply-To: <de70fddd0907151135r28ebd2a4ida1db324eb3cb09f@mail.gmail.com>
References: <de70fddd0907151135r28ebd2a4ida1db324eb3cb09f@mail.gmail.com>
Message-ID: <de70fddd0907301059q51336fe2t9b9826c01c403604@mail.gmail.com>

Dear pwscf users,
Has anybody got fully relativistic pseudopoential for Fe and N?
I've many due for th generations of PP. Please anyboby can send me this PP
with fully relativistic (norm converving)...!!

I will be grateful for any help.



-- 
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From arvifis at gmail.com  Thu Jul 30 19:52:55 2009
From: arvifis at gmail.com (Arles V. Gil Rebaza)
Date: Thu, 30 Jul 2009 14:52:55 -0300
Subject: [Pw_forum] Error with band.x
Message-ID: <de70fddd0907301052o7e1a2f00lf67c7e4a7741d014@mail.gmail.com>

Hi PW user's i'm new using Quantum Espresso code... I compiled QE whit
OpenMPI.  I've a error when run the example05 QE, all calculations is well
but when calculate bands.x shows the follow error:
[arles at bose results]$ bands.x <si.bands.in >si.bands.out
Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
Failing at addr:0x778a4f6c8
[0] func:/usr/lib64/openmpi/libopal.so.0 [0x3aeb521dc5]
[1] func:/lib64/tls/libpthread.so.0 [0x3aebe0c4f0]
[2] func:/usr/lib64/libblas.so.3(zdotc_+0x5e) [0x2b6d5108488e]
[3] func:bands.x(cgracsc_+0x5d) [0x435a4d]
[4] func:bands.x(punch_band_+0x221f) [0x42c3ff]
[5] func:bands.x(MAIN__+0x389) [0x42dae9]
[6] func:bands.x(main+0xe) [0x6547ce]
[7] func:/lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x3aeb71c3fb]
[8] func:bands.x [0x42a12a]
*** End of error message ***
Segmentation fault



Any idea with respect this error..???
Best.
Arles V. Gil Rebaza
Instituto de Fisica de La Plata
La Plata - Argentina
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From arvifis at gmail.com  Thu Jul 30 19:57:13 2009
From: arvifis at gmail.com (Arles V. Gil Rebaza)
Date: Thu, 30 Jul 2009 14:57:13 -0300
Subject: [Pw_forum] Error with band.x
In-Reply-To: <de70fddd0907301052o7e1a2f00lf67c7e4a7741d014@mail.gmail.com>
References: <de70fddd0907301052o7e1a2f00lf67c7e4a7741d014@mail.gmail.com>
Message-ID: <de70fddd0907301057n3dec4c8do8ff52f2e496b4ee8@mail.gmail.com>

Hi PW user's i'm new using Quantum Espresso code... I compiled QE whit
OpenMPI.  I've a error when run the example05 QE, all calculations is well
but when calculate bands.x shows the follow error:


> [arles at bose results]$ bands.x <si.bands.in >si.bands.out
> Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
> Failing at addr:0x778a4f6c8
> [0] func:/usr/lib64/openmpi/libopal.so.0 [0x3aeb521dc5]
> [1] func:/lib64/tls/libpthread.so.0 [0x3aebe0c4f0]
> [2] func:/usr/lib64/libblas.so.3(zdotc_+0x5e) [0x2b6d5108488e]
> [3] func:bands.x(cgracsc_+0x5d) [0x435a4d]
> [4] func:bands.x(punch_band_+0x221f) [0x42c3ff]
> [5] func:bands.x(MAIN__+0x389) [0x42dae9]
> [6] func:bands.x(main+0xe) [0x6547ce]
> [7] func:/lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x3aeb71c3fb]
> [8] func:bands.x [0x42a12a]
> *** End of error message ***
> Segmentation fault
>
>
>
> Any idea with respect this error..???
> Best.
> Arles V. Gil Rebaza
> Instituto de Fisica de La Plata
> La Plata - Argentina
>



-- 
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From somesh.kb at gmail.com  Thu Jul 30 20:13:13 2009
From: somesh.kb at gmail.com (Somesh Kumar Bhattacharya)
Date: Thu, 30 Jul 2009 20:13:13 +0200
Subject: [Pw_forum] Fwd: Help required
In-Reply-To: <op.uxvzpaa3a8x26q@paulax>
References: <e0e40e0d0907300614n2d2fc2c0qc1d4fef87e3d80e@mail.gmail.com>
	<e0e40e0d0907300809w186821a9x194a58b8ba2d333@mail.gmail.com>
	<op.uxvzpaa3a8x26q@paulax>
Message-ID: <e0e40e0d0907301113n2531893ci2d0ea0096552ee2f@mail.gmail.com>

Hi Lorenzo,

Thanks a lot for the reply. Below is a typical case of failed calc with
diagonalization = 'cg'.

As I was trying too many things, I don't have the output files for all cases
.... but can  send you later

See the input (below)  and output file attached (it was a big file so I
zipped it )  .

Regards,


input :


&CONTROL
  calculation = "scf",
  restart_mode = 'from_scratch',
  nstep  = 5000,
  tprnfor = .TRUE.,
  wf_collect = .TRUE.,
  max_seconds = 21000,
  pseudo_dir = '/scratch/userictp/ictpcm16/pseudo/'
  outdir = './'

/
&SYSTEM
    ibrav=  14,
    celldm(1) = 16.972000,
    celldm(2) = 1.,
    celldm(3) = 4.9733070,
    celldm(4) = 0.0,
    celldm(5) = 0.0,
    celldm(6) = -0.5,
    nat=  97,
    ntyp= 3,
    ecutwfc = 80.0,
    nbnd=160,
    nelec=264,
    nspin = 2,
    nelup = 132,
    neldw = 132,
  occupations = 'smearing',
    smearing = 'fd',
    degauss = 0.1D0,

/
&ELECTRONS
  diagonalization = 'cg',
  conv_thr    = 1.D-7,
  mixing_beta = 0.1D0,
  mixing_mode = 'TF'
/

ATOMIC_SPECIES
Cl 35.4527  Cl.blyp-mt.UPF
O  15.9990  O.blyp-mt.UPF
H   1.0008  H.blyp-vbc.UPF

ATOMIC_POSITIONS (bohr)
   Cl   0.442065E+01  0.306161E+01 -0.266987E+02
   O    0.000000E+00  0.000000E+00  0.000000E+00
   O    0.424300E+01  0.734909E+01  0.000000E+00
   O    0.851569E+01  0.000000E+00  0.000000E+00
   O    0.126108E+02  0.734909E+01  0.000000E+00
   O    0.438891E+01  0.244970E+01 -0.173220E+01
   O    0.848600E+01  0.956439E+01 -0.173220E+01
   O    0.127290E+02  0.271183E+01 -0.173220E+01
   O    0.169720E+02  0.944817E+01 -0.173220E+01
   O    0.428030E+01  0.725274E+01 -0.840389E+01
   O    0.841685E+01 -0.436113E-01 -0.861498E+01
   O    0.124692E+02  0.715221E+01 -0.903980E+01
   O    0.165969E+02 -0.158654E+00 -0.830754E+01
   O   -0.183694E+00  0.969090E+01 -0.719695E+01
   O    0.397887E+01  0.232368E+01 -0.681051E+01
   O    0.858600E+01  0.965094E+01 -0.682273E+01
   O    0.125603E+02  0.238309E+01 -0.670488E+01
   O   -0.544601E+00 -0.420609E+00 -0.133708E+02
   O    0.440102E+01  0.742833E+01 -0.137164E+02
   O    0.842565E+01  0.144513E-01 -0.136329E+02
   O    0.121833E+02  0.713481E+01 -0.145496E+02
   O    0.382665E+01  0.235481E+01 -0.139532E+02
   O    0.827943E+01  0.101149E+02 -0.163476E+02
   O    0.125329E+02  0.218570E+01 -0.160069E+02
   O    0.168335E+02  0.944957E+01 -0.143380E+02
   O    0.383163E+01  0.784639E+01 -0.197508E+02
   O    0.793527E+01 -0.657036E-01 -0.230354E+02
   O    0.118885E+02  0.671256E+01 -0.227310E+02
   O    0.172021E+02  0.506853E+00 -0.231756E+02
   O   -0.369799E+00  0.930820E+01 -0.234342E+02
   O    0.412088E+01  0.246691E+01 -0.190829E+02
   O    0.816263E+01  0.100876E+02 -0.219343E+02
   O    0.126415E+02  0.165939E+01 -0.210947E+02
   H    0.158053E+01  0.777030E+00 -0.615741E+00
   H    0.101349E+01  0.609887E+00 -0.136132E+02
   H    0.295433E-02 -0.174804E+01 -0.635311E+00
   H   -0.320957E+00 -0.200415E+01 -0.143969E+02
   H    0.409538E+01  0.747239E+01  0.182080E+01
   H    0.449351E+01  0.762299E+01 -0.118706E+02
   H    0.263941E+01  0.814680E+01 -0.681465E+00
   H    0.274098E+01  0.817016E+01 -0.141897E+02
   H    0.100102E+02  0.916500E+00 -0.623627E+00
   H    0.982207E+01  0.832598E+00 -0.145990E+02
   H    0.703605E+01  0.919996E+00 -0.686878E+00
   H    0.685374E+01  0.100312E+01 -0.138837E+02
   H    0.126555E+02  0.722834E+01  0.182702E+01
   H    0.121280E+02  0.702454E+01 -0.126965E+02
   H    0.126852E+02  0.551011E+01 -0.665021E+00
   H    0.123271E+02  0.535587E+01 -0.151826E+02
   H    0.421851E+01  0.243526E+01 -0.362234E+01
   H    0.382764E+01  0.225861E+01 -0.158333E+02
   H    0.434800E+01  0.422513E+01 -0.119546E+01
   H    0.396446E+01  0.423069E+01 -0.136939E+02
   H    0.694714E+01  0.871016E+01 -0.113223E+01
   H    0.677200E+01  0.916570E+01 -0.157926E+02
   H    0.995458E+01  0.865760E+01 -0.102494E+01
   H    0.971274E+01  0.902918E+01 -0.158122E+02
   H    0.126648E+02  0.260576E+01 -0.365650E+01
   H    0.126353E+02  0.188395E+01 -0.178750E+02
   H    0.142630E+02  0.176495E+01 -0.119721E+01
   H    0.139745E+02  0.128942E+01 -0.152125E+02
   H    0.153671E+02  0.871276E+01 -0.111388E+01
   H    0.151700E+02  0.870562E+01 -0.147042E+02
   H    0.169513E+02  0.112617E+02 -0.120529E+01
   H    0.166825E+02  0.112966E+02 -0.143418E+02
   H   -0.186080E+00  0.967497E+01 -0.534322E+01
   H   -0.410716E+00  0.111769E+02 -0.235014E+02
   H   -0.170693E+00  0.115036E+02 -0.772370E+01
   H    0.606586E+00  0.869850E+01 -0.248594E+02
   H    0.241458E+01  0.149908E+01 -0.745774E+01
   H    0.278675E+01  0.175538E+01 -0.201536E+02
   H    0.400545E+01  0.408502E+01 -0.747655E+01
   H    0.410033E+01  0.431163E+01 -0.194638E+02
   H    0.869216E+01  0.953273E+01 -0.496001E+01
   H    0.839309E+01  0.103335E+02 -0.201056E+02
   H    0.100559E+02  0.872566E+01 -0.757565E+01
   H    0.944654E+01  0.876504E+01 -0.223573E+02
   H    0.110200E+02  0.152522E+01 -0.737847E+01
   H    0.112050E+02  0.835252E+00 -0.219509E+02
   H    0.140384E+02  0.135637E+01 -0.730830E+01
   H    0.142191E+02  0.119371E+01 -0.220024E+02
   H    0.578777E+01  0.817933E+01 -0.778715E+01
   H    0.517532E+01  0.854101E+01 -0.208405E+02
   H    0.275644E+01  0.826658E+01 -0.801262E+01
   H    0.224952E+01  0.825531E+01 -0.206219E+02
   H    0.851028E+01  0.801689E-02 -0.105254E+02
   H    0.704752E+01  0.853268E+00 -0.244147E+02
   H    0.681312E+01  0.785612E+00 -0.813077E+01
   H    0.700809E+01  0.491320E+00 -0.215355E+02
   H    0.140548E+02  0.803540E+01 -0.859465E+01
   H    0.135749E+02  0.747089E+01 -0.228574E+02
   H    0.126118E+02  0.543782E+01 -0.830772E+01
   H    0.120930E+02  0.495909E+01 -0.221546E+02
   H    0.164613E+02 -0.340182E+00 -0.101937E+02
   H    0.183449E+02  0.123088E+01 -0.244582E+02
   H    0.167906E+02 -0.192736E+01 -0.769333E+01
   H    0.173328E+02 -0.135460E+01 -0.231944E+02
K_POINTS {automatic}
2 2 1 0 0 0


*
 *





On Thu, Jul 30, 2009 at 5:23 PM, Lorenzo Paulatto <paulatto at sissa.it> wrote:

> In data 30 luglio 2009 alle ore 17:09:14, Somesh Kumar Bhattacharya
> <somesh.kb at gmail.com> ha scritto:
> > finally it crashes.
>
> Dear Somesh,
> your system is huge, can you please provide the full output (if possible
> for the different cases you've tried), up to the point where it crashes so
> we can take a look without wasting all that CPU time?
>
> best regards
>
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/<http://people.sissa.it/%7Epaulatto/>
>
>     *** save italian brains ***
>  http://saveitalianbrains.wordpress.com/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Somesh Kr. Bhattacharya
Post Doctoral Fellow
Room No. 263,
Leonardo Building,
The Abdus Salam International Centre for Theoretical Physics
Strada Costiera, 11
I-34014 Trieste
Italy
Phone: +39-040-2240399
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From matteo at umn.edu  Thu Jul 30 20:18:35 2009
From: matteo at umn.edu (Matteo Cococcioni)
Date: Thu, 30 Jul 2009 13:18:35 -0500
Subject: [Pw_forum] occupation
In-Reply-To: <4A71C2FB.8040308@umn.edu>
References: <10309.19544.qm@web112513.mail.gq1.yahoo.com>
	<4A71C2FB.8040308@umn.edu>
Message-ID: <4A71E3FB.406@umn.edu>


the new tutorial on the calculation of U can be downloaded from this 
webpage:

http://www.quantum-espresso.org/wiki/index.php/QESB09#First_week


Matteo Cococcioni wrote:
> Dear Ali,
>
> on the wiki page of quantum-espresso you should be able to find a new 
> tutorial on the calculation of U. Please download it
> and run the scripts in there following the instructions.
>
>
>
> ali kazempour wrote:
>   
>> Dear all
>>
>> From Linear response calculation ,I get for TiO2 bulk U=5.73, But when 
>> I double the unit cell in z direction and again compute U ,I get three 
>> different value for Ti atoms.(U=5.63,5.46,5.70).
>>
>>     
>
> what are these three values? I assume they are what you get with 
> supercells of three different sizes. is this correct? if it is the only 
> strange thing is that the intermediate value is lower than the other 
> two. otherwise you got pretty nice convergence of U which is what you 
> want to achieve. Is there any particular reason (apart computational 
> cost) why you only enlarge the cell in z direction?
>
>   
>> Why these values are not same . what is the main reason? Does it in 
>> numerical variation errors?
>> ANother question:
>> When we perturb D level by alpha, it give rise to change in d 
>> occupancy . Is it correct that if we impose negative alpha , the 
>> occupation becomes less than initial state .?
>>
>>     
>
> no. positive alpha -- > decrease in total n. but you need to look at the 
> right n....
>
>   
>> for Ti isolated atom for apha=0.1  tr[ns(na)] after first-iteration 
>> equal to the 0.002 and at the end of calculation is 2.327 while we 
>> know that for Ti,  tr[ns(na)] =2.000. Does it seems to be correct.?
>>
>>      Number of iteration with fixed ns =  0
>>      Starting ns and Hubbard U :
>>  enter write_ns
>> U( 1) =  0.0000
>> alpha( 1) =  0.1000
>> atom  1   Tr[ns(na)]=   2.0000000
>> atom  1  spin  1
>> eigenvalues:  0.4000000 0.4000000 0.4000000 0.4000000 0.4000000
>>  eigenvectors
>>  1   1.0000000  0.0000000  0.0000000  0.0000000  0.0000000
>>  2   0.0000000  1.0000000  0.0000000  0.0000000  0.0000000
>>  3   0.0000000  0.0000000  1.0000000  0.0000000  0.0000000
>>  4   0.0000000  0.0000000  0.0000000  1.0000000  0.0000000
>>  5   0.0000000  0.0000000  0.0000000  0.0000000  1.0000000
>>  occupations
>>  0.400  0.000  0.000  0.000  0.000
>>  0.000  0.400  0.000  0.000  0.000
>>  0.000  0.000  0.400  0.000  0.000
>>  0.000  0.000  0.000  0.400  0.000
>>  0.000  0.000  0.000  0.000  0.400
>> atom  1  spin  2
>> eigenvalues:  0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
>>  eigenvectors
>>  1   1.0000000  0.0000000  0.0000000  0.0000000  0.0000000
>>  2   0.0000000  1.0000000  0.0000000  0.0000000  0.0000000
>>  3   0.0000000  0.0000000  1.0000000  0.0000000  0.0000000
>>  4   0.0000000  0.0000000  0.0000000  1.0000000  0.0000000
>>  5   0.0000000  0.0000000  0.0000000  0.0000000  1.0000000
>>  occupations
>>  0.000  0.000  0.000  0.000  0.000
>>  0.000  0.000  0.000  0.000  0.000
>>  0.000  0.000  0.000  0.000  0.000
>>  0.000  0.000  0.000  0.000  0.000
>>  0.000  0.000  0.000  0.000  0.000
>> nsum =   2.0000000
>>  exit write_ns
>>
>>     
>
> this is not the first iteration. this is what the initial guess of the 
> on-site occupations the code does to start the calculation
>
>
>   
>>  Atomic wfc used for LDA+U Projector are NOT orthogonalized
>>      Starting wfc are    9 atomic +    1 random wfc
>>
>>      total cpu time spent up to now is     13.34 secs
>>
>>      per-process dynamical memory:   326.3 Mb
>>
>>      Self-consistent Calculation
>>
>>      iteration #  1     ecut=    45.00 Ry     beta=0.70
>>      CG style diagonalization
>>      c_bands:  3 eigenvalues not converged
>>      c_bands:  2 eigenvalues not converged
>>      ethr =  1.00E-12,  avg # of iterations = 40.4
>>  enter write_ns
>> U( 1) =  0.0000
>> alpha( 1) =  0.1000
>> atom  1   Tr[ns(na)]=   0.0021401
>> atom  1  spin  1
>> eigenvalues:  0.0000001 0.0000001 0.0000001 0.0009883 0.0009883
>>  eigenvectors
>>  1   0.0000000 -0.8803392 -0.4743427  0.0000000  0.0013927
>>  2   0.0000000 -0.4743432  0.8803400  0.0000000 -0.0000040
>>  3   0.0000000  0.0012242  0.0006642  0.0000000  0.9999990
>>  4  -0.8886820  0.0000000  0.0000000 -0.4585240  0.0000000
>>  5   0.4585240  0.0000000  0.0000000 -0.8886820  0.0000000
>>  occupations
>>  0.001  0.000  0.000  0.000  0.000
>>  0.000  0.000  0.000  0.000  0.000
>>  0.000  0.000  0.000  0.000  0.000
>>  0.000  0.000  0.000  0.001  0.000
>>  0.000  0.000  0.000  0.000  0.000
>>
>>     
>
> this is the first iteration! the problem is, in my opinion, that you 
> didn't start this calculation from wfc and potential saved from the scf 
> unperturbed run, but from scratch (that's why the code has to make the 
> initial guess for the n).
>
> regards,
>
> Matteo
>   
>> ---------------------------------- and end of the file is
>> :
>>      End of self-consistent calculation
>>  enter write_ns
>> U( 1) =  0.0000
>> alpha( 1) =  0.1000
>> atom  1   Tr[ns(na)]=   2.3270531
>> atom  1  spin  1
>> eigenvalues:  0.1574294 0.1574294 0.1574294 0.9273825 0.9273825
>>  eigenvectors
>>  1   0.0000000 -0.4359030 -0.7986559  0.0000000  0.4148945
>>  2   0.0000000  0.7269732 -0.0406891  0.0000000  0.6854592
>>  3   0.0000000 -0.5305643  0.6004109  0.0000000  0.5983379
>>  4  -0.9258933  0.0000000  0.0000000 -0.3777851  0.0000000
>>  5   0.3777851  0.0000000  0.0000000 -0.9258933  0.0000000
>>  occupations
>>  0.927  0.000  0.000  0.000  0.000
>>  0.000  0.157  0.000  0.000  0.000
>>  0.000  0.000  0.157  0.000  0.000
>>  0.000  0.000  0.000  0.927  0.000
>>  0.000  0.000  0.000  0.000  0.157
>>
>>
>> Ali Kazempour
>> Physics department, Isfahan University of Technology
>> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733
>> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>   
>>     
>
>
>   


-- 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Matteo Cococcioni
Department of Chemical Engineering and Materials Science,
University of Minnesota
421 Washington Av. SE
Minneapolis, MN 55455
Tel. +1 612 624 9056    Fax +1 612 626 7246
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 


From arvifis at gmail.com  Thu Jul 30 20:35:16 2009
From: arvifis at gmail.com (Arles V. Gil Rebaza)
Date: Thu, 30 Jul 2009 15:35:16 -0300
Subject: [Pw_forum] Error with band.x
In-Reply-To: <de70fddd0907301052o7e1a2f00lf67c7e4a7741d014@mail.gmail.com>
References: <de70fddd0907301052o7e1a2f00lf67c7e4a7741d014@mail.gmail.com>
Message-ID: <de70fddd0907301135t5c2d92a5o2124b8c9271357c4@mail.gmail.com>

Hi PW user's i'm new using Quantum Espresso code... I compiled QE whit
OpenMPI.  I've a error when run the example05 QE, all calculations is well
but when calculate bands.x shows the follow error:
[arles at bose results]$ bands.x <si.bands.in >si.bands.out
Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
Failing at addr:0x778a4f6c8
[0] func:/usr/lib64/openmpi/libopal.so.0 [0x3aeb521dc5]
[1] func:/lib64/tls/libpthread.so.0 [0x3aebe0c4f0]
[2] func:/usr/lib64/libblas.so.3(zdotc_+0x5e) [0x2b6d5108488e]
[3] func:bands.x(cgracsc_+0x5d) [0x435a4d]
[4] func:bands.x(punch_band_+0x221f) [0x42c3ff]
[5] func:bands.x(MAIN__+0x389) [0x42dae9]
[6] func:bands.x(main+0xe) [0x6547ce]
[7] func:/lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x3aeb71c3fb]
[8] func:bands.x [0x42a12a]
*** End of error message ***
Segmentation fault



Any idea with respect this error..???
Best.
Arles V. Gil Rebaza
Instituto de Fisica de La Plata
La Plata - Argentina
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From giannozz at democritos.it  Thu Jul 30 22:09:21 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 30 Jul 2009 22:09:21 +0200
Subject: [Pw_forum] Error with band.x
In-Reply-To: <de70fddd0907301057n3dec4c8do8ff52f2e496b4ee8@mail.gmail.com>
References: <de70fddd0907301052o7e1a2f00lf67c7e4a7741d014@mail.gmail.com>
	<de70fddd0907301057n3dec4c8do8ff52f2e496b4ee8@mail.gmail.com>
Message-ID: <5D5487CB-2E64-4CB9-9D1B-7852CF180CBA@democritos.it>


On Jul 30, 2009, at 19:57 , Arles V. Gil Rebaza wrote:

>  [arles at bose results]$ bands.x <si.bands.in >si.bands.out
> Signal:11
> Any idea with respect this error..???

what does the code print on output (at the terminal,
no redirection)?

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




From arvifis at gmail.com  Thu Jul 30 22:38:30 2009
From: arvifis at gmail.com (Arles V. Gil Rebaza)
Date: Thu, 30 Jul 2009 17:38:30 -0300
Subject: [Pw_forum] Error with band.x
In-Reply-To: <5D5487CB-2E64-4CB9-9D1B-7852CF180CBA@democritos.it>
References: <de70fddd0907301052o7e1a2f00lf67c7e4a7741d014@mail.gmail.com>
	<de70fddd0907301057n3dec4c8do8ff52f2e496b4ee8@mail.gmail.com>
	<5D5487CB-2E64-4CB9-9D1B-7852CF180CBA@democritos.it>
Message-ID: <de70fddd0907301338q4e46f5fcraada7a55afa52238@mail.gmail.com>

This error appears in the terminal, ....no appears in si.bands.out
Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
Failing at addr:0x778a4f6c8
[0] func:/usr/lib64/openmpi/libopal.so.0 [0x3aeb521dc5]
[1] func:/lib64/tls/libpthread.so.0 [0x3aebe0c4f0]
[2] func:/usr/lib64/libblas.so.3(zdotc_+0x5e) [0x2b6d5108488e]
[3] func:bands.x(cgracsc_+0x5d) [0x435a4d]
[4] func:bands.x(punch_band_+0x221f) [0x42c3ff]
[5] func:bands.x(MAIN__+0x389) [0x42dae9]
[6] func:bands.x(main+0xe) [0x6547ce]
[7] func:/lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x3aeb71c3fb]
[8] func:bands.x [0x42a12a]
*** End of error message ***
Segmentation fault

2009/7/30 Paolo Giannozzi <giannozz at democritos.it>

>
> On Jul 30, 2009, at 19:57 , Arles V. Gil Rebaza wrote:
>
> >  [arles at bose results]$ bands.x <si.bands.in >si.bands.out
> > Signal:11
> > Any idea with respect this error..???
>
> what does the code print on output (at the terminal,
> no redirection)?
>
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
###--------->   Arles V.   <---------###
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From giannozz at democritos.it  Thu Jul 30 22:51:36 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 30 Jul 2009 22:51:36 +0200
Subject: [Pw_forum] Error with band.x
In-Reply-To: <de70fddd0907301338q4e46f5fcraada7a55afa52238@mail.gmail.com>
References: <de70fddd0907301052o7e1a2f00lf67c7e4a7741d014@mail.gmail.com>
	<de70fddd0907301057n3dec4c8do8ff52f2e496b4ee8@mail.gmail.com>
	<5D5487CB-2E64-4CB9-9D1B-7852CF180CBA@democritos.it>
	<de70fddd0907301338q4e46f5fcraada7a55afa52238@mail.gmail.com>
Message-ID: <FE88F4A6-5465-4409-B5D3-ADED29B7D5F4@democritos.it>


On Jul 30, 2009, at 22:38 , Arles V. Gil Rebaza wrote:

>
> This error appears in the terminal, ....no appears in si.bands.out

another one who can't read!!! execute WITHOUT REDIRECTING
OUTPUT TO A FILE
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From wshen02 at gmail.com  Thu Jul 30 23:09:27 2009
From: wshen02 at gmail.com (=?UTF-8?B?5paH5rKI?=)
Date: Thu, 30 Jul 2009 14:09:27 -0700
Subject: [Pw_forum] Does anybody have the same problem for the relax
	calculation about the atom force
In-Reply-To: <57CC674D-29AD-4F22-9773-64D8EE47CC0C@democritos.it>
References: <2c9df8a80907281437j48077c4dif65dd73e75304af3@mail.gmail.com>
	<4A702E4D.5020704@democritos.it>
	<2c9df8a80907291103k1e7393d1w46bcda14fa721f51@mail.gmail.com>
	<22D52536-AB66-45E6-A445-8693C8981438@democritos.it>
	<2c9df8a80907291202x615cc75vf182891512a9023a@mail.gmail.com>
	<57CC674D-29AD-4F22-9773-64D8EE47CC0C@democritos.it>
Message-ID: <2c9df8a80907301409y57aac6aep4bdfd1a584049db7@mail.gmail.com>

I checked that, the pseudopotential is fine.
Which version of Quantum espresso are you using?
I am using espresso-3.2.3

Best

Wen

On Wed, Jul 29, 2009 at 1:54 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Jul 29, 2009, at 21:02 , ?? wrote:
>
> > Can you tell me which type of Pseudopotential you were using?
>
> can you read?
>
> > > Can you tell me which pseudopotential are you using?
> >
> > those on the quantum espresso web site
>
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From arvifis at gmail.com  Thu Jul 30 23:13:31 2009
From: arvifis at gmail.com (Arles V. Gil Rebaza)
Date: Thu, 30 Jul 2009 18:13:31 -0300
Subject: [Pw_forum] Error with band.x
In-Reply-To: <FE88F4A6-5465-4409-B5D3-ADED29B7D5F4@democritos.it>
References: <de70fddd0907301052o7e1a2f00lf67c7e4a7741d014@mail.gmail.com>
	<de70fddd0907301057n3dec4c8do8ff52f2e496b4ee8@mail.gmail.com>
	<5D5487CB-2E64-4CB9-9D1B-7852CF180CBA@democritos.it>
	<de70fddd0907301338q4e46f5fcraada7a55afa52238@mail.gmail.com>
	<FE88F4A6-5465-4409-B5D3-ADED29B7D5F4@democritos.it>
Message-ID: <de70fddd0907301413h40be56b8wfd5b1d281cd57aa4@mail.gmail.com>

so sorry..!!  This appears in the terminal

  Program POST-PROC v.4.1 starts ...
  Today is 30Jul2009 at 18: 9:24

  Parallel version (MPI)

  Number of processors in use: 1

  Planes per process (thick) : nr3 = 20 npp = 20 ncplane = 400

  Proc/ planes cols G planes cols G columns G
  Pool (dense grid) (smooth grid) (wavefct grid)
  1 20 253 2733 20 253 2733 91 609

Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
Failing at addr:0x778a4f6c8
[0] func:/usr/lib64/openmpi/libopal.so.0 [0x3aeb521dc5]
[1] func:/lib64/tls/libpthread.so.0 [0x3aebe0c4f0]
[2] func:/usr/lib64/libblas.so.3(zdotc_+0x5e) [0x2b0663a1e88e]
[3] func:bands.x(cgracsc_+0x5d) [0x435a4d]
[4] func:bands.x(punch_band_+0x221f) [0x42c3ff]
[5] func:bands.x(MAIN__+0x389) [0x42dae9]
[6] func:bands.x(main+0xe) [0x6547ce]
[7] func:/lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x3aeb71c3fb]
[8] func:bands.x [0x42a12a]
*** End of error message ***
Segmentation fault



2009/7/30 Paolo Giannozzi <giannozz at democritos.it>

>
> On Jul 30, 2009, at 22:38 , Arles V. Gil Rebaza wrote:
>
> >
> > This error appears in the terminal, ....no appears in si.bands.out
>
> another one who can't read!!! execute WITHOUT REDIRECTING
> OUTPUT TO A FILE
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
###--------->   Arles V.   <---------###
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From xwzhang at uestc.edu.cn  Fri Jul 31 05:28:43 2009
From: xwzhang at uestc.edu.cn (xwzhang)
Date: Fri, 31 Jul 2009 11:28:43 +0800
Subject: [Pw_forum] fixed spin moment calculation does not give a correct
	lattice constant !?
Message-ID: <449007380.01764@eyou.net>

Dear All,

When I am trying to do FSM calculations to fcc-Fe, I met such strange things:
The equilibrium volume of magnetic fcc-Fe is about 72 (au)^3, and nonmagnetic one about 70 (au)^3(PRB,60, 3839).
When I fixed the magnetic moment, the total energy decreases with the increase of the volume over all the volume range I used: from 50 (au)^3 to 120(au)^3. One of the input is as follows: (in other calculations I just vary the celldm(1) )
 &CONTROL
                       title = fcc-fe ,
                 calculation = 'scf' ,
                restart_mode = 'from_scratch' ,
                      outdir = './' ,
                  pseudo_dir = './' ,
                  wf_collect = .true.,
                     tstress = .true.,
                      prefix = pwscf,
                     tstress = .false. ,
 /
 &SYSTEM
                       ibrav = 2,
                   celldm(1) = 6.60,
                         nat = 1,
                        ntyp = 1,
                     ecutwfc = 30 ,
                     degauss = 0.01,
                     ecutrho = 350,
                    smearing = 'mp',
                 occupations = 'smearing',
                       nspin = 2,
   constrained_magnetization = 'total',
      fixed_magnetization(3) = 0.0
 /
 &ELECTRONS
 /
 &IONS
 /
 &CELL
 /
ATOMIC_SPECIES
   Fe   55.84700  Fe.pw91-sp-van_ak.UPF
ATOMIC_POSITIONS alat
   Fe      0.000000000    0.000000000    0.000000000
K_POINTS automatic
  20 20 20   1 1 1
  
I do not know the reason. And the total energy is twice as the nonmagnetic calculation (nspin=1) . In my mind they should be the same if I set total moment to 0.0

Regards and happy weekend!

Dr. Wenxu Zhang

State Key Laboratory of Electronic Thin Films and Integrated Devices,
University of Electronic Science and Technology of China,
Chengdu 610054
China
Tel: +86-28-83201475
Fax: +86-28-83204938
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From giannozz at democritos.it  Fri Jul 31 08:24:24 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 31 Jul 2009 08:24:24 +0200
Subject: [Pw_forum] Does anybody have the same problem for the relax
	calculation about the atom force
In-Reply-To: <2c9df8a80907301409y57aac6aep4bdfd1a584049db7@mail.gmail.com>
References: <2c9df8a80907281437j48077c4dif65dd73e75304af3@mail.gmail.com>
	<4A702E4D.5020704@democritos.it>
	<2c9df8a80907291103k1e7393d1w46bcda14fa721f51@mail.gmail.com>
	<22D52536-AB66-45E6-A445-8693C8981438@democritos.it>
	<2c9df8a80907291202x615cc75vf182891512a9023a@mail.gmail.com>
	<57CC674D-29AD-4F22-9773-64D8EE47CC0C@democritos.it>
	<2c9df8a80907301409y57aac6aep4bdfd1a584049db7@mail.gmail.com>
Message-ID: <5BA35A99-8BE9-4D71-A1F7-5F007AA0FE9C@democritos.it>


On Jul 30, 2009, at 23:09 , ?? wrote:

> Which version of Quantum espresso are you using?

4.1 (it is printed in the first lines)

> I am using espresso-3.2.3


you should use a more recent version. You should also
try different compilers if the error persists

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




From paulatto at sissa.it  Fri Jul 31 12:19:18 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Fri, 31 Jul 2009 12:19:18 +0200
Subject: [Pw_forum] Fwd: Help required
In-Reply-To: <e0e40e0d0907301113n2531893ci2d0ea0096552ee2f@mail.gmail.com>
References: <e0e40e0d0907300614n2d2fc2c0qc1d4fef87e3d80e@mail.gmail.com>
	<e0e40e0d0907300809w186821a9x194a58b8ba2d333@mail.gmail.com>
	<op.uxvzpaa3a8x26q@paulax>
	<e0e40e0d0907301113n2531893ci2d0ea0096552ee2f@mail.gmail.com>
Message-ID: <op.uxxgag1sa8x26q@paulax>

In data 30 luglio 2009 alle ore 20:13:13, Somesh Kumar Bhattacharya  
<somesh.kb at gmail.com> ha scritto:
> As I was trying too many things, I don't have the output files for all  
> cases
> .... but can  send you later


It is not necessary, actually the code is not crashing, but stopping.

I would say there is something seriously wrong with the calculation since  
the very beginning:
starting charge  261.71475, renormalised to  264.00000

Where has those 2.3 electrons gone? Although the code could still work, it  
seems like the initial conditions are too off the mark for the  
diagonalization algorithms.

I've tested the Cl pseudopotential on its own, and it looks like it is  
indeed lacking some charge. Also if you look at the header of the  
pseudopotential file you can spot a couple of inconsistencies.

If it is due to a recently introduced bug in QE or it has always been like  
that, I cannot say at the moment. It may be related to the 3D orbital  
being "almost" unbound for Cl with BLYP.

Anyway, I have generated another Cl BLYP NC pseudopotential, starting from  
the same parameters (although using the "normal" occupations) and it seems  
to be reliable. I'll send it to you visa private email, so you can run the  
basic tests. Otherwise, you can also try to start from random  
wavefunctions, instead of atomic ones.

Last but not least, for a highly inhomogeneous system, as yours, you  
should use 'local-TF' mixing, 'TF' mixing is for homogeneous system!

best regards

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

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

From somesh.kb at gmail.com  Fri Jul 31 12:27:01 2009
From: somesh.kb at gmail.com (Somesh Kumar Bhattacharya)
Date: Fri, 31 Jul 2009 12:27:01 +0200
Subject: [Pw_forum] Fwd: Help required
In-Reply-To: <op.uxxgag1sa8x26q@paulax>
References: <e0e40e0d0907300614n2d2fc2c0qc1d4fef87e3d80e@mail.gmail.com>
	<e0e40e0d0907300809w186821a9x194a58b8ba2d333@mail.gmail.com>
	<op.uxvzpaa3a8x26q@paulax>
	<e0e40e0d0907301113n2531893ci2d0ea0096552ee2f@mail.gmail.com>
	<op.uxxgag1sa8x26q@paulax>
Message-ID: <e0e40e0d0907310327y64cc0402iad48d486183cc3b0@mail.gmail.com>

Hi Lorenzo,

thanks a lot for the help.

I must say here that prior to these PWSCF calc, I was doing CPMD calc for
the same system. Everything went right with CPMD.
I encountered the problem with PW only. So its not clear to me as whats
wrong ??? ( Also I am not acquainted with the PW code)

Thanks again for the PP of Cl. I will test it and let you know.

Regarding the 'local-TF', it was also not working. So just tried this stupid
thing ...sorry for that ..................

Regards,

Somesh

On Fri, Jul 31, 2009 at 12:19 PM, Lorenzo Paulatto <paulatto at sissa.it>wrote:

> In data 30 luglio 2009 alle ore 20:13:13, Somesh Kumar Bhattacharya
> <somesh.kb at gmail.com> ha scritto:
> > As I was trying too many things, I don't have the output files for all
> > cases
> > .... but can  send you later
>
>
> It is not necessary, actually the code is not crashing, but stopping.
>
> I would say there is something seriously wrong with the calculation since
> the very beginning:
> starting charge  261.71475, renormalised to  264.00000
>
> Where has those 2.3 electrons gone? Although the code could still work, it
> seems like the initial conditions are too off the mark for the
> diagonalization algorithms.
>
> I've tested the Cl pseudopotential on its own, and it looks like it is
> indeed lacking some charge. Also if you look at the header of the
> pseudopotential file you can spot a couple of inconsistencies.
>
> If it is due to a recently introduced bug in QE or it has always been like
> that, I cannot say at the moment. It may be related to the 3D orbital
> being "almost" unbound for Cl with BLYP.
>
> Anyway, I have generated another Cl BLYP NC pseudopotential, starting from
> the same parameters (although using the "normal" occupations) and it seems
> to be reliable. I'll send it to you visa private email, so you can run the
> basic tests. Otherwise, you can also try to start from random
> wavefunctions, instead of atomic ones.
>
> Last but not least, for a highly inhomogeneous system, as yours, you
> should use 'local-TF' mixing, 'TF' mixing is for homogeneous system!
>
> best regards
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/<http://people.sissa.it/%7Epaulatto/>
>
>     *** save italian brains ***
>  http://saveitalianbrains.wordpress.com/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Somesh Kr. Bhattacharya
Post Doctoral Fellow
Room No. 263,
Leonardo Building,
The Abdus Salam International Centre for Theoretical Physics
Strada Costiera, 11
I-34014 Trieste
Italy
Phone: +39-040-2240399
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From giannozz at democritos.it  Fri Jul 31 12:42:02 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 31 Jul 2009 12:42:02 +0200
Subject: [Pw_forum] Fwd: Help required
In-Reply-To: <op.uxxgag1sa8x26q@paulax>
References: <e0e40e0d0907300614n2d2fc2c0qc1d4fef87e3d80e@mail.gmail.com>	<e0e40e0d0907300809w186821a9x194a58b8ba2d333@mail.gmail.com>	<op.uxvzpaa3a8x26q@paulax>	<e0e40e0d0907301113n2531893ci2d0ea0096552ee2f@mail.gmail.com>
	<op.uxxgag1sa8x26q@paulax>
Message-ID: <4A72CA7A.2090307@democritos.it>

Lorenzo Paulatto wrote:

> starting charge  261.71475, renormalised to  264.00000
> Where has those 2.3 electrons gone? 

this is not necessarily an indication of a problem. One missing
electron comes from the required charge state (the neutral system
has 263 electrons); the remaining 1.3 electron difference could well
be due to the finite cutoff. Atomic charges and wavefunctions are
normalized, but when you project over a finite PW basis set, you
lose some normalization. Also note that the atomic charge is
typically the charge of the electronic configuration used in
pseudopotential generation, not necessarily a neutral state.

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

From paulatto at sissa.it  Fri Jul 31 14:52:34 2009
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Fri, 31 Jul 2009 14:52:34 +0200
Subject: [Pw_forum] Fwd: Help required
In-Reply-To: <4A72CA7A.2090307@democritos.it>
References: <e0e40e0d0907300614n2d2fc2c0qc1d4fef87e3d80e@mail.gmail.com>
	<e0e40e0d0907300809w186821a9x194a58b8ba2d333@mail.gmail.com>
	<op.uxvzpaa3a8x26q@paulax>
	<e0e40e0d0907301113n2531893ci2d0ea0096552ee2f@mail.gmail.com>
	<op.uxxgag1sa8x26q@paulax> <4A72CA7A.2090307@democritos.it>
Message-ID: <op.uxxndw0ka8x26q@paulax>

In data 31 luglio 2009 alle ore 12:42:02, Paolo Giannozzi  
<giannozz at democritos.it> ha scritto:
> the remaining 1.3 electron difference could well
> be due to the finite cutoff.

That specific pseudopotential is lacking 1.3 electrons even if you test it  
alone, with a huge cutoff..

> Atomic charges and wavefunctions are
> normalized, but when you project over a finite PW basis set, you
> lose some normalization. Also note that the atomic charge is
> typically the charge of the electronic configuration used in
> pseudopotential generation, not necessarily a neutral state.

Yes, and it has a net charge of +0.5 abs(e). Although, I see that the code  
takes valence charge (7.00) as the initial charge, not the sum of the  
orbital occupations (6.50). Nevertheless, if I construct a pseudopotential  
with valence charge = 6.5 (e.g. exactly equal to the original one), its  
initial charge is ~6.5, not 5.7.

My guess is that its PP_RHOATOM section of the UPF file has some problem.  
In fact if I regenerate the new potential with the same grid as the old  
one (xmin=-4.0, dx=0.0625, rmax=60.0) I can replace the atomic rho of the  
old pseudo with the one of the new, getting the (almost) correct starting  
charge.

Convergence is still a bit flaky at the beginning. Which is normal, due to  
renormalization of charge inflating 6.5 electron to 7.0 without reshaping  
them. If this would be enough to guarantee convergence in the more complex  
case, I cannot say without trying.

cheers

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

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

From manoj at phys.ufl.edu  Fri Jul 31 16:25:39 2009
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Fri, 31 Jul 2009 10:25:39 -0400 (EDT)
Subject: [Pw_forum] generating k point weights
Message-ID: <Pine.GSO.4.21.0907311023060.12226-100000@neptune.phys.ufl.edu>

Dear All, 
 I was wondering if someone can tell me, how to generate k point weights
in the BZ. Reference of a paper would be great! 

Regards, 
Manoj


From giannozz at democritos.it  Fri Jul 31 16:43:31 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 31 Jul 2009 16:43:31 +0200
Subject: [Pw_forum] Error with band.x
In-Reply-To: <de70fddd0907301413h40be56b8wfd5b1d281cd57aa4@mail.gmail.com>
References: <de70fddd0907301052o7e1a2f00lf67c7e4a7741d014@mail.gmail.com>	<de70fddd0907301057n3dec4c8do8ff52f2e496b4ee8@mail.gmail.com>	<5D5487CB-2E64-4CB9-9D1B-7852CF180CBA@democritos.it>	<de70fddd0907301338q4e46f5fcraada7a55afa52238@mail.gmail.com>	<FE88F4A6-5465-4409-B5D3-ADED29B7D5F4@democritos.it>
	<de70fddd0907301413h40be56b8wfd5b1d281cd57aa4@mail.gmail.com>
Message-ID: <4A730313.4090705@democritos.it>

It works for me (with MPI and 1 or 2 processors; not with
2 pools, but that's expected behavior).

> Signal:11

something really wrong happened when the following library:

> [0] func:/usr/lib64/openmpi/libopal.so.0 [0x3aeb521dc5]

part of mpi, was called by the following library:

> [1] func:/lib64/tls/libpthread.so.0 [0x3aebe0c4f0]

part of the op/sys? of mpi? called (for reasons I ignore)
by the following library:

> [2] func:/usr/lib64/libblas.so.3(zdotc_+0x5e) [0x2b0663a1e88e]

which is a blas, zdotc, that was called by bands.x etc etc.
All that is above here it out of control.

> [3] func:bands.x(cgracsc_+0x5d) [0x435a4d]
> [4] func:bands.x(punch_band_+0x221f) [0x42c3ff]
> [5] func:bands.x(MAIN__+0x389) [0x42dae9]
> [6] func:bands.x(main+0xe) [0x6547ce]
> [7] func:/lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x3aeb71c3fb]
> [8] func:bands.x [0x42a12a]

How did you compile?

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

From mastermik at gmail.com  Fri Jul 31 16:45:02 2009
From: mastermik at gmail.com (Mikiyas Tsegaye)
Date: Fri, 31 Jul 2009 10:45:02 -0400
Subject: [Pw_forum]  *.fc file in PW_SCF help.
Message-ID: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com>

Dear Professor Isaev,

I was hoping you could help me with the Force Constants file in  
Quantum espresso. I have read your description of this *.fc output on  
the forum, and it's very clear. However, my question is this: if R is  
given as, R = a*m1+b*m2+c*m3, then the nearest neighbors would be at  
R(1,1,1), which is the next unit cell. But what about the interaction  
terms for the atoms within the same unit cell?

- Mikiyas Tsegaye
ECE dept, UVA
charlottesville, VA, USA

From neelphysics at yahoo.in  Fri Jul 31 17:14:30 2009
From: neelphysics at yahoo.in (Neel Singh)
Date: Fri, 31 Jul 2009 20:44:30 +0530 (IST)
Subject: [Pw_forum] Error in DOS calculation
Message-ID: <473002.17673.qm@web95014.mail.in2.yahoo.com>

hi all,

?I have followed example 8 and calculated DOS but i am getting error as
?
from dos : error #???????? 1
???? reading inputpp namelist
?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
???? stopping ...

I have done scf and then nscf successfully and my inputs are below... Please help how to produce DOS and PDOS. Thanks in advance.....

?==================================================
SCF Inputs
================================================

?&control
??? calculation='scf',
??? restart_mode='from_scratch',
??? prefix='pbo'
??? pseudo_dir = '/home/physics/pseudo/',
??? outdir='/home/physics/work/dos/temp'
?/
?&system
??? ibrav =6, a=7.118300514, b= 7.118300514, c=6.289300454
, nat =24, ntyp= 3,? ecutwfc = 40.0,ecutrho=300,
?occupations='smearing', smearing='methfessel-paxton', degauss=0.02


?/
?&electrons
??? mixing_beta = 0.7
??? diagonalization = 'david'
??? conv_thr =? 1.0e-6
/
?&ions
?/

ATOMIC_SPECIES
?/
/
ATOMIC_POSITIONS {angstrom}
/
/
K_POINTS 
?26
0.000 0.000 0.000? 1
0.000 0.000 0.125? 1
0.000 0.000 0.250? 1
0.000 0.000 0.375? 1
0.000 0.000 0.500? 1??????????????????????????? 
0.125 0.125 0.500? 1?????????????????????????? 
0.250 0.250 0.500? 1????????????????????????? 
0.375 0.375 0.500? 1??????????????????????????? 
0.500 0.500 0.500? 1??????????????????????????? 
0.500 0.500 0.333? 1???????????????????????????? 
0.500 0.500 0.166? 1???????????????????????????? 
0.500 0.500 0.000? 1???????????????????????????? 
0.375 0.375 0.000? 1???????????????????????????? 
0.250 0.250 0.000? 1???????????????????????????? 
0.125 0.125 0.000? 1???????????????????????????? 
0.000 0.000 0.000? 1???????????????????????????? 
0.000 0.000 0.166? 1??????????????????????????? 
0.000 0.000 0.333? 1???????????????????????????? 
0.000 0.166 0.500? 1?????????????????????????? 
0.000 0.333 0.500? 1??????????????????????????? 
0.000 0.500 0.500? 1???????????????????????????? 
0.000 0.500 0.333? 1???????????????????????????? 
0.000 0.500 0.166? 1???????????????????????????? 
0.000 0.500 0.000? 1???????????????????????????? 
0.000 0.333 0.000? 1???????????????????????????? 
0.000 0.166 0.000? 1

=============================================
Nscf Inputs
============================================


?&control
??? calculation='nscf'
??? pseudo_dir = '/home/physics/pseudo/',
??? outdir='/home/physics/work/dos/temp',
??? prefix='pbo',
? 
?/
?&system
??? ibrav =6, a=7.118300514, b= 7.118300514, c=6.289300454, nat=24, ntyp=3, 
ecutwfc = 40.0,ecutrho=300, occupations='tetrahedra', nbnd= 115, 
??? 
?/
?&electrons
?? mixing_beta=0.7
?? conv_thr=1.0e-6
?diagonalization = 'david'
/
&ions
?/

ATOMIC_SPECIES
/
/
ATOMIC_POSITIONS {angstrom}
/
/
K_POINTS {automatic}
?6 6 6 0 0 0
============================================
=========================================
&inputpp
??? outdir='/home/physics/work/dos/temp'
??? prefix='pbo'
??? fildos='pbo.dos',
??? Emin=-10.0, Emax=15.0, DeltaE=0.5, ngauss=1,
=======================
Please help,

With regards,
Neel Singh



      Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/
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From giannozz at democritos.it  Fri Jul 31 17:19:41 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 31 Jul 2009 17:19:41 +0200
Subject: [Pw_forum] Error in DOS calculation
In-Reply-To: <473002.17673.qm@web95014.mail.in2.yahoo.com>
References: <473002.17673.qm@web95014.mail.in2.yahoo.com>
Message-ID: <4A730B8D.8080500@democritos.it>

Neel Singh wrote:

> from dos : error #         1
>      reading inputpp namelist

"You can observe a lot just by watching."
(Yogi Berra, who wasn't a physicist but a baseball player).
You can also find the source of many errors by reading
error messages.

> &inputpp
>     outdir='/home/physics/work/dos/temp'
>     prefix='pbo'
>     fildos='pbo.dos',
>     Emin=-10.0, Emax=15.0, DeltaE=0.5, ngauss=1,

...and? where is the termination character?
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

From giannozz at democritos.it  Fri Jul 31 17:33:54 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 31 Jul 2009 17:33:54 +0200
Subject: [Pw_forum] *.fc file in PW_SCF help.
In-Reply-To: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com>
References: <5C8F87B2-8650-4FFA-B83A-F3CB60D87342@gmail.com>
Message-ID: <4A730EE2.7000107@democritos.it>

Mikiyas Tsegaye wrote:

> what about the interaction  
> terms for the atoms within the same unit cell?

what do you think the set of indices before each block
of force constants stand for? alpha beta na nb, and
what follows is C_{na \alpha, nb \beta}(R)

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

From neelphysics at yahoo.in  Fri Jul 31 18:35:08 2009
From: neelphysics at yahoo.in (Neel Singh)
Date: Fri, 31 Jul 2009 22:05:08 +0530 (IST)
Subject: [Pw_forum] Error in DOS calculation
In-Reply-To: <4A730B8D.8080500@democritos.it>
Message-ID: <971735.67183.qm@web95014.mail.in2.yahoo.com>

Hi sir,
So sorry for such a mistake sir ... :) .... Surely , I will take care in future ..
Thanks

With regards,
Neel

--- On Fri, 31/7/09, Paolo Giannozzi <giannozz at democritos.it> wrote:

From: Paolo Giannozzi <giannozz at democritos.it>
Subject: Re: [Pw_forum] Error in DOS calculation
To: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Friday, 31 July, 2009, 3:19 PM

Neel Singh wrote:

> from dos : error #? ? ? ???1
>? ? ? reading inputpp namelist

"You can observe a lot just by watching."
(Yogi Berra, who wasn't a physicist but a baseball player).
You can also find the source of many errors by reading
error messages.

> &inputpp
>? ???outdir='/home/physics/work/dos/temp'
>? ???prefix='pbo'
>? ???fildos='pbo.dos',
>? ???Emin=-10.0, Emax=15.0, DeltaE=0.5, ngauss=1,

....and? where is the termination character?
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum



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From dimpy.sharma at tyndall.ie  Fri Jul 31 22:20:54 2009
From: dimpy.sharma at tyndall.ie (Dimpy Sharma)
Date: Fri, 31 Jul 2009 21:20:54 +0100
Subject: [Pw_forum] Volume in a supercell
Message-ID: <D4A761F73683694BBD69D634FF2980153AEB04@MAIL.tyndall.ie>


Hi Quantum espresso user,

I would like to know how do we fix the cell parameters for a supercell while running any calculation with quantum espresso as from the manual it has been mentioned about lattice vector which is not making it clear ?

How shall we relate the lattice parameter with the volume added in order to avoid any overlapping?

Thanks

Dimpy
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From giannozz at democritos.it  Fri Jul 31 23:06:15 2009
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 31 Jul 2009 23:06:15 +0200
Subject: [Pw_forum] Volume in a supercell
In-Reply-To: <D4A761F73683694BBD69D634FF2980153AEB04@MAIL.tyndall.ie>
References: <D4A761F73683694BBD69D634FF2980153AEB04@MAIL.tyndall.ie>
Message-ID: <7CD6A12E-0D7D-486B-B1C7-05AB64BBA019@democritos.it>


On Jul 31, 2009, at 22:20 , Dimpy Sharma wrote:
> I would like to know how do we fix the cell parameters for a  
> supercell while running any calculation with quantum espresso as  
> from the manual it has been mentioned about lattice vector which is  
> not making it clear ?
>

if your concept of "making it clear" is expressed in such a question,
I hope that the manual does not "make it clear" anything

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




From bogus@does.not.exist.com  Fri Jul 24 13:42:27 2009
From: bogus@does.not.exist.com ()
Date: Fri, 24 Jul 2009 11:42:27 -0000
Subject: No subject
Message-ID: <mailman.2.1249620984.24399.pw_forum@pwscf.org>

blog.sina.com.cn/nkasir to find some information about Yambo installaiton.

--=20
____________________________________
Hui Wang
School of physics, Nankai University, Tianjin, China

--000e0cd561dc9587100470860eeb
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

<div>Dear Jiayu Dai=EF=BC=9A</div>
<div>
<blockquote class=3D"gmail_quote" style=3D"PADDING-LEFT: 1ex; MARGIN: 0px 0=
px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">It&#39;s so exciting to see the =
new release of espresso-4.1, and a lot of new parts in<br>the code. But i w=
ould like to know if it includes the parts of TDDFT and GW? They<br>
have been discussed a lot before, and expected to be done soon?</blockquote=
>
<div>
<div>=C2=A0</div>
<div>As=C2=A0I only use 4.0.5, I do not know whether=C2=A0QE 4.1can perform=
 GW and TDDFT calculation.</div>
<div>If you want to do GW and TDDFT righti now, you can try Yambo.</div>
<div>
<p align=3D"justify">Yambo is a FORTRAN/C code for Many-Body calculations i=
n solid state and molecular physics. Yambo can take PWscf output files as i=
ts input file and do GW and TDDFT calculation. And Yambo is free. You can f=
ind it here <a href=3D"http://www.yambo-code.org/index.php">http://www.yamb=
o-code.org/index.php</a>=C2=A0.</p>
</div></div></div>
<div>From you address, I know you=C2=A0are Chinese. You can visit =C2=A0<a =
href=3D"http://blog.sina.com.cn/nkasir">blog.sina.com.cn/nkasir</a>=C2=A0to=
 find=C2=A0some information about Yambo installaiton.</div>
<div><br>-- <br>____________________________________<br>Hui Wang<br>School =
of physics, Nankai University, Tianjin, China </div>

--000e0cd561dc9587100470860eeb--

From bogus@does.not.exist.com  Fri Jul 24 13:42:27 2009
From: bogus@does.not.exist.com ()
Date: Fri, 24 Jul 2009 11:42:27 -0000
Subject: No subject
Message-ID: <mailman.3.1253281549.24399.pw_forum@pwscf.org>

DFT-Cohesive energy is decided by the functional and the pseudo-potential.
If the pseudo-potential and the functional predict correctly the ground
state of isolated atom and the bulk, we usually get less than 10% error.
This is the case of Al with GGA (I believe). For some other, especially in
transition metal where the ground states of isolated atoms (and/or bulks)
are not well predicted within DFT, the error in cohesive energy could be 20%
or more.
When a pseudo-potential is generated, it must be well tested before
releasing. It's safe to use.

On Wed, Sep 16, 2009 at 2:19 AM, udayagiri sai babu <udayagiri3 at gmail.com>wrote:

> Dear PWSCF users
> I calculated the cohesive energy for aluminium using GGA potential, which
> came out to be 3.59 ev/atom. When i compared this value with that of given
> in Kittel (3.34ev/atom) the error is 7.5%. Here i would like to know how
> much error in cohesive energy is acceptable and also if somebody can comment
> on error tolerance in lattice parameter and Bulk modulus (for GGA as well as
> LDA) as well it would be nice.
> Thanks in advance
>
> --
> U.Saibabu
> PhD student,
> Deformation mechanisms modeling group,
> Materials engineering department,
> IISc Bangalore,
> India.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


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

--00163646be844c72110473da595f
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

<div>From my understanding, correct me if I am wrong.</div><div><br></div>D=
FT-Cohesive energy is decided by the functional and the pseudo-potential. I=
f the pseudo-potential and the functional predict correctly the ground stat=
e of isolated atom and the bulk, we usually get less than 10% error. This i=
s the case of Al with GGA (I=A0believe). For some other, especially in tran=
sition metal where the ground states of isolated atoms (and/or bulks) are n=
ot well predicted within DFT, the error in cohesive energy could be 20% or =
more.<div>

<br></div><div>When a pseudo-potential is generated, it must be well tested=
 before releasing. It&#39;s safe to use.<br><br><div class=3D"gmail_quote">=
On Wed, Sep 16, 2009 at 2:19 AM, udayagiri sai babu <span dir=3D"ltr">&lt;<=
a href=3D"mailto:udayagiri3 at gmail.com">udayagiri3 at gmail.com</a>&gt;</span> =
wrote:<br>

<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;">Dear PWSCF users<br>I calculated the cohesi=
ve energy for aluminium using GGA potential, which came out to be 3.59 ev/a=
tom. When i compared this value with that of given in Kittel (3.34ev/atom) =
the error is 7.5%. Here i would like to know how much error in cohesive ene=
rgy is acceptable and also if somebody can comment on error tolerance in la=
ttice parameter and Bulk modulus (for GGA as well as LDA) as well it would =
be nice.<br>


Thanks in advance<br clear=3D"all"><font color=3D"#888888"><br>-- <br>U.Sai=
babu<br>PhD student,<br>Deformation mechanisms modeling group,<br>Materials=
 engineering department,<br>IISc Bangalore,<br>India.<br>
</font><br>_______________________________________________<br>
Pw_forum mailing list<br>
<a href=3D"mailto:Pw_forum at pwscf.org">Pw_forum at pwscf.org</a><br>
<a href=3D"http://www.democritos.it/mailman/listinfo/pw_forum" target=3D"_b=
lank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>
<br></blockquote></div><br><br clear=3D"all"><br>-- <br>-------------------=
-------------------------------<br>Duy Le<br>PhD Student<br>Department of P=
hysics<br>University of Central Florida.<br>
</div>

--00163646be844c72110473da595f--

From bogus@does.not.exist.com  Fri Jul 24 13:42:27 2009
From: bogus@does.not.exist.com ()
Date: Fri, 24 Jul 2009 11:42:27 -0000
Subject: No subject
Message-ID: <mailman.4.1258546999.24399.pw_forum@pwscf.org>


From bogus@does.not.exist.com  Fri Jul 24 13:42:27 2009
From: bogus@does.not.exist.com ()
Date: Fri, 24 Jul 2009 11:42:27 -0000
Subject: No subject
Message-ID: <mailman.5.1258547000.24399.pw_forum@pwscf.org>

no thermostat.
When I tried to add nose thermostat, the "econt" of the system became to NaN
and the vnhp became to Inf.
And then the program crashed with the information that "ortho went bananas"

here is a part of my input files,
 &CONTROL

                       title = 'CPMD'
,
                 calculation = 'cp'
,
                restart_mode = 'from_scratch'
,
                      outdir = '/tmp/' ,
                      wfcdir = '/tmp/'
,
                  pseudo_dir = '/home/vega/espresso-4.0/pseudo/' ,
                      prefix = 'cp_dissociation1' ,
                      nstep = 99999 ,
                          dt =
1,
 /

 &SYSTEM

                       ibrav =
8,
                   celldm(1) =24.8624,
                   celldm(2) = 0.8520,
                   celldm(3) = 1.6964,
                         nat =
147,
                        ntyp = 3,
                        nr1b = 20,
                        nr2b = 20,
                        nr3b =
20,
                       nosym = .true.
,
                   ecutwfc   =   30,
                   ecutrho   =  300,
 /


 &ELECTRONS
                 mixing_mode ='local-TF',
                 mixing_beta = 0.4,
                 electron_dynamics = 'damp',
 /

 &IONS

                ion_dynamics = 'none',
             ion_temperature =
'not_controlled',
 /
AUTOPILOT
    on_step =  20  : dt=3
    on_step =  20  : electron_dynamics = 'damp'
    on_step =  80  : dt=5
    on_step =  80  : ion_dynamics    = 'damp'
    on_step = 150  : ion_temperature = 'nose'
ENDRULES

ATOMIC_SPECIES

......
......
......

could you please do me a favor to tell me what is going wrong.

best wishes,

vega

On Wed, Nov 18, 2009 at 7:53 PM, vega lew <quantumdft at gmail.com> wrote:

> Dear sir,
>
> thank you for your information.
>
> could anyone tell me something about how to visualize the geometry of the
> output file?
> Is there a small tool to read the output file directly instead of
> converting the XYZ coordinations into another format and feeding it to VMD
> or VEGAZZ?
>
>
> thank you in advance.
>
> best wishes.
>
> vega
>
> On Wed, Nov 18, 2009 at 3:00 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:
>
>>
>> On Nov 18, 2009, at 6:17 , vega lew wrote:
>>
>> > I have a question about the option "nr1b, nr2b, nr3b" in &SYSTEM
>> > namelist.
>> > Could you please tell me something more about it?
>>
>> http://www.quantum-espresso.org/user_guide/node30.html
>> >
>>
>>
>> P.
>> ---
>> Paolo Giannozzi, Dept of Physics, University of Udine
>> via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
> --
>
> ==================================================================================
> Vega Lew ( weijia liu)
> Graduate student
> State Key Laboratory of Materials-oriented Chemical Engineering
> College of Chemistry and Chemical Engineering
> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
>
> ******************************************************************************************************************
> Email: vegalew at gmail.com
> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#,
> Nanjing, Jiangsu, China
> ******************************************************************************************************************
>
>



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

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--001636b2b50d9ae9480478a44ee9--

From bogus@does.not.exist.com  Fri Jul 24 13:42:27 2009
From: bogus@does.not.exist.com ()
Date: Fri, 24 Jul 2009 11:42:27 -0000
Subject: No subject
Message-ID: <mailman.6.1259952137.24399.pw_forum@pwscf.org>

German

ORNL



On Fri, Dec 4, 2009 at 4:26 AM, Paolo Giannozzi <giannozz at democritos.it> wrote:
> German Samolyuk wrote:
>
>> I'm little bit confused by comment
>> "notice that vel is not the real velocity" in the subroutine.
>
> I think it is just a reminder that "vel" is not the velocity
> but the velocity times Delta T
>
> P.
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
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